FUNDAMENTAL GENOMICS RESEARCH - Biblioteca do Paraíso

Interested in European research?Research*eu is our monthly magazine keeping you in touch with main developments (results, programmes, events, etc.). It isavailable in English, French, German and Spanish. A free sample copy or free subscription can be obtained from:European CommissionDirectorate-General for ResearchCommunication UnitB-1049 BrusselsFax (32-2) 29-58220E-mail: research-eu@ec.europa.euInternet: http://ec.europa.eu/research/research-euEUROPEAN COMMISSIONDirectorate-General for ResearchDirectorate F- HealthUnit F.4- Genomics and Systems BiologyContact: Christina KyriakopoulouOffice CDMA -1/19B-1049 BrusselsTel. (32-2) 29-59890Fax.(32-2) 29-60588E-mail: Christina.Kyriakopoulou@ec.europa.eu

EUROPEAN COMMISSIONFrom Fundamental Genomicsto Systems Biology:UNDERSTANDING THE BOOK OF LIFESynopses of EU collaborative research projects funded in FundamentalGenomics under the Sixth Framework Programme for the Thematic Priority«Life Sciences, genomics and biotechnology for health»FP6 and FP7 research policies in Fundamental Genomics and Systems Biologyedited by Christina Kyriakopoulou2008Directorate-General for ResearchLife Sciences, Genomics and Biotechnology for HealthEU-funded collaborative research projectsEUR 23132

AcknowledgementsThis publication could have only been accomplished thanks to the essential contribution of the project coordinators and theinput of my colleagues in the Health Directorate. Thanks to my colleagues, scientific officers, in the Genomics and SystemsBiology unit: Christian Desaintes, Tomasz Dylag, Iiro Eerola, Sasa Jenko, Fred Marcus, Sandra Pinto Marques and IoanaSiska. Thanks to the former colleagues of the fundamental genomics area Henriette Van Eijl, Indridi Benediktsson, Bill Baigand Elena Bordini. My special thanks to Mrs Josefina Enfedaque, scientific officer on health communication activities forher valuable input. Finally, my special gratitude to Patrik Kolar, Bernard Mulligan and Jacques Remacle for their continuoussupport and valuable guidance.Christina KyriakopoulouEUROPE DIRECT is a service to help you find answersto your questions about the European UnionFreephone number (*):00 800 6 7 8 9 10 11(*) Certain mobile telephone operators do not allow access to 00 800 numbers or these calls may be billedLEGAL NOTICENeither the European Commission nor any person acting on behalf of the Commission is responsible for the use whichmight be made of the following information.The views expressed in this publication are the sole responsibility of the author and do not necessarily reflect the viewsof the European Commission.A great deal of additional information on the European Union is available on the Internet.It can be accessed through the Europa server (http://europa.eu).Cataloguing data can be found at the end of this publication.Luxembourg: Office for Official Publications of the European Communities, 2008ISBN 978-92-79-08004-3DOI 10.2777/49314© European Communities, 2008Reproduction is authorised provided the source is acknowledged.Printed in BelgiumPRINTED ON WHITE CHLORINE-FREE PAPER

Contact details for the Genomics and Systems Biology unitEuropean CommissionDirectorate-General for ResearchDirectorate F- HealthUnit F4- Genomics and Systems BiologyDr Patrik Kolar, Head of Unit (patrik.kolar@ec.europa.eu)Dr Bernard Mulligan, Deputy Head of Unit (Bernard.mulligan@ec.europa.eu)Dr Jacques Remacle, Scientific officer (Jacques.remacle@ec.europa.eu)Dr Christian Desaintes, Scientific officer (Christian.desaintes@ec.europa.eu)Dr Tomasz Dylag, Scientific officer (tomasz.dylag@ec.europa.eu)Dr Iiro Eerola, Scientific officer (iiro.eerola@ec.europa.eu)Dr Sasa Jenko, Scientific officer (sasa.jenko@ec.europa.eu)Dr Christina Kyriakopoulou, Scientific officer (christina.kyriakopoulou@ec.europa.eu)Dr Beatrice Lucaroni, Scientific officer (beatrice.lucaroni@ec.europa.eu)Dr Fred Marcus (fred.marcus@ec.europa.eu)Dr Sandra Pinto Marques (Sandra.pinto-marques@ec.europa.eu)Dr Ioana Siska (ioana.siska@ec.europa.eu)Further information:http://cordis.europa.eu/fp7/health/home_en.htmlhttp://cordis.europa.eu/lifescihealth/genomics/home.htm5

TABLE OF CONTENTSForewordAbbreviationsPart ASection 1Section 2Section 3Section 4Section 5Section 6Section 714151616192022252727Overview of FP6 and FP7 research policies in Fundamental Genomics and Systems BiologyThe importance of Fundamental Genomics research in the European Union’s FrameworkProgrammes for RTDFundamental Genomics programme in FP6: sub-areas and their objectivesScientific Excellence and impact of European Fundamental Genomics Collaborative ResearchThe way forward in FP7: From Fundamental Genomics to Systems BiologyContent of the present publicationEC’s financial contribution in Fundamental Genomics & Systems BiologyCollaborative ResearchScientific sub-areas supported in the FP6 and FP7 in Fundamental Genomics andSystems Biology7.1 27 Tools and technologies for functional genomics7.1.1 29 Tools and technologies for gene expression7.1.2 31 Tools and technologies for proteomics7.1.3 32 Tools and technologies for molecular imaging7.1.4 33 Tools and technologies for gene integration and recombination7.2 33 Regulation of gene expression7.2.1 34 Transcriptional regulation7.2.2 34 Epigenetic regulation7.3 35 Structural Genomics and Structural Proteomics7.4 40 Comparative Genomics and Model organisms7.4.1 40 Mouse7.4.2 42 Rat7.4.3 43 Zebrafish7.4.4 43 Other models7.5 44 Population Genetics and Biobanks7.6 48 Bioinformatics7.7 51 Multidisciplinary functional genomics approaches to basic biological processes7.7.1 53 Biological pathways and intracellular and extracellular signalling7.7.2 54 Tissue and organ development, homeostasis and disease7.7.3 56 Stem cell biology7.7.4 57 RNA biology7.7.5 57 Chronobiology7.7.6 58 Biology of prokaryotes and other organisms7.8 58 Systems BiologyAnnexesAnnex IAnnex IIAnnex IIIAnnex IVAnnex VAnnex VI64646970727578Basic facts and figures for Fundamental Genomics activity areaFunding instruments-schemes in FP6 and FP7Development of the specific scientific topics for calls for proposalsin the FP6 Fundamental Genomics programmeEuropean Commission’s strategic workshops in different scientific areasof fundamental genomics and systems biologyEvaluation process in the FP6 and FP7 Fundamental Genomics programmeEvaluation criteria in FP6 and FP7Basic facts and figures for Fundamental Genomics activity area in FP6From Fundamental Genomics to Systems Biology: Understanding the Book of Life 7

Part BSynopses of projects funded in Fundamental Genomics in FP61. Tools and technologies for functional genomics1.1 Tools and technologies for gene expressionMolTools 86 Advanced Molecular Tools for Array-Based Analyses of Genomes,Transcriptomes, Proteomes and CellsREGULATORY GENOMICS 90 Advanced Genomics Instruments, Technology and Methods forDetermination of Transcription Factor Binding Specificities: Applicationsfor Identification of Genes Predisposing to Colorectal CancerTat machine 92 Functional genomic characterisation of the bacterial Tat complex as a nanomachinefor biopharmaceutical production and a target for novel anti-infectivesTransCode 94 Novel Tool for High-Throughput Characterisationof Genomic Elements Regulating Gene Expression in ChordatesEMERALD 96 Empowering the Microarray-Based European Research Areato Take a Lead in Development and ExploitationAutoscreen 98 Autoscreen for Cell Based High-throughput and High-contentGene Function Analysis and Drug Discovery ScreensTargetHerpes 100 Molecular intervention strategies targeting latentand lytic herpesvirus infectionsFGENTCARD 102 Functional GENomic diagnostic Toolsfor Coronary Artery DiseaseMODEST 104 Modular Devices for Ultrahigh-throughput and Small-volume Transfection1.2 Tools and technologies for proteomicsINTERACTION PROTEOME 108 Functional Proteomics: Towards defining theinteraction proteomeNEUPROCF 112 Development of New Methodologies for LowAbundance Proteomics: Application to Cystic FibrosisCAMP 114 Chemical Genomics by Activity Monitoring of ProteasesProDac 116 Proteomics Data Collection1.3 Tools and technologies for molecular imagingMOLECULAR IMAGING 120 Integrated Technologies for In vivo Molecular ImagingTips4Cells 124 Scanning Probe Microscopy techniques for real time,high resolution imaging and molecular recognition infunctional and structural genomicsCOMPUTIS 126 Molecular Imaging in Tissue and Cells by Computer-Assisted Innovative Multimode Mass Spectrometry1.4 Tools and technologies for gene integration and recombinationGENINTEG 130 Controlled gene integration: a requisite for genomeanalysis and gene therapyPLASTOMICS 132 Mechanisms of transgene integration and expressionin crop plant plastids, underpinning a technology forimproving human healthTAGIP 134 Targeted Gene Integration in Plants: Vectors,Mechanisms and Applications for Protein ProductionMEGATOOLS 136 New tools for Functional Genomics based onhomologous recombination induced by double-strandbreak and specific meganucleases8 From Fundamental Genomics to Systems Biology: Understanding the Book of Life

2. Regulation of gene expression2.1 Transcription regulationTRANS-REG 142 Transcription Complex Dynamics Controlling SpecificGene Expression ProgrammesX-TRA-NET 144 ChIP-Chip to Decipher Transcription Networks of RXRand Partners2.2 Epigenetic regulationTHE EPIGENOME 148 Epigenetic plasticity of the genomeHEROIC 152 High-Throughput Epigenetic Regulatory Organisationin ChromatinChILL 156 Chromatin Immuno-linked ligation: A novelgeneration of biotechnological tools for researchand diagnosisSMARTER 158 Development of small modulators of gene activationand repression by targeting epigenetic regulators3. Structural Genomics and Proteomics3DGENOME 164 3D Genome Structure and FunctionBIOXHIT 166 Bio-Crystallography on a Highly IntegratedTechnology Platform for European Structural Genomics3D-EM 170 New Electron Microscopy Approaches for StudyingProtein Complexes and Cellular Supramolecular ArchitectureGeneFun 174 Prediction of gene functionE-MeP 176 The European Membrane Protein ConsortiumFSG-V-RNA 180 Functional and Structural Genomics of Viral RNAVIZIER 182 Comparative structural genomics on viral enzymesinvolved in replicationUPMAN 186 Understanding Protein Misfolding and Aggregation by NMRNDDP 188 NMR Tools for Drug Design Validated on Phosphatases3D repertoire 190 A Multidisciplinary Approach to Determine theStructures of Protein Complexes in a Model OrganismFESP 194 Forum for European Structural ProteomicsE-MeP-Lab 196 E-MeP-Lab Training events in membrane proteinstructural biologyHT3DEM 198 High throughput Three-dimensional Electron MicroscopyNMR-Life 200 Focusing NMR on the Machinery of LifeExtend-NMR 202 Extending NMR for Functional and Structural GenomicsIMPS 204 Innovative tools for membrane structural proteomicsSPINE2-COMPLEXES 206 From Receptor to Gene: Structures of Complexes fromSignalling Pathways linking Immunology,Neurobiology and CancerOptiCryst 210 Optimisation of Protein Crystallisation for EuropeanStructural GenomicsTEACH-SG 212 Training and Education in High Volume and HighValue Structural GenomicsFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life 9

EUROSPAN 284 EUROpean Special Populations Research Network:Quantifying and Harnessing Genetic Variation forGene DiscoveryDanuBiobank 286 The Danubian Biobank Initiative — TowardsInformation-based MedicineImpacts 288 Archive tissues: improving molecular medicineresearch and clinical practiceEpiGenChlamydia 290 Contribution of molecular epidemiology and hostpathogengenomics to understand Chlamydiatrachomatis disease6. BioinformaticsBioSapiens 296 A European Network for Integrated Genome AnnotationATD 300 The Alternate Transcript Diversity ProjectEMBRACE 302 A European Model for Bioinformatics Research andCommunity EducationENFIN 306 An Experimental Network for Functional IntegrationEUROFUNGBASE 310 Strategy to build up and maintain an integratedsustainable European fungal genomic databaserequired for innovative genomics research on, important for biotechnology andhuman health7.Functional Genomics approaches for Basic biological processes7.1 Biological pathways and signallingMAIN 316 Targeting Cell Migration in Chronic InflammationWOUND 320 A multi-organism functional genomics approach tostudy signalling pathways in epithelial fusion/wound healingMitoCheck 322 Regulation of Mitosis by Phosphorylation-A Combined Functional Genomics, Proteomics andChemical Biology ApproachSIGNALLING & TRAFFIC 326 Signalling and Membrane Trafficking inTransformation and DifferentiationTransDeath 328 Programmed cell death across the eukaryotic kingdomPeroxisomes 330 Integrated Project to decipher the biological functionof peroxisomes in health and diseaseDNA Repair 334 DNA Damage Response and Repair MechanismsSTEROLTALK 338 Functional Genomics of Complex RegulatoryNetworks from Yeast to Human: Cross-Talk of SterolHomeostasis and Drug MetabolismRUBICON 342 Role of Ubiquitin and Ubiquitin-like Modifiers inCellular RegulationEndoTrack 346 Tracking the Endocytic Routes of Growth FactorReceptor Complexes and their Modulatory Role on SignallingAnEUploidy 350 AnEUploidy: understanding gene dosage imbalancein human health using genetics, functional genomicsand systems biologyFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life 11

7.2 Tissue and organ development and homeostasisNFG 356 Functional Genomics of the Adult and Developing BrainLYMPHANGIOGENOMICS 358 Genome-Wide Discovery and Functional Analysis ofNovel Genes in LymphangiogenesisEuroHear 362 Advances in hearing science: from functionalgenomics to therapiesMYORES 366 Multiorganismic Approach to Study Normal andAberrant Muscle Development, Function and RepairEuReGene 370 European Renal Genome ProjectEVI-GENORET 374 Functional genomics of the retina in health and disease7.3 Stem cellsFunGenES 380 Functional Genomics in Engineered ES cellsPlurigenes 384 Pluripotency Associated Genes to DedifferentiateNeural Cells into Pluripotent CellsESTOOLS 386 Platforms for biomedical discovery with human ES cellsEuTRACC 390 European Transcriptome, Regulome & CellularCommitment Consortium7.4 RNA biologyRIBOREG 396 Novel non-coding RNAs in differentiation and diseaseFOSRAK 398 Function of small RNAs across kingdomsCallimir 400 Studying the biological role of microRNAs in theDlk1-Gtl2 imprinted domainEurasnet 402 European Alternative Splicing Network of ExcellenceBACRNAs 408 Non-coding RNAs in Bacterial PathogenicityRNABIO 410 Computational approaches to non-coding RNAsSirocco 412 Silencing RNAs: organisers and coordinators ofcomplexity in eukaryotic organisms7.5 ChronobiologyEUCLOCK 418 Entrainment of the Circadian ClockTEMPO 422 Temporal Genomics for Tailored Chronotherapeutics7.6 Biology of prokaryotes and other organismsBACELL HEALTH 426 Bacterial stress management relevant to infectiousdisease and biopharmaceuticalsDIATOMICS 428 Understanding Diatom Biology by FunctionalGenomics Approaches12 From Fundamental Genomics to Systems Biology: Understanding the Book of Life

ForewordThe last decade has witnessed unprecedented advances in the life sciences. The sequencingof the human (2001) and other genomes has revolutionised biology, with genomesequences becoming the ‘periodic table’ of biology. The global understanding of the completefunction of approximately 22 000 human genes constitutes a major challenge forunderstanding normal and pathological situations. Therefore, to tackle this challenge, theEuropean Commission made fundamental genomics research into health and disease oneof the main action lines in the Life Sciences thematic priority under the Sixth FrameworkProgramme for RTD (FP6) (2002-2006).The European Commission identified the importance of genomics quite early, and has playeda cohesive role in addressing the fragmentation of the genomics and post-genomics researchcommunity in Europe by funding collaborative research projects via the EU Framework Programmesfor RTD. The rationale for structuring and integrating fundamental genomics researchat European level to tackle fragmentation and research capacity gaps is based on its immensepotential contribution to the understanding of the processes underlying human disease, andhence offering unprecedented opportunities to improve human health and stimulate industrialand economic activity. This research requires a collaborative approach, is by nature highlymultidisciplinary, and needs expertise and critical mass that do not exist in a single laboratory.Integrated multidisciplinary research and a strong interaction between high-throughput technologydevelopment and biology are vital in the fundamental genomics field for translatinggenome data into practical applications.The European Commission has allocated some 594 million over four years in FP6 for fundamentalgenomics research activities with the overall aim to foster the basic understandingof genomic information by developing the knowledge base, tools and resources needed todecipher the function of genes and gene products relevant to human health, and to exploretheir interactions with each other and with their environment. The present publication providesa brief description of the goals, expected results, achievements and expected impact of allthe projects supported during FP6 in the Fundamental Genomics priority area in the followingsub-areas: tools and technologies development for functional genomics; regulation of geneexpression; structural genomics and proteomics; comparative genomics and models organisms;population genetics and biobanks; bioinformatics; and multidisciplinary fundamentalgenomics research for understanding basic biological processes in health and disease andthe emerging area of systems biology. During FP6, the European Commission supported severalsystems biology initiatives which paved the way for further developing the genomicsand systems biology programme in the Seventh Framework Programme for RTD (FP7) (2007-2013). The introduction provides an overview on FP6 research policies and the steps taken tostrengthen the European Research Area in each of the scientific sub-areas, as well as the FP7concept in genomics and systems biology collaborative research.The European Commission via its Life Sciences and Health programme has been acting asa catalyst for strengthening European excellence in genomics and systems biology research.The path to scientific discovery and innovation is long and complex and we have realisedthat further investment will continue to be necessary for this important area. We are proud ofthe European scientists who collaborate in top-class research projects and we are certain thatthese projects will lead to substantial advances in the understanding of the links between thehuman genome and diseases, strengthen Europe’s position in this important field of research,and eventually benefit society.Manuel HallenActing DirectorHealth Research14From Fundamental Genomics to Systems Biology: Understanding the Book of Life

AbbreviationsAGCACPCP-FPCP-IPECERAEUFGFPFP5FP6FP7GDPHTPINCOIPNoERNARTDSBSGSMESME-STREPSPSSASTREP(Advisory Group)(Coordination Action)(Collaborative Project)(Small-Medium Scale Focused Research Collaborative Project)(Large Scale Integrating Collaborative Project)(European Commission)(European Research Area)(European Union)(functional genomics)(EU’s Framework Programme)(Fifth Framework Programme for RTD)(Sixth Framework Programme for RTD)(Seventh Framework Programme for RTD)(gross domestic product)(high-throughput)target countries (International Cooperation target countries)(Integrated Project)(Network of Excellence)(ribonucleic acid)(Research and Technological Development)(systems biology)(structural genomics)(small- to medium-sized enterprise)(SME-Specific Targeted Research Project)(structural proteomics)(Specific Support Action)(Specific Targeted Research Project)From Fundamental Genomics to Systems Biology: Understanding the Book of Life15

Part A: Overview of FP6 and FP7 research policiesin Fundamental Genomics and Systems BiologySection 1The importance of fundamental genomics research inthe European Union’s framework programmes for RTDOver the last 23 years, the European Union (EU), via the implementation of subsequent EU Framework Programmes(FPs) for supporting Research and Technological Development (RTD) activities in the European Union,has funded European collaborative and multidisciplinary research projects. This multi-laboratory, multinationalcollaboration represents the ‘reason of existence’ of the FPs for RTD, often essential for assembling critical mass,tackling fragmentation and strengthening European excellence in important research areas. The expected impactlies in enabling breakthroughs in important research areas in order to boost European biomedical and biotechindustry competitiveness, and ultimately to improve citizens’ quality of life.A significant part of different FPs’ budgets is dedicated to supporting collaborative research in life sciences andbiomedical research. The overall budget of the Sixth Framework Programme for RTD (FP6) was 17.5 billion, ofwhich an important proportion of 2.5 billion was allocated to the thematic priority of ‘Life Sciences, Genomicsand Biotechnology for Health’ in the period 2002 - 2006. The overall budget of the Seventh FrameworkProgramme for RTD (FP7) is 50.5 billion; it will run for seven years, with approximately 6 billion dedicatedto health-related collaborative research support. billion60504030201001984-19871987-1991 1990-1994 1994-1998 1998-2002 2002-2006 2007-2013FP7Fig. 1: Graphical representation of the budgetsof the EU Framework Programmes for RTD (FP1–FP7, 1984–2013)The European Research Area (ERA) was launched in 2000 by the EU as a key concept in implementing the Lisbonstrategy to make the EU “the most dynamic and competitive knowledge-based economy” by 2010; this was laterfollowed by the goal to increase spending on R&D in the EU up to 3% of the gross domestic product (GDP), wheretwo thirds would originate from private investments. FP6 set the implementation of the ERA as its major objectiveand addressed the fragmentation of EU research more intensively.16 From Fundamental Genomics to Systems Biology: Understanding the Book of Life

The ERA concept encompasses three interrelated aspects:■ a European ‘internal market’ for research, where researchers, technology and knowledge can circulate freely;■ effective European-level coordination of national and regional research activities, programmes and policies;■ initiatives implemented and funded at European level.The FP is the main financial instrument to implement the ERA at EU level, but it is clear that many other EU initiativesand particularly initiatives at national and regional level will have to be undertaken.A New European Research StrategyA joint effort by the EU and MS to address structural deficits in European researchFragmentationUnder-resourcingUnfavourable environment for research and innovationEuropean Research Area (ERA)European Research AreaNationalprogrammesFrameworkprogrammeOpenCoordinationEuropeanresearch policyEuropeanorganisationsFig. 2: Graphical representation of the concept of ERAThe European Commission (EC) identified the importance of genomics quite early, and has played a cohesiverole in addressing the fragmentation of the genomics and post-genomics research community in Europe by fundingcollaborative research projects via the EU FPs for RTD. The rationale for structuring and integrating fundamentalgenomics research at European level to tackle fragmentation and research capacity gaps is based onits immense potential contribution to the understanding of the processes underlying human disease, and henceoffering unprecedented opportunities to improve human health and stimulate industrial and economic activity.This research is by nature highly multidisciplinary, requires a collaborative approach, and needs expertise andcritical mass not available in any single laboratory. Integrated multidisciplinary research and strong interactionbetween high-throughput (HTP) technology development and biology is vital in the fundamental genomics fieldfor translating genome data into practical applications.From Fundamental Genomics to Systems Biology: Understanding the Book of Life17

Why research at European level?Resources are pooled to achieve critical massLeverage effect on private investmentsInteroperability and complementarity of big scienceStimulate training and international mobility of researchersImprove S&T capabilitiesStimulate competition in researchCreate scientific base for pan-European policy challengesEncourage coordination of national policiesEffective comparative research at EU-levelEfficient dissemination of research resultsFig. 3: The importance of European collaborative researchBetween 1990 and 2002 (from the Third Framework Programme (FP3) through the Fifth Framework Programme(FP5)), the EU invested in genomics research. This resulted in several major breakthroughs: the sequencing of thefirst eukaryotic genome (yeast), the sequencing of the first plant genome (Arabidopsis thaliana), and the assemblingof the physical and genetic maps of the human genomes — important and necessary tools for the furthersequencing of the human genome.During FP5 (1998–2002), the EC invested 120 million in genome research. In 2002, 39.4 million was providedto three large-scale research projects in genomics research for human health: GenomEUtwin, a major effortin population genetics (see www.genomeutwin.org); EUMORPHIA, a large integrated project (IP) devoted to thedevelopment and standardisation of mouse models phenotyping tools (see www.eumorphia.org); and SPINE, amajor structural proteomics effort that solved approximately 300 new protein structures (www.spineurope.org).These three projects, the first of such scale in FP5 in the life sciences, played an important role in structuring theresearch community in the respective areas.The publication of the first complete sequence of the human genome in 2001, as well as the sequencing of manyother genomes, heralded a new age in modern biology and biomedicine, offering unprecedented opportunitiesto improve human health and to stimulate industrial and economic activity. If science was looking for a milestoneto mark the entry into the 21 st century, it seems that revealing the sequence of the letters of the ‘book of life’ wasthe most important one. Researchers in the post-genomics era have doubled their efforts, with the major goal of‘reading’ the ‘book of life’, and understanding its ‘syntax’ and ‘language’ by putting the ‘words’ (our genes andtheir functions) in the correct order.The three billion ‘letters’ that make up our genetic code contain all the information needed to turn a fertilised egginto an adult human being. Thanks to the human genome project, we now know the sequence of letters constitutingthe approximately 22 000 human genes.However, the global understanding of the complete function of our genome, including the function of approximately22 000 human genes and the interactions amongst them and with the environment, still constitutes amajor challenge for the understanding of normal and pathological situations.DNA and protein microarrays and other technologies for HTP molecular profiling have expanded our horizonsand have provided a context for the information on the human organism: there are approximately 20 000 to25 000 protein-encoding genes, more than 100 000 transcript splice variants of those genes and perhaps 10 6protein states of possible functional significance.18 From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Early results in post-genomics research have already challenged established views about the nature of the genome.A surprising result of the human genome sequencing experiments was that only a very small proportion(1.5%) of the entire genome encodes for proteins. It was once thought that a large proportion of our genomewas inactive ‘junk DNA’, but today we know that many of these genomic regions have turned out to be regulatorysequences, which are responsible for activating or silencing genes when necessary.All the latest technological and knowledge breakthroughs and the accumulation of HTP novel data continueto highlight how little we still know about the effect of genes on the development of healthy and diseasedphenotypes.Therefore, to tackle these challenges, the EC made genomics and post-genomics research a research priority inFP6 (2002–2006). Indeed, of the total 2 500 million allocated to the priority of ‘Life Sciences, Genomics andBiotechnology for Health’, approximately 594 million was invested over four years in the FP6 FundamentalGenomics programme. Investing substantially in this EU Fundamental Genomics programme area was also importantin meeting the scientific community’s strong expectations, illustrated by the high number of expressionsof interest (550) submitted in this area during the 2002 launching of FP6.Section 2The Fundamental Genomics Programme in FP6:sub-areas and their objectivesFunctional genomics is the branch of genomics that determines the biological function of the genes and theirproducts using the development and application of global (genome-wide or systems-wide) experimental approaches(i.e. genomics, transcriptomics, proteomics, in silico functional prediction, etc.).Life sciences R&D - chainBiology: DNA,RNA, proteinTools/assaysAnalysis/interpretationApplicationssequencesvariationfunctioncellssystemsmicroarraysNMR, specgenotypingsiRNAmodel organismsimagingbioinformaticscomparative genomicsstructural genomicsfurther researchdiagnostics +disease markerstarget validationdrugs / therapiespharmacogenomicsFundamental genomicsFig. 4: Fundamental genomics research in the life sciences and biomedicine landscapeThe EU FP6 Fundamental Genomics Programme identified its strategic objectives: to foster the basic understandingof genomic information by developing the knowledge base, tools and resources needed to decipher thefunction of genes and gene products relevant to human health, and to explore their interactions with each otherand with their environment.From Fundamental Genomics to Systems Biology: Understanding the Book of Life19

Research in FP6 supported the following scientific sub-areas:■ Gene expression and proteomics with the aim of enabling researchers to better decipher the functionsof genes and gene products, as well as to define the complex regulatory networks (biocomplexity) thatcontrol fundamental biological processes. Research focused on developing high throughput tools andapproaches for monitoring gene expression and protein profiles and for determining protein functionsand protein interactions.■ Structural genomics with the overall objective to enable researchers to determine, more effectively and ata higher rate than currently feasible, the three-dimensional (3-D) structure of proteins and other macromolecules,important for elucidating protein function and essential for drug design. Research focused on developing HTPapproaches for determining high-resolution 3-D structures of macromolecules.■ Comparative genomics and population genetics with the goal of enabling researchers to use wellcharacterisedmodel organisms for predicting and testing gene function and to take full advantage of specificpopulation cohorts available in Europe, so as to determine the relationship between gene function and healthor disease. Research focused on developing model organisms and transgenic tools, and developing geneticepidemiology tools and standardised genotyping protocols.■ Bioinformatics with the aim of enabling researchers to access efficient tools for managing and interpretingthe ever-increasing quantities of genome data, and for making it available to the research community inan accessible and usable form. Research focused on developing bioinformatics tools and resources fordata storage, mining and processing, and on developing computational biology approaches for in silicoprediction of gene function and for simulation of complex regulatory networks.■ Multidisciplinary functional genomics approaches to basic biological processes withthe overall objective of enabling researchers to study fundamental biological processes by integrating theabove mentioned innovative approaches. Research will focus on elucidation of the mechanisms underlyingfundamental cellular processes, to identify the genes involved and to decipher their biological functions inliving organisms.With the rise of the era of systems biology, which signalled a new approach in understanding biological processes,the latter sub-area supported pilot projects applying systems biology approaches for understanding basic biologicalprocesses in health and disease.Although these areas represent different sections of the fundamental genomics programme during FP6, manyprojects were found to be cross-cutting in nature, using multidisciplinary approaches. For this reason, the authorsdecided to present the projects funded in fundamental genomics according to common scientific theme, rather thanto use the ‘artificial’ sections mentioned above: this is more comprehensible for the reader. The grouping of all theprojects funded in FP6 in scientific sub-areas is presented in Section 7, along with an introduction explaining whichEC Actions reinforce which areas, the steps taken towards the ERA and a set of representative project examples.Section 3Scientific excellence and impact of Europeanfundamental genomics collaborative researchThe EC identified the importance of genomics quite early, and has played a cohesive role in addressing the fragmentationof the genomics and post-genomics research community in Europe by funding collaborative researchprojects via the EU FPs for RTD. The rationale for structuring and integrating fundamental genomics research at theEuropean level to tackle fragmentation and research capacity gaps is based on its immense potential contribution20 From Fundamental Genomics to Systems Biology: Understanding the Book of Life

to the understanding of the processes underlying human disease, and hence offering unprecedented opportunitiesto improve human health and stimulate industrial and economic activity. This research is by nature highly multidisciplinary,requires a collaborative approach, and needs expertise and access to methodologies, technologies, data,facilities and critical mass not accessible in any one laboratory, in order to accelerate breakthrough discoveries.Integrated multidisciplinary research and strong interaction between high-throughput (HTP) technology developmentand biology is vital in the fundamental genomics field, for translating genome data into practical applications.While it is still premature to predict the success of European projects supported under the Fundamental Genomicsprogramme under FP6, one may conclude that EU is funding top-class, ambitious and state-of-the-art projects, involvingexcellence in Europe (as exemplified by the seven European Nobel prize winners participating in projects infundamental genomics):■ Harmut Michel: Nobel Prize Winner in Chemistry 1988 (project E-MEP)■ Christiane Nüsslein-Volhard: Nobel Prize Winner in Physiology or Medicine 1995 (project ZF-MODELS)■ Rolf Zinkernagel: Nobel Prize Winner in Physiology or Medicine 1996 (project MUGEN)■ John E. Walker: Nobel Prize Winner in Chemistry 1997 (project E-MeP)■ Tim Hunt: Nobel Prize Winner in Physiology or Medicine 2001 (project MITOCHECK)■ Kurt Wüthrich: Nobel Prize Winner in Chemistry 2002 (project UPMAN)■ Aaron Ceichanover: Nobel Prize Winner in Chemistry 2004 (project RUBICON)The first FP6-funded projects started in 2004, some have already been finalised, others are still ongoing. It is alreadyevident that many of these projects have already generated major discoveries on novel gene functions, andresulted in high-level publications (see project websites for further details). Most importantly, these projects haveplayed an important role in integrating the research community in Europe, thereby increasing their visibility at national,European and international level. They have also substantially contributed towards reducing fragmentationof research in Europe in their respective fields, thereby implementing the concept of the ERA and creating a realmultidisciplinary integrated programme of activities, as is illustrated with relevant figures in each sub-area’s activitiesdescription (see Section 7).All the projects funded in the area of fundamental genomics have very ambitious objectives. To achieve theseobjectives, it is necessary to apply a multidisciplinary transnational approach and to create the necessary criticalmass of researchers utilising a large set of different cutting-edge technologies. This multidisciplinary approachis only possible at European level by networking the research capacities and excellence available in differentcountries via the EU collaborative projects (CPs).KIKILAUCSICLULAUCNRSCNRSEBILUBIOZMPI-BMPI-FCSICEMBIMPI-BBIOZEMBLFEIMPI-FUOXFUOXFEBIBirkbeckFEIUUImperialBirkbeckUUImperialFig. 5: The structuring effect and the added value of collaborative projects: an exampleof active interactions between partners at the start point to the mid-term of a four year projectFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life21

Section 4The way forward in FP7:from fundamental genomics to systems biologyThe last decade has witnessed unprecedented advances in the life sciences. The rise of genomics after the sequencingof the human and other genomes has revolutionised biology, with genome sequences becoming the‘periodic table’ of biology. The spectacular development of the field of functional genomics and other ‘-omics’research has dramatically changed the research landscape in the life sciences.Life sciences research is moving away from a reductionist approach towards a new paradigm shift and a systemsbiology approach that attempts to understand biology in an integrative manner as large amounts of novel databecome available.In this new era of biology, scientists combine data, produced by a multidisciplinary set of functional genomicstools and technologies, into biological models with the power of computer science, mathematics or engineeringto understand the phenomena of life. Researchers are increasingly realising that complex organisms cannot easilybe subdivided into individual, independent components. Rather, genes, proteins, cells and organs interactwith each other and the environment in numerous, complex ways.Systems biology aims to shed new light on these interactions, which are vital for the holistic understanding ofmany major diseases such as cancer and diabetes.The FP7 programme (2007–2013) has already been launched and is expected to play an important role in developingthe field of systems biology in Europe by supporting the necessary critical mass of multidisciplinary expertise(‘-omics’, mathematics, physics, etc.) needed to produce the complex models underlying important biological processes.This will require modelling of complex systems involving networks of tens of thousands of genes, gene productsand other molecules. By understanding these biological processes in their complexity, systems biology promisesto make real progress towards understanding, preventing and combatting major complex diseases.Although the deciphering of the human genome sequence represents a major step towards understanding humanbiology, many questions still remain unanswered, including the function of most of the genes. New large-scaledata-gathering initiatives (e.g. population genetics including biobanks, large-scale proteomics, etc.) will be essentialfor generating new knowledge on gene functions and their interactions in complex regulatory networks inhealth and disease for future systems biology approaches.Furthermore, to catalyse progress in functional genomics and systems biology, it is important to develop new andimprove existing ‘-omics’ high-throughput (HTP) research tools. The tools will catalyse experimental progress byenhancing the generation and acquisition of data by orders of magnitude, and by significantly increasing ourknowledge base to gain insight into the functioning of cells, tissues, organs and entire organisms.Based on the continuation concept and building on the strong FP6 European collaborative activities that have takenplace, the priority area of fundamental genomics is evolving towards the systems biology era. The structure ofthe Genomics and Systems Biology programme in FP7 (2007–2013) ) is subdivided in the following sub-areas:■ High-throughput researchThe objective of this activity is to develop new research tools for modern biology that will significantly enhancedata generation and improve data and specimen (biobanks) standardisation, acquisition and analysis. The focuswill be on new technologies for:22 From Fundamental Genomics to Systems Biology: Understanding the Book of Life

■ sequencing■ gene expression■ genotyping and phenotyping■ structural genomics■ bioinformatics■ systems biology■ other ‘-omics’ fieldsPotential impact and European added value of high-throughput research initiativesFunctional genomics is a field of research offering many opportunities for technological innovation. Newtools and technologies will be essential to enhance our knowledge on gene functions in health and disease:increasing data output and considerably decreasing the cost for sample analysis will permit thetransfer of these technologies to the clinical environment. Developing new HTP research tools and technologiesfor collecting and processing vast amount of new and high-quality data will dramatically increase ourknowledge of complex biological processes.The development of these new tools and technologies requires a large multidisciplinary and coordinatedeffort, involving expertise in molecular biology, engineering, robotisation, electronics, material sciences andphysics. Only coordinated efforts at European level can harvest this diverse expertise with the common goalof developing new cutting-edge technologies. Importantly, any technological innovation obtained through acoordinated European effort greatly facilitates wider access to these new technologies in Europe.In several technological areas (e.g. imaging, proteomics, structural genomics, transgenics), Europe is verycompetitive and a wide range of direct medical applications have been or are being developed. Theintegrated collaborative efforts launched in FP6 and future efforts in FP7 will reinforce this competitive position.The development of groundbreaking technologies will support knowledge-based European competitivenessand their applications are expected to have a great impact on biomedical and biotechnologicalindustry, including small to medium-sized enterprises (SMEs).■ Integrating biological data and processes:large-scale data gathering and systems biology■ Large-scale data gatheringThe objective is to use HTP technologies to generate data for elucidating the function of genes and gene productsand their interactions in complex networks. The focus will be on the following:■ genomics■ proteomics■ population genetics■ comparative genomics■ functional genomicsFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life23

Potential impact and European added value of large-scale data gathering initiativesNew large-scale and systematic data-gathering initiatives in functional genomics (e.g. on the human proteome)will be essential for human biology in providing new knowledge on gene functions. Furthermore,standardisation of approaches will be achieved by developing European norms to facilitate efficient datainterchange. The data will be freely available for the scientific community in Europe.In the recent past, several large-scale European initiatives were proven to be successful. In FP6, severalnew initiatives have been initiated, including, for example, the large-scale genome annotation programme,the whole mouse genomes in situ hybridisation projects and several structural genomics efforts.Many Member States have cutting-edge post-genomics infrastructures, capacities and expertise. However,to launch new large-scale data-gathering initiatives, these will need to be networked in a well-coordinatedand integrated effort that will generate the necessary critical mass of scale and scope. They will offer possibilitiesto smaller Member States with more limited resources and capacities. Furthermore, considerableeconomy of scale and resources can be achieved by networking these research capacities in a coordinatedand integrated way. This coordinated approach at European level has proven to be successful forseveral large data-gathering initiatives: the sequencing of the first yeast and plant genomes, and morerecently, the determination of the 3-D structure of proteins important for human health, via the structuralgenomics collaborative efforts.These large-scale initiatives require a multidisciplinary approach involving different types of expertise.One of the bottlenecks in the translational process is how to translate a massive amount of data into usefulknowledge that is directly applicable. For this purpose, it is important to closely associate the bioinformaticscommunities with these initiatives, so as to develop the integrated databases necessary for widedissemination of results. Industry must be closely associated with these efforts, providing the requiredtechnical innovation and assistance.■ Systems biologyThe focus will be on multidisciplinary research that will integrate a wide variety of biological data and will developand apply system approaches to understand and model biological processes.Potential impact and European added value of systems biology initiativesSolving biological problems in health and disease requires understanding of complex networks, involvingtens of thousands of genes, gene products and other molecules. To further our understanding of biologicalphenomena, there is a need for quantitative approaches and systematic modelling, and analysis ofthe enormous amounts of information gathered by HTP technologies. With such approaches, collectivelytermed ‘systems biology’, we can gain new insight into the functioning of living systems, from the molecularlevels to the organism and population levels. This research involves a wide variety of disciplines,including modelling and simulation of the complex dynamic interactions. Eventually, systems biologicalresearch will open the way towards predictive biology and medical applications, when sufficiently powerfulmodels, fed with enormous amounts of data from different sources, become widely available.Projects operating in this category will contribute to the ERA by combining dispersed forces from around Europe.Scientists working on a particular system system (e.g. a cell, an organ or a disease) in different locationswill be able to work together towards a thorough understanding of the systems. Enabling this type of researchto be carried out at European level will secure Europe’s place in an increasingly competitive field and so helpemployment prospects, industrial development (including SMEs) and wealth creation. Exploiting biologicaldata in an integrated way is one of the most cost-effective means of supporting all life sciences, as well ashelping to achieve the Lisbon objectives with the move towards a dynamic knowledge-based society.Such an interdisciplinary approach is difficult, if not impossible, to carry out in a single institute, companyor even a single country. This research can only be undertaken in a large consortium which ideally shouldbe multinational. The requirement for such varied expertise renders the area ideal for European pro-24 From Fundamental Genomics to Systems Biology: Understanding the Book of Life

grammes, where national strengths in different disciplines can be combined for the benefit of all. Europewidecollaboration best averts the duplication of efforts and is a strong starting point for joining or drivinginternational collaboration.Under FP6, several projects are under way, that either work towards enabling system biology, or gatherdata that are suitable for such approaches (examples are Biosapiens and Eurohear). Many researcherscurrently working on various systems are moving into systems approaches and the trend is likely to continuein the coming decade. The genome era has enabled us to accumulate enormous quantities of dataon both our genome and that of other organisms. The amount of data is certain to increase exponentiallyfor the foreseeable future. Paradoxically, utilising this data is becoming feasible on the one hand, andincreasingly complex on the other. The high hopes for new drugs and other treatments from the genomicdata can only become reality if the potential is realised through approaches such as systems biology.Multidisciplinary projects : in a holistic approach to address complexbiological systems in health and diseaseFig. 6: The multidisciplinary nature of systems biologySection 5Content of the present publicationAlthough the sub-areas set out in Section 2 represent different sections of the fundamental genomics programmein FP6, many projects were found to be cross-cutting in nature, involving multidisciplinary approaches. Forthis reason, we thought the reader would find it clearer to present the list of projects funded in fundamentalgenomics arranged according to common scientific theme rather ‘artificially’ distributed based on the actionlines mentioned above.The present publication provides a brief description of the goals, expected results, achievements and expectedimpact of all the projects supported during FP6 in the fundamental genomics priority area in the following scientificsub-areas:■ tools and technologies development for functional genomics■ regulation of gene expressionFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life25

■ structural genomics and proteomics■ comparative genomics and models organisms■ population genetics and biobanks■ bioinformatics■ multidisciplinary fundamental genomics researchfor understanding basic biological processes in health and disease■ the emerging area of systems biology.For each of these sub-areas, an introductory section describes the importance and impact in the post-genomicsera of each field, including highlights from several projects and a short description of the activities implementedin the FP7 first call for proposals. The introductory section also provides an overview of FP6 research policies andthe steps taken to strengthen the ERA in each of the scientific sub-areas, as well as the FP7 vision in genomics andsystems biology collaborative research. However, owing to space limitations in this publication, we could nothighlight all 130 projects funded in the fundamental genomics programme, in the introductory section. Naturally,this by no means minimises the importance of the projects not cited.Table 1: EC Funding of different thematic sub-areas in fundamental genomicsand systems biology collaborative research in FP6 and in FP7’s first call selected projectsFundamental Genomics Research in FP6 (2002–2006)Scientific sub-areaNumber ofprojectsEC financialcontribution(million )Tools and Technologiesfor Functional Genomics20 68.0Regulation of Gene Expression 6 32.6Structural Genomicsand Structural Proteomics19 87.2Comparative Genomicsand Model Organisms15 82.4Population Genetics and Biobanks 10 19.4Bioinformatics 5 32.0Multidisciplinary Approachesfor Basic Biological Processes32 219.4FP6 Pilot Projects on Systems Biology 23 53.0 Genomics and Systems Biology Research in FP7 (2007–2013) (first call)Tools-Technologies for HTP research 3 35.7Large-Scale Data Gathering 7 80.0Systems Biology 4 45.8 26 From Fundamental Genomics to Systems Biology: Understanding the Book of Life

All the projects are highly multidisciplinary and include several areas of fundamental genomics in their researchplan. We thought it would be easier for the reader if we classified the projects using the respective scientificthemes they have in common. Having said that, there are several areas, like bioinformatics and databases,which are an essential part of all the projects and particularly of all the projects funded in the area of multidisciplinaryfunctional genomics, for understanding basic biological processes.Section 6EC financial contribution in fundamental genomicsand systems biology collaborative researchThe EU FP6 thematic activity on ‘Life Sciences, Genomics and Biotechnology for Health’ has had a clear focusin the post-genomics era, rising to the challenges following the sequencing of the human and other organisms’genomes. More specifically, the Fundamental Genomics Research programme received support of approximately594 million under FP6 for a large number of collaborative projects (CPs) (small- to medium-scale (89) and largescale(41)), out of a total 2 500 million allocated to the priority of ‘Life Sciences, Genomics and Biotechnologyfor Health’. The EC has committed approximately 635 million for 87 projects under Health research for the FP7first call selected projects which started in the beginning of 2008. More specifically, in the Genomics and SystemsBiology area, 14 large-scale integrating projects were supported, constituting 161.5 million (for further details,see Table 1). Specific explanatory notes on the definition of the funding instruments in FP6, namely IntegratedProjects (IPs), Networks of Excellence (NoE), Specific Targeted Research Projects (STREPs), Co-ordination Actions(CAs) and Specific Support Actions (SSAs) are presented in Annex I of this publication.Section 7Scientific sub-areas supported in FP6 and FP7in fundamental genomics and systems biologyAll processes in biology and medicine reflect the flow of information from the genome of the organism to itsphenotype. Since the identification of the structure of the DNA molecule more than 50 years ago, progress inunderstanding these processes has been driven by new technologies such as cloning, DNA sequencing, measurementsof ribonucleic acid (RNA) and protein, and use of robotics and microarrays. The genome sequencingproject has created a milestone for the deeper understanding of the function of the genes in a genome-wide, HTPmanner and set the challenges for the post-genomic era in the area known as functional genomics.Functional genomics focuses on a series of dynamic aspects of cellular biology such as gene transcription,translation and protein-protein interactions, including function-related aspects of the genome itself, such as mutationanalysis and the measurement of molecular activities. It utilises the development and application of global(genome-wide or systems-wide) experimental approaches e.g. genomics, transcriptomics, proteomics, in silico(in italics) functional prediction, etc.). HTP technologies are a hallmark of functional genomics experimentation,with their capacity for collecting data on a genome-wide scale.From Fundamental Genomics to Systems Biology: Understanding the Book of Life27

Functional genomics is a field of research offering many opportunities for technological innovation. These technologieshave proven strategically important for both academia and industry. Developing new HTP researchtools and technologies for collecting and processing vast amounts of new and high-quality data will dramaticallyincrease our knowledge of complex biological processes.Despite all the progress being made, there are a number of bottlenecks currently affecting functional genomicsresearch. The success of functional genomics lies in the development of novel tools to solve the practical limitationsit suffers today. It should also be noted that there is a high degree of fragmentation of technologies, resources andexpertise, which makes it difficult to exchange information and address the bottlenecks in a coordinated effort.Such collaboration is particularly important in view of the speed with which these technologies are moving andalso because of their multidisciplinary nature. Another important issue is the tools standardisation aspect: this isrequired to provide high-quality reproducible data and to enable valid exchange and comparison of experimentaldata. In addition, due to the large quantity of data produced by these techniques, the development of sophisticatedbioinformatics tools is necessary to increase the power of the functional genomics technologies. Most importantly,the development of new tools and technologies in functional genomics requires a large multidisciplinary and coordinatedeffort involving expertise in molecular biology, engineering, robotisation, electronics, material sciences andphysics. Only coordinated efforts at European level can bring together this diverse expertise with common goals ofdeveloping new cutting-edge technologies, and therefore the area is well suited for EU support.FP6 activitiesIn order for Europe to keep its competitive position in the development of new and improved functional genomicstools, a substantial number of projects have been supported in FP6 and several important actions have beenlaunched in the first three FP7 calls for proposals.In summary, the fundamental genomics programme in FP6 supported projects that aimed to improve existing ordevelop new tools and technologies for functional genomics research.The projects addressing such technologies are grouped in four categories, namely:■ technologies for gene expression■ technologies for proteomics■ technologies for molecular imaging■ tools and technologies for gene integrationPlenty of other projects developing tools and technologies are presented in the different sub-areas of structuralgenomics, model organisms, population genetics and bioinformatics in the following sections.The FP6 European projects have been successful in bringing together the tools, the developers and the experimentalistsfor developing the most appropriate state-of-the-art technology and for validating them in experimentalconditions. The HTP, high-precision technologies that are being established as a result of FP6-relatedprojects are expected to be of major importance to research, improving the competitiveness of Europe on theworld stage. Importantly, any technological innovation obtained through a coordinated European effort greatlyfacilitates wider access to these new technologies in Europe and to the international scientific community. Thefuture applications of functional genomics technologies in health research are endless: cellular mechanismscan be delineated, gene expression chips are already being used in early diagnosis, and proteins potentiallyhave enormous value as clinical biomarkers.FP7 activitiesThe EC recognises the immense potential of the technologies in functional genomics for innovation and strengtheningof European biotechnological and biomedical industry competitiveness. Therefore, FP7 has prioritised the28 From Fundamental Genomics to Systems Biology: Understanding the Book of Life

area of HTP research with a focus on new technologies for the following: sequencing, gene expression, genotypingand phenotyping, structural genomics, bioinformatics, systems biology and other ‘-omics’ fields.During the FP7 first call for proposals, EC supported three large integrating projects launched in 2008, amountingto 36 million overall, in the following subjects:■ development of human genetic variation databases integration (Gen2Phen);■ tools and technologies development for spatial and temporal proteomics (PROSPECTS);■ on technologies for DNA sequencing and genotyping (READNA).During the FP7 second call for proposals, a broad topic on SME-driven small-scale focused research CPs fordeveloping tools and technologies for HTP research was published. Several projects were selected for fundingamounting to approximately 30 million, covering areas on tools for gene expression, proteomics, sequencing,phenotyping (currently under negotiation). The funding upper limit was 3 million EC contribution per project,with 40% allocated to SMEs, which is expected to reinforce SMEs’ scientific and technological bases.The EC, continuing its efforts in the functional genomics tools area, published the FP7 third call forproposals in September 2008, with the aim of attracting proposals in the following areas:■ computational tools for genome annotation and genotype/phenotype data integrationtools, which will enable integration of the vast amounts of functional genomics data, facilitate data miningand catalyse progress in systems biology;■ HTP tools and technologies to analyse samples in large-scale human biobanks, which willdeliver high-quality and standardised data and accelerate epidemiological studies and biomarker discovery;■ tools, technologies and resources for the characterisation of protein functions, which willhelp to overcome bottlenecks in the investigation of protein functions in cells, leading to a better understandingof biological processes in health and disease.For the first time in EU CPs in health research, a two-stage selection process will be implemented, with proposaltopics that are broader in scope and that will invite a larger number of pre-proposals (of maximum 5 to 10 pages)for the first stage. In this way, the scientific community will be consulted for their ideas on research projects,aiming to keep Europe at the forefront of technology and resources development in HTP research.Europe is very competitive in the development of several groundbreaking technologies for functional genomics,and their applications are expected to have a great impact in biomedicine and in the biotechnology industry,including SMEs. Only coordinated efforts at European level can gather this different expertise with the commongoal of developing new cutting-edge technologies. Therefore, the FP7 Health priority via its Genomics and SystemsBiology programme will continue its support for catalyzing progress in this important area.The ability to functionally explore the effect of genes on cellular phenotypes and signalling in a HTP fashion is offundamental importance in all fields of life sciences and biomedicine and has also attracted the attention of thebiotechnology and biomedical industries.Developments in large-scale, high throughput technologies and robotics now allow researchers to simultaneouslyprofile vast numbers of different genes and gene products in parallel. Examples are DNA microarrays, wheremany thousands of genes are spotted onto an area no bigger than a microscope slide, allowing researchers tosample thousands of genes in parallel for expression analysis in health and disease.From Fundamental Genomics to Systems Biology: Understanding the Book of Life29

In view of the importance of spatial and temporal proteomics in the area of HTP tools development, at the FP7first call for proposals the EC supported the project PROSPECTS, a large scale integrating project fundedwith 12 million, to overcome current bottlenecks in the proteomics technologies. This multidisciplinary projectbrings together the world leaders in proteomics to make a major advance, both by developing much morepowerful instrumentation and by applying novel proteomics methods that will quantitatively annotate the humanproteome with respect to protein localisation and dynamics. These technological developments will be appliedso as to gain unique insights into the molecular basis of multiple forms of human disease, specifically neurodegenerationand other diseases related to folding stress.To keep Europe at the forefront of technology development in proteomics research, the EC, via its Health priority,published the FP7 second call for proposals for SME-targeted focused CPs in HTP research. Several proteomicsprojects have been selected for funding and are currently under negotiation. Continuing the efforts, the ECpublished the FP7 third call for proposals in September 2008 with the aim of developing tools, technologiesand resources for the characterisation of protein functions, to be implemented via a bottom-up approach and a twostageselection procedure. In this way, the scientific community will be consulted for their ideas on research projectsdeveloping state-of-the-art proteomics research.Further advances in proteomics techniques will help overcome bottlenecks in the investigation of protein functionsin cells, leading to a better understanding of biological processes in health and disease, and fostering Europeanresearch excellence and technological innovation.Although we need to continue to sequence genomes and to indentify individual proteins involved in a given biologicalresponse, the ultimate challenge will be to utilise the enormous amount of data generated and to convertthis into a dynamic picture of the subcellular, cellular or whole organism level. In the dynamic cellular environment,proteins and other cellular components undergo many processes — all primarily designed to maintaincellular function and homeostasis.Most of the current knowledge on gene expression, regulation and delivery in mammalian systems results from invitro or ex vivo studies. It is worthwhile reflecting on the fact that study of a biological system over time is generallyconstructed from a series of data obtained from different specimens, which often fail to represent accuratelythe true order of events in vivo. This situation, coupled with our inability to easily monitor multiple molecularspecies simultaneously, seriously limits our ability to study cellular processes, keeping in mind that biology isfundamentally dynamic.Biomedical methods have elucidated many cellular pathways and continue to do so. However, the desire to capturemicrosecond and nanosecond cellular changes and interactions in living cells in their natural environment, as wellas the need for high spatial and temporal specificity have led to the development of increasingly sophisticated imagingtechnologies. These techniques are becoming more powerful with the contribution of computing power.FP6 activitiesThe EC has supported FP6 collaborative projects (CPs), aiming at the development of new imaging technologiesfor monitoring gene and protein expression in situ and in vivo (often in tissues or living cells and whole animals).MOLECULAR IMAGING is an IP aiming to develop novel non-invasive imaging techniques that enablemonitoring of the dynamics of multiple molecules within living systems, and whole animals .The Tips4Cells focused project aims at further developing scanning probe microscopy (SPM); this is currentlythe imaging method of choice for measuring intermolecular and intramolecular forces in biomolecules at thesingle molecule level and for providing high-level information on structural details of biological samples in theirnative environment. The COMPUTIS focused project is developing new and improved technologies for molecularimaging mass spectrometry (MIMS), enabling innovative methods of investigation in functional genomics,proteomics and metabolomics, as well as investigation in cells and tissues.32 From Fundamental Genomics to Systems Biology: Understanding the Book of Life

High-resolution imaging of living cells and subcellular components is essential for functional and structuralgenomics. Developments in this field are expected to transform our understanding of biology, making experimentalinvestigations much more efficient, speeding up research into life sciences. Multidisciplinary consortia establishedin FP6, comprising physicists, mathematicians, biologists and chemists, addressing in vivo molecular imaging,resulted in the formation of ‘centres of excellence’, enabling greater technological developments and commercialopportunities. Imaging tools have potential for direct applicability in the biomedical sector; therefore partnershipsamongst academy, industry and the medical sector would facilitate the future transition from the laboratory anda wider diffusion and application of these technologies.One of the most important goals in the post-genomics era is to systematically determine the function of all genesand regulatory sequences within living cells. The so-called reverse genetics approaches rely on the targetedintegration of artificial gene constructs by homologous recombination to delete (knock-out) or alter (knock-in)chromosomal sequences.The modification of the cell’s genome by methods of gene targeting has traditionally been used in modern biologyfor gene function analysis and for development of tools for gene therapy. Therefore, controlled gene integrationand in particular targeted integration are key technologies for the exploitation of the full function of genomicinformation. Targeted gene integration also fulfils a critical role in medical research, as it allows the establishmentof animal disease models for advancing research in disease pathogenesis and treatment.Gene targeting allows researchers to precisely modify the genetic blueprint of living cells in vivo. The mechanismof gene integration into the chromosomes of living cells is far less known, and can occur either randomly or betargeted by homologous recombination.In FP6, the EC supported several focused research projects developing tools for gene integration and the study ofthe mechanisms of gene integration in different model organisms.The GENINTEG project seeks to establish a greater understanding of the mechanism of gene targeting and developnew generic tools for enhancing gene integration by applying an interdisciplinary and multi-organism comparativeapproach. TAGIP is a focused project that aims to develop gene targeting via homologous recombination as aroutine technology in plants that will facilitate the cost-efficient and large-scale production of therapeutic proteins.The PLASTOMICS project will define the mechanisms and improve the understanding of the genes and proteinsinvolved in several key stages of plastid transformation and foreign proteins expression. The focused projectMEGATOOLS studies meganuclease-induced recombination; this approach could provide a practical alternativeto current approaches and represents an extremely powerful tool for gene alteration.The clarification of gene function by transgenesis is important for our understanding of biological processesand disease pathogenesis. Therefore, investment in further developing gene integration technology promisesadvances not only in basic research, but also in drug development.Research into regulation of gene expression will enable scientists to decipher the functions of genes and theirprotein products, and acquire a clearer picture of the complex regulatory networks that control fundamentalbiological processes.The gene expression process is of fundamental importance for all living organisms. Regulation of gene expressionrefers to cellular control of the quantity and the timing of changes to the appearance of the functional product ofthe gene. Most genes reside in the chromosomes located in the cell nucleus and express themselves via proteinssynthesised in the cytoplasm. The genetic information is transcribed from DNA to RNA, and then translated fromFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life33

RNA into protein, the so-called central dogma in biology. Any of the steps leading to the expression of a genemay be modulated, from DNA or RNA transcription to the post-translational modification of a protein. Generegulation allows a cell to have control over its structure and function, which is the basis for cellular differentiation,morphogenesis and the versatility and adaptability of any organism to its environment.The sequence of an organism’s genome does not directly determine how the genome is used to build the organism.Buried deep in the primary code is a second regulatory code, which must also be deciphered.To address the importance of the gene regulation in the post-genomics era, the majority of FP6-funded projectswere oriented towards the understanding of:■ transcription regulation■ epigenetic regulation.The knowledge and methods developed within the FP6-funded projects will improve EU scientific competitivenessin the rapidly developing field of regulatory genomics, hopefully giving European scientists a head startin the race to decipher the regulation of the genetic code.Our genome consists of approximately 22 000 protein coding genes. However, only a fraction of these are usedin each cell. Which genes are expressed (i.e. govern the synthesis of new proteins) is controlled by the machinerythat copies DNA to mRNA in a process called transcription. In the gene expression pathway, the first regulated andin most cases rate-limiting step is the process of transcription. This process, in turn, can be modulated by variousfactors. A number of conceptual as well as mechanistic questions still need to be answered before we can attain acomplete picture of the principles employed by living organisms to control this process. One of the main gaps in ourknowledge is the limited insight we have regarding transcription regulation in the nuclear environment.The goal of the TRANS-REG focused project is to obtain a comprehensive knowledge of the mechanism ofregulation of model genes during cell differentiation, cell proliferation and signal transduction. The consortiumis undertaking concerted efforts to develop and apply different molecular and cell biology approaches to studythe molecular characteristics.The X-TRA-NET project develops and employs chromatin immunoprecipitation technology combined with sequencingto explore the complex transcriptional network of nuclear receptors signalling pathways and regulation. Theseunique methods will be used to investigate the impact of binding site diversity on the mechanism of gene activationwith potential impact in the treatment of major diseases such as cancer, insulin resistance and atherosclerosis.The completion of the human genome has provided a wealth of information about our genetic wiring. Epigeneticsis defined as the study of the heritable changes in genome function that occur without a change in DNAsequence. It seeks to determine how genome function is affected by mechanisms that regulate the ways the genesare controlled. There are hundreds of different kinds of cells in our bodies. Although each one derives from thesame starting point, the features of a neuron are different from a liver cell. As cells develop, their fate is governedby the selective use and silencing of genes. This process is subject to epigenetic factors where DNA methylationplays an important role in all the phenomena where genes are switched on and off. Epigenetics also provides ameans by which genetic material can respond to changing environmental conditions.Over recent years, the study of epigenetics (chromatin and/or DNA modifications not attributed to changes inthe DNA sequence but surviving across generations) has received increased attention due to its possible role inpathogenesis and in a series of the organism’s phenotypic characteristics.34 From Fundamental Genomics to Systems Biology: Understanding the Book of Life

The huge interest in epigenetic regulation of gene expression has led to a number of excellent European-fundedinitiatives. In the later stages of FP6, strong links were established between these projects, thereby developing aEuropean critical mass in this field.The EPIGENOME project has established a network of excellence (NoE) providing a platform for the developmentof the European epigenetic research. It seeks to promote the ERA in the field, not only by means of a strong researchprogramme, but also by integrating and disseminating the project’s activities, including an efficient communicationinfrastructure to enable internal communication of geographically dispersed teams and to foster public dialogue.The HEROIC project advances epigenetic research with HTP technology in the context of the whole genometo help unravel the meaning of the epigenetic code. It performs research into gene regulatory systems at thelevel of the chromatin structure and nuclear organisation, employing the most extensive multidisciplinary consortiumever assembled at European level. Although the chromatin immunoprecipitation (ChIP) assay plays acrucial role in deciphering patterns of epigenetic marks that govern gene transcription, it still suffers from lowresolution and low sensitivity. The CHILL project will overcome this by developing Chromatin Immuno-LinkedLigation (ChILL) technology resulting in a better understanding of the epigenetic code. The SMARTER projectwill help in the treatment of cancers by investigating the small molecules that target histone deacetylases andby opening up new avenues of research.Epigenetic research is anticipated to have far-reaching implications for medicine. Using a combination of genomictools, researchers are trying to better understand processes like DNA methylation in order to use theinformation for more effective early diagnosis of complex diseases (such as cancer) and to develop innovativetreatments directly targeting the molecules involved in these processes.The way molecules such as proteins and ribonucleic acids (DNA and RNA) interact with one another and withother molecules (such as drugs) is determined by their 3-D structure. Understanding the 3-D structure of these macromoleculesis critical for the understanding of their role in complex biological processes, and is essential for drugdesign. Most molecular interactions can only take place as a result of the molecules’ chemical architecture, creatingactive sites where they can link together with complementary molecules or interact as a part of cellular machinery,in order to acquire the functional state required in a living organism. In proteins, these sites depend on the way thelong chains of amino acids of which they are constituted are intricately folded to give a final 3-D structure. Mostdrugs target particular protein functions, either of proteins of human origin or of a specific pathogen, and the developmentof new drugs relies heavily on knowledge of the targeted protein’s structure. Compounds with potentialpharmaceutical activity can be designed and tested to determine their potential by altering the protein structure.Structural genomics researchers are using and developing a variety of techniques to study the 3D structure of macromolecules((X-Ray crystallography, nuclear magnetic resonance or NMR, 3-D Electron Microscopy). During, thelast decade, the major bottleneck in the technological developments described above, from the stage of samplepreparation to the analysis of structural data, has been the low-throughput outcome. The techniques did not permita sufficiently HTP analysis of samples and the determination of the structures of the thousands of macromolecules isstill to be solved. Research effort has therefore been focused on the automatisation of many stages in the proceduresto reduce bottlenecks and increase throughput.The concept of structural genomics arose in the late 1990s in the US and Japan as a response of the successof HTP sequencing methods applied to whole genomes. It was anticipated that similar HTP methods could beapplied to obtain 3-D structures of all the proteins. This vision led to the investment of substantial funds into largescalestructural genomics projects in the US (between 2000 and 2005) and in Japan. Europe was slow to enterthe area of structural genomics and proteomics, and European investment in this area has been on a considerablysmaller scale.In Europe, the first large collaborative initiative in implementing HTP approaches to structural biology waslaunched in 2002 (pilot FP5 IP) with the project SPINE: Structural Proteomics in Europe (www.spineurope.org).The challenge set for SPINE was to push forward cutting-edge technologies aimed at biomedically relevant tar-From Fundamental Genomics to Systems Biology: Understanding the Book of Life35

gets, while at the same time generating a pan-European integrated effort directed towards biomedically orientedstructural proteomics. The project produced approximately 300 novel protein structures and also developed Europeanstandards in protein crystal handling for X-ray crystallography studies. The success of the SPINE project,and its catalytic effect on the area, led to a new generation of CPs.FP6 activitiesThe effort in structural genomics and structural proteomics activity area was substantially increased in the EU’sFP6 Programme for RTD (2002–2006), with objectives to enable researchers to determine, more effectively andat a higher rate than was currently feasible, the 3-D structure of proteins and other macromolecules, which isimportant for elucidating protein function and essential for drug design.Whereas, in general, the projects elsewhere have tended towards a HTP approach, which would cover anorganism, an organelle or a category of proteins, most of the European projects are oriented towards technologydevelopment or high-value targets, in most cases associated with diseases (drug targets, viral pathogens,membrane receptors, signalling complexes involved in neuronal development and degeneration, immunology,and cancer).The FP6-funded projects in structural genomics and proteomics, whose objectives, results and potential impactare presented in this publication, cover the three main technological disciplines (X-Ray crystallography, NMR,and Electron Microscopy), which in many cases are integrated into the same consortium for the first time.In summary, the FP6 projects can be classified into three categories:1. Projects that are biologically focused and generate high-value 3-D structuresof proteins and complexes of fundamental and biomedical importance.These projects aim at the following:■ 3-D structure determination of viral pathogensVIZIER: The aim of this IP is to gather knowledge on viral replication needed to develop new drugs toprevent new viral outbreaks. RNA viruses include more than 350 different major human pathogens. Theproject, unprecedented in size, has set out the sequence of the genomes of hundreds of viruses, definedthe proteins essential for replication, and through a major 3-D structural effort is identifying common sitesof these proteins that could be a target for new antivirals with a large spectrum of action. FSG-V-RNAis a more targeted complementary project, which aims at developing and improving tools for the rapidstructural analysis of RNA and RNA-protein complexes in several RNA viruses.■ 3-D structure determination of membrane proteinsE-MeP is an IP that aims at solving the bottlenecks that preclude the determination, at HTP, of highresolutionstructures of membrane proteins and membrane protein complexes; an integrated databasecataloguing E-MeP’s results, protocols and other pertinent data is being developed.■ 3-D structures of components of important signalling pathwaysSPINE-2-COMPLEXES is a second-generation SPINE project that aims at investigating signalling pathwaysfrom receptor to gene by combining the knowledge of genomes with HTP methods for structuralproteomics. The complexes under study are extremely important with respect to human health and aredrawn from the common theme of signalling pathways with targets from key areas of biology, includingcell cycle, neurobiology, cancer and immunology, as well as pathogen proteins that modulate or subverthuman signalling pathways.■ 3-D structures of large complexes3D-Repertoire aims at determining the structures of all amenable complexes from the budding yeastat medium or high resolution by electron microscopy, X-ray crystallography, and in silico methods; thesestructures will serve to integrate toponomic and dynamic analyses of protein complexes in a cell.36 From Fundamental Genomics to Systems Biology: Understanding the Book of Life

2. Projects that develop new and/or improving existing technologies and methodsas well as bioinformatics tools for structure determination of proteins and complexes.These projects aim at the following:■ New and improved tools for 3-D electron microscopy3D-EM is bringing together European excellence in electron microscopy approaches for studying proteincomplexes and cellular supramolecular architecture. This NoE addresses the development and improvementof existing 3D-EM techniques, the standardisation of data processing, the integration of researchactivities and the transfer of knowledge. HT3DEM is a more focused project aimed at developing aninnovative technological platform for HTP screening and analysis of native protein complexes and proteincrystals that will reduce processing time and cost.■ New and improved tools for X-ray crystallographyBIOXHIT is mobilising both all European synchrotron facilities with beamlines equipped for macromolecularcrystallography (either already in existence or planned for the future), and also most of the softwaredevelopers active in fields relevant to HTP structure determination. It aims to build a common platform forEuropean researchers in the field of biological crystallography. It focuses on the development of hardwaresynchrotron technologies, HTP crystallisation technologies and standardisation of methodologies in synchrotrondata acquisition and treatment. This IP represents the greatest possible mobilisation of resourcesat the European level, both in terms of infrastructure and scientific excellence.Furthermore, the optimisation of methods for the production of proteins is important for retrieving sufficientquantities for crystallisation purposes. OptiCryst is a focused project with the goal of improvingand automating methods for protein crystallisation and the objective of increasing speed and crystallisationsuccess rates. IMPS aims at innovative techniques for expressing, stabilising, purifying and crystallisingmembrane proteins.■ New and improved tools for NMR structure determinationNDDP is a focused project that develops cutting-edge NMR techniques for the dynamic characterisationof drug-receptor interactions to support structure-based drug design for phosphatases, a major class ofproteins for a broad range of medical applications. UPMAN is studying the structural states of proteinsfrom unfolded monomers to oligomers and fibrillar aggregates. A variety of NMR techniques coupledwith novel computational approaches are used in order to define the misfolded structures’ characteristicsand are then applied to representative samples of the various types of proteins that are associated withmisfolding diseases.■ In silico tools for structure determinationExtend-NMR deals with the development of novel computational tools that extend the scope of NMRand that make possible functional and structural studies of larger proteins and biomolecular complexeswhich are not amenable to crystallisation. is developing improved bioinformatics tools forreliably assigning function to genes, with an emphasis on in silico protein-protein interaction and 3-Dstructure determination. The developed function prediction methods should improve the in silico functionalannotation of the genome.3. Projects that network and coordinate research efforts in Europe,as well as promoting high-level training. These projects aim at the following:■ High-value training in structural genomics in EuropeE-MeP-Lab is an SSA, where for the first time Europe’s membrane protein structural biology communitywill organise high-level training with advanced practical courses in the best-equipped laboratories in Europe.TEACH-SG is an SSA that provides a platform for training young scientists and those from smallerlaboratories and new EU Member States in the HTP technologies developed in the area of structural genomics,by organising a series of workshops and meetings with hands-on training.■ Networking and coordination in SG/SPNMR-Life promotes the networking and coordination of NMR research in structural genomics via theexchange of personnel and good practices, the organisation of meetings and the implementation of a vir-From Fundamental Genomics to Systems Biology: Understanding the Book of Life37

tual laboratory. FESP is a CA that aims at a thorough assessment of the existing structural genomics andstructural proteomics projects and infrastructures at national, European and international levels. Its majorgoal is to develop a strategy for structural genomics and structural proteomics in the broader context ofanticipated developments in biological research, resulting in recommendations for future European policiesin this area.In total, the EU investment in structural proteomics increased substantially in FP6, reachingmore than 90 million. Thanks in large part to EU-funded projects, in the last few years the structuralproteomics field has had good publicity and achieved international stature comparable to large-scale projectsin the US and Japan. While it is still premature to predict the success of the FP6 structural genomics projects,we could say that these projects have played an important part in integrating the research community in Europe,thereby increasing visibility at national, European, and international level, and improving the capacityto tackle ambitious challenges in research in a collaborative manner. By doing so, these projects are reducingthe fragmentation of research in Europe and are realising the concept of the ERA in structural genomics. Infigure 7, the steps towards the ERA in structural genomics are presented.Mature FieldInterdisciplinaryInitiatives in Structural Genomics/ProteomicsBiologically-FocusedResearchVIZIER(RNA Viruses)FSG-V-RNA(viral RNA)E-MeP(Membraneproteins)3D-Repertoire(Large Complexes)SPINE2-COMPLEXESSignalling Pathways-Structures of complexesIMPS (tools forMembrane proteins)OptiCryst (ProteinCrystallization)Extend-NMR(NMR)HT-3DEM (highthroughput3D-EM)1 st call - 20022 nd call - 20033 rd call - 20044 th call - 2005TechnologicalDevelopmentsGeneFun (in silicostrucure prediction) BIOXHIT3DGENOME(3D microscopy)(X-rayCrystallography)UPMAN (proteinmisfoldingaggregation)3D-EMNDDP (NMRphosphatases)(ElectronMicroscopy)Coordination, Fora,Workshops, TrainingFESP (Forum forEuropean StructuralProteomics)NMR-Life(coordinationaction)E-Mep-Lab(Training inMembrane proteins)TEACH-SG(Training inStructural Genomics)IP, NoESTREP, CA, SSAEuropeanFP5 Pilot projectFP5 foundations for European Structural Genomics:SPINE (pilot IP 2002-2005)Fig. 7: Steps to ERA in Structural Genomics and Structural Proteomics in FP6 (2002-2006)FP7 activitiesThe future of the field relies on combining integrated structural biology with cell biology so that the atomic dissectionof the cell can be reconstituted into a functional system (3-D cellular structural biology). FP7 will continue tosupport projects aiming at developing new and/or improving existing tools and technologies for protein and protein-complexstructure determination. Most importantly, in FP7, structural genomics projects will be implementing38From Fundamental Genomics to Systems Biology: Understanding the Book of Life

large-scale data gathering initiatives, but will also participate in multidisciplinary systems biology approaches.Understanding membrane protein function remains one of the research frontiers in cellular biology. Membraneproteins constitute approximately one third of all human proteins and are important drug targets. However, inthe current literature, membrane protein structure determination represents only 0.3% of all the protein structuresexisting in the public databases. To increase our knowledge in this important family of proteins, the EC set as apriority the structure-function analysis of membrane transporters and channels for the identification of potentialdrug target sites, in the FP7 first call for proposals in large-scale data gathering functional genomics initiatives.The following two complementary large IPs were funded and started in the beginning of 2008.EDICT: European Drug Initiative on Channels and TransportersAt a funding level of 12 million, this IP aims at characterising the structure-function of membrane superfamiliesin human and pathogenic microorganisms, covering a wide variety of human diseases. The main strength ofEDICT (where two of the partners are Nobel Prize winners) is its powerful HTP structural genomics pipeline. In addition,high-resolution images coupled with sophisticated computational methods will identify new drug targets.NeuroCypresAt a funding level of 11 million, this IP focuses on channel proteins of the central and peripheral nervous systeminvolved in severe neurodegenerative diseases. Its main strength is its multidisciplinary approach with a focus onbiology for understanding the link between dysfunction and disease.Figure 8 shows the runtime of current EU-funded CPs in structural genomics and structural proteomics between2002 and 2008, including all FP6 and the FP7 first call funded projects.This drastic change in investment implemented via the European FPs for RTD (FP5, FP6 andFP7 first call for proposals), resulted in a major investment of approximately 120 millionallocated to Collaborative Structural Genomics projects between 2002 and 2008.Project Acronym 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 FPSPINEBIOXHIT3D-EM3DGENOMEE-MePVIZIERNDDPUPMANGeneFunFSG-V-RNA3D-RepertoireExtend-NMRHT3DEMIMPSOptiCrystSPINE2-COMPLEXESFESPE-MeP-LabNMR-LifeTEACH-SGEDICTNeuroCypresIP13.7mIP10mNoE10mSTREP 2.2mIP10.35mIP13mSTREP 1mSTREP 1.9mSTREP 1.5mSTREP 2.4mIP13mSTREP 2mSTREP 1.8mSTREP 1.9mSTREP 2.3mIP12mSSA 0.3mSSA0.3mCA1.1mSSA 0.5mIP11.9mIP11.03m2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012FP5FP6FP7Fig. 8: Runtime of current EU-funded collaborative research projects in structural genomics and structural proteomics(funding period started in 2004 for FP6 projects-most projects extend well beyond 2007; funding period started in 2008 for the FP7 fi rst call projects)From Fundamental Genomics to Systems Biology: Understanding the Book of Life39

Comparative genomics is the analysis and comparison of genomes from different species. The purpose is to gaina better understanding on the genetic differences between species and to determine the function of the genes.Researchers have learned a great deal about the function of human genes by examining their counterparts inmodel organisms such as the mouse.The sequencing of the human genome has revealed that our genetic material is composed of about 22 000 differentgenes. Despite their morphological differences, model organisms and humans share a strong conservation of genesas well as fundamental biological pathways. This extensive conservation has promoted the use of model organismsas a means to study conserved processes.However, just identifying a gene does not tell us much about its potential function in health and disease. To investigatethis, it is necessary to mutate the gene in a model organism. Several model organisms are extensivelystudied to understand particular biological phenomena, with the expectation that discoveries made in thesemodels will provide insight into the workings of other organisms. In particular, model organisms are widely usedto explore potential causes and treatments for human disease in instances where experimentation on humanswould be unfeasible or unethical.FP6 activitiesIn FP6, substantial resources were invested in comparative genomics, in particular for research in rodentmodels like the mouse and the rat, but also in other vertebrate models like the zebrafish and the frog. Projectsinvolving invertebrate models (e.g. nematodes, yeast, etc.) were been funded in FP6. Finally, bacterial andplant functional genomics projects were also partially supported as cross-cutting activities with other FP6 fundamentalgenomics thematic areas.The identification of all the genes in mice and humans in the Human Genome Project has shown that about 99%of the genes in mice have an equivalent gene (or homologue) in humans. This is important as, to date, around5 000 diseases have been shown to be caused by an error in our genetic make-up (in our genes), for examplecystic fibrosis and Down’s syndrome. In several more complex diseases, such as diabetes, an error in the geneticmake-up is a contributory factor.In addition, powerful conditional mutagenesis technology has been developed that currently can only be appliedin the mouse to specifically inactivate any gene in a time- and space-dependent manner. This approach allowsus to very precisely unravel the genetic networks underlying disease. All things considered, the mouse is one ofthe model organism of choice for human disease research.EUMORPHIA was the first major integrated research programme (funded at the end of FP5) on mouse researchthat brought together a large consortium of 18 mouse research centres in 8 European countries. Themain goal of this large initiative was the development and standardisation of new approaches in phenotyping,mutagenesis and informatics leading to improved characterisation of mouse models for the understanding ofhuman physiology and disease. The project delivered an extensive database of standardised phenotypingprotocols (EMPReSS) that is now widely used in many mouse laboratories across Europe (Brown S.D. et al.,Nature Genetics, 2005, 11, 1113–20). Furthermore, this project has also played an important role in structuringthe research landscape in mouse research in Europe.In FP6, building on the success of EUMORPHIA, several mouse large-scale functional genomics initiatives(EUCOMM, EUMODIC, EUREXPRESS, and MUGEN) were funded that may be grouped as follows:40 From Fundamental Genomics to Systems Biology: Understanding the Book of Life

1. Projects that develop tools and resources for mouse functional genomicsEUCOMM integrates European skills, resources, and infrastructure to produce, in a systematic, HTP way,mutations throughout the mouse genome. A collection of up to 20 000 mutated genes will be generatedin mouse embryonic stem (ES) cells using conditional gene trapping and gene targeting approaches. Thismutant resource will be of crucial importance for health research since it will allow scientists to dissectgene functions within a living organism (in vivo) more accurately and to mimic human disease conditionsmore closely. By networking their effort at the European level with the EUCOMM project, Europeansresearchers are playing a leading role in the International Mouse Knockout Consortium that was launchedrecently (Collins F.S., Cell 2007, 128, 9–13; Qiu J., Nature 2006, 444, 814–816) and which joinedEUCOMM, KOMP (funded by the National Institutes of Health) and NorCOMM (funded by GenomeCanada). FLPFLEX is a more focused project aiming to develop flexible genomic insertion cassettescarrying modifications to allow recombinase-mediated cassette exchange of effector genes of interest.Molecular Imaging is another project (mentioned earlier in the functional genomics tools section) whichaims to develop non-invasive imaging tools for whole animals (mice) in vivo.2. Projects that develop tools and technologies for large-scaleand HTP phenotyping studiesEUREXPRESS and EUMODIC are both focused on phenotyping. EUREXPRESS’s main goal will be todeliver expression patterns for 20 000 mouse genes during embryonic development and in adult tissues.EUMODIC will phenotype in depth, using the EMPReSS standardised protocols (about 650 mutant lines)produced from the EUCOMM project. MUGEN is another FP6 major research initiative using functionalgenomics tools to analyse more that 200 mouse mutant strains showing defects in the immune systems in astandardised way.3. Plenty of projects support biologically focused research, using mouseas an essential model to understand diseases mechanismsThese projects cover a great variety of basic biological processes; several projects use predominantlymouse as the animal model of choice.MUGEN aims to structure and shape a world-class network of European scientific and technologicalexcellence in the field of murine models of human immunological diseases that will advance understandingof the genetic basis of disease and enhance the innovation and translatability of research efforts.The main objective of HEROIC is to make significant advances in the mechanistic questions of epigeneticregulation, characterise the epigenetic modifications that occur, and then understand the implications forgene expression in different cell types. The approach focuses on the use of HTP-enabling technologies onpredominantly primary and established mouse cell lines, particularly ES cells.The majority of the projects funded under the areas on multidisciplinary approaches to basic biologicalprocesses (see Part B,Chapter 7) are either using established mouse models or creating novel mouse modelsto understand health diseases. One example is the FunGenES consortium, which addresses fundamentalissues of stem cell biology differentiation and functional genomics, pursuing an integrated strategy basedon cultured mouse ES cells. Another, the EUROHEAR IP develops novel mouse models to understand themechanisms of hearing deficiencies.4. Projects that network and coordinate research efforts in EuropeAlong with the research initiatives, the EC has financed two CA projects: PRIME and CASIMIR. The aim ofPRIME is to build on existing national and European mouse research programmes, resource centres andinfrastructures by focusing and integrating them, rather than establishing new programmes. The long-termaim is to establish mechanisms to define future research policies and directions in a coordinated manneracross Europe. CASIMIR focuses on coordination and integration of databases set up in support of FP5and FP6 projects containing experimental data, including sequences, and material resources such asbiological collections, relevant to the use of the mouse as a model organism for human disease.From Fundamental Genomics to Systems Biology: Understanding the Book of Life41

Integrated European Mousefunctional Genomics ProgrammeBiologicallyFocused ResearchMUGEN(mouse modelsfor immunologicaldiseases)FunGenES(mouse ES cellsdifferentiation)HEROIC(Epigenetics inMouse ES cells)EUROHEAR(mouse modelsfor hearingdeficiencies)PhenotypingEURExpress(high-throughputin situhybridisation)EUMODIC(European mouseDisease clinic)1 st call - 20022 nd call - 20033 rd call - 20044 th call - 2005IP, NoESTREP, CA, SSATools and ResourcesCoordination, Fora,WorkshopsEuropeanPilot projectMolecular Imaging(in-vivo imagingtechnologies)PRIME(Co-ordination of mouse functionalgenomics programmes)FLPFLEX(transgenic tools)EUCOMM(genome-widemutagenesis)CASIMIR(Co-ordination/integrationof databases)FP5 foundations for European Mouse Functional GenomicsProgramme: EUMORPHIA (pilot IP 2002-2005) onstandardised phenotyping protocolsFig. 9 : Steps to ERA in mouse functional genomics research in FP6 (2002-2006)In FP5 and FP6 the European Commission has invested substantially in mouse functional genomics.All projects are very ambitious and highly complementary to each other, thereby creating an integrated European Research programmein mouse functional genomics. By joining their forces at the European level via these collaborative projects,Europe is now at the forefront of mouse functional genomics research at the international level.Europe has a large community of researchers using the rat as a model. Indeed, over the last 50 years, therat has also intensively been used by physiologists to investigate molecular determinants of diseases such asdiabetes. The availability of the rat genome sequence (since December 2004) and genome-scale technologies,along with the ability to clone fertile adult rats, has substantially advanced the potential for functional genomicsresearch in the rat model.The EURATools IP draws together leading European researchers in rat genetics, pharmacology, toxicology, diseasepathophysiology, and genome biology and informatics. The central aim of this project is the developmentof integrated genome tools that will generate knowledge that can be translated into improvements in healthcarefor highly prevalent diseases in the EU. Besides scientific excellence, EURATools is expected to have a strongEuropean structuring effect in the rat research community.In addition, two smaller-scale projects, MED-RAT and STAR, were also funded in FP6. These two projects arecomplementary to the EURATools project: one is developing new tools to generate transgenic and knock-out ratmodels (MED-RAT) while the other is generating a SNP and haplotype map for the rat model (STAR).42 From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Zebrafish is a vertebrate model that offers numerous advantages compared to the rodent models. It is smaller insize and less costly to grow and maintain. Many transgenic approaches are also possible in this animal, facilitatingthe study of genes highly conserved in vertebrates and having functions in health and diseases.Furthermore, for developmental biologists, the zebrafish model offers additional advantages. Indeed, the developmentalprocesses can be easily observed in the fish since the embryo develops outside the mother body andis also fully transparent. ZF-MODELS IP aims to utilise the zebrafish model to harvest large datasets on genefunctions underlying development and disease. Fish with genetic disorders corresponding to human diseases areproduced by chemical mutagenesis (forward genetics) and targeted knock-out (reverse genetics) and are phenotypicallycharacterised. These disease models will aid clinical researchers and the European pharmaceuticalindustry in the development of new therapies. This project will also contribute to improving basic knowledge ofhuman development, since key genes involved in development are often reactivated in adult life in many congenitaldiseases and cancers.Furthermore, the zebrafish embryo model also shows great potential to be incorporated into preclinical drugscreening pipelines. ZF-TOOLS aims to develop a case study for an anti-tumour drug screening system, basedon implantation of fluorescently labelled tumour cells into zebrafish embryos. This system allows for the powerfulcombination of visual monitoring with HTP analysis of expression of marker genes with a predictive value fortumour progression or for defence responses to developing tumours.The EC is also supporting functional genomics research projects in other model organisms including Xenopuslaevis (X-OMICS) and C. elegans nematode (NEMAGENETAG). Under the Systems Biology umbrella, theEC is also supporting a large IP (AGRONOMICS) on leaf development in Arabidopsis thaliana and a largeIP (BaSysBio) in Bacillus subtilis. These projects are also cross-cutting in nature, relating to other FP6 thematicpriorities, in particular with Priority 2, related to Food Safety.Importantly, an essential part of the thematic sub-area ‘Multidisciplinary functional genomics approaches to studybasic biological processes’ is devoted to model organism research used as tools to understand a particular basicbiological process. These projects are presented in a separate section in the current publication.In conclusion, between 2002 and 2007, the EC’s FPs (FP5, FP6) provided more than 150million for collaborative research projects on model organisms, such as mouse, rat,zebrafish, plant, nematode worm and bacteria. These projects are playing an important role instructuring the research landscape in Europe and creating the knowledge base to understand health anddisease. Furthermore, they are generating important and freely available data and/or animal resources thatwill catalyse progress in biomedical research.FP7 activitiesIn FP7, support of research on model organisms continues, and considering that FP6 funded several projectsin rodent models, we have proposed calls for proposals on establishing consortia on genome-wide associationstudies in non-rodent mammalian models that develop diseases analogous to those seen in humans.At the beginning of 2008, the EC launched the 12 million IP LUPA, which aims at elucidating the molecularbasis of common complex human disorders using the dog as a model system. This project brings together expertsin genomics, the world’s leading scientists in complex trait genetic analysis, and interconnects the majorveterinary centres of Europe, utilising HTP molecular tools. It should also be emphasised that particular attentionis being paid to following strict national guidelines for animal welfare.From Fundamental Genomics to Systems Biology: Understanding the Book of Life43

For the first two calls of the FP7, in the genomics and systems biology area, no specific topics related to large IPs inrodent model organisms were proposed. This area, and in particular research in mouse, was well covered in FP6and there was a need for the currently funded projects to reach the required maturity for novel evolving ideas.A policy workshop was organised by the Genomics and Systems Biology unit in the Health Directorate in March2007, in cooperation with other funding agencies, (including, the US National Institutes of Health and GenomeCanada), to explore the future research needs in the field of mouse functional genomics. The recommendationsof that workshop, which brought together the world-leaders in the field, also served as a foundation to reflecton future FP7 activities in the area. In the FP7’s third call for proposals, published in September 2008, the ECproposed a bottom-up approach, implementing (for the first time in the Health priority) a two-stage selectionprocedure, to attract proposals on large-scale functional genomics efforts in multicellular model organisms. Theexpected impact is to continue progressing in the understanding of the function of all human genes, their complexinteractions, and their role in disease.Project Acronym 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 FPEUMORPHIAEURExpressMUGENFLPFLEXEUCOMMPRIMEEUMODICCASIMIRSTARMED-RATEURAToolsZF-MODELSZF-TOOLSTP PlantsNEMAGENTAGX-OMICSLUPAIP17.3mIP10.8mNoE11mSTREP 1.7mIP10.3mCA0.8mIP12mCA1.3mSTREP 2.4mSTREP 1.6mIP11mIP12mSME-STREP 1.7mSSA 0.56mSME-STREP 1.8mCA0.8mIP11.9m2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012Fig. 10: Runtime of current EU-funded collaborative research projects in model organisms(funding period started in 2004 for FP6 projects-most projects extend well beyond 2007; funding period started in 2008 for the FP7 fi rst call projects)Common diseases of major public health importance are phenotypically complex, with many having a heritablecomponent. Population genetics approaches are used to characterise complex diseases and associated pathophysiologicalstates in respect to the genetic and environmental determinants involved. An important element of populationgenetics research is the study of the genetic variations and/or mutations that are correlated to the healthyand diseased phenotype. The estimated 22 000 protein-encoding genes are calculated to contain myriad possiblevariations, called polymorphisms, which increase the complexity of our genes. The human genome comprises about3 x 10 9 base pairs of DNA, and the extent of human genetic variation is such that no two humans, even identicaltwins, will be genetically identical. The amount of genetic variation is about 0.1%, meaning that about 1 base pairout of every 1 000 will be different between any 2 individuals. Some of these variations determine physical characteristics,but others can determine the susceptibility to certain diseases, or the response to drug therapies.Access to databases containing genotypic, clinical, and environmental and lifestyle information on individuals,along with corresponding clinical samples/specimens (biobanks), are an essential component for population geneticsresearch. The systematic collections of genetic material and other relevant information on individuals, namelybiobank collections, make it easier for researchers — using HTP analytical tools for monitoring DNA variationscombined with powerful bioinformatics — to systematically search for links between gene variation and disease.44 From Fundamental Genomics to Systems Biology: Understanding the Book of Life

There has been relatively little success in finding genes for complex disease or complex traits, most likely due tothe expected small effect of individual genes on complex disease. Because of the complex relationship betweendisease and genetic, environmental and lifestyle factors, population geneticists need access to very large numbersof samples to ensure that any patterns they observe are statistically significant. For this reason, populationstudies increasingly necessitate international collaboration to ensure that large data sources can be shared. Theethical, legal and social aspects of this type of research are also extremely important factors in ensuring thatindividuals’ data are respected.In several European countries, a multitude of national and regional population and disease-oriented biobankshave been systematically collected for decades via the national healthcare systems, representing a uniqueEuropean strength. Significant advantage could be gained by pooling the resources already available orunder construction. This could give researchers access to greater cohort size and data sets, so that the researchoutcome from associations’ studies between genotype, environment, and lifestyle at individual andpopulation level could lead to greater statistical significance and prediction. The lack of standardised andquality-controlled protocols for data and sample collection, storage, retrieval, analysis and access, as well asthe diversity of national legal regulations, have created a great deal of fragmentation and created obstaclesfor collaboration at European level. It would make an enormous difference if the protocols involved in humanpopulation genetics research at national level could be harmonised to become representative and accessibleat European and international level.Building the ERA in population genetics research via a coordinated and collaborative approach will address theexisting bottlenecks and would pave the way for advances in biomedicine and improvement of the public health.The EC, recognising the power of population-based approaches in the study of genetic susceptibility for disease,has funded a number of networking activities and collaborative research projects between 2002 and 2008.In Europe, the first large collaborative initiative on genetic epidemiology on common diseases utilising samplesfrom large- and medium-sized population biobanks and involving cross-border transfer of data and samples waslaunched in 2002 (pilot FP5 IP) with GenomEUtwin (www.genomeutwin.org). The main objective for Genom-EUtwin was to perform genome-wide analyses of European twin and population cohorts with the aim of identifyinggenes predisposing the carrier to common diseases. During the four-year period, the partners harmonisedand integrated the study cohorts’ data (a combined cohort of 850 000 twins and a cardiovascular diseasescohort of 160 000 volunteers). Genome-wide studies have the potential to systematically identify the contributionsof common genetic variants to human disease. This unique project has provided the basis for the detectionof small genetic infuences on common diseases, which may not be detected in small-scale family studies. Importantly,the project has developed an Ethics Manual defining policies for the transfer of data and samples betweencountries. GenomEUtwin is a cornerstone of European genetic epidemiological research, because it paved theway for harmonisation of collected data, easy access to available data by creating a unified database structureand genome-wide analysis of the existing cohorts.FP6 activitiesThe success of the GenomeEUtwin project, and its catalytic effect on the area, led to new CPs in FP6. Theseprojects are taking full advantage of specific population cohorts available in Europe for determining the relationshipbetween gene function and health or disease. These projects may be classified into the followinggeneral categories.1. Projects developing tools and technologiesThese projects bring together the critical mass to catalyse the development of techniques and technologiesfor population genetics research.MOLPAGE is an IP that develops and validates a range of ‘-omics’ technology platform tools (metabonomic,genomic, proteomic) for molecular phenotyping in large epidemiological studies. These tools will beused for identification of biomarkers, prediction of disease, and risk determination or response to therapy.The consortium develops and disseminates standards for the collection, processing and storage of biologi-From Fundamental Genomics to Systems Biology: Understanding the Book of Life45

cal samples that are suitable for use in large sets of individuals, applicable to biological fluids and solidtissue samples, and optimised for future ‘-omics’ platform analysis. The project is expected to significantlycontribute to the development of international scientific standards in molecular phenotyping.2. Projects performing large and medium-scale epidemiological studiesAll these projects perform large-scale studies on genetic epidemiology on common diseases and relatedtraits, utilising samples in large- and medium-sized biobanks and involving cross-border transfer of dataand samples.The EUROSPAN focused project has the objective of quantifying genetic variation in established diseasedgenes across population cohorts in Europe, with the goal of identifying novel disease variants. It will createa large database of phenotypic and genotypic data from genetic isolated populations and will thusimprove European competitiveness in gene discovery.GenOSept is a STREP which uses a multidisciplinary fundamental genomics approach to examine geneticpredisposition to sepsis by harmonising HTP genotyping and quality control between major European centres.3. Projects for networking and coordinationThe EC is also financing several CAs (such as PHOEBE and IMPACTS), as well as SSAs (such as DanuBiobankand EUHealthGen). PHOEBE promotes harmonisation of epidemiological biobanks in Europe. IMPACTScoordinates the standardisation of tissue archives. EUHealthGen organised a Wellcome Trust/EU EC conference(‘From Biobanks to Biomarkers’) to enable dialogue on the potential of human population geneticsresearch. The aim of Danubiobank is to establish a biobank foundation for ageing disorders by networkinguniversities, teaching in hospitals, developing prevention programmes and clinics along the Danube River, viathe organisation of workshops and conferences.On the whole, these projects have the following aims: to exchange information on research biobanks inEurope and beyond; to standardise and harmonise existing protocols for the acquisition, management andanalysis of data and samples from different sources; to develop common quality assurance schemes; andto standardise approaches to ethical and legal issues.By networking existing national capacities, FP6-funded projects have provided the critical mass to catalyse thedevelopment of techniques and technologies for population genetics and to conduct large epidemiological studies.Together, these projects will enable researchers to better understand the ways in which interactions betweengenes and environmental factors are involved in the causes of common diseases and to determine the influenceof specific genetic variations on the development or severity of these diseases.FP7 activitiesThe FP7 Health theme has several objectives, one of which is to integrate the vast amounts of genomics, epidemiologicaland biological data with a view to translating this data into the understanding of major diseases andthe ultimate development of new preventive, diagnostic and therapeutic methods. That is why population geneticsand biobanks research aiming to develop tools and harmonisation principles is essential in FP7.In the future, the integration of traditional population epidemiological genetic studies with HTP ‘-omics’ tools(genomics, transcriptomics, and metabolomics) and bioinformatics as an essential component, is expected totremendously boost the field of population genetics.With this in mind, in the FP7 first call for proposals under the HTP research activity area, the EC funded a large scaleintegrating project to develop groundbreaking techniques for DNA sequencing and genotyping, which is expectedto increase the efficiency and cost of existing tools and lead to wider applicability in the clinical environment.The READNA project, with 12 million of funding, focuses on next-generation nucleic analysis technologies anddevices. The tools developed should increase the sensitivity, rapidity and efficiency of existing tools for sequenc-46 From Fundamental Genomics to Systems Biology: Understanding the Book of Life

ing and genotyping, with a target of 1 000 for the sequence of a complete human genome, while at the sametime leading a revolution in cost-effective, non-invasive early screening of large cohorts for diseases.In FP7’s first call for proposals, the large-scale data-gathering activity area supported two highly complementaryprojects (started in 2008) for performing molecular epidemiological studies in existing well-characterised Europeanpopulation cohorts, with the objective of identifying candidate susceptibility genes to multifactorial diseasesby integrating genome-wide association studies and the advances of ‘-omics’ developments.The ENGAGE project, with 12 million of funding, sets as its main objective the integration of the results frommany large-scale genetic studies underway in Europe and Australia, and the identification of novel diseaseandtrait-susceptibility variants for multifactorial diseases. The scale is large, with more than 650 000 DNAsamples from various cohorts involved; the focus is primarily on cardiovascular and metabolic diseases, butcan be expanded to other common disorders.The HYPERGENES project, with 10.2 million in funding, aims to dissect complex genetic traits using hypertensionas the disease model. The consortium will identify, by means of a whole genome association approach,genes contributing to essential hypertension (EH) and to EH-associated target organ damage, utilising wellcharacterisedEuropean cohorts. A combination of the most up-to-date methods of genomics, molecular genetics,molecular epidemiology and bioinformatics, together with learning-based modelling of the data, is expected toproduce a disease model.To keep Europe at the forefront of technology development in population genetics and biobanks research, the ECpublished the third FP7 call for proposals in September 2008, via its Genomics and Systems Biology programme;a bottom-up approach via a two-stage selection procedure was implemented for the first time in the Health priority.In the activity area of HTP research, the scientific community is invited to submit proposals for large integratingprojects on the following topics:■ The development of HTP tools and technologies to phenotype samplesin large-scale human biobanks.The projects are expected to accelerate epidemiological studies and biomarker discovery by increasingthe molecular analysing capacity of biobanks, and will deliver high-quality and reproducible data set toenable standardised approaches for large-scale biobanks.In the activity area of large-scale data gathering initiatives, the FP7 third call for proposals invites proposals onthe following topics:■ Characterisation of human genetic variation in Europe.The projects should aim at characterising genetic variation in populations from different regions and ethnicminorities in Europe, involving normal and/or disease phenotypes. A large-scale comparative study of geneticvariation in human populations in Europe is expected to facilitate ongoing and new epidemiologicalstudies, and fill in the information gaps on genetic variability in healthy and/or disease phenotypes.■ Large-scale functional genomics efforts to identify molecular determinants of cancer.The projects should implement multidisciplinary functional genomics approaches (e.g. sequencing, transcriptomicsand/or epigenetics) to characterise in detail a large number of human cancer tumour samples,so as to identify molecular determinants that contribute to human oncogenesis. They should establish thestandards and norms on the manipulation and storage of tumours samples, thereby facilitating the comparisonbetween different data sets.Recognising the power of population-based approaches in the study of genetic susceptibility for disease, theEC’s FPs for RTD provided more than 60 million to collaborative research projects in thisarea between 2002 and 2008 (see fig.11 representing the steps towards the ERA in population geneticsresearch). In future calls, the Health theme will continue supporting this area, which will allow the EU todevelop and maintain a leading global position in genetic epidemiology and population genetics.From Fundamental Genomics to Systems Biology: Understanding the Book of Life47

Integrated research in Population Genetics & BiobanksGenetic epidemiologyof common diseasesENGAGE(genetic epidemiology-Commondiseases)GenOSept (geneticpredispositionsepsis)HyperGenes(geneticepidemiologyhypertension)EUROSPAN(genetic variation)Technological DevelopmentsMolPAGE(molecularphenotyping tools)READNA(sequencing/genotypingtechnologies)1 st call - 20022 nd call - 20033 rd call - 20044 th call - 2005FP7 1 st call - 2006IP, NoESTREP, CA, SSACoordination, Fora,WorkshopsFP5 EuropeanPilot projectEUHEALTHGEN(impact ofpopulation genetics)Microsat(workshop onmicrosatellites)Impacts(Tissue archivesstandardisation)DanubioBank(age-relatedbiobanks)PHOEBE(harmonisation ofpopulation biobanks)HUMGERI(Human GenomicsIntegration)FP5 foundations for Population Genetics:GenomEUtwin (pilot IP 2002-2005)EpiGenChlamydia(host-pathogengenomics)Fig. 11: Steps to ERA in Population Genetics and Biobanks in FP6 (2002-2006) and FP7 first call projectsAs we move towards understanding biology at the systems level, access to large data sets of many different typeshas become crucial. The data obtained from such technologies (such as genome-sequencing, microarrays, proteomicsand structural genomics) have provided ‘parts lists’ for many living organisms, and bioinformatics provides thesystematic cataloguing and interpretation of this data. Researchers are now focusing on how the individual componentsfit together to build systems. The hope is that scientists will be able to translate their new insights into improvingquality of life. The functional genomics HTP revolution is generating a vast amount of data. There is an ongoing (andgrowing) need to collect, store and curate all this information in ways that allow its efficient retrieval and exploitation.By making these data available to the academic and industrial research communities in an accessible andusable form, bioinformatics research ensures that the potential for genomics and health research is maximised.FP6 activitiesThe FP6 objectives for the field of bioinformatics were to enable researchers to access efficient tools for managingand interpreting the ever-increasing quantities of genome data, and for making it available to the researchcommunity in an accessible and usable form.The foundations for meeting these challenges were laid in FP5, especially with the major large-scale IP TEM-BLOR, which supported the development of major databases, including those for protein structure and sequence,protein-protein interaction, gene expression and integration of this and other data. The capabilities establishedand strengthened by TEMBLOR brought Europe to a level similar to that of other major world centres in the keyareas of life sciences research.In FP6, an ERA has been established in bioinformatics, building on the foundations in FP5. This bioinformaticsERA forms the basis for a wide range of applications for health research, and will be a key element in a futureERA in systems biology, already under development in FP6 as well.48From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Three major NoE in bioinformatics were established in FP6, which constitute the core of the bioinformaticsERA. All of them also involve the European Molecular Biology Laboratory and the European BioinformaticsInstitute (EMBL-EBI), which is a major core facility in Europe, and dozens of other major and smaller partnersin Europe and worldwide.In bioinformatics, BIOSAPIENS has created a European Virtual Institute for Genome Annotation, bringingtogether the best laboratories in Europe, including informaticians and experimentalists. The institute hasgreatly improved bioinformatics research in Europe by providing a focus for annotation, and by organisingEuropean meetings and workshops to encourage cooperation, rather than duplication of effort. The Institutehas established a permanent European School of Bioinformatics, to train bioinformaticians and to encouragebest practice in the exploitation of genome annotation data for biologists. The tools developed have alreadybeen applied to gain important insights into the mechanisms of genetic mutation in major diseases such asHIV/AIDS and Down’s syndrome.The EMBRACE NoE integrates the major databases and software tools in bioinformatics in Europe by creating abioinformatics computer grid for easy and integrated data access, analysis and services. The integration effortsare being driven by an expanding set of test problems representing key issues for bioinformatics service providersand end-user biologists. As a result, groups throughout Europe will be able to use the EMBRACE service interfacesfor their own local or proprietary data and tools. ATD aims to understand the mechanisms that are responsiblefor the formation of transcript isoforms on a genome-wide scale by creating a value added database of alternatetranscripts from human and model species.Finally, ENFIN is connecting bioinformatics and wet-lab capabilities with a Europe-wide integration of computationalapproaches in systems biology. Computational work includes the development of a distributed databaseinfrastructure appropriate for small laboratories and development of analysis methods including Bayesian networks,metabolite flux modelling and correlations of protein modifications to pathways. ENFIN will deliver aplatform for database provision of diverse biological data, integrated analysis tools, guides for wet laboratoryutilisation, and ‘best practice’ guidelines for systems biology.Furthermore, bioinformatics is included as an essential component by creating integrated databases in manymultidisciplinary functional genomics projects aiming to understand basic biological processes in health and disease(see next section). There are several characteristic project examples: MITOCHECK (which creates a publicallyaccessible database for all the proteins involved in mammalian cell cycle), MYORES (a NoE on muscledevelopment in different model organisms, which implements a database for muscle research), EVI-GENORET(which is creating a state-of-the-art relational database integrating functional genomics data and clinical diseasedata for genes involved in retina development, degeneration and disease).The development of computational biology and integrated bioinformatics databases of diverse ‘-omics’ data is anessential component for the successful implementation of systems biology approaches. Several systems biologyprojects funded in FP6 (see following section) are focused on the development of computational tools. There areseveral characteristic examples: EMI-CD is developing a software platform connecting several modules necessaryfor the in silico modelling of complex disease processes, while COMBIO combines a unique group of experimentalists,bioinformaticians and simulation groups in order to gain detailed understanding of key processeslike the P53-MDM2 regulatory network. Also, COSBICS is establishing and applying a novel computationalframework to investigate cellular signalling pathways and subsequent target gene expression. The DIAMONDSproject aims to demonstrate the power of a systems biology approach in the study of the regulatory networkstructure of the most fundamental biological process in eukaryotes: the cell cycle, in different species.FP7 activitiesContinuing the efforts to strengthen the ERA in bioinformatics, in the FP7 first call for proposals under the HTPresearch activity area, the EC funded a large scale integrating project to unify human and model organism geneticvariation databases; this is expected to achieve effective linkage between databases and would facilitateanalysis in population genetics studies.The GEN2PHEN project, with 12 million level of funding, implements an integrated approach towards unifyingFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life49

human- and model-organism genetic variation databases, in such a way that the resulting holistic view of genotypeto-phenotypedata can be blended with other biomedical databases via the central genome browser ENSEMBL.The project will help to overcome existing access and usage barriers for genotype-to-phenotype relationships, byproviding an integrated informatics structure. It will further facilitate easy access to the stored information and associatedresources through development of a Web portal knowledge centre.To keep Europe at the forefront of bioinformatics developments, the EC, via its Genomics and Systems Biologyprogramme, published the third FP7 call for proposals in September 2008, implementing a bottom-up approachvia a two-stage selection procedure for the first time in the Health priority.In the activity area of HTP research, the scientific community is invited to submit proposals for large IPs on thefollowing topic.■ Computational tools for genome annotation and genotype/phenotype data integration.The projects are expected to develop new computational tools and methods for genome/proteome annotationto catalyse the progress of systems biology by describing, for example, molecular interactions, pathwaysand networks. The development of new computational tools for genome annotation and genotype/phenotype data integration will enable integration of vast amounts of data generated on gene functiongenomics to facilitate data mining and catalyse progress in systems biology.In summary, between 2002 and 2008, the EC’s FPs for RTD provided approximately 75 millionto collaborative research projects in the area of bioinformatics. Before FP6, although therewas a strong European core at the European Bioinformatics Institute, there were a wide range of databasesand capabilities scattered across Europe with suboptimal access and interaction. By the end of FP6, databases,services, analysis tools, and scientific research were strengthened locally and linked together at European levelto produce highly coordinated resources in support of biology and health-related research, a fact that has greatlyincreased our understanding of the wealth of data being generated in Europe and the rest of the world.Bioinformatics Databases,Computational tools for Systems BiologyComputational BiologyENFIN(computationaltools for SB)COSBICS (modellingCellular signalling)EMI-CD(Disease modelling)DIAMONDS (cellcycle modelling)COMBIO(P53 and spindlemodelling)1 st call - 20022 nd call - 20033 rd call - 20044 th call - 2005FP7 1 st call - 2006Databases focusedon a biological themeClassical Bioinformaticsand DatabasesMYORES(muscle developmentnetwork)BioSapiens(GenomeAnnotation)EMBRACE(BioinformaticsGrid)MITOCHECK(mammaliancell cycle)ATD(Alternativetranscripts)EVI-GENORET(retina development& disease)GEN2PHEN(genotype/phenotypeDatabases grid)IP, NoESTREP, CA, SSAEuropeanFP5 Pilot projectFP5 foundations for European Bioinformatics:TEMBLOR (Cluster of 4 proposals) 2002-2004Plus individual smaller projectsFig. 12: Steps to ERA in Bioinformatics in FP6 (2002-2006) and FP7 first call projects50 From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Extremely strong bases in the bioinformatics area have been established. However, just as existing fields areshowing an ‘explosion’ of data (as new fields are being established in the various ‘-omics’ disciplines suchas metabolomics, regulomics) and as these data and analysis tools are being linked together and used as thedriving force for systems biology analysis, so bioinformatics research also needs to grow.The full potential of systems biology research has not yet been achieved in Europe, because basic databases andresearch methods have not yet provided the entire basis needed to fully apply a systems approach. The approachesplanned in FP7 should allow us to overcome the future challenges in bioinformatics and computational biology. The different approaches to functional genomics described in the earlier sections — gene expression, proteomics,structural genomics, model organisms and population genetics and bioinformatics — provide researcherswith an extremely powerful multidisciplinary ‘toolbox’ which they can use to study and manipulate fundamentalbiological processes.By picking the most appropriate genomic tools, or combination of these tools, researchers are developing innovativeways to study the basic understanding of cellular processes, by revealing the function and interactions ofcellular components in health and disease. The multidisciplinary approaches provide opportunities to view theseprocesses from different angles and gain new insights into the underlying cellular functions.Diseases are often the result of important biological processes dysfunctioning, either because of external stimuli,such as pathogens or environmental factors, or because of inherited or acquired gene mutations resulting inincorrectly coded gene products unable to perform the appropriate cellular function. By understanding normalcellular processes in organisms as diverse as micro-organisms, plants and animals, researchers will be able tomanipulate the cellular processes involved in disease, enabling therapeutic advances.In FP6, this research sub-area funded projects implementing innovative and multidisciplinary approaches of functionalgenomics to study basic biological processes in health and diseases. A series of large-and medium-scaletransnational projects were supported in FP6, where the main goal is to develop innovative ways to understandbasic biological processes such as transcription regulation, DNA repair, cell cycle, epigenetics, hearing and visionprocesses, immune system, intra- and inter-cellular signalling, and developmental processes. The innovation is aresult of the integration of the most appropriate multidisciplinary functional genomics tools; in this way we can gainnew knowledge on the complexity of the underlying mechanisms of life that constitute the footprint of a physiologicaland/or pathological situation.In summary, the sub-area of multidisciplinary approaches to basic biological processes in FP6supports projects that may be grouped into the following categories:■ basic biological pathways in intracellular and extracellular signalling■ tissue and organ development, homeostasis and diseases■ stem cell biology■ RNA biology■ chronobiology■ biology of prokaryotes and other organismsFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life51

Several projects aim to discover the genes involved in the regulation of fundamental processes such as cell cycle,DNA repair (examples are MITOCHECK, DNA REPAIR, RUBICON). A series of projects, such as EVI-GENORET,EUROHEAR and MYORES, provide new knowledge on the fundamental molecular and cellular biology of differenttissues/organs as well as their development and malfunction, with the ultimate goal of therapeutic advances.Large-scale functional genomics initiatives were funded to shed light to fundamental questions in embryonic/adult stem-cell research: how multipotent stem cells and early progenitors become committed to a single developmentalpathway and then differentiate to the specific cell type (examples are FunGenes and ESTOOLS). Theexciting discoveries in RNA biology of the ‘second genome’ and the non-protein coding genes as organisers andcoordinators of the organism’s complexity are tackled by several projects (SIROCCO and RIBOREG), includingthe increasing importance of post-transcriptional regulation of gene expression (EURASNET).In FP6, between 2002 and 2006, the EC provided approximately 220 million to collaborativeresearch projects in the area of multidisciplinary approaches for fundamental biologicalprocesses. All these European efforts have created the critical mass that will boost European excellencein the respective fields by increasing integration and reducing fragmentation. It is important to mention thateven though the projects are focused on fundamental biology, for the first time several of them are integratingbasic biologists, clinical scientists and industry (including SMEs) where appropriate, to facilitate the transferof basic knowledge to clinical applications. Several projects are improving functional genomics tools for thegenome-wide understanding of gene function that would be applicable in all areas of cell biology. Trainingcourses in multidisciplinary expertise of the next generation of biologists has been implemented in several,mostly large-scale projects. Importantly, the issues of setting up standard operational procedures on methodologiesand data collection, and the creation of integrated bioinformatics databases have been addressed— the latter being an essential element of collaborative effort in Europe.In summary, the FP6 projects have already generated a comprehensive list and map of the multiple set of genesand proteins related to a basic biological process in normal and/or pathological situations. Indeed, majordiscoveries on novel gene functions have already been made that have resulted in high-level publications bycollaboration of various laboratories, previously working in isolation. Most importantly, these projects haveplayed an important role in integrating the research community in Europe, thereby increasing their visibilityMultidisciplinary Initiativesfor understanding basic biological processesTissue/organDevelopment and disease,Stem cell biologyEUROHEAR(Hearing processand deficiencies)EureGene (kidneydevelopmentand disease)EuTracc(transcriptionalregulationin ES cells)ESTOOLS(hESdifferentiation)1 st call - 20022 nd call - 20033 rd call - 20044 th call - 2005Biological pathwaysand signallingMAINChronicinflammationDNA RepairEndoTrack(endocytosis)SIRROCO(SmallregulatoryRNAs)In silico tools,Integrated bioinformaticsdatabasesBIOSAPIENS(Human GenomeAnnotation)EMBRACE(Bioinformaticsgrid)IP, NoECA, STREPTools and technologicsfor ”-omics”Basis for advances in post-genomics era: High-throughputTools for Proteomics, transcriptomics, model organisms, imagingFig. 13: Steps to ERA in multidisciplinary functional genomics approachesfor understanding basic biological processes in FP6 (2002-2006)52 From Fundamental Genomics to Systems Biology: Understanding the Book of Life

at the national, European and international level. They have also substantially contributed towards reducingfragmentation of research in Europe in their respective fields, thereby implementing the concept of the ERA andcreating a real multidisciplinary integrated programme of activities, as is illustrated in Fig. 13.The FP6 investment constitutes the largest programme ever (in Europe and worldwide) that addresses fundamentalbiology in such a multidisciplinary collaborative way, implementing state-of-the-art functional ‘-omics’ approaches.However, it must be recognised that cellular components interact in subtle and complex ways, even in the simplestorganisms. The understanding of the enormous complexity of the interacting gene networks that are responsible formost biological processes will require integrative and quantitative forms of analysis of diverse data. It is important toemphasise that the ‘multidisciplinary approaches to basic biological processes’ action line, has already provided arichness of large-scale ‘-omics’ data that constitutes the foundation for future systems biology initiatives in Europe.Cellular signalling helps govern basic cellular activities and coordinates cellular function. A cell’s ability to respondcorrectly to its surrounding environment is the basis of normal cellular growth and tissue homeostasis, aswell as development and repair. Dysfunctions of the transmission and process of signalling within the cell mayresult in many diseases. An improved understanding of the basic biological pathways involved in intracellularand extracellular signalling will lead to more effective therapies for these diseases.In general, the FP6 projects funded in this broad sub-area could be classified into two groups: those focusing onbasic biological processes in healthy conditions, and others focusing on disease.1. Projects applying multidisciplinary approachesfor understanding basic biological processes in healthy conditionsMITOCHECK involves research into the regulation of mitosis and into the mammalian cell cycle, abnormalitiesof which can contribute to cancer. The project applies cutting-edge technologies: the use ofRNA interference genome-wide screens to identify in a systematic manner (functional genomics) all genesinvolved in mammalian cell-cycle, and proteomics approaches to identify novel protein complexes andphosphorylation sites. A web-based database is created with such information as, the list of genes requiredfor mitosis, the sub-unit composition of mitotic complexes, and genome-wide RNAi screens phenotypic datathat will provide a valuable source of information to the whole cell biology community.The RUBICON NoE focuses on the better understanding of post-translational modifications of proteins byubiquitination. It will establish the link to diseases such as infectious and inflammatory conditions, cancer,and neurodegenerative disorders. This goal is achieved by applying multidisciplinary functional genomicsto elucidate the functions of genes and gene products, and by defining the regulatory networks controllingubiquitination.The EndoTrack project aims at gaining conceptual advances into the signalling function of growth factorsfrom an unconventional perspective, namely by exploring the role of endocytic trafficking in the modulationof signalling and gene expression regulation. It further aims to translate such basic knowledge intonovel opportunities for the development of a new generation of tools to combat diseases like cancer, andcardiovascular, metabolic, and infectious and neurodegenerative diseasesThe PEROXISOMES project, using cutting-edge proteomics tools, identifies and characterises the functionsof novel peroxisomal proteins and establishes a catalogue of peroxisomal proteins in human liver,kidney and brain. The consortium will evaluate the role of peroxisomes as modulators or modifiers of diseasesof complex inheritance, such as cancer and neurodegenerative disorders.TRANSDEATH will investigate the functional relationships between the different forms of programmedcell death by using appropriate models. These mechanisms will then be used to understand correspondingtypes of cell death in mammals, and particularly in humans.From Fundamental Genomics to Systems Biology: Understanding the Book of Life53

SIGNALLING & TRAFFIC will establish the connections between signalling pathways and membranetrafficking in the context of migrating, dividing and adhering mammalian cells. Through the study ofmembrane traffic in the course of cell differentiation, dedifferentiation, and during mitosis, the projectexplores how membrane traffic can influence signalling cascades.2. Projects applying multidisciplinary approachesfor understanding basic biological processes in diseaseThe MAIN project is identifying and characterising the molecular mechanisms underlying chronic inflammatoryresponses and will produce cutting-edge technological approaches for use in cell migration. Itprimarily studies the migration of leukocytes from the bloodstream into inflamed tissues, and their local activationby inflammatory substances and pathogens. A bioinformatics database is being created, enablingrapid data retrieval and analysis, and cross-correlation of functional genomic and functional proteomicdata, facilitating biological hypothesis-making and ‘systems’-level investigations.Aneuploidy is the term used to describe the abnormal copy number of genomic elements. The ANEU-PLOIDY project is studying the phenotypic consequences of gene dosage imbalance in humans at cellularand organism level, by focusing on two prototype human model phenotypes: trisomy 21 and monosomy.The project will allow the identification of genes and biological pathways potentially involved in new aneuploidysyndromes.The DNA REPAIR consortium is using an integrated multidisciplinary approach to improve understandingof DNA damage response and repair systems in living organisms. Genomics tools are used to identify newcomponents of DNA damage response pathways. The project will extrapolate the findings from modelorganisms to humans, by the investigation of cells from patients suffering from genome instability, cancerpredisposition and premature ageing syndromes.WOUND will identify evolutionary conserved genes and major signalling pathways involved in epithelialfusion and wound healing, using model systems.The project STEROLTALK has undertaken a systematic post-genomic evaluation of cholesterol homeostasisand its cross-talk to drug metabolism and will contribute towards understanding the effects andside-effects of hypolipidemic therapy and combined therapies.All the projects described in this section have set very ambitious and technically challenging objectives whichclearly exceed the capacity of a single laboratory. The combination of a critical mass of excellent Europeanresearchers with a readiness to develop new concepts and highly innovative methods as part of European consortiahas stimulated a European corporate identity in their respective fields and is expected to greatly reinforcecompetitiveness. To overcome the duplication of efforts in the production of research tools and data, the majorityof the projects have established shared databases to include ‘-omics’ data which are shared between collaborativelaboratories. The availability of state-of-the-art HTP technologies is currently restricted to a relatively smallnumber of laboratories at larger institutions. All these projects have promoted access to advanced technology.The development of these technologies, as well as the integration of industry and SMEs in most of the projects,further facilitates the transfer of basic knowledge to future commercial applications.FP6 has built a strong basis by funding several projects applying multidisciplinary ‘-omics’ approaches to understandthe molecular pathways and identify novel genes involved in tissue and organ development, degenerationand disease. All projects apply functional genomics approaches and bring together multidisciplinary expertisein the same consortium for the first time, and several of them are validating the knowledge produced for developmentof gene and stem cell therapies. The focal point for most of these projects lies in fundamental research.However, the involvement of clinical expertise, the use of disease population cohorts and industry (includingSME) involvement, promises rapid translation of the basic knowledge to clinical applications.54 From Fundamental Genomics to Systems Biology: Understanding the Book of Life

The LYMPHANGIOGENOMICS consortium brings together leading researchers established in the fieldof lymphangiogenesis and provides fundamental insights into the molecular and cellular basis of the lymphaticdiseases. The project promotes the development of therapies for the treatment of cancer, inflammatorydisease, tissue ischemia and lymph oedema, and has been one of the main drivers behind the recentgrowth in the field of lymphatic biology.The MYORES NoE integrates the work of European laboratories previously working in isolation. Theproject aims at identifying the genetic determinants of muscle normal development, degeneration and disease,and at developing technologies for HTP screening in order to isolate novel molecules and rapidly testtheir suitability for muscle function and repair in animal models. The creation of the MyoBase database asa main integrating activity will become the main source of information in muscle biology.The aim of EVI-GENORET is to understand the fundamental molecular and cellular biology of the retina,of its development and of the way it is perturbed by genetic mutation, environmental factors and age.The project integrates population genetics, clinical and experimental phenotyping, molecular geneticsapproaches, and HTP transcriptomics and proteomics analysis for the pathophysiology of the retina. Thecreation of a state-of-the-art bioinformatics database that will integrate diverse ‘-omics’ data with clinicaldata it is expected to accelerate diagnosis, disease screening, drug target evaluation and the developmentof new therapeutic strategies for inherited and age-related retinal diseases.The EUROHEAR IP has two closely interrelated objectives: to provide fundamental knowledge on thedevelopment and function of the inner ear and to identify the molecular effects underlying hereditary hearingimpairments, including presbycusis. The involvement of hearing-impaired individuals and their familiesin research is essential for the understanding of normal and abnormal auditory function. The EUROHEARproject demonstrates vigorous cross-disciplinary expertise with strong interaction between human and animalmodels geneticists, development of biophysical and bioimaging techniques combined with functionalgenomics, as well as a sound inner-ear training programme for young European scientists.EuReGene integrates European excellence in research relevant to renal development, pathophysiologyand genetics. The main objective is to discover genes responsible for renal development and disease.The consortium involves the multidisciplinary expertise of leading scientists, including clinicians and SMEpartners, and focuses on the development of novel technologies and discovery tools in functional genomicsand their application to kidney research. Knowledge generated will be available to the scientificcommunity and to the stakeholders through freely accessible databases and repositories.All of the above projects, representing an investment of more than 60 million, constitute the most coordinatedand integrated approach in Europe and internationally in the fields of kidney, inner ear, retina, muscle and lymphatictissue health and disease.All the above projects are developing standardisation of protocols, and several of them standard operating proceduresfacilitating the cross-comparison of results between geographically isolated laboratories. Several of themare developing a strong bioinformatics database that for the first time will integrate diverse data existing in differentlaboratories to be shared and analysed by members of the consortia in collaboration. An advantage in thesefields is access to large-scale population cohorts as well as access to HTP genomics and genetic platforms.Given the genetic complexity of different organs and tissues, the cooperation between the European groups isexpected to be instrumental both in terms of resource sharing and complementary expertise. These consortia byuniting their efforts, have created a structure unequalled elsewhere.Disorders affecting normal organ and tissue function have an impact in the quality of life of large populations andhave a serious economic impact on the European economy. The knowledge produced will contribute strategies tocombat common and rare diseases as well as inherited and age-related diseases related to organ developmentand degeneration, and to identify novel disease genes and novel targets for diagnosis and therapy.From Fundamental Genomics to Systems Biology: Understanding the Book of Life55

The EU has supported stem cell research for a number of years in successive FPs. Stem cells have enormous potential,not only in regenerative medicine for replacing damaged tissue in various diseases, but also for applicationsin drug discovery, toxicology and pharmacogenomics. Stem cell research is also crucial in understandingthe basic underlying processes that lead to serious pathological conditions.In fundamental genomics and under the area in which multidisciplinary approaches are applied to basic biologicalprocesses, the EC funds several projects with the aim of generating knowledge on the fundamental processesgoverning stem cell differentiation in human and model organisms. If we can learn more about this fundamentalprocess, we might be able to reprogramme the body’s own cells, for example, to replace diseased or damagedtissue. Various sources of stem cells are studied and compared, including ES cells, adult stem cells and inducedpluripotent stem (iPS) cells originating from somatic cells.FUNGENES applies multidisciplinary approaches with an emphasis on microarray expression analysis to mouseES cells that are in a state of self-renewal or that have been induced to differentiate in various tissues of the threemajor differentiation pathways. It delivers a gene expression atlas on the genetic pathways for cell differentiationinto heart cells (cardiomyocytes), nerve cells (neurons), smooth muscle cells, vascular endothelial cells, fat cells(adipocytes), liver cells (hepatocytes) and insulin-producing cells of the pancreas. The data are analysed by methodsof bioinformatics to produce new knowledge regarding genetic pathways, to identify novel genes that areinvolved in different aspects of development, and lastly to validate the candidate genes by genetic engineeringof mouse ES cells. The project is expected to have an impact on future novel therapeutic strategies for diseasesincluding cancer, liver disease, diabetes and cardiovascular and neurodegenerative diseases.ESTOOLS applies multidisciplinary genomic techniques and genetic tools to uncover the basic mechanisms controllingthe choice that human ES cells make between self-renewal and differentiation into the neuronal lineage, byutilising 52 human ES cell lines. It will develop internationally agreed standardised protocols and tools for growingand manipulating ES cell lines, and for monitoring their phenotypic, genetic and epigenetic stability. This knowledgewill be disseminated to the wider scientific community to make the best use of the existing stem cell lines, andultimately will allow the culture and exploitation of hES cells.It will also address the technology for deriving inducedPluripotent Stem (iPS) cells and explore whether iPS cells have genetic, epigenetic and developmental propertiesequivalent to human ES cells. If this technology can be established, and if the derived cells are indeed identical toES cells, then this approach may in the future reduce the need for working with embryo-derived stem cells.A first step towards regenerative medicine involves finding a means to cause controlled dedifferentiation ofadult tissue. The project PLURIGENES investigates the controlled de-differentiation of adult tissue in order todiscover the function of genes controlling pluripotency and de-differentiation in the central nervous system, soas to ultimately combat diseases such as brain injury and/or ageing. The project is based on the identificationof candidate pluripotency associated genes evolutionarily conserved between different model organisms. Theknowledge generated on self-renewal pathways (which are often deregulated in cancer stem cells) might alsolead to improved outcomes in the treatment of human tumours.One of the big challenges for the next decade is to understand the regulatory network of TFs that control cellularfunctions. EuTRACC determines the regulation of the genome by mapping the regulatory pathways andnetworks of TFs (the ‘Regulome’) that control the activity of ES cells and the process of differentiation into neuraltissues and the blood system. The project utilises multidisciplinary approaches by applying genetics, proteomicsand genomics tools in the mouse mainly, which are complemented by functional assays in other model organisms.The neural and hematopoietic tissue types were selected because of their well-characterised differentiationpathways and their existing clinical applications.Several of these projects cooperate closely with international efforts. ESTOOLS will play a significant role in thedevelopment of standardised techniques for hES cells not only in Europe, but throughout the world, by workingtogether with the International Stem Cell initiative (ISCI), which addresses issues of standardisation of markersand techniques for studying human ES cell lines. will collaborate with the International RegulomeConsortium (IRC), a worldwide consortium that will map the genetic regulatory nodes and networks that controlthe function and lineage determination of embryonic and adult stem cells, with immense implications for developmentalbiology, disease and regenerative medicine.56 From Fundamental Genomics to Systems Biology: Understanding the Book of Life

The flow of genetic information from DNA via mRNA to protein has been termed as the central dogma of molecularbiology. Early results in post-genomics research have already challenged established views about the nature of thegenome. A surprising result of the human genome sequencing experiments was that only a very small proportion(1,5%) of the entire genome encodes for proteins. It was once thought that a large proportion of our genome was inactive‘junk DNA’, but today we know that many of these genomic regions are regulatory sequences responsible foractivating or silencing genes when necessary. A major surprise in the human and mouse genome sequences wasthe discovery that humans do not have considerably more genes than other mammals. However, the mammaliantranscriptome is largely constituted of many non-protein coding transcripts (many more than the number of genes),which might be associated with the level of cellular complexity in mammalian species. Many of these transcripts arenon-coding RNAs, while others are conserved across species and others are unique in species, yet their functionsin health and disease remain largely unknown.The discovery of the RNA-interference mechanism that can degrade mRNA from a specific gene was reportedin 1998 and led to the 2006 Nobel Prize in Medicine and Physiology. This mechanism is activated by doublestrandedRNA which leads to degradation of the target mRNA so that the corresponding gene is silenced and noprotein is produced. RNA interference occurs in plants, animals, and humans and is already being widely usedin basic science as a method to study the function of genes and it may lead to novel therapies in the future. Thesediscoveries have revealed a previously unknown role for RNA as a silencer of gene expression, to its previouslyunderstood role as a cellular messenger that directs protein synthesis.The exciting discoveries in RNA biology and the non-protein coding RNAs as the ‘second genome’ are tackledby several FP6 CPs (SIROCCO and RIBOREG are examples), including the increasing importance of post-transcriptionalregulation of gene expression (an example is EURASNET).The SIROCCO project studies the role of non-protein coding genes as organisers and coordinators of the organism’scomplexity. It investigates the role of small regulatory RNAs (sRNAs) in health and disease, with particularemphasis on cancer, neurological diseases and developmental regulation, by using HTP technologies and bioinformatics.It will determine the tissue and cell-type miRNA expression, optimise methods of sRNAs detection,characterise the molecular machines responsible for both miRNA and siRNA biogenesis, and dissect sRNAregulatory networks through the combination of multidisciplinary methods.The RIBOREG project identifies novel non-coding RNA (ncRNA) genes linked to cell differentiation and diseaseand analyse their mechanisms of action by developing a multidisciplinary approach integrating bioinformatics,cell biology, genetics and genomic strategies. The BACRNAs project will identify non-coding RNAs involvedin bacterial pathogenicity and the identification of targets (virulence factors) controlled by ncRNAs involved invirulence. RNABIO is an SSA: its main contribution was the organisation of an international workshop on computationalapproaches to non-coding RNAs, with the main objectives of presenting and discussing the state ofRNA computational biology so as to identify needs and propose new developments.The human genome contains a surprisingly low number of protein-coding genes — approximately 22 000. However,the human proteome consists of approximately 100 000 protein isoforms. Part of the answer is alternative messengerRNA (mRNA) splicing. The EURASNET NoE aims to develop an integrated approach to the study of alternative splicing:it will provide durable structures that will change the way research in this field is carried out in Europe; establishan ambitious, innovative and multidisciplinary programme of joint research activities with high impact; spread excellencewithin Europe; disseminate knowledge about alternative splicing in molecular biology and particularly inmedical communities; and foster public awareness of genomics and RNA research and their applications.The circadian clock is a basic biological process that enables organisms to anticipate daily environmentalchanges by adjusting behaviour, physiology and gene regulation. It impacts health and quality of life inregulating sleep and well-being, in the consequences of shift work, in medical diagnosis and therapy, and inage-related changes.From Fundamental Genomics to Systems Biology: Understanding the Book of Life57

In EUCLOCK, European researchers join forces to investigate the circadian clock under entrainment. Utilisingthe most advanced methods of functional genomics and phenomics, the team will compare genetic modelorganisms and humans. Important findings such as the prerequisites for large-scale non-invasive research onhuman entrainment as well as the first animal models for shift-work will be developed. These findings will enablethe field of chronobiology to exploit the advantages of systems biology research on circadian timing, andto perform and integrate findings at the level of the genome, the proteome, and the metabolome.The general objective of TEMPO combines functional genomics, proteomics, cell signalling, systems biology andpharmacokinetics, and will design mouse and in silico models to allow the prediction of optimal chronotherapeuticdelivery patterns for anti-cancer drugs.The EC is also supporting multidisciplinary functional genomics research projects in prokaryotic organisms suchas bacteria and other organisms.The BACELL HEALTH consortium aims to unravel the integrative cell stress-management systems and stressresistanceprocesses required to sustain a bacterial cell when exposed to types of environmental signals. Thereare also other projects using bacteria to understand the function of basic biological processes (like BaSysBio) andapplying systems approaches to understand transcriptional regulation.DIATOMICS will make use of whole genome sequences from diatoms to provide information on gene functionand its relationship to ecology and evolution.Systems biology, now an emerging discipline, has gained popularity over the past few years. Each cell, organor tissue is a dynamic biological system. The cellular functions are controlled by many genes, proteins and signallingand metabolic processes. Technological and computational advances have enabled the acquisition andanalysis of large datasets obtained by diverse biological systems at multiple levels. Global measurements ofDNA have yielded data on sequence and genotype and information about chromatin structure. RNA measurementshave enabled genome-wide transcriptional profiling and information about alternative splicing and noncodingRNAs. Proteomics approaches using mass spectrometry and more recently protein arrays have permittedthe global identification and quantification of proteins in their biological context. Furthermore, these technologieshave allowed the quantification of post-translational modifications and revealed dynamic protein-protein andprotein-DNA interactions. Great progress has also been made in measuring metabolic fluxes, and emergingimaging technologies are providing important insights into biological function.However, despite these advances, the link between complex biological networks and phenotype remains anenormous challenge.In order to gain deeper insights and ultimately a quantitative understanding of the complex and dynamic processesof living organisms (e.g. environmental adaptation, ageing, and immune defence) of the cells, it is necessaryto view the systems as a whole.Systems biology promises to build up an integrated picture of the regulatory processes at all levels, from genometo proteome, from organelles to cells and tissues, and the understanding of the whole organism, by integratingfunctional data into a cohesive model. This stands in contrast to the standard reductionistic approaches of thetwentieth century, with biologists analysing functional information on organisms based on a single gene or asingle protein at a time.There are two approaches proposed in systems biology. The top-down approach presupposes that it is not necessaryto know all the details of the ways in which cells work in order to make useful predictions about how organism58 From Fundamental Genomics to Systems Biology: Understanding the Book of Life

cells work. This method starts with a model of how the system works and then compares the model with informationfrom the real biological system. At the opposite end, stands the ‘bottom-up’ approach, which starts from the propertiesof individual molecules and builds models at increasingly higher scales. Therefore, the bottom-up approachessentially requires complete information, including the dynamics of each step, to build a system model. Whencomplete, such a detailed model should be capable of describing exactly how the system works under any circumstance.The combination of the advantages of the above approaches leads to the so-called ‘middle-up’ approach.The ultimate goal of biology is to understand biological systems in sufficient detail to enable accurate, quantitativepredictions about the behaviours of biological systems, including predictions of the effects of modificationsof the systems such as disease. The hope of the rapid translation of genomic information into novel drugs hasfoundered on the reality that disease biology is complex. Systems biology aims ultimately to develop predictivemodels of human disease. Currently, integration of ‘-omics’ data within the context of controlled gene expressionor drug perturbations of complex cell and animal models (and in the context of clinical data) is the basis forsystems biology efforts at a number of drug companies.Such research has a strong multidisciplinary nature and the collaboration between different stakeholders, university,research institutes, biotech companies and clinical centres is a prerequisite for success. The subject requirescollaboration between a broad spectrum of scientific disciplines including biology, physics, chemistry, computerscience and engineering. A collaborative approach is a prerequisite to achieving major breakthroughs.FP6 activitiesThe EU is emerging as a major world player in the development of systems biology in Europe. An important fundingeffort has been initiated in FP6 through the support of collaborative research projects and through a numberof key studies and workshop events that have helped to integrate this emerging community.In FP6, a number of systems biology projects predominantly initiated in 2005 have already demonstrated thata systems approach can indeed work, to provide both a deeper understanding of biological processes and predictivepotential for applications. These projects have major links to ongoing worldwide research programmes,national programmes, and Europe-wide support and links (EMBL, EMBL-EBI).Within FP6, the EC has already funded several pilot research projects paving the way toward systems biology.These projects may be grouped into the following general categories:1. Projects applying systems biology approaches in fundamental cellularsignalling pathwaysSome of these projects (COMBIO, COSBICS and DIAMONDS) are already applying systems biology approachesto model cellular signalling pathways. Other projects (QUASI and AMPKIN) aim for a systematicquantitative understanding of intracellular and extracellular signalling pathways of disease relevance, withultimate goals of building predictive pathway models. All of these projects demonstrate that the developmentof computational biology and integrated bioinformatics databases of diverse ‘-omics’ data is an essentialcomponent for the successful implementation of systems biology approaches.COMBIO implements an integrative approach to cellular signalling by combining a unique group ofexperimentalists, bioinformaticians and simulation groups in order to gain detailed understanding of keyprocesses, like the P53-MDM2 regulatory network. COSBICS establishes and applies a novel computationalframework to investigate cellular signalling pathways and subsequent target gene expression.The DIAMONDS project aims to demonstrate the power of a systems biology approach to study theregulatory network structure of the most fundamental biological process in eukaryotes, the cell cycle, indifferent species.In the AMPKIN project, experimental and theoretical studies will be integrated to achieve an advanced understandingof the dynamic operation of the AMP-activated protein kinase signalling pathway. This pathway playsa central role in monitoring the cellular energy status and controlling energy production and consumption.From Fundamental Genomics to Systems Biology: Understanding the Book of Life59

In the last FP6 call, the EC also financed an integrated project (BaSysBio) which uses systems biologyapproaches for the understanding of the dynamic transcriptional regulation in bacteria. It studiesthe transcriptional regulation and metabolism in B. subtilis and B. anthracis, and the cellular transcriptionalresponses in pathogenesis. The project AGRONOMICS applies integrative functional genomicsapproaches to systematically investigate the components controlling growth processes in plant cells(genome sequences, proteins and metabolites) and to explain quantitative growth phenotypes at themolecular level. Finally, mathematical and statistical methods will be employed in order to model basicplant processes. The aim is to investigate those further and test them in close collaboration with computerscientists, statisticians and experimentalists.2. Projects applying systems biology approachesfor understanding complex diseases phenotypesEMI-CD, ESBIC-D and BioBridge are using systems biology approaches to gain new insight into highlycomplex diseases, such as trisomy related illnesses (Down’s syndrome) and various cancers.The main purpose of EMI-CD is to provide a software platform complex enough to cope with various experimentaltechniques, connecting several modules necessary for the in silico modelling of complex diseaseprocesses such as cancer and diabetes.VALAPODYN validates predictive dynamic models of complex intracellular pathways related to the celldeath and survival. It develops a new systems biology approach to model the dynamics of molecular interactionnetworks related to neurodegeneration. The ultimate goal is to select and validate drug targets forhuman pathologies associated with neurodegeneration.SysProt develops a new paradigm for the integration of proteomics data into systems biology. It will producequantitative proteomics data, and study post-translational protein modifications via the development of computationalanalysis, in order to gain understanding on the progression of complex diseases such as diabetes.BioBridge focuses on the application of simulation techniques for integrated genomic, proteomic, metabolomicand kinetic data analysis, in order to create models for understanding complex diseases at the systemiclevel, with an emphasis on heart failure, chronic obstructive pulmonary disease and type II diabetes.3. Projects aiming at coordination and networking in systems biologyTo prepare the best research environment in Europe for systems biology, the EC is already supporting severalSSAs and CAs.EUSYSBIO laid the foundations for the successful start of European systems biology research,implementing networking activities and identifying the strengths and weaknesses in European systemsbiology. SYMBIONIC is creating a broad European network of research institutions and industries withinterdisciplinary expertise in the systems biology field, which will be a driving force for future ambitiousinitiatives in neuronal cell modelling.ESBIC-D aims at organising a Europe-wide systems approach to combat complex diseases. The projectwill network leading groups in the fields of cancer research, genomics, proteomics and computational biologyto strengthen the expertise and research infrastructure in Europe.SYSBIOMED explores the potential application of SB to medical research in major disease areas (infectious,neurodegenerative, metabolic and cardiovascular diseases and cancer), and its applications in drugdevelopment. A series of workshops will be organised to promote European collaboration and to contributeto the breaking down of barriers — between theoreticians, basic researchers and clinicians interested inmedical applications.YSBN is a CA which focuses on defining standards, methods and concepts of systems biology using themodel organism S. cerevisiae.60 From Fundamental Genomics to Systems Biology: Understanding the Book of Life

It is worth mentioning that the EU-supported large-scale functional genomics initiatives in FP6 have produced arichness of HTP ‘-omics’ data, which has provided new knowledge on basic biological processes such as themammalian cell cycle, tissue development and degeneration (muscle, retina, inner ear and kidney), human andanimal stem cell differentiation processes, organelle function, endocytosis and post-translational modifications.These large initiatives will pave the way for future systems biology initiatives in Europe. An essential element infuture systems biology are the integrated bioinformatics and computational biology tools. In FP6, important fundinghas been provided in the area of bioinformatics, which will contribute to the ERA of systems biology.ERA in Systems BiologyFP6 Pilot SystemsBiology ProjectsDIAMONDS(modelling cell cycle)QUASI (MAPKkinasesignalling)SysProt (systemsanalysis of proteinModification)COMBIO(P53 pathway)BaSysBio(Bacterial TranscriptionRegulation)COSBICS (modellingCellular signalling)ESBIC-D (SB forcomplex diseases)BioBridge(SB forchronic diseases)Fundamental genomics forbasic Biological processes;“-omics” data gatheringMITOCHECK(mammaliancell cycle)EUROHEAR(Hearing processand deficiencies)ESTOOLS(hESdifferentiation)SIRROCO(Small regulatoryRNAs)1 st call - 20022 nd call - 20033 rd call - 20044 th call - 2005Integrated bioinformatics,databases,Computational biologyBIOSAPIENS(Human GenomeAnnotation)EMBRACE(Bioinformaticsgrid)ENFIN(computationaltools for SB)IP, NoECA, STREPExperimental Tools andtechnologies for ”omics”Tools for Proteomics, transcriptomics, structural genomics,population genetics, metabolomics, imagingFig. 14: Steps to ERA in Systems Biology in FP6 (2002-2006)FP7 activitiesThe EU FP7 programme is already playing a major role in this important and rapidly expanding research fieldby establishing multidisciplinary networks in Europe that will catalyse progress and excellence in this field. TheFP7 first call for proposals provided an important boost for large-scale European initiatives, by allocatinga total budget of 45 million to the following large scale integrating projects.SYBILLA, a large scale integrating project, aims to understand at the systems level, how T-cells discriminateforeign from auto-antigens and will address modelling of T-cell activation. The project will develop technologicaland mathematical tools to generate and integrate high-density quantitative data describing T-cell activationin health and disease, placing particular emphasis on multiple sclerosis. T-cell activation is a complex process,relying on multiple layers of tightly controlled intracellular signalling modules, defects in which can cause severeand chronic disorders such as autoimmune diseases.The APOSYS project studies the basic cellular mechanisms of apoptosis. This multidisciplinary consortium bringstogether and networks experimental biologists, biomathematicians, biostatisticians, computer scientists and clinicalscientists to examine cell death pathways in health and disease, with an emphasis on cancer and AIDS. Itcomplements the systems approach with a series of in silico, in vitro and in vivo model organisms and tissueFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life61

samples from patients suffering from cancer and AIDS. The project is expected to enhance our understanding ofclinical data and lead to the development of new diagnostic tools and drugs.UNICELLSYS set as an overall objective the quantitative understanding of fundamental characteristics of eukaryoticunicellular organism biology, using yeast as model organism. The project goes far beyond the state of the art in termsof dynamic modelling of cellular subnetworks controlling complex biological processes such as control of cell growthand proliferation. It is expected to deliver new knowledge on important biological processes relevant to human health(cell growth and proliferation) but will also generate economic value in the form of new computational tools and approachesfor systems biology that will be of general applicability to other systems in more complex organisms.EuroSyStem is a large European effort that brings together elite European research teams to create a worldleadingprogramme in fundamental stem cell biology, with the main focus on the paradigmatic mammalian stemcells: haematopoietic, epithelial, neural and embryonic. Cutting-edge multidisciplinary technologies such ascytometry, transcriptomics, RNA interference, proteomics and single cell imaging, will be used to generate newknowledge on stem cells differentiation in terms of cellular hierarchy, signalling, epigenetics, de-regulation, andplasticity. An important bioinformatics and computational platform will be established to mine information andsubsequently to model these complex differentiation pathways.From biological pathways in unicellular eukaryotic organisms to human cells and organs, there is a need tocombine, integrate and extend existing data sources and screen different heterogeneous data resources. Theselarge-scale projects on systems biology are expected to integrate dispersed capabilities and assemble the criticalmass necessary to enable systems approaches, as well as to secure European excellence and competitivenessand the exploration of new directions for the field. The quantitative data delivered should serve as the basis fromwhich to design robust models with predictive value. They should produce new knowledge on basic biologicalprocesses relevant to health and diseases.Project Acronym 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 FPEYSYSBIOSYMBIONICEMI-CDQUASICOMBIOCOSBICSDIAMONDSEU-US WorkshopELifeESBIC-DYSBNAMPKINRIBOSYSEUROBIOFUNDVALAPODYNAGRON-OMICSBaSysBioBioBridgeSYSBIOMEDSysProtStreptromicsSYSCOProustAPOSYSSYBILLAUNICELLSYSEuroSysStemSSASSA0.5m0.2mSTREPSTREPSTREP1.9m1.9m2mSTREP 1.7mSTREP 2.5mSSA 0.06mSSA 0.48mSTREPCASTREPSTREPSSA1.9m1.3mSME-STREPIPIP2.1m2.4m0.9mIPIP1.5mIPIP12mSME-STREP 1.8mSSA 0.36mSME-STREP 2.1mSME-STREP 2.9mSME-STREP 1.8mSSA 1.5m12m11.1m11.1m11.03m11.03mFP6FP72002 2003 2004 2005 2006 2007 2008 2009 2010 2011 20122013FPFig. 15: Runtime of current EU-funded collaborative research projects in systems biology(funding period started in 2004 for FP6 projects-most projects extend well beyond 2007; funding period started in 2008 for the FP7 fi rst call projects)62 From Fundamental Genomics to Systems Biology: Understanding the Book of Life

In systems biology, not every research area requires a large collaborative effort. During the FP7 second callfor proposals, approximately 15 small-scale research projects were selected, and are currentlyunder negotiation with a total of 45 million to be committed at the end of 2008 or beginningof 2009. These projects may be categorised as follows: (i) projects aiming to enable systems biologyapproaches for diseases like inflammatory response, cancer, neurological diseases, and bacterial infections; (ii)projects applying systems biology for basic signalling pathways like DNA damage and repair, oxidative stress,cellular organelle function, and stem cell differentiation; and (iii) support actions for tackling future challenges insystems biology. All these projects are multidisciplinary and they are focused on collecting, analysing and applyingquantitative data to enable systems biological approaches.For an emerging and booming field like systems biology, it is rather difficult to identify which are the timely ideasto investigate using an EU large-scale coordinated approach. The large-scale CPs will create the critical massof multidisciplinary expertise that is necessary for enabling complex systems approaches. Therefore, the EC viaits Genomics and Systems Biology programme published the FP7 third call for proposals in September 2008,implementing a bottom-up approach via a two-stage selection procedure for the first time in the Health priority.The scientific community is invited to submit proposals for large integrating projects on the following topic:■ Systems biology approaches for basic biological processes relevant to healthand diseaseThe projects should focus on modelling important biological processes at any appropriate levels of systemcomplexity by generating and integrating quantitative data sets (e.g. transcriptomics, proteomics, metabolomics,structural biology, RNAi screening, physiology and/or pathophysiology). These large multidisciplinaryefforts should integrate the critical mass of excellence in Europe that is necessary for generating andvalidating the models using systems biology.In summary, to face the challenges of the systems biology era, the EC’s FPs for RTD have alreadyprovided, between 2003 and 2008, more than 150 million for collaborative researchprojects. With such substantial funding, the EU is emerging as a major world player in the development ofsystems biology in Europe and will continue to do so in the future.System Biology in FP7 & HealthSB: organismsSB: tissues/organsSB: Cells: Mammalian cellsSB: Cells: yeast/bacteriaSB: pathwaysBiological processes: data gatheringBioinformatics/ Data bases/software/computational biology2003200420052006200720082009201020112012201320142015201620172018201920202021FP6FP7Fig. 16: The future developments of systems biology in FP7The FP6 fundamental genomics programme paved the way by supporting multidisciplinary projects collecting large amountsof “-omics” data on basic biological processes, and by developing the bioinformatics and computation tools base.From Fundamental Genomics to Systems Biology: Understanding the Book of Life63

AnnexesBasic facts and figures forthe Fundamental Genomics activity areaAnnex IFunding instruments and schemes in FP6 and FP7Compared to FP5 (1998–2002), which mainly supported small and medium collaborative research projects, FP6(2002–2006) has additionally offered more ambitious ‘new funding instruments’, namely IPs and networks of excellence(NoE). These two project types are more ambitious in size and scope than the research projects fundedpreviously by the EU. Both types of projects aim to stimulate and sustain world-class research in a specific area offundamental genomics and to improve the organisational aspects of European research in the specified topic. However,IPs and NoE have a different centre of gravity. With an IP the balance is towards achieving ambitious, clearlydefined scientific objectives; with a NoE the balance is shifted towards tackling the fragmentation of Europeanresearch in a specific field, so as to provide an improved organisational structure in which research can flourish.It is clear that the ‘new instruments’ of FP6 have enabled European scientists to achieve a major critical mass invery competitive areas of functional genomics and have really given European research a global profile.For further information, see http://www.cordis.lu/fp6/instrument-ip/.Integrated Projects (IPs)IPs are large-scale projects aiming to support world-class objective-driven research, where the primary deliverableis generating new knowledge. In addition, by mobilising a critical mass of resources, IPs should also havea structuring effect on European research (see Figure 17 for the graphical representation on the goals of an IP).The activities integrated by an IP may cover the full research spectrum from basic to applied research, andshould contain:■ objective-driven research;■ technological development, innovation-related and demonstration components, as appropriate;■ the effective management of knowledge and, when appropriate, its exploitation;■ a training component, where appropriate.All these activities should be integrated within a coherent management framework.An IP should bring together a critical mass of research excellence and resources to achieve its ambitious objectives.The European Community funding for an IP in the fundamental genomics programme ranges from 8 to13 million, their duration from 36 to 60 months, with an average of 11.2 million per project and 48 monthsduration for the majority of the projects.64 From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Integrated ProjectsTo integrate the critical mass of activities/resources needed for :Addressing major societal needsIncreasing EU competitivenessEthical aspects, science-society dialogueTrainingRTD 4 RTD 5RTD 3 ManagementRTD 2DemonstrationRTD 1Technology transfer, exploitationPredefined S/Tresults andclear deliverablesStrongmanagementstructureImplementationPlanFig. 17: Graphical representation of the structure and the goals of an Integrated Project in FP6 (2002-2006)Networks of Excellence (NoE)NoE are large-scale projects with the goal of overcoming fragmentation in the European research landscapeand strengthening European excellence in a given area (see Figure 18 for a graphical representation of thegoals of a NoE). Their purpose is to reach a durable restructuring/shaping and integration of efforts andinstitutions or parts of institutions (labs, departments, units, teams, etc.) in areas where this is necessary. Thesuccess of a NoE is not measured only in terms of scientific results, but also by the extent to which the fabric forresearchers and research institutions in a given field has changed due to the project, and the extent to whichthe existing capacities have become more competitive as a result of this change.A NoE is implemented through a Joint Programme of Activities, which encompasses the following:■ Integrating activities: These aim at structuring and shaping the way participants carry out research inthe topic (e.g. coordinated programming, sharing research facilities, tools and platforms, joint managementof the knowledge portfolio, schemes for increasing staff training and mobility, staff exchanges, sharedinformation and communication systems).■ Jointly executed research: A world-class research programme is an obligatory part of the JointProgramme of Activities or JPA (for example, to generate new knowledge in the research topic and to developnew research tools and platforms for common use).■ Activities for spreading excellence: An essential mission of a NoE is to spread excellence beyondits boundaries. Typical examples of such activities would be the following: joint programmes for trainingresearchers and other key staff to ensure the sustainability of Europe’s excellence in the topic, communicationcampaigns for disseminating results (and raising public awareness of science), and networking activities toencourage knowledge transfer and innovation.NoE should pursue ambitious goals and gather the critical mass needed to ensure their achievement. The EuropeanCommunity grant to a NoE in the fundamental genomics areas ranges from 10 to 12.5 million, theirduration from 48 to 60 months, with an average of 10.7 million per project and 60 months duration for themajority of the projects.From Fundamental Genomics to Systems Biology: Understanding the Book of Life65

Networks of ExcellenceGoverning CouncilFunding BodiesRepresentativesEuropean CommissionManagementGroupTo structure the EU research potentialby integrating existing research capacitiesJoint research activitiesIntegrating activitiesSpreading of excellence (training)Common managementResearch team leaderPartner Organisation RepresentativeFig.18: Graphical representation of the goals and the structure of a network of excellence in FP6 (2002-2006)Specific Targeted Research Projects (STREPs)STREPs are multi-partner research projects, with the goal to support research, technological development anddemonstration or innovation activities of a more limited scope and ambition than IPs. They are an evolved form ofthe shared-cost RTD projects and demonstration projects used in FP5, and their main deliverables are to producenew knowledge and improved tools and technologies in fundamental genomics.The European Community financial support for a STREP in fundamental genomics ranges from 1.5 to 2.5 million,their duration from 36 to 48 months, with an average of 2.1 million per project and 36 months durationfor the majority of the projects.STREPs were also funded during the fourth call of FP6 with the specific goal of supporting projects for developingand/or improving tools and technologies development, and of encouraging SMEs’ research and innovationefforts. The goal was that 30% of the EC contribution to be allocated to the SMEs. These projects areentitled SME-STREPs in the current publication.Co-ordination Actions (CAs)CAs do not support research and development activities per se; they promote and support the networking andcoordination of research and innovation activities aiming at improved integration of European research. CAs area continuation of the concerted actions/thematic networks used in FP5, in a reinforced form.A CA could contain activities such as:■ the definition, organisation and management of joint or common initiatives;■ the organisation of conferences and meetings;■ the performance of studies and analyses;66 From Fundamental Genomics to Systems Biology: Understanding the Book of Life

■ the exchange of personnel;■ the exchange and dissemination of ‘good practices’;■ the setting up of information systems and expert groups;■ specific training courses or seminars.The European Community financial contribution for a CA in fundamental genomics ranges from 0.5 to 1.3million, their duration from 24 to 48 months, with an average of 0.8 million and 36 months respectively.Specific Support Actions (SSAs)SSAs are more limited in scope than the accompanying measures of the previous FPs. They aim to:■ promote and facilitate the dissemination, transfer, exploitation, assessment and/or broad take-up ofpast and present programme results (over and above the standard diffusion and exploitation activities ofindividual projects);■ contribute to strategic objectives, notably regarding the ERA (e.g. pilot initiatives on benchmarking,mapping, networking, etc.);■ prepare future community RTD activities, (e.g. via prospective studies, exploratory measures, pilot actions,etc.).The European Community funding contribution for an SSA in fundamental genomics ranges from 0.06 to 0.5million, their duration from 12 to 36 months, with an average of 0.3 million and 24 months respectively.FP7 projects are all categorized with the general term collaborative projects.Large scale collaborative Projects (Large scale integrating projects) (CP-IPs)The large integrating projects could be considered an evolution of the IPs in FP6.These projects will support objective-driven research projects aiming at developing new knowledge, newtechnologies, products, demonstration activities or common resources for research, to improve Europeancompetitiveness or to address major societal needs.They include the following activities:■ RTD — the core activities of the project;■ demonstration, where applicable;■ project management;■ other activities such as dissemination of research results, etc.The European Community funding contribution for CP-IPs in the Health theme should be more than 6 millionand maximum of 12 million. In the Genomics and Systems Biology programme during the implementationof the FP7 first call for proposals, the funding ranges from 11 to 12 million, their duration from 48 to 60months, with an average of 11.7 million and 48 months respectively.From Fundamental Genomics to Systems Biology: Understanding the Book of Life67

Small or medium scale collaborative Projects(Small-Medium Focused Research Projects) (CP-FPs)These projects could be considered as a continuation of FP6 STREP projects and are research projects withlower ambitions than IPs.The European Community funding contribution for CP-FRPs in the Health theme should be 3 million to lessthan 6 million. In the Genomics and Systems Biology programme during the implementation of the FP7second call for proposals (with a September 2007 deadline), currently under negotiation, the funding rangesfrom 2.5 to 2.99 million, their duration from 36 to 48 months, with an average of 2.7 million per projectand 36 months duration for the majority of the projects.Coordination and Support Actions (CSAs)These projects refer to Coordination and Support Actions (CSAs) and do not support research per se butrather coordination activities with objectives similar to those of FP6.The European Community funding contribution for CP-CSAs in the Health theme is generally in the rangeof up to 1.5 million, although there is no upper limit. In the Genomics and Systems Biology programmeduring the implementation of the FP7 second call for proposals (projects currently under negotiation), theEC funding ranges from 0.5 to 2.7 million, and the duration from 24 to 36 months.68 From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Annex IIDevelopment of the specific scientific topicsfor calls for proposals in the FP6 FundamentalGenomics programmeAt the beginning of FP6, a global expression of interest was established for the first time in the FP, and the mostinnovative ideas for European collaborative research were selected. This concept has been applied in the wholethematic area of Life Sciences, Genomics and Biotechnology for Health. In this section, we will concentrate onthe Fundamental Genomics activity area. The European scientific community has submitted 550 expressions ofinterest, and these have been evaluated by eminent scientists both within and outside Europe. This high-levelevaluation process led to the strategic areas of research that defined the specific topic for calls for proposals,mostly for the large-scale projects in the FP6 first, second and third call topics.The rest of the calls have been developed by consulting the scientific community via EC’s strategic workshops(see Annex III). The Scientific Advisory group was set up by the EC to provide input on the strategy and the implementationof the work programme in the Life Sciences theme in FP6: this group’s valuable advice is an importantsource of consultation on the work programmes (for more information, please see http://cordis.europa.eu/fp6/eags.htm and http://ec.europa.eu/research/fp7/index_en.cfm?pg=eag).The EC also acknowledges the important role of the Member States’ recommendations in the final implementationof the work programme.From Fundamental Genomics to Systems Biology: Understanding the Book of Life69

Annex IIIThe EC organisation of strategic workshopsin different scientific areas of fundamental genomicsand systems biologyDuring FP6, the EC organised a number of successful workshops in collaboration with the scientific community,to identify the challenges and the future developments in different areas of fundamental genomics, along withnew initiatives that have contributed to strategies in FP7. The following workshops were organised by the Unit ofFundamental Genomics — this name was updated to the Genomics and Systems Biology Unit in FP7 (for furtherinformation, see http://cordis.europa.eu/lifescihealth/genomics/home.htm).■ Bioinformatics Structures for the Future, in March 2003, with the goal of setting a research agendain the field for structuring European bioinformatics research;■ Workshop on Mouse Genetics, in July 2003, with the aim of setting priorities for mouse functionalgenomics research in Europe;■ Computation Systems Biology: its Future in Europe, in September 2003, with the aim of defininga research and policy agenda to promote the field of computational systems biology (CSB) in Europe;■ Meeting on population genetics in Europe, in September 2003, in order to identify priorities forresearch in population genetics and related areas;■ Workshop on Structural Genomics, in October 2003, with the aim of identifying the strengths,weaknesses and future opportunities for structural genomics in Europe;■ Conference on European Structural Genomics & Proteomics Research combined with thejoint meeting of EU-funded projects, in October 2004, with the aim of creating synergies between theprojects by clustering and networking, of disseminating best practices and success stories to establishgateways between disciplines; of debating and formulating a proposal on the current and future policiesneeded for SG in Europe;■ Functional Genomics Research: Future Perspectives in October 2004, with the aim of identifyingthe future challenges and developments of the functional genomics field for future research policies actions,in view of establishing genomics research for FP7;■ Workshop on Systems Biology in December 2004, where European scientists identified key areas insystems biology for development in the near future;■ Conference on Funding Basic Research in Life Sciences: Exploring opportunities for Europeansynergies in December 2004, a joint effort of Directorate F (Life Science, Genomics AndBiotechnology for Health in FP6 & Directorate E (Food Quality And Safety);■ EUROMOUSE conference: Understanding human disease through mouse genetics — TheEuropean Dimension in October 2005, for creating synergies among projects using mouse as a modelorganism and discussing priorities in mouse functional genomics;■ Human genetic variation workshop in March 2006, exploring the need for a grid-linked set ofdatabases in this area;■ Mouse functional genomics workshop in March 2007, concluding with recommendations forinternational collaboration in the field of mouse as a model for human disease;70 From Fundamental Genomics to Systems Biology: Understanding the Book of Life

■ EU-US Task Force Workshop on Infrastructure Needs for Systems Biology in May 2007 (US),with the aim of making recommendations for infrastructure support to enable systems biology research;■ EU-US workshop on ‘How Systems Biology Could Advance Cancer Research’ in May 2008,drawing up suggestions for international collaboration on systems biology of cancer.For more information, including the published reports for some of the workshops, see http://cordis.europa.eu/lifescihealth/genomics/home.htm. Information can also be found on the FP7 Health website, at http://cordis.europa.eu/fp7/health/home_en.html.From Fundamental Genomics to Systems Biology: Understanding the Book of Life71

Annex IVEvaluation process inthe FP6 and FP7 Fundamental Genomics programmeThe present section provides a short overview of the evaluation procedure in the thematic priority of Life Sciences,and more specifically focuses in the area of Fundamental Genomics.The procedure for evaluation of proposals is based entirely on the ‘Guidelines on proposal evaluation and projectselection procedures’, which can be found at: http://fp6.cordis.lu/lifescihealth/call_details.cfm?CALL_ID=148,and which serves as the basis for the following brief presentation.Role and code of conduct of evaluatorsThe EC appoints independent experts to assist in the evaluation of proposals. In general, independent expertsare expected to have skills and knowledge appropriate to the areas of activities in which they are asked to assist.Details of potential independent experts are maintained in a central database. This database may be madeavailable, on request, to national authorities in the Member States and countries associated to the FPs. The namesof the independent experts assigned to individual proposals are not made public; however, at regular intervals,the EC publishes the list of independent experts used per activity/research area, on the Internet.The EC takes all reasonable steps to ensure that each expert is not faced with a conflict of interest in relation tothe proposals on which he/she is required to give an opinion. To this end, the EC requires experts to sign a declarationthat no such conflict of interest exists at the time of their appointment and that they undertake to informthe EC if one should arise in the course of their duties. When so informed, the EC takes all necessary actions toremove the conflict of interest. The experts are obliged to maintain the confidentiality of the information containedwithin the proposals they evaluate and of the evaluation process and its outcomes and to act with strict impartiality.A conflict of interest and confidentiality declaration will be signed by independent experts.The proposal evaluation and project selection processThe overall evaluation and project selection process is summarised in the following diagram.The evaluation procedure consists of the following steps:Step 1: Briefing of the independent expertsAll independent experts are briefed in writing and orally before the evaluation by representatives of the EC’sservice in charge of the call, in order to inform them of the general evaluation guidelines and the objectivesof the research area under consideration.Step 2: Individual evaluation of proposalsThe proposals are sent to the expert evaluators at their normal place of work. Each proposal is evaluatedagainst the applicable criteria relevant to each funding instrument independently by several experts who fillin individual evaluation forms giving marks in each criterion and providing justification of marking. Thesecomments serve as input to the consensus discussion and related consensus report that takes place in Brussels.The number of evaluators legally required is five for IPs/NoE and three for the other instruments. The EC hasestablished as a general practice the evaluation by a number of seven to nine evaluators for IPs/NoEs andfive for the other instruments, in order to further strengthen the quality of the evaluation procedure.Written opinions from external reviewers are applied specifically for the large projects (IPs, NoE), where mostof the top European specialists in the field are involved in a given proposal. Therefore, to obtain an independenthigh-quality assessment, several specialists in the field, mainly from outside Europe, are invited to review72 From Fundamental Genomics to Systems Biology: Understanding the Book of Life

The Proposal Evaluation And Project Selection ProcessProposalEligibilityIndividual EvaluationConsensusThresholdsEthical Issues(OPTIONAL)HearingsPanelRanking by ECEC Rejection DecisionNegotiationNegotiation ResultConsultation of ProgrammeCommittee if requiredEC Funding Decisionand/or Rejection Decisioneach proposal. The external reviewers are asked to provide their written opinion of the scientific quality of theproposal. These written opinions are provided to the expert evaluators prior to the meeting of the consensusgroup in Brussels, but after the expert evaluators have completed and forwarded to the EC services their individualassessment reports on the proposals assigned to them. Consideration of the written opinions of theexternal reviewers makes up an important aspect of the consensus group’s discussions in Brussels.Different consensus groups operate in parallel in different groups of closely related topics. The proposalspassing the thresholds are reviewed by a final panel composed of several experts from each of theseveral consensus groups. The final panel produces a ranking list of proposals in order to advise the ECon which projects to select for funding.Step 3: Consensus panelsSeparate parallel consensus panels are convened in Brussels. The goal is that for each proposal all theexperts reach an agreement on a consensus mark for each of the blocks of evaluation criteria based onthe comprehensive discussion. They justify their marks with comments suitable for feedback to the proposalcoordinator. The discussion of the proposal continues until a consensus is achieved, i.e. a conclusionwith which all agree regarding the marks for each criterion and the accompanying comments. In theevent of persistent disagreement, the EC official supervising the evaluation of that proposal may bring inup to three additional evaluators to examine the proposal.From Fundamental Genomics to Systems Biology: Understanding the Book of Life73

In order to facilitate discussion among the experts, the EC officials act as moderators for the group andassign an expert as ‘proposal rapporteur’. The proposal rapporteur introduces the proposal(s) assigned tohim/her and summarises the opinions of the external reviewers (in the case of IPs and NoE). The proposalrapporteur is responsible for amalgamating the individual experts’ views, for initiating the discussion anddrafting the consensus report. The outcome of the consensus step is the consensus report signed by all independentexperts and the moderator. The moderating EC official is responsible for ensuring that the consensusreport faithfully reflects the consensus reached. For all proposals passing the thresholds, the consensusgroup is asked to give an opinion on the appropriateness of the level of Community funding requested inrelation to the tasks and activities to be carried out.Final evaluation panelImmediately after completion of the consensus panels, an integrated final panel discussion is convened in Brusselsto examine and compare the consensus reports and marks of the independent consensus panels, to reviewthe proposals with respect to each other and, in specific cases (e.g. equal scores) to make recommendations ona priority order of proposals. A panel rapporteur (who may also be the panel chairperson) is appointed to draftthe panel’s advice. An EC official may act as moderator of the panel. The role of the EC moderator is to ensurefair and equal treatment of the proposals in the panel discussions. The outcome of the panel meeting is the panelreport recording the deliberations of the panel containing the following: an evaluation summary report (ESR) foreach proposal and a ranked list of proposals passing thresholds, along with a final mark and the panel recommendationsfor priority order.After the evaluationAt this stage, the EC services review the results of the evaluation by independent experts, make their assessmentof the proposals based on the advice from these experts and prepare the final evaluation results.The EC services draw up a final ranked list of all the proposals evaluated and of those passed the required thresholds.Due account is taken of the marks received and of any advice from the independent experts concerning thepriority order for proposals. The list of proposals to be retained for negotiation takes into account the budget available.Negotiation may cover any scientific, legal or financial aspects of the proposal, based on the comments of theindependent experts and on any other issue that was taken into consideration at the ranking stage. If negotiationsare successful, the EC may then enter into the contract with the coordinator and the other contractors.Evaluation procedures in FP7The procedure for evaluation of proposals is based entirely on the ‘Rules for submission and the related evaluation,selection and award procedures’, which can be found at ftp://ftp.cordis.europa.eu/pub/fp7/docs/calls/fp7-evrules_en_pdf.zip.The basic structure of the procedure is similar to the one described in FP6, with some minor adaptations.The evaluation criteria in FP7 have been consolidated to avoid repetition and the high level of complexity experiencedduring the FP6 evaluations.74 From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Annex VEvaluation criteria in FP6 and FP7Evaluation criteria in FP6The evaluation criteria applied for each funding instrument in FP6 are described below.Each of the criteria may differ depending on the type of the funding instrument (described in Annex I). The evaluationcriteria are ranked as follows:0: the proposal fails to address the issue under examination or cannot be judged againstthe criterion due to missing or incomplete information;1: poor;2: fair;3: good;4: very good;5: excellent.Evaluation criteria for an Integrated Project (IP):■ relevance (threshold score: 3), which means the extent to whichthe proposed project addresses the objectives of the work programme/call;■ potential impact (threshold score 3);■ scientific & technological excellence (threshold score: 4);■ quality of the consortium (threshold score: 3);■ quality of the management (threshold score: 3);■ mobilisation of resources (threshold score: 3).The total score for an IP could be a maximum of 30 with threshold 24.Evaluation criteria for a Network of Excellence (NoE):■ relevance (threshold score: 3, which means the extentto which the proposed project addresses the objectivesof the work programme/call);■ potential impact (threshold score: 3);■ excellence of the participants (threshold score: 3);■ degree of integration & the joint programme of activities (threshold score: 4);■ organisation and management (threshold score: 3).The total score for a NoE could be a maximum of 25 with threshold 20.Evaluation criteria for a Specific Targeted Research Project (STREP):■ relevance (Threshold score: 3);■ scientific and technological excellence (threshold score: 4);■ potential impact (threshold score: 3);■ quality of the consortium (threshold score: 3);■ quality of the management (threshold score: 3) ;■ mobilisation of resources (threshold score: 3).The total score for STREP could be a maximum of 30 with threshold 21.From Fundamental Genomics to Systems Biology: Understanding the Book of Life75

Evaluation criteria for a Co-ordination Action (CA):■ relevance (Threshold score: 3);■ quality of the support action (threshold score: 4);■ potential impact (threshold score: 3);■ quality of the consortium (threshold score: 3);■ quality of the management (threshold score: 3);■ mobilisation of resources (threshold score: 3).The total score for CA could be a maximum of 30 with threshold 21.Evaluation criteria for a Specific Support Action (SSA):■ relevance (Threshold score: 3);■ quality of the co-ordination (threshold score: 3);■ potential impact (threshold score: 3);■ quality of the management (threshold score: 3);■ mobilisation of resources (threshold score: 3).The total score for an SSA could be a maximum of 25 with threshold 17.5.Evaluation criteria in FP7Evaluation criteria for Collaborative Projects (CPs)■ Scientific and/or technological excellence (relevant to the topics addressed by the call) (threshold score: 3).Under this criterion, the following aspects will be evaluated: soundness of concept and quality of objectives;progress beyond the state of the art; and quality and effectiveness of the S/T methodology andassociated work plan. The relevance of a proposal is considered in relation to the topic(s) of the workprogramme open in a given call, and to the objectives of a call. When a proposal is partially relevantTable 2: Quality of funded projects in the Fundamental Genomics area: an overview of the average total scores of the funded projectsFundamental Genomics Research in FP6 (2002–2006)Funding instrumentRange of total scorein funded projectsAverage normalisedscore in fundedprojects* Genomics and Systems Biology Research -FP7 (2007–2013) (first call) * The total score is divided by the number of the criteria per funding instrument, in order to have a normalised scorecomparison between different types of projects.** The number of criteria has been reduced to 3 in FP7, and hence the maximum score is 15.76 From Fundamental Genomics to Systems Biology: Understanding the Book of Life

ecause it only marginally addresses the topic(s) of the call, or if only part of the proposal addresses thetopic(s), this condition is reflected in the scoring of the first criterion.■ Quality and efficiency of the implementation and the management (threshold score: 3). under this criterionthe following aspects will be evaluated: appropriateness of the management structure and procedures;quality and relevant experience of the individual participants; quality of the consortium as a whole (includingcomplementarity and balance); and appropriateness of the allocation and justification of the resourcesto be committed (budget, staff, equipment).■ Potential impact through the development, dissemination and use of project results (threshold score: 3). Underthis criterion, the following aspects will be evaluated: contribution, at European and/or international level, tothe expected impacts listed in the work programme under relevant topic/activity; appropriateness of measuresfor the dissemination and/or exploitation of project results, and management of intellectual property.Impact is considered in relation to the expected impact listed in the work programme. The total score for a CPcould be a maximum of 15 with threshold 10.Table 3: Number of proposals evaluated, proposals funded and success rates in all the calls for proposals in FP6in the Fundamental Genomics activity area, including the first call of FP7Fundamental Genomics Research in FP6 (2002–2006)Call*Number ofproposalsevaluatedNumber ofproposalsfundedAveragepercentage ofsuccess rate** All FP6 calls Genomics and Systems Biology Research in FP7 (2007–2013) (first call) * Four calls for proposals with an overall budget of 594 million were open in the Fundamental Genomics programmein FP6 during 2002 and 2005. Some 441 proposals were evaluated and 127 projects were selected for funding, withan overall average success rate of 29%.** The average success rate represents the success rate for all types of funding instruments. If we would calculate thesuccess rate, separately for IPs/NoEs, STREPs/CAs and SSAs, which had different budget allocations, one wouldnote a variation on the success rate. The average percentage per call is calculated by dividing the total number ofproposals funded in all funding instruments by the total number of proposals evaluated.*** In FP7, the success rate generally concerns the large IPs for the first call. On the whole, the average success rate for theHealth theme ranges from 15% to 17% and could vary considerably in some areas, in relation to the higher numberof applications received.From Fundamental Genomics to Systems Biology: Understanding the Book of Life77

Annex VIBasic facts and figures forthe Fundamental Genomics activity areaTable 4: Number of funded proposals per funding instrument and total budget allocated per funding instrumentFundamental Genomics Research in FP6 (2002–2006)FundinginstrumentNumber offunded projectsTotal ECfinancialcontribution(million )Percentagebudget spent/type of fundinginstrument Total FP6 130 594.1 100Genomics and Systems Biology Research in FP7 (2007–2013) (first call) 78 From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Table 5: Average funding level, average number of partners and average duration per funding instrument,in FP6 in the Fundamental Genomics activity area, including the first call of FP7Fundamental Genomics Research in FP6 (2002–2006)FundinginstrumentAverage ECcontribution*(million /instrument)Averagenumber ofpartners**/instrumentAverage duration(months)/instrument Genomics and Systems Biology Research in FP7 (2007–2013) (first call) * The budget is indicative and is calculated based on the maximum EC contribution at the start of the project; it does notrelate to the final spent by the project for projects not finalised.** A partner is an independent legal entity, which might include several independent scientific groups belonging to the samelegal entity; partners (independent legal entities) are calculated based on information including amendments of the FP6projects until the end of 2007.From Fundamental Genomics to Systems Biology: Understanding the Book of Life79

Table 6: Distribution of partners and percentage of EC contribution per activity type of partnerFundamental Genomics Research in FP6 (2002–2006)Activity type ofpartners*Number partners/activity type of partnersPercentage ECcontribution/activitytype of partners * HES: higher education; RES: research institutes; IND: industry; OTH: other (for example, international organisations).The number of partners has been calculated based on information which includes amendments of the FP6 projects untilthe end of 2007. Figures do not include calculation of inclusion or termination of partners — with these included,numbers may vary.** The total EC contribution allocated to SMEs in the fundamental genomics area constitutes approximately 7% of the totalEC contribution during FP6 (2002–2006), with an allocated budget of more than 40 million; SME participationconstitutes 84% of the number of industrial activity partners.80 From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Table 7: Distribution of partners and percentage of EC contribution among different groups of countriesFundamental Genomics Research in FP6 (2002–2006)CountriesNumber of partners/country groupPercentage ECcontribution/countrygroupEU-25* (New Member States) Candidate countries**Associated countries Third countries*** * During FP6, the EU comprised 25 Member States; Bulgaria and Romania became Member States in 2007.The new Member States (from May 2004) are the Czech Republic, Estonia, Cyprus, Latvia, Lithuania, Hungary, Malta,Poland, Slovenia, Slovakia.The associated countries are Switzerland, Israel, Iceland, Norway, and Lichtenstein** Candidate countries for accession in EU during FP6 were Bulgaria, Romania, Croatia and Turkey; Bulgaria and Romaniawere candidate countries and are therefore included in this group in the FP6 statistics for the Fundamental Genomicsprogramme.*** Third countries. The FP6 programme was open for participation to the International Cooperation target group countries,which may be found in the relevant FP6 work programmes Annexes. Other third countries, for example industrialisedcountries like the US, Canada, Australia and Japan may participate on a case-to-case basis if during the evaluation theirparticipation is considered essential for implementing the objectives of the respective project; generally speaking, in FP6 theindustrialised countries did not receive EC contributions.Table 8: Distribution of non-EU-25 partners in FP6 Fundamental Genomics projectsFundamental Genomics Research in FP6 (2002–2006)Candidate countries Associated countries Third countriesBulgaria (1) Croatia (2) Australia (2)Turkey (1) Canada (5) China (1)Gambia (1)Japan (1)Lebanon (1)Russia (4)South Africa (2)Tunisia (2)US (5) From Fundamental Genomics to Systems Biology: Understanding the Book of Life81

1.TOOLS ANDTECHNOLOGIES FORFUNCTIONAL GENOMICS

1.1TOOLS & TECHNOLOGIESFOR GENE EXPRESSIONMolToolsREGULATORY GENOMICSTat machineTransCodeEMERALDAutoScreenTargetHerpesFGENTCARDMODEST

MolToolswww.moltools.orgProject Type:Integrated ProjectContract number:LSHG-CT-2003-503155Starting date:1 st January 2004Duration:42 monthsEC Funding:9 000 000State-of-the-Art:The recording of complete genome sequences now for the first time, provides opportunities tocharacterise comprehensively the flow of information from genetic variation at the DNA level,over messages expressed as RNA and to their protein products, and to functions of the cell.By eavesdropping on these processes, it will be possible to identify genetic variations underlyingmalignancy, diabetes and other common diseases, and to monitor and ultimately explainmolecular processes involved in these and other important conditions.Recent years have seen rapid growth of techniques for high-throughput analyses of genes,transcripts, proteins and cells using microarrays, but current methods still capture only a smallfraction of the information embodied in the molecules. This project brings together leadingEuropean laboratories and one American lab involved in the development of molecular tools,to study the molecules that make up our genomes and all their products. Our purpose is tobuild an infrastructure to develop a next-generation toolbox for large-scale molecular analyses.The suite of microarray-based technologies developed in the course of this project willbe of strategic value throughout biological research, and for the biotech and pharmaceuticalindustries. Gradually the techniques should also become available to clinical medicine toguide diagnosis and therapy, and in agriculture and environmental monitoring.Scientific/Technological Objectives:A series of interrelated research problems are being dealt with in collaboration betweenpartners in academia and in biotechnology companies. The partners provide the complementaryexpertise required to establish an individualised genome analysis technology byachieving the following objectives: and haplotyping, and the elucidation of duplications profiling read out on microarrays nucleic acids in the complexity of biological samples alterations in cells by establishing technologies for cell array studies.Expected Results:The ambitious plan for the MolTools project is to have developed, by 2007, a next-generationtoolbox for large-scale molecular analyses on arrays and in cells, with the abilityto detect even single molecules. The tools will increase throughput and decrease costs foranalyses of genomes, transcriptomes, proteomes and functional cells. Important progresstowards these goals has been made during the course of the project.Regarding the development of techniques for single-molecule detection and for the analysisof single cells, Uppsala and Aarhus Universities, in a joint project, have developed86From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Advanced Molecular Toolsfor Array-Based Analyses of Genomes,Transcriptomes, Proteomes and CellsAn image of serum analyses onarrays made of 700 antibodiesa method for in situ genotyping, visualising single nucleotide allelic variations in singlemolecules, directly in cells and tissues, using a combination of padlock probes and rollingcircle replication. An article was published in Nature Methods on how the technology wasapplied to genotyping mitochondria in individual cells. Since then, the technology has beenfurther refined and now permits analysis of nuclear single-copy genes in fixed cell preparations.The Uppsala lab has published a paper describing a related technology that allowsindividual and interacting pairs of protein molecules to be detected in cells.Progress has also been made on working towardsestablishing methods for high-sensitivity, highthroughputand low-cost gene expression profiling.Very often the molecular characterisation of clinicalsamples is complicated and limited due to theavailable amount of samples. During the MolToolsproject, the so-called TAcKLE technique has been developedat DKFZ. This method generates amplified,antisense-orientated fluorescent representations ofinitial mRNA for the sensitive parallel detection oftranscripts on oligonucleotide arrays..In situ genotyping single-nucleotidevariation in single mitochondrialgenomes. Larsson et al.Nature Meth., 1. 227-232 2004Potential Impact:The MolTools project brings together some of Europe’s leading groups developing technologiesfor molecular medicine to overcome fragmentation, create synergy and speed up thedevelopment process. The high-throughput, high-precision technologies established in thisprogramme are expected to be of decisive importance in many forms of molecular biologicalresearch, and the programme can therefore provide leverage in academic research,increasing competitiveness in the European Research Area in a global context. The projectalso addresses one of Europe’s main challenges in biotechnology: translating technologicalinnovations into commercially successful products, thereby increasing competitiveness ofthe European biotech industry.From Fundamental Genomics to Systems Biology: Understanding the Book of Life87

MolToolsThe MolToolsconsortium at the2004 annual meetingin Berlin, GermanyMolTools participants have strongrecords of developing techniques,which are now used by companiessuch as Affymetrix, Agilent, AppliedBiosystems, GE Healthcare,BiopsyTec, Biotage, Bruker Daltonics,DynaMetrix, Epigenomics,GPC-Biotech, Hybaid, Integragen,Lynx, Micro Discovery, MolecularStaging, Mosaic Technologies,PEPperPRINT, Prot@gen, PSF AGand Scienion. By strengtheningthe interactions between researchgroups in this consortium, wehope to provide a critical massthat will stimulate the transfer ofinventions from academia to establishedindustries, and that willalso promote the establishmentof new companies. During thecourse of MolTools, one new company,Olink, has been establishedin Sweden and another will soonbe founded in Denmark.Keywords: genomics, proteomics, diagnostics88From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Advanced Molecular Tools for Array-Based Analyses of Genomes,Transcriptomes, Proteomes and CellsPartnersProject Coordinator:Prof. Ulf LandegrenUppsala UniversityDepartment of Genetics and PathologyDag Hammarskjoldsvag 20P. O. Box 25675185 Uppsala, Swedenulf.landegren@genpat.uu.seProject Manager:Dr. Carolina RydinUppsala UniversityDepartment of Genetics and Pathology75185 Uppsala, Swedenmolecular.medicine@genpat.uu.seProf. Delores CahillUniversity College of Dublin in IrelandCentre for Genomics and BioinformaticsDublin, IrelandProf. Ivo GutCentre National de GénotypageEvry, FranceDr. Jorg HoheiselDeutsches KrebsforschungszentrumFunctional Genome AnalysisHeidelberg, GermanyDr. Michael TaussigThe Babraham InstituteTechnology Research GroupCambridge, UKProf. Arvydas JanulaitisFermentas UABVilnius, LithuaniaDr. Ove OhmanAmic ABUppsala, SwedenProf. Anthony BrookesUniversity of LeicesterDepartment of GeneticsLeicester, UKProf. Marc ZabeauMethexis GenomicsGhent, BelgiumDr. Michael DahmsFebit AGTechnology DepartmentMannheim, GermanyProf. Olli KallioniemiVTT Technical Research Centre of FinlandMedical BiotechnologyTurku, FinlandDr. Jorn KochUniversity of AarhusInstitute of PathologyAarhus, DenmarkProf. Hans LehrachMax-Planck-Institute for Molecular GeneticsDept of Vertebrate GenomicsBerlin, GermanyProf. Andres MetspaluEstonian BiocentreLaboratory of Gene TechnologyTartu, EstoniaProf. Edwin SouthernOxford Gene Technology (Operations) LtdOxford, UKFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life89

REGULATORY GENOMICShttp://research.med.helsinki.fi/regulatorygenomicsProject Type:Specific TargetedResearch ProjectContract number:LSHG-CT-2004-512142Starting date:1 st September 2004Duration:48 monthsEC Funding:2 200 000State-of-the-Art:Determination of the sequence of the human genome, and knowledge of the genetic codethrough which mRNA is translated have allowed rapid progress in the identification ofmammalian proteins. However, less is known about the molecular mechanisms that controlexpression of human genes, and about the variations in gene expression that underlie manypathological states, including cancer. This is caused, in part, by lack of information aboutthe second genetic code – binding specificities of transcription factors (TFs). Decipheringthis regulatory code is critical for cancer research, as little is known about the mechanismsby which the known genetic defects induce the transcriptional programmes that control cellproliferation, survival and angiogenesis. In addition, changes in binding of transcriptionfactors caused by single nucleotide polymorphisms (SNPs) are likely to be a major factor inmany quantitative trait conditions, including familial predisposition to cancer.Scientific/Technological Objectives:We aim to develop novel genomics tools and methods for the determination of transcriptionfactor binding specificity. These tools will be used for the identification of regulatory SNPsthat predispose to colorectal cancer, and for characterisation of downstream target genesthat are common to multiple oncogenic TFs.The specific aims are:1. to develop novel high-throughput multiwell-plate and DNA chip-based methods fordetermination of TF binding specificity2. to determine experimentally the binding specificities of known cancer-associated TFs3. to predict computationally, and to verify experimentally, elements that are regulatedby these TFs in genes that are essential for cell proliferation4. to develop an SNP genotyping chip composed of SNPs that affect the function of TFbindingsites conserved in mammalian species5. to use this chip for the genotyping of patients with hereditary cancer predisposition,as well as controls in three European populations, for identification of regulatorySNPs associated with cancer.Expected resultsThis project aims to understand the basic principles involved in growth regulation by oncogenicTFs, and is expected to have a major impact on understanding cancer. Identificationof SNPs associated with low penetrance cancer predisposition would be a majorbreakthrough in the effort to understand inheritance of quantitative trait loci, and will haveimplications on healthcare at the population level.The methods developed within the project¹ have already allowed genome-scale predictionof regulatory elements in the human genome, and the methods developed should makefeasible the analysis of DNA-binding specificities of all TFs, and consequently significantlyimprove our understanding of the regulation of gene expression.¹ Hallikas O, Palin K, Sinjushina N, Rautiainen R, Partanen J, Ukkonen E and Taipale J: Genome-wide Prediction of MammalianEnhancers Based on Analysis of Transcription Factor Binding Affinity. Cell. 124:47-59, 2006.90From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Advanced Genomics Instruments,Technology and Methods for Determinationof Transcription Factor Binding Specificities:Applications for Identification of GenesPredisposing to Colorectal CancerPotential impactWe expect that the project will lead to the identification of genes that associate with colorectalcancer. This will have direct implications on diagnosis and treatment of a cancer typethat affects more than 200 000 Europeans each year.Methods, tools and instrumentation for advanced genomics developed within the proposedproject will improve EU scientific competitiveness in the rapidly developing field of regulatorygenomics, and will allow EU scientists to be in a very good starting position to decipherthe genetic code controlling regulation of gene expression.Keywords:genomics, molecular genetics, cancer, transcription factorsPartnersProject Coordinator:Prof. Jussi TaipaleUniversity of HelsinkiFaculty of MedicineGenome-Scale Biology Research ProgrammeYliopistonkatu 400014 Helsinki, Finlandjussi.taipale@helsinki.fiDr. Jörg HoheiselDeutsches KrebsforschungszentrumFunctional genome AnalysisHeidelberg, GermanyDr. Markus BeierFebit Biotech GmbHHeidelberg, GermanyProf. Torben ØrntoftAarhus University Hospital, Skejby SygehusMolecular Diagnostic LaboratoryDepartment of Clinical BiochemistryAarhus N, DenmarkProf. Jan LubinskiPomeranian Medical UniversityInternational Hereditary Cancer CenterSzczecin, PolandFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life91

Tat machinewww.tatmachine.netProject Type:Specific TargetedResearch ProjectContract number:LSHG-CT-2004-005257Starting date:1 st November 2004Duration:48 monthsEC Funding:2 000 000State-of-the-Art:Bacterial protein secretion is a fundamental biological process that is of the utmost relevanceto human health. On the one hand, it can be exploited to enhance health through the biotechnologicalproduction of biopharmaceuticals. On the other hand, secreted bacterial toxinsand virulence factors represent a major threat to health. The twin-arginine translocation (Tat)machinery represents a recently discovered, but highly conserved, system for bacterial proteinsecretion. This multi-sub-unit nanomachine can transport fully folded proteins, and thus has immensepotential for biopharmaceutical production in the bacterial species already being usedfor this purpose, including , coli and . Moreover, it has beendemonstrated that critical virulence factors are secreted via Tat in important pathogens, such as and E. coli O157.Scientific/Technological Objectives:The goal of the multidisciplinary Tat machine consortium is to carry out the functional genomiccharacterisation of the Tat nanomachine, for both biotechnological and biomedicalpurposes. It has two specific objectives: firstly, to eliminate the current bottlenecks in the Tatnanomachine that limit biopharmaceutical production in , and ,and secondly, to characterise the structure and function of Tat nanomachines in a few selectedGram-positive and Gram-negative bacteria, including major pathogens. To achieve thesegoals, the full potential of bioinformatics, comparative and structural genomics and proteomicswill be exploited. The Tat machine consortium has a proven track record in the applicationof these cutting-edge technologies.The consortium’s principal technological objective is to generate a platform for the secretionof a wide range of heterologous proteins, in particular those of therapeutic value, based onthe Tat machinery. Its principal scientific objective is to obtain a clear picture of the ‘global’role of Tat in a range of pathogenic and non-pathogenic organisms, and to obtain detailedinformation on the Tat structure that will lay the foundations for the future design of specificinhibitors. It is already clear that the Tat system is vital to the pathogenesis of a range ofbacteria. Some bacteria export major virulence factors by this pathway, and disruption of theTat pathway impairs the viability of others. Because Tat sub-units are also unique in structuralterms, and completely absent from mammals, the Tat machine represents a superb target fornovel anti-infectives.Expected Results:The consortium aims to produce the following results: (1) A detailed structure of Tat complexesfrom representative Gram-negative and Gram-positive species. This is an ambitious target.The project is geared to the efficient delivery of a wide range of Tat complexes, to partnerswith track records in the elucidation of membrane protein structures; (2) Development of supersecretingstrains of B. subtilis and S. coelicolor that are capable of exporting heterologousproteins with high efficiency. These strains will fill major gaps in the present repertoire of bacterialvehicles for protein production; (3) Understanding of the overall role of Tat in a limitedseries of pathogenic bacteria, including identification of specific virulence determinants thatemploy this export pathway; (4) In-depth understanding of the Tat translocation mechanism.This will be achieved through a combined biochemical/genetic analysis of the Tat translocationprocess, and the results will benefit all the elements of this project, mentioned above.Potential Impact:The expected deliverables of the Tat machine project include knowledge of a fundamentalbiological system, the Tat nanomachine, which is of vital relevance to human health. The92From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Functional genomic characterisation of thebacterial Tat complex as a nanomachinefor biopharmaceutical production and atarget for novel anti-infectivesresults will serve to reinforce efforts to design anti-infectives and to produce novel biopharmaceuticals.In addition, the consortium will add to the stock of highly trained young Europeanscientists working in this area, and will disseminate knowledge via scientific booksand journals, scientific meetings and practical training courses. These deliverables will beachieved through multidisciplinary research involving biochemistry, proteomics, functionalgenomics, structural genomics and comparative genomics approaches, in combination withrobust project management.Keywords: anti-infectives, biopharmaceuticals, human health, nanomachines,twin-arginine translocation, Bacillus, E. coli, Staphylococcus, SpecificTargeted, Research Projecttomyces, Mycobacterium, bioinformatics,structural genomics, drug targetsPartnersProject Coordinator:Prof. Jan Maarten van DijlUniversity Medical Center GroningenDepartment of Medical MicrobiologyHanzeplein 1P. O. Box 300019700 RB Groningen, The Netherlandsj.m.van.dijl@med.umcg.nlProject Manager:Dr. Sierd BronUniversity of Groningen andUniversity Medical Center GroningenKerklaan 309751 NN Haren, The Netherlandss.bron@rug.nlProf. Colin RobinsonUniversity of WarwickDepartment of Biological SciencesCoventry, UKProf. Oscar KuipersUniversity of GroningenGroningen Biomolecular Sciences andBiotechnology InstituteMolecular GeneticsGroningen, The NetherlandsProf. Marc KolkmanGenencor InternationalMicrobial and Molecular ScreeningLeiden, The NetherlandsProf. Matthias MüllerUniversität FreiburgInstitute for Biochemistry and Molecular BiologyFreiburg, GermanyDr. Tracy PalmerUniversity of DundeeCollege of Life SciencesDivision of Molecular & Environmental MicrobiologyDundee, UKDr. Long-Fei WuCentre National de la Recherche Scientifique (CNRS)Laboratoire de Chimie Bacterienne UPR 9043Marseille, FranceProf. Michael HeckerErnst-Moritz-Arndt-UniversitätInstitute for Microbiology and Molecular BiologyGreifswald, GermanyProf. Werner KühlbrandtMax-Planck-Institute for BiophysicsStructural BiologyFrankfurt, GermanyProf. So IwataImperial College of ScienceCentre for Structural BiologyDivision of Molecular BiosciencesLondon, UKProf. Roland FreudlJülich Research InstituteJülich, GermanyFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life93

Project Type:Specific TargetedResearch ProjectContract number:LSHG-CT-2004-511990Starting date:1 st January 2005Duration:39 monthsEC Funding:1 000 000TransCodeState-of-the-Art:http://transcode.tigem.it/The aim of this project is to develop open source tools enabling the identification of regulatoryelements controlling gene expression. In particular it is focused on elements which controlthe expression of transcription factors, which in turn control expression of all other genesin the genome. This field has undergone a rapid expansion since the sequencing of severalchordate genomes, which enabled researchers to identify elements through the disciplineof comparative genomics, i.e. a comparison of sequenced genomes in search of conservedelements, which are likely to harbour functional elements. The great challenge is identifyingeffectively the elements that do not encode well-understood protein-coding genes but tendto act as regulators of expression. Recent advances have identified several such elementsbut they are likely to be the tip of the iceberg. TransCode aims to unravel many more suchelements as well as some of the fundamental properties that characterise them.Scientific/Technological Objectives:The project aims to perform medium-scale studies on conserved non-coding elements acrossseveral chordate organisms, as well as tackling fundamental questions related to transcriptionfactor binding. The project will study a dozen transcription factor gene families and investigatein-depth for the presence of regulatory elements within the family across organisms. Thefollowing analyses will be performed on each gene family: aims to identify elements which have remained conserved in position within a phylumand elements that have ‘shuffled’, i.e. changed position during evolution, when comparingsequences across different phyla ingcurrent algorithms with knowledge derived from the project medium-scale verification of activity in mammalian cell-lines as well as Ciona embryos ferentiationassays and knock-out of transcription factors (TFs) in differentiated cells, toidentify TFs involved in enhancer activity in silico, invitro and in vivo This project represents a large-scale pluri-disciplinary effort to decipher the grammar of chordateregulatory sequences, and will have a strong impact by building tools and resources thatwill enable devising more sophisticated hypothesis regarding regulatory networks, especiallythose of TFs which are involved in fundamental biological processes.Expected Results:The project has completed its first year and has successfully completed the in silico analysisof selected transcription factor gene families, as well as the development of a central repositoryfor both in silico and in vivo data that is being collected. The repository is available atthe website (http://transcode.tigem.it/). It collates the in silico analyses so far performed,which indicate the sequence elements predicted to have functional potential based on publishedalgorithms, as well as algorithms developed by project members. Some elementshave undergone testing and for those tested in vivo results are also integrated, indicatingthose which have acted as enhancers or repressors and those which have yielded no results.94From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Novel Tool for High-ThroughputCharacterisation of Genomic ElementsRegulating Gene Expression in ChordatesIn the long term, the projectaims to collate this data on alarger scale and with morein-depth information regardingthe transcription factorsresponsible for the function ofeach element and their modeof action and interactions.PotentialImpact:Throughout our project we are contributing widely to the creation, refinement and good useof standards. We are using open source software and XML data transfers, and generatingnovel tools and experimental protocols that will set new standards in both dry and wetareas of biology, which will help others to explore further the language of gene regulation.The identification of regulatory modules that are responsible for well-defined expressionpatterns will be very useful in gene therapy, thus having a direct impact on health issues.Finally we are reinforcing European competitiveness by carrying out a transnational andco-operative project of international visibility via a tight collaboration of partners acrossfour European countries.Keywords: comparative genomics, conserved non-genic sequences,bioinformatics algorithms, gene expression regulationPartnersProject Coordinator:Dr. Sandro BanfiFondazione TelethonTelethon Institute of Genetics and MedicineMolecular Biology UnitVia G. Saliceto, 5000161 Rome, Italybanfi@tigem.itDr. Patrick LemaireUniversité de la MéditerranéeCentre National de la RechercheScientifique (CNRS)Marseille, FranceDr. Cristian BrocchieriUniversity of CambridgeDepartment of OncologyCambridge, UKDr. Ferenc MullerForschungszentrum KarlsruheInstitute of Toxicology and GeneticsEggenstein-Leopoldshafen, GermanyProf. Graziano PesoleUniversità di MilanoDipartimento di ScienzeBiomolecolari eBiotecnologieMilan, ItalyDr. Elia StupkaCBM Scrl – Consorzioper il Centro diBiomedicina MolecolareBioinformatic UnitTrieste, ItalyFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life95

EMERALDProject Type:Co-ordination ActionContract number:LSHG-CT-2006-037689Starting date:1 st November 2006Duration:36 monthsEC Funding:1 300 000State-of-the-Art:Data quality and meta-data (documentation) are the key to all microarray implementations,ensuring that maximum information is extracted from the data. The microarray communityhas long realised the importance of structured documentation accompanying microarraydata. To this end, a ‘grassroots movement‘, now the Microarray Gene Expression Data(MGED) Society, established guidelines for experimental description (Minimum InformationAbout a Microarray Experiment, MIAME) and description of a structured data exchangemodel (Microarray Gene Expression Markup Language, MAGE-ML). MGED initiatives havemainly focused on data context, and only recently has this focus expanded to include datacontent. Quality and coherence of microarray data compendia (for example in ArrayExpress)are major determinants of information extraction and model-building. EMERALD isdesigned to structure and organise these efforts at a European level, in close associationwith MGED and the External RNA Controls Consortium (ERCC).Intensity representation on anAffymetrix array (spatial plot).The false colours represent thespatial intensity distributionof the array. The colour scalewas chosen proportional to theintensity ranks. This graphicalrepresentation highlightsproblems that result fromthe experimentation such asfingerprints, artifactual intensitygradient or dye specific failuresfor instance.Scientific/Technological Objectives:The EMERALD consortium aims to establish and disseminate quality metrics (QC), microarraystandards and best laboratory practices (QA) throughout the European microarraycommunity, in order to improve the quality of microarray data.Its specific objectives are as follows:1. To investigate existing microarray data resources in ArrayExpress, preparinga full inventory of these and deriving fair and meaningful QC from them;2. To develop a normalisation and transformation ontology for the description ofdata pre-processing information;3. To bring together all major players in the European microarray community;4. To structure communication and information exchange within this community;5. To obtain microarray community agreement on QA;6. To assess microarray standards for QC. An analysis of QC relevant to variousdata production protocols and available hybridisation standards (spikes,reference RNAs) will in turn facilitate the development of QA for high dataquality;7. Key microarray laboratory volunteers to validate QA/QC;8. To validate the benefits of QA/QC in data compendium modelling;9. To disseminate microarray standards and best practices to the microarraycommunity, through a user community website and information exchange andsupport networks, and to provide training in their proper implementation;10. To extrapolate and apply these standards to developing technologies.Expected Results:The main result of EMERALD will be a quality metrics system for microarray data, accompaniedby ontologies for documentation of microarray meta-data. The project will also generate hybridisationstandards and, in general, integrate European efforts towards laboratory standardisationin this area. Recent scientific publications have shown that microarray data producedunder a series of standardisation constraints show improved significance and sensitivity.EMERALD will bring together the main research and innovation operators involved in the developmentof microarray standards and quality metrics, with stakeholders in the data productionprocess (core facilities, companies, technology innovators), data mining (computational andsystems biology research teams) and data information (toxicology, clinical diagnostics, prognostics,etc). The coordination and amalgamation of the activities and interests of these diversestakeholders will strengthen the European microarray community, consolidating an essentialcomponent of data-driven systems biology.96From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Empowering the Microarray-BasedEuropean Research Area to Takea Lead in Development and ExploitationPotential Impact:Data-driven modelling approaches that depend on data quality and coherence are essentialto systems biology. EMERALD aims to bring about the implementation of QA/QC,especially in the building of high quality, compendium-style data repositories. The SeventhFramework Programme (FP7) is expected to place an emphasis on the development of newbiological research tools that will significantly improve the acquisition and analysis of data,with a view to enhancing our understanding of complex biological systems. FP7 researchwill include the development of technologies related to sequencing, gene expression, genotypingand systems biology. EMERALD will contribute to these research goals by improvinglarge scale data gathering.Keywords: microarray technology, quality control, quality assurance, systemsbiology, data modelling, technology developmentPartnersProject Coordinator:Prof. Martin KuiperGhent University/Flanders Interuniversity Institutefor BiotechnologyDepartment of Plant Systems BiologyComputational Biology groupGhent, Belgiummartin.kuiper@psb.ugent.beProf. Arne SandvikNorwegian University of Science and TechnologyNorwegian Microarray ConsortiumTrondheim, NorwayDr. Alvis BrazmaEuropean Molecular Biology LaboratoryEuropean Bioinformatics Institute (EBI)Hinxton, UKDr. Carole FoyMicroarray Standardisation LGC LtdTeddington, UKProf. Joaquin DopazoCentro de Investigación Príncipe FelipeDepartment of BioinformaticsValencia, SpainDr. Heinz Schimmel,Joint Research Centre of the European CommissionInstitute for Reference Materials and MeasurementsGeel, BelgiumDr. Laszlo PuskasBiological Research Centre ofthe Hungarian Academy of SciencesLaboratory for Functional GenomicsSzeged, HungaryProf. Ulf LandegrenUppsala UniversityDepartment of Genetics and PathologyRudbeck LaboratoryUppsala, Sweden.From Fundamental Genomics to Systems Biology: Understanding the Book of Life97

AutoscreenProject Type:SME- Specific TargetedResearch ProjectContract number:LSHG-CT-2007-037897Starting date:1 st January 2007Duration:60 monthsEC Funding:3 217 280State-of-the-Art:As more and more genomes are being sequenced, efficient methods to elucidate the functionsof the many unknown genes need to be developed. Such methods will be an essentialprerequisite for turning biology from a qualitative, mostly descriptive, to a quantitative,ultimately predictive, science. Although quantitative tools such as DNA microarrays fortranscriptome analysis have been available for some years, they have not yet been used totheir full potential due to the overwhelming complexity.Cells are built from thousands of different proteins that are expressed, both temporally andspatially, over an extremely wide dynamic range. Proteins and other cellular componentsare regulated through variations of their location, their activity and their state of modification.Although DNA microarrays have proved to be important tools for gene discovery onthe tissue level, and, moreover, hold great promise for diagnostic applications, they havemajor shortcomings in their lack of cellular resolution. In order to obtain qualitative andquantitative data on cellular pathways, new equipment needs to be developed.Scientific/Technological Objectives:The overall objective of the AUTOSCREEN project is the establishment of an innovative andautomated screening instrument for high-throughput and high-content screens. This instrumentwill allow standardised, robust, automated and ultrasensitive high-resolution analysisof RNAs and proteins at cellular and subcellular resolution.The main goal of the project is to develop an innovative screening platform suitable for highthroughputand high-content cell-based assays and to demonstrate its suitability for high-resolutionin situ techniques. This instrument, named AUTOSCREEN, will not only provide thebasis for intelligent and efficient high-content screens, but will also be designed for low costgenetic, medical, chemical and pharmaceutical screens. It will constitute a significant competitiveadvantage for the European pharmaceutical and agro biotechnological industry.Expected Results:The main expected result of the project is the generation of an innovative screening instrument,named AUTOSCREEN. This instrument, which will consist of the modular iMIC imagingmicroscopy platform as a future microscopy standard, will integrate ultra-sensitive CCDtechnologyand novel software concepts that allow an adaptive, i.e. result-based, shapingof the ongoing experiment. An ultra-sensitive fluorescence-based scanning device for singlemoleculemeasurements and a fully automated plate feeder station for automated samplehandling and tracking will increase the flexibility and wide utility of AUTOSCREEN. Thissystem will be tested in a large number of applications for performance and excellence.The project is expected to permit the qualitative and quantitative monitoring of cellular constituents(RNA, proteins, and metabolites) in living cells at the highest possible cellular andsubcellular resolution and with maximal sensitivity and specificity. This will allow quantifyingprotein expression and monitoring its subcellular localisation, its state of modificationand its association with other proteins and ligands. Furthermore, it will allow measuring ofthe change of these processes over time.Potential Impact:AUTOSCREEN will have a strategic impact on functional genomic, biotechnological and biomedicalresearch by permitting qualitative and quantitative monitoring of cellular constituentsin cells at the highest possible cellular and subcellular resolution and with maximal sensitivityand specificity. This will allow, for example, quantifying protein expression, monitoring of subcellularprotein localisation and state of modification, and characterisation of the toponome.98From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Autoscreenfor Cell Based High-throughputand High-content Gene Function Analysisand Drug Discovery ScreensThe demonstration of the wide applicability of AUTOSCREEN to the quantitative monitoringof biological processes, within living cells, at highest currently possible resolution and withsensitivity to the limit set by the laws of physics, will have a significant impact on biomedicalresearch in general. By combining interdisciplinary activities from academic and industrialsources and by interfacing biological research with nanotechnology, computing and engineering,the team expects to create an important tool for biomedical research. Moreover,AUTOSCREEN-based assays will allow the monitoring of cellular networks and incorporate invivo protein interaction assays and features like protein concentration and kinetic parameters.Thus, available information on gene expression networks will not only be useful for identifyingpoints of the network affected by the drugs and for simulations of cellular processes, but willalso allow the assessment of drug side reactions at an early stage and facilitate the design ofnovel, less toxic compounds.The project will reveal new, faster and better possibilities to determine gene functions andregulatory networks in a much shorter period of time. The implementation of these technologieswill lead to a higher competitiveness of European biomedical SMEs, in the sense that theinstrumentation to be developed and assembled in this project will enable many EuropeanSMEs to efficiently perform their screens. The estimated low cost of this instrument is expectedto be of great benefit for SMEs as it will promote their market success.Keywords: imaging, screening, genomics, proteomics, drug screening, highthroughputtechnologiesPartnersProject Coordinator:Prof. Dr. Klaus PalmeUniversity of FreiburgInstitute for Biology IIFaculty of BiologyCenter for Applied BiosciencesFahnenbergplatz79085 Freiburg, Germanyklaus.palme@biologie.uni-freiburg.deDr. Stefanie KlemmTILL ID GmbHGräfelfing, GermanyDr. Andras FilepManz KftDebrecen, HungaryDr. Alois SonnleitnerUpper Austrian Research GmbHLinz, AustriaDr. Colin CoatesAndor Technology PlcBelfast, UKDr. Carmen PlasenciaAromics SLBarcelona, SpainDr. Martin OheimInstitut National de la Santéet de la Recherche Médicale(INSERM)Neurophysiology andNew Microscopies LaboratoryParis, FranceDr. Hartmann HarzLudwig-Maximilians-UniversitätBioImaging ZentrumPlanegg, GermanyDr. Benedetto RupertiUniversity of PadovaLegnaro, ItalyFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life99

Project Type:SME- Specific TargetedResearch ProjectContract number:LSHG-CT-2006-037517Starting date:1 st January 2007Duration:36 monthsEC Funding:2 351 818TargetHerpesState-of-the-Art:www.targetherpes.orgHerpes viruses cause many serious and life-threatening diseases, especially in immunocompromisedpatients, such as transplant recipients and HIV-infected individuals. Even inhealthy ones, herpesviruses can result in serious diseases. For example, the herpes simplexvirus (HSV) remains one of the most common sexually transmitted diseases, while humancytomegalovirus (HCMV) is a leading cause of birth defects, and human herpes virus 8(HHV-8) causes a number of cancers. At present, the options for antiviral therapy are limited,and owing to toxicity, the current anti-herpesvirus drugs cannot be administered topregnant women. There is a continuing need to develop new treatments, because drugresistantviruses are constantly evolving.A principal characteristic of herpesvirus infections, is that after primary infection (usuallyin childhood), the viruses establish a latent state that remains for life. Up to 90 percent ofthe population may be latently infected with one or more herpes viruses. The social andpsychological consequences of the herpesvirus infections are severe.Scientific/Technological Objectives:The major objective of TargetHerpes is to define novel drug targets and to identify newstrategies, for the control of herpesvirus infections. These targets and strategies will help, inthe long term, to provide the next generation of antiviral compounds, Specifically, TargetHerpeswill perform the following actions: (i) develop peptide inhibitors that interfere withvirus entry; (ii) generate synthetic peptides that enable antibody-dependent cellular cytolysisagainst herpesviruses; (iii) define, investigate and apply RNA silencing reagents that blockthe expression of viral genes that enhance herpesvirus replication; (iv) define, investigateand apply RNA silencing reagents that interfere with proviral host genes; (v) identify viraland cellular genes involved in herpesvirus-mediated oncogenesis, and define RNA silencingreagents and peptide inhibitors; and (vi) develop approaches to inhibit the reactivationof HSV from latency.This programme of work will provide innovative technologies for the identification and developmentof future products targeted at preventive and therapeutic interventions for humanherpesvirus diseases. Moreover, these strategies will likely be transferable to many otherpersistent infections.Expected Results:The TargetHerpes project is divided into six experimental work packages (WPs). The aim ofWP1 is the development of peptide molecules that will inhibit the functions of herpesvirusglycoproteins and elucidate their roles in entry of the virus particles into cells. Preliminarywork has provided proof-of-principle that mimetic peptides to HSV gH inhibit infection.Such peptides targeting HSV glycoproteins will be suitable for future animal experimentationand translational research by partners PRIMM and IBA. WP2 will generate syntheticpeptides that enable IgG antibodies to execute cell-mediated cytolysis against HSV andHCMV. Such peptides will be evaluated for their individual potency in vitro, then bioactivepeptides will be evaluated with regard to safety and harmlessness to cells, as well asoptimal stability in cultured cell systems. WP3, WP4, WP5 and WP6 will identify suitablemolecular targets for antiviral intervention by RNAi.These targets will include important herpes virus gene products that have known or suspectedroles in promoting viral replication directly or indirectly. In case of WP5, siRNAs100From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Molecular intervention strategies targetinglatent and lytic herpesvirus infectionstargeted at viral genes will be selected based on their capacity to interfere with HHV-8 mediatedcell transformation and immortalization. WP6 expects to identify the cellular interactionpartners of ICP0 (the viral protein that is necessary for HSV to reactivate from latency),and to define those elements that are required for its activity.Potential Impact:TargetHerpes will identify novel strategies, leading to the development of new approachesto inhibit replication of, or pathogenesis caused by, HSV, HCMV and HHV-8. Due to theconservation of genes and replication strategies within herpesviruses, the approaches discoveredwill be applicable to other human herpesviruses as well. For example, treatmentsthat target HSV-1 are highly likely to be effective against HSV-2 and may be adapted tocounteract varicella zoster virus (VZV). Similarly, treatments that are effective against HHV-8may also be applicable to Epstein-Barr virus (EBV). Given the figures on the health burdenand costs of herpesvirus infections, the potential impact of a successful outcome of the TargetHerpesproject is considerable.Keywords:herpesvirus; chemiotherapeutics; herpes simplex virus; human cytomegalovirus; human herpesvirus8; fusion; glycoproteins; siRNA; innate immunity; host response; IFNPartnersProject Coordinator:Prof. Gabriella Campadelli-FiumeUniversity of BolognaCentro Interdipartimentale Galvani (CIG)via S. Giacomo 12I-40126 Bologna, Italygabriella.campadelli@unibo.itDr. Roger EverettMedical Research CouncilVirology UnitGlasgow, UKProf. Hartmut HengelUniversity of DuesseldorfInstitute for VirologyDüsseldorf, GermanyDr. Joachim BertramIBA GmbHGöttingen, GermanyDr. Frank NeipelUniversity of ErlangenInstitut fuer Klinischeund Molekulare VirologieErlangen, GermanyDr. Michael NevelsUniversity of RegensburgInstitute for MedicalMicrobiology and HygieneFaculty of Medicine,Molecular Virology UnitRegensburg, GermanyDr. Angela PontilloPRIMM SrlMilan, ItalyDr. Ivan RossiBioDec SrlBologna, ItalyWolfgang Laepple-BoettigerARTTIC S.A.Office MannheimSchifferstadt, GermanyFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life101

Project Type:SME-Specific TargetedResearch ProjectContract number:LSHG-CT-2006-037683Starting date:1 st January 2007Duration:36 monthsEC Funding:3 000 000FGENTCARDState-of-the-Art:www.fgentcard.euThe general aim of FGENTCARD is to apply functional genomic and genotyping technologiesalong with the knowledge arising from mammalian genome annotations, in order todefine novel diagnostic tools for risk factors of Coronary Artery Disease (CAD) (glucoseintolerance, insulin resistance, hypertension, dyslipidaemia and obesity). FGENTCARD,supported by available functional genomic technologies, will tackle these increasingly frequentand prevalent inherited diseases. The project will ultimately generate fundamentalknowledge on the impact of functional genomics to identify disease biomarkers and testtheir use for disease prediction. The consortium is interested in focusing on CAD becauseof its frequency and prevalence in the general population, the strong impact on humanhealth and the burden of related healthcare costs. Pathological elements of CAD have beenshown to have complex etiology and pathogenesis that influence an individual’s relativerisk of developing these diseases. The genetic input is complex, and involves combinationsof multiple genes that contribute to susceptibility or resistance to CAD risk factors. In orderto take advantage of high density multimodal phenotyping, the consortium is preparing aninnovative infrastructure of both the techniques and materials that provide strategic supportfor CAD quantitative genetics in rodent models and humans.Scientific/Technological Objectives:One of the major objectives of the FGENTCARD is to identify biomarkers associated withCAD risk factors, by means of network biology that can be used as disease prediction tools inclinical studies and as targets for developing novel and more efficient drugs.FGENTCARD is objective-driven research which develops along the following lines:1) Characterization of CAD phenotypes, using classical physiological and biochemicalmethods in a large cohort of patients and in animal models;2) Generation of functional genomic quantitative trait datasets using plasma and urinemetabonomic profiling in animal models and humans, plasma proteomic profiling inanimal models and humans and tissue transcriptomic, proteomic and metabonomicprofiling in animal models;3) Genetic studies which aim at testing the association between plasma biomarkers andCAD risk factors in humans, at testing the inheritance of plasma, urine and organbiomarkers in animal models and at identifying underlying gene variants in animalmodels and humans.Close interactions with external international groups investigating related disorders in othermodels and human cohorts will provide resources for extension and validation of CAD biomarkers.In addition, interactions with other EC funded programmes of research, including MOL-TOOLS and MOLPAGE, will maximize the scientific and technical outputs of FGENTCARD.Expected Results:The consortium plans to deliver the following specific results:1) Multimodal phenotyping in a novel collection of 5,000 CAD patients, and in mouseand rat models of spontaneous and experimentally-induced pathologies relevant toCAD risk factors;2) A series of integrated functional genomic datasets defining biomarkers associatedwith CAD risk factors, through quantitative genetic studies in experimental crossesderived from animal models and further genetic association and linkage studies inhumans;3) CAD susceptibility loci and genes providing chromosomal targets for positional cloningexperiments and entry points to the development of novel drugs designed forspecific protein and metabolite disease biomarkers;102From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Functional GENomic diagnostic Toolsfor Coronary Artery Disease4) A set of standard operation procedures (SOPs) for the characterization of novel CADquantitative biomarkers, applicable to genetic and clinical studies in other cohorts ofpatients and controls.5) Data analysis using bioinformatics and statistical genetic tools developed in experimentalpopulations and human cohorts, which will further strengthen the impact ofcomparative genomics in biomedical research.Potential Impact:FGENTCARD brings together a comprehensive set of specific expertise in functional genomictechnologies (metabonomics, proteomics, transcriptomics), genotyping methods andstatistical genetics in rodent models and humans. This multidisciplinary approach is necessarywhen undertaking an integrated functional genomic approach that addresses geneticvariation, in the context of CAD risk factors.Overall, the potential wealth of information that can be obtained on gene expression, fromtranscription to protein effects, is enormous. It represents novel challenges in quantitativegenetics, and ultimately, significant advances for disease diagnosis and prevention as well.An important goal of this research in CAD patients and animal models lies in disease geneidentification. Knowledge of the effects of genetic variations on metabolic processes andmetabotype regulation will have a major impact in the field of polypharmacology, on thedevelopment of novel drugs designed to affect multiple targets simultaneously.Keywords: metabonomics, quantitative genetics, diagnostics, coronary artery,cardiovascular diseasePartnersProject Coordinator:Dr. Dominique GauguierUniversity of OxfordWellcome Trust Centrefor Human GeneticsRoosevelt DriveOxford, OX3 7BN, UKgdomi@well.ox.ac.ukProf. Mark Lathrop, Dr. Ivo G. GutCentre National de Génotypage (CNG)Evry, FranceDr. Ulla Grove SidelmannNovoNordisk A/SMalov, DenmarkDr. Jorg HagerIntegraGen SAEvry, FranceDr. Frank BonnerMetabometrix LtdLondon, UKProf. Jeremy K. NicholsonImperial CollegeFaculty of MedicineChemical and Molecular Systems BiologyLondon, UKDr. Pierre ZallouaLebanese American UniversitySchool of MedicineDepartment of Internal MedicineBeirut, LebanonFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life103

MODESTProject Type:SME- Specific TargetedResearch ProjectContract number:LSHG-CT-2007-037291Starting date:1 st April 2007Duration:36 monthsEC Funding:2 755 356State-of-the-Art:The pharmaceutical industry is highly interested in using primary cells instead of cell linesfor cell-based screening campaigns in drug development since primary cells are freshlyisolated from the organism’s tissue, and have not gone through any transformations, whichis the prerequisite for the unlimited growth of conventional cell lines. With more predictivescreens in terms of both the relevance of a target and the pharmaco-kinetics/-dynamics of adrug compound, it becomes much easier to make adequate decisions as to which targets orcompounds to focus on for further development. While conventional transfection methods,such as lipofection or electroporation, usually yield satisfactory results for standard cell lines,many other cell lines — as well as most primary cells — are difficult or even impossible totransfect with these methods. Viral vectors - as an alternative for DNA delivery - work wellin some cases, but are labour-intensive, not versatile, and remain connected with significantsafety issues. As a consequence, most primary cells are considered non-transfectable. Thisrepresents a tremendous disadvantage in highly relevant research areas, as primary cellsare the ones that most closely resemble the situation of the living organism.Development of automated cellmanipulation in the 384-wellformat will add an important toolfor biomedical research and drugdevelopment.Besides the delivery of DNA, RNA or small molecules to primary cells, throughput of transfectionexperiments is of extreme importance. The emerging RNA interference (RNAi) technology,continued growth of (drug) compound libraries, and the increasing number of potentialtargets to be screened, have resulted in the high pressure to increase the throughputof screening to higher formats, the so-called ultrahigh-throughput screening (uHTS). However,cell-based assays still use the 96- or occasionally the 384-well format and screeningof millions of compounds may take months instead of days.Scientific/Technological Objectives:The principle objective of the MODEST project is the development and use of an ultrahighthroughputdevice for nucleofection (uHTN device) as well as protocols for highly efficient,small volume ultrahigh-throughput screenings of primary cells, mainly in the areas of immunology,neurology and liver metastasis with the aim of accelerating basic research, target identificationand validation as well as drug development.These uHTN device will represent a major breakthrough, since it would allow high-throughputscreenings in efficiently transfected and differentiated networks of primary cells. In addition,the concept of disposable modular multi-well plates for transfection is perfectly suited for preplatingsubstances, for storage and for later use, thus allowing flexible approaches, e.g. forhigh-throughput screening campaigns.Application of these tools is planned in order to investigate medically highly relevant disorders.On the basis of the 96-well Nucleofector, which was launched by “amaxa” in 2006,the Consortium will develop ultrahigh-throughput devices. In parallel, protocols for cultivating,differentiation, nucleofection and functional screens of primary cells in very small volumes willbe elaborated on and, furthermore, adapted to the devices.Expected Results:Development of uHTS device is the main objective of this project. These devices will be distributedby the coordinator, “amaxa”. In order to efficiently commercialise this platform withina well-balanced marketing and sales strategy, the coordinator will combine a top-notchsales force in key markets and alliances with quality strategic and distribution partners. Thecommercialisation strategy aims to optimise short- and medium-term revenues, secure broadmarket access and share, and provide crucial market feedback to the company.104From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Modular Devices for Ultrahigh-throughputand Small-volume TransfectionThe scientific knowledge of the MODEST project shall be published in premium peer-reviewedjournals, and scientists involved in the project will present their data at national andinternational conferences.Potential Impact:The partners of MODEST will employ the results of the project to service pharmaceuticalcustomers who repeatedly have expressed the urgent need for devices, protocols and assaysfor primary cells or differentiated human neuronal stem cells in target discovery andvalidation. The results of the project will give the partners a clear competitive advantage.The use of primary cells in preclinical R&D will positively impact attrition rates and reducethe significant time and capital involved in drug development. The proximity to Europeanpharmaceutical research and the size of the international pharmaceutical research marketstrengthen the logic for the creation and implementation of the MODEST project.Keywords:nucleofection, primary cells, hard-to-transfect cell lines, RNAi, siRNA, ultra high throughputtransfection, adult stem cells, neuronal cells, apoptosis, lead, gene silencing/knockdown,screeningPartnersProject Coordinator:Dr. Birgit Nelsen-SalzAmaxa AGNattermannallee 150935 Cologne, GermanyBirgit.nelsen-salz@amaxa.comDr. Alexander ScheffoldDeutsches Rheuma ForschungszentrumBerlin, GermanyDr. Joerg PoetzschRNAx GmbHBerlin, GermanyDr. Kaia PalmProtobios Ltd.Tallin, EstoniaHelmut LoiblFOTEC Forschungs- und Technologietransfer GmbHWiener Neustadt, AustriaJosef Anton PallanitsHTP High Tech Electronics GmbHNeudoerfl, AustriaDr. Naiara TelleriaDominion Pharmakine S. L.Derio, SpainThomas SchaumannPrevas ABVästerås, SwedenFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life105

1.2TOOLS & TECHNOLOGIES FORPROTEOMICSINTERACTION PROTEOMENEUPROCFCAMPProDac

INTERACTION PROTEOMEwww.interaction-proteome.orgProject Type:Integrated ProjectContract number:LSHG-CT-2003-505520Starting date:1 st January 2004Duration:66 monthsEC Funding:11 999 527State-of-the-Art:The main objective of the INTERACTION PROTEOME project is the establishment of a broadlyapplicable platform of routine methods for the analysis of protein interaction networksin biomedical research. A multidisciplinary approach will address different aspects of thegeneration of protein-interaction data, their validation by cell biological, biochemical andbiophysical methods, their collection in a new type of public database and their exploitationand use for in silico simulations of protein-interaction networks.These goals represent substantial state-of-the-art advances in these technologies. The innovationsgenerated in INTERACTION PROTEOME will thus provide the basis for an efficientanalysis and systems modelling of fundamental biological processes in health and disease.More specifically, INTERACTION PROTEOME will develop novel technologies, including ahigh-end mass spectrometer with an extremely large dynamic range, high-density peptide arraysand improved visualisation technology for light and electron microscopy. These technologieswill be validated through model systems of great relevance to medicine and biotechnology.In order to cope with the massive increase in experimental data on protein interactionsobtained by using the novel technologies, extensive bioinformatics support will be a keyelement in facilitating this work. In particular, the efficient integration of disparate data setsrepresents a vital challenge in proteomics and functional genomics.Localisation of proteins within acell: Protein complexes (coloured)are depicted at various levels ofresolution in their cellular context(background). This technologyenables the visualisation of the3-dimensional architecture andsupramolecular structure of cells.Within the context of interaction data already included within the scientific literature writtenby a community of ‘traditional biologists’, the analysis of the newly discovered interactionswill represent an essential prerequisite for the success of the consortium. For this purpose,the consortium includes the creation of the only European protein-interactions database,called MINT.Scientific/Technological Objectives:The aim of INTERACTION PRO-TEOME is to establish Europe as theinternational scientific leader in thefield of functional proteomics, and inparticular in the analysis of proteinproteininteractions. One of the majorobjectives includes the establishmentof a broadly applicable platform ofroutine methods for the analysis ofprotein interaction networks.The interaction partners of morethan 100 relevant protein domainsand more than 3,000 peptides willbe characterised using these noveltechnologies, while the data obtained during the project will be collected in an improvedversion of the European MINT database. At the same time, novel bioinformatics tools forthe prediction of protein interactions and their relation to post-translational modificationswill be created. In addition, software for in silico modelling of protein interactions will bedeveloped and validated with the projects’ model systems.108From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Functional Proteomics:Towards defining the interaction proteomeExpected Results:The aim of INTERACTION PROTEOME is to establish groundbreakingtechnology for the analysis of protein-protein interactions.During the first two years of the project, major goalshave already been achieved.In terms of technology, a major breakthrough by INTERAC-TION PROTEOME was the development of a novel massspectrometer, the LTQ-Orbitrap, and its introduction to themarket in June 2005 by the project partner Thermo Electron(Bremen). The Orbitrap is the first fundamentally new mass analyser in more than 20 years.Compared to a state-of-the-art high performance mass spectrometer (LTQ-FT), the Orbitrapexhibits a 10-fold increase in sensitivity along with a four-fold extension of the dynamicrange. Based on highly accurate mass determination combined with high resolution andsensitivity, the novel instrument not only allows for routine analysis with high-throughput,but also for straight forward analysis of peptide mixtures without chemical or enzymaticmodifications.From a methodological point of view, the Orbitrap is the ideal instrument for the two novel“2D-Gel-free” proteomics approaches developed within the project, namely the “SILAC”(Stable Isotopic Labelling by Amino acids in Cell culture) technology developed by the teamof Matthias Mann at the University of Odense/Max Planck Institute of Biochemistry, Martinsried,and the “COFRADIC” (COmbined FRActional DIagonal Chromatography) createdby the team of J. Vandekerckhove from Flanders Interuniversity Institute of Biotechnology,Ghent. Both technologies have been successfully applied to a number of the project’s modelsystems, including, among others, the analysis of protein processing in apoptosis by COF-RADIC, as well as the analysis of Chaperone-dependent protein folding and of signalling(de)differentiating stem cells by SILAC.In the first two years of its existence, INTERACTION PROTEOME has published over 30peer-reviewed publications in internationally renowned journals. During the project’s midtermreview in December 2005, external experts evaluated INTERACTION PROTEOMEas a clear “showcase project for EU research”. By the end of year four of the project, thenumber of publications issued has risen up to 120.Visualisation of the cytoskeletonof a Dictyostelium cell. Colourswere subjectively attributedto mark the actin filaments(reddish); other macromolecularcomplexes, mostly ribosomes(green); and membranes (blue).Potential Impact:Protein folding by the Chaperonemachinery: an unfoldedsubstrate protein is inserted intothe barrel-shaped GroEL cage,which is subsequently lockedwith the GroES lid. Foldingproceeds within the secludedchaperonin cage, which finallyreleases either correctly foldedfunctional protein (upper), oran incompletely folded proteinwhich may undergo either anotherfolding cycle or degradationin the cytosol.From Fundamental Genomics to Systems Biology: Understanding the Book of Life109

INTERACTION PROTEOMEClusters of phosphorylation sitesassigned according to the temporalprofiles of their modulationafter EGF stimulation of the cells.Prominent members are indicatedabove each cluster.The technology andmethodology producedin INTERACTION PRO-TEOME will facilitatea large-scale analysisof protein interactionsin various fields of biomedicine.The interdisciplinarycollaborationwithin the project willsupport the developmentof coherent standards inmethodology and dataformats, foster furtherhorizontal integrationof research centres andfacilitate the exchangeand comparison of dataobtained in different laboratories. Although this coherence will initially be observed onlywithin the consortium, its scientific success will promote the spreading of its standards toEuropean proteomics centres outside the partnership. The active contribution of individualpartners to various other networks at national and international level will also facilitate thedissemination of standards and promote the coherence of the proteomics field in Europe.In terms of human resources, the impact of INTERACTION PROTEOME in the many expandingareas of biomedicine will be considerable. Young scientists involved in the projectwill acquire multidisciplinary skills, including training in bioinformatics, and will thus representa valuable resource for the growing biomedical and biotechnological industry. Inaddition, highly qualified technical personnel in this novel interdisciplinary research fieldwill become available through the project. Finally, administrative staff involved in themanagement of this large EU project will gain experience for future careers as managersof international projects.Keywords: protein-protein interaction, signalling network, proteomePhototaxis in Halobacteriumsalinarum. A) Halobacteria arerepelled by blue light (left) andattracted by orange light (right).B) Components of the halobacterialsignal transduction chainmodulating clockwise (CW) andcounterclockwise (CCW) rotationof the flagellar motor.110From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Functional Proteomics: Towards defining the interaction proteomePartnersProject Coordinator:Prof. F. Ulrich HartlMax-Planck-Institute of BiochemistryDepartment of Cellular BiochemistryAm Klopferspitz 1882152 Martinsried, Germanyuhartl@biochem.mpg.deProject Manager:Dr. Anne Katrin WerenskioldMax-Planck-Institute of BiochemistryEU Project Acquisition & ManagementAm Klopferspitz 1882152 Martinsried, Germanyproteome@biochem.mpg.deProf. Luis SerranoCentre De Regulació Genómica (CRG)Systems Biology Research unitBarcelona, SpainDr. Philippe BastiaensEuropean Molecular Biology Laboratory (EMBL)(EMBL)-HeidelbergCell Biology and Cell Biophysics ProgrammeHeidelberg, GermanyDr. Mike SchutkowskiJT Peptide TechnologiesBerlin, GermanyProf. Wolfgang Baumeister, Prof. Dieter Oesterhelt,Prof. Matthias MannMax-Planck -Institute of BiochemistryMartinsried, GermanyProf. Joel VandekerckhoveFlanders Interuniversity Institute of BiotechnologyDepartment of Medical Protein ResearchGhent, BelgiumProf. Gianni CesareniUniversity of Rome Tor VergataDepartment of BiologyLaboratory of Molecular GeneticsRome, ItalyProf. Søren BrunakTechnical University of DenmarkCenter for Biological Sequence AnalysisLyngby, DenmarkDr. Raymond WagnerFEI Electron Optics BVEindhoven, The NetherlandsProf. Walter KolchBeatson Institute for Cancer ResearchSignalling & Proteomics LaboratoryGlasgow, UKDr. Marius UeffingGSF - National Research Centerfor Environment and HealthInstitute of Human GeneticsNeuherberg, GermanyDr. Reinhold PeschThermoElectron (Bremen) GmbHBremen, GermanyFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life111

NEUPROCFProject Type:Specific TargetedResearch ProjectContract number:LSHG-CT-2004-512044Starting date:1 st July 2005Duration:36 monthsEC Funding:2 355 000State-of-the-Art:In the search for new diagnostic and prognostic biomarkers for the development of newdrugs for cystic fibrosis (CF), the identification of new low- and medium-abundance proteinsinvolved in its pathophysiology is a very promising field. The characterisation of suchmarkers requires the development of several high performance techniques and the creationof standards for these new approaches. Several ways will be explored to bring newknowledge to the CF community, applying and developing state-of-the-art mass spectrometry,chromatography and electrophoresis methods to the inflammation mechanisms in CF,interaction between proteins, mainly the cystic fibrosis transmembrane regulator (CFTR),and other molecules, like DNA, other proteins or lipids. In addition to the biomarkers, thisshould bring a better understanding of CF pathophysiology with regard to transepithelialion transport, inflammatory processes and the identification of factors responsible for thedifferent CF phenotypes.Scientific/Technological Objectives:The aim is to identify new low abundance protein biomarkers in serum. In the meantime,the project will generate new basic knowledge for inflammation, protein-, lipid- and DNAinteractionin all fields related to scientific fields, such as cancer, neurodegenerative diseasesand asthma that are considered as priorities for EC science.Another strategic impact concerns prognostic biomarkers: the phenotype of CF is quite variable,even in patients bearing the most frequent mutation delta F508. To tackle the problemsposed by this disease and to try to decipher the underlying mechanisms, large-scalestudies at the protein level would certainly accelerate discoveries, in particular by detectinglow abundance proteins. This will imply new standard protocols for sample collection andtechnologies by: which will be useful for the proteomic community; cationof lipid molecules which interact with CF-related proteins; pathogenesis of CF; Expected Results:Methodological improvements in mass spectrometry, to be patented if applicable, willmaintain the very high level of skills in this field in Europe, and open new lipidomic-DNAproteomicapproaches.Here is a list of expected results: CF patients; Potential Impact:Through the NEUPROCF results and the ability to monitor low- and medium-abundance CFbiomarkers, the objective is to give a better prognostic of the disease severity. The treat-112From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Development of New Methodologiesfor Low Abundance Proteomics:Application to Cystic Fibrosisments could be then adapted, being lighter fora less severe affection, hence improving the patient’squality of life.In addition, the input of knowledge on themechanisms underlying CF phenotypes in a databasecould prove to be a decisive asset inthe perspective of transferring the knowledgeto biotech or pharmaceutical groups, togetherwith standard protocols for sample collectionand high-tech technology.One of the NEUPROCF strategiesto identify biomarkers: highresolution MS/MS analysispeptide map.© Dr. M. Dadlez (IBB-MS)Keywords: low abundance proteins, proteomics, cystic fibrosisPartnersProject Coordinator:Dr. Aleksander EdelmanInstitut National de la Santé etde la Recherche MédicaleFaculte de Medecine Necker Inserm U467156, rue de Vaugirard75730 Paris, Franceedelman@necker.frDr. Michal DadlezPolish Academy of SciencesDepartment of BioinformaticsWarsaw, PolandDr. Dorota SandsInstitute of Mother and ChildCF CentreWarsaw, PolandDr. Lena HjelteKarolinska InstitutetHuddinge University HospitalStockholm Cystic Fibrosis CenterStockholm, SwedenDr. Josef VogtUniversitätsklinikum UlmDepartment of AnaesthesiologyUlm, GermanyProf. Margarida AmaraFundacao da Faculdade deCiencias de Universidade de LisboaDepartment of Chemistry andBiochemistry - Laboratory ofMolecular GeneticsLisbon, PortugalDr. Peter BergstenUppsala UniversityDepartment of Medical Cell BiologyUppsala, SwedenProf. Jasminka Godovac-ZimmermannUniversity College LondonDepartment of Medicine Rayne InstituteLondon, UKDr. Robert DormerUniversity of WalesDepartment of Medical Biochemistry& Immunology School of MedicineCardiff, United KingdomDr. Laure-Emmanuelle BenhamouINSERM - TransfertEuropean Projects ManagementSaint-Beauzire, FranceDr. Michael CahillProteoSys AgMainz, GermanyProf. Gérard LenoirAssistance Publique - Hopitaux deParisHôpital Necker Departmentof PediatricsParis, FranceFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life113

Project Type:Specific TargetedResearch ProjectContract number:LSHG-CT-2006-018830Starting date:1 st January 2006Duration:36 monthsEC Funding:2 700 000CAMPState-of-the-Art:http://camp.bioinfo.cipf.esProteases are key molecules in biological systems. They modify numerous proteins by hydrolyticcleavage, thus controlling and executing many physiological processes. Their intricatenetworks require rigorous regulation to prevent fortuitous proteolysis. Where this regulationfails, proteases trigger pathologies such as neurodegeneration, inflammation, and cancer.Many therapeutic approaches are directed towards proteases or their natural inhibitors, andare already leading to drugs for life threatening diseases. However, the tight regulation ofproteases by posttranslational modifications makes current functional genomics technologiesunsuitable for fully establishing biological relevance. The project “Chemical Genomics by ActivityMonitoring of Proteases” (CAMP) will lay the groundwork for the study and understandingof proteases through activity labelling and functional imaging in cells. Specifically, CAMPwill investigate the substrate specificity of proteases by using large peptide libraries, derivefluorescent labelling molecules from the sequence information gathered, and use these moleculesto investigate proteolytic activities in cellular environments. Given the estimated numberof 600 proteases to 1100 proteases in the human genome, the team’s selected set constitutesa significant representation and will establish the feasibility of the project’s approach to addressthe protease proteome. CAMP’s proteases will serve as prototypes to develop novelprotease-specific technologies and probes for studying expression and folding, the activitystate of proteases and their endogenous interaction partners in vitro and in vivo. The gatheredinformation will be annotated in a public repository. The team expects the derived insights ofCAMP to foster high-throughput approaches and research, leading to new avenues in drugdiscovery, using integrated data on the protease proteome.Structure of the LCI-CPA2 complexStructure of Caspase 2Scientific/Technological Objectives:The CAMP project will develop and integrate novel technologies in the areas of recombinantprotein production, High Throughput (HT) structure determination and bioinformatics, togetherwith the development of specific chemical tools for functional annotation, localizationand characterization. Ultimately, CAMP will provide the following: information on syntheticpeptide substrates of proteases; chemical probes as tools to investigate the physiological roleof proteases in cellular environment; identification of physiological substrates of proteasesproviding information about protease signalling pathways, essential for understanding biologicalroles in health and disease, and an assessment of the tools developed in the project;and novel crystal structures of proteases in the activated form (either alone or in complex withinhibitors), as well as in the zymogen state. The team has selected a total of 45 targets fromthe cysteine proteases (papain-like lysosomal proteases and caspases) and metalloproteases(carboxypeptidases, matrix metalloproteases and ADAM-TS metalloproteases) to develop,implement and demonstrate the feasibility of the team’s proteomics-oriented approaches forproteases. The aim of CAMP is to establish the interdisciplinary core infrastructure and technologiesthat will be required for a subsequent full-scale protease proteomics approach. Theteam’s choice of protease targets has been based on two criteria: implication in importantphysiological processes, as well as novelty with respect to function.Expected Results:Besides the proteomics-focused technological aims, CAMP focuses on a selected and medicallyhighly relevant subset of human proteases. The team further expects to substantiallyincrease the current knowledge (at the level of genomic annotation) of four selected clans ofproteases, encompassing 45 prototypic representatives. Many of them are critically involvedin medical problems and pathologies, such as those related to hormone and neuropeptideprocessing and maturation (i.e.N/E carboxypeptidases), inflammation and joint diseases(cathepsins, caspases, ADAM-TSs), stroke and cardiovascular arteriosclerosis (caspases,TAFI, MMPs, ADAM-TSs) andcancer (cathepsins, caspases, MMPs).114From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Chemical Genomicsby Activity Monitoring of ProteasesPotential Impact:The data resulting from CAMP will promote and stimulate novel applied research based onthe enzyme targets, which have been poorly interconnected or neglected so far owing tothe lack of an integrated and generally available platform for protease-specific proteomics.Within the present project, the selected proteases will be used as a training set to developsuch proteomics technologies. Proteases have been recognized as valid drug targets, andmany inhibitors of proteases have been designed that resulted in drugs, e.g. to treat HIV infections,thrombosis, or hypertension. Therefore, a significant expansion of knowledge on theseenzymes and on molecules controlling them (such as natural or artificial inhibitors) will have adirect impact on the landscape of biomedical sciences and technologies in Europe. The resultsand technologies of CAMP should facilitate the efficient generation of structural and functionaldata for this set at a full proteomic scale. Furthermore, the tools developed in CAMP shouldfacilitate the future application of the developed technologies to other hydrolytic enzymes. Bydeveloping and integrating family-specific technologies for high-throughput expression, biochemistry,inhibitor design and structural proteomics, CAMP aims to enable a future functionaland structural annotation of the entire protease proteome.Complex between TIMP-1 andthe catalytic domain of MMP-3Keywords: chemogenomics, chemoproteomics, functional probing, proteolyticenzymesPartnersProject Coordinator:Prof. Francesc Xavier AvilesUniversitat Autonoma de BarcelonaInstitut de Biotecnologia i de BiomedicinaProtein Engineering and Enzymology Unit08193 Bellaterra (Barcelona), Spainfrancescxavier.aviles@uab.esDr. Matthias WilmannsEuropean Molecular Biology Laboratory(EMBL) – Hamburg unitGerman Synchrotron Research CenterHamburg, GermanyProf. Boris TurkJ. Stefan Institute ProteolysisResearch GroupDepartment of Biochemistry andMolecular BiologyLjubljana, SloveniaProf. Markus G. GruetterUniversity of ZurichDepartment of Biochemistryof the University of ZurichZurich, SwitzerlandDr. Ernst MeinjohannsArpida ASCopenhagen, DenmarkDr. Ulrich WendtSanofi-AventisDeutschland GmbHValorisation & InnovationFrankfurt, GermanyProf. Dr. Wolfram BodeMax-Planck Institute ofBiochemistryMartinsried, GermanyFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life115

Project Type:Co-ordination ActionContract number:LSHG-CT-2006-036814Starting date:1 st November 2006Duration:30 monthsEC Funding:1 000 000ProDacState-of-the-Art:www.fp6-prodac.euBased on the work of the Human Proteomics Organisation (HUPO), the Proteomics StandardsInitiative (PSI) and the experience of the HUPO Brain Proteome Project (HUPO BPP), ProDaCaims to develop and implement international standards for the representation of high-performanceproteomics data. The main focus of the project is standardised data collection aswell as standardised data analysis of protein identification by mass spectrometry. In total, 12core partners (European Bioinformatics groups and proteomics laboratories) and 31 associatedpartners (non-EU laboratories, both academic and commercial) will participate in the30-month project. Data providers from experienced European proteomics laboratories willprovide appropriate data, derived from state-of-the-art proteomics technologies, for proof ofconcept; moreover, they will utilise the newly developed software tools. The project will besupported by a number of high-ranking scientific journals, which will be actively involved inthe standards’ development, including the defining of mandatory supplementary informationfor submitting articles.Scientific/Technological Objectives:In phase one, all ProDaC partners will contribute to the finalisation of the analysisXMLstandard for the representation of protein identifications; they will also contribute to the PSIGPS modules for the overall representation of a proteomics experiment, in particularthe sample description, sample handling, and separation modules.In phase two, ProDaC core partners will establish submission pipelines from experimentaldata providers and data analysis centres to the PRIDE proteomics repository.In phase three, the strategies developed will be implemented by a much broader group ofproject participants, building on the previous project experience, and supported by dedicatedtechnical advisors. At the end of phase three, it is expected that the PSI proteomicsstandards will be adopted by major European and worldwide proteomics data providers.To demonstrate the immediate benefit of central data collection to data producers, we willextend PRIDE functionality to allow for the comparison of submitted, but nonetheless privatedata in pre-publication status, to other, publicly available datasets. Through the dataexchange between proteomics repositories, the scope of proteomics data integration intosequence databases will reach out to other repositories, such as Proteios, ProteinScape, andPeptideAtlas; ultimately, this may improve or validate (or both), or even sequence databasesthemselves.Expected Results:ProDaC expects that the following results will be produced:1. PSI standards finalised and tested;2. Implementation of mzData and analysisXML capabilities in ProteinScape;3. PROTEIOS, Phenyx and Mascot and PRIDE (and conversion of existing data);4. Identification of relevant proteomics tools used in the consortium, and of developmentneeds to ensure functional data submission pipelines from data producers toPSI-compatible repositories;5. Tools for compiling raw data into standard file formats (mzData and analysisXML);6. Evaluation of existing data storage solutions at the participants’ sites;7. Elaboration, testing and optimising of the data submission pipeline;8. Elaboration and testing of submitted supplementary data sets for publications;9. Collection of data packages;10. Establishing of a steering committee and the network structure;11. Implementation of the intranet and other communication platforms;12. Coordination of software implementation116From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Potential Impact:Proteomics Data CollectionSystematic coordination in the ProDaC context may boost proteomics data standardisationand collection on a global level, and may significantly reduce the timeframe in which theseaims could otherwise be achieved, to boot. Moreover, the European core component of theProDaC proposal will help to retain Europe’s strong position in the field of proteomics, whilethe significant global participation of associated partners will ensure broad acceptance ofthe project in the global proteomics community.The ProDaC consortium comprises commercial and open source proteomics tool providerswho will implement PSI standards in their products, thus minimising the effort necessary fordata conversion and submission. Moreover, the participation of scientific publishers in Pro-DaC will ensure that the developed standards, tools and repositories meet the requirementsof the publication process, and will in turn, promote the application of these standards onbehalf of their authors, thus increasing the transparency, quality and public value of proteomicspublications.Keywords: proteomics, databases, standardisationPartnersProject Coordinator:Prof. Helmut E. MeyerRuhr-Universitaet BochumMedizinisches Proteom-CenterUniversitätsstrasse 15044801 Bochum, Germanyhelmut.e.meyer@ruhr-uni-bochum.deDr. Rolf ApweilerEuropean Molecular BiologyLaboratory (EMBL)European Bioinfomatics Institute (EBI)Hinxton, UKProf. Rudi AebersoldFederal Institute of TechnologyETH ZurichZurich, SwitzerlandProf. Joel VandekerckhoveUniversity of GhentDepartment of MedicalProtein ResearchGhent, BelgiumProf. Michael J. DunnUniversity College DublinConway Institute of Biomolecularand Biomedical ResearchDublin, IrelandDr. Frederique LisacekSwiss Institute of BioinformaticsProteome Informatics GroupGeneva, SwitzerlandDr. Jari HäkkinenLund UniversityDepartment of TheoreticalPhysicsLund, SwedenDr. Simon HubbertManchester UniversitySchool of BiologicalSciencesManchester, UKDr. Pierre-Alain BinzGenebioGeneva, SwitzerlandMartin BlüggelProtagen AGDortmund, GermanyProf. Herbert ThieleBruker Daltonics GmbHBremen, GermanyDr. John CottrellMatrix ScienceLondon, UKFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life117

1.3TOOLS & TECHNOLOGIESFOR MOLECULAR IMAGINGMOLECULAR IMAGINGTips4CellsCOMPUTIS

Project Type:Integrated ProjectContract number:LSHG-CT-2003-503259Starting date:1 st January 2004Duration:60 monthsEC Funding:11 000 000Single-molecule fluorescence closeto an absorbing nanostructure.The emission rate is stronglymodified by the local-fieldenhancement and the nonradiativecoupling with the object.MOLECULAR IMAGINGState-of-the-Art:www.molimg.grAdvances in molecular biology have provided considerable information concerning thesequence, structure and function of genes. This has opened new perspectives for the understandingof fundamental biological processes underlying human disease and for thedevelopment of innovative diagnostic, prognostic and therapeutic tools. Strategies for genomicresearch and therapeutic interventions at the genetic level will benefit from increasedcapability to monitor in vivo the effects of genetic manipulations in cells and living organisms.Ironically, although biology is fundamentally dynamic, most of the current knowledgeon gene expression, regulation and delivery in mammalian systems relies on results fromin vitro or ex vivo studies. This, coupled with our inability to easily monitor multiple molecularspecies simultaneously, seriously limits our ability to study a wide range of biologicalprocesses. Furthermore, since empirical descriptions of the evolution of systems over timeare generally constructed from a series of data obtainedfrom different specimens, they often fail torepresent the true order of events accurately. Additionally,these invasive techniques tend to be timeconsuming and labour intensive, often leading todistortion or even destruction of native properties.Thus the current capacity to extract biological informationin intact microenvironments of living systemsis severely limited. MOLECULAR IMAGINGaims at developing new tools that will enable monitoringthe dynamics of multiple molecules withinliving systems and will transform our understandingof biology, making experimental investigationsmuch more efficient and accelerate the progress inlife sciences.Scientific/Technological Objectives:The goal of the Molecular Imaging Integrated Project is to generate and apply novel advancedtechnology for non-invasive imaging of biomolecular function in living systems rangingfrom single cells to whole animals. The main areas for technological innovation are: Different imaging scales involvedin the MOLECULAR IMAGINGIntegrated Project120From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Integrated Technologiesfor In vivo Molecular ImagingWe will combine multidisciplinary research in biology, bioorganic chemistry, theoreticalphysics and biomedical optics with the objective of developing novel imaging tools that willenhance genomic and post genomic research, and biotechnological capabilities in Europe.It is expected that our combined effort will provide spectacular new opportunities for phenotypingfunctional (molecular) analysis in cells and animal models.Expected Results:The expected results are: 3D tomographic approaches provedmicroscopic molecular imaging techniques probes and biosensors become available to a variety of end-users in the scientific community.The development of such tools will offer multilevel information, (spatial, temporal and relative)so that reliable and complex conclusions can be reached faster. This proposal aims tocoordinate the development of functional in vivo imaging capabilities in order to addressfundamental biological questions. This will be achieved by partnering high-resolution imagingwith post-genomic molecular technology. Much of the technology and techniques tobe developed under this integrated project will be directly applicable to high-throughputscreening and genomic and proteomic microanalysis.Non-invasive phenotyping will drastically reduce the number of sacrificed animals necessaryfor accurately addressing biological problems and will: a) b)a) Visualisation of the intestinallymphatic systemb) Flow chart of the differentsubprojects and work packagesFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life121

MOLECULAR IMAGINGInteraction betweendisciplines in theMOLECULAR IMAGINGIntegrated ProjectPotential Impact:The proposed consortium of physicists,mathematicians, biologists and chemistsoffers a unique opportunity to address thechallenge of in vivo molecular imaging ina concentrated but Europe-wide effort. Webelieve that this project will lead to the formationof centres of excellence in the nearfuture that will attract scientists to join thosecountries and institutions that are able toprovide this technology. Such research centreswould promote the commercialisationof this technology in partnership with highendindustry to make it widely availableand widely deployed in the near future.This will create many new jobs for highly educated scientific and technical personnel. Specificinnovation aspects include:a) New probes. These will be engineered, taking into account the natural absorbanceproperties of tissue and will be suitable for imaging in organs and animals.b) Simultaneous spatially and temporally resolved detection of multiple physiologicalevents.c) Novel theoretical tools to model light propagation and atomic-scale interactions.d) New optical instruments with improved depth detection that allows the identificationof fluorescent organs or structures within the animal body non-invasively in vivo.e) New optical instruments that allow the localisation of individual cells and their distributionand migration within organs.f) Novel multimodal nanometric imaging setups that will allow follow up of atomic interactionsin vivo.Fluorescence moleculartomography (FMT) imagingof T-cell regulation. (A) FMTsetup where the specimenrotates along an axis, anexcitation source (Ar+ laser) isscanned over the surface andexcitation and emission imagesare collected using appropriatefilters. (B) 3D reconstruction ofGFP concentration in the spleenfor GFP-tagged T-cells in a F5mouse. This figure indicates thepotential that FMT has to imagebiological processes in vivo.Keywords: genetic engineering, applied optics, molecular chemistry, tomography,microscopy, fluorescence, inverse problem, functional genomics,phenotypingPartnersProject Coordinator:Prof. Eleftherios EconomouFoundation for Research and Technology – HellasInstitute of Electronic Structure and Laser (IESL)Institute of molecular biology and biotechnology (IMBB)P.O Box 1385, Vassilika Vouton71 110 Heraklion, Creteeconomou@admin.forth.grProf. Stefan Andersson-EngelsLund UniversityDepartment of PhysicsLund, SwedenProf. Simon ArridgeUniversity College LondonDepartment of Computer ScienceLondon, UK122From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Integrated Technologies for In vivo Molecular ImagingProf. Dr. Christoph BremerUniversity of MünsterDepartment of Clinical RadiologyMünster, GermanyProf. Remi CarminatiCentrale Recherche SALaboratoire EM2CParis, FranceProf. Juan Jose SaenzUniversidad Autonoma de MadridDepartamento de Fisica dela Materia CondensadaMadrid, SpainProf. Maria Carmo-FonsecaInstitute of Molecular MedicineLaboratory of Cell BiologyLisbon, PortugalDr. Paul FrenchImperial College of ScienceTechnology and MedicinePhysics DepartmentLondon, UKProf. Theodorus GadellaUniversity of AmsterdamSwammerdam Institute for Life SciencesAmsterdam, The NetherlandsDr Dimitris KioussisMedical Research CouncilDivision of Moleculer Immunology,National Institute for Medical ResearchLondon, UKDr. Carsten SchultzEuropean Molecular BiologyLaboratory (EMBL)Gene Expression ProgrammeHeidelberg, GermanyProf. Vahid SandoghdarSwiss Federal Institute ofTechnology (ETH)Department of ChemistryZurich, SwitzerlandDr. Konstantin LukyanovRussian Academy of SciencesInstitute of Bioorganic ChemistryMoscow, RussiaDr. Oliver DornUniversidad Carlos III de MadridDepartment of MathematicsMadrid, SpainProf. Frank GrosveldErasmus Medical Centre RotterdamDepartment of Cell BiologyRotterdam, The NetherlandsProf. Carlos Martinez,Prof. M. Nieto-Vesperinas, Prof. N. GarciaConsejo Superior de InvestigacionesCientíficasMadrid, SpainProf. Cristoph CremerRuprecht-Karls-Universitat HeidelbergKirchhoff-Institute for PhysicsHeidelberg, GermanyDr. Martin InglePhotek LtdSt Leonards-on-Sea, UKDr. Patrick CourtneyPerkinelmer Life andAnalytical ScienceCambridge, UKDr. Levin ShimonLenslet Labs LtdRamat-Gan, IsraelDr. Paul WynnKentech Instruments LtdDidcot, UKDr. Jens SteinUniversity of BernTheodor Kocher InstituteBern, SwitzerlandDr. James SharpeCentre for GenomicRegulation (CRG)Barcelona, SpainDr. Miguel TorresCNIC Fundación CentroNacional de InvestigacionesCardiovasculares Carlos IIIMadrid, SpainFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life123

Tips4Cellswww.tips4cells.orgProject Type:Specific TargetedResearch ProjectContract number:LSHG-CT-2005-512101Starting date:1 st February 2005Duration:36 monthsEC Funding:1 713 000State-of-the-Art:High resolution imaging of living cells and subcellular components is essential for functionaland structural genomics. Scanning Probe Microscopy (SPM) is currently the imagingmethod of choice, because it yields the greatest number of structural details of biologicalsamples in their native, aqueous environment and at ambient conditions. Due to the high lateralresolution and sensitive force detection capability of SPM, it is now possible to measureintermolecular and intramolecular forces in biomolecules at the single molecule level. This,in turn, has made it possible to examine the physiological consequences of the interactionof a single ligand molecule with its cognate receptor. The Tips4Cells consortium proposesto develop SPM still further. New technologies, such as faster scanning force microscopy(SFM) at lower forces, improved tip chemistry and integration of optical imaging techniqueswill be used to analyse ligand-receptor interactions in the plasma membrane and in downstreamsignalling events in living cells, and to study the structure, transport and dynamics ofnuclear pore complexes (NPC) in functional nuclei.Scientific/Technological Objectives:The general goal of the consortium is to develop new SPM technologies for functional andstructural genomics. More specifically, its goals are as follows:1) To develop new SFM hardware, including fast scanning hardware (scanner, miniaturecantilevers) and electronics (high speed data acquisition, Q control);2) To develop molecular recognition force microscopy (MRFM), via the intermediarydevelopment of the following: (i) Chemically functionalised tips/beads; (ii) The chemistryof the drugs that are put on those tips/beads; (iii) Imaging and spectroscopymodes for recognition (pulsed force mode and recognition mode);3) To integrate optical techniques into SFM, to improve detection of signalling afteradministering a chemical to a cell, by approaching it with a functionalised tip;4) To validate the new technologies in the study of cell biology systems, such as the nongenomiceffects of steroids (e.g. aldosterone), the Wnt signalling pathway and thestructure, transport and dynamics of NPC in functional nuclei.Expected Results:The consortium expects to achieve higher data acquisition rates through faster electronics,and faster sensors with higher force sensitivity through miniaturised cantilevers. Fasterscanners will move more rapidly around the surfaces to be scanned, allowing for framerates above 100 images per second. The consortium also expects to improve the speedof MRFM. More general functionalisation protocols will allow a wider range of chemicalsto be attached to SFM tips. Through the use of linkers between tip and molecule that areoptimised in length, a higher resolution will be achieved in molecular recognition imaging.Genomics knowledge will be advanced through high resolution imaging and docking siteidentification, the development of new tools for biomolecular analysis of drugs for orphanreceptors, the introduction of new chemistries for drugs on tips, and new substitutes for mappingreceptor distribution in living cells. The commercialisation of novel imaging platformswill be managed by the consortium’s SME partners, thereby bringing these techniqueswithin reach of a broad range of researchers.124From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Scanning Probe Microscopy techniquesfor real time, high resolution imagingand molecular recognition in functionaland structural genomicsPotential Impact:The project will generate improved research tools and insights in SPM. It is anticipated thatthe breakthroughs in nanoscience and technology will serve to stimulate industry, generatingemployment opportunities. The SMEs involved in Tips4cells specialise in hardware development,and will clearly benefit from the commercial opportunities generated by the research.The multinational, multidisciplinary nature of the consortium will facilitate broad disseminationof new knowledge, both across Europe and across academia and industry. The consortiumwill also foster novel collaborations between research institutes and industry.Keywords: scanning force microscopy, imaging techniques, high resolution,molecular recognitionPartnersProject Coordinator:Dr. Tjerk OosterkampLeiden Institute of PhysicsLeiden UniversityNiels Bohrweg 22333 CA Leiden, The Netherlandsoosterkamp@physics.leidenuniv.nlDr. Peter HinterdorferUniversity of LinzInstitute of BiophysicsLinz, AustriaProf. Michael HortonUniversity College LondonDepartment of MedicineLondon, UKDr. Ziv ReichWeizmann Institute of ScienceDepartment of Biological ChemistryRehovot, IsraelProf. Mervyn MilesUniversity of BristolH.H. Wills Physics LaboratoryBristol, UKDr. Torsten JähnkeJPK Instruments AGBerlin, GermanyDr. Gertjan van BaarleLeiden Probe MicroscopyLeiden, The NetherlandsDr. Gerald KadaAgilent TechnologiesÖsterreich GmbHAustriaProf. Hans OberleithnerUniversity Hospital MünsterDepartment of PhysicsInstitut für Physiologie IIMünster, GermanyFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life125

COMPUTISProject Type:Specific TargetedResearch ProjectContract number:LSHG-CT-2005-518194Starting date:1 st January 2006Duration:42 monthsEC Funding:2 200 000State-of-the-Art:Significant improvements in desorption and ionisation techniques, such as SIMS (secondaryion mass spectrometry) or MALDI-MS (matrix-assisted laser desorption ionisation – massspectrometry ) associated with TOF-MS (time of flight – mass spectrometers), offer levels ofsensitivity and mass accuracy which allow detection, and analysis of large organic moleculeslike peptides or proteins with very small sample amounts.Recent developments showed the possibility of extrapolating these techniques to produceactual molecular images of flat samples with a full mass spectrometry at each pixel downto micrometric scales.The growing interest of this approach and its high potential will lead to the development,optimisation, combination and correlation of these SIMS and MALDI-MS techniques.Scientific/Technological Objectives:This project aims to develop new and improved technologies for molecular imaging massspectrometry (MIMS), enabling innovative methods of investigation in functional genomics,proteomics and metabolomics, as well as investigation in cells and tissues.It is the goal of the project to develop, optimise, combine, correlate and apply methods ofmass spectrometric molecular imaging, especially various specialised methods of SIMS andMALDI associated with various types of mass spectrometers.The three principal objectives of the project are: novel desorption, ionisation and detection techniques the study of molecular images cells or tissue growth.This project will provide innovative analytical capabilities for mapping a variety of biologicalcompounds directly at the tissue or cell level by superposing information from differentsources in the same image.MIMS needs further development to make it routinely accessible to users. Application ofthese methods to analytical problems requires appropriate instrumentation, sample preparationmethodology, and computerisation with high performance massive data acquisitionand processing.Expected Results:The objectives of the project will be achieved by significant improvements in desorptionand ionisation techniques, leading to a new protocol of sample preparation for bettermatrix deposition control. Instrumentation developments include the setup of UV confocalmicroscopy integrated into the MALDI imaging instrument and the adaptation of new ionguns favouring secondary ion emission for SIMS analysis. Dedicated software tools willbe implemented for high performance data acquisition and processing with, in particular,the realisation of the superposition of data from different analytical sources in the sameimage. The project will conclude with definition, implementation and testing of new analyticalconcepts, as well as criteria for diagnostics of chosen pathologies or diseases, and thedevelopment of an industrial concept. In addition, a validation phase through the applica-126From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Molecular Imaging in Tissue and Cellsby Computer-Assisted InnovativeMultimode Mass Spectrometrytion of MIMS to the three selected biological problems is imperative for the acceptance ofthe methodology.Potential Impact:MIMS techniques connected with proteomics and bioinformatics pave the way to in situ inspectionof cell and tissue physiology. They could be extended towards pathophysiologicalinspections of human tissues performed at the molecular level on a large-scale.Imaging MS eliminates the need to know in advance about the specific proteins that may havechanged in a comparative study. So, these new analytical methods will be performed ideallywith almost no a priori knowledge about markers and gene products expressed in normaland pathological specimens. Improved image acquisition, image processing and connectivitywith existing biological databases will have a critical impact for applications in humanhealthcare.Keywords: bioanalytical chemistry, mass spectrometry, massive data processing andinformation treatmentPartnersProject Coordinator:Dr Haan Serge, Dr Robbe Marie-FranceCommissariat à l’Energie Atomique CEA)LIST/DETECSCentre de Saclay, Bat. 451P.O. Box 91191 CedexGif-sur-Yvette, Franceserge.haan@cea.frmarie.france.robbe@cea.frProf. Bernhard SpenglerJustus Liebig UniversityInstitute of Inorganic andAnalytical ChemistryGiessen, GermanyProf. Ronald MA HeerenStichting FOM (FundamenteelOnderzoek der Materie)AMOLFAmsterdam, The NetherlandsDr. Olivier LaprevoteCentre National de la RechercheScientifique (CNRS)Institute de Chimie des SubstancesNaturelles (ICSN)Gif-sur-Yvette, FranceDr. Ronald SchutPCC UvA BVAmsterdam, The NetherlandsDr. Fedor SvinartchoukGénéthonDépartement Rechercheet DéveloppementEvry, FranceDr. Markus StoeckliNovartis Pharma AGDiscovery TechnologiesAnalytical andImaging SciencesBasel, SwitzerlandFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life127

1.4TOOLS & TECHNOLOGIESFOR GENE INTEGRATION ANDRECOMBINATIONGENINTEGPLASTOMICSTAGIPMEGATOOLS

GENINTEGProject Type:Specific TargetedResearch ProjectContract number:LSHG-CT-2003-503303Starting date:1 st January 2004Duration:48 monthsEC Funding:1 846 561State-of-the-Art:Despite the enormous potential of using transgenesis for gene function analysis and genetherapy, little is known about the mechanism of gene integration in eukaryotic cells. Transgeneintegration into the chromosomes of living cells can occur either randomly or targetedby homologous recombination. The latter type of integration is the most useful, because itallows precisely sequences to be precisely deleted or modified at defined chromosomal positions.The GENINTEG consortium was formed to study gene integration by recombinationin a number of different model organisms. As DNA repair is conserved during evolution, acomparative genomics approach was proposed to discover evolutionary conserved principlesof gene integration.Scientific/Technological Objectives:The main objective is to understand and enhance gene integration through interdisciplinaryand comparative genome analysis in different model organisms. As DNA structureand DNA repair are conserved during evolution, the gained knowledge and resourceswill improve gene integration across plant and animal species and facilitate large-scalegene function analysis and transgene expression for biotech and medical applications.Other objectives are: (1) better insight into the genetics, the regulation and the mechanismof homologous recombination; (2) new protocols to increase targeted gene integration inprimary cells and cell lines either by modification of gene constructs or the gene deliverymode; (3) adaptation of existing site specific recombination system for safe and stable geneexpression and long range chromosome engineering; (4) use of improved gene integrationfor gene function analysis; (5) exploitation of the generated knowledge and resources forcommercial application through the protection of intellectual property and product development;(6) new protocols for transgenesis of whole organisms.Expected Results:Controlled gene integration and in particular targeted integration has to be considereda key technology for exploiting the wealth of recently obtained genome information. Thisis due to the fact that traditional transgenesis can only add bits of poorly controlled informationto the genome, whereas targeted integration can be used to modify the genomeprecisely at any chosen position. The proposed work will therefore significantly reinforcegenome research and support many of the activities envisioned for funding within FP6. Althoughsuccessfully employed in yeast and murine embryonic stem cells, a major stumblingblock for the widespread use of targeted integration is the tendency of most eukaryotic cellsto insert transfected DNA at random chromosomal positions. More efficient gene targetingwill expedite reverse genetics in a variety of cells and organisms enabling truly comparativegenome function analysis across species boundaries. Targeted gene integration also fulfillsa critical role for medical research, as it allows the experimental verification of the findingsof human genetics and the establishment of animal disease models for further detailed researchof pathogenesis and treatment.Potential Impact:To realize the full potential of transgenesis for genome research, biotechnology and medicalapplications, only a concerted European initiative can bring together and focus the availableexpertise in academia and industry. The GENINTEG consortium has recruited someof the best laboratories working on gene integration and also balances the work amongdifferent species to allow for a truly comparative genomics approach.The availability of genome sequences helps traditional genetics approaches and it promotesreverse genetics as a means to modify the genotype in precisely defined terms.130From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Controlled gene integration:a requisite for genome analysisand gene therapyThe clarification of gene function by transgenesis is paramount to our understanding ofbiological processes and disease pathogenesis. Consequently, investment in further developmentof controlled gene integration technology promises rich returns not only for basicresearch, but also for drug development.Keywords: gene, homologous recombination, transformation, biotechnology,genomic function, transgenes, site-specific, integrationPartnersProject Coordinator:Prof. Dr. Jean-Marie BuersteddeGSF-Forschungszentrum fur Umwelt und Gesundheit GmbHInstitute of Molecular Radiation BiologyIngolstädter Landstraße 185764 Neuherberg, Germanybuerstedde@gsf.deDr. William BrownUniversity of NottinghamQueen’s Medical CentreInstitute of GeneticsNottingham, UKProf. Ann DepickerFlanders Interuniversity Institute for Biotechnology (VIB)Ghent University TechnologieparkDepartment of Plant Systems BiologyGhent, BelgiumDr. Francis FabreCommissariat à l’Energie Atomique (CEA)Fontenay-aux-Roses, FranceProf. Dr. Martin FusseneggerCistronics Cell Technology GmbHZurich, SwitzerlandDr. Andrzej M. KierzekUniversity of SurreySchool of Biomedical and Molecular SciencesGuildford, UKDr. Bernd ReissMax Planck Society for the Advancement of ScienceMax-Planck Institute for Plant Breeding Research MPIZCologne, GermanyProf. Dr. Walter SchaffnerUniversity of Zurich-IrchelInstitute of Molecular BiologyZurich, SwitzerlandFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life131

PLASTOMICSProject Type:Specific TargetedResearch ProjectContract number:LSHG-CT-2003-503238Starting date:1 st February 2004Duration:42 monthsEC Funding:2 384 000State-of-the-Art:Plastid transformation is the most precise method of integrating foreign genes in plants. Itoffers the possibility of cheap and large-scale production for therapeutic proteins, such ashormones and vaccines, and also for food of improved nutritional quality. Plastid transformationand high level expression of foreign proteins in chloroplasts in tobacco leaves is wellestablished. However, the commercial success of plastid transformation as a productionplatform, depends mainly on the successful high level expression in non-green plastids (suchas chromoplasts and amyloplasts), using crops that are amenable to processing.Scientific/Technological objectives:The aim of the project was to define the mechanisms and to improve the understanding ofthe genes and proteins involved in several key stages of plastid transformation and foreigngene expression, in different plastid types, in tobacco, tomato and potato. Genomics andproteomics approaches were used to identify genes and proteins involved in several processes:1) transgene integration and marker gene excision via homologous recombination;2) regulated gene expression in chloroplasts, chromoplasts and amyloplasts; 3) proteindegradation in different plastid types.The project was divided into 3 work packages (WPs). WP1 relates to transgene integrationand marker excision. WP2 relates to regulated plastid gene expression. WP3 relatesto protein degradation in different plastid types. WP3 aimed to identify the proteolysissystems in plastids that may limit the expression of transgenes in plastids. It also aimed todevelop cleavable protein-fusion systems that may protect foreign proteins from proteolysisand simplify protein purification.Expected results:WP1’s achievements are as follows:1. Identification (using database searches) of genes encoding putative components of theplastid recombination system in higher plants and isolation of tobacco cDNAs encodingsome of these plastid recombination proteins.2. Characterization of transgenic tobacco plants with altered expression of genes encodingplastid recombination proteins to examine the effects on transgene integration andmarker excision3. Optimization of plastid transformation vectors, with different amounts of flanking plastidDNA, and with foreign genes of different length, orientation and control sequences.4. Proof-of-concept of an novel system of automatic marker excision, using transformationvectors with the selectable marker gene located outside the plastid sequences flankingthe transgene.WP2’s achievements are as follows:1. Determination of the complete nucleotide sequences of the plastid genomes of tomatoand potato.2. Use of DNA microarrays and macroarrays for examining transcripts of all plastid genesand open reading frames in tomato fruits and in potato tubers.3. Characterization of nuclear-encoded RNA polymerases (NEP) and identification ofNEP-transcribed plastid genes.4. Production of improved plastid transformation vectors, with altered sequences in thevicinity of the translation initiation codon.WP3’s achievements are as follows:1. Identification by database searches of genes and cDNAs encoding components ofplastid proteolysis systems in tobacco, tomato and potato, and production of transgenictobacco with alteration of levels of ClpC.2. Production and introduction of gene constructs into the tobacco plastid genome forthree cleavable protein-fusion systems.132From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Mechanisms of transgene integrationand expression in crop plant plastids,underpinning a technologyfor improving human healthPotential impact:The PLASTOMICS team expects the project to result inimproved understanding of processes involved in plastidtransformation, and in improved efficiency of plastid transformationand transgene expression in tomato and potato.This has the potential to impact significantly on the area ofplant biotechnology applied to human health, through theproduction of protein products of benefit to human healthand food, with better nutritional value.Keywords: gene integration, gene expression,protein degradation, plastid transformation,proteomics, plant modelsPartnersProject Coordinator:Prof. John GrayUniversity of CambridgeDepartment of Plant SciencesDowning StreetCB2 3EA Cambridge, UKjcg2@mole.bio.cam.ac.akDr. Anil DayVictoria University of ManchesterSchool of Biological SciencesManchester, UKProf. Philip DixNational University ofIreland MaynoothBiology DepartmentMaynooth, Co Kildare, IrelandProf. Zach AdamHebrew University of JerusalemDepartment of Agricultural BotanyJerusalem, IsraelProf. Ralph BockMax-Planck Institute ofMolecular Plant PhysiologyGolm, GermanyDr. Janusz BujnickiInternational Institute ofMolecular and Cell BiologyLaboratory of BioinformaticsWarsaw, PolandDr Teodoro CardiConsiglio Nazionale Delle RicercheCNR-IGV, Institute of Plant GeneticsResearch Division PorticiRome, ItalyProf. Tony KavanaghTrinity College DublinSmurfit InstituteDepartment of GeneticsDublin, IrelandDr. Stefan HerzIcon Genetics AGResearch Centre FreisingMunich, GermanyDr Silva Lerbs-MacheUniversité Joseph Fourier Grenoble 1Laboratoire Plastes etDifferenciation CellulaireGrenoble, FranceFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life133

Project Type:Specific TargetedResearch ProjectContract number:LSHG-CT-2005-018785Starting date:1 st December 2005Duration:36 monthsEC Funding:1 980 972TAGIPState-of-the-Art:www.eurotagip.comPlants can be considered as natural, solar energy powered, and environmentally friendlyprotein factories that can be genetically improved for the production of proteins with therapeuticvalue. It is crucial that the production of target proteins is well controlled in terms ofhigh and steady yield, and tissue-specific deposition allowing for easy harvest, extractionand purification. However, current transgenesis technologies are not accurate enough tosecure a protein production scheme that demands such high reliability and precision.Random chromosomal integration of transgenic inserts often causes unpredictable misregulationof their transcription, including complete gene silencing. Therefore, the abilities to modifythe plant genome in a precise manner and/or control the chromatin environment of transgenicinserts, are arguably the most important missing technologies in the toolkit of plant biologists.DNA integration, via homologous recombination (Gene Targeting, or GT) has provedto be a powerful technology in many species. In particular, it enables not only targeted genedisruption or replacement of an endogenous locus by a modified or different gene, but alsoexpression of a new protein in the genomic context of the native gene. GT enables a precisealteration of genomes, from single nucleotide modifications to gene replacement or knockout.It is an invaluable tool for functional genomics as well as for biotechnology. Despite its successin other organisms, GT has not yet become a routine technique in plants, owing to the naturallylow frequencies of homologous, as compared to non-homologous, DNA integration.Scientific/Technological Objectives:New findings, several of which originate from the TAGIP partners, as well as advances infunctional genomics, suggest that the precise engineering of plant genomes structure by GT,via DNA integration at any locus or at specific sites, has recently become a realistic goal.Achieving this goal will involve the following activities: 1) gaining fundamental knowledgein the field of genome maintenance/modifications via DNA recombination; 2) applying thisknowledge to develop new technologies for precise engineering of plant genomes in themodel organism Arabidopsis and in selected crop plants; and 3) using this knowledge forthe production of proteins of high value in the most suitable crop.There are three specific objectives:1) Stimulation of GT via reduction of non-homologous DNA recombination pathways;2) Enhancing the rate of GT in Arabidopsis via over-expression of GT-related proteins;3) Testing for synergistic interactions between partner proteins, to stimulate GT.Expected Results:The exploitable products expected from this project include a technological platform for GTin crops and a technological platform for protein production in plants (based on GT). Thisproject will speed up the acceptance of new GM corn in Europe. The Biogemma consortium,which includes key EU players for crop improvement, guarantees the preservation ofEU Plant Biotech and Seed Business company competitiveness. This will ensure that in thefuture era of GM crops in Europe, EU companies will not have to pay large royalties to UScompetitors, to gain access to GT technologies necessary for the registration of GM traits.Potential Impact:Industry competitiveness and societal problems:An important aspect of this project is that in the EU, public reluctance to consume GMOproducts has slowed down progress in agricultural biotechnology, while in other countries(such as the USA, China, Japan), this Agro-biotech revolution is taking place. A technol-134From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Targeted Gene Integration in Plants:Vectors, Mechanisms andApplications for Protein Productionogy such as GT, enables precise and controlled alteration of thegenome.The European added-value:One reason to carry out this work at European level is that researchin DNA recombination in plants is far more advanced in Europethan in the USA, and it should be further supported to maintainthis competitive edge. The proposed TAGIP project brings togetherleading groups in the field of DNA recombination in plants, thusfurther increasing the competitiveness of the EU in this field.Innovation aspects:At a technological level, the project plans to turn GT into a routine tool in plants. This technologyhas a very high potential economic impact in the Agro-biotech industry, as well as onthe pharma industry via “molecular farming” for protein production in plants. At a scientificlevel, the mechanism whereby GT occurs is still poorly understood in higher eukaryotes. Theteam will test several genes, working at different levels of the DNA recombination process(initiation, invasion, strand exchange, heteroduplex formation and resolution), for their effecton GT.Keywords: homologous recombination, gene targeting, protein production,model organisms, Arabidopsis, genome structure and maintenance,functional genomics, plant technologiesABSize MarkerskDa12479483825181311One single protein, Poly PhenolOxydase (PPO), consitutes 60%of the proteins in trichomes (leafhairs) of tomato. Trichome arethus ideally suited for proteinproduction and purification. Oneof the goals of TAGIP is to replacePPO by a gene of interest forhigh and specific expression andfor simple purification.PartnersProject Coordinator:Prof. Avi LevyWeizmann Institute of ScienceFaculty of BiochemistryDepartment of Plant SciencesHerzl St. 27600 Rehovot, Israelavi.levy@weizmann.ac.ilDr. Charles WhiteCentre National de la RechercheScientifique (CNRS)UMR47, Université Blaise PascalAubière, FranceProf. Holger PuchtaUniversity of KarlsruheBotanical InstituteKarlsruhe, GermanyDr. Karel J. AngelisInstitute of ExperimentalBotany ASCRMolecular Farming andDNA Repair LaboratoryPrague, Czech RepublicProf. Jerzy PaszkowskiUniversity of GenevaDépartement de BiologieVégétaleGeneva, SwitzerlandDr. Pascual PerezBiogemma SAS Les CrezauxAubière, FranceDr. Hagai KarchEvogene LtdRehovot, IsraelProf. Barbara HohnNovartis ForschungsstiftungZweigniederlassungFriedrich MiescherInstitute for BiomedicalResearchBasel, SwitzerlandDr. Pnina DanOSM-Dan LtdRehovot, IsraelFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life135

MEGATOOLSwww.cellectis.com/megatoolsProject Type:SME- Specific TargetedResearch ProjectContract number:LSHG-CT-2006-037226Starting date:1 st October 2006Duration:36 monthsEC Funding:1 999 962Purpose of MEGATOOLSand strategy for meganucleaseengineeringState-of-the-Art:The genome sequence programmes have contributed a huge amount of information, andcreated many possibilities. An exhaustive catalogue of genes is now available for manyorganisms, but the real meaning of this information remains to be deciphered. Thus, thesuccess of functional genomics definitively lies in the development of novel tools breakingthrough the practical limits it suffers today. Meganucleases-induced recombination couldprovide a practical alternative to current approaches. Meganucleases are, by definition,sequence-specific endonucleases with large (>14 bp) recognition sites. However, the inactivationor modification of any and all known genes, or genomic sequence, depends on theavailability of Meganucleases that cleave within or in the vicinity of each gene sequences.This issue would be addressed if it was possible to rapidly engineer the specificity of naturalMeganucleases.Scientific/Technological Objectives:The first objective of the project is to provide the means to modify a large number of sequencein rodent genomes. The second is to develop the tools to engineer a large numberof rodent genes, for functional genomic purposes. Since meganuclease-induced recombinationrepresents an extremely powerful tool for gene alteration, we will focus on the generationof four kinds of results:1) A large collection of novel meganucleases. This collection of novel proteins shouldgreatly enhance the repertoire of natural meganucleases and thus allow for the targetingof a large number of genes in organisms whose genome has been sequenced,with a strong focus on rodent genomes.2) The means to exponentially increase this collection. The collection of novel meganucleasesshould provide a unique database of characterised DNA binders. Structural andstatistical studies should reveal the laws governing these interactions, and this datacould in turn be used in a predictive way, for the design of novel meganucleases.3) The methods, procedures and quality standards to make these meganucleases widelyusable as research tools.4) A refined method to use these meganucleasesin cells. The focus will beon mouse cells for functional genomics,providing a direct validation.Expected Results:1) Protein engineering: Partner 1 hasestablished the basis of a combinatorialprocess to assemble functionalengineered meganucleases. We expectthis combinatorial strategy toprovide a functional meganucleasefor most chosen gene.2) Computational biology: The FoldX algorithmcan successfully predict theeffect of protein mutation on the specificityof protein-DNA recognitionspecificities. Subsequent versions of136From Fundamental Genomics to Systems Biology: Understanding the Book of Life

New tools for Functional Genomicsbased on homologous recombinationinduced by double-strand breakand specific meganucleasesFoldX should allow for more efficient design of meganucleases combinatorial process.3) Structural Biology: A continuous flow of novel structures that will contribute to thecomputational steps is expected.4) Standardisation of protein storage and use: An efficient purification and characterisationprocess for each engineered protein is expected.5) Validation of the general approach: The whole approach should eventually be validatedby the use of engineered meganucleases on real chromosomal targets in rodentcells. A general, standard protocol for rodent cells is expected.Potential Impact:The possibility of correcting errors in a genome through targeted homologous recombinationor modifying at will any DNA sequence is clearly enormously attractive to the scientificcommunity. Although it is clearly valuable to understand how genomic information is translatedinto function, rational modification of the DNA sequence of an organism has beenlimited by the time consuming process it requires, despite the development of new tools forthe construction of targeting vectors. Thus, the possibility of having new tools that will allowtargeting of any DNA sequence for insertion, deletion or repair could introduce a newrevolution in the field of functional genomics and could also bring a new paradigm and anew momentum to human gene therapy.Keywords:genome engineering, protein engineering, meganucleases, gene targeting, homologousrecombination, functional genomics, tools and technologiesPartnersProject Coordinator:Dr. Frédéric PâquesCELLECTIS SA102 Route de Noisy92 235 Romainville Cedex, Francepaques@cellectis.comProf. Guillermo Montoya BlancoCentro Nacional de Investigaciones Oncologicas (CNIO)Structural BiologyMacromolecular Cristolography GroupMadrid, SpainProf. Luis SerranoCentro de Regulacio GenomicaSystem Biology LaboratoryBarcelona, SpainDr. Arvydas LubysFermentas UABVilnius, LithuaniaFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life137

2.REGULATION OFGENE EXPRESSION

2.1TRANSCRIPTIONREGULATIONTRANS-REGX-TRA-NET

TRANS-REGwww.imbb.forth.gr/people/talianidis/strep.htmProject Type:Specific TargetedResearch ProjectContract number:LSHG-CT-2003-502950Starting date:1 st April 2004Duration:36 monthsEC Funding:1 860 000State-of-the-Art:In the pathways of gene expression, the first regulated and, in most cases, rate-limiting stepis the process of transcription. Despite the detailed picture that is emerging, a great numberof conceptual as well as mechanistic questions still need to be resolved. One of the maingaps in our knowledge is the limited insights we have on transcription regulation in the nuclearenvironment. The general goal of the project is to obtain a comprehensive knowledgeon the mechanism of regulation of model genes during cell differentiation, cell proliferationand signal transduction. The consortium will undertake concerted efforts to develop andapply fluorescent imaging techniques, coupled with genetic, proteomic and conventionalmolecular and cell biology approaches to study the molecular characteristics and functionsof individual multiprotein complexes, and their dynamic interplay in the context of uniquechromatin structures in living cells.Scientific/Technological Objectives:The objectives of this project are: calisationstudies by indirect immunofluorescence assays in vivo and in situ proteinproteininteraction studies by FRET (fluorescence resonance energy transfer) known nuclear structures under different conditions course of assembly of complexes on model genes induced during cell differentiation,cell proliferation and signal transduction in situ analysis by FLIP (fluorescence loss in photobleaching) and FRAP (fluorescencerecovery after photobleaching) of the time course of assembly of complexes on amodel gene and its relationship with transcription initiation spondingto euchromatin and heterochromatin during gene activation/ repression role in subnuclear targeting drosophila and mice, and cross-speciescomparisons of the individual complex components.Expected Results:The successful execution of the project is expected to result in:1. new knowledge on the in situ dynamics of the RNA polymerase-II machinery2. new knowledge on the molecular mechanism of transcription regulation that leads topathway-specific gene expression programmes3. development of new technologies and research tools.The results of the first 18-month period resulted in 4 joint publications and 27 individualpublications in high impact scientific journals. These and other results of the research canbe found on the project’s website.Potential Impact:The consortium is developing and applying state-of-the-art in vivo imaging techniques basedon FRET, with improved spatial and temporal resolution and mathematical tools to extractthree-dimensional information from two-dimensional spatial images. Development of highsensitivity and quantitative assays for chromatin immunoprecipitation is also an importantdeliverable of the project. While the work focus is on transcription complexes, we be-142From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Transcription Complex DynamicsControlling Specific GeneExpression Programmeslieve that the technologies andthe research tools generatedin parallel will be useful for abroader range of biologicalapplications.The project combines and expandsindividual activities witha more comprehensive collaboration.Keywords:gene expression, transcription,RNA polymerase-II, transcriptionregulation, transcriptionfactors, complex-complex interactions,signal transductionLocalization of TBP and TBP2(TBP-related factor 3) duringmouse folliculogenesis. TBP andTBP2 exhibit different localizationpattern. TBP expression is absentin the oocyte but present insurrounding follicular cells. TBP2is detected exclusively in oocytes.PartnersProject Coordinator:Prof. Iannis TalianidisFoundation for Research and Technology – HellasInstitute of Molecular Biology and BiotechnologyVassilika Vouton P.O. Box 152771110 Heraklion, Greecetalianid@imbb.forth.grProf. Imre BorosUniversity of SzegedFaculty of ScienceDepartment of Genetics and Molecular BiologySzeged, HungaryDr. Marc TimmersUniversity Medical Centre – UtrechtLaboratory for Physiological ChemistryUtrecht, The NetherlandsDr. Laszlo ToraInstitut de Génétique et deBiologie Moléculaire et CellulaireIllkirch, FranceDr. Annick Harel-BellanCentre National de la Recherche Scientifique (CNRS)Institut André LwoffVillejuif, FranceProf. Dr. Michael MeisterernstGSF-Forschungszentrum für Umweltund GesundheitNational Department of Gene ExpressionMunich, GermanyDr. Alexander PintzasNational Hellenic Research FoundationInstitute of Biological Research andBiotechnologyAthens, GreeceFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life143

X-TRA-NEThttp://rxrnet.dk/Project Type:Specific TargetedResearch ProjectContract number:LSHG-CT-2005-018882Starting date:1 st September 2005Duration:42 monthsEC Funding:1 950 000State-of-the-Art:The majority of nuclear receptors signal as heterodimers with the promiscuous retinoid Xreceptors (RXRs). Heterodimerisation introduces several key regulatory features to the RXRfamily, as it specifies response element recognition and allows dual ligand input in an HDspecificmanner. Together these features allow the large family of RXR heterodimerisingnuclear receptors to establish a plethora of cognate ligand-dependent gene networks thatregulate major aspects of cell and organ function during embryogenesis and in the adult.Importantly, nuclear receptors are “druggable” and play central roles in major diseaseslike cancer, diabetes and atherosclerosis. Hitherto, heterodimer target gene regulation hasonly been investigated by a gene-by-gene approach. Thus, key aspects of this regulatorynetwork, such as the identity of primary targets and their response dynamics, sharing oftargets by different heterodimers, nuclear receptor subtype and ligand dependency, areentirely unknown.Scientific/Technological Objectives:The main objective of X-TRA-NET is to develop and employ chromatin-immunoprecipitation(ChIP) in combination high throughput sequencing (ChIP-seq) to explore the complex transcriptionalnetwork of RXR and its partners. X-TRA-NET will use this combination to investigate theimpact of position and binding site diversity on the mechanisms of RXR target gene activation.The complex interplay between cellular context, target site diversity and receptor subtypespecificity will also be addressed. Furthermore, the genome-wide ChIP analyses will be usedto investigate how treatment of cell culture and animal models with different ligands targetingthe heterodimerization partner, or RXR itself, differentially affects recruitment of the NRs andtheir associated co-factors to target sites. Thus, X-TRA-NET aims to provide the first “proof ofconcept” for the use of genome-wide ChIP technology in NR ligand profiling. This would representa major leap forward in NR pharmacogenomics by providing the missing link betweenin vitro ligand binding studies and testing these putative drugs in animals.Expected Results:Global RXR target site profiles will be generated by ChIP-seq. These analyses will allow usto gain insight into several aspects of the RXR transcriptional network. These will include:1) the impact of position and binding site diversity on the composition, kinetics andspatio-temporal action of transcription-factor/co-factor complexes recruited2) molecular mechanisms underlying nuclear receptor subtype specific action3) molecular mechanisms of RXR agonists4) molecular mechanisms of selective nuclear receptor modulators, thereby providingproof of concept that the ChIP-seq approach is suitable nuclear receptor profiling.Potential Impact:The ChIP-seq approach pioneered by X-TRA-NET will serve as a model to tackle othertranscription factor families. In addition, due to the central role of nuclear recepors in anumber of major diseases, the new insight into the nuclear receptor field would significantlyimprove our understanding of the molecular mechanisms of the etiology and treatment ofmajor diseases like cancer, insulin resistance and atherosclerosis. In addition, proof of con-144From Fundamental Genomics to Systems Biology: Understanding the Book of Life

ChIP-Chip to DecipherTranscription Networks of RXR and Partnerscept that ChIP-seq technology can be used in nuclear receptor drug discovery will providecompanies with hitherto unsurpassed insight into the molecular mechanisms underlying thephysiological effects of their drugs. Thus X-TRA-NET is likely to increase competitiveness ofEuropean biotechnology and pharmaceutical companies.Keywords:chromatin-IP, nuclear receptors, global target site array, ligand specific effects, co-factors,pharmacogenomics, transcription factors, high-throughput techniques, ChIP-chipPartnersProject Coordinator:Prof. Susanne MandrupUniversity of Southern DenmarkDepartment of Biochemistry andMolecular BiologyCampusvej 555230 Odense M, Denmarks.mandrup@bmb.sdu.dkProf. Hendrik G. StunnenbergStichting Katholieke UniversiteitDeptartment of Molecular BiologyNijmegen, The NetherlandsDr. Hinrich GronemeyerCentre Européen de Recherche en Biologieet Médecine - Groupement d’IntérêtEconomiqueInstitut de Génétique et de BiologieMoléculaire et Cellulaire (IGBMC)Illkirch, FranceProf. Bart StaelsUniversité de Lille 2 - Droit et SantéDepartment of AtherosclerosisInstitut Pasteur de LilleLille, FranceDr. Dean HumGENFITLoos, FranceFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life145

2.2EPIGENETICREGULATIONTHE EPIGENOMEHEROICChILLSMARTER

THE EPIGENOMEwww.epigenome-noe.netProject Type:Network of ExcellenceContract number:LSHG-CT-2004-503433Starting date:1 st June 2004Duration:60 monthsEC Funding:12 500 000State-of-the-Art:In this “post-genomic” era, advances in epigenetic research represent a new frontier that ispredicted to yield novel insights into gene regulation, cell differentiation, stem cell plasticity,development, human diseases, cancer, infertility and ageing. According to an importantemerging concept, there is an “epigenetic code”, which greatly extends the potentialinformation of the genetic code. Based on this concept, one genome can generate many“epigenomes”, as the fertilised egg progresses through development and translates its informationinto a multitude of cell fates.In general, epigenetic research covers many topics that are of key interest to the public andscientists alike, such as embryonic and adult stem cells. Epigenetic research is thereforeanticipated to have far-reaching implications for medicine and for the understanding of thebasic processes of cell fate determination. The developments of research in this field willtherefore undoubtedly impact academic and industrial research communities and will forman important knowledge-base for policymakers and public bodies that contribute to thesocio-economic future of our “post-genomic” society.Europe has many world-leading laboratories in epigenetic research. The Network of Excellence(NoE) project EPIGENOME, proposes to follow a progressively expanding strategy.In the initial phase of the project, 25 teams with a proven record as leaders in their fieldwill combine their expertise and resources and will constitute the “virtual core centre” ofthe project.During the course of the project, 22 additional “junior” researchers (newly establishedteams, or NETs) will be supported and integrated via the NET programme, which will providethem with access to a world class epigenetic research platform.Scientific/Technological Objectives:The EPIGENOME NoE aims at reinforcing existing synergies to build a strong base for scientificexcellence. Furthermore, it seeks to promote the ERA not only by means of a strongresearch programme, but also by integrating and disseminating the project’s activities,including an efficient communication infrastructure to enable internal communication ofgeographically dispersed teams and to foster a dialogue with the public.The NoE comprises around 25 of the leading European research groups to study epigeneticmechanisms. Together, they constitute the critical mass for an internationally competitiveresearch programme. This programme is structured into 8 research topics to build on thecurrent strengths of the NoE. Within this framework, the 8 sub-programmes will address anumber of the ‘big questions’ in epigenetic research, thereby providing a coordinate approachto establish a research force of world-class standard.There are 8 sub-programes:1. Chromatin modification2. Nuclear dynamics3. Non-coding RNA & gene silencing4. X-inactivation & imprinting5. Transcriptional memory6. Assembly & nuclear organisation7. Cell fate & disease8. Epigenomic mapsThe major advantage of the NoE is that the common theme of chromatin modificationswill ideally interconnect most of the projects carried out by the individual members. Thus,although there are progressively increasing layers of experimental approaches in differentorganisms to study the complex mechanisms of epigenetic control in regulating informationof the chromatin template, all 8 research topics can be integrated into a logical platform,central to the unravelling of the many questions that will lead to a deeper understanding ofstem cell plasticity and disease.148From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Epigenetic plasticity of the genomeBased on the resources and expertises provided by this NoE, andfostered by the numerous collaborations even broader initiatives canbe envisaged. These can include large-scale profiling for decipheringthe epigenetic plasticity of the genetic information by genomewidemicroarray analyses. The availability of genomic micro-arraysin genetically tractable organisms, together with the expertises ofChIP-on-chip technology and modification-specific histone antibodiesplaces this NoE in a strong position to analyse the differencesbetween stem cells versus committed cells and to map epigenetictransitions along entire chromosomes (chromosome landscaping).With respect to model organisms, THE EPIGENOME represents amultidisciplinary project covering S.cerevisiae, S.pombe, plants,Drosophila, mouse and human. It integrates high-end genetic, biochemical,cytological and micro-array approaches for a functionalanalysis of epigenetic control.The strength of this NoE is in its focus on molecular mechanismsrather than on descriptive analyses. In addition, thanks to the expertiseof the NoE members, some of the most important questionsin modern epigenetic research may be addressed. The implicationsof epigenetic research are far-reaching and range from agricultureto human biology and disease, including our understanding of stemcells, cancer and ageing.The programme of EPIGENOME NoE rests on 5 pillars, namely, a joint research programmethat is directed towards elucidating epigenetic mechanisms; a Newly EstablishedTeam (NET) programme to integrate ‘junior’ scientists into the NoE; measures ensuringnetwork development and durability; communication platforms to address the needs of bothscientific exchange, and public consulting and a management structure that will underpinthe network.Expected Results:Research into epigenetics represents the new frontier for addressing many questions that,despite a vast resource of existing genetic data, still remain unanswered. The importanceof the “epigenetic code” concept explains why it is essential to have a better understandingof the processes of cell fate determination: better knowledge means better understanding ofdisease and development, and will therefore, improve intervention strategies for multifactorialdisease.The recent discoveries related to an epigenetic “histone code” and the function of the RNAimachinery in epigenetic silencing only serve to highlight the emerging new concepts inepigenetic research. In this sense, the creation of a NoE will not only provide an importantnucleation point for durable structure research, but will also overcome the problem of fragmentationby promoting the longer-term aims of scientific progress, and by contributing toan expanding and dynamic community.Our increasing understanding of epigenetic control should therefore foster the developmentof innovative strategies for therapeutic intervention based on regulatory pathways of epigeneticmechanisms.Epigenetics covers many topics of key interest to the general public, including embryonicand adult stem cells, their medical use and the cloning of whole animals. Advances in epigeneticresearch are expected to have far-reaching implications for medicine and humanhealth. By acknowledging its responsibility towards the public, the NoE is committed toensuring the dissemination of knowledge regarding epigenetic research and its societal implications.With these measures the NoE aims to provide a benchmark for a new Europeanpartnership between science and society.Genomes vs EpigenomesFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life149

THE EPIGENOMETHE EPIGENOME groupPotential Impact:In defining a coordinated joint programmeof activities (JPA), this NoE will assimilate existingsynergies for building a structure thatcan feed three important needs: advancescientific discoveries, integrate Europeanresearch and establish an open dialogue.The project’s main objectives will contributeto the long-lasting determination of a coherentEuropean Research Area (ERA) onepigenetic research. In the short term, THEEPIGENOME aims at constituting a frameworkfor important discoveries in Europe,thus establishing the NoE as an internationallycompetitive research force. As a consequence,the NoE will provide a platformfor the development of epigenetic research,benefiting not only the NET members, butalso the wider scientific communityA major goal of THE EPIGENOME is tosupport post-doctoral research, thereby allowingthe team to gain visibility at internationalmeetings and to disseminate their results.The NoE organises annual meetings,workshops and the ‘Alan Wolffe’ EpigeneticsConference, which provides a venue toeffectively showcase the NoE’s excellence.The EPIGENOME also promotes initiativesfor dialogue and disseminates information tothe public via organised events, the media,and the World Wide Web. This will help thepublic keep pace with new developmentsin knowledge, technology and innovation,and facilitate a greater acceptance of scientificendeavours. As a consequence, thepublic could have a more informed role inscientific governance, particularly on importantissues for society, which also raise ethicalquestions.Keywords:chromatin modification, RNA silencing, epigeneticcode, cell fate determination, reprogrammingPartnersProject Coordinator:Prof. Thomas JenuweinResearch Institute for Molecular Pathology (IMP)Dr. Bohr-Gasse 71030 Vienna, Austriathomas.jenuwein@imp.univie.ac.atDr. Denise BarlowResearch Center for Molecular MedicineVienna, AustriaProf. Ingrid GrummtDeutsches Krebsforschungszentrum HeidelbergDivision Molecular Biology of the Cell II / A030Heidelberg, GermanyProf. Jörn WalterUniversität des SaarlandsDepartment of GeneticsSaarbrücken, GermanyProf. Peter Becker, Philipp KorberLudwig-Maximilians-UniversitätAdolf-Butenandt-Institut MolekularbiologieMunich, GermanyProf. Gunter ReuterMartin-Luther-Universität Halle-WittenbergInstitut fur GenetikHalle, GermanyProf. Frank Grosveld, Peter VerrijzerErasmus Medical CenterRotterdam, The NetherlandsProf. Robin Allshire, Dr. Adrian Bird, Dr. Irina StanchevaUniversity of EdinburghWellcome Trust Centre for Cell BiologyEdinburgh, United KingdomProf. Wendy Bickmore, Prof. Neil BrockdorffProf. Amanda FisherThe Medical Research CouncilFaculty of MedicineMRC Clinical Sciences CenterLymphocyte Development GroupEdinburgh, United Kingdom150From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Epigenetic plasticity of the genomeProf. Bryan TurnerThe University of BirminghamSchool of MedicineDepartment of AnatomyBirmingham, UKDr. Wolf Reik, Dr. Patrick Varga-WeiszDr.Miguel ConstanciaThe Babraham InstituteDevelopmental Genetics & Imprinting LaboratoryCambridge, United KingdomProf. Azim SuraniThe University of CambridgeGurdon InstituteCambridge, United KingdomProf. Peter MeyerThe University of LeedsLeeds, UKDr. Genevieve Almouzni, Dr. Edith HeardCentre National de la Recherche Scientifique (CNRS)Institut CurieParis, FranceProf. Philip AvnerCentre National de la Recherche Scientifique (CNRS)Institut PasteurParis, FranceProf. Jerzy PaszkowskiUniversité de GenèveGeneva, SwitzerlandProf. Ueli GrossniklausUniversität ZürichInstitute of Plant BiologyDepartment of Plant Developmental BiologyZurich, SwitzerlandDr. Asifa Akhtar, Dr. Andreas LadurnerEuropean Molecular Biology Laboratory (EMBL)Heidelberg, GermanyDr. Fred van Leeuwen, Dr. Bas van SteenselHet Nederlands Kanker InstituutAmsterdam, The NetherlandsDr. Valerio OrlandoFondazione TelethonDulbecco Telethon InstituteNaples, ItalyProf. Susan Gasser, Dr. Antoine PetersDr. Dirk SchübelerFriedrich Miescher Institute for Biomedical ResearchBasel, SwitzerlandDr. Ana Losada, Dr. Oskar Fernandez-CapetilloCentro Nacional de Investigaciones OncológicasMadrid, SpainDr. Ortrun Mittelsten ScheidGregor Mendel-InstitutVienna, AustriaDr. Leonie RingroseInstitute of Molecular BiotechnologyVienna, AustriaDr. Deborah Bourc’hisInstitut National de la Santé et de la RechercheMédicale (INSERM)Institut Jacques MonodParis, FranceDr. Wolfgang FischleMax Planck Institute for Biophysical ChemistryGoettingen, GermanyDr. Robert SchneiderMax Planck Institute of ImmunobiologyFreiburg, GermanyProf. Renato ParoEidgenössische TechnischeHochschule ZürichBasel, SwitzerlandDr. Karl EkwallKarolinska InstitutetUniversity College SödertörnStockholm, SwedenDr. Vincent ColotCentre National de la Recherche Scientifique (CNRS)Plant Genomics Research UnitInstitut National de la Recherche Agronomique (INRA)Evry, FranceDr. Giacomo CavalliCentre National de la Recherche Scientifique (CNRS)Institut de Génétique HumaineMontpellier, FranceThe complete list of the 22 newly established groups integrated might not appear due to space limitations;see project web site for updated informationFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life151

HEROICProject Type:Integrated ProjectContract number:LSHG-CT-2004-018883Starting date:1 st November 2005Duration:52 monthsEC Funding:12 000 000State-of-the-Art:At last the completed genetic code of many organisms gives science the chance to understandhow genes build organisms. Unfortunately, like all truly great codes, simply decodingthe letters does not explain how life is manifest, since buried deep in the primary geneticcode is a second regulatory code, which we need to decipher to understand how the genomeworks. This regulatory code is encrypted in chromatin and 3D nuclear organisation,and functions to regulate the accessibility of the primary genetic information. We knowthat there is linear genome organisation and that genes subject to similar regulatory controlsare adjacent to each other. What we do not yet know is the extent of these ‘genomedomains’ – if domains operate between different chromosomes, or how domains are setup and maintained. Answers to these questions will depend upon global and long-rangegenome strategies that need the development of high-throughput technologies. HEROIC willtake a two-pronged approach. First, it will develop global biochemical and high-throughputgenomic tools and screens that will identify novel gene regulators and determine whenand where transcription factors, histone modifying enzymes and chromatin remodellingproteins interact with the primary genetic code. Then well-characterised progenitor-differentiationsystems, such as pluripotent mouse ES cells and paradigm silencing models fromgenomic imprinting and X-inactivation, will be studied using high-throughput ChIP-on-chip,chromosome interaction and whole genome nuclear localisation assays to provide basicinformation on linear and 3D genome organisation. HEROIC will provide knowledge thatcontributes to a functional understanding of gene regulation in a genome context. It willinject epigenetic research with high-throughput technology on a genome-wide scale, thusmaking a wider contribution to understanding the primary genetic code that will eventuallyallow society the full benefit expected from its decryption.Scientific/Technological Objectives:The main objective of HEROIC is to make significant advances in the mechanistic questionsof epigenetic regulation, characterise the epigenetic modifications that occur, andthen understand the implications for gene expression in different cell types. The approachfocuses on the use of high-throughput enabling technologies on predominantly primary andestablished mouse cell lines, particularly ES cells.To characterise the epigenome, high-throughput bisulphite sequencing, advanced massspectrometry applied to histone post-translational modifications, ChIP-on-chip, and threedimensional interaction mapping and profiling DNA replication timing across the genomewill be applied to ES cells, mutated ES cells and macrophages differentiated from these EScell lines. This will allow a comparison of pluripotent to differentiated aspects and changesof the epigenome in a model case. As a complement, aspects of the epigenome will bemapped in the haematopoietic compartment in the mouse.Expected Results:The histone codeHEROIC aims to unravel the meaning of the epigenetic code. This requires comprehensivedocumentation of coding combinations, the hierarchies and cross signalling within the codeand understanding what the code means.152From Fundamental Genomics to Systems Biology: Understanding the Book of Life

High-Throughput Epigenetic RegulatoryOrganisation in ChromatinWhole genome epigenetic andtranscription factor profilingHEROIC will screen whole genometile path arrays to identifyand compile a definitive set ofnon-coding regulatory elementsfor the mouse genome yieldinga TRR microarray. HEROIC willscreen high-density oligonucleotidearrays at nucleosomeresolution to study the epigeneticresponse of cells in cultureto short-term treatment withhormones in relevant regions ofthe genome. It will use the TRRmicroarrays to profile changesin gene expression and chromatinstructure that underlie thereprogramming of differentiatedB-lymphocytes towards the myeloidlineage by the enforced expression of the transcription factor CEBP.Overview ofHEROIC’s scientific goalsIn-depth DNA methylation and epigenetic profiling of mouse Chromosome 17HEROIC aims to provide a comprehensive map of epigenetic layers of chromosome 17ranging from histone marks, factors that read, write and interpret the marks, DNA methylationand parental imprinting to understand how transcription networks and epigeneticinformation contribute to the formation of specialised cell types in multicellular organisms.HEROIC will focus on two fundamental areas: pluripotency and lineage restriction.The epigenetic dimension of global genome structure and nuclear organisationHEROIC addresses epigenetic aspects of nuclear architecture and its relevance to cell commitmentand memory by exploiting well-defined cellular systems to examine how generegulation is affected by global genome structure and nuclear organisation.BioinformaticsHEROIC will accumulate all epigenetic data generated as well as public data. The accumulateddatasets will be analysed for currently unknown patterns of epigenetic states.Potential Impact: The main impact of the HEROIC IP will be research into gene regulatory systems atthe level of chromatin structure and nuclear organisation, with high-throughput technologyapproaches in the context of the whole genome. Never before has such anextensive multidisciplinary consortium been assembled at European level. The yield of cumulative joint research carried out in this IP will stimulate competitivenesswithin Europe and between other developed countries, such as the US andCanada. HEROIC will also act as a focal point within Europe for the development ofnovel technology applied to chromatin and nuclear organisation studies.From Fundamental Genomics to Systems Biology: Understanding the Book of Life153

HEROIC The undertaking of proactive training will contribute to extending the widespread useof the technology employed by consortium members to address other research questions. HEEROIC aims to disseminate actively but also protect research results where commercialexploitation is a possibility. Dissemination will occur in the form of joint publicationsand within the network through conferences and workshops. Researchers of HEROIC will be called upon as expert voices in discussions withinEurope on topics such as stem cell therapy, novel genetic and epigenetic diagnosticscreening methods and gene therapies involving RNAi.Keywords: epigenetics, chromatin, gene regulation, high-throughput techniques©Shutterstock, 2007154From Fundamental Genomics to Systems Biology: Understanding the Book of Life

High-Throughput Epigenetic Regulatory Organisation in ChromatinPartnersProject Coordinator:Prof. Henk StunnenbergStichting Katholieke UniversiteitDepartment of Molecular BiologyGeert Grooteplein 286500 HB Nijmegan, The Netherlandsh.stunnenberg@ncmls.ru.nlProject Manager:Dr. Adrian CohenScientific ManagerNijmegen Centre for Molecular Life Sciences (NCMLS)P.O. Box 91016500 HB Nijmegen, The NetherlandsProf. Denise BarlowCeMM - Forschungszentrum fürMolekulare Medizin GmbHInstitute of Microbiology and GeneticsVienna, AustriaProf. Matthias MerkenschlagerMedical Research CouncilMRC Clinical Sciences CentreLymphocyte Development GroupLondon, UKDr. Miguel BeatoCentre de Regulació GenòmicaDepartment of Chromatin & Gene ExpressionBarcelona, SpainDr. Edith HeardInstitut Curie ParisNuclear Dynamics and Plasticity of the GenomeParis, FranceDr. Kurt BerlinEpigenomics AGScience DepartmentBerlin, GermanyProf. Rolf OhlssonUppsala UniversityDepartment of Development & GeneticsUppsala, SwedenDr. Matthias MannMax-Planck Society for the Advancement of SciencesProteomics and Signal TransductionMartinsreid, GermanyProf. Francis StewartTechnische Universität DresdenBiotec and GenomicsDresden, GermanyDr. Stephan Beck, Dr. Dave VetrieGenome Research LtdWellcome Trust Sanger Institute,Immunogenomics LaboratoryCambridge, UKDr. Ewan BirneyEuropean Molecular Biology Laboratory (EMBL)European Bioinformatics Institute (EBI)Hinxton, UKDidier AllaerDiagenode SAScience DepartmentLiege, BelgiumFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life155

ChILLProject Type:SME- Specific TargetedResearch ProjectContract number:LSHG-CT-2006-037462Starting date:1 st October 2006Duration:36 monthsEC Funding:1 800 480State-of-the-Art:The sequence of an organism’s genome does not directly determine how the genome isused to build the organism. A second, more complex regulatory code - the epigenetic code- is encrypted in the chromatin structure and the 3D nuclear organisation of chromosomes.Epigenetic information is encoded in DNA modifications (namely methylation), chromatincomposition and modification, and nuclear topology, or the dynamic organisation of thegenome within the nucleus.Epigenetic information not only provides the first cue to allow a cell to interpret the genome,it can also be heritably transmitted through cell division to maintain cellular identity. Moreover,while many heritable disorders in humans are caused by DNA sequence changes (mutations)that abolish gene expression, a number of diseases are caused by inappropriategene silencing brought about by epigenetic modifications. Indeed, most cancers involve theepigenetic silencing of genes that normally control cell proliferation. The principal forms ofepigenetic modification are DNA and histone methylation.A challenge that is central to modern biology is the identification of the spatial and temporaldynamics of epigenetic factors in a number of physiological situations. The ChromatinImmuno-Precipitation (ChIP) assay has played a pivotal role in deciphering patterns ofepigenetic marks that govern gene transcription. Besides ‘classical’ ChIP, several similartechniques have been described in the literature. Recently, new technologies designed toimprove on the existing ChIP and native ChIP (NChIP) technologies, have emerged.In addition, low resolution and reproducibility problems are often encountered. These severelimitations of the ChIP method are overcome by the Chromatin Immuno-Linked Ligation(ChILL) method, , which could provide the foundation for a new generation of biotechnologytools and methods.Scientific/Technological Objectives:The objective of this project is to develop and validate a new technology which has thepotential to replace the various ChIP technologies, and to transform the way the molecularanalysis of chromatin is performed. The ChILL technique has been patented by one of thepartners of this project, leaving the consortium free to operate with regard to intellectualproperty rights. The ChILL method is based on specific ligations which occur between DNAstretches under diluted conditions. In this environment, ligation partners can only interact ifthey are in close proximity.This proximity is created by new oligonucleotide-antibody conjugates (nucleoproteic probes,or oligo-ab), which physically place the target DNA in contact with the oligonucleotide reportersequences. The ligation products are then amplified by the polymerase chain reactionand analysed with real-time instruments and/or classical gel electrophoresis.Due to the ligation step taking place under diluted conditions, the ChILL method will generatedata comparable to those obtained with ChIP, but with increased sensitivity and asimpler protocol that omits the tedious immuno-precipitation step. As a proof of principle,the ChILL method has already been shown to be at least 100 times more sensitive than theregular ChIP assay.ChILL will not only facilitate analysis of very small samples, such as early embryos or diagnosticsamples from patients, but will also radically improve the resolution of the epigeneticmarks. In addition, strong detergents used in the ChILL assay open up the chromatin structure,rendering it more accessible to antibodies than in conventional ChIP assays.Another major advantage of ChILL will be its ability to interrogate several parameters in asingle sample. For this purpose, a variant of ChILL called combinatorial ChILL will be developed.This will represent a major breakthrough, because it will mean that several epigeneticmarks can be collected from a single tube, making it easier to build up what might be calledan “epigenetic profile” of the biological material in question.156From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Chromatin Immuno-linked ligation:A novel generation of biotechnologicaltools for research and diagnosisExpected Results:The Chromatin Immuno-Precipitation (ChIP) assay plays an absolutely pivotal role in decipheringpatterns of epigenetic marks that govern gene transcription. While the ChIP assayis a versatile tool, it suffers from low resolution and low sensitivity. These strong limitationsof the ChIP method are overcome by the Chromatin Immuno-Linked Ligation (ChILL) method.ChILL will not only facilitate analysis of very small sample sizes, such as early embryosor diagnostic samples from patients suffering from a range of diseases, but also radicallyimprove the resolution of the epigenetic marks. The ChILL approach also offers opportunitiesto examine simultaneous co localization of two or more factors on the same chromatintemplate, and the epigenetic marks will be resolved in unprecedented detail.The expected results of the program would be to make ChILL technology accessible to allEuropean research laboratories via validated procedures, reagents or kits. We also expectedto launch diagnostic kits using ChILL technology for the diagnosis of diseases linkedto epigenetic disorders.Potential Impact:The first impact of ChILL will be a better understanding of the epigenetic code. Of course,the commercial impact of the ChILL method might consequently also be very important forDiagenode with the possible development of tools for the research or diagnostic market.Keywords:chromatin remodeling, transcription regulation, epigenetics, ChIP assay, histones,DNA methylationPartnersProject Coordinator:Didier AllaerDiagenode SAAvenue de L’Hopital, 1 Tour Giga B344000 (Sart Tilman) Liège, Belgiumdidier.allaer@diagenode.comProf. Dr. Rolf I. OhlssonUppsala UniversityDevelopment andGenetics Evolution CenterUppsala, SwedenProf. Dr. Henk G. StunnenbergRadbout University NijmegenDepartment of Molecular BiologyNijmegen, The NetherlandsDr. François FuksFree University ofBrusselsFaculty of MedicineLaboratory ofMolecular VirologyBrussels, BelgiumDr. Duncan ClarkGeneSys LtdCamberley, UKFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life157

SMARTERProject Type:SME-Specific TargetedResearch ProjectContract number:LSHG-CT-2006-037415Starting date:1 st December 2006Duration:48 monthsEC Funding:2 499 999State-of-the-Art:The identity of a given cell within a metazoan organism is primarily defined by the expressionpattern of its genes. The activation and repression of genes is tightly regulated by the concertedaction of transcription factors that recognise and bind specific DNA sequences withinregulatory regions. Work done over the last 20 years established this basic regulatory mechanismof gene activation and repression, while recent experiments have exposed an additionallayer of regulation involving modifications of DNA and bound histones. These modificationsare involved in cellular inheritance of transcriptional states through cell division and development,and as they are not coupled to DNA sequence, are referred to as epigenetic.Many factors that impact on epigenetic phenomena are clearly distinct from basic transcriptionfactors and are involved in regulating chromatin structure. Modulation of chromatinstructure is frequently achieved by intrinsic enzymatic activities that either mark particularregions within the genome for activity or repression, or use the hydrolysis of ATP to remodelnucleosomal arrays. This alteration of gene expression patterns in response to external andinternal signals has a major influence on stem cell differentiation, the maintenance of tissueintegrity, and the adaptation of organisms to environmental changes.Recently, small molecules that target histone deacetylases (HDAC) have been used in thetreatment of cancer, opening up new avenues in therapeutic research. However, smallmolecules targeting epigenetic regulators have so far not been the major focus of drugdiscovery efforts.The SMARTER project aims to develop such compounds, and this is also the primary missionof Chroma Therapeutics, the SME participating in the consortium. The interaction betweenleading European chromatin labs and Chroma is expected to greatly strengthen thecompany’s knowledge base, and thus, have a powerful impact on its ability to enter drugcandidates for clinical trials.Scientific/Technological Objectives:The SMARTER project has the following goals:1) Identification of small molecule inhibitors that target various histone-modifying enzymes(SMARTERs);2) Validation of these inhibitors through in vivo analysis of histone modification states;3) Establishment of histone modification states as standard readouts for drugs that targetepigenetic modifiers;4) Improvement of known epigenetic modulators through medicinal chemistry;5) Identification of target genes that are regulated by the SMARTER molecules and6) Application of the SMARTER molecules in standard animal model systems to verifytheir activity in living organisms.Expected Results:After 48 months, SMARTER will provide:1) SMARTER molecules that are selective for specific histone deacetylases and two additionaltargets, with high potency;2) An assay system for new epigenetic modifiers that is applicable to high throughputscreen for small molecule inhibitors;3) Definition of SMARTER effects on histone modification patterns and kinetic analysisof effects on chromatin;4) Identification of one or several bona fide target genes for direct SMARTER effects;158From Fundamental Genomics to Systems Biology: Understanding the Book of Life

5) Establishment of one or several SMARTER molecules for one or several targets thatshow an in vivo effect in mice;6) Demonstration of global and gene-specific effects of SMARTERs on the epigeneticpattern of lymphomas in a model of radiation-induced lymphomagenesis, with aview to investigating the chemotherapeutic potential of SMARTERs.Potential Impact:Development of small modulatorsof gene activation and repressionby targeting epigenetic regulatorsThe SMARTER project is specifically designed to increase the knowledge base of ChromaTherapeutics, a SME located in the UK. Chroma will profit from the collaboration, becausethe consortium will greatly facilitate the analysis of SMARTER molecules that have been andwill be discovered by the company. The project will also allow Chroma to direct improvementof the small molecules through medicinal chemistry, and to test them rapidly in variousbiological systems. Being a SME-targeted STREP, the project will contribute significantly tothe Lisbon objective of Europe becoming the most competitive knowledge-based economyin the world by 2015.The knowledge gained through this project will be disseminated and translated into newtherapies and clinical practice. SMARTER will have a strategic impact on European R&Dthrough facilitating the generation of small molecules that are cell-permeable and that durablychange chromatin modification states. In order to fully understand how the eukaryoticgenome in general and the human genome in particular operate, knowledge about theirDNA sequence, epigenetic control systems and dynamic structure in relation to gene expressionmust be integrated.Keywords: epigenetics, small molecules, gene regulationPartnersProject Coordinator:Prof. Axel ImhofLudwig Maximilians University of MunichAdolf-Butenandt InstituteHistone Modifications GroupProtein Analysis Core FacilitySchillerstr. 4480336 Munich, Germanyimhof@lmu.deDr. Scott CuthillChroma Therapeutics LtdOxford, UKDr. Dirk SchübelerFriedrich Miescher Institute forBiomedical ResearchBasel, SwitzerlandDr. Manuel EstellerSpanish National Cancer CentreCancer Epigenetics LaboratoryMadrid, SpainProf. Tony KouzaridesUniversity of CambridgeThe Wellcome TrustCancer ResearchUK Gurdon InstituteCambridge, UKFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life159

3.STRUCTURAL GENOMICS& STRUCTURALPROTEOMICS

3.STRUCTURALGENOMICS3DGENOMEBIOXHIT3D-EMGeneFunE-MePFSG-V-RNAVIZIERUPMANNDDP3D repertoireFESPE-MeP-LabHT3DEMNMR-LifeExtend-NMRIMPSSPINE2-COMPLEXESOptiCrystTEACH-SG

3DGENOMEhttp://3dgenome.uva.sara.nl/3dg.htmlProject Type:Specific TargetedResearch projectContract number:LSHG-CT-2003-503441Starting date:1 st December 2003Duration:42 monthsEC Funding:2 173 803State-of-the-Art:Understanding the molecular mechanisms that underlie the orchestration of many thousandsof genes in higher eukaryotes is a key target in modern biomedical research. Our knowledgeabout gene regulation at the single gene is rapidly expanding. However, understandingof the coordination of gene regulation, for example during cell differentiation and disease,is still remarkably limited. There is considerable evidence that the three-dimensionalfolding of the DNA chain, packaged as chromatin, plays an important role in gene control.The 3DGENOME project has the ambition to force a breakthrough in our understanding ofthe relationship between the functioning of the human genome and its 3D structure insidethe cell nucleus. To this end we analyse the 3D folding of the human genome inside its naturalenvironment, i.e. the cell nucleus, and relate this to its transcriptional activity. This studycombines 3D light microscopy with genome-wide information about gene activity.Scientific/Technological Objectives:The 3DGENOME project is based on the systematic and large-scale combination of twomain technologies: in situ hybridisation (FISH) followed by 3D light microscopy A major challenge is created by the large cell-to-cell variation of 3D chromatin structure inotherwise identical (cultured) human cells. Novel methods are developed to identify significantstructural features that stand out against this ‘noisy’ background. At the same time it isessential to quantify and characterise this cell-to-cell variation precisely. Results will tell whichaspects of chromatin structure are important for genome function and which are not.An integral part of this approach is the development of novel high-throughput 3D imagingroutines in combination with automated 3D image processing and quantitative imageanalysis. Specific aspects of 3D chromatin structure will be analysed by high-resolution lightmicroscopy, including 4Pi microscopy.Most of the work is carried out with primary human cells and cell lines. In addition, Drosophilais used as a system in which specific changes can be made in the genome, afterwhich the effect of 3D chromatin structure can be analysed.Expected Results:The 3DGENOME project is unveiling the link between the folding of the chromatin/chromosomefibre inside the interphase nucleus and the functional (primarily transcriptional) propertiesof the human genome. It builds on the human transcriptome, which shows genes of hightranscriptional activity in a limited number of gene-dense clusters in the genome. Results ofthese studies will give new insight into how the eukaryotic genome in general, and the humangenome in particular, operates inside the living cell. This project will lay the groundwork forunderstanding how, beyond the regulation at the individual gene level, a large-scale chromatinstructure affects the complex gene regulation networks in normal and deceased cells.Potential Impact:1. Fundamental insight into the relationship between gene regulation and 3D structureof the eukaryotic genome. To understand fully how the eukaryotic genome ingeneral, and the human genome in particular, operate, knowledge about its DNAsequence, its epigenetic control systems and its dynamic 3D structure in relation togene expression must be integrated.164From Fundamental Genomics to Systems Biology: Understanding the Book of Life

3D Genome Structure and Function2. High resolution 3D microscopy and related software tools 3DGENOME will bringforth new developments on the areas of high-resolution 3D light microscopy, 3D imageprocessing and quantitative analysis of acquired images. Furthermore, we willdevelop methods to quantitatively compare and statistically analyse 3D structuresand distribution in biological specimens.Keywords: 3D structure, fluorescent in situ hybridization, gene expression, highthroughput imaging analysisPartnersProject Coordinator:Prof. Roeland Van DrielUniversiteit van AmsterdamScience FacultySwammerdam Institute for Life SciencesKruislaan 3181098 SM Amsterdam, The Netherlandsvan.driel@science.uva.nlDr. Hans van der VoortScientific Volume Imaging BVHilversum, The NetherlandsProf. Dr. Thomas CremerLudwig-Maximilians-Universität München (LMU)Department of Biology IIMartinsried/Munich, GermanyProf. Dr. Christoph CremerAngewandte Optik undInformationsverarbeitungKirchhoff Institut für PhysikHeidelberg, GermanyProf. Dr. Roland EilsDeutsches Krebsforschungszentrum (DKFZ)Division of Theoretical BioinformaticsHeidelberg, GermanyProf. Dr. Giacomo CavalliCentre National de la Recherche Scientifique (CNRS)-IHGInstitute of Human GeneticsMontpellier, FranceProf. Dr. Rogier VersteegUniversity of AmsterdamAcademisch Medisch CentrumAmsterdam, The NetherlandsProf. Dr. Stanislav KozubekAcademy of Sciences of the Czech RepublicInstitute of BiophysicsBrno, Czech RepublicFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life165

BIOXHITwww.bioxhit.orgProject Type:Integrated ProjectContract number:LSHG-CT-2003-503420Starting date:1 st January 2004Duration:54 monthsEC Funding:9 993 849State-of-the-Art:The recently acquired knowledge pertaining to numerous genome sequences provides aunique opportunity to quantitatively decipher the roles of biological molecules in complexprocesses within cells, organs and organisms. An essential step in accomplishing this taskis to determine their atomic structures; this permits a more comprehensive description of theroles of molecules in living systems, in the context of both health and disease. The acquisitionof structural information on biological macromolecules on a genomic scale lies at thecore of Structural Genomics (SG).At present, the only techniques appropriate for determining three-dimensional (3D) structuresof biological macromolecules in atomic detail, and at a rate appropriate for SG, arebiological X-ray crystallography (biocrystallography) and NMR-spectroscopy. Biocrystallographyhas been responsible for roughly 85% of all biomolecular structures (and for 95%of all the smallest proteins) deposited in the Protein Data Bank (http://www.rcsb.org/pdb)and the Molecular Structural Database (http://www.ebi.ac.uk/msd).Biocrystallography has undergone a tremendous transitional period over the past decade.Formerly, determining a macromolecular crystal structure required years; today it wouldtypically require a few weeks, if not days. And crucially, the potential for further improvementis far from exhausted. Furthermore, recent technological advances have made a widerange of new biological problems responsive to crystallographic study. Although obtaininglarge amounts of a protein in soluble form is still in many cases an important issue, biocrystallographyis in principle applicable to the complete spectrum of biological macromolecules,derived from all organisms (from eubacteria and archeae, to human organisms),and of all sizes (from small domains to gigantic ribosome or virus particles).BOIXHIT GroupScientific/Technological Objectives:The central objective of the BIOXHIT project entails tackling the challenge posed by theStructural Genomics initiatives already underway in the USA and in Japan, and to develop,assemble, standardise and provide a highly integrated technology platform for HighThroughput Structural Biology. This goal will be attained as a result of coordinated effortswith the present and future European synchrotron radiation facilities, and a team of internationallyrecognised European leaders in hardware and software development, directlyassociated with high-throughput methodologies.166From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Bio-Crystallography ona Highly Integrated Technology Platformfor European Structural GenomicsBiocrystallography is the method of choice, and synchrotron radiation the principal sourceof X-rays, for data acquisition. This technology encompasses the components necessary toproduce an efficient pipeline linking crystallisation to completed 3D-structure determination.It will operate with minimal user intervention, and will be fully accessible to the wider lifesciences research community.Expected Results:BIOXHIT aims to deliver the following results: smaller crystallisation drops, with less protein consumption; X-ray beam; and easy-to-operate beamlines, providing high-quality stable X-rays, that are automaticallydelivered to the sample; in order to optimally plan the actual diffraction experiment; the success of the experiment at the earliest possible stage, and to allow direct feedbackfor data collection and crystallisation; control; tionedabove, and high-level training in new hardware; within and external to the BIOXHIT consortium.Potential Impact:BIOXHIT provides a substantial component in scientific as well as technical innovation. Thetask of building such integrated platforms entails numerous developments in instrumentationand in hardware automation. Instances of this are the complete tracking of crystal samplesduring synchrotron experiments, and interaction with the project information managementsystems of the users; the automated handling of crystal samples by robots, their automaticrecognition and centring on the goniometric hardware; and their automated screening.The BIOXHIT project activities include innovative developments in many of these directions,(as exemplified in the mini-kappa goniometer and its control software), and therefore provideaccess to new categories of data collection strategies hitherto inaccessible. Anotherprominent feature of BIOXHIT is the assembly of a computational crystallographic pipeline,which aims at automating the sequence of steps involved in determining macromolecularcrystal structures. This requires a dramatic paradigm shift in X-ray crystallographic methodology,as compared to the old paradigm, whereby the successive steps of structure determinationwere performed by crystallographers running computer programs interactivelythrough graphical interfaces, to a new pipeline operating with little or no human intervention.The immediate demand for such integration will be met by connecting these programs,From Fundamental Genomics to Systems Biology: Understanding the Book of Life167

BIOXHITBIOXHIT: Integration and Activity AreasStandardisationSamplepreparationandmanipulationCore hardwaredevelopmentsCore softwaredevelopmentsDiffractionExperimentLogistics / remoteoperation / integrationThe BIOXHIT project: Relationshipbetween activity areas, partnercontributions, workpackagesand sections. Each link defines acontribution of a Partner to a WP.1Crystallisationtechnologies2Synchrotrontechnologies3Beamline endstationsand datacollection4Data processing andstructure determination5Databases andnetworkingthus emulating the actions of a crystallographer by the execution of suitable scripts. Thecomplexity of this approach should not be underestimated; it will serve to deliver a firstgeneration of integrated structure determination pipelines.BIOXHIT ultimately proposes to achieve a genuine integration of all of the processes intoa single, seamless computational scheme that will be structured around a conceptual unificationof the structure determination process. This demands a radical rethinking of X-raycrystallographic methods, and a profound reorganisation of their software implementationaround the modern techniques of object-oriented programming. In return, it will deliver amarkedly powerful second generation of integrated pipelines, as well as considerably improvedsoftware for general use. The combination of hardware and software innovationswill in turn render new phasing techniques accessible, such as routine phasing by means ofanomalous dispersion from sulphur and phosphorus.The number of scientists from the structural biology community subsequently becoming newusers of the synchrotron facilities has increased rapidly during recent years. Synchrotronradiation centres have had long experience in training users, but training of the increasingnumber of new users represents a challenge that would be impossible to meet by the hardwarecore-facilities alone. These efforts will be amplified throughout the BIOXHIT projectlifetime. A number of Training, Implementation and Dissemination TID-centres will be establishedoutside the participating laboratories as the vital tools for the dissemination of thedeveloped know-how.Keywords: synchrotrons, hardware and software pipeline, protein crystallisation,X-ray crystallography, robotics, automation techniques, standardisation,technology platform, structural genomicsPartnersProject Coordinator:Dr. Victor LamzinEuropean Molecular Biology Laboratory (EMBL)Outstation HamburgMacromolecular Crystallography22603 Hamburg, Germanyvictor@embl-hamburg.deProject Research Director:Dr. Manfred WeissEuropean Molecular Biology Laboratory (EMBL)Outstation HamburgMacromolecular Crystallography22603 Hamburg, Germanymsweiss@embl-hamburg.de168From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Bio-Crystallography on a Highly Integrated Technology Platformfor European Structural GenomicsProject Manager:Natalie SebastianEuropean Molecular BiologyLaboratory (EMBL)Outstation Hamburgc/o DESYNotkestr. 85, building 25A22603 Hamburg, Germanynatalie.sebastian@embl-hamburg.deDr. Raimond Ravelli(since 2008 replaced by Dr. Andrew McCarthy)European Molecular Biology Laboratory (EMBL)Outstation GrenobleGrenoble, FranceDr. Kim HenrickEuropean Molecular Biology Laboratory (EMBL)European Bioinformatics Institute (EBI)Hinxton, UKDr. Sean McSweeneyEuropean Synchrotron FacilityGrenoble, FranceDr. C. Schulze-BrieseSwiss Light Source (SLS)Villigen, SwitzerlandDr. Gerard BricogneGlobal Phasing LtdCambridge, UKDr. Anastassis PerrakisHet Nederlands Kanker Instituut Antonivan LeeuwenhoekziekenhuisAmsterdam, The NetherlandsDr. Roberto PuglieseELETTRA TriesteSincrotrone Trieste S.C.P.A.Trieste, ItalyProf. Keith Sanderson WilsonUniversity of YorkStructural Biology LaboratoryDepartment of ChemistryYork, UKDr. Uwe MuellerFreie Universität BerlinProteinstrukturfabrik c/o BESSY GmbHBerlin, GermanyDr. Peter John BriggsCouncil of the Central Laboratoryof Research CouncilsWarrington, UKProf. George SheldrickGeorg-August-Universität GöttingenGöttingen, GermanyDr. Andrew ThompsonSociete Civile Synchrotron SOLEILGif-sur-Yvette, FranceDr. Thomas SchneiderFondazione Italiana perla Ricerca sul CancroMilan, Italy(Since 2007 at the projectcoordinator’s site)Dr. Marjolein ThunnissenLund UniversityDepartment of Molecular BiophysicsLund, SwedenProf. Sine LarsenUniversity of CopenhagenDepartment of ChemistryCopenhagen, DenmarkDr. Elizabeth Duke, Dr. Colin NaveDiamond Light Source LtdDidcot, UKDr. J. JuanhuixCampus UniversitatAutònoma de BarcelonaConsorci Laboratori deLlum de SincrotóBarcelona, SpainDr. Edgar WeckertDeutsches ElektronenSynchrotronHamburg, GermanyDr. Gábor Mihály LammEMBLEM EnterpriseManagementTechnology Transfer GmbHHeidelberg, GermanyDr. Kristina Djinovic-CarugoUniversity of ViennaInsittute for BiomolecularStructural ChemistryVienna, AustriaFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life169

3D-EMwww.3dem-noe.orgProject Type:Network of ExcellenceContract number:LSHG-CT-2004-502828Starting date:1 st March 2004Duration:60 monthsEC Funding:10 000 000State-of-the-Art:Currently, the primary challenge for biological research lies in understanding the cellularfunction in molecular detail, based on genomic and proteomic information. Detailed knowledgeof the structure of macromolecules and macromolecular complexes, and also of theinteraction networks that underlie cellular function, allow for progress in the study of biologicalprocesses in health and disease. This project will specify potential targets for therapeuticintervention, as well as identify pharmaceutical lead structures.Three-dimensional (3D) visualization is the best way to appreciate the complex interactionsof macromolecules, such as proteins. Visual techniques, especially electron microscopy (EM),can complement and extend quantitative data obtained using other methods in this field.EM is a powerful tool that derives 3D structural information from biological specimens. Thespecific EM technologies provide 3D projections in a wide spectrum of resolutions rangingfrom atomic to cellular. Electron crystallography is applied when studying symmetric 2Dcrystals of molecules, such as membrane proteins, showing the same structure and orientation.Single particle analysis enables the 3D reconstruction of noncrystalline and asymmetricassemblies. The application of electron tomography reveals macromolecular interactionsin native cellular contexts. A near physiological preservation of small cells and viruses isachieved by rapid freezing in vitreous ice.The sectioning of these vitreous samples and subsequent cryo-electron tomography, as wellas the 3D reconstruction based on low contrast 2D images, represent technical challenges.European laboratories and companies are taking the lead in different EM techniques, andalso in their related aspects, like that of image processing. Such interdisciplinary cooperationis required to standardise, develop, improve and combine EM techniques.Scientific/Technological Objectives:The 3D determination of macromolecular structures, such as proteins, will play an essentialrole in future life-science research. The 3D-EM network was initiated so as to create a forumfor internationally recognised European manufacturers and institutions, in various fields of3D structural research. The activities of the network focus on 3D imaging of macromoleculesand molecular machines, as well as cells and cell organelles.The main objectives of 3D-EM are the following:1) Improvement and development: 3D-EM improves existing techniques, and also developsnovel techniques necessary for 3D visualization of macromolecules and theirfunctions within cells.2) Provision of training: The European Molecular Biology Organization (EMBO) annuallyoffers a continually oversubscribed training course on cryo-EM. A novel courseprogramme has been established in close collaboration with EMBO. 3D-EM expertstrain advanced students and scientists in specific EM techniques, data analysis andimage processing. The courses provide hands-on training, as well as lectures andseminars concerning the theoretical background of EM methods. Basic skills in stateof-the-artEM technologies will increase, since new knowledge is included in the advancedtraining courses. The training programme, access to central registration andfurther details are available on the Internet (http://www.3dem-noe-training.org/).170From Fundamental Genomics to Systems Biology: Understanding the Book of Life

New Electron Microscopy Approachesfor Studying Protein Complexesand Cellular Supramolecular Architecture3) Exchange of knowledge: Expertise gained in EM techniques, especially the innovativecryo-electron microscopy of vitreous sections (CEMOVIS), is disseminated toscientists both within and external to 3D-EM. In addition to the course programme,workshops have also been organised, intended to promote discussion and the awarenessof new developments in electron microscopy.4) Standardisation: the processing and comparison of data obtained with the differentEM methods are extremely time-consuming. Standards for 3D image reconstructionmust be identified, developed and tested. An EM data base and an optimal standardsoftware platform (based on these standards), will be established. User-friendlyinterfaces, operating between electron crystallography, single particle analysis andelectron tomography, will reduce processing time. Knowledge and excellence arespread via collaborations, training courses, scientific meetings and publications.The results achieved by 3D-EM have been presented at numerous conferences and workshops.Furthermore, they have been published in over 65 scientific articles in peer-reviewedjournals, and are listed in detail on the project web page, mentioned above.Expected Results:Towards the end of its second year, 3D-EM was reviewed by external experts. These advisorsrated the overall project performance as excellent. Over the full project duration, thefollowing results are expected:1) Improvement of methods and technologies related to electron microscopy, e.g. specimenpreparation and image processing2) Integration of software packages and tools with instrumentation? User-friendly, universalinterfaces between electron crystallography, single particle analysis and electrontomography3) Development and use of standards for 3D image reconstruction Expansion of thenetwork in the direction of Eastern EuropeSetting 3D-EM guidelines for software development and data exchange some highlights ofthe current results are: 240 participants, beginners and advanced, were trained in 21 coursesScientists from several European labs have already been trained in the technology developedby CEMOVIS. The outstanding results achieved thus far include the development ofseveral software tools, packages and algorithms, such as the TOM Toolbox and the IPLT(Image processing library & toolbox) programme.From Fundamental Genomics to Systems Biology: Understanding the Book of Life171

3D-EMPotential Impact:In the field of electron microscopic technologies, 3D-EM provides a platform for the jointsolution of issues. A standardised comparison and exchange of experimental data obtainedwith differing EM methods, will facilitate these efforts and contribute to the understandingof cellular function in molecular detail.The close cooperation of individuals, respectively grounded in academic and applied research,guarantees an immediate transfer of knowledge and experience from the field ofbasic research to industrial application. In addition, the added benefit of improved toolsor instrumentation, suitable for research requirements, strengthens the market position ofEuropean companies.A growing market for structural biology in Europe generates novel employment opportunitiesin this sector, associated with the need for experienced personnel. In collaboration withthe European Molecular Biology Organization (EMBO), 3D-EM created a novel trainingprogramme covering specific aspects of electron microscopy, applicable to both beginnersand experienced scientists.3D-EM trains and supports groups with experience in electron microscopy to bring themto the state-of-the-art in terms of methodology and equipment. This strategy will generate anetwork of electron microscopy centres across Europe. The network defines future needs forresearch, standardisation and instrumentation.Keywords:3D electron microscopy, protein complexes, cryoelectron microscopy, electron tomography,single particle, electron microscopy techniques, imaging, structural biologyTraining ProgramWP 1Electron TomographyWPs: 4, 5, 6, 8, 13ElectronCrystallographyWP 7Single ParticleAnalysisWPs: 9, 10, 11Co-ordinationand NetworkManagementWP 12Setting 3D-EM GuidelinesWPs: 2, 3172From Fundamental Genomics to Systems Biology: Understanding the Book of Life

New Electron Microscopy Approaches for Studying Protein Complexesand Cellular Supramolecular ArchitecturePartnersProject Coordinator:Prof. Andreas EngelUniversity of BaselM.E. Miller Institute for Structural BiologyBiozentrumKlingelbergstrasse 70CH-4056 Basel, Switzerlandandreas.engel@unibas.chProject Manager:Dr. Urs MüllerUniversity of BaselM.E. Miller Institute for Structural BiologyBiozentrumKlingelbergstrasse 70CH-4056 Basel, Switzerlandu.mueller@unibas.chProf. Wolfgang BaumeisterMax-Planck Institute of BiochemistryDepartment of Molecular Structural Biology (MPIB)Martinsried, GermanyProf. Werner KühlbrandtMax-Planck Institute of BiophysicsFrankfurt am Main, GermanyProf. Jose CarrascosaConsejo Superior de Investigaciones CientificasCentro Nacional de Biotecnologia (CNB)Madrid, SpainDr. Kim HenrickEuropean Molecular Biology Laboratory (EMBL)European BioInformatics Institute (EBI)Hinxton, UKDr. Achilleas FrangakisEuropean Molecular Biology Laboratory (EMBL)Heidelberg, GermanyDr. Werner HaxFEI CompanyEindhoven, The NetherlandsProf. Stephen FullerUniversity of OxfordDivision of Structural BiologyOxford, UKProf. Marin van HeelImperial CollegeCentre for Biomolecular Electron MicroscopyCentre for Structural BiologyLondon, UKProf. Helen SaibilBirkbeck University of LondonDepartment of CrystallographyLondon, UKProf. Jacques DubochetUniversity of LausanneLaboratory of Ultrastructural AnalysisLausanne, SwitzerlandDr. Nicolas Boisset † , Dr. Slavica JonicUniversité Pierre et Marie CurieParis, FranceProf. A.J. (Bram) KosterLeiden University Medical CenterDepartment of Molecular Cell BiologyElectron Microscopy DivisionLeiden, The NetherlandsProf. Christian SpahnCharité – Universitätsmedizin BerlinInstitut für Medizinische Physikund BiophysikBerlin, GermanyDr. Sergio MarcoCentre de Recherche LaboratoireRaymond LatarjetInstitut CurieCentre Universitaire d’OrsayOrsay, FranceProf. Bertil Daneholt, Prof. Hans Hebert,Prof. Oleg Shupliakov, Prof. Ulf SkoglundKarolinska InstitutetMedical Nobel InstituteStockholm, SwedenProf. Nicolas Boisset † , Dr. Eric LarquetCentre National de la Recherche Scientifique (CNRS)Paris, FranceProf. Arie VerkleijUniversity of UtrechtFaculty of BiologyUtrecht, The NetherlandsFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life173

GeneFunProject Type:Specific TargetedResearch projectContract number:LSHG-CT-2004-503567Starting date:1 st March 2004Duration:52 monthsEC Funding:1 500 000State-of-the-Art:Deciphering the information on genome sequences in terms of the biological function of genesand proteins is a major challenge of the post-genomic era. Most function assignments for newlysequenced genomes are performed using bioinformatics tools that infer the function of agene on the basis of sequence similarity with other genes of known function. This approach is,however, error-prone. Continuing to use it without clearly defining the limits of its applicabilitywould lead to an unmanageable propagation of errors. On the other hand, various novelbodies of data are being generated. These provide information on the physical and functionalinteractions between genes and proteins, and on whole networks and processes. In parallel,structural genomics efforts are providing much better coverage of proteins structures and interactions.This novel data offers an unprecedented opportunity for incorporating higher-levelfunctional features into the annotation pipeline, and the GeneFun project addressed theseimportant aspects. To limit error propagation, criteria will be developed for evaluating the reliabilityof the annotations currently available in databases, and derived reliability scores willbe incorporated into standard annotation pipelines. To incorporate higher-level features intofunctional annotations, the project will combine sequence and structure information in orderto identify non-linear functional features (eg. interaction sites), and will also integrate availableand newly developed methods for inferring function from information on protein domainarchitecture, protein-protein interaction, genomic context, etc.Scientific/Technological Objectives:The main objective of the GeneFun project is to develop improved methods for reliably assigningfunction to genes. To that end it will pursue the following specific scientific and technicalobjectives: (1) Quantifying error rates (error baseline) for classical sequence similarity-basedfunctional annotations from the analysis of meaningful descriptions of protein families andsub-families, and functional annotations currently available; (2) Developing automatic proceduresfor deriving detailed functional descriptors for individual protein families by mappingsequence family information onto the experimental or modelled 3D structure, then usingthis information to improve functional annotation from sequence; (3) Combining objective 1and objective 2, in order to enable more efficient and reliable prediction of function fromsequence; (4) Exploiting information on domain architecture to infer context-based functionalproperties, including domain and protein interactions; (5) Developing new methods foridentifying protein-protein interactions by combining information on sequence families, 3Dstructure, domain and genome architecture; (6) Benchmarking existing and newly developedmethods for the prediction of interactions, which use context-based approaches, combineinformation on sequences families and 3D structure, and analyse various data sets on proteinproteininteractions (obtained through experiments and automatic analyses of published literature);(7) Integrating sequence similarity-based and context-based prediction methods, andapplying them to verify and improve available annotations of eukaryotic genes and to inferfunction for the still important number of non-annotated regions of these genes; (8) Performingexperimental validation of the predicted function and other related features, for a selectedset of proteins of strategic importance for evaluating the performance of the various functionprediction algorithms. Methods and data produced in this project will be made available tothe scientific community through the Internet. This will include a web server for assessing homology-basedannotation reliability, a downloadable protocol for performing the assessment,and a comprehensive set of protein family trees with structure-annotated functional groups.Other tools will include an automated system for predicting enzyme function, sites for specifichigh affinity recognition, and interaction partners for peptide-binding modules.Expected Results:www.genefun.orgThe expected results of the GeneFun project are as follows: (1) improved procedures forinferring function on the basis of sequence similarity; (2) a set of procedures for predicting174From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Prediction of gene functionnon-linear functional features from sequence and 3D structure in a more automated way; (3)benchmarked procedures for predicting context-based functional features. Major efforts willbe devoted to devising protocols that optimally combine the results from several methods.In particular, web-based servers for the individual and combined procedures will be developedand made available to the scientific community. The community will be introduced tothese new tools through open workshops and training sessions.Potential Impact:The developed function prediction methods should make a significant contribution towardsimproving the in silico annotation of gene function, and thereby have an important impacton the entire life-science sector, which heavily depends on these annotations.Keywords: Function prediction, protein structure, protein-protein interactions,interaction networks, structural genomicsPartnersProject Coordinator:Prof. Shoshana WodakUniversité Libre de BruxellesService de Conformation deMacromoleculesBiolgiques et BioinformatiqueBiologie MoleculaireAvenue F Roosevelt CP 194/6B-1050 Brussels, Belgiumshoshana.wodak@rogers.comDr. Alfonso ValenciaCentro Nacional de InvestigacionesOncologicasMadrid, SpainDr. Arne ElofssonStockholm UniversityStockholm Bioinformatics CenterStockholm, SwedenProf. Cheryl ArrowsmithOntario Cancer InstituteUniversity Health NetworkToronto, CanadaDr. Christian BlaschkeAlma Bioinformatics SlMadrid, SpainProf. Luis SerranoCenter for Genomic Regulation (CRG)Systems Biology LaboratoryBarcelona, SpainProf Peer BorkEuropean Molecular Biology Laboratory (EMBL)Heidelberg OutstationHeidelberg, GermanyDr. Chen Ceasar. Prof. Daniel FischerBen-Gurion UniversityDepartment of Computer ScienceBeer Sheva, IsraelDr. Leszek RychlewskiBioInfoBank InstitutePoznan, PolandFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life175

E-MePwww.e-mep.orgProject Type:Integrated ProjectContract number:LSHG-CT-2004-504601Starting date:1 st May 2004Duration:60 monthsEC Funding:10 347 066State-of-the-Art:E-MeP’s research platform focuses on developing and implementing new technologies tosolve the bottlenecks that preclude the determination, at high throughput, of high-resolutionstructures of membrane proteins and membrane protein complexes. This has been achievedby integrating the activities of many of the world leaders in membrane protein structuralbiology. The E-MeP consortium focuses on developing methods and exchanges laboratoryand in silico tools, with the aim of solving the structures of membrane proteins, which comprisemore than 30% of known proteomes.Specifically, the heterologous production, purification and crystallisation of a library ofbioinformatically-selected membrane proteins are being streamlined by elucidating the parametersresponsible for success and failure at each of these key stages. In the process, newtechnologies are being developed and commercialised, to overcome existing bottleneckspeculiar to membrane protein structural genomics, which cannot be solved using existingmethods. A mobilisation of European expertise to address this timely issue, will ultimatelycontribute to understanding membrane protein-related human diseases.Scientific/Technological Objectives:E-MeP has several scientific objectives, including the following: tainingmilligram quantities; pertinent data.Crystal Structure of a DivalentMetal Ion Transporter CorA at 2.9Angstrom Resolution.176From Fundamental Genomics to Systems Biology: Understanding the Book of Life

The European MembraneProtein ConsortiumThere are also several specific technological objectives, namely: structural genomics platform. Overall, the aim is to build a European Membrane ProteinStructural Genomics Research Area.Expected Results:The resolution of membrane protein (MP) structures is important for health. The findings ofE-MeP will contribute to scientific communities’ understanding of key biological processes,and will also serve as templates for structure-based drug design.Potential Impact:An increase in the number of membrane protein (MP) structures will help to understand manybasic phenomena underlying the cellular functions essential to human health, and may leadStructure of a LTC4 synthase;2.15 Å. Published in Nature,2007, 448: 613-616From Fundamental Genomics to Systems Biology: Understanding the Book of Life177

E-MePdirectly to products with both societal impact and commercial value. E-MeP will contributeto important social requirements related to health, because structural genomics, togetherwith functional genomics, transcriptomics and proteomics, will open up new routes to fightdisease and will explore new dimensions in biotechnology and bio-nanotechnology.Keywords:membrane proteins, protein production, X-ray crystallography, structure determination, 3Dstructure, structural genomicsPartnersProject Coordinator:Dr. Roslyn BillAston UniversityDepartment of Life and Health SciencesAston TriangleBirmingham B4 7ET, UKr.m.bill@aston.ac.ukProject Manager:Eric BourguignonAston UniversityDepartment of Life and Health SciencesAston TriangleBirmingham, BA 7ET, UKe.bourguignon@aston.ac.ukProf. So Iwata, Prof. Naomi ChayenImperial College of Science, Technology and MedicineDivision of Molecular Biosciencesand Division of Biomedical Sciences –Biological Structure and Function SectionLondon, UKProf. Peter Henderson, Prof. John FindlayThe University of LeedsAstbury Centre for Structural – Molecular Biologyand Faculty of Biological SciencesInstitute of Membrane and Systems BiologyLeeds, UKSir John Walker, Dr. Edmund R. S. KunjiMedical Research CouncilDunn Human Nutrition UnitCambridge, UKDr. Franc PattusCentre Européen de Recherche en Biologieet Médicine (CERBM)Groupement d’intérêt économiqueIllkirch, France178From Fundamental Genomics to Systems Biology: Understanding the Book of Life

The European Membrane Protein ConsortiumProf. Christian CambillauUniversité de la MediterranéeArchitecture et Fonctiondes Macromolecules Biologiques,UMR 6098, CNRS-Université Aix-Marseille I & IIMarseille, FranceDr. Etienne L’HermiteBioXtal SAMundolsheim, FranceProf. Hartmut MichelMax-Planck-Institut für BiophysikMolecular Membrane BiologyFrankfurt am Main, GermanyProf. Lars-Oliver EssenPhillipps-Universität MarburgDepartment of ChemistryMarburg, GermanyProf. Pär NordlundKarolinska InstituteMedical Biochemistry and BiophysicsStockholm, SwedenProf. Richard NeutzeGothenburg UniversityDepartment of ChemistryBiochemistry & BiophysicsGothenburg, SwedenProf. Richard CogdellUniversity of GlasgowInstitute of Biomedical & Life Sciences -Division of Biochemistry & Molecular BiologyGlasgow, UKProf. Paula BoothUniversity of BristolDepartment of BiochemistryBristol, UKDr. Nicolas Le NovèreEuropean Molecular Biology Laboratory (EMBL)European Bioinformatics Institute (EBI)Hinxton, UKProf. Horst VogelEcole Polytechnique Fédérale de LausanneLaboratoire de Chimie Physique des Polymèreset Membranes (LCPPM)Institut des Sciences et Ingénierie Chimiques (ISIC)Lausanne, SwitzerlandProf. Arnold Driessen, Prof. Bert PoolmanUniversity of GroningenGroningen Biomolecular Sciences andBiotechnology InstituteKerklaan, The NetherlandsProf. Rainer RudolphMartin-Luther-Universität Halle-WittenbergInstitut fur BiotechnologieHalle, GermanyProf. Wim de GripStichting Katolieke UniversiteitUniversity Medical Centre NijmegenNijmegen, The NetherlandsFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life179

Project Type:Specific TargetedResearch projectContract number:LSHG-CT-2004-503455Starting date:1 st July 2004Duration:51 monthsEC Funding:2 400 000FSG-V-RNAwww.fsgvrna.nmr.ru.nlState-of-the-Art:We will develop and improve tools and approaches to facilitate the generation of newknowledge in functional and structural genomics of viral RNAs. The project exploits availableRNA sequence data but will also expand our knowledge of viral RNA sequence elementsand their variations.The biomedical importance of RNA as a research target is stressed by the fact that viralinfections are global public health problems. The outcomes of the project can initiate the developmentof novel drugs that target viral RNA molecules and thus have strong implicationsfor public health. The innovative tools developed will open the way for efficient analysis ofa wide range of RNA-based processes extending far beyond the analysis of viral RNAs.Scientific/Technological Objectives:RNA is a central molecule in all living organisms. They can adopt a wide variety of conformationsranging from single-stranded to complex tertiary structures tightly associated withtheir functions. To understand the function of RNAs, and to act on these functions with smallmolecules, it is essential to expand our knowledge of the structure of these molecules and oftheir interactions. A multidisciplinary research approach is taken in the project to addressthis need, by integrating the research facilities of a number of leading European labs aswell as an SME.The main objectives of the consortium are:1. to develop new methods and tools for rapid and efficient structure determination of (large)RNA and (large) RNA-protein complexes and RNA ligand screening, including:a) new and streamlined methods for site-specific and segmental 2H, 13C, 15N isotopelabelling of RNAs via in-vitro and/or in-vivo methodsb) to establish, experimentally and theoretically, chemical shift-structure relationships(CSRs) for 1H, 13C, 15N, 31P of RNAsc) to implement these (CSRs) and other easily accessible NMR parameters, such asRDCs and CSAs, in efficient NMR structure calculation protocolsd) to implement scanning probe microscopy (SPM) tools for morphology and interactions.2. to apply these methods on key viral RNA targets (from HBV, HCV and HIV), which arecurrently considered major public health threats. The efforts will be three-fold:a) characterise the RNA sequences involvedb) perform structural analysis on key RNA elements and/or reconstituted viral RNA andRNA-protein assemblies either by NMR or SPM for the larger objectsc) produce and identify new antiviral compounds (small molecules, siRNA, modifiedoligonucleotides) capable of binding these RNAs. These compounds could providethe basis for developing new viral agents.Expected Results:Novel tools will be developed and implemented, which will provide improved methods forstructural analysis of RNA and RNA-protein complexes. The molecular details obtained byapplying these tools to viral and other important RNA molecules will provide a basis forthe identification and screening of small molecule inhibitors that target key RNA structures.The unique combination of technological platforms available within the consortium willadd new fundamental knowledge on HCV translation and HBV replication by generatingnovel three-dimensional data on the corresponding RNAs and RNA-protein complexes. Thiswill provide an opportunity to correlate RNA 3D structure with function, and to make theHCV, HBV and HIV RNA elements and their protein complexes new targets for the rationaldesign of drug leads. The results of the project will allow a comparative analysis of smallcompounds targeting viral RNA elements and antiviral RNAs.180From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Functional and Structural Genomicsof Viral RNAPotential Impact:New and optimised research tools for the structure/function analysis of RNA and RNAbasedprocesses will be generated. The potential of these tools in correlating structure andfunction of RNA molecules and the identification of inhibitors will enhance basic researchon RNA splicing, translation and the recently discovered essential mechanisms for the posttranscriptionalregulation of gene expression that involve non-coding RNAs. These tools arealso expected to enhance our understanding of viral RNAs significantly and to further thedevelopment of new antiviral drugs. The consortium allows the setting up a multidisciplinaryresearch-project that addresses biomedical questions in a unique way that extends beyondcurrent research programmes.Keywords: labelling, synthesis, NMR, screening, function, RNA structure, genomics,RNA viruses, RNA, RNAi, HBV, HIV, HCVPartnersProject Coordinator:Prof. Sybren WijmengaRadboud University NijmegenIMM/Faculty of ScienceMathematics and InformaticsToemooiveld 16525 ED Nijmegen, The Netherlandss.wijmenga@science.ru.nlProject Manager:Susanna BicknellRadboud University NijmegenFaculty of ScienceFinance and Economic AffairsS.Bicknell@science.ru.nlProf. Dr. Michael SattlerHelmholtz Zentrum MünchenGerman Research Centerfor Environmental HealthAnd Lehrstuhl BiomolekulareNMR-SpektroskopieDepartment ChemieTechnische Universität MünchenGarching, GermanyProf. Frédéric DardelCentre National de la RechercheScientifique (CNRS)Laboratory of Crystallography andBiological NMRParis, FranceProf. Vladimir SklenarMasaryk UniversityNational Center for Biomolecular ResearchBrno, Czech RepublicProf. Michael NassalUniversitätsklinikum FreiburgDepartment of Internal MedicineLaboratory of Molecular BiologyUniversity Hospital FreiburgFreiburg, GermanyDr. Karin Kidd-LjunggrenLund UniversityDepartment of Medical Microbiology,Dermatology and Infectious DiseasesLund, SwedenDr. Richard BlaauwChiralix B.V.Nijmegen, The NetherlandsFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life181

VIZIERwww.vizier-europe.orgProject Type:Integrated ProjectContract number:LSHG-CT-2004-511960Starting date:1 st November 2004Duration:48 monthsEC Funding:12 905 986State-of-the-Art:This project aims to have a significant impact on the identification of potential new drugtargets against RNA viruses through comprehensive structural characterisation of a diverseset of viruses. RNA viruses include more than 350 different major human pathogens andmost of the etiological agents of emerging diseases: viruses of gastroenteritis (1 milliondeaths annually), measles (45 million cases and 0.6 million deaths annually), influenza(100 million cases annually), dengue fever (300 million cases annually), enteroviruses andencephalitis (several million cases of meningitis annually), and hepatitis C virus (170 millioninfected people in the world).The SARS outbreak has dramatically demonstrated how high the economic cost of an epidemiccaused by an emerging virus could be. This possibility is growing every day asmany governments are being forced to make costly arrangements to cope with the threat ofbio-terrorism, which lists some deadly RNA viruses in its arsenal. To meet these challenges,science needs to look for new therapeutic and prophylactic substances active against RNAviruses since those currently available are scarce and of low potency. The common strategiesused for the development of antiviral drugs are mainly based on the knowledge accumulatedthrough studies of virus genetics and structure. Yet, genomic and structural characterisationof RNA viruses was not accepted as a priority until very recently. The VIZIERproject proposes to fill the existing gap between the necessary scientific characterisation ofemerging viruses and pre-clinical drug design.Crystal structure of the 3Cproteinase of coxsackievirus B3Scientific/Technological Objectives:To address society’s needs, scientists need to anticipate potential threats and be readyshould they arise. The participants of the VIZIER project have created a team that bringstogether the leading authorities on RNA viruses in the EU and other countries as well asmany leading European structural biologists. This team includes three partners with P4facilities, as well as leaders in the field of structural genomics. The development of protocolsfor high-throughput (HTP) protein production means that a concerted programme ofstructure determination is now appropriate and feasible. The VIZIER consortium will characteriseRNA viruses that do not include a DNA stage in their replicative cycle. These virusclasses employ profoundly different replicative mechanisms driven by poorly characterisedreplication machineries. Although virus-specific, they are the most conserved and essentialviral components and thus the most attractive targets for antiviral therapy. In the frameworkof this project the core enzymes/proteins of the replication machinery, carefully selectedamong 300 different RNA viruses, including strains of medical interest, will be characterised.One unique feature of VIZIER, compared to other structural genomics projects, is theintegration of major structural effort within a broad multidisciplinary study, having virologyupstream and target validation (candidate drug design) downstream. As a result, the implementationplan of the VIZIER project is structured into five interacting scientific sections:(1) bioinformatics, for genome annotation, target selection and data integration (2) virusproduction and genome sequencing (3) HTP protein production (4) HTP crystallisation andstructural determination (5) target validation to assess the function of enzymes and designstrategies for virus inhibition (6) training, implementation and dissemination. This organisationwill allow in record time the full characterisation of a viral target that can quickly beused to design drugs, either by the pharmaceutical industry through the VIZIER industrialplatform or by any research and development institution.182From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Comparative structural genomicson viral enzymes involved in replicationExpected Results:VIZIER will produce an unprecedented wealth of data on replicases of RNA viruses with awindow into the antiviral drug development. A representative set of RNA-based viruses thatbelong to three major classes which are profoundly different in their replicative strategies,will be characterised by a concerted and multidisciplinary effort unparalleled to date. Atthe end of this programme, the percentage of sequenced genomes of RNA virus species thatinfect vertebrates will virtually double from 30% to 55%. As a case example, the genomiccharacterisation of Flavivirus (ssRNA+) and Arenavirus (ssRNA-) genera, which include alarge number of human pathogens, will be systematically executed. A dramatic advanceis expected in the number and diversity of 3D structures of the replicative subunits, nowin the one-digit range. VIZIER will aim to identify lead molecules inhibiting the replicativeenzymes, but will not enter into the broad field of drug development. Offers of cooperationwill be made on a contractual basis to the pharmaceutical and biotechnology industriesfor further drug development, and through the VIZIER industrial platform, which connectsupfront scientific results to the pharmaceutical industry.Potential Impact:With no equivalent integrated programme in the world, the VIZIER project will undoubtedlyhave a profound impact on the field of structural genomics of emerging viruses. Inparticular, it is expected that VIZIER will contribute very significantly to the sequencing ofnew viruses (viral genomics) as well as to the deposition of new crystal structures of viralproteins in the Protein Data Bank. These viral proteins can then be considered as targets fordrug design. There is expected to be considerable scientific impact on drug design throughconcepts and methods implemented up to the design stage. Indeed, current drug discoverystill often relies on screening compounds in a blind manner. Thousands or millions ofcompounds are screened on infected cells or purified enzymes, and ‘hits’ are selected. Thisis followed by confirmation of the inhibitor activity and basic toxicology studies, which isa frequently tedious and uncertain phase for a project. It is widely believed that structuralbiology is capable of speeding up the whole process. HTP crystallography, coupled witha strong validation section such as that proposed in VIZIER, will undoubtedly reinforce thistrend by leading the field. Indeed, the concept of finding a drug and its target together withthe putative bottlenecks in further improvement can prove to be scientifically challenging,innovative, and promising.VIZIER will develop new products, technologies and strategies. The products are RNA virusgenomic sequences, soluble viral protein domains, their 3D structures, assigned proteinfunctions, and inhibitors or ligands for selected protein targets (drug leads). All these productswill have a substantial impact on our (currently limited) understanding of the RNA viralreplication machinery. They will also identify entirely new targets for the development ofspecific drugs, with a high level of detail. Collectively such information is seen as being ofstrong strategic value, not only for the health issues described, but also for the developmentof industrial enterprises. Although diverse DNA-based cellular and viral parasites are alsoresponsible for a large fraction of human infections, none of them are so poorly controlledby drugs as the RNA viruses. Consequently, drug development against RNA viruses, theultimate goal of the VIZIER project, is becoming a top priority for global health-care programmes.From Fundamental Genomics to Systems Biology: Understanding the Book of Life183

VIZIERKeywords: RNA viruses, genomics, structural genomics, antiviral drugs, crystalstructure, bioinformatics, protein production, high-throughput,screening3D StructureDrug-designPartnersProject Coordinator:Dr. Bruno CanardUniversité de la MéditerranéeCentre National de la Recherche Scientifique (CNRS)Laboratoire Architecture et Fonction desMacromolecules Biologiques UMR 6098Marseille, Francebruno.canard@afmb.univ-mrs.frDr. Andrei M LeontovichMoscow State UniversityA N Belozersky Institute of Physico-Chemical BiologyDepartment of Mathematical Methods in BiologyGenebee GroupMoscow, RussiaProf. Miguel CollConsejo Superior De Investigaciones CientificasInstituto De Biologia Molecular De BarcelonaMadrid, SpainProf. Johan NeytsKatholieke Unversiteit LeuvenDepartment of Microbiology and ImmunologyDivision of Virology and ChemotherapyLeuven, BelgiumDr. Etienne L’HermiteBioXtal SAMundolsheim, France184From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Comparative structural genomics on viral enzymes involved in replicationDr. Paul TuckerEuropean Molecular Biology Laboratory (EMBL)Hamburg OutstationHamburg, GermanyDr. Segolene ArnouxAlma Consulting Group SasInnovation DepartmentHoulbec Cocherel, FranceDr. Herve BourhyInstitut PasteurLaboratoire de la RageParis, FranceDr. Gerard Bricogne,Global Phasing LtdCambridge, UKProf. Dave StuartUniversity of OxfordWellcome Trust Centre for Human GeneticsDivision of Structural BiologyOxford, UKProf. Martino BolognesiNational Institute for the Physics of Matter - GenovaUdr GenovaGenoa, ItalyProf. Andrea MatteviUniversity of PaviaDepartment of Genetics and MicrobiologyLaboratory of BiocrystallographyPavia, ItalyProf. Alwyn T. JonesUppsala UniversitetUppsala, SwedenDr. Alexander GorbalenyaLeiden University Medical CenterDepartment of Medical MicrobiologyLeiden, The NetherlandsDr. Boris KlempaSlovak Academy of SciencesInstitute Of ZoologyBratislava, SlovakiaDr. Jacques RohayemTechnische Universität DresdenInstitut für Virologie - The Calcilab Medical FacultyCarl Gustav CarusDresden, GermanyProf. Rolf HilgenfeldUniversität LübeckInstitute of BiochemistryLübeck, GermanyProf. Paolo La CollaUniversità Degli Studi di CagliariDipartimento di Scienze E Tecnologie BiomedicheCagliari, ItalyProf. Par NordlundStockholm UniversityDepartment of Biochemistry and BiophysicsStockholm, SwedenDr. Eric Leroy, Dr. Jean Paul GonzalesInstitut de recherche pour le développementParis, FranceDr. Stephan GüntherBernhard-Nocht-Institute (BNI)Centers for Disease Control and PreventionHamburg, GermanyDr. Gerhard PuerstingerUniversität InnsbruckInnrain 52aInstitut für PharmazieInnsbruck, AustriaProf. Ernest GouldNatural Environment Research CouncilCEH OxfordPolaris HouseSwindon, UKDr. Helene NorderSwedish Institute for Infectious Disease ControlVirological Department, Hepatitis SectionSolna, SwedenFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life185

UPMANhttp://schwalbe.org.chemie.uni-frankfurt.de/upmanProject Type:Specific TargetedResearch projectContract number:LSHG-CT-2004-512052Starting date:1 st November 2004Duration:42 monthsEC Funding:1 900 000State-of-the-Art:To gain biological function, polypeptide chains generally need to fold into specific 3Dstructures – their native states. Aberrant folding of proteins can lead to a range of otherscenarios, including the development of highly organised and intractable aggregates thatare deposited inside or outside cells. Such misfolding events are at the origins of a rangeof neurological and systemic diseases that increasingly compromise the quality and expectancyof life and the health resources of advanced societies. The focus of this applicationis the development of novel methods to study the structural states of proteins that areparticularly relevant to understanding protein misfolding and aggregation. In most of thesestates, polypeptide chains acquire structures that differ substantially from those of the nativeproteins, which are accessible from conventional approaches of structural biology or fromstructural genomics procedures.Scientific/Technological Objectives:In this STREP, a range of complementary NMR approaches will be developed. These approachesinclude a variety of NMR techniques, which will be coupled with novel computationalapproaches able to define even the disorganised ensembles characteristic of some ofthe most interesting and biologically relevant species. These techniques will then be appliedto representative examples of the various types of proteins that are associated with misfoldingdiseases. These range from native unfolded species (such as a-synuclein associated withParkinson’s disease) and partially unfolded intermediates (such as forms of superoxide dismutaseassociated with motor neuron disease), to the precursors of aggregation prone fragments(such as the Alzheimer precursor protein) and the prion proteins, which are uniquelyassociated with transmissible conditions. One of the major aims of this project is to providea novel unified view of the conformational behaviour of protein molecules, which will havea broad significance for understanding important aspects of functional genomics, includingthe fundamental links between genetic mutations and disease, and the mechanisms bywhich normally soluble proteins can sporadically misfold, giving rise to a wide range ofdisorders associated with diet, medical and agricultural practices and ageing.NMR is able to provide both dynamic and structural information about proteins in a varietyof different states at atomic resolution. It has the potential for probing residual structure, thesize of aggregating molecules and variation in the internal dynamical properties based ondiffusion-weighted NMR spectroscopy, heteronuclear relaxation measurements, paramagneticenhancement of relaxation induced by paramagnetic spin labels, and residual dipolarcouplings.Expected Results:Fundamental Research, Structural Studies:1) Structure of protein-folding intermediates2) Time course of the folding process3) Structure of protein aggregates4) New technologies to characterise protein folding and aggregation at atomic resolution5) Common factors underlying the development of protein-folding diseases.Potential Impact:By generating structural information about prefibrillar states that are currently assumed to bethe most toxic states of protein folding diseases, this STREP research project would help todevelop pharmaceutical products against some of the most debilitating conditions in mod-186From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Understanding Protein Misfoldingand Aggregation by NMRern society. However, in contrast to many other major diseases, thefundamental mechanism of protein misfolding and aggregation isless well studied. Therefore, studies aiming at providing a structuralbasis for protein misfolding and aggregation are not only at theforefront of innovative research but are also important assets for theLife Science and Health priority area of the European Commission.Keywords: mutation genetics, protein depositiondisorders, molecular evolutionPartnersProject Coordinator:Prof. Harald SchwalbeJohann Wolfgang Goethe-UniversitätCenter for Biomolecular Magnetic ResonanceInstitute for Organic Chemistry and Chemical BiologyMarie-Curie-Atr. 1160439 Frankfurt am Main, Germanyschwalbe@nmr.uni-frankfurt.deProf. Lucia BanciUniversity of FlorencePolo ScientificoCentro Risonanze Magnetiche (CERM)Sesto Fiorentino, ItalyProf. Rolf BoelensUtrecht UniversityBijvoet Center for Biomolecular ResearchNMR Spectroscopy Research GroupUtrecht, The NetherlandsProf. Chris DobsonUniversity of CambridgeThe University Chemical LaboratoryCambridge, UKProf. Astrid GräslundStockholm UniversityThe Arrhenius Laboratories for Natural SciencesDepartment of Biochemistry and BiophysicsStockholm, SwedenProf. Flemming Martin PoulsenUniversity of CopenhagenDepartment of Molecular BiologyStructural Biologyand NMR LaboratoryCopenhagen, DenmarkDr. Ago SamosonNational Institute of ChemicalPhysics and BiophysicsTallinn, EstoniaProf. Kurt WüthrichETH ZurichInstitute of MolecularBiology and BiophysicsZurich, SwitzerlandDr. Jesús ZurdoZyentia LtdBabraham Research CampusCambridge, UKThe different states a proteinmolecule can attainFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life187

NDDPwww.projects.bijvoet-center.nl/nddpProject Type:Specific TargetedResearch ProjectContract number:LSHG-CT-2004-512077Starting date:1 st November 2004Duration:42 monthsEC Funding:1 000 000State-of-the-Art:The instruments for drug discovery include high-throughput synthesis and subsequent screening,biological assays, molecular biology, computational modelling, electron microscopy,X-ray crystallography, and NMR spectroscopy. Only NMR and X-ray diffraction providehigh-resolution information about the protein-ligand interactions at atomic resolution.While the technology for high-throughput X-ray crystallography of protein-ligand complexeshas been optimised such that it is now routinely used in all major pharmaceutical companies,this is not the case for NMR spectroscopy, despite its tremendous potential, relativeto and complementary to X-ray crystallography. NMR can provide both structural and dynamicinformation on the protein-ligand complex at atomic resolution, information that ishighly desirable for efficient drug design. Potentially, NMR can provide such informationvery rapidly and without the constraints of co-crystallization.Scientific/Technological Objectives:This structure-based drug design will use cutting-edge nuclear magnetic resonance (NMR)techniques. The NDDP project will speed up drug design efforts for typical drug targets andwill shorten the lead time for new drugs.Fast, reliable and robust NMR techniques will be developed by the team, for an exactstructural and dynamic characterisation of drug-receptor interactions at atomic resolution,thus enabling and/or improving the directed development of drugs by demonstrating themaximum desired interaction characteristics in a relatively short time.Protocols for obtaining the NMR parameters needed for the characterisation of proteins,inhibitors and protein-inhibitor complexes will be developed, starting from known X-raystructures. These parameters will establish a tight connection between NMR and X-ray technology,enabling the optimal exploitationof the complementary strengths of the twotechniques.The NMR technologies to bedeveloped will be complemented by new,fast computer modelling approaches forprotein-inhibitor complexes, and also byspecific advanced tailored protein expressionmethods.Schematic project presentation.The NDDP project aims to developan efficient screening protocolusing high-field NMR andadvanced modelling techniquesthat allows to dock lead targetsto pharmaceutical receptors suchas phosphatases.X-ray structures of unknown phosphataseswill be determined, and these structures willbe used as molecular models to provide ahighly detailed picture of the proteins inquestion. Knowing the X-ray structure of theprotein target, the NDDP consortium willbe able to provide a streamlined protocolfor the rapid identification of its protein-ligandcomplexes. Such a protocol will boostthe impact of NMR technology on structurebaseddrug discovery. It is the intention ofthis consortium to provide the means to determineprotein-ligand complexes, with aturnaround of three structures per high-fieldinstrument per week.188From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Expected Results:In order to show the potential impact of NMR techniques on drug development, NMR protocolswill be developed and tested using phosphatases, a major class of drug targets fora broad range of medical indications. The majority of cellular functions depend on phosphorylationby kinases and dephosphorylation by phosphatases. High eukaryotes encodeapproximately 500 protein kinase and 100 protein phosphatase schemes, correspondingto three percent of their genome. While the importance of kinases in cellular regulation hasled to substantial drug design activities, the importance of phosphatases has only recentlybecome appreciated.Potential Impact:NMR Tools for Drug DesignValidated on PhosphatasesProtein phosphatases regulate insulin signalling, cell growth and the cell cycle. The inhibitionof phosphatases is therefore relevant NDDP to the treatment of diabetes, obesity andvarious types of cancer, for instance. The availability of the human genome provides researcherswith access to a wide variety of phosphatases, and allows systematic drug designusing sophisticated techniques to identify potential inhibitors.Keywords: NMR spectroscopy, phosphatases, drug design, structural genomicsPartnersProject Coordinator:Prof. Rolf BoelensUtrecht UniversityBijvoet Center for Biomolecular ResearchFaculty of SciencesHeidelberglaan 83584 CS Utrecht, The Netherlandsr.boelens@uu.nlProf. Harald SchwalbeJohann Wolfgang Goethe-UniversitätCenter for Biomolecular Magnetic ResonanceInstitute for Organic Chemistry andChemical BiologyFrankfurt am Main, GermanyProf. Ivano BertiniConsorzio Interuniversitario di Risonanze Magnetichedi Metalloproteine ParamagneticheMagnetic Resonance Centre (CERM)Sesto Fiorentino, ItalyProf. David BarfordInstitute of Cancer Research Section ofStructural BiologyChester Beatty LaboratoriesLondon, UKProf. Egon OgrisUniversity of ViennaDepartment of Medical BiochemistryVienna, AustriaDr. Wolfgang StirnerSynthacon GmbHFrankfurt am Main, GermanyFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life189

3D repertoirewww.3drepertoire.orgProject Type:Integrated ProjectContract number:LSHG-CT-2005-512028Starting date:1 st February 2005Duration:54 monthsEC Funding:12 997 641State-of-the-Art:The major current initiatives in structural biology can be divided into two general types. Researchersare channelling their efforts into structural genomics, with the aim of determiningstructures for all individual protein structures in an organism or system. At the same time,efforts have been intensified to obtain structures of individual large complexes. Despite allthe efforts that have been made, an initiative aimed at the structural resolution of all proteincomplexes in a living organism, has not yet been formulated. Such an initiative, if combinedwith other EU-oriented initiatives such as BIO-XHIT or SPINE, would give Europe the edge overall non-European competitors.Recent proteomics studies with the budding yeast Saccharomyces cerevisiae have indicatedthat the number of complexes that exist, transiently at least, in a cell, has been largely underestimated.The techniques of isolation and purification that are traditionally used in biochemistryoften include many steps, and due to this, the most robust and abundant complexes tend to beselected. This is especially true as many complexes are transient, occurring, for example, onlyduring a certain stage of the cell cycle, or in the presence of a specific co-factor, such as GTP,calcium or phosphorylated subunits. More recent technologies, including the Tandem AffinityPurification (TAP), which has been developed at the EMBL and commercialised by the Europeancompany Cellzome, allow purification of weaker complexes. There are also a numberof means to identify both new components of complexes, or entirely new assemblies, throughthe use of other sources of protein interaction data (experimental and in silico). Such methodsare currently being developed by members of the consortium project 3D Repertoire.Large-scale proteomic approaches suggest that single proteins interact, on average, withseven other proteins. Even if this is an overestimation, it is clear that many more complex structuresare needed, in order to complete the structural view of the cell. Analysis of proteins in thecontext of complexes has the advantage of revealing new protein folds, to help complete theknown repertoire in nature, as well as adding to the set of protein-protein interaction surfaces.The latter advantage cannot emerge from an analysis of single proteins or domains. The aimof 3D-Repertoire is to determine the structures of all amenable complexes in a cell at mediumor high resolution, which will later serve to integrate toponomic and dynamic analyses ofprotein complexes in a cell.Scientific/Technological Objectives:3D Repertoire will develop novel approaches and technologies for the expression andisolation of protein complexes, as well as for the analysis of their constituents by massspectrometry. New methods for the production of yeast protein complexes will be testedand validated, to become part of the standard technology for the production of proteincomplexes from any source of biochemical characterisation and structural analysis. In particular,3D-Repertoire will focus on the development of combined Free Flow Electrophoresis(FFE) separation techniques, specifically for the separation of protein complexes, and on thedevelopment and production of a prototype instrument. The performance of the prototypeinstrumentand the underlying separation techniques will be tested in the case of the enrichmentand isolation of complexes of interest. 3D-Repertoire will develop new tools for fasterand more accurate image processing in single particle electron cryomicroscopy, whichshould help to speed up 3D structure determination at increasingly higher resolution.190From Fundamental Genomics to Systems Biology: Understanding the Book of Life

A Multidisciplinary Approachto Determine the Structures of ProteinComplexes in a Model OrganismThe instrumentation of electron microscopes will be improved to allow for automated datacollection. Improved sample preparation techniques will also be developed to make eventhe most difficult complexes accessible to structural studies by cryo-EM. Furthermore, 3DRepertoire will develop X-ray crystallography and electron microscopy technologies, particularlysuited for the structural analysis of large macromolecular assemblies. In particular,automated crystal screening procedures to detect optimally diffracting crystals and to improveinitial crystal diffraction by systematically applying shrinking, annealing or derivatisationprotocols will be developed.Moreover, major technological advances are expected in the automation of single-particleelectron microscopy data collection, which will considerably speed up data acquisition.Special emphasis will be placed on the development of technologies at the interface betweenX-ray crystallography and electron microscopy, where improved docking proceduresand validation of these fits are required, to allow such hybrid approaches to become standardprocedure in structural biology. In addition, the collaboration of a leading laboratoryin electron tomography will stimulate the development of new technologies suited to theanalysis of protein complexes within the cell. It will provide a unique platform for the subcellularlocalisation of protein complexes.Expected Results:The project’s deliverables include a series of high and medium resolution structures of theyeast complexes as well as improved protocols and vectors, for expression and purificationof large complexes. Furthermore, the partners aim to develop software to automaticallybuild protein complexes using structural information regarding the complex components, orrelated proteins as well as innovative software to automatically fit modelled complexes intolow resolution structures. Within the 3D Repertoire consortium, partners will create a databaseresource containing structural, functional and experimental information on all proteincomplexes of S. cerevisiae, as well as on homologues in other organisms. Finally, trainingin new protein expression, and purification and software technologies, will be provided toresearchers both within and outside the 3D-Repertoire consortium.Potential Impact:The era of post-genomic research is characterised by the necessity to develop high throughputprocedures, in order to exploit the vast amount of information generated by the largenumber of genome projects. This is of particular relevance for the health sector, where theeffective identification of functional protein-protein interactions in multiprotein complexes,e.g. in cell signalling, provides the basis for the development of novel diagnostics andtherapeutics. Recently, some 50 biologists and officials from government-funding agenciesmet at the NIH campus in Bethesda, Maryland, to explore the interdisciplinary science andorganisation of the emerging field of structural proteomics. This field aims to discover macromolecularcomplexes and characterise their three-dimensional structures and functionalmechanisms, in space and time.The goal of structural proteomics may appear daunting, but the consensus is that the predictableoutcome is well worth the effort invested, especially given the importance of molecularmachines and functional networks in biology and medicine. Identification of assembliesand transient complexes combined with their structural and functional characterisationThe RNA Polymerase III:protein purification andcomposition (left), negativelystained particles (middle)and cryo-EM structure (right).From Fundamental Genomics to Systems Biology: Understanding the Book of Life191

3D repertoirewill allow us to understand, control, design and change the functioning of larger biologicalsystems, and to contribute to drug target discovery, lead discovery, and lead optimisationfor treatment of human disease.To maintain Europe’s international competitiveness in this field, it is essential to promoteinterdisciplinary cooperation of the continent’s most innovative research centres. Europeplaying a leading role in the structure genomics field will also yield economic benefits, sincethe number of drugs developed or improved using 3D structures is growing every year. Inaddition, it will allow Europe to be well positioned for the next challenge in biology, namelythe quantitative understanding of the cell.3D Repertoire will contribute to rendering this task feasible, through the establishment ofsuitable technological platforms. The project’s main contribution comprises large data setsand material for protein complexes, which will be produced for biomedically relevant componentsof the cell.Keywords: protein complexes, 3D-electron microscopy, electron tomography,X-ray crystallography, structural genomics, yeast, bioinformaticsPartnersProject Coordinator:Prof. Luis SerranoCentre de Regulació Genòmica (CRG)Systems Biology LaboratoryDr. Aiguader 8808003 Barcelona, Spainluis.serrano@crg.esProject Manager:Dr. Michela BerteroCentre de Regulació Genòmica (CRG)Dr. Aiguader 8808003 Barcelona, Spainmichela.bertero@crg.esProf. Alfred Wittinghofer, Dr. Susanne EschenburgMax-Planck Institute for Molecular PhysiologyDortmund, GermanyProf. Wolfgang Baumeister, Dr. Stephan Nickel,Prof. Elena ContiMax-Planck Institute of BiochemistryAbteilung Molekulare StrukturbiologieMartinsried, GermanyDr. Holger StarkMax-Planck Institute for Biophysical ChemistryResearch Group 3D Electron Cryo-MicroscopyGoettingen, GermanyProf. Herman van TilbeurghInstitut de Biochimie et de BiophysiqueMoléculaire et Cellulaire (IBBMC)Centre National de la RechercheScientifique (CNRS) UMR8619Université Paris-SudOrsay, FranceProf. Bertrand SéraphinCentre National de la RechercheScientifique (CNRS)Center for Molecular GeneticsGif-sur-Yvette, FranceProf. Patrick CramerLudwig-Maximilians-Universität MünchenGene Center MunichDepartment of Chemistry and BiochemistryMunich, GermanyDr. Anastassis Perrakis, Dr. Titia SixmaNetherlands Cancer InstituteMolecular CarcinogenesisAmsterdam, The NetherlandsDr. Andrea MusacchioEuropean Institute of OncologyMilan, ItalyDr. Guillermo Montoya, Dr. Jeronimo BravoSpanish National Cancer Research CentreMadrid, Spain192From Fundamental Genomics to Systems Biology: Understanding the Book of Life

A Multidisciplinary Approach to Determine the Structuresof Protein Complexes in a Model OrganismProf. Helen SaibilBirkbeck College LondonDepartment of CrystallographyBloomsbury Centre for Structural BiologyLondon, UKProf. Jose L. CarrascosaCentro Nacional de BiotecnologiaMadrid, SpainProf. Miquel CollInstitute for Research in Biomedicine(IRB Barcelona)Barcelona, SpainProf. Hanah MargalitThe Hebrew UniversityFaculty of MedicineThe Institute of MicrobiologyJerusalem, IsraelProf. Carol RobinsonUniversity of CambridgeChurchill CollegeCambridge, UKDr. Matthias WilmannsEuropean MolecularBiology Laboratory (EMBL)Hamburg OustationHamburg, GermanyDr. Patrick AloyInstitute for Research inBiomedicineBarcelona, SpainDr. Andrzej DziembowskiWarsaw UniversityInstitute of Geneticsand BiotechnologyWarsaw, PolandDr. Michael SattlerHelmholtz Zentrum Muenchen (HMGU)Neuherberg, GermanyDr. Francisco BlancoCentro de Investigación Cooperativa en BiocienciasCICBioGUNEBilbao, SpainDr. Gordana ApicCambridge Cell Networks LtdSt. John’s Innovation CentreCambridge, UKDr. Hervé GinistyGTP TechnologyImmeuble BiostepLabège, FranceDr. Joan AymamiCrystax LtdBarcelona, SpainDr. Rob Russell, Dr. Elena Conti, Dr. Bettina Boettcher,Dr. Klaus Scheffzeck, Dr. Dietrich Suck, Dr. Peer Bork,Dr. Anne-Claude Gavin, Dr. Christoph MuellerEuropean MolecularBiology Laboratory (EMBL)Heidelberg OutstationHeidelberg, Germany(*Dr. Sattler moved to GSF as of 01/10/2007)Dr. Darren HartEuropean MolecularBiology Laboratory (EMBL)Grenoble OutstationGrenoble, FranceFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life193

FESPwww.ec-fesp.orgProject Type:Specific Support ActionContract number:LSSG-CT-2005-018750Starting date:1 st July 2005Duration:30 monthsEC Funding:300 000hAChe-FAS-IIState-of-the-Art:The main goal of the project is to perform a thorough assessment of the existing structuralgenomics (SG) and structural proteomics (SP) projects throughout the world. This will includethe assessment of the existing infrastructures in Europe relevant to SG and SP, andtheir comparison with those active in the rest of the world. The requirements, in terms ofthematic areas and infrastructures, will also be evaluated. This SSA will result in staged publications,a complete register of the structural genomics and structural proteomics projectsworldwide, and a position paper on strategic plans for a European policy in the area ofstructural genomics and proteomics.Scientific/Technological Objectives:The objectives are:1) an assessment of the existing infrastructures relevant to SG and SP projects in Europein comparison with the rest of the world, and the evaluation of EU requirements,especially for new EU members2) an assessment and analysis of existing SG and SP projects at national and EU levelsand worldwide, and a comparison with respect to their strategic objectives, organisation,budgetary aspects, their outcomes (i.e. structures determined, contribution todata banks, etc.) and their impact on academia and industry3) an assessment of industrial needs for SG and SP and of their impact on health andthe economy in the EU4) establishing of a database resource to serve as a completeregister of structural genomics and structural proteomicsprojects worldwide5) drafting a series of staged publications based on the assessmentand compilation of a position paper that will includean assessment of SG and SP activities in the EU, anda strategic road map to guide future directions of structuralgenomics and structural proteomics initiatives in Europe.Nuclear pore particleExpected Results:A database will be established and it willserve as a complete register of the structuralgenomics/proteomics projects worldwide.A position paper will be compiled which willinclude an assessment of structural genomics/proteomics,and the infrastructures andactivities in Europe and the rest of the world.A strategic road map will be prepared toguide future directions of SG and SP initiativesin the EU.NMR Structure194From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Forum for European Structural ProteomicsPotential Impact:1) The open discussion that we plan to stimulate anddirect within the SG/SP European communityshould raise the awareness of structural biologycentres among high-throughput SG/SP researchersin healthcare and academia, and in big pharmacologicaland biotech companies throughoutthe EU.2) The staged documents, based on our assessmentsand discussions with a wide spectrum of scientists and national scientific officersworldwide, should help the EC in formulating policies for future scientific calls in LifeSciences, in general, and in SG/SP in particular.3) The position paper will provide guidelines for an overall strategic direction that the ECcan consider adopting for future directions for European research in the SG/SP area.Keywords: structural proteomics, structural genomics, research policiesPartnersProject Coordinator:Prof. Joel L. SussmanWeizmann Institute of ScienceDepartment of Structural BiologyHerzel Street P.O. Box 2676100 Rehovot, IsraelJoel.Sussman@weizmann.ac.ilProject Manager:Bracha VakninWeizmann Institute of ScienceIsrael Structural Proteomics CenterDepartment of Structural Biology100 Herzel StreetP.O. Box 2676100 Rehovot, Israelispc@weizmann.ac.ilProf. Lucia BanciUniversity of FlorenceCentro RisonanzeMagnetiche (CERM)Sesto Fiorentino, ItalyProf. Udo HeinemannMax-Delbrück-Center forMolecular MedicineDepartment of CrystallographyBerlin, GermanyProf. Gunter SchneiderKarolinska InstitutetDivision of MolecularStructural BiologyDepartment of MedicalBiochemistry and BiophysicsStockholm, SwedenProf. Wolfgang BaumeisterMax-Planck Institut für BiochemieAbteilung Molekulare StrukturbiologieMartinsried, GermanyFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life195

E-MeP-Labwww.e-mep.org/?rub=labProject Type:Specific Support ActionContract number:LSHG-CT-2005-512011Starting date:1 st July 2005Duration:48 monthsEC Funding:250 000State-of-the-Art:E-MeP is an EC funded FP6 integrated project. Its research will develop new technologies tosolve the bottlenecks that preclude the determination, at high throughput, of high-resolutionstructures of membrane proteins and their complexes. This will be achieved by integratingthe activities of world leaders in membrane protein structural biology. E-MeP-Lab is aproposal for a Specific Support Action to exploit this confluence of talent. For the first time,Europe’s membrane protein structural biology community will converge as teachers anddemonstrators in a Master Class and five Advanced Practical Courses in the best equippedlaboratories in their fields in Europe. This research field is important because membraneproteins comprise the major target area of study within modern structural genomics. Moreover,the field of membrane protein study involves approximately 70 percent of human patientsthat qualify for therapeutic intervention.Scientific/Technological Objectives:E-MeP-Lab’s objectives are to:1) Increase the pool of appropriately skilled young researchers in membrane proteinstructural genomics;2) Provide access for all European researchers to training programmes;3) Integrate with other Structural Genomics programmes to facilitate a coherent EuropeanStructural genomics strategy on membrane and soluble proteins.Expected Results:In addition to working with researchers from European member states, the project aimsto harness the considerable scientific talent in the new Member States to ensure their fullparticipation within the European Structural Genomics community, through the provision ofring-fenced funding. Together with an analysis provided by an expert in gender and mobilityissues, this will provide an excellent opportunity to evaluate the potential impact of anincrease in scientific mobility and more equal gender participation. Thus, achievement ofbalanced growth in the wider ERA will be achieved with a particular focus on the transferof knowledge in the structural genomics of membrane proteins.E-MeP-Lab Training workshop196From Fundamental Genomics to Systems Biology: Understanding the Book of Life

E-MeP-Lab Training events inmembrane protein structural biologyPotential Impact:By providing training to eliminate bottlenecks that preclude the structural determination ofmembrane proteins and membrane protein complexes to atomic resolution, the E-MeP-Labproject addresses this issue head-on. Intelligent, structure-based drug design will short-circuitcurrent brute force random screening of drugs and will therefore save pharmaceuticalcompanies time and money. Even in the absence of structures, the provision of the skill set toproduce functional eukaryotic membrane proteins for targeted drug screening by high-techSMEs will be an important outcome from E-MeP-Lab. This will give Europe a competitiveedge in the pharmaceutical and biotechnology markets.Keywords: structural proteomics, structural genomics, research policiesPartnersProject Coordinator:Dr. Roslyn BillAston UniversityDepartment of Life and Health SciencesAston TriangleBirmingham, B4 7ET, UKr.m.bill@aston.ac.ukProject Manager:Eric BourguignonAston UniversityDepartment of Life and Health SciencesAston TriangleBirmingham, B4 7ET, UKe.bourguignon@aston.ac.ukProf. Peter HendersonUniversity of LeedsAstbury Centre for Structural - Molecular BiologyLeeds, UKFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life197

Project Type:Specific TargetedResearch projectContract number:LSHG-CT-2005-018811Starting date:1 st October 2005Duration:42 monthsEC Funding:1 802 501HT3DEMState-of-the-Art:www.ht3dem.orgMembrane proteins, unlike soluble proteins, are generally not easily amenable to 3D crystallization.The most regular organization of a membrane protein amenable to crystallographyis a 2D crystal (2DX). It comprises only a single layer of the regularly packed protein,which is reconstituted in a lipid bilayer. Electrons must be used for the diffraction analyses.The availability of membrane proteins suitable for electron crystallography is of high importancefor rational drug design since about 70% of all drug targets are membrane proteins.The potential of this approach has long been recognized, and the first structure of a humanchannel protein, aquaporin-1, has been solved to a 3.8 Å resolution. An innovative technologyplatform for high throughput screening and analysis of native protein complexes andprotein crystals by EM would reduce processing time and cost and greatly increase theprobability of obtaining high quality 2D crystals of membrane proteins.Scientific/Technological Objectives:The objective of the HT3DEM project is to develop an automated pipeline for sample preparationand analysis by electron microscopy. The novel hardware and software under developmentincludes: (1) a 2D crystallisation robot: Membrane protein reconstitution is criticallydependent on lipid mixtures, lipid-to-protein ratio and cofactors such as divalent cations,ionic strength and pH. Such a multi-parameter optimisation for each protein investigatedcan only be satisfyingly screened using a high-throughput approach; (2) a sample preparationrobot. This robot is designed to prepare negatively stained samples from cytosolicfractions or 2D crystallisation experiments. The robot will be compatible with the 96 wellplate format and the autoloader of the EM; (3) An automated grid loader (AutoLoader)and a cassette revolver fitting on the EM and the corresponding software are in development.These robots will enable the automatic loading of up to 96 samples and thus be fullycompatible with the sample preparation robot; (4) development of software for instrumentalcontrol and screening acquisition schemes. Automatic acquisition and screening software,involving novel developments and improvement of existing routines will allow a first qualityassessment and the selection of suitable sample areas for further in-depth investigations; (5)development of a versatile, self-learning image analysis and pattern recognition system forthe automated identification of interesting sample areas and directing the pertinent imageacquisition at different magnifications; (6) design of a versatile, user friendly database toallow storage and analysis of all pertinent experimental data.Expected Results:Regions Of Interest (ROI)identification at mediummagnification: after an edgedetection of the membranes (B),the ROI (red squares) are placedaround the detected edges. Then,a selection process retains themore significant ones (C).1) A fully integrated high throughput system for screening and analysis of native proteincomplexes and protein crystals by electron microscopy is expected. Good progresshas been achieved in all parts of the project.2) 2D-Cryrsallisation Robot: The alpha version of the robot (96 well plate) has beenworking reliably for a few months. Proteins have already been processed to yieldhigh quality crystals. (Picture).3) Sample Preparation Robot: A first version of a robot has been used with encouragingresults. New developments to improve the automated staining are in progress.4) Autoloader and Cassette Revolver: Both robots are in a well advanced state of developmentand will be ready in six to nine months.5) Software for instrumental control and screening acquisition: The software to controlthe automatic grid loading hardware (AutoLoader) has been tested and will be integratedas soon as the EM is ready. The software design of the screening and acquisitionprocess suitable for crystalline objects and particles is well advanced.6) Image analysis and pattern recognition software for crystal detection and analysis198From Fundamental Genomics to Systems Biology: Understanding the Book of Life

has been developed for low, medium and highmagnification.7) Database: A first version of the database isready for data entry. The statistical analysis ofdata is in development.Potential Impact:The development of a versatile platform enabling theautomated screening and analysis of various types ofsamples by electron microscopy closes a gap in the generaluse of this technology. It will speed up the structuralanalysis of several classes of fundamentally important specimens, such as macromolecularcomplexes, and, most importantly, membrane proteins. 2D crystals can provide 3D structuralinformation of membrane proteins in their native environment by EM analysis and on surfaceproperties by AFM analysis, including molecular interactions. This development thus fits inwith the European effort to advance leadership in electron microscopy and with the enhancementof European competitiveness in the field of structural genomics. In the greater context,the project will also aid competitiveness in life sciences and the European pharma industry.Keywords: high throughput, three-dimensional electron microscopy,membrane proteins, 2D crystallisationPartnersHigh throughput Three-dimensionalElectron MicroscopyProject Coordinator:Prof. Andreas EngelUniversity of BaselM E Mueller Institute for Structural BiologyBiozentrumNadelberg 64054 Basel, Switzerlandandreas.engel@unibas.chAlpha version of the 2D-crystallisationrobot at Partner BIOZ(Right). High quality crystals ofAeromonas hydrophila Aerolysinobtained with the cy-clodextrinmethod. Scale bars represent100 nm. (Left)(Prof. Gisou vander Goot and Ioan Iacovache areacknowledged for kindly providingus with Aero-lysin).Project Manager:Dr. Urs MuellerUniversity of BaselM E Mueller Institute forStructural BiologyBiozentrumNadelberg 64054 Basel, Switzerlandu.mueller@unibas.chProf. Wolfgang BaumeisterMax-Planck Institute ofBiochemistryDepartment of MolecularStructural BiologyMartinsried, GermanyDr. Werner Hax, Dr. Marc StormsFEI Electron Optics BVEindoven, The NetherlandsDr. Bart van der SchootSeyonic SANeuchatel, SwitzerlandProf. Jean-Philippe UrbanUniversité de Haute AlsaceFaculté des Sciences etTechniquesMulhouse, FranceFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life199

Project Type:Co-ordination ActionContract number:LSHG-CT-2005-018758Starting date:1 st December 2005Duration:39 monthsEC Funding:1 070 000Endothelin-1 bound toEndothelin-B receptorNMR-LifeState-of-the-Art:Structural genomics originally aimed at the full structural coverage of the proteome. In themeantime, the investigation of the whole network of interacting proteins produced by aliving organism (the ‘interactome’), and of how these interactions are being modulated bychanging concentrations of small molecules, has become an emerging field of researchproviding information on the biochemical processes which occur through protein-proteinand protein-DNA/RNA interactions. NMR spectroscopy is particularly suited for the studyof weak and/or transient intermolecular interactions.The present project will implement coordination activities focused on the scientific areas ofprotein-protein, protein-DNA/RNA, and protein-ligand interactions, and membrane proteins.These scientific areas share common technical and methodological aspects, whichrepresent crucial issues for the development of the whole field of biological NMR. Theproject will contribute to standardising and disseminating best practices.Scientific/Technological Objectives:Coordination activities will be developed to achieve the following main goals: focuses, mainly through the common vertical aspects methodological approaches the spreading of innovative methods and tools netby maintaining a common virtual laboratory The above coordination activities will be crucial in guaranteeing that on-going research andmethodological innovation in Europe, such as the development of new software tools, arecarried out by promptly tackling the needs of the European scientific community. This willbe achieved by guaranteeing the awareness of the potential stakeholders, and by avoidingboth the duplication and exclusion of efforts (as much as possible), which may later becomebottlenecks for the evolution of the whole field of biological NMR.Expected Results:Actions to be taken within the project are planned by the managing committee (MC) on ayearly basis. Actions will involve: tionsof high potential impact, unprecedented scientific challenges and opportunities,proposition of new standards, etc. demonstrations or road shows presenting new advances, etc. These actions are complemented by an annual meeting involving all participants in theproject, organised by the coordinator in collaboration with all MC members.Potential Impact:www.postgenomicnmr.netThe impact of this Coordination Action is that it brings together scientists, creating a com-200From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Focusing NMR on the Machinery of Lifemon reference basis in terms of experimental approaches, data elaboration and analysisthrough exchanges of good practices and/or by sharing procedures and results. Thecoordination of research activities is important when making breakthroughs or advancingtechnologies achieved by the various scientists in the field, by avoiding needlessduplication of efforts, thus enhancing and allowing the extensive scientific productivity ofEuropean researchers. This will help reinforce the European lead in the field of biologicalNMR, and the interaction with pharmacological and biotech companies will lead toindustrial applications.Keywords: protein interactions, protein ligand interactions, membrane proteins,immobilised proteins, NMRPartnersProject Coordinator:Prof. Ivano BertiniConsorzio Interuniversitariodi Risonanze Magnetiche diMetalloproteine Paramagnetiche,Magnetic Resonance Center (CERM)Via Luigi Sacconi, 650019 Sesto Fiorentino, Italybertini@cerm.unifi.itProject Manager:Kathleen McGreevyConsorzio Interuniversitario diRisonanze Magnetiche diMetalloproteine Paramagnetiche,Magnetic Resonance Center (CERM)Via Luigi Sacconi, 650019 Sesto Fiorentino, Italymcgreevy@cerm.unifi.itDr. Michael SattlerGSF – National Research Centerfor Environment and HealthLehrstuhl BiomolekulareNMR-SpektroskopieDepartment ChemieTechnische Universität MünchenGarching, GermanyProf. Rolf BoelensUtrecht UniversityBijvoet Center for Biomolecular ResearchNMR Spectroscopy Research GroupUtrecht, The NetherlandsProf. Harald SchwalbeJohann Wolfgang Goethe-UniversitätCenter for Biomolecular Magnetic ResonanceInstitute for Organic Chemistry and Chemical BiologyFrankfurt am Main, GermanyProf. Hartmunt OschkinatLeibniz-Institut für MolekularePharmakologie (FMP)Berlin, GermanyProf. Geoffrey BodenhausenEcole Normale Supérieure de ParisDépartement de chimieLaboratoire de ResonanceMagnetique BiomoleculaireParis, FranceProf. Flemming Martin PoulsenUniversity of CopenhagenStructural Biology andNMR Laboratorythe Institute ofMolecular BiologyCopenhagen, DenmarkProf. Vladimir SklenarMasaryk UniversityNational Center forBiomolecular ResearchBrno, Czech RepublicProf. Ernest D. LaueUniversity of CambridgeCambridge, UKProf. Iain CampbellUniversity of OxfordDepartment of BiochemistryOxford, UKNMR Structure of the yeastAtx1: Copper(I): Ccc2a adductStructure of a protein:single-stranded DNA complexFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life201

Extend-NMRwww.ccpn.ac.uk/ccpn/projects/extendnmr/extend-nmr-project-informationProject Type:Specific TargetedResearch projectContract number:LSHG-CT-2005-018988Starting date:1 st January 2006Duration:42 monthsEC Funding:2 000 000State-of-the-Art:In comparison with better-established methods like X-ray crystallography, computationaltools for the extraction of information from NMR spectra of large proteins and complexes,and its analysis and interpretation, are much less well developed. As a result, the full powerof the method cannot be exploited at present. Novel tools that allow the identification ofsignals in crowded NMR spectra of larger proteins and complexes, and their quantification,are urgently needed. The resulting information will, in turn, provide the starting point for thedevelopment of novel algorithms that facilitate structure determination of protein complexesin situations where NMR can play a key role; for example, where one or more componentsare only partly structured, or for solid-state studies of membrane proteins.Scientific/Technological Objectives:The objectives of the project are:1. the development of novel computational tools that allow rapid assignment of NMRspectra for studies of interactions and dynamics by making optimal use of existing (inparticular structural) information, i.e. the NMR equivalent of molecular replacementin X-ray crystallography,2. extending the scope of NMR spectroscopy by developing novel tools that allow thecalculation of structures without the need for prior spectral assignment,3. the development of improved tools for the identification and quantification of signalsfrom NMR data.These three objectives will be facilitated by the development and implementation of a seriesof computational algorithms involving Bayesian analysis, maximum entropy reconstruction,multi-dimensional decomposition, principle component analysis, and statistical and expertsystem-based analysis tools. These algorithms will be implemented within a common softwareframework developed by the CCPN project, so that they can be flexibly employedin the development of the different tools. We will develop novel tools for the validation ofstructures and experimental results and mine databases for NMR and structural informationcrucial to the aims of the project.Expected Results:The expected result is the development ofa highly integrated set of computationaltools, which will extend the scope of NMRspectroscopy and allow researchers tocarry out studies flexibly in functional andstructural genomics, as well as NMR-baseddrug design.Potential Impact:An integrated system allowing the extractionof information from raw NMR dataand the direct calculation of the final 3Dstructure, without the need for assignmentof that information to specific atoms in the202From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Extending NMR for Functionaland Structural Genomicsmolecule, would be highly desirable and make a significant impact in NMR programmesof functional/structural genomics. In a similar vein, a method that allowed one to obtainassignments with the aid of a structure of a homologous protein would be extremely usefulfor functional studies. The development of novel algorithms will therefore greatly stimulatethe use and usefulness of NMR in functional/structural genomics, having a crucialimpact on increasing the potential of NMR for studies in biology and medicine in thepost-genomic era.Keywords: nuclear magnetic resonance, NMR, structural genomics, functionalgenomics, biomolecular complexes, spectrum assignment, structurecalculation, high-throughput techniquesPartnersProject Coordinator:Professor Ernest D. LaueUniversity of Cambridge80 Tennis Court RoadCambridge, CB2 1GA, UKe.d.laue@bioc.cam.ac.ukProject Manager:Charles ShannonResearch Services Division16 Mill LaneCambridge, CB2 1SB, UKcharles.shannon@rsd.cam.ac.ukDr. Kim HenrickEuropean Molecular BiologyLaboratory (EMBL)European Bioinformatics Institute (EBI),Hinxton, UKDr. Michael NilgesCentre National de la Recherche Scientifique (CNRS) -Institut PasteurUnité de Recherche Associeé (URA)Unité de Bioinformatique Structurale,Paris, FranceDr. Gert VriendRadboud University Nijmegen Medical CentreNijmegen Centre for Molecular Life Sciences (NCMLS)Centre for Molecular and Biomolecular Informatics (CMBI)Nijmegen, The NetherlandsDr. Martin BilleterGothenburg UniversityBiochemistry and BiophysicsDepartment of ChemistryGothenburg, SwedenDr. Hans-Robert KalbitzerUniversity of RegensburgInstitute of BiophysicsRegensburg, GermanyDr. Bruno GuigasBruker BioSpin GmbHMagnet DivisionKarlsruhe, GermanyDr. Alexandre BonvinUtrecht UniversityNMR Research GroupBijvoet Center forBiomolecular ResearchUtrecht, The NetherlandsFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life203

IMPSProject Type:Specific TargetedResearch projectContract number:LSHG-CT-2005-513770Starting date:1 st January 2006Duration:36 monthsEC Funding:1 900 000State-of-the-Art:The objective of IMPS is to explore innovative approaches to membrane protein (MP) overexpression,stabilization and crystallography. Establishing the structure of MPs is of majorimportance in basic life sciences as well as drug development. Yet fewer than 1% of proteinstructures currently available correspond to MPs, most of them devoid of pharmacologicalinterest. The reason for the paucity of crystallographic structures can be traced mainly to thefollowing factors: (1) most MPs purified from natural sources are in short supply, hence theneed for overexpression; (2) most MPs become unstable once extracted from their naturalmembrane environment, hence the need for improved handling conditions; (3) MPs do notcrystallize easily, hence the need for alternative crystallization approaches to improvingcrystal quality and for specialized methods to deal with microcrystals. IMPS is an integratedattempt to develop novel, original ways of circumventing these three bottlenecks.Scientific/Technological Objectives:MPs play key roles in innumerable biological processes. Even though their genes are nowaccessible, solving their structure remains time-consuming and most often unsuccessful. Giventheir physiological and biomedical importance, this constitutes a major problem in basic lifesciences as well as public health care. Tools have been developed to overexpress, solubilize,stabilize, purify and crystallize MPs, and they are currently being used in large-scale initiativesfor structure determination. Unfortunately, most MPs resist one or more of these steps.The objective of IMPS is to develop imaginative, broad-range tools for membrane structuralproteomics. The project brings together experts in chemistry, biochemistry, molecular genetics,electron microscopy and X-ray crystallography, and aims at developing original, innovativetools to attack each of these stumbling blocks. A strong core of crystallographers with demonstratedexpertise in MP structure determination will apply these novel techniques to a representativetest set of MPs. The approaches to be developed include original overexpressionsystems (insect photoreceptor cells and the chloroplast), unconventional surfactants (amphipathicpolymers, fluorinated surfactants, novel detergents and additives) and unconventionalcrystallization systems (lipid cubic phase crystallization, other non-detergent environments,molecular scaffolding). As the project progresses, some of these objectives are being adapted,extended, or, in some cases, superseded by alternative novel approaches that have yieldedparticularly promising results. These novel methodologies will be made available to the scientificcommunity through a distributed technological platform including workshops, hands-ontraining, and dissemination of the new molecules, whose large-scale synthesis and distributionwill be carried out by a participant SME. The circulation of scientists between IMPS laboratoriesand the organization of workshops ensures the rapid spread of know-how.Expected Results:The general philosophy of the project has been outlined above. The resources and experiencebrought by the eight partners and four associated laboratories are highly complementary.Thirteen MPs have been selected either as models for technological development and/or as pharmacologically important targets. At the onset of the project, some proteins werealready available in mg amounts, either from natural sources or following overexpression,while others were at the stage of setting up overexpression systems. As methodologies develop,new proteins are being chosen to further explore their domain of applicability, a ruleof the game being the sharing among IMPS laboratories of plasmids, novel molecules andknow-how. The main results to be expected are the following:1) validation and dissemination of the most promising of the novel approaches to MPoverexpression, stabilization and crystallization;2) solving, or making significant steps towards solving, the structure of some of the targetMPs;3) training the members of IMPS and other laboratories and creating the basis for collaborationsextending beyond the end of the project.204From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Innovative toolsfor membrane structural proteomicsPotential Impact:Solving the structure of MPs that constitute important pharmacological targets is currently ahigh-risk endeavor, calling for long-term work-intensive investments. Providing new tools towardsthis goal will speed up structure resolution and cut down on its cost, which can havea significant economic impact in a field where research investments represent hundreds ofmillions of dollars. Most of the innovative approaches developed by IMPS partners originatedin Europe. IMPS provides an opportunity to consolidate the leadership that Europeanlaboratories currently hold in these new developments and speed up their optimizationand the definition of their field of applicability. Once validated, the novel methods will bedisseminated throughout European laboratories, thanks, in particular, to workshops andcollaborations involving both IMPS and external laboratories.Keywords: membrane proteins, overexpression, crystallization, stabilization,novel surfactants, microcrystallography, lipid cubic phases, amphipols,Drosophila, yeastPartnersProject Coordinator:Dr. Jean-Luc PopotCentre National de la Recherche Scientifique (CNRS)/Université Paris-7 UMR 7099Institut de Biologie Physico-Chimique13, rue Pierre-et-Marie-Curie75005 Paris, Francejean-luc.popot@ibpc.frProf. Eva Pebay-PeyroulaCentre National de la Recherche Scientifique (CNRS)CEA/Université Joseph FourierInstitut de Biologie StructuraleGrenoble, FranceDr. Isabelle Mus-VeteauCentre National de la Recherche Scientifique (CNRS)Université de Nice-Sophia AntipolisNice, FranceProf. Irmgard SinningRuprecht-Karls-UniversitätHeidelberg, GermanyProf. Bernard PucciUniversité d’Avignon et des Pays du VaucluseAvignon, FranceProf. Wolfram WelteUniversität Konstanz, F R GMathematisch-Naturwissenschaftliche SektionFachbereich BiologieLehrstuhl BiophysikKonstanz, GermanyDr. Jean-Pierre SallesTargeting System PharmaEguilles, FranceProf. Kaspar HegetschweilerUniversität des SaarlandesFakultaet 8 Chemie PharmazieBiowissenschaftenWerkstoffwissenschaftenSaarbrücken, GermanyDr. Gebhard SchertlerMRC-LMBMedical Research CouncilCambridge, UKFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life205

SPINE2-COMPLEXESwww.spine2.euProject Type:Integrated ProjectContract number:LSHG-CT-2005-031220Starting date:1 st July 2006Duration:42 monthsEC Funding:12 000 000State-of-the-Art:SPINE2-COMPLEXES builds on the technological developments in structural genomics/proteomicsof the last decade and aims to break new territory in this field. The concept of structuralgenomics arose in the USA at the end of the 1990s, as a response to the availabilityof whole genome information, and also as a response to the success of high throughput(HTP) methods in genome sequencing. At that time, it was foreseen that similar HTP methodscould be applied to obtain 3-D structures of all the proteins (the proteome) of an organism,thus generating an efficient way of filling in the gaps in observed fold-space. This vision ledto the investment of immense sums of money into large-scale structural genomics projects.Instances of this are noted both in Japan, e.g. the massive RIKEN project, (http://www.rsgi.riken.go.jp/), and in the USA, e.g. nine multi-million dollar projects funded by the NIH/NIGMS Protein Structure Initiative, costing around $270 million and stretching over a 5year period, ending in June 2005 (http://www.nigms.nih.gov/psi/ ).These projects were characterised by the following elements: the concentration of resourcesinto a small number of large centres, the development of novel, automated technologies permittinga high-throughput, a pipeline approach to structure determination, a focus on novelfolds as the major target criterion, and immediate public deposition of structural data.Europe has been slower off the mark in implementing structural genomics. The ProteinStructure Factory in Berlin, Germany (http://www.proteinstrukturfabrik.de/) first made themove, followed by the OPPF in Oxford, England (http://www.oppf.ox.ac.uk/), and theGenopoles in France (notably Gif, Marseille and Strasbourg, http://rng.cnrg.fr/). However,it was not until October 2002 that the first Europe-wide project began. This was athree-year project funded by the EU FP5 programme called SPINE: Structural Proteomicsin Europe (http://www.spineurope.org). SPINE, a second generation structural genomicsproject, made some radical departures from previously funded initiatives, and has benefitedfrom the experience and developments in technology arising from previous findings in thisfield. SPINE2-COMPLEXES plans to push developments beyond the previous limits.Scientific/Technological Objectives:SPINE2-COMPLEXES’ aim is to investigate challenging biological systems by combiningknowledge of genomes with HTP methods for structural proteomics. The project targetsthe development and application of HTP methods, for an efficient determination of atomicresolution structures of protein-protein and protein-ligand complexes. These complexes,which are extremely important with respect to human health, are drawn from the commontheme of signalling pathways from receptor to gene.Overall, the success of SPINE2-COMPLEXES will be assessed on the scientific impact ofits output.The project work is divided into 3 sections:Section 1 involves 3-D structure determination of complexes within the target focus ofsignalling pathways from receptor to gene. This is the major section of SPINE2-COM-PLEXES, both in terms of allocation of manpower, and in terms of scientific importance.Targets are drawn from key areas of biology, including cell cycle, neurobiology,cancer and immunology, as well as pathogen proteins that modulate or subverthuman signalling pathways. This section has been subdivided into a set of WPs which206From Fundamental Genomics to Systems Biology: Understanding the Book of Life

From Receptor to Gene:Structures of Complexes from SignallingPathways linking Immunology,Neurobiology and Cancerbring together Partners working in specific areas. Since the apparently diverse cellularprocesses often involve the same components and pathways, this will providewide opportunities for inter-Partner synergies.Section 2 involves the development of technologies addressing the difficult problemsassociated with the production of human protein complexes in quantities sufficientfor structural studies, and also with the provision of an interdisciplinary approachfor determining protein complex structures. This will build on and extend the HTPprotein expression and crystallisation technologies initiated and implemented withinthe SPINE project.Section 3 deals with the dissemination and organization of the emerging data andknowledge, through a series of training session and symposia on an annual basis.Expected Results:To date, the SPINE2-COMPLEXES project has made progress in several areas, as detailedbelow:1) Significant progress has been made towards the development of protein complexspecifictarget tracking software, to enable the rigorous capture, storage and analysisof protein expression and structure determination data. This tracking software will bePIMS compatible and will utilise a similar interface for data acquisition and retrieval.2) A SPINE2-COMPLEXES website (http://www.spine2.eu) has been set up and will befurther developed over the next months, after which it will form the centre of the consortiumcommunication strategy.3) A planned timetable of training workshops, demonstrating the state-of-the-art technologiesrelevant to protein structure determination, will be implemented in the first twelvemonthreporting period of the project.4) All Partners have started work on the structure determination of their nominated proteincomponents. These component proteins have been identified as members of the cellsignalling pathways, which in turn, form the biological focus of the project. Some proteinstructures are expected to be delivered in the first twelve-month reporting period.Potential Impact:SPINE2-COMPLEXES has several deliverables, and they are as follows: 1) high value 3Dstructures of complexes of fundamental and biomedical importance; 2) novel methods forthe production, characterisation and structure determination of eukaryotic proteins andcomplexes; 3) new bioinformatics tools; and 4) an interactive and co-ordinated Europewidenetwork of laboratories engaged in training and research in structural proteomics.These deliverables will ensure the profound impact of this project both in Europe and beyond.SPINE2-COMPLEXES intends to further develop and streamline the high throughputtechnologies, so as to tackle not only individual proteins, but also more challengingprotein/protein and protein/nucleic acid complexes. The success of the consortium willdemand technological innovation, resulting in new and/or improved HTP procedures atall stages, from cloning, expression and purification, through biophysical and biochemicalcharacterization of individual proteins and complexes, to crystallization, data collection,and solution of their structures, as well as solution of smaller protein structures by NMR, andelectron microscopy (EM) studies on complexes.From Fundamental Genomics to Systems Biology: Understanding the Book of Life207

SPINE2-COMPLEXESThe SPINE2-COMPLEXES project goes far beyond the capacities of individual laboratories,which work in isolation, lacking both the infrastructure and the critical mass to tackle sucha far-reaching and ambitious project. At European level, the added value of the project willfind expression in several ways. Firstly, consortium members will be able to take advantageof infrastructures and expertise, especially in protein production, bioinformatics and LIMS,NMR and synchrotron facilities that are offered by consortium partners. The training andmobility programme of SPINE2-COMPLEXES will facilitate interactions and dissemination.Secondly, major emphasis will be placed on Internal Networking. This will utilize a website,with adjunct internal databases, linked to LIMS systems in the member laboratories.Keywords: crystallography, protein expression, nanodrop technology, proteincomplexes, ligand interfaces, signalling pathways, protein structure,structural genomics, high-throughput techniquesPartnersProject Coordinator:Prof. David StuartWellcome Trust Centre for Human GeneticsDivision of Structural BiologyRoosevelt Drive, HeadingtonOxford, OX3 7BN, UKdave@strubi.ox.ac.ukProject Manager:Dr. Susan DaenkeScientific Program ManagerEuropean ProjectsWellcome Trust Centre for Human GeneticsRoosevelt Drive, HeadingtonOxford, OX3 7BN, UKsusan@mail.strubi.ox.ac.ukProf. Joel SussmannWeizmann Institute of ScienceThe Israel Structural Proteomics CenterDepartment of Structural BiologyRehovot, IsraelDr. Stephen CusackEuropean Molecular Biology Laboratory (EMBL)Grenoble OutstationGrenoble, FranceDr. Matthias WilmannsEuropean Molecular Biology Laboratory (EMBL)Hamburg OutstationHamburg, GermanyDr. Dino MorasCentre Européen de Recherche en Biologie eten Médecine – Groupement d’Intérêt ÉconomiqueUPR9004/CERBM G.I.E.Illkirch, France208From Fundamental Genomics to Systems Biology: Understanding the Book of Life

From Receptor to Gene: Structures of Complexes from Signalling Pathwayslinking Immunology, Neurobiology and CancerProf. Gunter SchneiderKarolinska InstitutetDepartment of Medical Biochemistry and BiophysicsStockholm, SwedenProf. Keith WilsonUniversity of YorkDepartment of ChemistryStructural Biology LaboratoryYork, UKDr. Rolf BoelensUniversity of UtrechtBijvoet Center for Biomolecular ResearchNMR SpectroscopyUtrecht, The NetherlandsProf. Titia SixmaNetherlands Cancer Institute (NKI)Division of Molecular CarcinogenesisAmsterdam, The NetherlandsProf. Ivano BertiniMagnetic Resonance Center (CERM)SestoFiorentino (FI), ItalyDr. Beata VertessyHungarian Academy of SciencesMetabolism and Repair DepartmentInstitute of EnzymologyBudapest, HungaryDr. Jan DohnalekUstav makromolekularnii chemieAkademie ved Ceske republikyDepartment of Structure AnalysisGroup of Analysis of Molecular StructurePrague, Czech RepublicProf. Maria Armenia CarrondoInstituto de Technolgie Quimica e BiologicaProtein crystallography laboratoryOeiras, PortugalDr. Renos SavvaDomainex LimitedBirkbeck College, University of LondonRosalend Franklin LaboratoryLondon, UKProf. Sine LarsenEuropean Synchrotron Radiation Facility(Installation Européenne deRayonnement Synchrotron)Grenoble, FranceProf. Udo HeinemannMax-Delbruck-Center for Molecular MedicineDepartment of CrystallographyBerlin, GermanyProf. Miquel CollConsejo Superior de Investigaciones CientíficasInstitut de Biologia Molecular de BarcelonaBarcelona, SpainDr. Yves BourneInstitute de Biologie Structurale et MicrobiologieArchitecture et Fonction desMacromolecules BiologiquesMarseille, FranceDr. Herman van TilbeurghUniversité Paris-SudIBBMC-Institut de Biochemie et deBiophysique Moleculaire et CellulaireCentre National de la RechercheScientifique (CNRS) UMR 8619Orsay, FranceFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life209

OptiCrystwww.opticryst.orgProject Type:SME- Specific TargetedResearch ProjectContract number:LSHG-CT-2006-037793Starting date:1 st December 2006Duration:36 monthsEC Funding:2 270 000State-of-the-Art:The wealth of information obtained by Structural Genomics has allowed protein structurebaseddrug design to complement screening and combinatorial chemistry to provide moreefficient drug development. Ultimately, this approach will reduce the time of productioncycles and therefore cost per drug.Structural Genomics has coincided with the era of high-throughput, resulting in major advancesin the automation of protein preparation and X-ray crystallographic analysis, and inautomating and miniaturising crystallisation trials (thousands per day). Despite this, the successrate in going from cloned gene to high-resolution protein structure is still relatively lowin all current Structural Genomics projects, with a major bottleneck situation from purifiedprotein to diffracting crystals. This problem clearly needs to be addressed. This can be donethrough the production of a design that will offer new and improved optimisation methods,in order to turn crystal leads into useful diffracting crystals.Scientific/Technological Objectives:The key objective of the OptiCryst project is to address the critical post-protein productionbottleneck area in the field of Structural Genomics. To date, this area has been consistentlyignored by initiatives worldwide. We propose to enhance the state-of-the-art in proteincrystal optimisation by increasing the success rate of the production of diffraction-qualitycrystals from the current rate of 21 percent to at least 40 percent.Expected Results:Moving away from current approaches, and applying methods based on understanding thefundamental principles of crystallisation, the OptiCryst project will focus on designing techniquesto actively control the crystallisation environment as the project progresses throughits stages.Potential Impact:Structural Genomics is a key discipline in post-genomic biology, and today the pressure toproduce diffraction-quality crystals that can yield new protein structures is greater than ever.As a result, the science of crystallisation is becoming a rapidly developing field and it isgathering new momentum. The work being carried out by the Opticryst project will go a significantlylong way towards addressing the outstanding needs within that research area.Masterclass Opticryst 2007210From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Keywords:Optimisation of Protein Crystallisationfor European Structural Genomicsprotein crystallization, phase diagrams, nucleation, robotics, high throughput, structuralgenomicsPartnersProject Coordinator:Dr. Roslyn BillAston UniversityDepartment of Life and Health SciencesAston TriangleBirmingham, B4 7ET, UKr.m.bill@aston.ac.ukProject Manager:Eric BourguignonAston UniversityDepartment of Life and Health SciencesAston TriangleBirmingham, B4 7ET, UKe.bourguignon@aston.ac.ukProf. Naomi ChayenImperial College of Science, Technology and MedicineBiomedical SciencesBiological Structure and FunctionLondon, UKDr. Patrick Shaw StewartDouglas Instruments LtdHungerford, UKDr. Flip HoedemaekerKey Drug PrototypingAmsterdam, The NetherlandsDr. Anthony SavillMolecular Dimensions LtdNewmarket, UKDr. Rafael Rubio CruzTriana Science & TechnologyArmilla, SpainProf. Rolf HilgenfeldUniversity of LübeckInstitute of BiochemistryLübeck, GermanyDr. Marcus J. SwannFairfield Scientific LtdCrewe, UKProf. Juan Manuel Garcia-RuizConsejo Superior de InvestigacionesCientificas (CSIC)Laboratorio de Estudios CristalograficosArmilla, SpainProf. Christian BetzelPLS Design GmbHHamburg, GermanyProf. Lena GustafsonGothia Yeast Solutions ABGothenburg, SwedenFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life211

Project Type:Specific Support ActionContract number:LSSG-CT-2004-503468Starting date:1 st January 2007Duration:30 monthsEC Funding:490 000TEACH-SGState-of-the-Art:Since 2002, momentum has been gathering in European structural genomics. EU funding forsix major projects, along with other initiatives in Europe (SGC, PSF, OPPF, Genopoles andPSB) has provided a broad base to build a comprehensive and competitive European structuralgenomics research effort. These early programmes have excelled in the development and implementationof automated, computational and high throughput methods for protein structuredetermination in a number of organisms. The challenge is to broadcast this knowledge to Europeanlaboratories as the scientific and strategic goals of structural genomics are expandedand refined to address important issues for human health. TEACH-SG provides a focus fortraining in all the main methodological areas of structural genomics, bringing together expertisefrom each programme to provide an integrated skill resource for researchers in the field.Scientific/Technological objectives:The principal objective of TEACH-SG is to institute a programme to train and educate thenext generation of biomedical and computational scientists in the methods and technologiesof high throughput and high value structural proteomics. TEACH-SG will provide training inseveral formats:1) Practical workshops on state-of-the-art structural genomics/proteomics methodology.2) Networking meetings bringing together several projects under the European structuralgenomics umbrella, TEACH-SG, will host joint meetings with representativesfrom other structural genomics programmes.3) Unrestricted web-based training information: All workshop and conference programmeswill be published on a dedicated TEACH-SG website.4) European Structural Genomics Newsletter: As part of the information dissemination,a newsletter will be established5) Visits from world-class scientific researchers in SG.Expected results:TEACH-SG will provide a platform for training young scientists and those from smaller laboratoriesand new EU member states in the technologies developed in Structural Genomics,particularly in high throughput techniques. Training will be provided in: i) bioinformaticsapproaches to target selection and data handling; ii) high throughput automated methodsin cloning and protein expression in prokaryotic and eukaryotic systems; iii) automatedprotein characterization iv) high volume crystallogenesis and evaluation; v) computationalstructural determination methods. The programme of networking meetings will have a specificStructural Genomics/Proteomics theme, presenting recent technological and methodologicaladvances in the field with the aim of fostering a constructive dialog between developersof similar or complementary technologies.Potential impact:www.teach-sg.euTEACH-SG will provide essential focus for training in all the main methodological areasof high throughput structural biology, bringing together expertise from each programme toprovide integrated skills resource for researchers. Productive associations with the commercialand industrial sector will also identify and support the transfer of developmental workinto the highly focused area of new drug design. TEACH-SG will provide a scale of trainingand opportunity that is not always met with a limited budget available within a multidimensionalbut largely research-driven programme. TEACH-SG will be able to concentrateon providing these resources, particularly practical hands-on experience of emerging andfast-moving technologies and will be in an excellent position to monitor the impact of thisprogramme in subsequent years.212From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Training and Education in High Volumeand High Value Structural GenomicsKeywords:structural proteomics, training, workshops,website, networking, crystallography,structure determinationPartnersProject Coordinator:Prof. David StuartUniversity of OxfordWellcome Trust Centre forHuman GeneticsDivision of Structural BiologyRoosevelt DriveHeadington, OX3 7BN, UKdave@strubi.ox.ac.ukProject Manager:Dr. Susan DaenkeUniversity of OxfordWellcome Trust Centre forHuman GeneticsRoosevelt DriveHeadington, OX3 7BN, UKsusan@mail.strubi.ox.ac.ukProf. Joel L. SussmanWeizmann Institute of ScienceDepartment of Structural BiologyFaculty of ChemistryRehovot, IsraelDr. Stephen CusackEuropean Molecular BiologyLaboratory (EMBL)Grenoble OutstationGrenoble, FranceProf. Dino MorasCentre Européen de Rechercheen Biologie et en Médecine –Groupement d’Intérêt EconomiqueUPR9004/CERBM G.I.E.Illkirch, FranceProf. Keith WilsonUniversity of YorkDepartment of ChemistryStructural Biology LaboratoryYork, UKDr. Anastassis PerrakisNetherlands Cancer Institute (NKI)Division of Molecular CarcinogenesisAmsterdam, The NetherlandsDr. Beata VertessyHungarian Academy of SciencesMetabolism and Repair DepartmentInstitute of EnzymologyBudapest, HungaryDr. Jan DohnalekUstav makromolekularniichemie Akademie vedCeske republikyDepartment of Structure AnalysisGroup of Analysis of MolecularStructurePrague, Czech RepublicDr. Maria Armenia CarrondoInstituto de Technolgie Quimica e BiologicaProtein crystallography laboratoryOeiras, PortugalProf. Miquel CollInstitute for Research inBiomedicine (IRB Barcelona)Barcelona, SpainProf. Lucia BanciUniversity of FlorencePolo ScientificoCentro RisonanzeMagnetiche (CERM)Sesto Fiorentino, ItalyFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life213

4.COMPARATIVEGENOMICS& MODEL ORGANISMS

4.1MOUSEEURExpressMUGENPRIMEFLPFLEXEUCOMMEUMODICCASIMIR

EURExpresswww.eurexpress.org/ee/Project Type:Integrated ProjectContract number:LSHG-CT-2004-512003Starting date:1 st January 2005Duration:48 monthsEC Funding:10 800 000State-of-the-Art:This EURExpress integrated project responds to the priority topic “Global in situ gene expressionanalysis in rodent models and human tissues”. EURExpress integrates Europeanskills, efforts, resources and information in the field of systematic gene expression analysis.Expression data of approximately 20 000 genes will be generated by RNA in situ hybridisation(ISH) on E14.5 wild type murine embryos which will result in detailed description(at a cellular level) of gene expression patterns. A ‘transcriptome atlas’ will be generatedusing a newly developed automated RNA ISH system. Automated scanning microscopeswill collect image data which will be electronically sent out in a digital format for annotation.The latter will be performed using a web-based ‘virtual’ microscope and entered ina hierarchical database designed to hold large amounts of image data and display themin a user-friendly format. For a subset of genes, mainly those directly involved in humandiseases, expression data will also be generated by using human and murine tissue arrays.This will offer the opportunity to compare human and mouse expression patterns in adulttissues. This project builds up a strong European concentration of skills in gene expressionanalysis and mouse genomics. It will allow integration with existing European projects,such as mouse mutagenesis and mouse phenotyping projects, which critically depend ondetailed information on gene expression patterns. Integration of the efforts of several Europeanlaboratories will result in the standardisation of methods to generate, collect anddisplay gene expression data. Furthermore, technological expertise will be disseminatedby training and exchange programmes. All expression data will be made readily availableto the scientific community via the EURExpress web-linked database, advancing ourknowledge of gene function and having a significant impact on the identification of geneexpression markers of disease processes.Scientific/Technological Objectives:The scientific and technological objectives of this grant proposal are: represent the major source for the transcriptome atlas. Additional priorities includedisease genes and genes subject to alternative splicing of approximately 20 000 genes mantissues using tissue microarray analysis with medically relevant genes and synergistically integrate with other European mouse functional genomics effortssuch as EUMORPHIA.Expected Results:EURExpress proposes a transcriptome-wide acquisition of expression patterns chiefly bymeans of in situ hybridisation (ISH) with non-radioactive probes and will use this data toestablish a web-linked, interactive digital transcriptome atlas of embryonic mouse. In addi-218From Fundamental Genomics to Systems Biology: Understanding the Book of Life

A European Consortium to Generatea Web-Based Gene Expression Atlasby RNA in situ HybridisationClone SelectionTemplateGenerationEURExpressTranscriptomeAtalsTrackingDatabaseAUTOMATED in situImage AnnotationAutomated MicroscopyWork Flow. In SituHybridization (ISH)tion to generating large sets of embryonic expression data in mouse, EURExpress will takea detailed look at expression in human tissues. Over >1000 disease-related genes willbe analysed using tissue microarrays containing several hundred mouse and adult humantissues. A publicly accessible transcriptome atlas database will be created to store andretrieve all image, experimental and annotation data.The consortium will undertake an integrated approach to create a web-based gene expressionatlas by RNA in situ hybridisation.The direct results at the end of the project will be:The establishment of a tracking database that will allow monitoring and integrating dataflow. This database will be accessible across the project, facilitating the management ofdata production.The establishment of high-throughput ISH technology in Europe.Eurexpress will contribute to setting up a structure in which scientists can be trained in thefield of gene expression and database management.The generation and management of approximately 20 000 murine templates.The implementation of simple search interfaces to the transcriptome database and of aninitial set of programmatic interfaces to other bio-informatics resources to support functionalgenomics analyses.High-resolution expression data throughout brain development for a subset of brain-specificgenes.From Fundamental Genomics to Systems Biology: Understanding the Book of Life219

EURExpressleft: Saggittal section of anE14.5 embryo showing theexpression pattern of Fgfb3(Fibroblast binding protein 3) inthe developing CNS.middle: Expression of anuncharacterized gene in the CNS,in the sympathetic ganglion andin the dorsal root gangliaright: Example of a gene (Otx2)with strong expression in thedeveloping retinaThe gene expression data for approximately 20 000 genes.The generation of ISH data for tissue microarray sections.The implementation of user interfaces, which will provide public access to EURExpress dataand will facilitate its application in functional genomics.The generation of a web-based gene expression atlas.Potential Impact:The era of ‘post-genomic research’ is characterised by the requirement of high-throughputprocedures to exploit the vast amount of information generated in genome projects. Highresolutionanalysis of gene expression can be performed by RNA in situ hybridisation,which allows definition of gene expression with great accuracy. Europe is not only at theleading edge in studies in mammalian genetics and the use of mouse models to elucidatethe genetic bases of disease, but has undertaken the lead in a number of new researchand development areas in the field of mouse functional genomics. EURExpress intends toadd to this European effort by creating an atlas of mouse gene expression in the form ofa searchable database that will be available to the scientific community. The expressionpattern of a gene in a multicellular organism is a basic feature of the biological function ofany gene. The mouse is strategic for this type of study because the mouse genome encodesan experimentally tractable organism and has emerged as a pre-eminent organism for thestudy of human diseases and gene function. More than 98% of human genes are presentin the mouse.The potential impact on the study of human development and disease is enormous: phenotypes evaluate disease prognosis and to measure therapeutic benefits.Keywords:RNA in situ hybridisation, mouse, gene expression analysis, functional genomics, transcriptomeatlas, automated RNA ISH system, web-based virtual microscope, web-linked geneexpression database220From Fundamental Genomics to Systems Biology: Understanding the Book of Life

A European Consortium to Generate a Web-Based Gene Expression Atlasby RNA in situ HybridisationPartnersProject Coordinator:Prof. Andrea BallabioFondazione TelethonTIGEM-Telethon Institute of Genetics and MedicineVia Pietro Castellino 11180131 Naples, Italyballabio@tigem.itDr. Uwe RadelofRZPD German Resource Center for Genome ResearchBerlin, GermanyProf. Gregor EicheleMax-Planck Institute of Biophysical ChemistryGöttingen, GermanyDr. Marie-Laure YaspoMax-Planck Institute for Molecular GeneticsBerlin, GermanyDr. Duncan DavidsonMedical Research CouncilMRC Human Genetics UnitEdinburgh, UKProf. Stylianos AntonarakisUniversity of GenevaFaculty of Medicine/ Division of Medical GeneticsGeneva, SwitzerlandProf. Salvador Martinez PerezUniversidad Miguel HernandezInstituto de Neurociencias -Laboratorio deEmbriología ExperimentalAlicante, SpainDr. Pascal DolleCentre Européen pour la Recherche en Biologieet MédecineMouse Clinic InstituteIllkirch, FranceDr. David TannahillWellcome Trust Sanger InstituteWellcome Trust Genome CampusHinxton, UKProf. Pier Paolo Di FioreIFOM, The FIRC Institute for Molecular OncologyMilan, ItalyDr. Stefan KruseOrgarat GmbHEssen, GermanyDr. Paolo SarmientosPRIMM SrlMilan, ItalyFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life221

MUGENwww.mugen-noe.orgProject Type:Integrated ProjectContract number:LSHG-CT-2004-005203Starting date:1 st January 2005Duration:60 monthsEC Funding:11 000 000State-of-the-Art:Immunological diseases are complex diseases. They encompass a wide variety of disorders,affecting a steadily increasing proportion of people living in modern societies. Duringthe past decade, dramatic advances have been made in understanding the mechanismsregulating the immune system, its pathological processes and the processes of immune deviation.Central to this was the ability of studying individual genes in the immune system oflive animals using gene-targeting technologies. At the same time, this allowed the developmentof models of immune diseases.Life Sciences have entered the post-genomic era. A surprisingly small number of 30 000or less genes comprise our genome. Thus, it is feasible to apply technologies such as DNAmicroarrays and proteomics to analyse almost all genes and proteins simultaneously. Thisprovides the unprecedented opportunity to map genes and gene networks systematically.By applying functional genomics to models for immunological diseases, gene-networks canbe mapped and genes underpinning immune deviations and diseases can be identified.This will unlock a huge potential for generating novel diagnostic tools and identifying novelpharmacological targets. The next major contribution to our understanding of the immunesystem is expected to come from a systematic coordinated application of functional genomicsapproaches to animal models for immune disorders or processes.Scientific/Technological Objectives:MUGEN aims to structure and shape a world-class network of European scientific and technologicalexcellence in the field of murine models of human immunological diseases thatwill advance understanding of the genetic basis of disease and enhance the innovation andtranslatability of research efforts. The network is pursuing three parallel approaches: mumuse of the common resources to identify new target genes for immune processesand diseases expertise able to provide all MUGEN participants with the services necessary for anefficient application of post-genomic protocols relational database for the integration and management of knowledge and informationin the area of immunological research.Expected Results:MUGEN aims to bridge the gaps in immunological research by assembling, coordinatingand exploiting the animal model resources of its participants, and employing a unifyingfunctional genomics approach to efficiently predict and validate dominant gene function withpathogenic relevance for human immunological disease. In the first phase, the project is assimilatingexpertise in key areas of immunological research that can be divided roughly intothe three categories: basic immunological processes, immunological diseases and immunogenetics.Following this assimilation, a selective functional genomics strategy will lead to theidentification of putative genetic networks in human immunological diseases. A comparativeanalysis of the data produced by the first phase will allow us to decide on key genetic targets222From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Integrated Functional Genomicsin Mutant Mouse Models as Toolsto Investigate the Complexity ofHuman Immunological Diseasefor immune diseases. Integratingfunctional genomic platforms willbe implemented to validate thegenetic targets in animal modelsystems and allow for the developmentof biotechnological productstargeting pathological processes.This will produce new basicknowledge on immune processesand additional targets for humanimmunological diseases.Through the integration of thisknowledge into the MKE, the resultsfrom this network will helpformulate new concepts for clinicalapplications. Besides the scientificand technological components, thenetwork is keen on spreading itsscientific and technological excellence.The primary objective is topromote training-through-researchto a new generation of scientists.MUGEN also wants to create animpact on the public awareness ofthe pan-European dimension of researchefforts into immunologicalproblems.TNFRI positiveFollicular Dendritic CellsMUGEN is dedicated to extendingevery effort to promote the exploitation,dissemination and communicationof its scientific and technologicalexcellence to key stakeholders in the area of immunological diseases, includingphysicians, patients, policy-makers, the industry, academia and the public at large.Potential Impact:Immune pathologies encompass a wide variety of disorders with epidemiological relevance,hence the discovery of therapeutic targets is a major priority in European health policies.Previous work in immunological research resulted in independent knowledge, complementaryexpertise and resources. The benefit of the consortium lies in the integration of laboratoriesthat are expert in the modelling of immunological processes or disease, state-of-the-arttechnologies in genome research and functional genomics, with the aim of enhancing ourunderstanding of mechanisms in immunity and disease.The coordinated application of functional genomics approaches to existing mouse modelsand the integration of the research results into a common knowledge environment is expectedto have a significant impact on our understanding of pathways and gene networks underlyingimmunological diseases. With the notion that the major drug candidates in clinicalTNFRI deficientFollicular Dendritic CellsFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life223

MUGENdevelopment were either predicted or validated in mouse models, this approach promises toadd significantly to future diagnostic and treatment options of immune related diseases.Thus, the successful implementation of the network will have a major structural impact forbiomedical research in Europe, which will persist well after the end of the duration of theproject. MUGEN’s achievements and deliverables are expected to benefit research beyondits borders and will therefore be of broad scientific and socioeconomic value.Keywords:functional biology, molecular genetics, animal immunology, targeted mutagenesis, animalmodels, molecular pathways, exploratory drug discovery, functional genomicsProject FlyerThis is the first project flyerdescribing participation andactivities throughout the firstJoint Programme of Activities,running from month 1-18.© BSRC Al. FlemingPartnersProject Coordinator:Dr. George KolliasBiomedical Sciences Research Center34 Al. Fleming Street16672 Vari, Greeceg.kollias@fleming.grProf. James DisantoInstitut PasteurUnité des Cytokines et Developpement LymphoideParis, FranceDr. Günter HaemmerlingDeutsches Krebsforschungszentrum (DKFZ)Molekulare ImmunologieHeidelberg, GermanyProf. Bernard MalissenCentre National de la Recherche Scientifique (CNRS),Delegation ProvenceMarseille, FranceProf. Paola Ricciardi-CastagnoliUniversity of Milano-BicoccaDepartment of Biotechnology and BioscienceMilan, ItalyProf. Maries Van Den Broek, Prof. Rolf ZinkernagelUniversity of ZurichInstitute of Experimental ImmunologyZurich, SwitzerlandDr. Werner MüllerGBF Gesellschaft für Biotechnologishe Forschung mbHDepartment of Experimental ImmunologyBraunschweig, GermanyProf. Anton BernsNetherlands Cancer InstituteAntoni van Leeuwenhoek HospitalDivision of Molecular GeneticsAmsterdam, The Netherlands224From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Integrated Functional Genomics in Mutant Mouse Models as Tools toInvestigate the Complexity of Human Immunological DiseaseProf. Alvis BrazmaEuropean Molecular Biology Laboratory (EMBL)European Bioinformatics Institute (EBI)Microarray Informatics TeamOutstation HinxtonHinxton, UKProf. Lars Fugger, Prof. Dimitris KioussisMedical Research CouncilHuman Immunology UnitOxford, UKProf. Rikard HolmdahlLunds Universitet – Medical Inflammation ResearchDepartment of Cell and Molecular BiologyLund, SwedenProf. Paola Ricciardi-CastagnoliGenopolis ConsortiumUniversity of Milano-BicoccaDepartment of Bioscience and Biotechnology/U4Milan, ItalyDr. Antonio LanzavecchiaInstitute for Research in BiomedicineBellinzona, SwitzerlandProf. Klaus PfefferHeinrich-Heine-Universitat DüsseldorfInstitut für Medizinische MikrobiologieDüsseldorf, GermanyDr. François RomagneInnate Pharma SASMarseille, FranceDr. Martin BachmannCytos Biotechnology AGZurich-Schlieren, SwitzerlandJesper ZeuthenBiomedical Venture, Bankinvest GroupCopenhagen, DenmarkDr. Alberto MantovaniInstituto Clinico HumanitasRozzano, ItalyDr. Bjorn LowenadlerBiovitrum ABGothenburg, SwedenDr. Manolis PasparakisUniversity of CologneInstitute of GeneticsDepartment for Mouse Genetics and InflammationCologne, GermanyDr. Lefteris ZachariaBioMedCode Hellas SAVari, Athens, GreeceProf. Andreas RadbruchDeutsches Rheuma-ForschungszentrumBerlin, GermanyProf. Glauco Tocchini-ValentiniConsiglio Nazionale delle RichercheIstituto di Biologia CellulareRome, ItalyProf. Jurg TschoppUniversity of LausanneInstitute of BiochemistryEpalinges, SwitzerlandDr. Klaus RajewskyThe CBR Institute for Biomedical Research IncHarvard Medical SchoolBoston, USADr. Andreas PersidisBiovista – A. Persidis & Sia O.E.Elliniko, Athens, GreeceFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life225

Project Type:Coordination ActionContract number:LSHG-CT-2005-005283Starting date:1 st June 2005Duration:48 monthsEC Funding:799 417PRIMEState-of-the-Art:www.prime-eu.orgAt present, the genetic make-up or genome of the mouse is familiar to scientists. The next challengefor biomedical science is to determine the function of these genes, and the manner inwhich their alterations can cause disease. This is what is referred to as functional genomics.The mouse model plays a pivotal role in the investigation of human diseases and their diagnosisand treatment. Most EU member states perform research into mouse functional genomics.This research is funded at two levels: nationally, and by the European Commission. Mousefunctional genomics research in Europe would benefit significantly from a pan-European approach,which would integrate both national and EU programmes. Greater interaction betweenresearch scientists and national policymakers would in fact allow for research prioritiesto be formulated.The European Commission provides support for infrastructures, such as the developmentof databases of anatomy, or the European Mutant Mouse Archive (EMMA). Collaborationamongst policy makers within the member states may promote the development of new strategies,which would secure funding to support these essential infrastructures.Scientific/Technological Objectives:In delivering a new coordinating action to improve the structure and integration of Europeanmouse functional genomics, we propose 3 phases for PRIME, namely:1. Benchmarking, mapping and assessment of European activities committed to mousefunctional genomics;2. Exploring methods for convergence of policy, communality of research and communication;3. Extending and consolidating the new coordination activities.The aim is to ensure that Europe delivers research of outstanding quality, by employing moreintegrated approaches and by more effectively harnessing existing resources (both biologicaland informational); the development of new resource and infrastructure opportunitieswill likewise further this cause. Achieving these goals will allow us to more advantageouslycompete for funding, utilise available opportunities, and ultimately acquire financial backingfrom both national and European sources.Networking meetings will be held, with the intention of determining how far Europe isalready integrated in terms of research policy, and how the means for achieving suchconvergence might be enhanced. It is also important to assess how communication andinformational resources can assist in this matter. Following networking meetings, dialoguebetween expert groups of scientists and policy makers will establish new means for improvedconvergence of policy, communality of research and communication. The followingkey areas will be addressed:Convergence of research policy1. Initiation of dialogue between key research funders and policy makers;2. Exploration of research policies and mechanisms of research support.Communality of research currency1. Determination of current resource centres (including infrastructures), inclusive of thoseunder development, and those requiring assistance;2. Determination of informatics currently used to keep records, and provide access tothese resource centres;226From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Priorities for mouse functional genomicsresearch across Europe: integrating andstrengthening research in Europe3. Determination of areas with standard protocolsin place, and areas lacking such protocols;4. Determination of the presence and absence ofquality control.Improved communication1. Determination of websites and databases currentlyavailable, and of means to improvetheir inter-communication;2. Exploration of training needs, and means tofund training;3. Determination of available expertise at individualinstitutes within the project, and potentialfor training provision.Potential Impact:The Eumorphia programme of mouse phenotyping delivered pan-European standards fora mouse phenotyping platform (www.empress.har.mrc.ac.uk). PRIME will investigate standardisationin other areas of mouse functional genomics, by investigating means of producingcommon and standardised information systems for mouse resources, as well as improvingintegration and common data standards.PRIME will find ways to avoid duplication in research, by facilitating interaction betweenresearch groups working in common research areas; improve access to resources and databases,ensuring that data can be shared and avoiding duplication; and work to commonstandards and protocols, allowing data to be directly compared by laboratories, reducingthe need to duplicate the research. In addition, the project will genuinely benefit the causeof animal welfare, by reducing the number of animals used for research purposes.Keywords: mouse functional genomics, animal models, integrating research,resources, infrastructures, research policiesPartnersProject Coordinator:Prof. Steve BrownMedical Research CouncilMammalian Genetics UnitMRC HarwellOxfordshire, OX11 0RD, UKs.brown@har.mrc.ac.ukProf. Johan AuwerxInstitut Clinique de la SourisIllkirch, FranceProf. Philip AvnerInstitut PasteurParis, FranceProf. Martin Hrabé de AngelisGSF-National Research Center forEnvironment and Health GmbHInstitute of Experimental GeneticsNeuherberg, GermanyProf. Andrea BallabioTIGEM, Telethon Institute of Genetic MedicineNaples, ItalyFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life227

FLPFLEXProject Type:Specific TargetedResearch ProjectContract number:LSHG-CT-2005-513769Starting date:1 st July 2005Duration:42 monthsEC Funding:1 698 000State-of-the-Art:The aim of FLPFLEX is to develop a novel genetic approach to the manipulation of geneexpression in the mouse in order to dissect complex genetic pathways and to providemore accurate models of human disease. Most major human diseases are caused by smallcumulative changes in cell function that are often related to inherited susceptibility to differentdiseases. Recapitulating these multiple genetic susceptibilities in an animal model hasremained a major challenge to modern medical research. The FLFPLEX system engages thecell’s own gene regulatory circuits to capture subtle gene expression patterns, and at thesame time provides a means to target different small changes to specific genes, allowingrapid assessment of the effect of gene mutations that cause human disease. This novel technologyprovides powerful and adaptable tools for designing increasingly complex geneticmodels of human physiology and pathology.Scientific/Technological Objectives:The project will develop readout vector technologies, establish the FLPFLEX cell library anddevelop flexible genomic insertion cassettes carrying modifications to allow recombinasemediatedcassette exchange of effector genes of interest. The FLPFLEX vector carrying a multifunctionaltag will be randomly incorporated into the genome of embryonic stem (ES) cells.The team will also sequence and identify 10 000 FLPFLEX cassette integration sites usingmouse genomic information. Fifty FLPFLEX clones will be selected for further characterisationand focused studies in vivo. Different effector genes will be introduced in selected FLPFLEXcell clones. The consortium will engage and refine the FLPFLEX system in a series of proof-ofconceptexperiments that focus on genes whose disease relevance is well documented, butmutations which have yet to be modelled in the mouseExpected Results:Once proven, the system can be scaled to produce the desired change in virtually anygene of clinical interest. The project also intends to provide an efficient mechanism for generating,characterising and disseminating these models. FLPFLEX is strategically designedto provide an efficient mechanism for generating, characterising and disseminating thesemodels. Information and reagents generated will be disseminated on a publicly accessibledatabase.Potential Impact:These studies will be correlated with work in related EU-funded projects on mouse gene expressionpatterns and mutagenesis and the models will be disseminated to the internationalscientific community for further analysis and testing, broadening the knowledge base ofgene expression in mice for future testing.Keywords:medical genetics, molecular genetics, genetic engineering, animal models228From Fundamental Genomics to Systems Biology: Understanding the Book of Life

abPartnersProject Coordinator:Prof. Nadia RosenthalEuropean Molecular Biology Laboratory (EMBL)Mouse Biology UnitMonterotondo OutstationCampus “A Buzzati-Traverso”Via Ramarini 3200016 Monterotondo, Italyrosenthal@embl-monterotondo.itProf. Andrea BallabioTIGEM, Telethon Institute of Genetics and MedicineRome, ItalyProf. Dr. Wolgang WurstHelmholtz-Zentrum MuenchenGerman Research Center for Environmental HealthInstitute of Developmental GeneticsNeuherberg, GermanyProf. Riccardo Cortese(Partner until project month 24)Istituto Di Ricerca Di Biologia Molecolare P AngelettiPomezia, ItalyDr. Hansjorg HauserHelmholz Center for Infection ResearchDepartment of Molecular BiologyBraunschweig, GermanyA Flexible Toolkit for ControllingGene Expression in the MouseThe transgene has the samepattern of expression of theendogenous SPNR gene, asvisualized by in situ hybridizationwith both SPNR and GFP probesand by direct GFP fluorescence(a) Diagram of direct (geo) andflipped (hygro-GFP) insertions inthe third intron of the SPNR locus(b) Sagittal sections of wholeembryos at 13.5 d.p.c. ofheterozygous SPNR +/GFPmice, hybridized with a DIGlabeledprobe of the endogenousSPNR gene and the GFP gene,indicate a specific signal in thetelencephalon, mesencephalonand spinal cord. Direct GFPvisualization of the adjacentsections shows the same patternof expression of the transgene.From Fundamental Genomics to Systems Biology: Understanding the Book of Life229

EUCOMMwww.eucomm.orgProject Type:Integrated ProjectContract number:LSHM-CT-2005-018931Starting date:1 st January 2006Duration:48 monthsEC Funding:13 000 000State-of-the-Art:The EUCOMM project responds to the most important topic defined by Priority 1, LifeSciences and Biotechnology for Health, Genome-wide Mutagenesis in Mouse. EUCOMMintegrates European skills, efforts, resources and infrastructure to produce, in a systematichigh-throughput way, mutations throughout the mouse genome. A collection of up to 20000 mutated genes will be generated in mouse embryonic stem (ES) cells using conditionalgene trapping and gene targeting approaches. This library will enable mouse mutants tobe established worldwide in a standardised and cost-effective manner, making mouse mutantsavailable to a much wider biomedical research community than has been previouslypossible. For a subset of genes relevant for human disease, mutant mice will be established,archived and analysed. This will offer an opportunity to decipher molecular diseasemechanisms and, in some cases, provide a foundation for the development of diagnostic,prognostic and therapeutic strategies. This project is built on exceptionally strong Europeanexpertise in mouse molecular genetics, genomics and bioinformatics, and enables automationof targeting vector production and professional dissemination of material. EUCOMMfosters integration with existing European consortia which address mouse gene expressionanalysis, mutant phenotyping, imaging and archiving. Progress of all of these projects willbe enhanced by EUCOMM mouse mutants. All targeting vectors, mutant ES cells, mouseresources and standard operating procedures generated by EUCOMM are displayed to thescientific community via the EUCOMM web-linked database, other EU consortia databasesand the Ensembl browser, and distributed by two professional distribution units. Taken together,EUCOMM will make a major contribution to the analysis of gene function. Finally,EUCOMM resources will represent major opportunities for exploitation by SMEs and thepharmaceutical industry.Chimeric mice © GSF - IDGPhoto: Ralf KuehnScientific/Technological Objectives:EUCOMM presents a work plan for a pan-European effort in mouse mutagenesis that buildson existing resources in mutagenesis, gene expression analysis, phenotyping, archivingand bioinformatics to move towards a comprehensive annotation of gene function in themouse genome. EUCOMM aims at making a significant contribution to the internationaleffort to establish a library of conditionallymutated mouse ES cells whichare available to the scientific community.An ES cell library containingup to 20 000 independently mutatedgenes will be created using conditionalgene trapping and conditionalgene targeting approaches. From themutant ES cell resource, by EUCO-MM itself, up to 320 mutant mouselines will be established focusing ondisease-relevant gene mutations. EU-COMM’s mutant ES cells, vectors andmouse models are publicly accessiblevia an interactive website, and materialis disseminated via two professionaldistributing units.230From Fundamental Genomics to Systems Biology: Understanding the Book of Life

The European Conditional MouseMutagenesis ProgrammeSchematic presentation ofEUCOMM organisationExpected Results:The expected EUCOMM results after the end of the funding period will be: conditional gene targetingmutations in mouse EScells, including mutationsassociated with humandisease archiving of up to 320mutant mouse lines 20 ligand-inducible Crerecombinaseexpressingtransgenic mouse lineswhich differ in theirexpression characteristics an online database todisseminate EUCOMMmaterial worldwideMouse embryonic stem (ES) cellcolonies ©GSF - IDGPhoto: Ralf KuehnFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life231

EUCOMM integration of EURExpress, FLPFLEX, EMAGE, PRIME, FunGenES, EUMODIC, EMMA,and others.Potential Impact:EUCOMM’s repository of conditionally mutated ES cells will allow the establishment ofsophisticated mouse models for a wide range of human diseases including neurologicaland psychiatric diseases, cardiovascular diseases, cancer and diseases related to ageingprocesses. EUCOMM’s deliverables will also be very useful for target identification andvalidation in the development process of human disease diagnostics and therapeutics, implementedby companies. EUCOMM will secure intellectual property rights and the benefitfor the European industry, especially SMEs, in exploiting the respective results. Altogether,EUCOMM will have a great impact on societal needs as well as on the strengthening of theEuropean biotech industry.Furthermore, EUCOMM will contribute to the establishment of a European Research Area:1) EUCOMM’s repository of conditionally mutated mouse ES cells will allow the establishmentof mouse models in a systematic, standardised, and non-redundant manneracross the European scientific community, thus helping to overcome fragmentation ofresearch efforts.2) EUCOMM will establish a close interaction with several other EU research consortia,including the integration of all the projects’ databases, thereby supporting the establishmentof a European Research Area in web area terms. In addition, EUCOMMco-operates with complementary mouse functional genomics initiatives at the globallevel (KOMP, TIGM in the United States, and NorCOMM in Canada) in the frameworkof the International Knockout Mouse Consortium (IKMC).Keywords: functional analysis of the mouse genome, mouse disease models,conditionally mutated mouse ES cell libraryCell culture robot(HAMILTON MICROLAB STAR)Detail of a HAMILTON MICROLABSTAR, showing the independentlyspreadable channels and a96-channel pipetting head inthe background. ©Hamilton LifeScience Robotics allowed the useof the picture for this purpose.Photo: Alexander Starcevic232From Fundamental Genomics to Systems Biology: Understanding the Book of Life

The European Conditional Mouse Mutagenesis ProgrammePartnersProject Coordinator:Prof. Wolfgang WurstHelmholtz Zentrum München, German Research Centerfor Environmental Health GmbHInstitute of Developmental GeneticsIngolstaedter Landstrasse 185764 Neuherberg, Germanywurst@helmholtz-muenchen.deProject Co-Coordinator:Prof. Allan BradleyGenome Research LtdWellcome Trust Sanger InstituteWellcome Trust Genome CampusHinxton, CB10 1SA, UKabradley@sanger.ac.ukProf. Nadia RosenthalEuropean Molecular Biology Laboratory (EMBL)EMBL Monterotondo OutstationMouse Biology UnitMonterotondo, ItalyProf. Steve BrownMedical Research CouncilMammalian Genetics UnitHarwell, UKProf. Glauco Tocchini-ValentiniConsiglio Nazionale delle RicercheIstituto di Biologia Cellulare (CNR-IBC)Monterotondo Scalo, ItalyProject Manager:Dr. Cornelia KaloffHelmholtz Zentrum München, German Research Centerfor Environmental Health GmbHInstitute of Developmental GeneticsIngolstaedter Landstrasse 185764 Neuherberg, Germanycornelia.kaloff@helmholtz-muenchen.deProf. Martin Hrabé de AngelisHelmholtz Zentrum München,German Research Center for EnvironmentalHealth (GmbH)Institute of Experimental GeneticsNeuherberg, GermanyProf. Harald von MelchnerUniversity Hospital of the Johann WolfgangGoethe University FrankfurtDepartment of HaematologyFrankfurt am Main, GermanyProf. Patricia RuizCharité Universitaetsmedizin BerlinCenter for Cardiovascular ResearchBerlin, GermanyProf. Francis StewartTechnische Universitaet DresdenDepartment of Biotec, GenomicsDresden, GermanyProf. Johan AuwerxCentre Européen de Recherche en Biologieet Médecine - Groupement d’Intérêt EconomiqueInstitut Clinique de la SourisIllkirch, FranceFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life233

EUMODICwww.eumodic.orgProject Type:Integrated ProjectContract number:LSHG-CT-2006-037188Starting date:1 st February 2007Duration:48 monthsEC Funding:11 999 832State-of-the-Art:The major challenge for genetics in the 21st century is the determination of the function ofall the proteins encoded by the human genome and, moreover, the role of these proteins indisease. Model organisms will be the key to this endeavour as the EUMODIC team are ableto manipulate the genes and investigate the consequences for the organism. The EUMODIC(http://www.eumodic.eu) consortium is made up of 18 laboratories across Europe and includesleading experts in the field of mouse functional genomics and phenotyping who havea track record of successful collaborative research in the FP5 EUMORPHIA project.The mouse occupies a unique position in determining the genetics of disease for a numberof reasons. Firstly, it demonstrates a remarkably similar development, physiology and biochemistryto the human. Secondly, mouse geneticists have developed a very extensive genetictoolkit that enables defined targeted alteration of genes in the mouse genome. Thirdly,previous research has revealed the complete sequence of the mouse genome.As a first step towards a functional annotation of the mouse genome, EUMODIC will undertakea primary phenotype assessment of up to 650 mouse mutant lines. In addition, a numberof these mutant lines will be subject to a more in-depth secondary phenotype assessment.Scientific/Technological Objectives:The EUMODIC project will provide the tools to determine the function of the genes, by passingthe mice through a series of screens that will fully identify the characteristics (or phenotype)of a mouse that has had its genes altered. These screens are designed to identify abroad range of characteristics to determine the function of the gene. The screens will givereproducible results so information from different groups of mice with different alterations totheir genes can be compared.The EUMODIC consortium will build on the findings of the EUMORPHIA project, whichdelivered a comprehensive database EMPReSS (European Mouse Phenotyping Resourceof Standardised Screens) of Standard Operating Procedures (SOPs) that can be used todetermine the phenotype of a mouse (http://www.empress.har.mrc.ac.uk). EUMODIC hasdeveloped a selection of screens, EMPReSSslim, which is structured for comprehensive,primary, high-throughput phenotyping of large numbers of mice. Primary phenotype assessmentusing EMPReSSslim will be undertaken in four large-scale phenotyping centres. Theyare: GSF (Germany), ICS (France), MRC Harwell (UK) and the Sanger Institute (UK). Phenotypedata from these mice will be made publicly available to the wider scientific communityvia the EuroPhenome database (http://www.europhenome.eu).Mutant lines will be made available from another EU initiative, the EUCOMM (EuropeanConditional Mouse Mutagenesis) project which aims to produce conditional mutations in20,000 mouse genes (www.eucomm.org). EUMODIC will undertake a comprehensive primaryphenotype assessment of up to 650 mouse mutant lines generated by the EUCOMMconsortium in the null configuration.. A distributed network of centres with in-depth expertisein phenotyping domains will undertake more complex, secondary phenotyping screens andapply them to a subset of the mice which have shown interesting phenotypes in the primaryscreen. Phenome data on the mouse lines will be disseminated to the wider biomedical sciencescommunity via the EuroPhenome database (www.europhenome.eu). EUMODIC will234From Fundamental Genomics to Systems Biology: Understanding the Book of Life

The European Mouse Disease Clinic:A distributed phenotyping resourcefor studying human diseasealso undertake further refinement of a number of phenotypingapproaches to speed mouse phenotyping.Overall, EUMODIC is a first step towards tackling theneed for large-scale phenotyping in the mouse and thecomprehensive study of mammalian gene function andits role in disease.Expected Results:The aim of the EUMODIC project is to generate comprehensivephenotype data covering most body systemson a large number of mouse mutants.Moreover, EUMODIC plans a major discovery phase of the programme where many of themost interesting mutants will undergo more detailed secondary phenotyping. The secondarydata recovered will add considerable value to the primary phenome data on many of themutant lines. Each virtual centre will deliver a set capacity to analyse a number of mutantlines for one or more secondary screens. In addition, EUMODIC may direct particular linesof high interest directly to the secondary phenotyping centres, depending on a variety offactors such as the putative functional domains of the relevant gene, its expression patternsor interactions with other genes of known function.Potential Impact:One of the key objectives of the LifeSciHealth priority has been to translate genomic informationinto an improved understanding of the role of genes in disease. Research onthe determination of the gene function has been supported by the availability of completesequences of both human and a number of model organism genomes. The provision of wellannotated complete sequences of the mouse genome is an important starting-point for thedetermination of the function of mammalian genes and the role they play in disease.With the extensive toolkit that is available to generate mutants, this team is now in a positionto generate mutations for all of the genes in the mouse genome and to examine the phenotypicoutcome for each mutant allele. The information provided would bolster and underpinmany of the projects in both human and mouse genetics that are at the core of Europeanfunding and objectives of the LifeSciHealth Priority. The EUMODIC project will ensure thatEurope will remain competitive in the development of phenotyping tools and approaches.The EUMODIC project is crucial for increasing momentum in the key goals of mouse functionalgenomics by applying phenotyping platforms to the mouse mutant resources that arebeing developed. Moreover, the proposed links with disease genetics groups across Europein the selection of mutants to be phenotyped will underpin the competitiveness of Europeanfunctional genomics programmes.Identifying the genetic bases for human disease is a fundamental goal of biomedical sciencesprogrammes. The investigation of gene function through mouse mutagenesis andphenotyping is a central element in achieving this goal and we can expect that the identificationof the many disease models that will arise from the EUMODIC programme willFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life235

EUMODICconsiderably inform our understanding of disease genetics. The EUCOMM programmewill be complemented by a major effort in the US to develop a knock-out mouse mutant resource(the KOMP initiative). A large-scale gene trap initiative has been recently announced(NorCOMM) in Canada as well. An international Complex Trait Consortium (CTC) is alsoprogressing with the generation of recombinant inbred mice strains which would complementthe mutants created on both sides of the Atlantic.Keywords:phenotyping, mouse disease models, animal models, human disease modelsPartnersProject Coordinator:Prof. Steve BrownMedical Research CouncilMammalian Genetics UnitMRC HarwellHarwell, OX11 0RD, UKs.brown@har.mrc.ac.ukProf Johan AuwerxCentre Européen de Recherche enBiologie et en Médecine GIEInstitut Clinique de la SourisIllkirch, FranceProf. Dr. Martin Hrabé de AngelisHelmholtz Zentrum MünchenGerman Research Center forEnvironmental HealthInstitute of Experimental GeneticsNeuherberg, GermanyProf. Karen SteelWellcome Trust Sanger InstituteWellcome Trust Genome CampusHinxton, UKDr. Werner MuellerHelmholtz-Zentrum fürInfektionsforschung GmbHHelmholtz Centre for Infection ResearchBraunschweig, GermanyProf. Glauco Tocchini-ValentiniConsiglio Nazionale delle RicercheIstituto di Biologia CelluareMonterotondo Scalo, ItalyProf. Ludwig NeysesUniversity of ManchesterHeart Failure GroupManchester, UK236From Fundamental Genomics to Systems Biology: Understanding the Book of Life

The European Mouse Disease Clinic:A distributed phenotyping resource for studying human diseaseProf. Nadia RosenthalEuropean Molecular Laboratory (EMBL)EMBL Monterotondo OutstationMouse Biology UnitMonterotondo, ItalyProf. George KolliasAlexander Fleming BiomedicalSciences Research CenterVari, GreeceProf. Mariano BarbacidCentro Nacional de Investigaciones Oncológicas (CNIO)Spanish National Cancer Research CentreMadrid, SpainDr. Jacqueline MarvelEcole normale supérieure de LyonAni.Rhône-AlpesDR2 Centre National de la RechercheScientifique (CNRS)Lyon, FranceProf. Karen B. AvrahamTel Aviv UniversitySackler School of MedicineDepartment of Human Molecular Geneticsand BiochemistryTel Aviv, IsraelProf. Fatima BoschUniversitat Autònoma de BarcelonaCenter of animal biotechnology and genetictherapy (CBATG)Bellaterra, SpainProf. Walter WahliUniversité de LausanneCentre Integratif de GénomiqueLe GénopodeLausanne, SwitzerlandDr. Yann HeraultCentre National de Recherche Scientifique (CNRS)Institut de Transgenose,Laboratoire d’Immunologie et EmbryologieMoléculaires (IEM)Orléans, FranceDr. Paul SchofieldUniversity of CambridgeDepartment of Physiology,Development and NeuroscienceCambridge, UKProf. Andrea BallabioTelethon Insitute of Genetic andMedicine (TIGEM)Naples, ItalyFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life237

Project Type:Co-ordination ActionContract number:LSHG-CT-2006-037811Starting date:1 st February 2007Duration:36 monthsEC Funding:1 300 000CASIMIRState-of-the-Art:www.casimir.org.ukIn Europe, much of the current effort in functional genomics, as well as knowledge of thebiology of human disease, is underpinned by a scattered collection of databases. Failureto sustain and integrate these databases will ultimately damage Europe’s competitiveness inthese areas of research. CASIMIR is designed to coordinate and integrate databases thathave been set up in support of the Fifth, Sixth and Seventh Framework Programmes for thestorage of experimental data, including sequences; and of material resources, such as biologicalcollections, that are relevant to the mouse as a model for human disease. Ensuringthat databases are inter-operable will generate enormous synergy in the provision, integrationand analysis of data, significantly enhancing the value of research.Scientific/Technological Objectives:CASIMIR will deliver a series of scientific meetings, reports and papers addressing the currentstate of databases supporting mouse functional genomics in Europe, and will recommenda feasible and widely applicable model for their inter-operability and sustainability. Itwill also address the mobilisation of national resources, where databases are funded solelyor partly by Member States. The consortium’s specific objectives are set out below:1) Standardisation of data representation and its semantics;2) Standardisation of data transfer and database-querying protocols;3) Creation of the modes of database use that are required by the community, andprovision of appropriate interfaces;4) Dissemination of information regarding the existence of, and means of accessing,databases throughout Europe;5) Consideration of legal issues surrounding the deposition of data in public databases.Failure to address these issues could damage European research in future, if data resourcesremain fragmented. CASIMIR will also, therefore, address three aspects of the sustainabilityof databases and informatics infrastructures: (1) Scientific sustainability, as measured bythe willingness of scientists to use them and to deposit their data in them, for the benefit ofthe whole scientific community; (2) Financial sustainability, measured mainly in terms of theprovision of curators, database developers and informaticians; (3) Technical sustainability,i.e. the need to accommodate innovations in database and (semantic) web technologies,to keep databases compatible with evolving worldwide standards, once they have beenestablished.Expected Results:In the first phase of the project, which will last nine months, the consortium will gatherinformation concerning interested parties with a stake in informatics infrastructures and databases,beyond the consortium itself, and establish a presence on the world wide web, inorder to inform the community of its existence and to invite external views. It will make useof reports from an existing European project known as PRIME, to obtain information aboutthe current state-of-the-art, in mouse databases in Europe.In the second phase of the project, the consortium will prepare a set of recommendationsfor data standards and semantics, together with reports on strategies for financial sustainabilityand an assessment of the impact of legal considerations on data deposition. Anannual public meeting will be held, which, along with scientific publications, will contributetowards the dissemination of the project’s findings.238From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Co-ordination And Sustainability ofInternational Mouse Informatics ResourcesPotential Impact:CASIMIR will produce a coherent strategy for the technical integration and scientific sustainabilityof the database infrastructure required for mouse functional genomics and relatedinvestigations into human disease. It will lay the foundations for a coherent and sustainableinformatics infrastructure, which will produce added value for both the EuropeanCommission and for funding agencies of the EU Member States. In doing so, it will supportthe following activities: (1) The functional analysis of mammalian genes; (2) The developmentof animal models of human disorders; (3) The development of widely applicableresources for the understanding of gene function and the dissection of genetic networks,which, in turn, will aid comparison of conserved and species-specific functions betweenvarious model organisms and man.Europe currently has a competitive edge over the rest of the world, in terms of academicand industrial research using the mouse as a model. If that advantage is to be retained,a coherent strategy must be settled for maintaining and developing the existing databaseinfrastructure. To this end, CASIMIR will drive integration, the free flow of information andultimately, innovation in the health sciences.Keywords: bioinformatics, databases, mouse, animal modelsPartnersProject Coordinator:Dr. Paul SchofieldUniversity of CambridgeDepartment of PhysiologyDevelopment and NeuroscienceDowning StreetCambridge, UKps@mole.bio.cam.ac.ukDr. John HancockMedical Research CouncilMammalian Genetics UnitHarwell, UKDr. Duncan DavidsonMedical Research CouncilHuman Genetics UnitEdinburgh, UKProf. Nadia RosenthalEuropean Molecular BiologyLaboratory (EMBL)EMBL Monterotondo OustationMouse Biology Unit,Monterotondo, ItalyProf. Glauco Tocchini-ValentiniIstituto di Biologia CellulareConsiglio Nazionale della RicercheMonterotondo Scalo, ItalyDr. Tom WeaverGeneservice LtdCambridge, UKProf. Rudi BallingHelmholtz-Zentrum fürInfektionsforschungBraunschweig, GermanyProf. Martin Hrabé de AngelisHelmholtz Zentrum MünchenGerman Research Center forEnvironmental Health (GmbH)Institute of Experimental GeneticsNeuherberg, GermanyDr. Ewan BirneyEuropean Molecular BiologyLaboratory (EMBL)European Bioinformatics Institute (EBI)Hinxton, UKProf. George KolliasInstitute of ImmunologyBiomedical Sciences ResearchCentre ‘Alexander Fleming’Vari, GreeceFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life239

4.2RATSTAREURAToolsMed-Rat

STARwww.mdc-berlin.deProject Type:Specific TargetedResearch ProjectContract number:LSHG-CT-2004-005235Starting date:1 st January 2005Duration:24 monthsEC Funding:2 400 000State-of-the-Art:The rat is an important model organism for systems biology, providing the most relevantmodels of common multifactorial human disease, and is by far the leading model speciesin pharmacology and toxicology. Decades of exquisite phenotyping and detailed analysisof crosses of inbred rats have resulted in initial localisation of hundreds of loci involved incomplex disease and quantitative phenotypes, but with very few eventual gene identificationsto date. A clear understanding of the origin and structure of the genetic variation in therat will provide a missing key piece of this puzzle. The proposed SNP-based haplotype mapprovides a valuable tool for functional genomics, specifically by focusing positional cloningof QTLs through the reduction of regions obtained through linkage analysis, the selection ofideal strain combinations for further reduction of critical regions, and the use of correlationacross many inbred strains to identify very short gene-harbouring regions.Scientific/Technological Objectives:Taking advantage of the access to novel gene functions promised by mouse and rat QTLstudies, there is a need for new innovative and straightforward approaches that providestrategic support for QTL research in the rat in Europe. The proposed haplotype map willbe represented to the genetics community to facilitate QTL gene identification. The developmentof a set of 150 000 high-quality candidate SNPs is a prerequisite for the constructionof a detailed haplotype map across the rat genome. Ancestral segments of rats representingthe most commonly used rat strains in life science will be used to identify very short genomicregions, which are most likely to harbour the corresponding disease genes. A clear understandingof the haplotype structure and origin of genetic variation in these strains will be akey progress in biology and will have deep impact on understanding disease developmentand health.Expected Results:STAR will lead a comparative molecular analysis across many disease relevant strains. Itwill provide essential tools that will be immediately useful to focus positional cloning of QTLsthrough the reduction of regions obtained through linkage analysis via identification of segmentsshared by the strains used for the cross, and the selection of ideal strain combinationsfor further reduction of critical regions through simple intercross/backcross experiments.Also, the use of correlation between phenotype and ancestral sequence origin across manyinbred strains will help to identify the very short genomic regions most likely to harbourresponsible genes.The research will be objective-driven and carried out in the following steps:1. identification of sufficiently large sets of sequence variation throughout the rat genomewithin transcribed sequences and within genomic sequences2. establishment of a haplotype map3. display of results to integrate into existing databases.242From Fundamental Genomics to Systems Biology: Understanding the Book of Life

A SNP and Haplotype Map for the RatPotential Impact:STAR’s focus is to gather fundamental knowledge and basic tools for functional genomicsby conducting research on sequence variation across the rat genome to define the ancestralhaplotype blocks. It has strong innovative aspects and will contribute towards strengtheningthe competitive position of European research, but it has also a potentially very significantsocietal impact in the mid to longer term regarding the improvement of healthcare.The STAR consortium will internally generate standard operational procedures for defininghaplotype blocks and widely applicable genotyping panels, which will provide a valuablebasis for the creation of standards in SNP typing and validation.Keywords: rat model, SNP, haplotype map, genetic variation, positional cloning,phenotypingPartnersProject Coordinator:Dr. Norbert HübnerMax-Delbrück-Center for Molecular MedicineExperimental Genetics of Cardiovascular DiseasesRobert-Rössle-Strasse 1013092 Berlin, Germanynhuebner@mdc-berlin.deDr. Ivo Glynne GutConsortium National de Rechercheen Génomique (CNRG)Technology DepartmentEvry, FranceDr. Dominique GauguierUniversity of OxfordWellcome Trust Centre for Human GeneticsOxford, UKDr. Ewan BirneyEuropean Molecular Biology Laboratory (EMBL)European Bioinformatics Institute (EBI)Hinxton, UKDr. Roderic GuigóInstitut Municipal d’Assitència SanitariaGenome Bioinformatics Research LabBarcelona, SpainDr. Edwin CuppenHubrecht LaboratoryNetherlands Institute for Developmental BiologyFunctional Genomics GroupUtrecht, The NetherlandsDr. Richard ReinhardtMax-Planck-Institute for Molecular GeneticsHigh Throughput Technology and Service UnitBerlin, GermanyDr. Roderic GuigóCentre de Regulació GenòmicaResearch Group on BiomedicalInformatics (GRIB-IMIM)Barcelona, SpainFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life243

EURAToolswww.euratools.euProject Type:Integrated ProjectContract number:LSHG-CT-2005-019015Starting date:1 st March 2006Duration:48 monthsEC Funding:11 000 000State-of-the-Art:The EURATools Consortium will address fundamental issues of genetic and phenotypic variationin mammalian biology. The project will be carried out in an integrated manner by using anumber of innovative approaches. EURATools methodology is credited with making it possibleto anticipate that progress will be clearly demonstrable against the state-of-the-art.The use of whole-genome scans to identify Quantitative Trait Locus (QTL) is a powerful way toinvestigate the genetic basis of susceptibility to complex human diseases. Although QTL mappinghas become easier with the availability of many genetic markers, identifying the genesthat underlie the QTL that are associated with common phenotypes has proved to be a challenge.The new genome data generated by EURATools will build on, and markedly improve,the recently assembled draft rat genome sequence, thus improving gene models as well as theutility of the sequence for rat genetics.Optimisation of nuclear transfertechniques for standardisedcreation of cloned ratsGenome projects are, bynature, highly collaborative,as it is unusual forany single centre (or evena single country) to embarkon genome projectsalone. This makes theEURATools proposal verysuited to EU funding, andwill place the EU in anextremely competitive position.Collaborative workwith the USA, Canadaand Japan will give theEU a strong place in negotiationson future resources and initiatives in these countries, and will build on the significantinvestment already made by the EU in the area of rat biology and genetics.Moreover, the advancement in knowledge and associated reagents and resources will contributesignificantly to the scientific communities’ understanding of the genetic programmesthat underpin multifactorial diseases. Progress in this area will play a key role in providing theessential tools for the development of future strategies. The main goals of these strategies areto identify susceptibility genes for epidemiologically important disorders; to optimise strategiesfor new drug design; and to identify new targets for therapies for treatment of commonhuman diseases.Scientific/Technological Objectives:The main scientific and technological objectives of the EURATools project are the following:1) Development of high-throughput genomic tools for annotation and identification ofcomplex trait disease genes in the rat;2) Optimization and facilitation of germline modification procedures, refinement andadaptation of nuclear transfer protocols;244From Fundamental Genomics to Systems Biology: Understanding the Book of Life

European Rat Toolsfor Functional Genomics3) Provision of a resource for depositing,exchanging, preserving anddistributing inbred, congenic andmutant rat strains, mapping of multiplephysiological phenotypes;4) Coordination of genome sequence,gene models, mapping resourcesand expression data, developmentof data mining resources and trainingof bioinformatics expertise;5) Definition of genes and regulatorypathways underlying control ofgene expression and protein abundance in relation to disease phenotypes, integrationof expression profiling and linkage analysis;6) Positional cloning of genes in minimal congenic strains representing cardiovascularand inflammatory diseases as models for human diseases, dissection of the complexityof pathway controls.Expected Results:After 4 years, the EURATools programme plans to deliver the positional cloning of several ratcomplex trait genes. Presently, two have been definitively identified, but several more havetantalising results based on very small, minimalcongenic regions and strong positional candidates.Given the development of proposed genome resourcesand tools, the development of this is likelyto accelerate to such an extent that the team couldanticipate entering an exponential phase of QTLgene discovery and characterisation.Based on past successful progress and existing expertiseof EURATools Partners in the field of nucleartransfer and oocyte biology; achieving robust protocolsfor rat cloning and homologous recombinationby the end of the project is anticipated. Resultsfrom the project would potentially give rise to aquantum leap in the research on rat genetics andwould lead to mechanistic experiments of test hypothesesthat, through observational phenotypingexperiments in the rat, have arisen in hundreds oflaboratories world-wide over the past 50 years.Computerised measurementof blood pressure by radiotelemetry in conscious, freemovingratsEURATools programme plans to offer very significantopportunities for translating investment in basicscientific discovery to improvements in healthand opportunities for wealth generation. The toolsto be put in place under these proposals will providethe stimulus for an exciting period of discoveryin biomedical science and translational research.Development of a rat congenicstrain for genetic analysisof rat arthritisFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life245

EURAToolsNuclear donor cellin the pipette prior to transfer– a preparation for rat cloningPotential Impact:The project has strong innovative aspects that will contribute to strengthening the competitiveposition of European research. Specifically, EURATools will merge European researchresources and, most importantly, will use and consolidate common tools and protocols thatwill allow genomics data to be effectively used to understand the biology of the genomefor a large number of inbred strains. The Consortium will also develop a collection of novelmolecular tools to mark and select disease specific inbred strains.EURATools has a potentially significant societal impact regarding the improvement of healthcare.Its integrative and multidisciplinary approach will considerably contribute to the restructuringand strengthening of EuropeanR&D activities. Comparative and functionalgenomics studies are likely to provide datafor annotating the human genome sequence,for building better animal models, for assistingin the development of new therapeuticagents, and for understanding gene regulation.As the genomic sequence is annotatedwith more and more function, it will become increasingly easy to formulate testable hypothesesfor common diseases. In addition, the project will have a broad stimulating effect ongene target validation and drug development in pharmaceutical industries.Keywords:complex traits, drug development, disease mechanisms, informatics, gene targetingPartnersProject Coordinator:Prof. Timothy J. AitmanMedical Research CouncilPhysiological Genomics and MedicineMRC Clinical Sciences CentreHammersmith HospitalDu Cane RoadLondon, W12 0NN, UKt.aitman@csc.mrc.ac.ukProject Manager:Dr. Erik WernerMedical Research CouncilPhysiological Genomics and MedicineMRC Clinical Sciences CentreHammersmith CampusDu Cane RoadLondon, W12 0NN, UKerik.werner@csc.mrc.ac.ukDr. Laurence GameMedical Research CouncilMicroarray CentreLondon, UKProf. Norbert Hübner, Prof. Michael BaderMax-Delbrück-Centrum fürMolekulare Medizin (MDC)Berlin, GermanyProf. John Mullins, Sir Ian WilmutUniversity of Edinburgh (UEDIN)Edinburgh, UKDr. Michal Pravenec, Dr. Vladimír Landa,Prof. Vladimír KrenCzech Academy of Sciences (CAS)Prague, Czech RepublicDr. Ewan Birney, Dr. Xosé M. FernándezEuropean Molecular Biology Laboratory (EMBL)European Bioinformatics Institute (EBI)Hinxton, UK246From Fundamental Genomics to Systems Biology: Understanding the Book of Life

European Rat Tools for Functional GenomicsProf. Anna F Dominiczak, Prof. Walter KolchUniversity of Glasgow (UGL)Glasgow, UKProf. Rikard HolmdahlLund UniversityMedical Inflammation ResearchLund, SwedenDr. Alexandre FraichardgenOway SALyon, FranceProf. Roland WolfCXR Biosciences Ltd. (CXR)Dundee TechnopoleDundee, UKProf. Claude SzpirerUniversité Libre de BruxellesInstitut de Biologie etde Medecine Moleculaires (IBMM)Brussels, BelgiumProf. Mark Lathrop, Dr. Ivo Gut,Dr. Jean WeissenbachCommissariat à l’Energie AtomiqueCentre National de Séquençage (CNS),Centre National de Génotypage (CNG)Evry, FranceProf. Dominique GauguierProf. Jonathan FlintUniversity of OxfordWellcome Trust Centre for Human GeneticsOxford, UKProf. Alberto Fernández-TeruelUniversitat Autònoma de BarcelonaDept. of Psychiatry and Forensic MedicineBellaterra (Cerdanyola del Vallès), SpainProf. Tomas OlssonKarolinska InstituteNeuroimmunology UnitCenter for Molecular Medicine (CMM)Stockholm, SwedenProf. Qi ZhouChinese Academy of Sciences (IOZ CAS)Institute of ZoologyState Key Lab of Reproductive BiologyBeijing, Peoples Republic of ChinaDr. Richard ReinhardtMax-Planck-Institute forMolecular Genetics (MPIMG)Berlin, GermanyProf. Jean-Paul RenardInstitut National de la Recherche Agronomique (INRA)Unité de Biologie du DéveloppementJouy en Josas, FranceFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life247

Med-RatProject Type:Specific TargetedResearch ProjectContract number:LSHG-CT-2006-518240Starting date:1 st March 2006Duration:36 monthsEC Funding:1 575 000State-of-the-Art:The post-genomic era offers opportunities to improve the quality of life in Europe. Whilstprojects involving mice and human genome have revealed the basic genomic information,complex modelling systems are now required to transfer knowledge into functional biologyand medicine. Transgenic (TG) animal models play an important role in the attempt to discoverthe genetic basis of human disease. In particular, there is a need for animal modelsinstead of cell culture because of the complexity of the biological processes that form the basisof most diseases. To date, most information on genomics has been generated through themouse model. However, the potential of this is limited because the anatomy and physiologyof mice are not always adequate for studying human disease. In addition, the sophisticatedtechniques used for the mouse model have, through the procedure of nuclear replacement,now become available for studies in non-murine species.The MED-RAT project aims to exploit these advances, and, by generating transgenic modelsin other species, bridge the gap between mouse models and treatment of human diseases.Many species have metabolism and organs more similar to humans than to mice. However,the lack of stable stem cell lines in animal species other than mice has impeded the use ofrefined genetic tools for specific targeted genetic models.Mouse clonesScientific/Technological Objectives:The aim of the MED-RAT project is to establish Europe as a leader in animal models for comparativefunctional genetic research by 2008. The establishment of transgenic laboratory animalmodels will reveal the correlation between the genetic code and the biological functions andthis approach will potentially clarify the genetic base of many diseases including Alzheimer’s,cardiovascular diseases, diabetes and cancer.As part of the 6th Framework Programme, the primary objective of MED-RAT is to produce atechnological platform for the generation of novel targeted genetic animal models, thus providinga powerful tool for European functional genomics with great potential for medical research.Additional objectives include: 1) validating the nuclear replacement as a technical platform toproduce transgenic mouse models; 2) clarifying the role of mitochondrial inheritance in nuclearreplacement; 3) improving gene targeting methods in somatic cells cultures; 4) developing animproved system for banking and distributing the newly generated model animals.Expected Results:The examples reported above demonstrate the need to understand gene function differencesin various species. The aim of MED-RAT is to create models in rats with targeted genetic modifications.This will result in the creation of new models to compare the functional genomicsof rats with those of mice. The application ofthese conclusions will create new or improvedmethods for somatic cell gene targeting, gameteand embryo cryopreservation, and newknowledge on the role of mitochondria in nuclearreplacement, Activation of mitochondrialand ribosomal RNA genes following nuclearreplacement will altogether contribute to thecreation of a novel technological platform.The safety and reliability of this platform willbe validated in the mouse model, by applyingan already existing state-of-the-art mousegeno- and phenotyping system.248From Fundamental Genomics to Systems Biology: Understanding the Book of Life

New Tools to Generate Transgenicand Knock-out Mouse and Rat ModelsPotential Impact:The development of novel and more efficient animal nuclear replacement techniques formammalian animal models in mouse and rat with targeted genetic modifications, is crucialfor the generation of precisely defined transgene conditions and defined genomic backgrounds.This is an important prerequisite for the standardised and reproducible appraisalof transgene-induced phenotypic variations. The parallel animal nuclear replacement andphenotype studies within this consortium will allow the standardisation of animal nuclearreplacement procedures and result in interpretation. Development and dissemination of animalmodels are fundamental for making them accessible for the wider scientific community.A separate work package focuses on the cryopreservation of gametes of newly generatedanimal models in mouse and rat. Banking of such gametes and their international exchangewill allow the laboratories involved to study a standardized genetic background model.Forecasts in different countries point out that in 2020, close to 40 percent of the populationwill be older than 65 years. The ageing population is prone to various diseases, causingimmense social and economic problems. Gene medicines will be effective in primary preventionand in the treatment of chronic diseases as they interfere with their molecular cause,and will thus provide better treatment at lower cost.Keywords: gene targeting, somatic cell, nuclear replacement, mouse, rat, comparativefunctional genomics, animal modelsPartnersProject Coordinator:Dr. Andras DinnyesAgricultural Biotechnology CenterGenetic Reprogramming GroupSzent-Gyorgyi A. u. 42100 Godollo, Hungarydinnyes@abc.huProject Manager:Nora BurgmannAgricultural Biotechnology CenterGenetic Reprogramming GroupSzent-Gyorgyi A. u. 42100 Godollo, Hungaryburgmann@abc.huDr. Johannes BeckersHelmholtz Zentrum MünchenDeutsches Forschungszentrumfür Gesundheit und Umwelt(HMGU) (former GSF)Neuherberg, GermanyProf. Mathias MüllerUniversity of Veterinary MedicineInstitute of Animal Breedingand GeneticsVienna, AustriaProf. Poul Maddox-HyttelUniversity of CopenhagenDepartment of Basic Animaland Veterinary SciencesFrederiksberg, DenmarkProf. Keith CampbellUniversity of NottinghamDivision of Animal PhysiologySchool of BiosciencesNottingham, UKDr. Andras DinnyesBioTalentum LtdGodollo, HungaryFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life249

4.3ZEBRAFISHZF-MODELSZF-TOOLS

ZF-MODELSwww.zf-models.orgProject Type:Integrated ProjectContract number:LSHG-CT-2003-503496Starting date:1 st January 2004Duration:60 monthsEC Funding:12 000 000State-of-the-Art:In recent years, model organisms have played an increasingly important role in genomeresearch, both in addressing basic biological questions and in making the best possible useof sequence information for human health (drug design and diagnostics). While Drosophilaand have yielded valuable information, many aspects of human developmentand gene regulation require a vertebrate model. In this context, the zebrafish hasseveral unique advantages, such as transparent, easily accessible embryos, simple breedingand a short generation time. It has therefore become the pre-eminent, non-mammalianvertebrate model organism, complementing the most widely used mammalian organism,the mouse.Zebrafish mutants have been characterised, that affect a large number of developmentalprocesses, such as early embryogenesis, organ formation and simple behaviour. The functionsof most zebrafish genes have been shown to be conserved in other vertebrate groups,and a large proportion of the known zebrafish mutations are candidates for human diseasegenes. The importance of the zebrafish for functional genomics is illustrated by the recentestablishment of several SMEs that focus on zebrafish research. To provide a systematicbasis for the cloning of zebrafish mutations, increasingly powerful genomic tools have beendeveloped, both in Europe and in the USA. The Fishman lab in Boston, for example, hasproduced 4,000 microsatellite markers, while the zebrafish genomics group currently ledby Robert Geisler, in Tübingen, Germany, has mapped several hundred mutations and createda radiation hybrid map for the zebrafish.Scientific/Technological Objectives:The ZF-MODELS consortium will produce new insights into how genes control developmentand ageing in vertebrates, insights that could potentially lead to the development of newor improved therapies for human diseases. Its targets include common pathologies such ascancer, neurodegenerative diseases, muscular dystrophies and eye diseases, as well asresistance to infections, the process of wound-healing and behavioural disorders.Zebrafish development252From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Zebrafish Modelsfor Human Development and DiseaseThe specific, scientific objectives of the project can be described as follows: (1) Two largescalemutagenesis projects, offering scientists the opportunity to examine zebrafish carryinggenetic mutations. The first such screen, organised by the Max-Planck Institute for DevelopmentalBiology, was initiated in January 2005; the second, organised by the University ofFreiburg, got underway in mid-2005. In contrast to previous zebrafish mutagenesis screens,the ZF-MODELS project places an emphasis on the genes relevant to human disease, andon mutations affecting the adult as well as the developing fish; (2) Analysis of gene expressionpatterns. Thousands of fish are being generated, in which the expression of greenfluorescent protein is under the control of enhancer sequences of specific genes (enhancerdetection screening). Under blue light, the tissues of these fish light up where the gene inquestion is being expressed. Three-dimensional patterns of gene expression will also beanalysed during development, on a large scale, using in situ hybridisation; (3) Expressionprofiling and proteomics. The activity (expression) of tens of thousands of zebrafish genesis being analysed on gene chips (microarrays), in an effort to discover how genes regulateeach other’s activity during normal development, and how this regulation is disturbed in mutants.In addition, proteins expressed in normal and mutant zebrafish are being analysed,to elucidate how protein expression is affected.Expected Results:The expected results of the ZF-MODELS project are as follows: (1) Disease models. Fish withgenetic disorders corresponding to human diseases will be produced by chemical mutagenesis(forward genetics) and targeted knockout (reverse genetics), and characterised bythe consortium. These disease models will aid clinical researchers and the European pharmaceuticalindustry in developing new therapies; (2) Drug targets. The vast majority of zebrafishgenes are orthologues to human genes, over half of which have yet to be assigneda function in the Human Genome Project. ZF-MODELS will discover novel candidate genesfor regulatory pathways by their expression patterns and mutant phenotypes. These geneswill be made available to the European pharmaceutical industry for evaluation as potentialdrug targets, in small molecule screens, for instance; (3) Analysis of regulatory pathways.The consortium will elucidate previously unknown pathways of gene regulation that arerelevant to human development. This information will be obtained by expression profilingZebrafish adultFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life253

ZF-MODELSand proteomics, in combination with more traditional approaches in developmental genetics,such as phenotypic and functional analysis of mutants. Improving basic knowledge ofhuman development is central to understanding the causes of many congenital diseasesand cancers.Potential Impact:ZF-MODELS will provide new tools and large data sets for functional genomics of the zebrafish,allowing European researchers to access genomic data from the ongoing sequencingproject in novel ways. There are currently estimated to be nearly 300 research groupsusing zebrafish data and screening methods, of which almost 200 are located in the USA.The American research groups are focusing on the development and deployment of newfunctional genomics tools, in anticipation of sequencing information to be generated by theUK’s Wellcome Trust Sanger Institute. It is important that European groups also have thetools to use this resource, in order to compete on an international level, and to strengthenthe European science base in comparative genomics, and its applications in understandingthe basis of human diseases.The geographical distribution of zebrafish research groups in Europe reflects past investmentsin research as well as the historical development of the field. One of ZF-MODELS’main goals is to spread expertise and to encourage the use of the zebrafish as a non-mammalianvertebrate model in groups emerging beyond the traditional centres of strength — inparticular, in groups in EU Candidate States, which lack the large-scale facilities requiredfor genome sequencing and high-throughput functional genomics, but which could benefitgreatly from use of the zebrafish model, in addressing their specific research questions.The ZF-MODELS consortium will therefore encourage the participation of researchers fromemerging groups across the EU and the Candidate States in its training programmes andworkshops. Arrangements will be made for the training of technicians, and advice will beoffered on means of setting up new laboratories and screening facilities. There will alsobe opportunities for emerging groups to join the consortium — opportunities that will beannounced publicly as and when they rise, through mailing lists, websites and internationalmeetings, as well as through direct contact with those emerging European groups knownto the consortium. With its strong focus on human disease, ZF-MODELS expects to advancebasic, early clinical and translational research.Keywords:functional genomics, model organisms, animal models, disease mechanisms, drug targets,bioinformatics, zebrafish, human developmentPartnersProject Coordinator:Dr. Robert GeislerMax Planck Institute for Developmental BiologyDepartment of GeneticsTübingen, Germanyrobert.geisler@tuebingen.mpg.deProf. Christiane Nüsslein-VolhardMax Planck Institute for Developmental BiologyTübingen, GermanyCarl-Philipp HeisenbergMax Planck Institut of Molecular CellBiology and GeneticsDresden, GermanyDr. Matthias HammerschmidtMax-Planck-Institut für ImmunbiologieFreiburg, Germany254From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Zebrafish Models for Human Development and DiseaseProf. Jane RogersGenome Research LtdWellcome Trust Sanger InstituteCambridge, UKDr. Christine ThisseCentre Européen de Recherche en Biologieet en Médecine (CERBM)Institut de Génétique et de Biologie Moléculaireet Cellulaire (IGBMC)Illkirch, FranceProf. Ronald H. A. PlasterkHubrecht LaboratoryNetherlands Institute for Developmental BiologyUtrecht, The NetherlandsProf. Philip W. InghamThe University of SheffieldCentre for Developmental GeneticsSheffield, UKProf. Stephen WilsonUniversity College LondonDepartment of Anatomy and Developmental BiologyLondon, UKDr. Philippe HerbomelInstitut PasteurDépartement de Biologie du DéveloppementUnité Macrophages et Développement de l’ImmunitéParis, FranceProf. Herman SpainkLeiden UniversityInstitute of BiologyLeiden, The NetherlandsProf. Uwe SträhleForschungszentrum Karlsruhe GmbHInstitut für Toxikologie und GenetikKarlsruhe, GermanyDr. Michael BrandTechnische Universitaet DresdenBIOTEChnologisches ZentrumDresden, GermanyProf. Stephan C. F. NeuhaussUniversität ZürichInstitute of ZoologyZurich, SwitzerlandDr. Frédéric RosaInstitut National de la Santé et de la RechercheMédicale (INSERM)U368 INSERM: “Biologie Moléculaire duDeveloppement”Paris, FranceProf. Wolfgang DrieverAlbert-Ludwigs-Universität FreiburgLaboratory of Developmental BiologyFreiburg, GermanyDr. Thomas BeckerUniversity of BergenSars Centre for Marine BiologyBergen, NorwayDr. Francesco ArgentonUniversita’ degli Studi di PadovaDipartimento di BiologíaPadova, ItalyDr. Laure Bally-CuifGSF-Research Center for Environment and HealthInstitute of Developmental GeneticsNeuherberg, GermanyFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life255

ZF-TOOLSProject Type:SME- Specific TargetedResearch ProjectContract number:LSHG-CT-2006-037220Starting date:1 st January 2007Duration:36 monthsEC Funding:1 739 000State-of-the-Art:Human disease research and drug development rely heavily on the use of animal models.Among these, the mouse model is the most intensively studied. However, over the last decadethe zebrafish has emerged as an attractive alternative model and has progressivelygained importance. This is due to the fact that the zebrafish offers exciting novel researchopportunities because of the optical transparency of its embryos and its amenability togenetics. To date, the value of zebrafish in pharmacological studies has not yet been extensivelyexplored and exploited. However, findings emphasise the potential of using zebrafishin several phases of drug discovery processes and in toxicological screens.Scientific/Technological Objectives:The ZF-TOOLS project comprises the coordinated effort of three research laboratories andthree SMEs aimed at achieving the following two main objectives: Firstly, a genomic-basedmarker discovery for biomedical screens in zebrafish and, secondly, the use of high-throughputmarker analysis and tumour cell implants for the identification of tumour growth andmetastasis factors and organismal defence factors.Transparent zebrafish embryoMore specifically, the project aims to develop a case study for an anti-tumour drug screeningsystem, based on the implantation of fluorescently labelled tumour cells into zebrafishembryos. This innovative tumour cell implantation system is currently being developed byone of the SME partners and has the major advantage that it does not involve the use oftransgenic animals. Growth and metastasis properties of implanted tumour cells can be efficientlymonitored by fluorescence microscopy during the development of the transparentzebrafish embryos. This system resembles the natural situation of tumour growth, as thetumour cells are derived from zebrafish cell cultures of embryonic origin and implantedback into zebrafish embryos. It is envisaged that a powerful screening system can arise bycombining high-throughput marker analysis with the possibility to visualise tumour growthand metastasis in an optically transparent vertebrate model organism.However, for the realisation of this complex screening system, the identification of relevantdisease marker genes in zebrafish represents a crucial step. In ZF-TOOLS, different genomicsapproaches will be used to discover novel markers, which will be suitable for applicationin the ZF-TOOLS tumour screening system and will also have a broader utility fordisease research in the zebrafish model.Expected Results:The strategic aim of ZF-TOOLS is the development of a zebrafish embryo screening systemas an innovative genomics tool. This system will be employed for high-throughput effectivenesstesting of pharmaceutical compounds that have the potential to influence disease processes,including tumour growth, metastasis and immune defence responses. This zebrafishscreening tool offers some unique features that make it very attractive in comparison withexisting tools.In order to establish the zebrafish screening tools, the project will undertake a multidisciplinaryfunctional genomics approach which integrates different global expression profilingtechniques and bioinformatics. Based on this approach, the ZF-TOOLS project expects toachieve the following results:1) Knowledge of tumour growth and metastasis factors and organismal defence factors;2) High-throughput tools for quantitative analysis of disease marker sets;3) A collection of constitutive and inducible, oncogenic and non-oncogenic reporter256From Fundamental Genomics to Systems Biology: Understanding the Book of Life

High-throughput Toolsfor Biomedical Screens in Zebrafishcell lines useful for basic disease research and for application in screeningsystems;4) Case study results of a novel anti-tumour drug screening system, based on theimplantation of fluorescently labelled tumour cells into zebrafish embryos.Potential Impact:The ZF-TOOLS project aims to reinforce European competitiveness by generatingstrategic knowledge thanks to its multidisciplinary research approach. The developedtools and technology will be exploited for basic research on vertebrate disease andfor strategic research and service activities on behalf of three high-tech SMEs.The lack of basic knowledge of disease marker genes is the current bottleneck forbiomedical research in zebrafish and for genomics-based compound screens in thismodel organism. The ZF-TOOLS project uses multidisciplinary functional genomicsapproaches to discover novel disease markers. The expected identification of factorsimportant for tumour growth and metastasis and organismal defence responses willgenerate fundamental knowledge relevant to human health and will open the door tothe establishment of zebrafish-based biomedical research and screening tools.Tumour screening systemKeywords: zebrafish, animal models, zebrafish embryo model, oncogenic cellimplants, anti-tumor drug discovery, reporter cell lines, tumor markers,immune response markers, expression profiling, screens, highthroughputtechniquesPartnersProject Coordinator:Dr. Annemarie H. MeijerLeiden UniversityInstitute of BiologyMolecular Cell BiologyWassenaarseweg 642333 AL Leiden, The Netherlandsa.h.meijer@biology.leidenuniv.nlProf. Dr. Herman P. SpainkZF-screens BVLeiden, The NetherlandsDr. Nicholas Simon FoulkesForschungszentrum Karlsruhe GmbHInstitute for Toxicology and GeneticsEggenstein-Leopoldshafen, GermanyDr. Bas ReichertBaseClear BVLeiden, The NetherlandsDr. Tamás ForraiZenon Bio LtdSzeged, HungaryDr. Mátyás MinkSzeged UniversityDepartment of Geneticsand Molecular BiologySzeged, HungaryFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life257

4.4OTHERMODELSNemaGENETAGTP Plants and HealthX-OMICS

NemaGENETAGhttp://elegans.imbb.forth.gr/nemagenetagProject Type:Specific TargetedResearch ProjectContract number:LSHG-CT-2003-503334Starting date:1 st January 2004Duration:36 monthsEC Funding:1 782 474State-of-the-Art:The nematode Caenorhabditis elegans is a widely appreciated, powerful platform onwhich to study important biological mechanisms related to human health. Numerous humandisease genes have homologues in C. elegans, and essential aspects of mammalian cellbiology, neurobiology and development are faithfully recapitulated in this worm. We aim todevelop cutting-edge tools and resources that will facilitate the modelling of human pathologiesin C. elegans, and advance our understanding of animal development and physiology.The final product of our focused project – a comprehensive collection of transposon-taggedalleles – together with the acquisition of efficient transposon-based tools for mutagenesisand transgenesis in C. elegans, should be of great value to the European and internationalscientific community.Scientific/Technological Objectives:Our initiative has three clear objectives.1. Optimisation/automation of the Mos1-based system for large-scale mutagenesis.The Mos1 system has already been established as an efficient tool for gene taggingin C. elegans. We will further characterise this system in terms of insertion bias andmutagenicity. Through such detailed characterisation, we will seek to optimise Mos1tools and reagents for high-throughput screenings.2. Development of novel transposon-based systems for mutagenesis, transgenesis andgenome engineering in C. elegans.Development of other transposon systems is important for two reasons. First, all transposonshave preferential insertion sites in genomes. Second, transposons can beused to introduce foreign sequences into the host genome and can accommodateexogenous DNA, but the frequency of transposition decreases exponentially withthe size of the insert. We plan to develop alternative transposon systems in C. elegansbased on the well-characterised and widely used Minos transposable element.Transposon insertions represent an entry point to further manipulate the locus wherethey were inserted. We aim to develop and optimise transposon-based tools fortransgene-instructed gene conversion as an alternative to homologous recombinationtechniques that are not available in C. elegans.3. Construction of an ordered library of transposon-tagged alleles covering at least85% of the C. elegans gene complement.Our aim is to use the tools and technologies described above to generate a comprehensivecollection of transposon-tagged nematode genes. Such a mutant collectionwill provide an extremely valuable resource because it will accelerate our understandingof gene function, which is a major challenge in biology.Expected Results:The expected results of our activities are categorised into two major types.Research results:1. Optimisation/automation of Mos1 transposon-based technologies2. Development of alternative systems for mutagenesis and transgenesis in C. elegansbased on the Minos transposon3. Generation of a comprehensive, ordered library of tagged nematode genes4. Case-studies/evaluation of the resource.Technological development, innovation and demonstration-related results:5. Platform technology development/deployment.260From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Potential Impact:The massive amount of raw data generatedby genome sequencing projects worldwidepresents the scientific community with the staggeringtask of making sense of the information.Upon completion of our programme, we willhave generated a comprehensive resource,highly valuable for functional genomics as wellas for individual case studies. This resource, togetherwith the acquisition of cutting-edge functionalgenomics tools, will transform the fieldof nematode functional genomics and allowstraightforward modelling of human pathologiesin C. elegans, in addition to greatly acceleratingresearch on important biological areas,ultimately interfacing with approaches aimingto improve human health and quality of life.Nematode Gene-Tagging Toolsand ResourcesKeywords: nematode, Caenorhabditis elegans, functional genomics, transposon-mediatedmutagenesis, transposable elements, transposon-taggedmutants, gene knock-out, heterologous transpositionPartnersProject Coordinator:Dr. Nektarios TavernarakisFoundation for Research and Technology – HellasInstitute of Molecular Biology and BiotechnologyVassilika VoutonP.O. Box 138571110 Heraklion, Greecetavernarakis@imbb.forth.grProcedure for generationof transposon-insertionmutantsDr. Jean-Louis BessereauInstitut National de la Santéet de la Recherche Médicale (INSERM)Paris, FranceDr. Jonathan EwbankCentre National de la Recherche Scientifique (CNRS)Institut National de la Santé etde la Recherche Médicale (INSERM)Centre d’Immunologie de Marseille-LuminyMarseille, FranceDr. Johan GeysenMAIA ScientificGeel, BelgiumProf. Patricia KuwabaraUniversity of BristolDepartment of BiochemistryBristol, UKDr. Laurent SegalatCentre National de laRecherche ScientifiqueUniversité Claude BernardLyon, FranceFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life261

TP Plants and HealthProject Type:Specific Support ActionContract number:LSSB-CT-2004-512149Starting date:1 st June 2004Duration:32 monthsEC Funding:555 840State-of-the-Art:In the 1970s and 80s plant science had a solid research base in Europe, but Europeanplant biotechnology activities have declined over the past decade. The Eurobarometer survey“Europeans and Biotechnology” in 2002 showed that most Europeans are in favour ofbiotechnology if it is related to medical research, but many remain sceptical of agriculturaland food-related biotechnology. The academic sector and plant biotechnology industry hasseverely curtailed biotechnology field research programmes in the EU in favour of thirdcountry trials. Also, at European universities the number of students interested in pursuingcareers in plant science, genomics and biotechnology has declined. This was recognisedas a matter of concern by the 2003 EU Council with a recommendation that the matter beaddressed.Scientific/Technological Objectives:The key objectives of the TP Plants and Health project were to: until 2025; based on the long term strategic plan; the development of plants and products offering a healthy, balanced diet.Expected Results:The project’s main result will be publication of the Plant Genomics and Biotechnology ActionPlan in 2010. Other results will be: 1) a common vision for plant genomics and biotechnologyresearch in the EU and a discussion of this amongst policy makers to develop coherent©Shutterstock, 2007262From Fundamental Genomics to Systems Biology: Understanding the Book of Life

The European Technology Platformon Plant Genomics and Biotechnology:Plants for healthy lifestylesand for sustainable developmentresearch policy measures; 2) an increased interaction between the public and private plantgenomics and biotechnology research sectors with the aim of stimulating knowledge to beturned into innovation leading to increased productivity and competitiveness in Europe; 3)a more balanced public debate recognising plant genomics, biotechnology, classical agriculturalpractices and organic farming all as natural and valid components of both researchand application.Potential Impact:The publications of TP Plants and Health will be used in meetings and consultations withdifferent stakeholders including academic institutions, industry, farmers, consumers, etc).The project will also have a long-term impact on policy makers at European level (EuropeanCommission and European Parliament) and at national level (Member State consultationsand several meetings organised by individual countries, for example by the UK during itsEU-presidency). This will continue and increase in the future, creating an impact on scienceand research policy at European level (the European Commission’sproposal for FP7) and at national level (ERA-PG, 1st National Research Programmes).Keywords:European technology platform, policy recommendations, genomics, plant models, stakeholderforumPartnersProject Coordinator:Dr. Karin MetzlaffEuropean Plant Science OrganisationTechnologiepark 927Ghent, Belgiumkarin.metzlaff@psb.ugent.beSimon BarberEUROPABIOThe European Association of BioindustriesPlant Biotechnology UnitBrussels, BelgiumFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life263

X-OMICSProject Type:Co-ordination ActionContract number:LSHG-CT-2004-512065Starting date:1 st January 2005Duration:48 monthsEC Funding:800 000State-of-the-Art:Elucidation of the function of the 25 000 genes in the human genome will be significantlyaccelerated by exploiting comparative genomic approaches in an integrative manner.The international community will soon have access to the complete genome sequence ofseveral organisms, already validated as excellent experimental models of developmentalbiology. European scientists need to coordinate an efficient interfacing in their strengthsin comparative bioinformatics and functional genomic approaches. Comparisons acrossseveral vertebrate and invertebrate systems allow us, by bioinformatics analysis, to identifysequenced-conserved orthologous genes with important biological roles which will mostlikely have conserved functions in mammals, including humans. The aim of the proposal isto organise the coordination of the research of several recognised European laboratoriesusing the amphibian Xenopus as a model to identify vertebrate genes of medical and developmentalinterest.Scientific/Technological Objectives:Our overall aim is to strengthen the coordination in functional genomics research in theEU in order to understand the genetic basis of human pathologies better. We will apply acomprehensive comparative functional genomics strategy, based on the amphibian Xenopusmodel organism, with the goal of identifying and assessing the function for conservedgenes during early and late development. This objective will be reached through a strongcoordination between European experts in several scientific areas: bioinformatics, genomicsand developmental genetics, using the vertebrate amphibian models Xenopus laevis andXenopus tropicalis. The consortium will coordinate the ‘vertical’ studies from in silico definitionof orthologous genes (comparisons across all available genomic models) down to geneexpression and function studies. Analyses of many genes by high-throughput techniques willbe followed by in-depth analysis of gene sets selected for their importance in human health.This project will be integrative through the generation of interactive databases linked tomouse and human electronic resources. More precisely, the objectives of the coordinationaction in Xenopus genomics are to coordinate: identified by genomic sequencing and those of other model organisms: Drosophila,Ciona, zebrafish, chick, mouse and human thousands of orthologous genes genes playing a role in development and differentiation amphibian well as general and specialised meetings and workshops.Expected Results:The first and central aspect of this project is to coordinate the use of integrated tools whichmeans that we go beyond the classical way of doing our science, and use and developtools for functional genomics. The functionally characterised genes will permit development ofdatabases directly providing comparative information between all model organisms includingman. They will also provide seamless integration with downstream applications, such as264From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Xenopus Comparative Genomics:Coordinating Integrated and ComparativeFunctional Genomics for UnderstandingNormal and Pathologic Developmenthigh-throughput screening of drug candidates and provide information for developing animalmodels of human diseases. Another side-product of our action is the dissemination of the improvementsof biotechnological techniques made by some of us for modulating gene functionin Xenopus. The end result of X-OMICS will be the disposal of comparative functional genomicsdata as alternative and complementary information with other organisms.Potential Impact:Novel gene functions and technological development resulting from Xenopus genomics willgive fuel to innovation activities and help in understanding human development and diseases.X-OMICS will facilitate efficient comparative genomics, the generation and comparisonacross species of gene expression data, the improvement of techniques for gene expressionanalysis, the development of accessible gene expression and function databases, compatiblewith human databases and the expansion of bioinformatic tools.Moreover, the in-depth functional analyses carried out within the consortium framework willlink genomic data to development and to several human diseases, thereby guaranteeing themedical impact of the project.Keywords: vertebrate models, Xenopus, zebrafish, mouse, systematic highthroughputgene expression studies, conserved genes, functionalin vivo studies, bioinformatics, genomics, developmental genetics,interactive databasesPartnersProject Coordinator:Dr. Andre MazabraudCentre National de la RechercheScientifique (CNRS)UMR 8080 Développement et EvolutionRue Michel-Ange 375794 Orsay, Franceandre.mazabraud@ibaic.u-psud.frDr. Nancy PapalopuluUniversity of CambridgeWellcome Trust Cancer ResearchCancer Gurdon InstituteCambridge, UKDr. Eric BellefroidUniversité Libre de BruxellesIBMM Laboratory of MolecularEmbryologyBrussels, BelgiumProf. Christoph NiehrsDeutsches KrebsforschungszentrumDepartment of MolecularEmbryologyHeidelberg, GermanyDr. Tim MohunMedical Research CouncilThe National Institute forMedical ResearchDivision of Development BiologyLondon, UKProf. Tomas PielerUniversity of Göttingen,Center of Molecular BiologyDepartment ofDevelopmental BiochemistryGoettingen, GermanyFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life265

5.POPULATION GENETICS& BIOBANKS

5.POPULATION GENETICS& BIOBANKSHUMGERIMolPAGEGENOSEPTMICROSAT workshopEUHEALTHGENPHOEBEEUROSPANDanuBiobankImpactsEpiGenChlamydia

HUMGERIwww.humangenom.huProject Type:Specific Support ActionContract number:LSSG-CT-2003-503405Starting date:1 st April 2004Duration:30 monthsEC Funding:285 000State-of-the-Art:The morbidity and mortality statistics of the Hungarian population are among the worst inEurope and it is assumed that genetic as well as epigenetic factors play a significant role inthis phenomenon. Genomic research is very likely to provide a new framework to approachthis problem. However, Hungarian genomic research is in its infancy, rather fragmentedand unfocused. The main objective of the project is to obtain specific support for changingthis unfortunate situation. A consortium of Genomic Research for Human Health in Hungaryhas been formed, which starts organising genomic research within this action by pullingtogether all the related activities in the country and providing an umbrella for medicallyorientated genomic research.Scientific/Technological Objectives:Based on studies and comparisons of European human genome projects, the objectives ofthis action are: nosticworks carried out in Hungary and making it available to the public and officialsof the healthcare system. 1) explore and integrate existing, genome-specific bioinformatics resources of themembers of the consortium2) develop a common website for the consortium including links to local activitiesof the partners, to their national and international collaborations, and to othergenome research networks3) organise an international workshop with experts from several existing Europeangenome research networks with the purpose of integrating the activities of theconsortium with European partners. 1) collect and provide information about the various, existing human tissue andDNA/RNA collections, their content and medical background or research project,and rules for access2) establish a nationwide quality assurance system for collecting, handling, storingand documenting human biological samples in Hungary3) establish the framework for sample collections from large volunteer cohorts, andmove towards a centralised national biobank. projects. Establish an, as yet, non-existing, integrated, non-profit network of biotechnologyorientated, primarily Hungarian-based SMEs. legal framework of R&D activity, the existing official network and procedure of theethical assessment of research protocols, and in particular genomic research programmeshave to conform to high European standards and regulations.Expected Results: proposition on the required computing environment270From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Human Genomic Research Integration Group sub-domains and partner pages (SME partnering, bioethics, genetic tests, projects,etc.) in Disease Development) questionnaires are on the website. There is a standard database and informationmanagement system for Hungarian biobanks. legislation.Potential Impact: will stimulate:a) further uncovering of inheritedrisk factors and identify candidategenes/SNPs for major diseasegroupsb) identification of genetic features/markers unique to the MiddleEuropean regionc) characterisation of theMHC (HLA) gene pool inHungary work,the EC will have access to all ofthe potential facets of the Hungariangenome-related SMEs. wardsneighbouring candidate countrieswill help integration of the regioninto the ERA. cialimpact on decision-makers to starta new funding system, providing theappropriate framework for a long-termgenomic programme in Hungary.PartnersProject Coordinator:Dr. László FésüsUniversity of DebrecenMedical and Health Science CenterDepartment of Biochemistry andMolecular BiologyEgyetem Ter 14032 Debrecen, Hungaryfesus@indi.biochem.dote.huKeywords:human genomics, research policiesFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life271

Project Type:Integrated ProjectContract number:LSHG-CT-2004-512066Starting date:1 st October 2004Duration:48 monthsEC Funding:12 000 000MolPAGEState-of-the-Art:www.molpage.orgIt is widely recognised that large-scale phenotyping studies are required in order to identifybiomarkers that will translate from bench to bedside. More specifically, such studies arenecessary for an examination of the influence of many environmental and genetic determinantsof disease. Because of the molecular heterogeneity that contributes to most of themajor common disease phenotypes studied in large populations, these studies must aim toanalyse large numbers of cases and controls.Currently, a number of biobank efforts are being carried out, not exclusively in the UK,but worldwide. These efforts will soon produce an unprecedented number of samples formolecular phenotyping. As a consequence, epidemiologists, clinical trial workers and experimentalscientists will potentially soon be presented with numerous opportunities forthe molecular phenotyping of large numbers of biological samples obtained from thesebiobank cohorts, patients or animal models.Although the development of genotyping technologies for the analysis of DNA markershas, to a degree, matured enough to allow for their use on an epidemiological scale, it isnot yet clear how the application of post-genomic technologies such as metabonomics andproteomics, (where standardisation of procedures and high throughput approaches are lesswell established), will be tackled.The MolPAGE (Molecular Phenotyping to Accelerate Genomic Epidemiology) project aimsto design a programme to bridge this gap. The four-year project MolPAGE brings togethera consortium of 18 leading academic institutions, and biotechnology and pharmaceuticalcompanies, with expertise from a wide variety of ‘omics’ technologies and computationalmethods, as well as from the biology of metabolic disease.The consortium partners are working to upscale and optimise a range of genomic, metabonomicand proteomic tools. In addition, the consortium is seeking to develop novel technicaldata analysis and integration protocols, to facilitate biomarker discovery and validationstudies conducted on an epidemiological scale (“genomic epidemiology”).Post-genomic technologies deriving from the project will be applied to biomarker discoveryand typing in metabolic diseases such as diabetes and its associated vascular complications,which constitute major causes of ill health and premature death, and which are reachingepidemic proportions in Europe and worldwide.Scientific/Technological Objectives:A major goal of the MolPAGE consortium, is to develop and upscale a range of ‘omic’technology platform tools (metabonomic, genomic, proteomic), and to apply these identifyingbiomarkers in predicting disease, determining risk and relating to disease activity orresponse to therapy.The programme is divided into three component parts. Firstly, the project aims to evaluatesample collection and storage methodologies, understand sources of technical and biologicalvariation and explore issues of analyte stability, so as to inform ongoing and futureendeavours in biobanking and biomarker discovery.Secondly, MolPAGE seeks to develop, upscale and validate tools that will allow molecularphenotyping at an epidemiologic scale. This includes the capacity to undertake analysis of(a) small molecules (metabonomics); (b) mRNA (transcript profiling); (c) proteins and peptides;(d) DNA methylation patterns; and (e) genome sequence variation.272From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Molecular Phenotypingto Accelerate Genomic EpidemiologyThe third part of the project entails the development of bioinformatic tools and statisticalmethods to support the storage, interrogation and analysis of the large complex data setsproduced. The analysis of longitudinal cohorts from Biobank projects will be used for thevalidation (and large-scale phenotyping) of risk biomarkers. A number of technologies internalto the consortium will be utilised for these tasks.The MolPAGE project is using two separate approaches to biomarker discovery and validation,namely a genome wide, systematic methodology (for example, transcriptomics, NMRand MS based metabonomics, and ms based proteomics) and a limited analysis which usessets of candidate biomarkers (methylation, affinity arrays, and tissue arrays).The MolPAGE consortium, which is coordinated by the University of Oxford, comprises 18partners from 5 SMEs, 2 international pharmaceutical organisations and 11 public bodies.The project is organized into work packages (WPs); from an operational point of view,these work packages fall into four main areas: sample-related (1); technology-related (2);informatics and analysis (3); and training and management (4).Expected Results:The MolPAGE project will significantly contribute to the development of international scientificstandards in molecular phenotyping. During the project the consortium will develop,establish and disseminate standards for the collection, processing and storage ofbiological samples that are firstly, suitable for use in large sets of individuals, secondly,applicable to blood, urine and solid tissue samples, and thirdly, optimised for future‘omic’ platform analysis of DNA, RNA, protein and other biological analytes.Another crucial aspect of the project is the development of standardised data handlingand analysis methods, which will be applicable to future molecular phenotyping effortsperformed on an epidemiological scale. The consortium has released an open sourceversion of our novel web-based sample management system (http://passim.sourceforge.net) for use by other projects. Furthermore, by the end of the project, the consortium willhave completed the development of a data warehouse, optimised for the submission, storageand integration of both raw and analysed data from a wide range of the MolPAGEtechnology platforms.Similarly MolPAGE is actively working to improve the statistical tools available for analysisof many of these types of data, and to develop approaches for deriving an integratedview of the transcriptional, proteomic and metabonomic changes which associate withand/or predict disease. Towards MolPAGE standard setting goals, the consortium andthe EU co-hosted an international workshop on ‘Standards and Norms in PopulationGenomics’, to establish a roadmap for developments standard setting and obtaining acceptanceby the wider scientific community.Significant efforts to upscale the enabling metabonomic and proteomic technology platformswere made in the first two years of the project; these efforts will continue on a selectedsubset of the most promising technology platforms for the remainder of the project.A medium-term goal of the MolPAGE consortium was to apply the methods developed inthe initial phase, to proof-of-principle biomarker discovery efforts. These studies are nowunderway, focused on metabolic and cardiovascular disease in samples from MolPAGEand from selected European longitudinal cohort projects. By the end of the funding period,we propose to make our recommendations regarding the most suitable technologyplatforms for application to molecular phenotyping of biobank samples, in a broad rangeof disease areas.From Fundamental Genomics to Systems Biology: Understanding the Book of Life273

MolPAGEDifferential geneexpression analysis of adiposetissue RNA comparing obeseand lean subjects froma rat model of diabetes.PotentialImpact:With MolPAGE’s initialfocus on biomarker discoveryand validation inmetabolic disease (type 2diabetes and cardiovasculardisease), the teamwill be addressing a majorpublic health problemin the EU community — aproblem of considerablehealth and economic proportionseven now, andone expected to escalatein the decades to come.The methodology to bedeveloped, however, willhave applications in everyform of common humandisease, including cancer,inflammatory diseasesand degenerative diseases.The involvement of fiveindustrial partners in theconsortium, has provided the power necessary for the distribution of the project’s resultsand experience, to corporate institutions. These corporate institutions are capable of convertingthe knowledge generated by the project into new drug opportunities and treatmentmodalities, which will benefit patient groups worldwide, and increase the competitivenessof the EU-based pharmaceutical industry.This project will therefore influence economic development in the EU in several distinctways. By establishing successful technology platforms, we expect to stimulate the technologyand diagnostic section of the health-care related economy. In addition, by addressingthe single largest causes of ill health and premature death, and through their direct healthbenefits as well as indirectly through facilitating discovery in the pharmaceutical sector,these studies have the potential to enhance economic development.Keywords: phenotyping, epidemiology, molecular phenotyping, genomics274From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Molecular Phenotyping to Accelerate Genomic EpidemiologyPartnersJoint Project Coordinators:Prof. John BellUniversity of OxfordRichard Doll Building, Roosevelt DriveHeadington, Oxford, OX3 7DG, UKregius@medical-sciences-office.oxford.ac.ukProf. Mark McCarthyUniversity of OxfordOxford Centre for DiabetesEndocrinology and Metabolism (OCDEM)Churchill Hospital SiteOld Road, HeadingtonOxford, OX3 7LJ, UKmark.mccarthy@drl.ox.ac.ukProject Manager:Dr. Maxine AllenUniversity of OxfordOxford Centre for DiabetesEndocrinology and Metabolism (OCDEM)Churchill Hospital SiteOld Road, HeadingtonOxford, OX3 7LJ, UKmaxine.allen@drl.ox.ac.ukProf. Peter Donnelly, Prof. Lon CardonUniversity of OxfordOxford, UKProf. Sir Edwin SouthernOxford Gene TechnologyOxford, UKProf. Vladimir StichCharles UniversityDepartment of Sports MedicinePrague, Czech RepublicDr. Alvis BrazmaEuropean Molecular BiologyLaboratory (EMBL)European BioinformaticsInstitute (EBI)Microarray GroupHinxton, UKDr. Juris ViksnaInstitute of Mathematicsand Computer ScienceRiga, LatviaProf. Jeremy NicholsonImperial College LondonDepartment of Biological ChemistryLondon, UKProf. Luisa BernardinelliUniversity of PaviaDepartment of Health SciencesPavia, ItalyDr. Stephan HoffmanGyros ABUppsala, SwedenProf. Tim SpectorKings College LondonTwin Research UnitLondon, UKDr. Dominique LanginInstitut National de la Santéet de la Recherche Médicale(INSERM)Obesity Research UnitToulouse, FranceDr. Fredrik PontenUppsala UniversityDepartment of Genetics andPathologyHuman Proteome ResearchUppsala, SwedenDr. Hanno LangenF. Hoffman-La Roche AGProtemics InitiativeBasel, SwitzerlandDr. Ivo GutCentre National de Genotypage (CNG)Evry, FranceDr. Kurt BerlinEpigenomics AGBerlin, GermanyDr. Rainer VoegeliDigilab BioVisioN GmbHHannover, GermanyDr. Esper BoelNovo Nordisk A/SNovo Alle, DenmarkProf. Mathias UhlenKTH BiotechnologyRoyal Institute of TechnologyAlbaNova University CenterStockholm, SwedenDr. Thomas BergmanAffibody ABBromma, SwedenFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life275

Project Type:Specific TargetedResearch ProjectContract number:LSHG-CT-2004-512155Starting date:1 st January 2005Duration:48 monthsEC Funding:2 000 000GenOSepthttps://www.genosept.euState-of-the-Art:GenOSept is a STREP which uses a multidisciplinary fundamental genomics approach (geneexpression, structural genomics and population genetics) to examine genetic predispositionto sepsis. Sepsis (a life-threatening infection) is a major public health problem throughoutEurope. In the USA, in 1995, it cost $17 billion to treat 751 000 patients with severe sepsis,of whom 28.6% died. The Centre for Disease Control suggests that sepsis-attributablemortality rates are rising. We hypothesise that susceptibility to expensive new treatmentsand fatal outcomes from severe sepsis are, in part, genetically determined.The GenOSept project will test this hypothesis. It will standardise protocols for genotyping,facilitate application of new knowledge in functional and structural genomics, harmonisehigh-throughput genotyping and quality control between major European centres, and contributeto reducing sepsis-related mortality in European healthcare.Scientific/Technological Objectives:Genetic predisposition for the incidence and outcome of sepsis has been recognised andsuggested as a possible powerful tool for future risk stratification and even as inclusion criteriafor therapeutic trials. GenOSept also contains a module which links patterns of geneexpression with patterns of genomic variation in corresponding genes.Genomic variants may influence the individual phenotype including gene expression levelsand patterns, as well as protein levels and protein structure. A possible result is that futureintensive care physicians may have access to readily available genetic risk patterns includingpharmacogenetics of their patients which not only allows for better risk stratification, butmay also help tailor individual patient care and drug therapy.The major milestones of GenOSept are: base; (ICUs); Expected Results:The expected results of GenOSept are that it will: flammation,and of programmed cell death.The novel genes identified by expression studies will add to a set of candidate genes usedin a subsequent epidemiologic study which will: functional and structural genomics; by coordinating major European genotyping centres; First project achievement: the diseases to be included in the study were refined and four willbe examined. The inclusion and exclusion criteria database have been developed.Potential Impact:The GenOSept findings will contribute to reducing sepsis-mortality and morbidity in Euro-276From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Genetics of Sepsis in Europepean ICUs. The project will link fundamental genomics to sepsis, a major European publichealth issue. The application of gene expression studies and structural genome analysisdetecting genomic variation will generate novel data on relevant genes as well as novelgenomic variations involved in the genetic predisposition of incidence and outcome fromsepsis. The evaluation and use of novel techniques, including the gene chip technology andthe establishment of a European network of clinical and laboratory groups working in thefield of critical care medicine, will strengthen European biotech industry.Keywords: intensive care medicine, sepsis, mortality, epidemiology, genetictesting, genetic predispositionPartnersProject Coordinator:Prof. Julian Bion, Dr. Nathalie MathyEuropean Society of IntensiveCare MedicineResearch Activities40 avenue Joseph Wybran1070 Brussels, Belgiumpublic@esicm.orgProf. Dr. Frank StüberRheinische Friedrich-Wilhelms-Universität BonnKlinik und Poliklinik für Anästhesiologie und spezielleIntensivmedizin UniversitätsklinikumBonn, GermanyProf. Jean-Daniel ChicheInstitut National de la Santé etde la Recherche Médicale (INSERM)Institut Cochin- Réanimation médicaleParis, FranceProf. Adrian HillUniversity of OxfordWellcome Trust Centre forHuman GeneticsOxford, UKProf. Vito Marco RanieriUniversita degli Studi di TorinoSezione di Anestesiologica eRianimazioneTurin, ItalyProf. Jordi RelloUniversity Rovira & VirgiliHospital Universitari Joan XXIIICritical Care DepartmentTarragona, SpainProf. Thomas MeitingerHelmholtz Zentrum MünchenInstitute of Human GeneticsNeuherberg, GermanyDr. Yoram WeissHadassah Medical OrganisationDepartment of Anaesthesiaand Critical Care MedicineJerusalem, IsraelProf. Dr. Stefan RusswurmSIRS-Lab GmbHR&D DepartmentJena, GermanyProf. Marion SchneiderUniversity Ulm Medical FacultySektion ExperimentelleAnästhesiologieUniversitätsklinikum UlmUlm, GermanyProf. Konrad ReinhartKlinikum der Friedrich-Schiller-Universität JenaDepartment forAnaesthesiology andIntensive Care MedicineJena, GermanyDr. Vladimir SramekMasaryk UniversityBrno Medical FacultySt Ann’s University HospitalDepartment of Anaesthesiologyand Intensive CareBrno, Czech RepublicDr. Ilona BobekNational Medical CenterDepartment of Anaesthesiaand Intensive CareBudapest, HungaryDr. Silver SarapuuTartu University ClinicsIntensive Care UnitTartu, EstoniaFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life277

MICROSAT workshopwww.microsatellites.orgProject Type:Specific Support ActionContract number:LSSG-CT-2004-013019Starting date:1 st January 2005Duration:24 monthsEC Funding:112 000State-of-the-Art:Tandem repeats are repeat sequences in the human genome. They occur in all genomes,including bacteria, yeast, plants and humans. Tandem repeats have been widely used inlinkage analysis in many organisms, where they are used as non-functional markers forinheritance of genetic loci. They have also been implicated in human disease, with microsatellitessuch as CAG triplet repeats causing a variety of neurological disorders and higherorder motifs such as the insulin gene VNTR influencing complex diseases such as diabetes.VNTRs affect gene expression and are useful for genetic fine mapping of complex diseaseloci; for example they were used to identify the neuregulin 1 gene which predisposes toschizophrenia. However, despite their clear importance, in recent years far more emphasishas been placed on single nucleotide polymorphisms (SNPs) than tandem repeats becauseof the unproven perception that SNPs are the major cause of complex diseases. The SNPConsortium Ltd is a non-profit foundation that was developed for the purpose of providingpublic genomic data. Its mission is to develop up to 300,000 SNPs distributed evenlythroughout the human genome and to make the information related to these SNPs availableto the public.Scientific/Technological Objectives:1) To stimulate international cooperation in functional genomics in Europe by bringingtogether researchers to examine microsatellite and variable number of tandem repeat(VNTR) markers in human and non-human genetics and genomics.2) To promote and facilitate international co-operation in microsatellite research by networkingscientists for a research consortium.3) To develop microsatellite and VNTR markers as tools for genomic and genetic analysiswith the potential to develop long term research funding and be a catalyst forcooperation, especially with SMEs and third world countries.4) To develop web-based resources to facilitate the use of microsatellite markers in genomicand genetic analysis.Expected Results:The consortium ran two workshops, one in the UK at the Institute of Psychiatry and one inHungary at the Hungarian Academy of Sciences (Institute of Enzymology) to train researchersto use microsatellites in genomic and genetic analysis, which will lead to self-financingworkshops in future years. The first workshop established the consortium and the secondprovided training in the field and allowed the dissemination of research findings and transferof knowledge and technologies which developed as a result of the first workshop. SMEsparticipated directly in two workshops and were encouraged to develop technology thatcan be commercially exploited. Researchers from China and Brazil played a direct role inthe consortium, and training and knowledge were transferred to other developing nationsin addition to European states. The fist self-funded microsatellite workshop will be held inColorado in February 2009.278From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Microsatellites and VNTRs: workshop onbioinformatics, genomics and functionalityPotential Impact:Microsat-SSA was focused on stimulating research into microsatellites and VNTRs as basictools for genome research, and as candidate polymorphisms for human and animal disease.A team working in a neglected area of genomics will have a significant impact ongenetic and genomics, including the areas of human and animal disease, by increasingthe variety of tools available to the scientists. This will improve our understanding of thebasic biology of the genome, as well as the ability to locate disease-causing genes and theunderlying variants, and to understand population genetics from a different perspective.Microsat-SSA will contribute to economic competitiveness by promoting the involvementof SMEs in activities related to microsatellite markers, including the provision of contractgenotyping and other intellectual property related research services.Keywords:microsatellite, VNTR, tandem repeat, population, genetics, mapping, association, comparative,linkagePartnersProject Coordinator:Prof. David CollierKing’s College, University of LondonDepartment of SocialGenetic and Developmental PsychiatryInstitute of PsychiatryDe Crespigny ParkLondon, SE5 8AF, UKd.collier@iop.kcl.ac.ukFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life279

EUHEALTHGENProject Type:Specific Support ActionContract number:LSHG-CT-2005-518144Starting date:1st September 2005Duration:12 monthsEC Funding:245 000State-of-the-Art:Member and Associated States across the European Research Area are supporting researchon population genetics in order to build upon the significant investments made insequencing the human genome. Significant added value can be obtained if the objectivesand protocols involved in human population genetics research at a national level can beharmonised to become representative of the entire EU population. The EU would therebydevelop and maintain a leading global position in genetic epidemiology and populationgenetics. Project coordination will be by a steering committee, which will meet twice duringthe planning phase of the proposed conference. It will then meet twice following theconference to agree the report and to lay the foundations for implementing the developedstrategy. The conference will be held at the Wellcome Trust Conference Centre, Cambridge,United Kingdom on 21-23 September 2005.Scientific/Technological Objectives:EUHEALTHGEN has been established to: across the ERA and restrict fragmentation tabaseinfrastructure needed for major population genetic studies in Europe careprofessionals, policy-makers and funders about human population genetics adoption of a joined-up and fully integrated strategy from basic research, throughclinical studies to the treatment of individual patients treatment to the identification of personal disease risk and the development of appropriatepersonalised prevention strategies.Expected Results:Some of the expected results are: ingtechnology and proteomic analysis for clinical research, thereby enhancing datageneration, standardisation, acquisition and analysis so achieve the better targeting of limited health resources 280From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Harnessing the Potentialof Human Population Genetics Researchto Improve the Quality of the EU Citizen to the large data sets needed to integrate biological data with clinical need thus promotingtranslational research for improved human health in this area and help improve the efficiency of translating the outcomes of clinicalresearch into clinical practice.Potential Impact:Human population genetics will play an important role in analysing the complex interactionsthat occur in determining susceptibility and cause of the priority disease areas.However, for this to be realised it will be necessary to ensure that the biobanks operatingacross Europe are compatible so that validated reagents, samples and information can beexchanged in a safe and ethically acceptable way. This provides further justification for themain aim of EUEALTHGEN, namely to develop a forward-looking strategy for translatingthe outputs of population genetics research into clinically useful and health enhancing initiatives,whilst improving EU industrial competitiveness in this area.Keywords: health sciences, population genetics, biobanks, human geneticsPartnersProject CoordinatorDr. Alan DoyleThe Wellcome TrustDepartment of Biomedical Resourcesand Functional Genomics215 Euston RoadLondon, NW1 2BE, UKa.doyle@wellcome.ac.ukFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life281

Project Type:Co-ordination ActionContract number:LSHG-CT-2006-518148Starting date:1 st March 2006Duration:36 monthsEC Funding:800 870PHOEBEState-of-the-Art:This coordination action aims to help create a harmonised network of population-basedbiobanks across Europe and Canada. The main purpose is to maximize the use of Europe’spopulation-based biobanks in the study of complex disease etiology.Scientific/Technological Objectives:The objectives can be categorized accordingto the following harmonization areas:Epidemiology: tion-basedbiobanks and longitudinalcohort studies in Europe to coordinated investigations of the geneticand environmental determinantsof complex diseasesIsolated populations: in Europe, with a focus on geneticallyisolated populations lectionand collection of data andsamples from these populationsBiobank information management: Information Management Systems edto the management of large andcomplex databases for biobanks level programming and developmentExpected Results:of flexible communication engines supportingreliable, efficient and securecommunication between biobanksGenotyping: the evaluation of large-scale genotypingefforts in population cohorts,Phenotypes and environmental exposures: approach to the assessment of a rangeof complex phenotypes and life-styleexposuresEthical, legal and governance issues: establish ethical, legal and governancecriteria consistent with the internationalnorms and European practices that willenable data and sample sharing for researchpurposesStatistics: nadianexpertise related to statisticalchallenges derpinningthe design, analysis andharmonization of population-basedbiobanks. cohorts in Europe, and information on the accessibility of data and status of the studies; isolates; and storage strategy and report on standards in European biobanks; population biobanks, genotyping quality and cost reports, a web-based SNP selectiontool, and procedures for collection and storage of genotyping data; phenotypes and exposures for future European biobanks; platform; Potential Impact:www.phoebe-eu.org comeexisting fragmentation of European population genomic research. sample sizes, and will help to promote collaborative international genetic epidemiologicalresearch.282From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Promoting harmonisationof epidemiological biobanks in EuropeKeywords: epidemiology, genetic epidemiology, biobanks, population-based cohorts,complex disease, isolated populations, bioethics, phenotyping,genotyping, GenomEUtwin, COGENE, P3G, data managementPartnersProject Coordinator:Dr. Jennifer HarrisNorwegian Institute of Public HealthDivision of EpidemiologyOslo, Norwayjennifer.harris@fhi.noProf. George Davey-SmithUniversity of BristolDepartment of Social MedicineBristol, UKProf. Max BauerUniversity of BonnInstitute of Medical BiometryInformatics and EpidemiologyBonn, GermanyProf. Paolo GaspariniUniversita degli Studi di TriesteFacolta di Medicina e ChirurgiaTrieste, ItalyProf. Jaume BertranpetitUniversitat Pompeu FabraDepartment de CienciesExperimentals i de la SalutBarcelona, SpainProf. Jan-Eric LittonKarolinska InstitutetDepartment of MedicalEpidemiology and BiostatisticsStockholm, SwedenAndy HarrisUK Biobank LtdManchester Incubator BuildingManchester, UKProf. Leena PeltonenNational Public Health InstituteDepartment of Molecular MedicineHelsinki, FinlandDr. Thomas J. HudsonMcGill UniversityMcGill University and QuebecInnovation CentreMontreal, CanadaProf. Dorret BoomsmaVrije UniversiteitDepartment of BiologicalPsychologyAmsterdam, The NetherlandsProf. Anne Cambon-ThomsenINSERM U 558Faculté de MédecineToulouse, FranceProf. Bartha Maria KnoppersUniversité de MontrealFaculté de Droit, Centre deRecherche en Droit PublicMontreal, CanadaProf. Paul BurtonUniversity of LeicesterDepartment Epidemiologyand Public HealthLeicester, UKProf.. Cornelia van DuijnErasmus Medical CenterDepartment of Epidemiologyand BiostatisticsRotterdam, The NetherlandsProf. Andres MetspaluUniversity of Tartu, IMCBEstonian BiocentreTartu, EstoniaProf. Milan MacekCharles University PragueInstitute of Biology and MedicalGenetics - Cystic Fibrosis CentrePrague, Czech RepublicProf. Pagona LagiouUniversity of AthensMedical SchoolDepartment of Hygieneand EpidemiologyAthens, GreeceProf. Paul ElliottImperial College of ScienceTechnology and MedicineDepartment of Epidemiologyand Public HealthLondon, UKFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life283

EUROSPANProject Type:Specific TargetedResearch ProjectContract number:LSHG-CT-2006-018947Starting date:1 st March 2006Duration:36 monthsEC Funding:2 400 000State-of-the-Art:This project will study five special populations throughout Europe which represent a uniqueresource for genomic research. It will quantify genetic variation in genes known to be involvedin health and disease and will harness this variation to identify novel variants. The project willbuild on the achievements of substantial existing investment in these special populations andwill pool expertise across Europe in phenotyping, genotyping, statistical genetics and socialand ethical aspects of genomic research. A common database of health and disease-relatedphenotypes will be established and cores of expertise established in the major project areas.This will create the largest database of phenotypic and genotypic data from genetic isolatepopulations and will thus improve European competitiveness in gene discovery. The projectwill also provide the platform for the evaluation of a novel gene discovery approach (hybrididentity profiling) which has been developed by a European SME.Scientific/Technological Objectives:The objectives regarding genetic variation in established disease genes are: (genetic isolate) populations in five European countries and in three outbred Europeanpopulations odsacross five special populations ly40 QTs influenced by these genes across five diverse environmental backgrounds.The objectives regarding employing genetic variation to identify novel genetic variants are: neticloci underlying traits (QTs) of public health importance in Europe and to employcross population mapping and high density SNP association approaches to fine-mapthese loci ingshared chromosomal regions that show IBD sharing by genome hybrid identityprofiling (HIP) values and high-density chip genotyping these special populations develop a statement of best practice for interaction with study populations in terms ofconsent, sharing of benefits, and communication with individuals and communities ducedin response to research findings, where this is appropriate.Expected Results:New Knowledge: tionsand three outbred populations in Europe will be described. ease-relatedphenotypes (QTs) will be described. identify new genetic loci related to these QTs will be performed.284From Fundamental Genomics to Systems Biology: Understanding the Book of Life

EUROpean Special Populations ResearchNetwork: Quantifying and HarnessingGenetic Variation for Gene DiscoveryTools: extreme QT values will also be assessed. Resources: putSNP genotyping and statistical genetics; ethical and social aspects of genomicresearch; phenotyping to serve the project partners.Potential Impact:EUROSPAN will give new information on genetic variations in traits underlying conditions ofpublic health importance in Europe and how this is related to disease risk. The project willresult in greater efficiency of effort, application of state-of-the art methods, pooling of intellectualresources to tackle scientific problems and, ultimately, more internationally competitiveresearch. The approach draws on genetic diversity across Europe and is distinct from existinginvestments in national biobanks and international twin studies. The social and ethicalissues raised, explored and resolved before and during the research process will have widerrelevance for genetic epidemiology and the meaning of research participation.Pulse waveKeywords: genomics, genetic variation, gene discovery, quantitative traits,endophenotypes, genetic isolatePartnersProject Coordinator:Prof. Harry CampbellUniversity of EdinburghPublic Health SciencesTeviot PlaceEdinburgh, EH8 9AG, UKharry.campbell@ed.ac.ukProf. Igor RudanUniversity of ZagrebDeptarment of Medical StatisticsEpidemiology andMedical InformaticsZagreb, CroatiaProf. Alan WrightMedical Research CouncilHuman Genetics UnitEdinburgh, UKProf. Cornelia Van DuijnErasmus Medical CenterEpidemiology & BiostatisticsRotterdam, The NetherlandsDr. Jorg HagerIntegraGen SAEvry, FranceDr. Peter PramstallerEURAC - European Academyof BolzanoDepartment of Genetic MedicineBolzano, ItalyProf. Ulf GyllenstenUniversity of UppsalaDepartment of Genetics and PathologyUppsala, SwedenProf. Thomas MeitingerGSF - Forschungszentrum für Umwelt und GesundheitInstitute of Human GeneticsMunich-Neuherberg, GermanyFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life285

DanuBiobankProject Type:Specific Support ActionContract number:LSSG-CT-2006-018822Starting date:1 st January 2006Duration:24 monthsEC Funding:480 000State-of-the-Art:Public healthcare systems in Europe are facing the challenge of a rapidly ageing populationwhich is susceptible to a wide variety of ageing-related disorders, such as heart diseaseand strokes, and metabolic disorders such as diabetes. People over 65 use 3 to 5 timesmore healthcare facilities than young people, and even though death rates from heart diseaseand strokes have decreased in recent years, these illnesses are making an increasingfinancial demand on health services. Setting up a comprehensive healthcare strategy fordealing with this problem is imperative.Scientific/Technological Objectives:The aim of Danubiobank is to establish a biobank foundation in molecular medicine forageing disorders in order to identify risk factors in population studies. Large clinical trialsof new medications can then take place. The project aims to connect universities, teachinghospitals, prevention programmes and clinics along the Danube River and in neighbouringareas. Danubiobank will study the field of ageing disorders, focusing mainly on diabetesrelatedendpoints including vascular disease and neuro-degenerative disorders. The projectalso aims to integrate biobanking into local and regional health care systems’ e-healthstructures and IT-based strategies along the Danube.Expected Results:The formulation of regional networks will help to realise a biobank model providing accessto the latest information and data concerning ageing-related disorders. Scientific meetings,networking, policy meetings and the publication of papers will bring attention to this fieldand encourage scientists and researchers to establish working alliances. A series of workshopsand a concluding conference will be organised to this effect. An interactive websitewill also be available with access for the general public. The project team hopes that otherconsortia will grow out of Danubiobank and will undertake research activities with nationalor international funding. The project also hopes to collaborate with self-help communitiessuch as Weight Watchers, and public health groups.Potential Impact:The project’s aim is to impact positively on the treatment of ageing-related disorders inEuropean health services through the biobank foundation and through its networks ofresearchers disseminating information through workshops, meetings, research and policymakingactivities.Keywords:metabolic disorder, ageing disorder, biobank, vascular disease, neuro-degenerative disorder286From Fundamental Genomics to Systems Biology: Understanding the Book of Life

PartnersProject Coordinator:Prof. Gerd SchmitzUniversity Hospital RegensburgInstitute of Clinical Chemistry and Laboratory MedicineFranz-Josef-Straub-Allee 1193053 Regensburg, Germanygerd.schmitz@klinik.uni-regensburg.deProf. Oswald WagnerMedical University of ViennaClinical Institute for Medical and ChemicalLaboratory DiagnosticsVienna, AustriaProf. Gyorgy KeriSemmelweis University BudapestCooperative Research CenterRational Drug Design LaboratoriesBudapest, HungaryDr. Jaroslav HubacekInstitute for Clinical and Experimental MedicineLaboratory of Molecular GeneticsPrague, Czech RepublicProf. Iwar KlimešSlovak Academy of SciencesInstitute of Experimental EndocrinologyDiabetes and Nutrition GroupBratislava, SlovakiaDr. Vita DolzanUniversity of LjubljanaFaculty of MedicineInstitute for BiochemistryLjubljana, SloveniaThe Danubian Biobank Initiative —Towards Information-based MedicineProf. Wolfgang König, Prof. Bernhard BoehmUniversity of UlmUlm, GermanyDr. Jaako Tuomilehto, Prof. Michael BraininDanube University KremsKrems, AustriaFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life287

Impactswww.impactsnetwork.euProject Type:Co-ordination ActionContract number:LSHG-CT-2007-037211Starting date:1 st February 2007Duration:24 monthsEC Funding:600 000State-of-the-Art:Today, most of the molecular research is carried out on cell culture and animal models, but it ispossible also to apply it directly to human clinical tissues. A very important tool for translationalresearch is represented by the large number of human archive tissues (AT) that are stored inhospitals all over Europe. Tissue specimens removed from patients for diagnosis or surgicaltherapy are fixed and paraffin-embedded in order to obtain a conclusive diagnosis. After afew sections are cut, the tissues are stored in archives for many decades. For each hospital anaverage of between 10 000 and 30 000 tissue samples are collected each year. We alreadyhave the technology that allows a molecular research at DNA and RNA level on fixed andparaffin embedded tissues, and new possibilities for proteomics analysis are emerging. InEurope, many laboratories are working with archive tissues at molecular level. DNA genomicanalysis is already widely spread in research and diagnostics (lymphomas and leukaemia etc).Less diffused and validated are the techniques for studying DNA methylation, comparative genomichybridization (CGH) or single nucleotide polymorphisms (SNP) in archive tissues. Manylaboratories also perform analysis at RNA level in order to detect RNA virus persistence or tostudy gene expression for functional genomics or micro-RNAs.Scientific/Technological Objectives:The project is capable of overcoming some of the major obstacles and limitations in the developmentof clinical molecular medicine, obstacles created by insufficient expertise at clinicallevel in the use of molecular methods and the collection of appropriate clinical materials. Theobjectives of IMPACTS are:1) to analyse the present knowledge and use of molecular analysis in archive human tissuesin Europe and to propose methods of validation and standardisation;2) to explore the range of technical availability and reproducibility of these new methodsfor research in functional genomics and clinical application;3) to establish a more organised European research effort. There are uncommon protocolsfor some of the molecular analysis in AT and every laboratory has its own experience.4) to compare methods and results by organising meetings and inter-laboratory comparisonsfor a proposal of method validation and standardisation.Expected Results:1) organisation of meetings2) publication of technical guidelines3) definition of future research proposals on archive tissues4) standardised protocols and guidelines diffusion5) validation of new tissue fixation procedures with better molecular preservation6) proposal of bioethics guidelines for human archive tissue multicentric research7) guidelines for archive tissue multicentric collection8) proteomic analysis protocols in archive tissues for research and clinical applicationsPotential Impact:This project will make a positive impact on the health of European citizens. Among the proponentsof the project are the scientists who first developed this type of molecular analysis.IMPACTS aims to integrate this expertise with others for the final goal of better managementof research. The project will also have an impact on research and development in Europeanindustry. Collaboration with pharmaceutical and biotechnological enterprises may stimulateindustrial activities with evident economic advantages. Preparing technological innovation isa basic aim of IMPACTS with the development of new procedures (new fixatives, standardisedmolecular methods and diagnostic kits) and suggestion of new devices for molecularanalysis. The project has also developed a network of laboratories and pathology archiveswith a very large number of tissues to validate new methods and clinical biomarkers.288From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Archive tissues: improving molecularmedicine research and clinical practiceKeywords: pathological anatomy, ethics in health sciences, molecular biology,molecular medicine, functional genomics, personalised medicine,biobanksPartnersProject Coordinator:Prof. Giorgio StantaUniversity of TriesteDepartment of ClinicalMorphological andTechnological Sciencesc/o Ospedale di CattinaraStrada di Fiume 44734149 TriesteandInternational Centre for GeneticEngineering and BiotechnologyMolecular Histopathology LaboratoryPadriciano 9934012 Trieste, Italystanta@icgeb.orgProf. J.H.J.M. Van KriekenRadboud UniversityNijmegen Medical CentrePO Box 90106500 GL Nijmegen, The NetherlandsProf. Fatima CarneiroUniversity of PortoInstitute of Molecular Pathologyand ImmunologyPorto, PortugalProf. Fred BosmanUniversity of LausanneLausanne, SwitzerlandProf. Generoso BevilacquaUniversity of PisaDepartment of OncologyPisa, ItalyProf. Gregor MikuzMedical University InnsbruckInstitute of PathologyInnsbruck, AustriaProf. Heinz HoeflerTechnical University MunichInstitute of PathologyMunich, GermanyProf. Manfred DietelCharite – Universitatsmedizin BerlinInstitut for Pathologie CCMBerlin, GermanyProf. Aldo ScarpaUniversity of VeronaDepartment of PathologyVerona, ItalyProf. Gianni BussolatiUniversity of TorinoDepartment of BiomedicalSciences and Human OncologyTurin, ItalyMarco BelliniMilestone SrlSorisole- Bergamo, ItalyProf. Mladen BeliczaUniversity Hospital“Sestre milosrdnice”University Department ofPathology “Ljudevit Jurak”Zagreb, CroatiaProf. Nina GaleUniversity of LjubljanaInstitute of PathologyLjubljana, SloveniaProf. Pierre BedossaCentre National de la RechercheScientifique (CNRS)UMR 8149 - Université Paris VHôpital BeaujonClichy, FranceProf. Maciej ZabelMedical University of WroclawDepartment of Histologyand EmbryologyWroclaw, PolandProf. Helmut PopperMedical University of GrazInstitute for PathologyGraz, AustriaProf. Thomas KirchnerLudwig-Maximilians-Universitaet MünchenDepartment of PathologyMunich, GermanyDr. Serena BoninInternational Centre for GeneticEngineering and BiotechnologyMolecular HistopathologyLaboratoryTrieste, ItalyProf. Samuel NavarroUniversity of ValenciaDepartment of PathologyValencia, SpainProf. Elias CampoHospital Clinico Provincialde BarcelonaDepartment of PathologyBarcelona, SpainProf. Gerald HoeflerMedical University of GrazInstitute for PathologyGraz, AustriaProf. Jaime PratHospital de la Santa Creui Sant PauBarcelona, SpainFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life289

Project Type:Co-ordination ActionContract number:LSHG-CT-2007-037637Starting date:1 st July 2007Duration:24 monthsEC Funding:450 000EpiGenChlamydiaState-of-the-Art:www.epigenchlamydia.euThe preliminary findings of members of EpiGenChlamydia estimate that there is a 40 percentgenetic predisposition to Chlamydia trachomatis (CT) infections. To allow full exploitationof this knowledge, it is essential to know which part of a person’s genetic make-up predisposesthem to CT infections. Therefore, genomic analysis on a large number of unrelatedindividuals needs to be performed.As no single entity has access to all the information, nor the necessary expertise to processall samples and data, a collaborative effort is required. This Coordination Action gives theconsortium the opportunity to thoroughly define the requirements for successful collaborationson this issue.Scientific/Technological Objectives:1) To provide state-of-the-art reports on the epidemiology of both ocular and sexuallytransmitted CT infections;2) To define and provide an approach based on the host-pathogen interaction for largescalegenetic typing;3) To generate a validated and integrated large biobank and efficient data warehouse;4) To integrate ongoing immunogenetic CT research lines in three European centres inwhich several participants are involved;5) To apply for research grants;6) To disseminate the EpiGenChlamydia consortium’s activities.Expected Results:1) A validated central biobank;2) Validated data warehouses;3) A validated EpiGenChlamydia website for the data warehouse;4) Research integration;5) Enhanced collaboration between partners and potential new partners;6) Dissemination of results;7) Media coverage, including publications and meetings. Reports and reviews will beproduced to keep the partners, the EC and the general public aware of the consortium’sachievements.Potential Impact:By the end of this CA, an integrated network of all key players for the genetic epidemiologicalstudy to determine the genetic predisposition to CT infection will have been formed.The collective knowledge acquired in this CA will allow for the development of tools for theearly detection of a predisposition to CT infection and diagnostics to detect CT infectionsindicative of non-regular treatment (persistent infections).Keywords: genetic epidemiology and standardisation, SNP-Chip, Chlamydiatrachomatis, screening-cohorts, sample collections, host factors, bacterialfactors, environmental factors, datawarehouse development290From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Contribution of molecular epidemiologyand host-pathogen genomics to understandChlamydia trachomatis diseasePartnersProject Coordinator:Dr. Servaas A. MorréVU University Medical CenterImmunogenetics of Infectious DiseasesDepartment of PathologyLaboratory of ImmunogeneticsDe Boelelaan 11171081 HV Amsterdam, The Netherlandssamorretravel@yahoo.co.ukProf. Chris Meijer, Prof. Salvador Peña,Bart CrusiusVU University Medical CenterDepartment of PathologyAmsterdam, The NetherlandsProf. David Mabey, Prof. Robin BaileyUniversity of LondonSchool of Hygiene and Tropical MedicineLondon, UKDr. Ioannis Ragoussis, Richard Mott,Prof. Michael Parker,Prof. Dominic KwiatkowskiUniversity of OxfordWellcome Trust Centre for Human GeneticsOxford, UKProf. Jorma PaavonenUniversity of HelsinkiUniversity HospitalDepartment of Obstetrics andGynaecologyHelsinki, FinlandDr. Helj-Marja SurcelNational Public Health InstituteHelsinki, FinlandDr. Han Fennema, Dr. Henry de VriesMunicipal Health ServiceAmsterdam, The NetherlandsDr. James Ito, Dr. Joe LyonsCity of Hope National Medical Centerand Beckman Research InstituteDepartment of Infectious DiseasesDuarte, California, USADr. Jean-Francois SchemannL’Institut de Recherche pour leDeveloppement (IRD)Paris, FranceDr. Ansumana SillahThe Gambia InternationalCentre for Eye HealthMinistry of HealthBanjul, GambiaDr. Björn HerrmannSwedish Institute of InfectiousDisease ControlSection of Sexually TransmittedInfectionsUppsala, SwedenDr. Björn Buan, Dr. Inger BakkenStiftelsen for Industriell og TekniskForskning ved Norges TekniskeHogskoleTrondheim, NorwayProf. Lars Ostergaard,Dr. Berit AndersenAahus University HospitalDepartment of ClinicalMicrobiologyArhus, DenmarkDr. Tjaco OssewaardeErasmus UniversityDepartment of MedicalMolecular MicrobiologyRotterdam, The NetherlandsDr. Yvonne PannekoekAcademic Medical CentreDepartment of MedicalMicrobiologyAmsterdam, The NetherlandsDr. Jan van BergenSTI AIDSAmsterdam, The NetherlandsProf. Jolande LandUniversity of MaastrichtMaastricht, The NetherlandsDr. Marianne van der SandeNational Institute of PublicHealth and the EnvironmentDepartment of InfectiousDiseases EpidemiologyBilthoven, The NetherlandsProf. Joseph IgietsemeMorehouse School of MedicineAtlanta, USAProf. Paul SavelkoulMicrobiome LtdHouten, The NetherlandsProf. Cathy Ison,Dr. Mary MacintoshHealth Protection AgencyCentre for InfectionSexually Transmitted BacterialReference LaboratoryLondon, UKFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life291

6. BIOINFORMATICS

6.BIOINFORMATICSBIOSAPIENSATDEMBRACEENFINEUROFUNGBASE

BioSapienswww.biosapiens.infoProject Type:Network of ExcellenceContract number:LSHG-CT-2003-503265Starting date:1 st January 2004Duration:60 monthsEC Funding:12 000 000State-of-the-Art:The genome projects have revealed for the first time the “blue-print” of life. The first draft ofthe human sequence was published in 2001, and there are now over 100 completed and70 draft genome sequences in the public domain. This explosion in genomic informationhas been achieved in a remarkably short period of time, and the flood of new sequencedata is likely to continue for the next decade. However, DNA sequence is merely a stringof letters; it must be interpreted in terms of the RNA and proteins that it encodes and thepromoter and regulatory regions that control transcription and translation.Annotation can be described as the process of “defining the biological role of a moleculein all its complexity” and mapping this knowledge onto the relevant gene products encodedby genomes. This involves both experimental and computational approaches and, indeed,absolutely requires their integration. The BioSapiens network provides the necessary expertiseand European infrastructure to allow distributed annotation, from both computationaland experimental laboratories. These expert annotations will be made available to everyoneover the web. To date, European scientists have been very active in the field of genomeand protein annotation, with Ensembl and SWISS-PROT being the primary resources in useworldwide. Many of the tools used in genome and protein sequence and structure annotation,prediction and validation, as well as in pathway analysis were developed in Europe.Many of the secondary resources derived from protein sequences and structures are alsoEuropean.However, the groups that develop the methods for improving genome annotation are widelydistributed throughout Europe and the best methods are often not incorporated into publiclyavailable genome annotations. Furthermore, these methods are continually changing andimproving, so keeping up to date becomes problematic. The fragmentation of currentlyavailable resources for genome annotation means that only a few bioinformatics expertsknow where to look for them. Consequently, most experimentalists cannot access all thebest information about a genome. This problem will only get worse as annotation methodsbecome more sophisticated and more bioinformatics laboratories are established to handleall the new data.Scientific/Technological Objectives:The objective of the BIOSAPIENS Network of Excellence is to provide a large-scale, concertedeffort to annotate genome data by laboratories distributed around Europe, usingboth informatics tools and input from experimentalists. The Network will create a EuropeanVirtual Institute for Genome Annotation, bringing together many of the best laboratories inEurope. The institute will help to improve bioinformatics research in Europe, by providing afocus for annotation and through the organisation of European meetings and workshops toencourage cooperation, rather than duplication of effort.An important aspect of the network activities is to try and achieve closer integration betweenexperimentalists and bioinformaticians, through a directed programme of genomeanalysis, focused on specific biological problems. The annotations generated by the Institutewill be available in the public domain and easily accessible on the web. This will beachieved initially through a distributed annotation system (DAS), which will evolve to takeadvantage of new developments in the GRID. European scientists have traditionally been296From Fundamental Genomics to Systems Biology: Understanding the Book of Life

A European Networkfor Integrated Genome AnnotationBIOSAPIENS Schoolvery active in the field of protein and genome annotation, and Ensembl and SWISS-PROT(now part of UniProt) are the primary resources in use worldwide.Many of the tools used in genome and protein sequence and structure annotation, predictionand validation, and pathway analysis have been developed in Europe. The BioSapiensNoE will further increase European competitiveness, through new discoveries, increasedintegration, expert training and improved tools and services, and enhance Europe’s role inthe academic and industrial exploitation of genomics.A further objective of the Network of Excellence is the establishment of a permanent EuropeanSchool of Bioinformatics, to train bioinformaticians and to encourage best practice inthe exploitation of genome annotation data for biologists. The courses and meetings will beopen to all scientists throughout Europe, and available at all levels, from basic courses forexperimentalists to more advanced training for experts.Expected Results:Some of the main results expected from the project will be the development of an integratedapproach to genome annotation from gene to function, and the establishment of an integratedand distributed website for Genome Annotation. The team expects a stimulationof cooperation between experimental scientists and computational biologists for genomeannotation, in the form of meetings and joint collaborations. Experimental validation ofpredictions made in silico will form part of these collaborations.The team will also focus on the developmentof improved computational methods for annotationthrough cooperation: new methods will be madeavailable via the web. Annotations from new methodswill be available on the BioSapiens website.Potential Impact:The BioSapiens Network of Excellence will have animpact on the establishment of a European researchstructure that will support the coordination of bioinfor-From Fundamental Genomics to Systems Biology: Understanding the Book of Life297

BIOSAPIENSDNAAnnotationProteomeAnnotationFunctionalAnnotation Gene Definition (alternative splicing) Protein Families Protein Structure & Modelling Sequence & Structure to Function Regulators & Promoters Expression Variation (haplotypes & SNP’s) Membrane Proteins & Ligands Post Translation Modification& Localisation Protein-Protein Complexes Pathways and Networksmatics research activities across different sub-areas, and across different areas of medicaland biotechnological application. It will promote the development of the required level ofcritical mass, which is essential if Europe should be able to compete with the major investmentsmade in this area in the USA, Canada and Japan.The integration between the groups in the BioSapiens Network of Excellence will have alasting impact on the European bioinformatics infrastructure, and on the sharing of humanresources, infrastructure databases and tools. Through cutting-edge research, high-leveltraining, and vigorous European interaction, the BioSapiens Network of Excellence willmake a substantial contribution to improving Europe’s knowledge base, and increase thepotential for creating new industries, new knowledge, and new employment.The exploitation of the biological informationenabled by the BioSapiens Networkof Excellence will in some cases be relativelydirect: e.g., improved health-carethrough better drugs, new vaccines, andpersonalised medicines for individualsand sub-populations, and by improvedunderstanding of diet and health.PartnersProject Coordinator:Prof. Janet ThorntonEuropean Molecular Biology Laboratory (EMBL)European Bioinformatics Institute (EBI)Wellcome Trust Genome CampusHinxton, CB10 1SD, UK.thornton@ebi.ac.ukProject Manager:Dr. Kerstin NybergEuropean Molecular Biology Laboratory (EMBL)European Bioinformatics Institute (EBI)Wellcome Trust Genome CampusHinxton, CB10 1SD, UKknyberg@ebi.ac.ukProf. Peer BorkEuropean Molecular Biology Laboratory,(EMBL)Heidelberg, GermanyKeywords:genome annotation,data integration, databasesProf. Dmitrij FrishmanHelmholz ZentrumNeuherberg, GermanyProf; Jacques van HeldenUniversité Libre de Bruxelles,Service de Conformation de MacromoléculesBiologiques et BioinformatiqueBrussels, Belgium298From Fundamental Genomics to Systems Biology: Understanding the Book of Life

A European Network for Integrated Genome AnnotationProf. Alfonso ValenciaSpanish National Cancer ResearchCentre (CNIO)Madrid, SpainDr. Roderic GuigoCentre for Genomic RegulationBarcelona, SpainDr. Tim HubbardGenome Research LtdWellcome Trust Sanger InstituteHinxton, UKProf. Thomas LengauerMax-Planck Institute for InformaticsSaarbrücken, GermanyProf. Michal LinialHebrew University of JerusalemDepartment of Biological ChemistryJerusalem, IsraelProf. Anna TramontanoUniversity of Rome ‘La Sapienza’Department of Biochemical SciencesRome, ItalyProf. Gunnar von HeijneUniversity of StockholmDepartment of Biochemistryand BiophysicsStockholm, SwedenDr. Richard MottUniversity of OxfordWellcome Trust Centre forHuman GeneticsOxford, UKProf. Christine Orengo, Prof. David JonesUniversity College LondonDepartment of Biochemistry andMolecular BiologyLondon, UKProf. Gert VriendRadboud UniversityNijmegen Medical CentreCentre for Molecular andBiomolecular InformaticsNijmegen, The NetherlandsDr. Anne-Lise VeutheySwiss Institute of BioinformaticsGeneva, SwitzerlandProf. Søren BrunakTechnical University of DenmarkCenter for Biological SequenceAnalysis (CBS)Lyngby, DenmarkProf. Esko UkkonenUniversity of HelsinkiDepartment of Computer ScienceHelsinki, FinlandProf. Stylianos AntonarakisUniversity of GenevaDivision of Medical GeneticsGeneva, SwitzerlandProf. László PatthyInstitute of EnzymologyBiological Research CenterHungarian Academy of SciencesBudapest, HungaryDietmar SchomburgTechnical University of BraunschweigDepartment of Bioinformatics andBiochemistryBraunschweig, GermanyAntoine DanchinInstitut PasteurDepartment Structure and Dynamicsof GenomesParis, FranceDr; Leszek RychlewskiBioInfo Bank InstituteBioinformatics LaboratoryPoznan, PolandProf. Martin VingronMax-Planck Institute forMolecular GeneticsBerlin, GermanyDr. Vincent SchachterGenoscopeEvry, FranceProf. Rita CasadioUniversity of BolognaDepartment of BiologyBologna, ItalyDr. Christos OuzounisInstitute of AgrobiotechnologyCentre for Research andTechnology Hellas (CERTH)Thessaloniki, GreeceFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life299

Project Type:Specific TargetedResearch ProjectContract number:LSHG-CT-2003-503329Starting date:1 st March 2004Duration:36 monthsEC Funding:2 000 000ATDState-of-the-Art:www.atdproject.orgA single human gene can produce a variety of alternative transcripts (ATs or mRNA isoforms),which differ in terms of their transcription initiation, splicing or polyadenylation patterns.Expression of alternative transcripts has been observed to be specific to tissue-typeor developmental stage. Disruptions in AT expression have serious consequences for anorganism and are associated with numerous diseases, including cancer, multiple sclerosis,heart failure and neurodegenerative disorders.The ATD project aims to understand the mechanisms responsible for the formation of differentATs. It is anticipated that studies in the field of ATs will develop into a significantresearch area, with direct applications for pharmaceutical industries. These applicationsare inclusive of disease diagnosis or prognosis of risk patients, as well as identification ofnew drug targets.Scientific/Technological Objectives:The ATD project is a collaborative multi-disciplinary project.It aims to comprehensively characterise alternative transcript(AT) forms throughout the human genome, and alsoto assess the differential expression of these forms in timeand space, in normal and disease-related tissues. This is accompaniedby adequate quality control procedures, suchas research for evolutionary proof through comparative sequencedata analysis, between human and mouse. Furthercharacterisation of the AT is implemented through activitiessuch as identification of regulatory patterns, and derivationof expression states (i.e. expression specificity in termsof association with diseases, developmental stages, or tissue-specificity).The project also aims to develop standardvocabularies and models that will represent gene structuresand their expression patterns.Expected Results:The validity of the bioinformatics prediction of diseasespecificATs is being examined through the execution ofRT-PCR experiments on selected tissues. The AT discoveryeffort is accompanied by database integration, and also bydissemination to the scientific community.The principal end results being targeted are as follows: gene, feature variants, transcript variants, annotations, derived expression states, proteinfunctionalities, results of experimental validations and associations with diseases.Fully developed query interfaces and toolboxes are available in the database, whichis accessible at: http://www.ebi.ac.uk/atd/; of vocabularies for the representation of annotations; human and mouse; 300From Fundamental Genomics to Systems Biology: Understanding the Book of Life

The Alternate Transcript Diversity ProjectPotential Impact:Alternative transcription has such a strong impact on gene products, that any disruption ofATs is potentially linked to fatal diseases. Diseases that have been linked to AT disruptioninclude cancer, multiple sclerosis, heart failure and neurodegenerative diseases; ATD hasthe capacity to facilitate and support those areas.Traditional molecular biology approaches founded on a “one gene at a time” basis, are nolonger practical when detecting new disease-specific ATs. There is currently a need for theexecution of genome-wide AT detection, followed by high-throughput analysis of transcriptexpression. It is predicted that these studies on alternative transcripts will develop into amajor research area, with direct applications for pharmaceutical industries.Keywords: transcriptome, gene expression regulation, splicing, diagnosis,disease markers, microarrays, basic biological processes, transcriptPartnersProject Coordinator:Prof. Daniel GautheretERM-0206 TAGCInstitut National de la Santé et de laRecherche Médicale (INSERM)75654 Marseille, Francedaniel.gautheret@u-psud.frProf. Peer BorkEuropean Molecular Biology Laboratory (EMBL)Structural and Computational Biology UnitHeidelberg, GermanyDr. Eleanor WhitfieldEuropean Molecular Biology Laboratory (EMBL)European Bioinformatics Institute (EBI)Hinxton, UKProf. Magnus von Knebel DoeberitzUniversity of HeidelbergDepartment of Applied Tumor BiologyHeidelberg, GermanyDr. Christiane Dascher-NadelInserm Transfert SAEuropean Project Management DepartmentMarseille, FranceProf. Jens ReichMax-Delbruck-Centrum fürMolekulare Medizin Berlin-BuchBioinformatics UnitBerlin-Buch, GermanyProf. Winston HideUniversity of the Western CapeSouth African National Bioinformatics InstituteCape Town, South AfricaDr Roderic GuigoCentre de Regualci GenmicaBioinformatics and Genomics UnitBarcelona, SpainDr. Jaak ViloEstonian BiocenterBioinformatics GroupTartu, EstoniaFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life301

EMBRACEwww.embracegrid.infoProject Type:Network of ExcellenceContract number:LHSG-CT-2004-512092Starting date:1 st February 2005Duration:60 monthsEC Funding:8 280 000State-of-the-Art:The EMBRACE project addresses the need for integration of data and analysis resources forbiological and biomolecular information. The many publicly available collections of biomolecularinformation do a reasonable job for a given domain. Software tools to organise andanalyse this information are available both from the public domain, and commercially. Inprinciple, cross-references in these databases allow inter-database navigation; however, thelinks are sparse and coarse-grained, and their exploitation requires biological knowledgeand expert programming. As a result, every serious bioinformatics centre is burdened notonly with the task of maintaining local data and software, but also of supporting users in thesubstantial task of exploring the natural biological connections between data. This requiresconsiderable human effort. Current trends in systems biology demand greatly improvedconnections between different domains of knowledge, and the weaknesses in informationintegration are becoming an intolerable hindrance. This network will address these weaknessesby enabling data providers and tool builders to standardise their data access andsoftware tools, using the new grid computing technologies that are ideally adapted to thetask. The use of these standard methods will allow data resources to be essentially selfdescribing,allowing software to work out the structure of the data, in large part automatically.Apart from facilitating widespread integration of software and data, this will makethe interacting systems easy to update; for example, it will reflect changes to the internalrepresentation of the data.Scientific/Technological Objectives:The objective of the EMBRACE Network of Excellence is to draw together a wide groupof experts throughout Europe who are involved in the use of information technology in thebiomolecular sciences. The EMBRACE network will optimize informatics and information exploitationby pure and applied biological scientists, in both the academic and commercialsectors. The result will be highly integrated access to a broad range of biomolecular dataand software packages. Groups in the network are involved in the following activities:1) collection, curation and provision of biomolecular information;2) development of tools and programming interfaces to exploit that information; and3) tracking and exploiting advances in information technology, with a view to applyingthem in bioinformatics training and also to reaching out to groups who can benefitfrom the work of the network.302From Fundamental Genomics to Systems Biology: Understanding the Book of Life

A European Modelfor Bioinformatics Researchand Community EducationThese groups work together to enable highly functional interactive access to a wide rangeof biomolecular data (sequence, structure, annotation, etc.), and tools with which to exploitthe data. This naturally includes many core databases and tools available from theEuropean Bioinformatics Institute (EBI), but, crucially, the methods used will support theintegration of dispersed, autonomous information. As a result, groups throughout Europewill be expected to integrate their own local or proprietary databases and tools into thecollaborative “information space” which constitutes the EMBRACEgrid — a ‘data grid’allowing integrated exploitation of data, analogous to a ‘compute grid’, which enablesunified exploitation of dispersed computer resources. EMBRACEgrid will serve as a comprehensivevirtual information source: virtual in the sense that it will have no single physicallocation, being rather a dispersed set of tightly coupled resources. EMBRACEgrid willbe a permanent product of the project.Expected Results:The results expected are as follows:1) Standardized application programming interfaces (APIs) with all the core biologicaldatabases at the EBI, as well as with several wide-ranging sources of other informationdistributed throughout Europe.2) Software tools that exploit the data through the new APIs, to provide a workingenvironment in which to access and analyze the data, and also to facilitate thedevelopment of further tools in a consistent programming environment.3) Technological standards for finding and describing the data and application servicesmentioned above.4) Training and outreach to enable biologists to get the best out of the resulting toolsand data, and bioinformaticians to develop ever better tools, in the knowledge thatthey are firmly connected to all the data.Potential Impact:There is currently a great deal of investment in post-genomics projects. About once a weekthe sequence of an entire species becomes available. Transcriptomics and proteomicsprojects are producing data avalanche after data avalanche. Each time that (bio)informaticianshave dealt with the data flow of one type of project, two new types of high throughputexperiment have been developed. All this data is finding its way to the biosciences, andfields such as pharma, health, food and agriculture are all likely to undergo major revolutions,that are expected to improve the quality of life for all, from infants to the elderly. Thisproject sits in the context of existing integration projects such as Integr8 and BioMart. Theseprojects, and information resources like Ensembl will exploit the standards developed inEMBRACE to provide common interfaces to data and tools across Europe, targeted to theneeds of experimental research.Keywords: bioinformatics, standards, web services, integrationFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life303

EMBRACEPartnersProject Coordinator:Dr. Graham CameronEuropean Molecular BiologyLaboratory (EMBL)European Bioinformatics Institute (EBI)Wellcome Trust Genome CampusHinxton, CB10 1SD, UKcameron@ebi.ac.ukProject Manager:Dr. Kerstin NybergEuropean Molecular BiologyLaboratory (EMBL)European Bioinformatics Institute (EBI)Wellcome Trust Genome CampusHinxton, CB10 1SD, UKknyberg@ebi.ac.ukDr. Andreas GiselInstitute of Biomedical TechnologiesSection BariConsiglio Nazionale della Ricerche (CNR)Bari, ItalyProf. Terri AttwoodUniversity of ManchesterSchool of Biological SciencesManchester, UKMarco PagniSwiss Institute of BioinformaticsLausanne, SwitzerlandDr. Erik Bongcam-RudloffSwedish University of Agricultural SciencesLinnaeus Centre for BioinformaticsUppsala, SwedenDr. Vincent Breton, Dr Christophe BlanchetCentre National de la RechercheScientifique (CNRS)Clermont-Ferrand and Lyon, FranceProf. Søren BrunakTechnical University of DenmarkCenter for Biological SequenceAnalysis (CBS)BioCentrum-DTULyngby, DenmarkJose-Maria Carazo GarciaSpanish National Research Council (CSIC)Madrid, Spain304From Fundamental Genomics to Systems Biology: Understanding the Book of Life

A European Model for Bioinformatics Research and Community EducationProf. Arne ElofssonUniversity of StockholmStockholm Bioinformatics CentreStockholm, SwedenDr. Daniel KahnINRIA-UCBLInstitut National de la RechercheAgronomique (INRA)Toulouse, FranceDr. Ralf HerwigMax-Planck Institute forMolecular GeneticsDepartment of Vertebrate GenomicsBerlin, GermanyDr. Eija KorpelainenCSC – Scientific Computing LtdEspoo, FinlandProf. Christine OrengoUniversity College LondonDepartment of Biochemistryand Molecular BiologyLondon, UKDr. Yitzhak PilpelWeizmann Institute of ScienceDepartment of MolecularGenetics/BiochemistryRehovot, IsraelDr. Gert VriendRadboud UniversityNijmegen Medical CentreCentre for Molecular andBiomolecular InformaticsNijmegen, The NetherlandsProf. Alfonso ValenciaInstituto Nacional De TecnicaAeroespacial (Centro DeAstrobiologia)Laboratory of BionformaticsCABMadrid, SpainProf. Inge JonassenBergen Center forComputational ScienceBergen, NorwayFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life305

ENFINwww.enfin.orgProject Type:Network of ExcellenceContract number:LSHG-CT-2005-518254Starting date:15 November 2005Duration:60 monthsEC Funding:8 967 500State-of-the-Art:Despite the progress made in bioinformatics methods and databases to date, even the bestexperimental laboratories use only a small number of computational tools in their work, andthey rarely exploit the potential of multiple datasets. The ENFIN network will transform theway computational analysis is used in the laboratory. The infrastructure will be entirely open,in the same way that genome information is accessible to all.To achieve its goals, the network will encourage close internal collaboration between experimentaland computational research groups, and will have a specific consumables budget fortesting predictions experimentally. The computational work includes the development of adistributed database infrastructure appropriate for small laboratories, and the development ofanalysis methods, including Bayesian networks, metabolite flux modelling and correlations ofprotein modifications to pathways.The experimental techniques used to test this system include mass spectroscopy, syntheticpeptide biochemistry and RNA interference knockdown. Where appropriate, the network haschosen experimental areas related to intracellular signalling, associated with the cell cycle.Scientific/Technological Objectives:ENFIN’s network’s specific objectives can be summarised as follows:1) Development of the ENFIN Core (EnCORE), by taking a number of pre-existingdatabase packages and providing a unified installation which can be used inlaboratories worldwide;2) Curation of appropriate pathway knowledge and hypotheses;3) Development and management of new experimental data standards;4) Discrete function prediction;5) Network reconstruction;6) Systems level modelling. (Objectives 4, 5 and 6 comprise the ENFIN analysislayer. Cycling between computational predictions and experimental validationfeedback will be used, to improve the accuracy of bioinformatics tools for predictingbiological features in this layer);7) Critical assessment and integration, i.e. bringing together groups across the analysislayer, both to critically assess the methods and also to uncover new synergiesbetween computational and experimental groups;8) Provision of graduate level training, coordinated with the European School of Bioinformatics,so as to arrange a short course for graduate level students;9) Documentation from a wet laboratory perspective, enabling the consortium to developa multi-authored resource, which is kept as current as possible through directediting by appropriate researchers within the network;10) Facilitating SME outreach, to raise awareness of ENFIN in the biotechnology community,and to increase the understanding of SMEs’ needs.306From Fundamental Genomics to Systems Biology: Understanding the Book of Life

An Experimental Networkfor Functional IntegrationExpected Results:EnCore, the network, will develop a set of existing databases for the storage and integrationof public and local data, such as microarray data, protein-protein interaction data andpathway information. This core will be available by all nodes of the ENFIN network, andwill form the backbone for the communication of datasets.The ENFIN analysis layer will work with EnCore as a series of computer programs to provideanalysis of the data stored in EnCore. Interaction between experimental and computationalresearchers is crucial in the development of these programs. There will be a criticalassessment of the computational tools using experimental information as a challenge.A truly multidisciplinary set of investigators will be gathered across Europe, spanning experimentalresearch in mitogenic signalling through to algorithm development in machinelearningtechniques. ENFIN will use a variety of experimental techniques to test and informcomputational work. This work will also provide insights into cancer, since the bulk of thenetwork’s experimental research concerns regulation of the cell cycle. These biologicalresults will prove the effectiveness of the network’s products and provide insights that couldbe used to enhance human health.ENFIN’s products will be disseminated, not principally as scientific results, but rather as atechnical solution for how to coordinate computational and experimental work. The productiveinteractions between computational and experimental researchers will be as importantas the technical programming aspect of the work. Through its dissemination programme,ENFIN will reach the post-doctoral student in the lab, the SME researcher, and biologicaland bioinformatics graduate students. The project will pass on developments in bioinfor-Systems Modeling MethodsFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life307

ENFINmatics best practice and software deployment to core biological labs, and will benefit fromfeedback on their use.Potential Impact:The main tangible benefit of ENFIN will be the development of a set of scientific proceduresfor understanding multi-component systems using computational techniques. The ENFINinfrastructure will be distributed firstly to all the network’s partners, and then to various identifiedcollaborators and other interested laboratories. Local installation of ENFIN will allowon-site processing of information, access to public archived data as well as local information,access to specific, designed analysis methods which have been tested experimentally,and access to documentation written from the wet laboratory perspective.ENFIN will have an impact on the understanding of complex human diseases such as cancerand diabetes. The systems-level vision of ENFIN is applicable to many other complexdiseases and biological processes in other fields. As well as mammalian cells, systemsbiology could potentially impact the understanding of many pathogenic organisms - botheubacteria and eukaryotes.In addition to the network’s research being fully integrated with that of leading molecularbiology laboratories, it will organise a public, highly visible conference to explicitly test theoutputs of systems biology predictions. The scientific approach taken by ENFIN will be ofgreat interest to many industrial groups. Through the industry programme at the EuropeanBioinformatics Institute (EBI), whose members include all the main life science companies,the network will be able to educate these industrial partners in new approaches.Keywords:systems biology, functional genomics, pathways, computational predictionsPartnersProject Coordinator:Prof. Ewan BirneyEuropean Molecular Biology Laboratory (EMBL)European Bioinformatics Institute (EBI)Wellcome Trust Genome CampusHinxton, CB10 1SD, UKbirney@ebi.ac.ukProject ManagerDr. Pascal KahlemEuropean Molecular Biology Laboratory (EMBL)European Bioinformatics Institute (EBI)Wellcome Trust Genome CampusHinxton, CB10 1SD, UKpkahlem@ebi.ac.ukDr. Jan EllenbergEuropean Molecular Biology Laboratory (EMBL)Heidelberg, GermanyDr. Henning HermjakobEuropean Molecular Biology Laboratory (EMBL)European Bioinformatics Institute (EBI)Hinxton, UKProf. Geoffrey J. BartonUniversity of DundeeDivision of Biological Chemistry andMolecular MicrobiologySchool of Life SciencesDundee, UKProf. Søren BrunakTechnical University of DenmarkCentre for Biological Sequence AnalysisLyngby, Denmark308From Fundamental Genomics to Systems Biology: Understanding the Book of Life

An Experimental Network for Functional IntegrationProf. Gianni CesareniUniversity of Rome Tor VergataDepartment of BiologyLaboratory of Molecular GeneticsRome, ItalyDr. John HancockMedical Research CouncilMammalian Genetics UnitHarwell, UKProf. Carl-Henrik HeldinLudwig Institute for Cancer ResearchUppsala, SwedenDr. Edda Klipp, Dr. James AdjayeMax-Planck Institute for Molecular GeneticsBerlin, GermanyDr. Jaak ViloOÜ QureTecTartu, EstoniaIoannis XenariosSerono Pharmaceutical Research InstituteGeneva, SwitzerlandProf. Alfonso ValenciaSpanish National Cancer Research Centre (CNIO)S-CompBioStructural Biology and Biocomputing ProgrammeMadrid, SpainDr. Jaap HeringaCentre for Integrative Bioinformatics VUAmsterdam, The NetherlandsProf. Erich NiggMax-Planck Institute of BiochemistryDepartment of Cell BiologyMartinsried, GermanyProf.Tomi MäkeläUniversity of HelsinkiFaculty of MedicineMolecular and Cancer Biology Research ProgramHelnsinki, FinlandProf. Christine OrengoUniversity College LondonDepartment of Biochemistry andMolecular BiologyLondon, UKDr. Christos OuzounisNational Center for Research and TechnologyInstitute of AgrobiotechnologyThessaloniki GreeceDr. Dietmar SchomburgTechnical University BraunschweigBioinformatics & BiochemistryBraunschweig, GermanyDr. Vincent SchachterConsortium national de rechercheen Genomique (Genoscope)Evry, FranceDr. Eran SegalWeizmann Institute of ScienceDepartment of Computer Science andApplied MathematicsRehovot, IsraelFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life309

EUROFUNGBASEwww.eurofung.netProject Type:Co-ordination ActionContract number:LSSG-CT-2005-018964Starting date:1 st November 2005Duration:36 monthsEC Funding:486 000State-of-the-Art:The biotechnology industries that exploit filamentous fungi are strong within Europe. Largecompanies and SMEs have participated in EUROFUNG projects within FP4 and FP5, andthis is a major strength. Similarly, European research into the pathogenesis of A. fumigatusis strong. On the other hand, genomic resources for filamentous fungi have not beena strong European feature. The sequencing efforts have been carried out largely outsideEurope (in the USA and Japan) although Europe has made modest contributions to sequencingof fungal genomes and ESTs. Genome sequence information has only recently becomepublicly available for the fungi to be used within this project. There are no gene arrayscurrently available for any of these fungal species that cover the entire genome, althoughpartial genome coverage has been achieved on slides in some cases. The internationalAspergillus Genomes Research Policy Committee, which was founded in 2004, concludedthat fabrication of A. nidulans microarrays is a top community priorityThere is no bioinformatics resource available that makes it possible to store and interconnecttranscriptomic and proteomic data, for filamentous fungi. The current state of theart for yeast-based data repositories is that platforms have been developed and will serveas the model for the filamentous fungi. Integration of the yeast data will provide the modelfor the fungal equivalent. European scientists within the consortium are international leadersin many areas of science that will exploit the filamentous fungal genome sequenceinformation.Scientific/Technological Objectives:The EUROFUNGBASE project is a Coordination Action. The objectives of the project areto develop the tools and technologies necessary, so as to enable innovative functionalgenomic research of hyphal fungi. In that context it is also essential, as a community, todevelop a strategy to set up and maintain a sustainable database.The project focuses on several filamentous fungi for different reasons. Aspergillus nidulanshas a long record of use as a fungal model organism. Aspergillus niger, Trichodermareesei and Penicillium chrysogenum are important cell factories used for the production ofenzymes and metabolites including compounds such as β-lactams with benefits to humanhealth. The human pathogen Aspergillus fumigatus not only serves as a model pathogen,but is becoming more and more of a serious threat to human health.This new genomics information will thus be beneficial to Europe’s biotechnology industries,and will help to improve the prevention and treatment of fungal disease.Expected results:The main results expected from this project are set out below: notationjamborees. laborationwith bioinformatics centres, and incorporation of the consortium’s data. munityand the European fungal biotech industry through meetings, workshops andweb-based information.310From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Strategy to build up and maintain an integratedsustainable European fungal genomic databaserequired for innovative genomics research on, important forbiotechnology and human health patingindustries, thus strengthening infrastructure for high quality fungal genomicsresearch in Europe and determining joint research targets for the future. and biotechnological research.Potential impact:Enlarging and maintaining genomic databases is of paramount importance in order tofurther develop systems biology for model organisms, including relevant filamentous fungi.Therefore, bioinformatics tools must become progressively more sophisticated, to allow forthe interpretation of the enormous amounts of data that already have been generated, andare increasing every day. In the end, not only the EUROFUNGBASE community but alsoother research communities will profit from the effort put in to maintaining a sustainabledatabase. The EUROFUNGBASE project will illustrate the impact described above.Keywords: fungal pathogenicity, fungal health applications, genomic databasesPartnersProject Coordinator:Prof. Cees van den HondelLeiden UniversityClusius LaboratoryWassenaarseweg 642333 AL Leiden, The Netherlandsc.a.m.van.den.hondel@biology.leidenuniv.nlDr. Dave UsseryTechnical University of DenmarkLyngby, DenmarkProf. Steve Oliver,Dr. Geoffrey RobsonUniversity of Manchester,School of Biological SciencesManchester, UKFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life311

7.FUNCTIONAL GENOMICSAPPROACHES FOR BASICBIOLOGICAL PROCESSES

7.1BIOLOGICAL PATHWAYSAND SIGNALLINGMAINWOUNDMITOCHECKSIGNALLING & TRAFFICTransDeathPEROXISOMESDNA REPAIRSTEROLTALKRUBICONEndoTrackAnEUploidy

MAINhttp://main-noe.orgProject Type:Network of ExcellenceContract number:LSHG-CT-2003-502935Starting date:1 st January 2004Duration:48 monthsEC Funding:10 000 000TNF-a stimulated HUVECsand T-lymphoblast, 12 mincoincubation. The projectionof a z-stack of 8 images.Acknowledgement: Jaime MillanState-of-the-Art:Chronic inflammation is a systemic disorder resulting from the dysregulation of multiple,mechanistically unrelated higher order biological processes. This consortium will promotethe integration of multi-disciplinary research groups to achieve a thorough understanding ofdirected inflammatory cell migration towardsand across injured tissues. To achieve itsgoals, the MAIN consortium will be based onfour developmental research programmes,three support facilities and one core facility.The research programmes are tightly interconnectedin a logical sequence of highlyintegrated activities. The tool developmentprogramme (TDP) will develop technologicaltools that are instrumental in making advancementsin the field of cell migration. Thetarget identification programme (TIP) willidentify signalling pathways and/or molecularnetworks involved in defined aspects ofinflammatory cell migration. The target validationprogramme (TVP) will validate targetsemerging from the TIP by testing them acrossin vitro and in vivo models, different inducingstimuli and manipulating conditions. The TVPcombines the products of the TDP and the TIPto provide a unified explanation on how multiple‘inputs’ received by inflammatory cellsresult in spatially and temporally coordinated‘outputs’, affecting the migratory behaviourof such cells. The drug development programme(DDP) will transfer selected targetsinto a pipeline of drug development, throughthe SMEs of the consortium. The support facilities(imaging, microarrays and proteomics)and the bioinformatics core will providetechnological and bio-computational supportto the programmes. To spread excellence through education and training, MAIN will implementa training and education programme (TEP), with practical courses and workshops forgraduate students and technicians.Scientific/Technological Objectives:The scientific goal of MAIN is to identify and characterise the molecular mechanisms underlyingchronic inflammatory responses, with emphasis on a crucial step in such responses,namely the transmigration of leukocytes (white blood cells) from the bloodstream into inflamedtissues and their local activation by inflammatory substances and pathogens. MAINhas gathered over 150 researchers and graduate students from 13 research institutes andtwo biotechnology companies of five EU Member States, and Switzerland and Israel. Theinternational dimension of MAIN is emphasised by the strong connection between MAIN316From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Targeting Cell Migrationin Chronic Inflammation scientists and the US Cell Migration Consortium’s (CMC) goal of exploring the complexmechanisms underlying cell migration in embryonic development, wound healing and cancer.MAIN and CMC share information/technology platforms and will develop a coordinatedagenda of scientific events to communicate their scientific achievements to a widerscientific audience and the public.Expected Results:Bioinformatic databases on the website: integrated suite of MAIN’s resources, bioinformaticssoftware tools, application databases enabling rapid data retrieval/analysis and crosscorrelationof functional genomic/proteomic data facilitating biological hypothesis-makingand ‘systems’ level investigations. It includes MAIN’s deliverables (public access) detailingwork packages, publications, patents, training, meetings and workshops, experimentaltools (main members’ access only)including a database of antibody, cell lines, peptides,plasmids, vectors, cDNA and transgenic organisms.Tutorials (the cell migration and inflammation section of website) explain the process to anon-expert public audience.‘Deciphering the Cell Migration Code’:students meeting held 30 April-3 May2005, Switzerland. The format was acombination of poster presentations,20 student presentations and guestspeakers/partners from the MAIN consortium.It was a unique opportunity tomeet other students from the consortium,encouraging mobility and enablingan exchange of scientific/technologytransfer expertise between theconsortium members via their youngscientists.MAIN published papers: Prof. B. Moser:‘Follicular B Helper T Cells in AntibodyResponses and Autoimmunity’and ‘Professional Antigen-PresentationFunction by Human gamma-delta TCells’, (Nature Reviews ImmunologyNovember 2005/Science Express 2June 2005); Prof. R. Alon: ‘How dorolling immune cells use their integrinsto arrest on inflamed blood vessels?’and ‘Immune Cell Migration in Inflammation:present and future therapeutictargets’, Nature Immunology May/December2005.Endothelial celljunctions delineated ina mouse cremastericvenule by the use of ananti-PECAM-1 mAbTracking of leucocyte(white) transmigrationthrough IL-1βstimulatedcremastericvenules immunostainedwith an anti-PECAM-1mAb (red)From Fundamental Genomics to Systems Biology: Understanding the Book of Life317

MAINInflamed mouse cremastericvenule stained for pericytes(a-SMA; red) and neutrophils(MRP-14; green)Inflamed mouse cremastericvenule stained for pericytes(a-SMA; red), neutrophils(MRP-14; green) and monocytes(CX3CR1; green)Potential Impact:The bioinformatics core facility will organise/disseminateMAIN’s informationinside and outside its boundaries.It is hoped that the TDP will producecutting-edge technological approachesfor widespread use in the cell migrationresearch community and refine existingtechnologies to make them appropriatefor use in the cell migration field. The TIPwill promote identification and characterisationof signalling pathways and/ormolecular networks involved in definedaspects of inflammatory cell migration,achieved by the implementation of jointresearch projects. The TVP aims at combiningthe TDP and TIP results to providea unified explanation of how multiple‘inputs’ received by inflammatory cellsresult in spatially and temporally coordinated‘outputs’, as applied to cellmigration and related biological processesoccurring in chronically inflamedtissues. The TVP aims to identify the mostpromising targets for further analysis/potential use in drug development. TheDDP will focus on selected target pathways/networksemerging from the TVPand will transfer them into a pipeline ofdrug development, using biotechnological/pharmaceuticalSMEs participating in the network. The TEP aims to develop PhDs withtop quality, up-to-date education in biotechnology/technology transfer. Training in differentEuropean institutions will encourage mobility and enable an exchange of scientific/technologytransfer expertise.Keywords: general pathology, immunology, medicine, cell migration, inflammation,signal transduction318From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Targeting Cell Migration in Chronic InflammationPartnersProject Coordinator:Prof. Ruggero PardiFondazione Centro San Raffaele Del Monte TaborDepartment of Molecular Biology andFunctional GenomicsVia Olgettina 5820132 Milan, Italypardi.ruggero@hsr.itProf. Francisco Sanchez-MadridUniversidad Autonoma de MadridHospital De La PrincesaDepartamento De MedicinaMadrid, SpainProf. Anne RidleyKing’s College LondonRandall Division of Cell &Molecular BiophysicsLondon, UKProf. Dietmar VestweberMax-Planck-Institute ofMolecular BiomedicineDepartment of Cell BiologyMuenster, GermanyDr. Jochen WittbrodtEuropean Molecular BiologyLaboratory (EMBL)Department of Molecular BiologyHeidelberg, GermanyDr. Christina CaschettoIFOM-Istituto FIRC di Oncologia MolecolareInstitute for Molecular OncologyMilan, ItalyProf. Antonio LanzavecchiaInstitute for Research in BiomedicineImmune Regulation LaboratoryBellinzona, SwitzerlandDr. Marlene WolfUniversity of BernTheodor-Kocher InstituteBern, SwitzerlandProf. Fritz KrombachLudwig-Maximilians-Universität MünchenInstitute for Surgical ResearchMunich, GermanyProf. Ronen AlonWeizmann Institute of ScienceDepartment of ImmunologyRehovot, IsraelProf. Dorian HaskardImperial College LondonNational Heart and Lung InstituteLondon, UKDr. Matthias P. WymannUniversity of BaselDepartment of Clinical &Biological SciencesBasel, SwitzerlandDr. Jean-Philippe GirardInstitut de Pharmacologie etde Biologie (IPBS)-Centre National de laRecherche Scientifique (CNRS)UMR 5089Department of Cancer BiologyToulouse, FranceDr. Daniele D’AmbrosioBIOXELL SpAResearch DepartmentMilan, ItalyDr Françoise CaillerEndocube SASProloque BiotechLabege, FranceDr. Marco BaccantiScience Park Raf SpABiotechnology TransferCentreMilan, ItalyFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life319

WOUNDhttp://pdg.cnb.uam.es/bioinfogp/woundProject Type:Specific TargetedResearch ProjectContract number:LSHG-CT-2003-503447Starting date:1 st January 2004Duration:48 monthsEC Funding:1 870 321State-of-the-Art:Understanding the properties of the signalling mechanisms involved in epithelial fusion andwound healing is of central importance for basic science and in clinical applications. A functionalgenomics approach has been chosen to unravel the signalling pathways involved inthese processes. It can provide direct information on the coordination of the cell communicationsystems directing these events and on the molecules and cellular activities that implementthem. Thus, the wealth of information and resources generated by efforts in genomics canbe directly translated into understanding the functioning of cells and tissues in vivo and toclinical applications. To achieve these goals, a multiorganism approach will be developedto analyse the control of gene expression during wound healing and related morphogeneticprogrammes. The result will be a truly comparable genomic description of a basic biologicalmechanism conserved throughout evolution. It is important to emphasise that this multiorganismanalysis will be performed in organisms which have had their genomes sequenced.The process of dorsal closureinitiales at 10 hours afteregg laying and is completedafter 13 hoursScientific/Technological Objectives:Wound healing disorders are major health problems that demand the development of effectivetherapeutics. This, however, requires a thorough understanding of the molecular mechanismsunderlying healing. The goal of this project is to identify evolutionary conserved genes andmajor signalling pathways that orchestrate the healing process, and to use model systems tohelp define their function. Previous studies demonstrated a strong conservation of the genesinvolved in murine and human wound repair and epithelial movement and fusion in Drosophilaand C. elegans. Therefore, we are performing a multi-organism functional genomicsapproach to identify genes that are under- or over-expressed during wound healing or thatare required during epithelial morphogenesis. Our first objective is to identify genes regulatedin more than one system. The second objective is to analyse their expression in situationsof impaired fusion/repair. The third objective is to use invertebrate models and monoculturesand organotypic mammalian culture systems to examine the function of the most highlyconserved genes. Finally, for a few selected genes, transgenic/knockout mouse studies andstudies using skin-humanised mice shall be performed to identify their in vivo function in repair.The ultimate goalis to identify and investigateselected genes astargets for the developmentof innovative therapeutics.Expected Results:The objective of this project is to define the conserved acting elements of the biomolecularnetworks involved in epithelial fusion/wound healing, to analyse their functions and toexplore their use as targets for the development of innovative therapeutics. Major specificgoals as identified below will be tackled in a logical sequential fashion. Each of them correspondsto independent subprojects with recognised deliverables:1) To identify the common pathways directing epithelial fusion both during morphogenesisand in the process of wound healing.2) To identify those conserved genes whose expression is altered in models of impairedepithelial fusion and wound healing.320From Fundamental Genomics to Systems Biology: Understanding the Book of Life

A multi-organism functional genomicsapproach to study signalling pathwaysin epithelial fusion/wound healing3) The functional characterisation of the relevant genes/pathways in different organismsby defining the expression pattern of selected genes and interfering with theirfunction.4) Translational research and preclinical studies.Potential Impact:In most cases, skin wounds heal without obvious problems. However, wound repair in thepostnatal mammalian organism does not lead to perfect regeneration, but to the formationof a scar that lacks the elasticity of the normal dermis and all appendages. Therefore, patientswith large wounds, for example. extended burn wounds, suffer from severe cosmeticand functional impairments. The identification of genes that are regulated in different woundhealing models in Drosophila,, mice and men using GeneChip hybridisation approacheswill help to define major conserved signalling pathways that are important for thehealing response. In the long run, this project will help to define new therapeutic targets toalleviate and eventually perhaps cure major wound healing disorders and thus improve thequality of life for the patients concerned.Keywords: wound healing, morphogenesis, skin, signalling pathways, conservedgenes.PartnersProject Coordinator:Dr. Enrique Martin-BlancoConsejo Superior de Investigaciones Cientificas (CSIC)Instituto de BiologiaMolecular de BarcelonaC/ Josep Samitier 1-508028 Barcelona, Spainembbmc@cid.csic.esProf. Sabine WernerSwiss Federal Institute of TechnologyDepartment of Biology, Institute of Cell BiologyZurich, SwitzerlandDr. Petra BoukampDeutsches KrebsforschungszentrumGenetics of Skin CarcinogenesisHeidelberg, GermanyDr. Michel LabouesseInstitut de Génétique et de Biologie Moléculaireet Cellulaire (IGBMC)Illkirch Graffenstaden, FranceDr. Jose Luis JorcanoCentro de Investigaciones Energeticas yMedioambientalesEpithelial Damage, Repair and TissueEngineering DepartmentMadrid, SpainDr. Osvaldo PodhajcerGene Therapy LaboratoryBuenos Aires, ArgentinaFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life321

MitoCheckwww.mitocheck.orgProject Type:Integrated ProjectContract number:LSHG-CT-2004-503464Starting date:1 st April 2004Duration:48 monthsEC Funding:8 578 177State-of-the-Art:The proliferation of cells depends on the duplication and segregation of their genomes. Thelatter is an immensely complex process that remains poorly understood at a molecular level.Mistakes during mitosis contribute to cancer, whereas mistakes during meiosis, causinganeuploidy, are the leading cause of infertility and mental retardation.During mitosis, sister DNA molecules are dragged towards opposite poles of the cell dueto their prior attachment to microtubules with opposite orientations (bi-orientation). Bi-orientationinvolves dissolution of the nuclear membrane, changes in chromosome organisationand reorganisation of the spindle apparatus. How mitotic cells coordinate these disparatebut interlocking processes is poorly understood.Protein kinases like Cdk1 have fundamental roles during cell division. However, Cdk1’sactual function remains mysterious despite recognition of its importance with a Nobel Prize.The same is true for other mitotic kinases, such as Plk1 and Aurora A and B. We need toknow which set of proteins are phosphorylated, what their functions are, and how phosphorylationchanges their activity. Identification of kinase substrates has been hampered by difficultiesin mapping phosphorylation sites, in experimentally controlling protein kinase activity,and in evaluating the physiological consequences of defined phosphorylation sites. Thepremise behind MitoCheck is that all three hurdles can be overcome by new technologies,namely the use of RNA interference to identify in systematic (functional genomics) mannerpotential substrates, iTAP-tagging to purify protein complexes, small molecules to inhibitspecific kinases in a controlled fashion and mass spectrometry to identify phosphorylationsites on complex subunits. As the concept behind MitoCheck’s project could be applied toother areas, the projects outcomes have the potential to impact on European cell biologyfar beyond the cell cycle community.Scientific/Technological Objectives:The main objective for the MitoCheck team is to understand how mitotic kinases orchestratethe many events of mitosis.MitoCheck is carrying out genome-wide RNAi screens in human cells to systematicallysearch for potential substrates of mitotic kinases. A genome-wide collection of syntheticsmall interfering RNAs (siRNAs) is introduced into human cells to deplete the entire 22, 000human genes one- by- one. The behaviour of the cells after transfection is then recorded bylive cell video microscopy. Genes whose depletion causes mitosis to go awry are crucialfor mitosis.322From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Regulation of Mitosis by Phosphorylation-A Combined Functional Genomics,Proteomics and Chemical Biology ApproachA subset of the proteins crucial for mitosis is currently being tagged with green fluorescentprotein (GFP) and with an affinity purification tag. The GFP tag will allow visualisation of thesubcellular localisation of these proteins during cell cycle, whereas the affinity tag will enablethe identification of binding partners of these proteins via affinity purification followedby mass spectrometry. Since the phosphorylation state of these proteins and their bindingpartners are thought to be crucial for their function during mitosis, much of MitoCheck’sefforts will be devoted to identifying the mitosis-specific phosphorylation sites on them bymass spectrometry and the mitotic kinases responsible for these phosphorylation events.Some mitotic kinases are over-expressed in human tumours. One important objective of MitoCheckis to develop assays to systematically evaluate the clinical utility of mitotic kinasesas diagnostic or prognostic markers.Expected Results:1) A list of mammalian proteins that have important roles during mitosis: This list will becompiled based on knowledge in the published literature, knowledge obtained in theMitoCheck labs and, most importantly, data from our genome-wide RNAi screens.2) Subunit composition of the mitotic protein complexes and their mitosis-specific phosphorylationsites: MitoCheck will employ mass spectrometry methods to identify thebinding partners of the selected mitotic proteins, and to map the mitosis-specific phosphorylationsites on them. We will further link particular mitotic kinases with specificphosphorylation sites.3) Expression profiles of mitotic kinases in tumour samples and the potential of the mitotickinases as diagnostic or prognostic markers in clinical oncology4) A web-based database: This database will contain important information such as alist of genes required for mitosis, subunit composition of mitotic complexes and theirphosphorylation sites. Furthermore, the dataset from the genome-wide RNAi screenswill also be displayed in the future. This dataset includes a wide range of cellularphenotypes, mitotic and non-mitotic. The MitoCheck database will therefore be aunique and highly valuable source of information, not only for the cell cycle field butalso for many other areas in the life sciences.Potential Impact:In order to gain insight into how cell division is controlled by phosphorylation, MitoCheckis developing a variety of genomic, proteomic and chemical approaches. Besides celldivision, protein phosphorylation is also essential in many other biological processes such asNormal rat kidney cells indifferent stages of cell divisionstained for chromosomes (blue)microtubules (green) and actin(red). (Courtesy of Dr. JanEllenberg, EMBL/Heidelberg)© Dr. Jan Ellenberg, EMBL/HeidelbergFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life323

MITOCHECKsignal transduction, gene expression andcellular differentiation. Abnormalities inprotein phosphorylation pathways cancontribute to human diseases such ascancer. The technologies MitoCheck isestablishing will therefore have an impacton other research areas, far beyond cellcycle field.Although MitoCheck focuses on basicresearch, it will also foster innovationsin applied research. In some cases itmay lead to new commercial products.For example, MitoCheck is developingbiological assays for measuring boththe amount and the activity of proteinkinases in human biopsy material. Thesemethods may be useful as diagnosticand prognostic assays in cancer therapy, where novel “biomarker” assays are urgentlyneeded to tailor therapies to the specific needs of patients.The potential impact of MitoCheck in the area of product development is reflected bythe participation of both a small biotech company (Gene Bridges GmbH) and a largecompany (Leica Microsystems CMS GmbH). Leica is one of the world’s leading bioopticalmanufacturers. It is expected that novel software tools developed by Leica as partof the MitoCheck project will be introduced to the market soon.Last, but not least, a unique strength of MitoCheck is its integration of leading experts frommany disciplines ranging from optical engineering to high throughput genomics, fromchemical biology to protein crystallography, and from bioinformatics to human pathology.This unusual diversity of expertise helps to foster innovation in technology development. It alsocreates opportunities for basic research that may lead to unforeseen important discoveries.324From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Regulation of Mitosis by Phosphorylation -A Combined Functional Genomics, Proteomics and Chemical Biology ApproachKeywords: mitosis, phosphorylation, RNAi, mass spectrometry, chemicalinhibitors, cancer, chemical biology, proteomics, functional genomics,regulation, cell cyclePartnersProject Coordinator:Dr. Jan-Michael PetersForschungsinstitut für Molekulare Pathologie GmbHDr. Bohrgasse 71030 Vienna, Austriapeters@imp.univie.ac.atProject Manager:Dr. Yan SunForschungsinstitut für Molekulare Pathologie GmbHDr. Bohrgasse 71030 Vienna, Austriasun@imp.univie.ac.atDr. Jan EllenbergGene Expression and Cell BiologyBiophysics ProgrammesEuropean Molecular Biology LaboratoryHeidelberg, GermanyProf. Dr. Roland EilsTheoretical BioinformaticsDeutsches KrebsforschungszentrumHeidelberg, GermanyFrank SieckmannLeica Microsystems CMS GmbHMannheim, GermanyProf. Dr. Tony HymanMax Planck Institute of Molecular Cell Biologyand Genetics (CBG)Dresden, GermanyGary StevensGene Bridges GmbHHeidelberg, GermanyDr. Andrea MusacchioEuropean Institute of OncologyDepartment of Experimental OncologyMilan, ItalyDr. Ariane AbrieuCentre de Recherche de BiochimieMacromoléculaire (CRBM)Centre National de la Recherche Scientifique (CNRS)Montpellier, FranceProf. Tim HuntCell Cycle Control LaboratoryClare Hall Laboratories, Cancer Research UKSouth Mimms, UKDr. Kai StoeberUniversity College LondonWolfson Institute for Biomedical ResearchLondon, UKDr. Richard DurbinWellcome Trust Sanger InstituteHinxton, UKFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life325

SIGNALLING & TRAFFICwww.signallingtraffic.comProject Type:Specific TargetedResearch ProjectContract number:LSHG-CT-2004-503228Starting date:1 st May 2004Duration:43 monthsEC Funding:1 600 000State-of-the-art:Intracellular communication in eukaryotes is largely achieved by the trafficking of membranescarrying membrane-bound and/or intravesicular signalling molecules. Inside cells,vesicles circulate from one intracellular compartment to another thus facilitating vectorialtransport of signals. Between cells, membrane anchored and secreted soluble moleculesmediate extracellular signalling. Exocytosis and endocytosis of receptors control the responseof sensitive cells to extracellular signals. The routes of membrane trafficking arecontrolled by cell signalling pathways but the underlying molecular machinery is scarcelycharacterised. Moreover, membrane trafficking has been studied mainly in differentiatedcells and rarely in cells changing phenotype during differentiation or dedifferentiation. Suchdrastic phenotypic changes occur during development when cells mature to differentiatedcells as complex as neurons, and during malignant transformation.Scientific/Technological Objectives:The goal of this STREP is to establish the connections between signalling pathways and membranetrafficking in the context of migrating, dividing and adhering mammalian cells. Throughthe study of membrane traffic in the course of cell differentiation, dedifferentiation, and duringmitosis, we aim to unravel how important signalling pathways remodel the intracellulartrafficking routes and conversely, how membrane traffic can influence signalling cascades.We will take advantage of several cellular models including neurons differentiating in cultureand cancer cells dividing and migrating. We will investigate proteins that play central rolesin membrane trafficking and secretion such as rabs, SNAREs and their partners. We willfocus on the trafficking of signalling molecules including cell-cell and cell-substrate adhesionmolecules, growth factors and their receptors, and also investigate the role of glycosylation.Through these approaches we will define the connections between Signalling and Traffic.Using modern cell biological approaches, the SIGNALLING & TRAFFIC consortium will studyseveral cellular models, including neurons differentiating and establishing contacts in culture,and cancer cells dividing and migrating. It will investigate proteins that play central roles inmembrane trafficking and secretion — such as Rabs, SNAREs and their partners — some ofwhich have already been linked to cancer and brain related diseases. It will also focus on thetrafficking of signalling molecules, including cell-cell and cell-substrate adhesion molecules,growth factors and their receptors.In the case of cancer, the goal is to shift the therapeutic emphasis (at least for some tumours)from surgical to pharmacological interventions, thereby reducing hospitalisation costs as wellas the financial, psychological and physical burden on patients and their families. In the caseof neurodegenerative diseases such as Alzheimer’s and Huntington’s diseases and neuropathies,there is an urgent need to identify effective therapies. This will depend on advances inknowledge concerning the physiopathological links between gene defects and symptoms.The project’s results will be disseminated through congresses, workshops and publications,and in classes in the partners’ universities. Its website will represent the hub of a communicationnetwork, intended to attract both students working in relevant academic fields, and thegeneral public.Expected Results:A number of results have already been reported by members of the consortium: (1) Tetanusneurotoxin-mediated cleavage of cellubrevin impairs epithelial cell migration and cell adhesion;(2) Expression of the cell adhesion molecule L1 augments cell motility, invasivenessand tumour growth in vivo; (3) Recycling of pro-transforming growth factor alpha regulatesthe activation of the epidermal growth factor receptor (EGFR), opening up the possibilitythat defects in trafficking may contribute to the development of tumours; (4) Two different326From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Signalling and Membrane Traffickingin Transformation and Differentiationpathways exist for the internalisation of the EGFR; (5) The Rab6A’ GTPase enzyme is requiredfor the metaphase/anaphase transition in mitosis; (6) Crosstalk exists between theactin-remodelling signalling pathway, activated by platelet-derived growth factor stimulationof cells, and endocytosis.Potential Impact:The intention of SIGNALLING & TRAFFIC is to open up new avenues in the development ofmolecular diagnostic and therapeutic tools for diseases demonstrating a membrane traffickingand/or signalling component. This will be relevant to a range of pathologies, from cancerand proliferative non-neoplastic diseases, to neurodegenerative diseases and neuropathies.Cancer and brain-related diseases are major causes of death in Europe and they representa large socioeconomic burden and an increasing challenge in Europe’s increasingly ageingpopulation. SIGNALLING & TRAFFIC is designed to develop new therapies and new diagnostictools, ultimately leading to improvements in health and quality of life for the Europeanpopulation.Keywords: Signalling, membrane trafficking, cell division, cell migration,cell adhesionPartnersProject Coordinator:Prof. Thierry GalliInstitut Jacques MonodTeam ‘Avenir’ INSERM2 Place Jussieu75005 Paris, Francethierry@tgalli.netProf. Peter AltevogtGerman Cancer Research CentreTumour Immunology ProgrammeHeidelberg, GermanyDr. Bruno GoudCentre National de laRecherche Scientifique (CNRS)Institut CurieUMR 144Paris, FranceDr Jonathan DandoInserm-TransfertDept International and European AffairsParis, FranceDr. Joaquín ArribasUniversity Hospital Research InstituteMedical Oncology Research ProgrammeBarcelona, SpainDr. Júlia CostaInstituto de Tecnologia Químicae BiológicaLaboratory of GlycobiologyOeiras, PortugalProf. Pier Paolo Di FioreFIRC Institute of Molecular OncologyFoundationMilan, ItalyProf. Jacqueline TrotterJohannesGutenberg-UniversitätInterdisciplinary Centrefor NeurosciencesMainz, GermanyDr. Letizia LanzettiInstitute for CancerResearch and TreatmentDivision of MolecularAngiogenesisTurin, ItalyFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life327

TransDeathProject Type:Specific TargetedResearch ProjectContract number:LSHG-CT-2004-511983Starting date:1 st December 2004Duration:36 monthsEC Funding:2 500 000State-of-the-art:Apoptosis is controlled by multiple pathways, which include extrinsic signalling via deathreceptors, and by intrinsic pathways involving the mitochondria and endoplasmatic reticulum.These inputs activate proteolytic caspase cascades and subsequent cell death. Pro- andanti-apoptotic Bcl-2 family members are important in controlling mitochondrial signals, includingcytochrome c, whose association with the downstream regulator Apaf-1 and procaspase-9forms the apoptosome that mediates caspase activation. Although homologs ofthe apoptotic machinery are not found in plants and lower eukaryotes, comparative phylogeneticanalysis of the domains conserved in these proteins indicates that they existed in thecommon ancestor of animals, plants, and fungi. These ancient domains were, and in somecases still are, components of ancestral signalling pathways for responses to pathogens andstresses, including starvation and DNA damage.A goal of the Transdeath program is to understand the mechanistic relations between extantPCD programmes in different organisms. For example, plant leaves senesce at the end ofgrowth seasons. How is this developmental form of PCD related to the more rapid PCDinduced during the plant hypersensitive response to pathogens?Scientific/Technological Objectives:Transdeath aims to define (phenomenologically and molecularly) distincttypes of cell death by using models appropriate for each type ofdeath. A main focus of the project is the research on the less studied celldeath types, which are caspase-independent and non-apoptotic. Thesemechanisms will then be used to understand corresponding types of celldeath in mammals, in particular humans.The general lines of inquiry followed in the WorkPackages (WPs) include:analysing distinct types of cell death in their respective optimalmodel(s); comparing cell death types within and between these models;and extending the study to corresponding cell death types in humans.Death in the mold – Top - duringfruiting body development in thesocial amoeba Dictyostelium, cellsof the stalk under programmedcell death. Bottom - cultured cellscan be induced to die and areused to study this process.The project has five scientific WPs. WP1 (Bioinformatics & Database)identifies genes of interest for experimental WPs, and provides a hubfor data used to develop gene-silencing experiments. WP2 (Apoptosis)uses phylogenetic comparison to elucidate apoptotic functions ofproteins involved in human diseases. WP3 (Autophagic PCD) aims toidentify and analyse phylogenetically conserved pathways, subcellularevents, and molecular mechanisms involved in autophagic/vacuolarcell death by using the most amenable models.WP4 (Necrosis & other PCD) analyses necrotic/non-apoptotic cell death using methodologiesin diverse model systems. This strategy permits the analysis of aspects of non-apoptoticcell death from different angles and in organisms of increasing complexity. This verticalapproach has the potential to reveal points of convergence for the underlying mechanismsthat would otherwise go unnoticed.Expected Results:The Transdeath project will potentially provide cutting-edge tools and resources for theEuropean and international scientific community, and additionally nucleate a larger pan-European network of laboratories aimed at exploiting these tools and resources to modelhuman diseases and to address gene function. Both of these objectives are immediatelyrelevant to the improvement of human health and quality of life.328From Fundamental Genomics to Systems Biology: Understanding the Book of Life

The partners are expected to identify all well-conserved and poorly-conserved eukaryotichomologs of cell death genes, and construct phylogenetic trees for all families. Furthermore,the team will identify potentially missing family members, and establish a functioning,basic web platform for data exchange between partners.Potential Impact:Programmed cell deathacross the eukaryotic kingdomThe results of Transdeath will be useful to the scientific community at large by makingdiverse PCD genes and models attractive and accessible platforms to study genes andbiological phenomena of particular importance to biomedicine. These developments willbridge the gap between development and progress in the United States with Europeanresearch on PCD in model organisms and biomedicine.The project will signify a major achievement in terms of consolidating the fragmentedEuropean PCD research base, strengthening the European model organism research communityand laboratories, and providing new opportunities for European biomedical andbiotechnology interests to acquire intellectual property.Keywords: apoptosis, bioinformatics, cancerDeath Suppressor Screen –A mutant, transgenic plant inwhich death can be chemicallyinducedwas used to screen~3 million progeny for secondarymutations that suppress death.The corresponding genes encodingdeath activators are now beingidentified.PartnersProject Coordinator:Prof. John MundyUniversity of CopenhagenInstitute of Molecular BiologyNorregade 101017 Copenhagen, Denmarkmundy@adm.ku.dkmundy@my.molbio.ku.dkProf. Kai-Uwe FröhlichUniversity of GrazInstitute of Molecular BiosciencesGraz, AustriaDr. Corinne ClavéCentre National de la RechercheScientifique (CNRS) IBGC-UMR 5095Unit with U. Bordeaux 2Bordeaux, FranceDr. Pierre GolsteinCentre National de la RechercheScientifique (CNRS) CIML-UMR 6102Unit with INSERM & U. Aix-Marseille IIMarseille, FranceDr. Guido KroemerCentre National de la RechercheScientifique (CNRS) IGR-UMR 8125Unit with INSERM & U. Paris XIParis, FranceDr. Nektarios TavernarakisFoundation for Researchand Technology HellasInstitute of MolecularBiology and BiotechnologyHeraklion, GreeceProf. Adi KimchiWeizmann Instituteof ScienceRehovot, IsraelProf. Roberto TestiUniversity of Rome‘Tor Vergata’Department ofExperimental MedicineRome, ItalyProf. Jonathan JonesThe Sainsbury LaboratoryNorwich, UKFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life329

Peroxisomeswww.peroxisome.euProject Type:Integrated ProjectContract number:LSHG-CT-2004-512018Starting date:1 st January 2005Duration:48 monthsEC Funding:8 000 000State-of-the-Art:Peroxisomes are single, membrane-bound organelles that are present in virtually all eukaryoticcells. In mammals, the size, number and protein content of peroxisomes varysignificantly, depending on the cell and tissue type as well as on the developmental andphysiological stage in question. Consequently, peroxisomes are considered to be multipurposeorganelles.In humans, impairments of these multiple functions lead to different peroxisomal disorderswhich can be divided into two groups. The first of these are peroxisome biogenesis disorders(PBDs), which are caused by a generalised or multiple loss of peroxisomal function dueto a defect in the formation of the organelle. Many PBDs were named before their associationwith the organelle was recognised. These include Zellweger syndrome (ZS), neonataladrenoleukodystrophy, infantile Refsum disease, and rhizomelic chondrodysplasia punctata.The second group of disorders is caused by a single peroxisomal enzyme deficiency.Although they are essential for life, the various functions and dynamics of peroxisomes inhealth and disease are poorly understood. Most inherited peroxisomal disorders in humanshave a low incidence, but collectively they represent an enormous burden on affectedindividuals, their families and society. At present, the number and nature of peroxisomalmatrix proteins are unknown. Each year, several novel peroxisomal matrix proteins are discovered,and the number of metabolic pathways known to exist within peroxisomes, grows.Evidence is now emerging that peroxisomes play a role in modulating diseases of complexinheritance, such as arteriosclerosis, cancer and Alzheimer’s disease (AD).Scientific/Technological Objectives:Using cutting edge proteomics tools, the Peroxisomes consortium will identify and characterisethe functions of novel peroxisomal proteins, and establish a catalogue of peroxisomalmatrix proteins in human liver, kidney and brain. In parallel, it will characterise andcatalogue the mouse peroxisomal proteome in liver, kidney and brain, in order to gain adeeper understanding of species differences - the basis for a more accurate interpretationof existing mouse models of peroxisomal diseases.The consortium will also evaluate the role of peroxisomes as modulators or modifiers ofdiseases of complex inheritance, such as AD and cancer. Tissue microarray analysis, cDNAchip and quantitative RT-PCR analysis will be used to verify the results, with the final goal ofdeveloping improved diagnostic and prognostic tools for these disorders.Many of the functions affected by peroxisomal disorders are related to processes whichtake place at the peroxisomal membrane. A complete catalogue of peroxisomal membraneproteins in mouse and man will contribute to our understanding of what kind of metabolitesare transported across this membrane, how peroxisomes import proteins and lipids, andhow the organelles divide and are transmitted to a new cell. The distinction between matrixand membrane-localised proteins is based mainly on technical considerations. As membraneproteins are notoriously under-represented in conventional proteomic approaches,the consortium will apply state-of-the-art techniques for membrane isolation.330From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Integrated Projectto decipher the biological functionof peroxisomes in health and diseaseExpected Results:Almost all peroxisomal diseases are associatedwith childhood pathology. Mostof them are incurable, and lead to deathbefore the first decade. The Peroxisomesconsortium’s fundamental studies on therole of peroxisomes, should shed light onthe pathogenesis of these devastating diseases,and may lead to novel treatmentregimens for them. It is clear that the expertisebrought together by this proposalwill drive significant advances in thisarea. The consortium will also create andapply novel tools, including peroxisomalmembrane anchor proteins for affinitypurification of peroxisomes from differentsources and tissues, transgenic animalspermitting the regulated inactivation ofperoxisomal function in distinct tissuesonly, and an automated tissue microarrayer.Finally, by means of this joint effort,it should be possible to decipher themolecular mechanisms of so far uncharacterisedperoxisomal disorders, therebycreating novel diagnostic and therapeuticopportunities.Plasmalogen-deficient knockoutmouse showing eye defectsand cataractPeroxisomes visualised asdark granules by catalaseimmunostaining in human fetalrenal cortexPotential Impact:The motivation for this project wasthe realisation that peroxisomes haveremained an ill-defined subcellularorganelle for years, even though theyare known to be essential for life, as isclearly demonstrated by the devastatingconsequences of the absence ofperoxisomes in patients affected by ZS.Lack of knowledge about peroxisomesis a serious obstacle to determining theirtrue significance in health and disease,and to designing effective diagnostic andtherapeutic strategies for such diseases.Some peroxisomal disorders, such asZS, have a rapid, lethal course, causingdeath in the first year. Patients with othertypes of peroxisomal disorders, however,may survive for long periods with severePeroxisomes visualised asdark granules by catalaseimmunostaining in humanfetal liverCytochemical incubation forcatalase activity in mouserenal cortex (proximal tubule)revealing peroxisomes aselectron-dense organellesFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life331

PEROXISOMESA molecular model of partof the structure of the (3R)-hydroxyacyl-CoA dehydrogenaseof human peroxisomal MFE-2showing two residues, Val218and Trp273, whose mutation toother residues causes dysfunctionof the enzyme in humanshandicaps which require chronictreatment and care, often in specialinstitutions for mentally retardedpeople. This is obviously costly tosociety, but it also imposes an enormousemotional and psychological burdenon the families affected. Clearly,increasing knowledge about thebiological role of peroxisomes couldreduce that burden, if it leads totherapeutic advances. Moreover,many patients with a likely defect ofperoxisomal function currently remainundiagnosed. If this project leadsto improvement in the diagnosis ofperoxisomal disorders, such patientswill benefit from a more rapid andmore accurate diagnosis, which willin turn mean they can then be treatedappropriately.Keywords:peroxisome, genomics, proteomics,human diseases, diagnosis, therapy,mouse modelsFluorescent image of peroxisomesMorphometry of peroxisomesin normal mouse liver332From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Integrated Project to decipher the biologicalfunction of peroxisomes in health and diseasePartnersProject Coordinator:Prof. Johannes BergerCentre for Brain ResearchMedical University of ViennaSpitalgasse 231090 Vienna, Austriajohannes.berger@meduniwien.ac.atProf. Ron Wanders, Dr. Antoine van KampenAcademic Medical CentreAmsterdam, The NetherlandsProf. Myriam BaesCatholic University of LeuvenLaboratory of Clinical ChemistryLeuven, BelgiumProf. Ralf Erdmann, Prof. Helmut MeyerRuhr-Universität BochumBochum, GermanyProf. Wilhelm JustUniversität HeidelbergBiochemie-Zentrum derUniversität HeidelbergHeidelberg, GermanyProf. Kalervo HiltunenUniversity of OuluBiocenter Oulu and Departmentof BiochemistryOulu, FinlandProf. Stefan AlexsonKarolinska InstitutetDepartment of Medical LaboratorySciences and TechnologyStockholm, SwedenProf. Gerald HoeflerMedical University GrazInstitute for Pathological AnatomyGraz, AustriaProf. Marc EspeelUniversity of GentDepartment of Anatomy, EmbryologyHistology and Medical PhysicsGhent, BelgiumProf. Andreas HartigUniversity of ViennaDepartment of BiochemistryVienna, AustriaProf. Norbert LatruffeUniversité de BourgogneLaboratoire de BiologieMoléculaire et CellulaireDijon, FranceProf. Klaus-Armin NaveMax-Planck Institute forExperimental MedicineDepartment of NeurogeneticsGöttingen, GermanyDr. Annamaria CiminiUniversity of L’AquilaDepartment of Basic andApplied BiologyCoppito, ItalyProf. Jorge E. AzevedoIBMC-University of PortoInstituto de Biologia Molecular e CelularPorto, PortugalFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life333

DNA Repairwww.dna-repair.nlProject Type:Integrated ProjectContract number:LSHG-CT-2005-512113Starting date:1 st May 2005Duration:48 monthsEC Funding:11 500 000State-of-the-Art:Understanding the pleiotropic effects of the time-dependent erosion of the genome, andthe complexity of cellular responses to DNA damage, requires a comprehensive, multidisciplinaryapproach ranging from molecule to patient. At the level of structural biologyand biochemistry, the DNA Repair consortium will analyse individual components and pathways,to identify new components and clarify reaction mechanisms. The interplay betweenpathways and crosstalk with other cellular processes will be explored using biochemicaland cellular assays.To better understand the function and impact of DNA damage response and repair systemsin living organisms, the DNA Repair consortium will take full advantage of its unique andextensive collection of models (mutant yeast cells and mice), to engineer and analyse newmutants whose genome stability is impaired. The latest genomic and proteomic technologieswill be exploited to identify novel genes involved in genome surveillance. Bioinformatics,high throughput gene expression analysis and proteomics will be used to identify theputative functions of these genes and their proteins.Figure 1. DNA repair proteins atwork. Treatment of cells withionising radiation can result incell death because the irradiationintroduces breaks in the DNA.DNA repair proteins counteractthe lethal effect of irradiationby restoring the integrity of theDNA. After irradiation the DNArepair proteins are organised intoclusters, called foci, at sites ofrepair. This dynamic relocalisationcan be visualised in living cellsby fusing DNA repair proteins toa naturally fluorescent protein.The cells in the image have beenirradiated and foci containing therepair protein become visible.Similar global genome analytical toolswill be used to identify interactions with,and effects on, other cellular processes.The ‘druggability’ of potential targets, inthe context of anti-cancer therapies, willbe tested in collaboration with SMEs.Through its existing contacts with clinicians,the consortium will continue to analysepatients with previously identified defectsin DNA damage response and repairmechanisms, and will also screen patientsfor new disorders.Scientific/TechnologicalObjectives:The study of the vast problem of DNAdamage requires an integrated, multidisciplinaryapproach. European researchteams have played a prominent role in increasing understanding of individual pathwaysinvolved in this phenomenon, but many challenges remain, including the following: (1) Understandingthe complex interplay between the various genome stability systems, and placingthe pathways which have already been described into an integrated cellular context;(2) Gaining insight into the clinical impact of the systems, both individually and collectively,from the cellular level to that of intact organisms and the human population; (3) Translatingthis knowledge into practical applications in the form of improved diagnosis, effectivetherapy and prevention or postponement of diseases associated with the functional declineof the genome.334From Fundamental Genomics to Systems Biology: Understanding the Book of Life

DNA Damage Responseand Repair MechanismsExpectedResults:DNA Repair expects to producethe following results:1) A detailed understandingof the biochemicalmechanism of DNArepair and checkpointpathways;2) Insight into the cellular functioning and consequences of defects in one of the genomesurveillance pathways;3) Identification of new components of DNA damage response pathways;4) Extrapolation of findings from model organisms to humans. The expected resultswill be accomplished firstly by the investigation of patients and cells from patientssuffering from genome instability, cancer predisposition and premature ageing syndromes,and secondly by an extensive comparison of mouse mutants with thesehuman conditions.Figure 2. Accumulation of theMre11 DNA repair complexat sites of DNA double-strandbreaks (DSBs). The left panelshows a cell immunostained forthe Mre11 complex (in green)at DSBs. The linear arrangementof the DSBs is caused by thepassage of an α-particle throughthe cell (DNA shown in blue).The length of the linear track isabout 10 μm. The panel on theright shows the archtitectureof the Mre11 DNA complex asdetermined by Atomic ForceMicroscopy. The arms protrudingfrom the globular domain are 50nm in length.Potential Impact:Our DNA is constantly under attack from physical and chemical agents that compromiseits integrity and represent a threat to genomic stability, potentially resulting in cancer andother health problems. A large number of chemical compounds in food have a potentiallyharmful influence on human genetic make-up, especially under conditions in which the DNArepair capacity is sub-optimal.The proposed research will be importantfor assessing potential risksposed by environmental hazards(such as food components and environmentalpollutants). A better understandingof genome-wide responsesto genotoxins, in relation to the DNArepair status of an organism, will enablethe evaluation of possible risksto consumer health and contribute tothe eventual elimination of identifiedtoxins.The consortium’s genomics andproteomics approaches could alsobe applied to the assessment of thehealth risks of such compounds forspecific sub-groups who carry subtlemutations in DNA repair genes, andfor the ageing population.Figure 3. Chromosomalaberrations, associated withcarcinogenesis, induced byinterstrand crosslink (ICL)-inducing agents. In the absenceof the Ercc1/Xpf DNA repairprotein ICLs cause numerouschromosomal aberrations, mostnotably fusion of chromatids.Shown is a metaphase spread ofan Ercc1/Xpf deficient Chineseovary hamster cell line.From Fundamental Genomics to Systems Biology: Understanding the Book of Life335

DNA REPAIRKeywords:genome (in)stability, cancer, ageing, molecular biology, genomics, proteomics, human disease,DNA damage, DNA repair mechanismsPartnersProject Coordinator:Prof. Jan HoeijmakersErasmus Universitair MedischCentrum RotterdamDept. of Cell Biology and Genetics‘s Gravendijkwal 2303015 CE Rotterdam, The Netherlandsj.hoeijmakers@erasmusmc.nlProject Manager:Dr. Rini de CromErasmus Universitair MedischCentrum RotterdamDept. of Cell Biology and Genetics‘s Gravendijkwal 2303015 CE Rotterdam, The Netherlandsdna.repair@erasmusmc.nlm.decrom@erasmusmc.nlProf. Roland Kanaar, Dr. Wim VermeulenDr. G.T.J. van der HorstErasmus Universitair Medisch Centrum RotterdamDepartment of Cell Biology and GeneticsRotterdam, The NetherlandsDr. Stephen West, Dr. Jesper Q. SvejstrupCancer Research UKGenetic Recombination LaboratoryLondon, UKProf. Jiri Bartek, Dr. Jiri LukasDanish Cancer SocietyInstitute of Cancer Biology andCentre for Genotoxic Stress ResearchCopenhagen, DenmarkProf. Karl-Peter HopfnerUniversity of MunichGene CentreMunich, GermanyProf. Stephen P. JacksonWellcome Trust/Cancer ResearchUK Gurdon InstituteUniversity of CambridgeCambridge, UK336From Fundamental Genomics to Systems Biology: Understanding the Book of Life

DNA Damage Response and Repair MechanismsProf. Josef JiricnyUniversity of ZürichInstitute of Molecular Cancer ResearchZurich, SwitzerlandDr. Graeme C. M. Smith, Dr. Mark O’ConnorKuDOS Pharmaceuticals LtdCambridge, UKProf. Alan R. Lehmann,Prof. Anthony M. Carr, Dr. Penelope A. JeggoUniversity of SussexGenome Damage and Stability CentreBrighton, UKProf. Hans E. KrokanNorwegian University of Scienceand TechnologyDept. of Cancer Research andMolecular MedicineTrondheim, NorwayProf. Leon H. F. MullendersLeiden University Medical CenterDepartment of ToxicogeneticsLeiden, The NetherlandsProf. Marco FoianiIstituto FIRC di Oncologia Molecolare(FIRC: Fondazione Italiana perla Ricerca sul Cancro)Milan, ItalyProf. Paolo PlevaniUniversity of MilanoDipartimento di Scienze Biomolecolarie BiotecnologieMilan, ItalyProf. Magnar BjøråsRikshospitalet OsloInstitute of Medical MicrobiologyOslo, NorwayProf. Noel LowndesUniversity of IrelandGenome Stability LaboratoryDepartment of BiochemistryGalway, IrelandProf. Jean-Marc EglyCentre National de la RechercheScientifique (CNRS)Institut National de la Santéet de la RechercheMédicale (INSERM)Université Louise PasteurIllkirch, FranceFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life337

STEROLTALKwww.steroltalk.netProject Type:Specific TargetedResearch ProjectContract number:LSHG-CT-2004-512096Starting date:1 st September 2005Duration:36 monthsEC Funding:2 200 000State-of-the-Art:Cardiovascular diseases remain one of the major causes of mortality in the developedworld. Dependence between cholesterol levels and mortality and the positive influence ofcholesterol lowering effects are clearly established. Even if statins are still considered asrelatively safe drugs, considerable attention is payed to the statin-based risk of muscularadverse drug reactions (ADR). Considering that 5-10% of population in developed societiesis treated with statins, this represents an important health risk problem. Drugs are generallymetabolized by the cytochrome P450 (CYP) system. Once bound to nuclear receptors,drugs modulate the expression of the responsive CYPs, which represents the basis of ADR:a modulated metabolism of xenobiotics (and enobiotics) that are metabolized by the sameCYP. Statins are often used in combination with other medications since patients with hyperlipidemiafrequently have other medical problems. 60% of statin-related rhabdomyolysis isattributed to ADR. Post-genomic approaches applied in Steroltalk offer venues to approachsuch complex physiological questions that have a great impact on human therapy.The STEROLTALK multidisciplinaryfunctional genomics approachesand models. Human primaryhepatocytes and normal, hyperlipidemicand nuclear receptor PXRand CAR knockout mice weretreated with known and noveldrugs. Transcriptome, limitedproteome and sterol metabolomehave been measured and dataincorporated into the in silicomodel, together with the humanizedyeast data and literatureinformation. The model is able tosimulate cholesterol homeostasisand the cholesterol loweringeffect of statins as well as novelchemical entities. This gives aninsight into the mechanism ofhypolipidemics action.Scientific/Technological Objectives:The vision of STEROLTALK is to develop a global approach by combining dedicated functionalgenomic tools, three model organisms and in silico modelling, for the discovery ofnew drug targets, new chemical entities and therapeutic strategies. Regulatory networks inhuman, mouse and S. cerevisiae will be assessed through integrative analysis of transcrip-338From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Functional Genomics ofComplex Regulatory Networks fromYeast to Human: Cross-Talk of SterolHomeostasis and Drug Metabolismtome, proteome, metabolome and by yeast engineering. For the first time this will allowthe deciphering of multi-level response of cholesterol homeostasis to known and candidatedrugs, and its modulation in pathologies. Typical investigation targets will be mouse liversand primary human hepatocytes. The first task of our project is to develop original tools forfunctional genomic analyses of drug-modulated responses of STEROLTALK genes, proteinsand metabolites in biological models. Tools include a dedicated microarray, an antibodyset, siRNA knockouts, humanised yeast and a database. Deposited analytical data will beevaluated by numerous bioinformatic approaches, to assist in building relevant in silicomodels with predictive values, ready for implementation in novel drug discovery strategies.These models will allow, for the first time, the identification of potential cholesterolhomeostasis-related targets that will be validated in vivo in biological models by the originalSTEROLTALK tools.Expected Results:The project STEROLTALK will for the first time undertake a systematic post-genomic evaluationof the cholesterol homeostasis and its cross-talk to drug metabolism and contributeto understanding the effects/side effects of the hypolipidemic therapy and the combinedtherapies. Original functional genomics tools will be developed with focus on the genes,enzymes and metabolites that are involved in cholesterol homeostasis and in drug metabolism.The Steroltalk tools include dedicated mouse and human Steroltalk microarrayscontaining genes of the cholesterol homeostasis and the entire CYP and nuclear receptorgene families, a structured Steroltalk database, a set of novel Steroltalk antibodies raisedagainst membrane-bound choelsterogenic enzymes, humanized yeast strains synthetizingcholesterol, representing novel drug screening tools and predictive in silico models. Thenovel tools will be used in combination with commercial tools, to experimentally determinethe cross-talk between cholesterol homeostasis and drug metabolism in drug-treated humanprimary hepatocytes and in livers of normal, hyperlipidemic and nuclear receptor-knockoutmice, at the level of transcriptome, proteome and metabolome.The original tools developed within the STEROLTALKproject. The Steroltalk microarray exists in the humanand mouse version, containing 300 gene of each species.The Steroltalk database contains protocols used withinthe consortium as well as data. It is restricted to accessby Steroltalk partners through a safe web portal. TheSteroltalk antibody set consists of over 20 antibodies.Some are commercial, some original and raised againstthe membrane proteins of the cholesterol homeostasisand drug metabolism network. The prototype Steroltalkprotein chips and protein maps are under development.Several humanized yeast strains have been developedby yeast engineering, synthetizing cholesterol and beingevaluated as novel hypolipidemic drug screening tools.The first set of data regarding the Steroltalktranscriptome, limited proteome and sterol metabolomeis available for drug treated mice and human primaryhepatocytes. Novel findings regarding statin and originalhypolipidemics action have been acquired and drugdiscovery strategies discussedFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life339

STEROLTALKThese data will be interpreted, and when appropriate, also included into in silico models.The Steroltalk tools and experimental data will together with mathematical models aid indetermining novel correlations and in resolving unknown molecular mechanisms of the cholesterolhomeostasis/drug metabolism network.Potential Impact:STEROLTALK will compare the effects of clinically approved ‘safe’ statins with novel, non-statinhypolipidemics, at the levels of transcriptome, proteome and metabolome. This will havea high impact on understanding the multi-level effects and potential side effects of drugs.This innovative functional genomic approach, which involves development of original anddedicated tools, will reinforce the competitiveness in developing new and, for humans, safehypolipidemics.Keywords:functional genomics, medical pathway modelling, yeast engineering, improved humanhealth340From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Functional Genomics of Complex Regulatory Networks from Yeast to Human:Cross-Talk of Sterol Homeostasis and Drug MetabolismPartnersProject Coordinator:Prof. Rita BernhardtSaarland UniversityDepartment of BiochemistryCampus, Building B2.266123 Saarbrücken, Germanyritabern@mx.uni-saarland.deProf. Damjana RozmanUniversity of LjubljanaInstitute of BiochemistryDepartment of Electrical EngineeringLjubljana, SloveniaDr. Denis PomponCentre National de laRecherche ScientifiqueCNRS-CGMGif-sur-Yvette, FranceProf. Steven KellyUniversity of Wales, SwanseaSchool of MedicineSwansea, WalesProf. Ingemar BjörkhemKarolinska InstitutetDivision of Clinical ChemistryStockholm, SwedenProf. Urs MeyerUniversity of BaselBiozentrumBasel, SwitzerlandDr. Patrick MaurelInstitut National de la Santé etde la Recherche Médicale (INSERM)U632Montpellier, FranceDr. Katalin MonostoryHungarian Academy of SciencesChemical Research CenterBudapest, HungaryDr. Drago KuzmanLek Pharmaceuticals d.d.Ljubljana, SloveniaDr. Andrej GustinCREA storitve in svetovanje, d.o.o.Ljubljana, SloveniaFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life341

RUBICONwww.rubicon-net.orgProject Type:Network of ExcellenceContract number:LSHG-CT-2005-018683Starting date:1 st January 2006Duration:60 monthsEC Funding:12 000 000State-of-the-Art:Numerous cellular proteins are post-translationally modified by a conjugation of ubiquitinand ubiquitin-like (UbL) proteins. Among them are cell cycle regulators, tumour suppressors,growth regulators, transcriptional activators and inhibitors, signalling proteins and regulatoryenzymes in key metabolic, replicative and quality control/stress pathways. Membraneproteins, which include cell surface receptors, ion channels and ER proteins, are also targetedby the system. Finally, mutated and denatured/misfolded proteins are specificallyrecognized and efficiently removed.With this diverse repertoire of substrates it is not surprising that the system regulates abroad array of cellular processes inclusive of the following: cell cycle and division, differentiationand development, signal transduction, regulation of transcription, modulation ofthe immune and inflammatory responses, intracellular trafficking of proteins, biogenesis oforganelles, morphogenesis of neuronal networks and axon guidance, modulation of cellsurface receptors, ion channels and the secretory pathway, DNA repair, long-term memory,circadian rhythms, and the cellular stress response and quality control machineries.Aberrations of the system are implicated in the pathogenesis of human diseases, seen inmany malignancies, neurodegenerative disorders and pathologies of the inflammatory andimmune response. Consequently, a great deal of effort has been channelled into the developmentof drugs, which target the different components of the system, namely enzymes,substrates and modifiers. One of these drugs is already on the market, while others are inthe pipeline. Within this context, a better understanding of the underlying mechanisms involvedin this complex post-translational modifying system has important biological, clinicaland therapeutic implications.Overview of the RUBICON project342From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Scientific/Technological Objectives:Malfunctions of the ubiquitin and ubiquitin-related systems are strictly connected to thepathogenesis of numerous diseases, including cancer and inflammation. Insights into therole of ubiquitin-dependent pathways in disease development, may ultimately lead to theidentification of novel therapeutic targets. A striking instance of this is the recent finding, onbehalf of network members, of the central role of ubiquitin in DNA repair in yeast, a findingthat impacts crucially on cancer research. This discovery highlights the potential importanceof basic research in the understanding of disease-related processes.Moreover, the understanding of functional genomics and protein-protein interactions is anessential prerequisite for rational structure-driven drug design. This is expected to havean impact on future drug discovery processes, on the competitiveness of pharmaceuticalindustries and, ultimately, on the health of the world population. Improved information onaltered signalling pathways and on modifications in the target structure is essential for theacceleration of the development of a drug. In this sense, it is expected that network researchwill lead to patent applications relevant to medical research and, ultimately, to the developmentof new drugs and therapeutic procedures in clinics.The RUBICON project aims to foster translational research, by bringing together basic scientists,clinicians and biotech SMEs. They will form a communication network that will providethe industry with new therapeutic avenues, which can be investigated and exploited ina mutually beneficial manner.Expected Results:Role of Ubiquitin andUbiquitin-like Modifiersin Cellular RegulationThe RUBICON consortium will substantially enhance the competitiveness of basic Europeanresearch on ubiquitin and ubiquitin-like molecules, and explore their role in the regulationof basic cellular processes. Moreover, the project will promote translational research onthe system’s involvement in human diseases; by acting as a catalyst, it will also encourageprogress, and facilitate further coordination of biotech research enterprises, within this keyarea of biomedicine.The European contribution to the ubiquitin field has been both pioneering and substantial,and Europe is currently home to some of this field’s world-leading scientific groups. Formany years, research funding for this field has been provided at a national level, and despitethe high degree of specialisation, it has resulted in poor dissemination of the acquiredknowledge to new and relevant research areas. RUBICON will overcome this apparentfragmentation and further the combined efforts of European laboratories, by establishingcollaborative multi-centre research projects.The “virtual core facilities” of RUBICON will allow all laboratories to access and employhighly specialised, cutting-edge technology on demand, thus accelerating scientific progress.The rapid dissemination of such sophisticated methodology is greatly hampered by the highstart-up and maintenance costs, and the lack of specifically trained technical personnel. Inaddition, RUBICON will support pre-existing technical platforms created through nationalfunding, making them available for use on behalf all the partners. RUBICON, through thedevelopment, collection and dissemination of commonly required research tools, will coordinateresearch activities, eliminate a duplication of effort, and allow for the faster and moreFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life343

RUBICONeconomic use of resources in ubiquitin research. RUBICON will generate new knowledge,which will be published in specialist journals and presented at international meetings, thusensuring the dissemination of the project’s findings to the scientific community. The website,press releases, media events and seminars in schools will be instrumental in transmittingdiscoveries to the general public.Potential Impact:RUBICON is expected to have a lasting impact on European research. The training ofresearch workers in networked laboratories will foster a rich source of young and talentedpeople, who will enter the academic and industrial spheres where they will continue conductingresearch and teaching in this area. Collectively, these multi-disciplinary researcherswill contribute to the ongoing effort to make Europe the global leader in this field.Moreover, interaction with researchers from countries in Eastern Europe, coupled with thetraining of young scientists from these countries, will have a long-standing impact on theEuropean scientific community. As a result, not only will these countries be able to rapidlyattain the highest international standards, but the position of Europe as a competitive participantin global science will also be strengthened.Finally, RUBICON will form research collaborations with SMEs and large pharmaceuticalcompanies in Europe. An improved understanding of the complementary needs of basic scienceand biomedical companies, will facilitate affiliations and encourage the developmentof new drugs for the treatment of human diseases.Keyword: ubiquitin344From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Role of Ubiquitin and Ubiquitin-like Modifiers in Cellular RegulationPartnersProject Coordinator:Prof. Maria MasucciKarolinska InstitutetDepartment of Cell and Molecular BiologyNobels vag 1617177 Stockholm, Swedenmaria.masucci@ki.seProf. Rene BernardsNetherlands Cancer InstituteAntoni van Leeuwenhoek HospitalDivision of Molecular CarcinogenesisAmsterdam, The NetherlandsProf. Ger StrousUtrecht University Medical CenterDepartment of Cell BiologyDivision of Biomedical GeneticsUtrecht, The NetherlandsDr Colin GordonMedical Research CouncilHuman Genetics UnitEdinburgh, UKProf. Ronald T. HayUniversity of DundeeDundee, UKProf. Ronald ThomasUniversity of DundeeDundee, UKDr. Anne De JeanInstitut PasteurUnité de Recherche OrganisationNucléaire et OncogenèseParis, FranceDr. Pascal GenschikCentre National de la RechercheScientifique (CNRS)Institut de Biologie Moléculaire desPlantes (IBMP) du CNRS UPR 2357Strasbourg, FranceProf. Stefan JentschMax-Planck Institute for BiochemistryMartinsried, GermanyProf. Frauke MelchiorBereich Humanmedizin derGeorg-August-Universitaet GöttingenStiftung Oeffentlichen RechtsGöttingen, GermanyProf. Martin ScheffnerUniversitat KonstanzKonstanz, GermanyDr. Thomas SommerMax-Delbrueck-Centrumfuer Molekulare MedizinBerlin, GermanyProf. Dieter H. WolfUniversität StuttgartInstitute of BiochemistryStuttgart, GermanyProf. Pier Paolo Di FioreIFOM Fondazione Istituto Fircdi Oncologia MolecolareMilan, ItalyProf. Aaron CiechanoverTECHNION - Israel Instituteof TechnologyHaifa, IsraelProf. Yinon Ben-NeriahHebrew University of JerusalemJerusalem, IsraelDr Hans LangedijkPepscan SystemsLelystad, The NetherlandsDr Henk ViëtorDrug Discovery Factory BVAbcoude, The NetherlandsDr Dominique ThomasCytomics Systems SAGif-Sur-Yvette, FranceDr Paul SheppardAffiniti Research Products Ltd(trading as BIOMOLInternational LP)Exeter-Devon, UKDr Yuval ReissProteologics LtdRehovot, IstraelFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life345

EndoTrackProject Type:Integrated ProjectContract number:LSHG-CT-2006-019050Starting date:1 st February 2006Duration:48 monthsEC Funding:11 000 000State-of-the-Art:Endocytic trafficking plays a more active role in the regulation of polypeptide growth factor(GF) signalling than was previously recognised. Despite great progress in the description ofthe endocytic routes and their molecular regulation, the scientific community is far from possessinga complete understanding of the endocytic trafficking of GF receptor (GFR) complexesand to what extent their signalling activity requires, and is modulated by, these routes. TheEndoTrack project aims to fill this gap by gaining a basic understanding of the relationshipbetween the endocytic transport and signalling activity of GFRs.EndoTrack combines leading European interdisciplinary research teams to pursue the followingaims:1) Define the trafficking routes of various GFR complexes in cultured cells with an unprecedenteddegree of precision, combining high-throughput microscopy with automatedimage analysis and electrochemiluminescence technology.2) Define the molecular machinery responsible for this transport using proteomics andfunctional genomics approaches, and generate proof of concept that trafficking contributesto GF signalling activity in cultured cells;3) Integrate the information from cultured cells with in vivo studies in animal model systems,in particular Drosophila, zebrafish, Xenopus and mouse;4) Test the relevance of the modulation of endocytic trafficking on signal transduction indisease model systems;5) Within four years, the use of knockdown approaches, reporter cell lines and animals,combined with target validation proprietary technology from biotech SMEs, will providea new generation of assays to measure GFR trafficking and signalling. Theseassays will lead to the identification of novel key regulatory components and hence,to a new generation of diagnostic markers and potential targets for modulation of GFsignalling in the treatment of human diseases. EndoTrack’s translational research willthus strengthen the innovation potential of the European biotech and pharmaceuticalindustries.Scientific/Technological Objectives:EndoTrack has twin objectives. The first is to fill a gap in basic knowledge by providingnew insights into how cells transduce extracellular stimuli in the form of polypeptide GFsto changes in gene expression, exploiting the enormous potential of the spatio-temporalregulation provided by the endocytic pathway. The second is to develop new concepts thatwill lead in future to novel opportunities for therapeutic intervention in human disease. Theresults of EndoTrack will be relevant to the treatment of many diseases that are currently eitherincurable or can only be treated inadequately, such as cancer and neurodegenerativeand cardiovascular disorders.The EndoTrack project is aimed at gaining conceptual advance into the signalling functionof GFs from an unconventional perspective, namely by exploring the role of endocytic traffickingin the modulation of GF signalling. It further aims to translate such basic knowledgeinto novel opportunities for the development of a new generation of tools to combat diseaseslike cancer, cardiovascular, metabolic, infectious and neurodegenerative diseases. Toachieve this ambitious goal, a multidisciplinary action plan carried out by a consortium ofacademic groups and SMEs will define the intracellular routes of GFR complexes, identify346From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Tracking the Endocytic Routesof Growth Factor Receptor Complexesand their Modulatory Role on Signallingselective regulators of trafficking, and provide mechanistic insights into the contribution ofendocytic trafficking to the signalling outcome. The plan will use in vitro, ex-vivo and in vivosystems. These efforts should result in the proof of principle that it is possible to qualitativelyand quantitatively modify the signal transduction output of a variety of GFs via the modulationof endocytic routes, with predictable consequences at the patho-physiological level.Expected Results:After 48 months, EndoTrack will provide:1) A new generation of cell-based assays tracking the endocytic routes of GFR complexesand the position of signalling components downstream of the GFRs alongthese routes;2) A comprehensive description of the machinery that regulates GFR trafficking alongthese endocytic routes;3) Proof of principle that modulation of trafficking can modulate the signalling output ofGFs;4) Proof of principle that trafficking modulators are novel potential therapeutic targetsfor the treatment of various human diseases.Schematic diagram of theendocytic pathway. Variousinternalization routes andinternal endocytic compartmentsare depicted. The continuouslines represent experimentallycharacterized trafficking routes;the dashed lines illustrate thepostulated or cell-type specifictransport steps. GEEC, GPIanchoredprotein enriched earlyendosomal compartment.From Fundamental Genomics to Systems Biology: Understanding the Book of Life347

EndoTrackPotential Impact:The societal impact of EndoTrack lies in the opportunity it provides to alter the textbookmodel of how cytoplasmic cascades transduce proliferation and differentiation signals fromthe plasma membrane to the cell nucleus. The current models barely acknowledge the importanceof endocytic trafficking routes, and when they do address them, they ignore theircomplexity at the subcellular level. Taking advantage of this opportunity implies gainingnovel mechanistic insights into the regulation of signalling pathways, and how these areintegrated in a multi-GF environment with the fundamental principles of cellular organisationand its overall significance in embryogenesis. Besides enhancing basic knowledge,advances in this area will also have implications for the treatment of severe diseases resultingfrom dysfunction of signal transduction and gene expression.The economic impact of the project will be most evident in the middle and long term.EndoTrack itself will not carry out screening of small molecule libraries to identify novelpotential drug candidates in disease model systems. Nevertheless, by defining new mechanisticprinciples, it will conduct the groundwork necessary for the development of novelopportunities for intervention. Specifically, these opportunities are based on the followingdeliverables:1) Development of new cell-based, multi-parameter assays that can be scaled up forhigh-throughput screening and will consequently be amenable to the screening ofchemical libraries;2) Identification of a large number of novel key signalling regulators that can serve aspotential drug targets.3) The generation of new cellular and animal models systems that recapitulate differentaspects of human disease.4) Proof of principle for the value of intervention via trafficking regulators to modulatesignalling functions required for normal development and which are altered in humandiseases. Altogether, at the end of the funding period, EndoTrack will deliver notonly new knowledge but also an entirely novel technology platform with the potentialto provide higher efficiency of drug development, hence improved cost effectivenessof health care and increased competitiveness of European biotech companies.Knocking down gene expressionof the kinase EEF2K in HeLacells via siRNA oligonucleotidesderegulated clathrin-mediatedendocytosis and led toa different phenotype.Keywords:high-throughput screen, high-throughput techniques, cancer metastasis, receptor trafficking,signalling, endocytosis348From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Tracking the Endocytic Routes of Growth Factor Receptor Complexes andtheir Modulatory Role on SignallingPartnersProject Coordinator:Prof. Marino ZerialMax-Planck Institute of MolecularCell Biology and GeneticsPfotenhauerstr. 10801307 Dresden, Germanyzerial@mpi-cbg.deProject ManagerDr. Jutta TatzelMax-Planck Institute of MolecularCell Biology and GeneticsPfotenhauerstr. 10801307 Dresden, Germanytatzel@mpi-cbg.deProf. Carl-Phillipp HeisenbergMax-Planck Institute of MolecularCell Biology and GeneticsDresden, GermanyProf. Danny HuylebroeckFlanders Interuniversity Institutefor Biotechnology (VIB)Department of Molecular andDevelopmental GeneticsKatholieke Universiteit LeuvenLeuven, BelgiumProf. Michael BrandTechnische Universität DresdenBiotechnology CenterDresden, GermanyProf. John HeathUniversity of BirminghamSchool of BiosciencesBirmingham, UKProf. Jim SmithUniversity of CambridgeWellcome Trust/Cancer ResearchUK Gurdon InstituteCambridge, UKDr. Carol MurphyFoundation for Research &Technology-HellasBiomedical Research InstituteUniversity of Ioannina,Ioannina, GreeceDr. Jérôme PansanelImaxio SALyon, FranceProf. Carl-Henrik HeldinUppsala UniversityLudwig Institute for Cancer ResearchUppsala, SwedenProf. Christof NiehrsDeutsches KrebsforschungszentrumDepartment of Molecular EmbryologyHeidelberg, GermanyDr. Marta MiaczynskaInternational Institute of Molecularand Cell BiologyWarsaw, PolandDr. Ruediger KleinMax-Planck Institute of NeurobiologyMartinsried, GermanyDr. Jean-Paul VincentNational Institute for Medical ResearchLondon, UKFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life349

AnEUploidywww.aneuploidy.euProject Type:Integrated ProjectContract number:LSHG-CT-2006-037627Starting date:1 st December 2006Duration:48 monthsEC Funding:12 000 000State-of-the-Art:AnEUploidy is the term used to describe the abnormal copy number of genomic elements(i.e. when one chromosome set is incomplete). This predisposition is one of the most commoncauses of morbidity and mortality in human populations. The importance of AnEUploidyis often neglected, because its effects only materialise in the embryonic and fetalperiods. The prototype of extra genomic material is trisomy 21 (Down syndrome), and somecommon microdeletion syndromes are the models of monosomies.It is likely that numerous other unknown pathologic conditions (including common phenotypes)are attributable to segmental aneuploidies. In addition, an extensive variability of thecopy number of numerous genomic regions has been found to be polymorphic in humanpopulations. Aneuploidy is related to gene expression perturbation and abnormalities, butthe molecular pathogenesis of the numerous aneuploid disorders is largely unknown.Scientific/Technological Objectives:The project has the ambitious goal of contributing to the understanding of the molecularbasis and pathogenetic mechanisms of aneuploidies. The project proposes to use experimentalstrategies that will incorporate and take advantage of recent achievements withinthis field of research. The project incorporates the following areas of existing research:1) human genome sequencing,2) comparative genome analysis,3) genome variation,4) mouse transgenesis,5) technological platforms for transcriptome and genotypic analysis,6) bioinformatics tools, and7) systems biology.The overall goal of this integrated project is to understand the molecular mechanisms of genedosage imbalance (aneuploidy) in humanhealth using genetics, functional genomicsand systems biology. The project will focuson the following 2 models of aneuploidy:1) trisomy 21 as the prototype for supernumerarycopies of a genomic segment, and2) monosomy for 7q11.23 (Williams-Beurensyndrome) as one prototype of haploinsufficiencyfor a genomic segment.In terms of looking at specific objectives, thephenotype of heart defect in the monosomy22q11 (VCFS) will be used. Furthermore,certain novel emerging syndromes of aneuploidyand Copy Number Variation (CNV)will be also used as experimental and discoverymodels.Karyotype350From Fundamental Genomics to Systems Biology: Understanding the Book of Life

AnEUploidy: understanding gene dosageimbalance in human health using genetics,functional genomics and systems biologyThe specific aims are as follows:1. To study the phenotypic consequences of gene dosage imbalance in humans at thecellular and organism level, by focusing on two prototype human model phenotypes:trisomy 21 (T21, Down syndrome; DS) and the monosomy model Williams Beurensyndrome (WBS at 7q11.23). We hypothesise that it is feasible to identify a smallnumber of genes, or even single genes, that are responsible for a given phenotype.2. To identify and characterise novel microaneuploidy syndromes. Clinically well-definedentities will be used as a starting point for high-resolution analysis of copynumber. In addition, patients with specific syndromes will be selected and screenedfor gene dosage alterations, using ultra high-resolution microarrays. The project willallow the identification of genes and biological pathways potentially involved in newaneuploidy syndromes. Furthermore, a catalogue of copy number variants (CNVs)and segmental duplications (SDs) of the human genome will be established in Europeans.3. To exploit the unique advantages of the mouse embryonic stem (ES) cell as an experimentalparadigm, so as to identify the effects of gene dosage imbalance on theglobal transcriptome and proteome. The effects of dosage imbalance on the abilityof pluripotent ES cells to differentiate into lineages that are relevant to human aneuploidyphenotypes, will also be investigated.The project will focus on two regions of the human genome, which are subject togene dosage imbalance: HSA21 and 7q11.23, respectively involved in DS andWBS. Global transcriptome and proteomics analysis of the cell lines will be performedthrough specific platforms, and systematic analysis and integration of transcriptomeand proteomics data will be carried out.4. To use a large number of mouse models of aneuploidyExpected Results:The AnEUploidy project will result in the identification of genes involved in Down Syndrome,Congenital Heart Defect, and of majordysregulated pathways in human cellsof Down Syndrome and Williams BeurenSyndrome patients; functional genomics andsystems biology analysis in Lymphoblastoidcell lines and isogenic lines will be appliedto this end.AnEUploidy will also identify new aneuploidysyndromes, assess their clinical significance,and develop appropriate diagnosticmethods. In addition, emerging aneuploidysyndromes will be characterised at a molecularlevel, so as to identify key dosageimbalanced genes. This project will generatea comprehensive ES-cell line resourceof single-gene and segmental overexpres-Down Syndrome KaryotypeFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life351

AnEUploidysion, comprising the largemajority of genes withinHSA21 and WBS regions.Microarray analysis, followedby systems biologyanalysis, will allow the consequencesof dosage imbalanceleading to the pathologyof these disordersto be revealed. The newmouse models for T21,HSA22q11.2 deletion syndromeand WBS, generatedduring this project, willelucidate the contribution ofdifferent genomic segmentsto the complex phenotypespresent in these aneuploidiessyndromes.The AnEUploidy project represents a complementary approach to the identification ofgenes involved in Down Syndrome Congenital Heart Defect, and to the identification ofnew aneuploidy syndromes. AnEUploidy will result in the characterisation of the functionalrole of conserved non-genic sequences, micro-RNAs and HSA21 transcription factors, andan exposition of their contribution to disease, in the context of dosage imbalance.Potential Impact:AnEUploidy has major clinical implications, and countless patients with their support networksof families and carers, are suffering from its consequences; the results of the project’s outcomewill go some way towards supporting the work undertaken in this field. The impact of theAnEUploidy project can be summarised as follows:1. The results of this research could lead to the identification of novel targets for therapeuticinterventions.2. This proposal could ultimately result in diagnostic tests of novel disorders, the identificationof diagnostic markers, or the improvement of exciting methodologies.3. All of the above will contribute to the overall improvement of health in Europe. Itshould not escape our attention that disorders of aneuploidy in Europe are relativelymore common than in many other countries, owing to the reduction of morbidity andmortality stemming from infectious diseases, and also because of the increased meanmaternal age (which is a result of better educational and professional opportunities forwomen).Furthermore, the individual component symptoms of trisomy 21, for example, are indistinguishablefrom those of other serious diseases; therefore, research on the mechanisms of thosecomponents will benefit not only aneuploidies, but also memory decline, mental retardation,autism, epilepsy, diabetes, muscle hypotonia, infertility, immune system deficiencies, leukemias,neoplasias and a very important aspect of the understanding of Alzheimer’s disease.Keywords: Aneuploidy, gene dosage imbalance, trisomy, monosomy, geneexpression, transcriptome, copy number polymorphisms, mousetransgenesis352From Fundamental Genomics to Systems Biology: Understanding the Book of Life

AnEUploidy: understanding gene dosage imbalance in human health usinggenetics, functional genomics and systems biologyPartnersProject Coordinator:Prof. Stylianos AntonarakisUniversity of GenevaFaculty of MedicineDepartment of Genetic Medicineand Development1, Rue Michel Servet1211 Geneva, SwitzerlandStylianos.Antonarakis@medecine.unige.chProject Manager:Dr. Jérôme WuarinUniversity of Geneva Medical SchoolDepartment of Genetic Medicineand DevelopmentJerome.Wuarin@medecine.unige.chDr. Yann HeraultCentre National de la RechercheScientifique (CNRS)Immunologie et embryologie moleculaireInstitut de TransgenoseOrleans, FranceProf. Yoram GronerWeizman InstituteBiomedical ResearchDepartment of Molecular GeneticsRehovot, IsraelDr. Maria del Mar DierssenCentre de Regulacio Genomica (CRG)Barcelona, SpainDr. Jean Maurice DelabarUniversité Paris 7Paris, FranceDr Dean NizeticBarts & the London Schoolof Medicine and DentistryInstitute of Cell and Molecular ScienceLondon, UKDr. Victor TibulewiczNational Institute for MedicalResearch (NIMR)Immune cell biologyInfection and immunityLondon, UKDr. Marie-Laure YaspoMax-Planck Instituteof Molecular GeneticsChromosome 21Gene expression and regulationBerlin, GermanyProf. Jiri ForejtAcademy of Sciencesof the Czech RepublicInstitute of Molecular GeneticsMouse Molecular GeneticsPrague, Czech RepublicDr Luis Perez JuradoUniversitat Pompeu FabraUnitat de GenèticaDepartament de CiènciesExperimentalsBarcelona, SpainProf. Han G. BrunnerRadboud UniversiteitNijmegen Medical CentreHuman GeneticsNijmegen, The NetherlandsProf. Joachim KloseCharite-Universitatsmedizin BerlinInstitute for Human GeneticsBerlin, GermanyProf. Andrea BallabioTelethon Institute of Geneticsand MedicineNaples, ItalyProf. Alexandre ReymondUniversity of LausanneCenter for Integrative GenomicsLausanne, SwitzerlandDr. Henri BléhautInstitut Jérôme LejeuneParis, FranceDr. Fabrice TroveroKey-Obs SAParis, FranceFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life353

7.2TISSUE ANDORGAN DEVELOPMENT,HOMEOSTASIS AND DISEASENFGLYMPHANGIOGENOMICSEuroHearMYORESEuReGeneEVI-GENORET

NFGState-of-the-Art:Project Type:Specific TargetedResearch ProjectContract number:LSHG-CT-2003-503221Starting date:1 st January 2004Duration:48 monthsEC Funding:1 849 600Neurons are not all the same — many thousands of different classes of neurons, defined bya variety of criteria such as morphology, patterns of connectivity, and expression of particularneurotransmitters and receptors, serve as the cellular building blocks of the brain. Each ofthese neuronal types has a specific physiological role in brain function. Neurological andpsychiatric diseases target particular neurons or neural circuits. The brain is a natural mosaicof a large variety of different cell types and a combined approach is necessary in order todescribe them fully. Northern blot analysis, RT_PCR amplifications and cDNA microarrayanalysisallow rapid testing of many genes, but lack spatial resolution. One promising alternativeis to tag individual genes in transgenic animals using a marker such a green fluorescentprotein (GFP), thereby revealing their pattern of expression in vivo. Not only does this techniquereveal cell morphologies with high resolution, it also allows particular cell types to beharvested for molecular analysis. The complexity of brain cell types and circuits is reflectedin the complexity of gene expression patterns in the brain. It is not yet known how many celltypes are in the brain, but it seems likely that a classification of neuronal types based on geneexpression, will reveal many more neuronal subtypes than can be recognized with traditionalelectrophysiological and morphological methods. Therefore, a proper classification cannotbe obtained through the exclusive use of anatomy and electrophysiology.The most efficient approach is to start mapping transcription factors for individual neurons:they may provide powerful markers for adult cell types and neural development. It is likely thata specific combination of transcription factors will determine many cellular properties, bothmorphological and electrophysiological, i.e. excitability, connectivity and synaptic properties.A cellular list for the nervous system is a powerful resource, not only for understanding thedevelopment of the nervous system, but also for understanding brain functions.Scientific/Technological Objectives:There will be three milestones involved in this process:1) Objective one focuses on delivering the first cDNA chips; developing the techniqueof single cell gene profiling; in part WKP 1 and 2 of the project are transferred to theelectrophysiological laboratories.2) This objective will ascertain whether preliminary experiments of gene expressionprofiling have been performed in specific parts of the project; whether specific taskshave been carried out; and lastly, whether the technique for the selective ablation ofspecific neuronal populations is working.3) At this point, NFG will further assess whether the characterisation of sensory, corticaland hippocampal neurons combining gene profiling, electrophysiology and morphologyhas been effectively obtained, and if real advancements towards the mainobjectives of the project have occurred.Expected Results:Functional genomics tools will be developed. This technological development consists of theconstruction of cDNA arrays, and of the optimisation of the procedure to harvest mRNAfrom single neurons, and for global amplification of single cell cDNA.Using the tools developed within the project it will be possible to examine the gene expressionprofile from single neurons identified either by their morphological or their electrophysiologicalcharacteristics. Such data enable the identification of gene abundantly expressedin particular classes of neurons, which can be used as markers. Having identified thesemarkers, transgenic mice will be constructed using BAC technology, in order to specificallylabel particular cell types with a fluorescent label, whose expression will be identical356From Fundamental Genomics to Systems Biology: Understanding the Book of Life

to the cell-specific marker. When specific neuronal populations have been marked with afluorescent label, they are selected by FACS, and can also be tagged with a toxin whoseexpression is driven by a promoter specific to the identified neuron of interest, allowingselective ablation of that neuronal population. This technological development is carriedout in a coordinated way in Cambridge, Trieste and Tokyo, and additional groups are performingthe electrophysiological experiments of the present project. Part of the NFG projectis dedicated to understanding the relation of sensory transduction and gene expression inolfactory sensory neurons and photoreceptors.Potential Impact:Functional Genomics of the Adultand Developing BrainNFG plans to answer questions relating to basic functional properties of the genome inolfactory sensory neurons and photoreceptors. The project’s findings will impact our knowledgeof the links between gene expression and sensory adaptation. Furthermore, it willimprove our understanding of existing and potentially new cell types in the cortex, basedon expression patterns using cortical neurons. Finally, NFG’s research into the hippocampuswill be aimed at elucidating the links between gene expression in identified neurons,and changes in their electrical and functional properties during the major changes associatedwith mammalian development. These developments are expected to further enhanceresearch efforts in the area of brain function, and potentially establish a clear Europeanadvantage in this field.Keywords: functional genomics, genetics, DNA chips, development, brainPartnersProject Coordinator:Prof. Anna MeniniSISSA (Scuola InternazionaleSuperiore di Studi Avanzati /International School for Advanced Studies)Neurobiology Sectorvia Beirut 2-434014 Trieste, Italymenini@sissa.itProf. Hugh Robinson, Dr. Frederick LiveseyUniversity of CambridgeCambridge, UKDr. Richard MilesInstitut National de la Santéet de la Recherche Médicale (INSERM)0224 Cortex et EpilepsieParis, FranceDr. Piero CarninciRIKEN (The Institute for the Physicaland Chemical Research)Wako, Saitama, JapanDr. Simona CapsoniLLG (Lay Line Genomics)Rome, ItalyFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life357

LYMPHANGIOGENOMICSwww.lymphomic.orgProject Type:Integrated ProjectContract number:LSHG-CT-2004-503573Starting date:1 st May 2004Duration:60 monthsEC Funding:9 000 000State-of-the-Art:The lymphatic vasculature is essential for the maintenance of fluid balance in the body, forimmune defence and for the uptake of dietary fat. Absent or damaged lymphatic vesselsmay lead to lymphoedema, a chronic and disfiguring swelling of the extremities whichsometimes necessitates the amputation of affected limbs. In addition, lymphatic vesselspromote metastatic spread of cancer cells to distant organs, a leading cause of death inpatients with cancer and a major obstacle to the design of effective cancer therapies. Thelymphatic vessels were identified hundreds of years ago, yet their development and function,and the molecular mechanisms underlying their role in disease processes is in effect,poorly understood.Scientific/Technological Objectives:The aim of this project is to discover novel genes that are important for lymphatic vascularversus blood vascular development and function, and to study the functional role and therapeuticpotential of their gene products in lymphangiogenesis, using state-of-the-art technologies.The methods planned by the consortium include large-scale knockout and knockdownof the mouse genome, embryonic stem (ES) cell technology, knockdown of zebrafish genesby morpholino-antisense technology and positional cloning of disease susceptibility genesinvolved in lymphangiogenesis.Although historically it has been somewhat neglected, the field of lymphatic biology has experienceda dramatic growth in the last year, this, due for the large part, to the availabilityof enhanced techniques and tools and a greatly improved understanding of basic aspects oflymphatic physiology. The LYMPHANGIOGENOMICS project has been an essential driverof this development. Lymphatic biologists, physiologists, biomedical engineers and physicianshave a great need for a forum in which to collaborate and discuss developments, soas to determine the future direction of research within this field. The project brings togetherthe leading laboratories working in lymphangiogenesis. The project has been brought intoaction, in an effort to understand, at the molecular level, the mechanism of growth of lymphaticvessels and the key molecules in the lymphatic differentiation programme.Expected Results:The project’s research outcomes may hold significant therapeutic potential for the twoforemost causes of morbidity and mortality in Europe: cancer and vascular diseases. Theproject will provide fundamental insights into the molecular and cellular basis of lymphangiogenesisand thereby enabling scientists to develop therapies that suppress (e.g. for thetreatment of cancer and inflammatory diseases), or stimulate the growth of lymphatic vessels(e.g. for the treatment of tissue ischaemia and lymphoedema).The consortium’s many and greatly significant achievements to date include the following:(1) Several new target candidate genes have been identified, some of which have beenvalidated in Xenopus and Zebrafish models; (2) The new amphibian genetic system, asdeveloped and validated for the analysis of lymphatic vascular development, has beenmade available to the consortium for semi-high throughput functional lymphangiogenomics;(3) Immortalised cell lines have been developed from primary lymphatic endothelial cells;358From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Genome-Wide Discoveryand Functional Analysis of Novel Genesin Lymphangiogenesis(4) Several neural molecules that provideguidance cues in the lymphatic vesseldevelopment have been discovered. Agreat advance was the identification of arole for vascular endothelial growth factorC (VEGFC) in the regulation of neuralprogenitor cells; (5) Protocols have beenoptimised for the isolation of multipotentadult progenitor cells from mouse and ratbone marrow, for the study of lymphaticendothelial cell (LEC) differentiation ; (6)Striking new results on the trans-differentiationof macrophage-like cells into lymphaticendothelium; (7) New vascularmalformation mutants have been identified,including a novel VEGFR-3 receptormutation in a sporadic lymphoedema; (8)Different monoclonal antibodies directedto human LECs have been obtained, insome cases from a human antibody phagedisplay library; (9) A web-accessible database,QRISP, that provides a platformfor integrated bioinformatics analysis ofconsortium and public expression data,has been implemented and is now fullyoperational; (10) An extensive databaseof blood vascular and lymphatic endothelialtranscriptomes has been compiled;(11) A company, Lymphatix Ltd, has beenestablished and has started to developVEGFC and VEGFD for the therapy oflymphoedema and tissue ischaemia.Potential Impact:While the focus of this project is on providingnew insights into the pathophysiologyand biology of lymphangiogenesis,its broad scope and multidisciplinary naturemean that it will also have a positiveimpact on the wider scientific communityand on society in general. This statementis supported by evidence of the centralrole that lymphangiogenesis plays in humandisease. It is estimated that in Europealone, three to five million people are affectedby secondary lymphoedema (dueto radiation therapy, cancer, surgery orinfections). This number increases whenone considers the role of the lymphaticFig. 1Fig. 2Fig. 3Images by: Tuomas Tammela,Molecular/Cancer Biology Laboratory,University of Helsinki, Finland.Fig.1. Lymphatic vessels in redare shown encircling a very smalltumor (0.1 mm in diameter) thatis grown in the mouse ear.The tumor secretes growthfactors that promote thegrowth of lymphatic vesselsinto the tumor. Individualtumor cells gain entry into thelymphatic vessels, and use themas routes for spreading to nearbylymph nodes.Fig.2. Lymphatic vessels(green) and blood vessels (red)intermingle in the mouse earskin. The lympahtic vessels areblind-ended vessels that takeup fluid, large molecules andcells, which leak out of the bloodvessels and return them back tothe blood circulation via largerlymphatic vessels.Fig.3. A high magnificationmicroscopic image of a smalllymphatic vessel (green) that hasbeen stimulated with a growthfactor protein called VEGF-C.Note the very thin projectionsof lymphatic endothelial cellssprouting from the vessel.VEGF-C does not affect thenearby blood vessels (red), whichindicates that it can be used tospecifically grow new lymphaticvessels for example in patientssuffering from lack or impairmentof lymphatic vessel function.From Fundamental Genomics to Systems Biology: Understanding the Book of Life359

LYMPHANGIOGENOMICSsystem and blood vessels in the spread of inflammatory and infectious diseases (e.g. tuberculosisand filariasis). If one also takes into account the millions of people who suffer frommetastatic spread of cancer via the lymphatic vasculature, it becomes clear that the integratedproject described here stands to have a profound impact on the burden of humandisease in Europe. Novel therapies for cancer, inflammatory diseases, lymphoedema andtissue ischaemia will also be developed.Keywords:vascular diseases, cancer, inflammatory diseases, vascular biology, molecularbiology, stem cells, lymphoedema, genomics, lymphangiogenesis360From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Genome-Wide Discovery and Functional Analysis ofNovel Genes in LymphangiogenesisPartnersProject Coordinator:Prof. Kari AlitaloUniversity of HelsinkiFaculty of MedicineBiomedicum HelsinkiMolecular Cancer Biology ProgramHaartmaninkatu 8P.O. Box 6300014 Helsinki, Finlandkari.alitalo@helsinki.fiProject Manager :Dr. Pirjo LaakkonenUniversity of HelsinkiMolecular Cancer Biology Programpirjo.laakkonen@helsinki.fiDr. Anne EichmannInstitut National de la Santé etde la Recherche Médicale (INSERM) U36Paris, FranceProf. Christer BetsholtzKarolinska InstitutetDepartment of Medical Biochemistryand BiophysicsStockholm, SwedenProf. Dontscho KerjaschkiMedical University ViennaClinical Institute of PathologyVienna, AustriaProf. Peter CarmelietFlanders Interuniversity Institutefor Biotechnology (VIB)Centre for Transgene Technology and Gene TherapyLeuven, BelgiumProf. Hellmut AgustinDeutsches KrebsforschungszentrumVascular MedicineHeidelberg, GermanyProf. Seppo Yla-HerttualaUniversity of KuopioA.I. Virtanen InstituteKuopio, FinlandDr. Per LindahlGothenburg UniversityInstitute of Medical BiochemistryGöteburg, SwedenDr. Jyrki IngmanLymphatix OyHelsinki, FinlandDr. Bernhard BarleonRELIATech GmbHBraunschweig, GermanyProf. Elisabetta DejanaFIRC Institute of Molecular OncologyMilan, ItalyProf. Gerhard ChristoforiUniversity of BaselInstitute of Biochemistry and GeneticsBasel, SwitzerlandProf. Lena Claesson-WelshUppsala UniversityDepartment of Genetics and PathologyRudbeck LaboratoryUppsala, SwedenProf. Miikka VikkulaChristian de Duve Institute of Cellular PathologyLaboratory of Human Molecular GeneticsBrussels, BelgiumFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life361

Project Type:Integrated ProjectContract number:LSHG-CT-2004-512063Starting date:1 st December 2004Duration:60 monthsEC Funding:12 500 000EuroHearState-of-the-Art:www.eurohear.orgHearing impairment is the most common human sensory deficit, affecting more than 10 percentof the European population (40 million people). This causes a considerable social andeconomic burden to those afflicted and to society, but early identification and interventionhas proved to be cost-effective. Seventy percent of human hearing impairment is geneticin origin and classified as non-syndromic hereditary hearing impairment, meaning it hasonly one symptom. The remaining 30 percent of human hearing impairments have othersymptoms and are therefore described as syndromic.Hearing impairment is the most common birth defect in humans. Of the non-syndromic,prelingual cases, about 80 percent are due to recessive inheritance, with the majority ofparents hearing normally. About 20 percent are due to dominant inheritance, with at leastone of the parents found to be hearing-impaired. Whereas single gene defects probablyaccount for over half of cases of childhood deafness, no such quantitative data exists for theproportion of hearing impairment in adults that may be due to hereditary causes.Over 45 genes responsible for isolated (nosyndromic) hearing impairment in humans areknown, but at least as many as this still need to be identified. The involvement of hearing-impairedindividuals and their families in research made these breakthroughs possible, and theirongoing support will be the key to future success in understanding the molecular basis of auditoryfunction. Moreover, as a result of their participation, molecular diagnostics have been developedand the quality of genetic counselling has been dramatically improved. The ultimategoal of this research is the development of new ways of treating hearing impairment.Scientific/Technological Objectives:The Eurohear project, comprised of 25 research teams, is building on their work on geneticand molecular mechanisms underlying hearing impairment.EuroHear aims to identify the molecules that play a critical role in the inner ear, and morespecifically in the cochlea or the auditory sensory organ. The project has three closely relatedobjectives:1) To identify the genes underlying sensorineural hearing impairment, in turn enablingresearch on these molecular mechanisms involved in the development and functioningof the inner ear. The consortium proposes to identify the human and mousegenes that underlie early and late onset forms of hearing impairment - both thosethat are monogenic and those that are multifactorial in origin. Special emphasis willbe placed on late-onset forms of hearing impairment (age-related hearing loss) andmore specifically on the sensorineural form, presbycusis, since these are better targetsthan congenital hearing impairment for preventive and curative therapies.Hair bundles2) To understand the mechanisms underlying normal and impaired hearing. EuroHearwill not only address the hair bundle, the ribbon synapse of the hair cells and outerhair cell electromotility mechanisms, it will also investigate the cochlear ion channels,transporters and gap junctions that contribute to potassium homeostasis.3) To develop tools for preventing and treating hearing impairment. This includes testingcandidate drugs in vivo, developing high throughput screening of organotypiccochlear cultures for testing of drugs, and in-depth exploration of three possibletherapeutic approaches (gene therapy, cell transplantation, and therapy based onthe use of inner ear progenitor/stem cells, especially hair cell progenitors). Experimentalevidence show that pharmacological compounds can significantly reduce theprogression of hearing impairment and this approach could lead to more efficient362From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Advances in hearing science:from functional genomics to therapiestreatment strategies. Recent observations on cell and gene therapy, as well as thediscovery of inner ear progenitor cells, suggest entirely new methods for treating theinner ear deficits. Within the next five years, EuroHear expects to realise some ofthese methods.EuroHear has a strong, cross-disciplinary training programme whose objective is to createa network of scientific expertise on the development and function of the inner ear and hearingimpairment. The training programme aims to provide high-standard, multi-curricular innerear training courses in Europe to favour the growth of a generation of young Europeanscientists with multi-disciplinary researchtraining.Expected Results:So far, Eurohear has made a significantadvance with the identification of severalnovel genes and their mutations responsiblefor different forms of deafness. Thiswas made possible by the active involvementof hearing-impaired patients andtheir families. Some of these results are:1) Mouse mutants are an invaluableresource for studying the mechanismsof hearing and deafness.The consortium has been workingon 21 mutant mice. Loci for14 mutants have been mappedand genes for 13 mutants havebeen cloned;2) Human deafness: 13 novel genescausative for isolated or syndromicforms have been discoveredby EuroHear;3) Dysfunction of the hair cell’s ribbon synapse has been shown by the project to bethe cause of human hereditary deafness. This finding is a major breakthrough in theunderstanding of how auditory information is relayed to the central nervous system,and reveals that cochlear implants are likely to be successful in the “treatment” ofchildren diagnosed with mutations in the Otoferlin gene;4) The amplification of low level sound signals by a motile protein localised in themembranes of hair cells is crucial for proper hearing. Eurohear’s research has recentlyidentified unique regions within the sequence of this protein that are essentialfor its function as a cellular motor;5) Mutations in the gene encoding connexin 26, a gap junction required for intercellularcommunication within the ear, are the major cause of deafness in humanbeings. Work carried out in the consortium has now identified two genes that aredownregulated as a consequence of the loss of connexin 26, and are likely therapeutictargets for intervention;6) Eurohear is also seeking tools for prevention and cure. Promising observations incell and gene therapy, as well as the recent discovery of progenitor cells (stemcells) in the inner ear, suggest new ways to treat the inner ear in the future. Testshave been initiated using several new in vitro models for drug screening, and novelmethods for stimulating the regeneration of the replacement of inner ear cells arebeing actively explored.The ear consists of external,middle, and inner structures.The eardrum and the three tinybones conduct sound from theeardrum to the cochlea.From Fundamental Genomics to Systems Biology: Understanding the Book of Life363

EuroHearSensory cells of the cochleaOther expected results of EuroHear include astandardisation of investigative protocols, theprovision of access to large-scale platformsfor genetics and genomic analysis, and thedevelopment and diffusion of physiologicaland biophysical techniques of relevance forfunctional investigations of the inner ear.Potential Impact:This research has direct implications for patients.For example, it will lead to improvementsin presymptomatic diagnosis, whichin the case of Usher syndrome type 1 (deafnessassociated with blindness) will allow cliniciansto provide hearing-impaired childrenwith cochlear implants at the best possiblestage, i.e. when they are young and beforethey lose their sight. It will allow the diagnosisof a predisposition to a form of hearingimpairment that is induced by aminoglycosides,so that the treatment of affected individualswith this class of antibiotics canbe avoided. It will also enable clinicians topredict, on the basis of information about apatient’s underlying genetic defect, whetheror not a cochlear implant will be successful.In the case of late onset hearing impairment,molecular diagnosis will allow susceptibleindividuals to make informed career choicesin order to avoid excessive noise exposure.Obviously, the effective treatment of hearingimpairment will significantly improve qualityof life for deaf or hard-of-hearing individuals.Among the molecular mechanisms thatcontribute to hearing impairment, those thatinvolve potassium homeostasis could becomea therapeutic target within a reasonabletimeframe.Keywords:hearing impairment, inner ear, synapse,K+ homeostasis, hair bundle, therapy, cellphysiology, functional genomicsPartnersProject Coordinator:Prof. Christine PetitInstitut National de la Santé etde la Recherche Médicale (INSERM)UMRS 587- Institut PasteurUnité de Génétique et Physiologie de l’Audition25 rue du Dr Roux75724 Paris, Francecpetit@pasteur.frProject co-Coordinator:Prof. Karen AvrahamUniversity of Tel AvivDepartment of Human Molecular Geneticsand Biochemistry, Sackler School of MedicineRamat Aviv39040 Tel Aviv, Israelkarena@post.tau.ac.ilProject Manager:Laurent CharvinINSERM Transfert7 rue Watt75013 Paris, Francelaurent.charvin@inserm-transfert.frProf. Jonathan AshmoreUniversity College LondonDepartment of PhysiologyLondon, UKProf. Stephen BrownMedical Research CouncilMammalian Genetics UnitOxfordshire, UKProf. Cor W. R. J. CremersUniversity Medical Centre Nijmegen (UMCN)OtorhinolaryngologyNijmegen, The NetherlandsProf. Dominik OliverPhilipps-Universität MarburgInstitut für Physiologie und PathophysiologieMarburg, GermanyProf. Jonathon HowardMax Planck Society for the Advancement of ScienceMax-Planck Institute of Molecular Cell Biologyand GeneticsDresden, GermanyProf. Thomas JentschMax-Delbrück-Centrum für Molekulare MedizinMetabolic Diseases, GeneticsGenomics and BioinformaticsBerlin, Germany364From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Advances in hearing science: from functional genomics to therapiesProf. Guy P. Richardson, Prof. Corné KrosUniversity of SussexSchool of Life SciencesBrighton, UKProf. Christian KubischUniversity Hospital of the University of CologneInstitut of Human GeneticsCologne, GermanyProf. Mark LathropConsortium National De Recherche EnGenomique (CNRG)Centre National de GénotypageEvry, FranceProf. Fabio MammanoIstituto Veneto Di Medicina Molecolare (VIMM)Centro Di Ricerca Della Fondazione PerLa Ricerca BiomedicalPadova, ItalyProf. Felipe MorenoFundación para la Investigación Biomédica delHospital Universitario Ramón y CajalUnidad De Genetica MolecularMadrid, SpainProf. Tobias MoserBereich Humanmedizin Georg AugustUniversität GöttingenDepartment of OtorhinolaryngologyGöttingen, GermanyProf. E. Sylvester ViziInstitute of Experimental MedicineHungarian Academy of SciencesDepartment of PharmacologyBudapest, HungaryDr. Christian VieiderACREO ABMicroTechnology DepartmentStockholm, SwedenDr. Jörg HagerIntegraGen SAResearch & DevelopmentEvry, FranceStéphane SilventeAffichemResearch and DevelopmentToulouse, FranceProf. Hammadi AyadiUniversity of SfaxFaculty of Medicine of SfaxHuman Molecular Genetics LaboratorySfax, TunisiaProf. Klaus WilleckeUniversity of BonnInstitute of GeneticsBonn, GermanyDr. Ulla PirvolaUniversity Of Helsinkilnstitute of BiotechnologyHelsinki, FinlandDr. Pascal Martinlnstitut Curie, Division de RechercheLaboratoire Physico-Chimie ‘Curie’ (UMR 168)Paris, FranceProf. Karen P. SteelGenome Research LtdWellcome Trust Sanger InstituteCambridge, UKProf. Mats UlfendahlKarolinska InstituteDepartment of Clinical NeuroscienceCenter for Hearing and Communication ResearchStockholm, SwedenProf.Guy Van CampUniversity of AntwerpDepartment of Medical GeneticsAntwerp, BelgiumFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life365

Project Type:Network of ExcellenceContract number:LSHG-CT-2004-511978Starting date:1 st January 2005Duration:60 monthsEC Funding:12 000 000MYORESState-of-the-Art:www.myores.orgIn Europe, over 300,000 people are affected by muscular dystrophies leading to decreasedmobility and loss of independence. This has severe consequences at both a personal andeconomic level. The aim of this proposal is to understand how these muscular defects canbe repaired.To date, the genetic mechanisms responsible for the emergence of these diseases have onlybeen identified for some of the most common muscular dystrophies, such as Duchenne orLimb Girdle dystrophies, and it is still necessary to identify the genetic determinants for anumber of other myopathies. In addition to identifying the genetic determinants of musclediseases, it is crucial to acquire a profound understanding of the molecular and physiopathologicalmechanisms associated with aberrant gene function in order to be able todesign efficient therapies.Satellite cell (in blue) andmuscle cell nucleiInherited diseases are not the sole pathologies associated with muscle dysfunction: the bedriddenand the elderly suffer from muscle degeneration too, which has huge implicationsfor the economy, particularly with the latter group as life expectancy continues to rise inEurope. For these reasons as well as the large economical burden that these diseases placeon our societies it is an urgent matter to find cures for muscle pathologies. Since a numberof avenues are explored by various laboratories in isolation around Europe it is becomingclear that the integration of European potential in this domain is an important step in designingsuccessful therapies. To address efficiently the problem posed by muscular diseases,three fundamental rules must be followed: i) breadth of investigations in order not to missimportant routes of research; ii) clear and focused research to provide patients with fastrelief; iii) rapid transfer of new information to health providers.All aspects of muscle differentiation will be investigated in this project and this will betranslated into the mechanisms of repair in the adult. Fundamental to the advancement ofour knowledge is the recent demonstration that throughout evolution many of the molecularmechanisms regulating muscle differentiation have been highly conserved. As molecularpathways can be easily assessed in invertebrates, the European Muscle Development Network(MYORES) will exploit this advantage and rapidly extend the knowledge gained inthese systems to determine gene function in higher vertebrates. This is a unique aspect ofthe proposal and places the consortium at the international forefront of understanding genefunction during normal muscle development and disease.Scientific/Technological Objectives:MYORES aims to target various aspects of muscle disease by bringing together Europeanspecialists in muscle development and function. This integrated approach is aimed at providinga critical mass of researchers with complementary expertise who will be able totackle more difficult problems and make more key advancements than when working alone.The MYORES participants will utilize different animal models to investigate various aspectsof muscle development, from myogenic induction morphogenesis to terminal differentiation.This is complemented by teams with expertise in muscle protein structure, muscle diseaseand degeneration and tissue engineering as well as human therapy or bio-computing. Inaddition, the MYORES project will maximise the scientific and commercial potential of Europeanresearch in muscle biology by: i) promoting the sharing of data and research tools;ii) enhancing exchanges of personnel between laboratories and through the organisationof training programmes; iii) developing and implementing an integrated multiorganismicapproach to accelerate investigations and improve understanding of normal muscle development,function and pathological dysfunction.366From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Multiorganismic Approachto Study Normal and Aberrant MuscleDevelopment, Function and RepairThe overall objectives of the project are:1) To integrate internationally recognised European specialists working on various aspectsof muscle biology and pathology in a number of model organisms.2) To coordinate research on well-defined aims and obtain a critical mass of researcherswho will be able to make significant scientific advancements.3) To create state-of-the-art technical platforms and resources.4) To organise the rapid transfer and application of knowledge acquired in geneticallyamenable organisms into specific applications for human muscle diseases.5) To publicise scientific actions broadly and, through education, attract a younger generationof scientists into this essential field of research.6) To contribute to reducing the incidence and impact of muscle diseases on the Europeanpopulation and help the European healthcare sector to compete internationally. Furthermore,MYORES is working to restructure the field of muscle biology, providing addedvalue by strengthening the impact of European research.In achieving its objectives, MYORES further aims to coordinate the efficient transfer of knowledgeand information from research projects to regulatory bodies and industrial sectors.Expected Results:A fundamental aspect of the MYORES network is the extensive use of recently developedtechnologies of high-throughput screening to isolate novel molecules and to rapidly testtheir relevance in the various aspects of muscle function and repair in a number of animalmodels. Special emphasis will be put on the interaction, coordination and efficient transferof knowledge between experimental models and clinical demands to ensure that the informationobtained is fully exploited.As a result of this collaborative effort, we expect to gain broad insight into the regulatoryinteractions and cellular pathways that underlie normal and aberrant muscle formation andfunction. Hopefully, this will lead to designing new therapeutic approaches for musculardiseases and muscle weakening in humans.We expect isolation of about 100 novel genes expressed during the various steps of myogenesisin invertebrates and/or vertebrates. The function of about 30 novel genes will bedetermined. The network expects to publish at least one collaborative publication per RP inthe second year of funding and at least two co-signed publications per RP in the next yearsof funding. Thus, by the end of the funding period MYORES plans to publish about 40 publications,co-signed by at least two of the network’s participants. An Internet resource willbe developed that will be used by MYORES participants and by the scientific community.The first release of MyoBase is expected during the second year of funding to augmentexchanges between scientists working in the muscle biology field in Europe. This will resultin an increase in competitiveness of European research in this field. MYORES members willalso contribute to the designing of novel therapeutic strategies and to the generation ofdiagnostic tools.An important aspect of the project is to transfer efficiently the knowledge present within theMYORES network to young researchers and doctors, and to this effect MYORES is organizingsummer schools and workshops to provide technical training and up-to-date knowledgein the field of mycology. In 2006, one summer school dedicated to various aspects ofmuscle biology took place in Spain with 20 students from MYORES laboratories attending.Moreover, in house training and mobility programmes have been initiated allowing technicaltraining for young researchers in collaborating laboratories within the network.Potential Impact:The MYORES network will create the necessary framework to accelerate the pace of muscleresearch, and generate, much more efficiently, the important advances in our understand-Drosophila transgenesis platformcreated in Clermont-Ferrand andsupervised by INSERM for gainand loss of function of autologousand heterologous genes in vivoFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life367

MYORESDrosophiliaCionaZebrafishwupA/TpnlExample of identified orthologmuscle-specific genes fromDrosophila, Ciona and Zebrafish.ing of muscle pathologiesand in definingArgKcures or treatments forhuman muscle diseases.EC funding will promotethe development of participatinggroups and improvetheir contributionto the EC as a whole, byallowing cross-disciplineand cross-border linksto be established andfostered. Shared use ofresearch infrastructuresand development ofmutual specialisation isexpected to result fromjointly undertaken participantactivities. Thesewill further strengthenboth the participants’ expertise and theEuropean knowledge base, and will havean important impact on the job market byattracting young researchers to the field ofmuscle biology. The MYORES network hasbeen structured to extend previously existingsmaller scale collaborations. Both shorttermand long-term projects are designed toprovide important information and researchtools for the academic and industrial sectors,and patient associations. An importantMYORES deliverable for the scientificcommunity will be the MyoBase database.The intention is that this regularly updateddatabase will become the main source ofinformation in muscle biology and representa durable contribution to the network, whichwill have far-reaching impacts on the entirescientific community.Keywords:degenerative diseases, developmental biology,molecular biology, myogenic specification,muscle differentiation, diversification ofmuscle fibres, muscle patterning, myoblastsfusion, functions of muscle-specific proteins,muscle stem cells, muscle regenerationPartnersProject Coordinator:Dr. Krzysztof JaglaInstitut National de la Santé et dela Recherche Médicale (INSERM) U38428 place Henri Dunant63000 Clermont-Ferrand, Francechristophe.jagla@u-clermont1.frProject Sub-Coordinator:Prof. Christophe MarcelleCentre National de la Recherche Scientifique (CNRS)LGPD UMR6545Université de la MéditerranéeDevelopmental Biology Institute of MarseilleLGPD, Campus de Lumigny13288 Marseille, Francemarcelle@lgpd.univ-mrs.frProject Manager:Anton OttaviINSERM Transfert SAHôpital du VinatierBat. 452b95 Bd Pinel69500 Paris, Franceanton.ottavi@inserm-transfert.frDr. Dominique Daegelen, Dr. Pascale Maire,Dr. Bénédicte Chazaud, Dr. Frédéric RelaixInstitut National de la Santé et dela Recherche Médicale (INSERM)Paris, FranceDr. Patrick Lemaire, Dr. Laurent Ségalat,Dr. Josiane Fontaine-Perus, Dr. Delphine DuprezCentre National de la Recherche Scientifique (CNRS)Paris, FranceDr. Anne-Gaëlle Boricky, Prof. Phil InghamUniversity of SheffieldCentre for Developmental GeneticsDepartment of Biomedical ScienceSheffield, UKProf. Beate Brand Saberi, Prof. Bodo ChristUniversitatklinikum FreiburgInstitut fur Anatomie und Zellbiologie IIFreiburg, GermanyDr. Baljinder Mankoo, Dr. Mathias Gautel,Dr. Simon Hughes, Dr. Susanne Dietrich,Dr. Philippa Francis-West, Dr. Peter ZammitKing’s College LondonRandall Centre for Molecular Cell BiologyGKT School of Biomedical SciencesLondon, UKDr. Andrea MunsterbergUniversity of East AngliaSchool of Biological SciencesCell and Developmental BiologyNorfolk, UKDr. Michael Victor TaylorUniversity of Wales, CardiffCardiff School of BiosciencesCardiff, UK368From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Multiorganismic Approach to Study Normal and Aberrant MuscleDevelopment, Function and RepairProf. Margaret Buckingham,Dr. Shahragim TajbakhshInstitut PasteurDépartement de Biologie du DéveloppementParis, FranceDr. Eileen FurlongEuropean Molecular BiologyLaboratory (EMBL)Developmental Biology andGene Expression ProgrammesHeidelberg, GermanyProf. Nadia RosenthalEuropean Molecular BiologyLaboratory (EMBL)Mouse Biology unitMonterotondo,ItalyProf. Bernard ThisseCentre Européen de Recherche enBiologie et en Médecine (CERBM)Institut de Génétique et de BiologieMoléculaire et CellulaireIllkirch, FranceProf. Hans Henning ArnoldTechnical University BraunschweigCell and Molecular Biology/BiosciencesBiochemistry and BiotechnologyBraunschweig, GermanyProf. Stefano SchiaffinoUniversita degli Studi di PadovaDipartimento di Scienze BiomedicheSperimentaliPadova, ItalyDr. Tomas SoukupInstitute of Physiology, Academy ofSciences of the Czech RepublicDepartment of Functional MorphologyPrague, Czech RepublicProf. Renate Renkawitz-PohlPhilipps-Universitat MarburgDevelopmental of Developmental BiologyMarburg, GermanyProf. Carmen BirchmeierMax-Delbruck-Centrum furMolekulare MedizinSignaltransduction andDevelopmental Biology GroupBerlin, GermanyProf. Alberto Ferrus, Dr. Mar Ruiz-GomezConsejo Superior deInvestigaciones CientificasInstituto CajalMadrid, SpainDr. Chava Kalcheim,Dr. Orna HalevyHebrew University of JerusalemDepartment of Anatomy and Cell BiologyJerusalem, IsraelProf. John Sparrow,Dr. Belinda BullardUniversity of YorkDepartment of BiologyYork, UKDr. Vincent MoulyUniversité Pierre et Marie CurieUMR 7000, Cytosquelette etDéveloppementParis, FranceProf. Thomas BraunMax-Planck Institute for Physiologicaland Clinical ResearchW.G. Kerckhoff-InstitutBad Nauheim, GermanyProf. Peter RigbyInstitute of Cancer ResearchRoyal Cancer HospitalSection of Gene Function andRegulation, Chester Beatty LaboratoriesLondon, UKYann DantalSoluscience SABiopôle Clermont-LimagneSt. Beauzire, FranceDr. Peter CurrieVictor Chang CardiacResearch InstituteDarlinghurst, AustraliaDr. Thierry TourselAssociation Françaisecontre les Myopathies (AFM)Direction Recherche etDéveloppement desTherapeutiquesEvry, FranceDr. Jonathan BeauchampRoyal Holloway andBedford New CollegeSchool of Biological SciencesEgham, UKProf. John SquireUniversity of BristolDepartment of PhysiologyBristol, UKFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life369

EuReGeneProject Type:Integrated ProjectContract number:LSHG-CT-2004-005085Starting date:1 st January 2005Duration:48 monthsEC Funding:10 500 000State-of-the-Art:Diseases of the kidney represent a major cause of morbidity and mortality in Europe. Theelderly are disproportionately affected, but renal disease is also a condition that severelyaffects children. An estimated 4.5 million Europeans suffer from renal disorders. The annualdeath rate in patients with renal failure is 20%.The focus of the European Renal Genome Project (EuReGene) is to challenge kidney diseases.Elucidation of human and other genomes heralds a new era in biomedical research,offering unprecedented opportunities to understand disease processes and to identify strategies,so as to improve health. The project embraces these opportunities and plans to implementan interdisciplinary research programme. EuReGene integrates European excellencein research relevant to renal development, pathophysiology and genetics. The goal is todiscover the genes responsible for renal development and disease, and to examine theirproteins and their actions. To this end, a consortium has been established, comprisingleading scientists, clinicians and SME partners that will focus on the development of noveltechnologies and discovery tools in functional genomics, and their application to kidneyresearch. Moreover, we will look to comparative genomic studies in many systems that provideutilitarian models, ranging from zebrafish to Xenopus, and from mice and rats to man.The studies will be performed at different levels, including the gene, the cell, the organ andthe organism. Ultimately, identification of disease genes will lead to a better understandingof renal disease processes, to improved diagnosis and to new concepts in therapy. Theprogramme will establish a paradigm for an integrated post-genomic approach to analyserenal disease-related developments that may be transferred to other organ systems or diseaseentities, in the future.Scientific/Technological Objectives:EuReGene will pursue objectives in four areas:1. Functional genomics technologies: EuReGene will develop new high throughput geneexpression analysis methods; renal organ cultures to study gene function; databasesfor tools, methodologies and results; and kidney atlas for spatio-temporal descriptionof renal mechanisms.2. Renal development: EuReGene will develop new cell lines for the study of developmentalprogrammes, as well as detailed gene expression maps of developing anadult kidney; and identify genes involved in nephrogenesis/differentiation.3. Pathophysiology: EuReGene will develop new mouse and rat models; study regulatorynetworks in cell differentiation, injury and repair and cellular transport; andidentify new targets for therapeutic intervention in renal diseases.4. Complex genetics: EuReGene will establish new ENU models in zebrafish and mice;map modifier QTLs for proteinuria and progressive renal injury in rats, and forglomerulosclerosis and renal stone disease in mice; and identify modifiers in diabeticnephropathy in mice.Expected Results:The project’s integrated research approach will have a fundamental impact on the currentunderstanding of renal development and disease in humans. At the end of the project(which has a 4-year duration) the following measurable results will be delivered:370From Fundamental Genomics to Systems Biology: Understanding the Book of Life

European Renal Genome ProjectEU CommissionAdvisory BoardElizabeth Robertson, Enyu Imai, Mathias Brandis, Nine KnoersAlastair Kent, Steve Hebert, Luigi Baroni, Karl-Heinz WilbersGeneralAssemblyProject coordinatorThomas WillnowSteering CommitteeProject ManagementOfficeIwan Meij,Dorothee SaarPanel “Training”Nick HastieTopic 1GenomeTechnologiesAndreas SchedlTopic 2RenalDevelopmentErik ChristensenTopic 3PathophysiologyCorinne AntignacTopic 4ComplexGeneticsDominik Müller,Carsten Wagner,Andreas Schedl,Raj Thakker,Seppo Vainio,Friedrich LuftTopic coordinatorsMDC BerlinMRC EdinburghUniversity NiceNecker Hospital, ParisUCL BrusselsETH ZürichMRC HarwellMario Negri Inst. BergamoUniversity ParisUniversity ZurichMPI HannoverUniversity OuluUniversity HamburgAarhus UniversityUniversity OxfordLMU MünichReceptIconJamie DaviesGregor EicheleThomas WillnowDuncan DavidsonJamie DaviesGregor EicheleSteffen OhlmeierMathias KretzlerAndreas SchedlAndré BrändliNick HastieAndreas SchedlOlivier DevuystAndré BrändliSeppo VainioPierre VerroustOlivier DevuystDominik MüllerFriedrich LuftPierre CourtoyPierre VerroustHeini MurerThomas JentschErik ChristensenAnders NykjaerRoger CoxCorinne AntignacCorinne AntignacRoger CoxGiuseppe RemuzziRaj ThakkerPanel “Exploitation, IPR”ReceptIcon,Ascenion,Thomas WillnowPanel “Ethics, Gender”Ariela Benigni,Mathias Kretzler,Raj Thakker,Friedrich Luft,Rikke NielsenEuReGene management structure1. Methods for high throughput in situ expression analysis at organ level2. Methods for 3D reconstruction of expression maps at organ level3. Bioinformatic tools to integrate data from various genomic approaches into an kidneyatlas of spatio-temporal relationships of developmental/pathophysiological processesat organ level4. A comprehensive kidney atlas of renal developmental and pathophysiological processes(as data and as 3D image reconstructions)5. Novel discovery tools including zebrafish, Xenopus, mouse and rat models (knockouts,knockdowns, transgenics, GFP reporter lines, Cre lines), as well as new cell andorgan cultures6. Repositories (models, cell lines, biopsies, DNA) and databases (expression maps)that are accessible throughout the scientific community7. A list of candidate genes responsible for (i) developmental, (ii) complex genetic and(iii) acquired renal diseases (diabetic nephropathy, glomerulosclerosis, nephrotoxicity,proteinuria, end-organ damage) representing major new targets for diagnosis,drug development, and therapeutic intervention8. A patent portfolio that protects the intellectual property rights of the EuReGene consortium,and forms the basis for commercial exploitation and funding beyond the FP6period9. Websites that inform stakeholders (patient advocacy groups, health care providers,scientists) of latest developments in renal disease research.Potential Impact:EuReGene’s integrated approach will have a profound impact on the current understandingof renal development and disease, and will contribute to fundamental knowledge production,and novel concepts for improving health. It will focus on innovative aspects of technologydevelopment such as animal models, organ cultures and imaging techniques. Theburden of renal disease is vast in terms of financial cost, as well as in increased mortalityFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life371

EuReGeneGraphic representationof the four interrelated topicswithin EuReGeneand medical and psychological morbidity of patients and their families. Through the identificationof the mechanisms underlying disease processes, EuReGene will have a majorimpact on lifting the societal and economic burdens caused by renal disease. It will alsoaddress the ongoing problem of fragmented research activities that hampers efficient medicalresearch in Europe.Keywords:animal models, transgenic animals, mouse, zebrafish, Xenopus, organogenesis, kidneydiseases, transcriptome analysis, cardiovascular diseases, renal pathogenesis, complexgenetics, QTL mapping, solute carrierExpression of Slc12a1in adult kidney visualisedby ISH on a 10micron paraffin sectionusing optimised methodsfor automated ISH372From Fundamental Genomics to Systems Biology: Understanding the Book of Life

European Renal Genome ProjectPartnersProject Coordinator:Thomas WillnowMax-Delbrück-Center for Molecular MedicineCardiovascular Research CentreDepartment of Cardiovascular ResearchLipids and Experimental Gene TherapyRobert Roesslestrasse 1013125 Berlin, Germanywillnow@mdc-berlin.deProject Manager:Dr. Iwan C. MeijMax-Delbrück-Center for Molecular MedicineCardiovascular Research CentreRobert Roesslestrasse 1013125 Berlin, Germanyi.meij@mdc-berlin.deProf. Friedrich Luft, Dr. Dominik MüllerProf. Thomas JentschMax-Delbrück-Center for Molecular MedicineBerlin, GermanyProf. Nick Hastie, Dr. Duncan DavidsonMRC Human Genetics UnitWestern General HospitalEdinburgh, UKDr. Jamie DaviesUniversity of EdinburghCentre for Integrative PhysiologyEdinburgh, UKDr. Roger CoxMedical Research Council HarwellMRC Mammalian Genetics UnitDiabetes, QTL and Modifier Loci GroupOxfordshire, UKProf. André BrändliSwiss Federal Institut of Technology ETHZInstitute of Pharmaceutical SciencesDepartment of Chemistry and Applied BiosciencesZürich, SwitzerlandDr. Giuseppe Remuzzi, Dr. Ariela BenigniMario Negri Institute for Pharmacological ResearchNegri Bergamo LaboratoriesBergamo, ItalyProf. Jürg Biber, Prof. Carsten WagnerUniversity of ZürichInstitute for PhysiologyZürich, SwitzerlandProf. Gregor EicheleMax-Planck Institute of Biophysical ChemistryGenes and Behaviour OrganisationGöttingen, GermanyProf. Seppo VainioUniversity of OuluBiocenter OuluDepartment of BiochemistryOulu, FinlandProf. Erik Ilsø Christensen, Dr. Anders NykjaerAarhus UniversityAarhus C, DenmarkProf. Raj ThakkerUniversity of OxfordNuffield Department of Clinical MedicineOxford Centre for DiabetesEndocrinology and MetabolismChurchill HospitalOxford, UKProf. Andreas SchedlInstitut National de la Santé et de la RechercheMédicale (INSERM) U 470Université Nice - Sophia Antipolis - Centre de BiochimieNice, FranceProf. Corinne Antignac, Prof. Pierre VerroustInstitut National de la Santé et de la RechercheMédicale (INSERM) U 574 & 538Necker Hospital, & Faculté de Médecine Saint-AntoineParis, FranceProf. Pierre Courtoy, Dr. Olivier DevuystUniversité Catholique de Louvain (UCL)Faculté de médecineBrussels, BelgiumFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life373

EVI-GENORETwww.evi-genoret.orgProject Type:Integrated ProjectContract number:LSHG-CT-2005-512036Starting date:1 st April 2005Duration:48 monthsEC Funding:10 000 000State-of-the-Art:About 90 percent of all the information humans use in order to interact in society, is receivedthrough their eyes. But despite major clinical and therapeutic achievements in ophthalmology,the number of people suffering from serious eye problems is growing. This paradoxreflects the fact that we have yet to find ways of stemming and repairing the damagecaused by diseases that affect the retina, such as Inherited Retinal Degenerations (IRD) andAge-Related-Macular Degeneration (ARMD). Furthermore, visual handicaps are a particularproblem in a society in which visual communication is ever increasing.The retina — the part of the eye that converts light into sight — is a highly complex systemthat accommodates both numerous tissue-specific and ubiquitously expressed developmentaland pathologic pathways. The number of genes identified in IRDs has steadily increased.Over the past 20 years, a massive accumulation of knowledge has led to the recognitionof more than 180 mapped loci and the identification of about 120 genes. The most commonform of visual impairment of people above 60, with 12.5 million people affected inEurope, is ARMD, caused by mostly unknown genetic factors. Preventing blindness from IRDand ARMD requires understanding of the genetic and cellular interactions controlling retinaldevelopment, maintenance and function. Understanding complex diseases of the retina isnot only challenging, but it also offers a major incentive to use the knowledge that can begathered by using state-of-the-art functional genomics technologies in order to generate amore comprehensive analysis of retinal degenerations.Scientific/Technological Objectives:In the EVI-GENORET project, 25 academic and industrial partners have formed five interactingcomponents — phenotyping, development, genetics, functional genomics and therapy— to establish working platforms and share tools and knowledge in the field of the retinawithin and outside the academic community.Developmentof standards and informationnetworking system374From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Functional genomics of the retinain health and diseaseThe aim of EVI-GENORET is to build on the current understanding of the fundamental molecularand cellular biology of the retina. The project will help to prevent blindness causedby IRD and ARMD by aiming its work at pursuing a greater understanding of the geneticand cellular interactions that control retinal development, maintenance and function. Theconsortium plans to overcome the lack of critical knowledge in single EU countries by structuringretinal research from leading scientists throughout Europe in order to offer a sourceof expertise for those involved in that research field.Further focus is on: (1) Obtaining and integrating the information on gene function throughnumerous human, animal and in vitro models of retinal degeneration available as well asdata from studies during development; (2) Standardising and analysing this information(databases, bioinformatics, transcriptome, proteome and expression studies); (3) Validationof the information (bioinformatics and functional assays); (4) Generating conceptualand biological models of genes, gene networks and pathways relevant to major functionsinvolved and/or impaired in retinal health and disease; (5) Designing novel cell-based andgenomic-based therapies that will potentially benefit patients but also validate the pathwaysand targets identified, using the above-described approaches.Expected Results:The project has already provided some significant results towards the above objectives, andthese are listed as follows: (1) Harmonisation of Standard Operating Procedure and developmentof the relational EVI-GENORET database. The EVI-GENORET database is a Europeandatabase devoted to fundamental and clinical scientists, as well as patients and aimsat the centralization, sharing, exploitation and dissemination of the data and knowledgerelated to retinal health and disease. The database integrates heterogeneous data encompassingpopulation genetics, experimental phenotyping of human and animals, moleculargenetics, high throughput functional genomics. Its design is specifically oriented towardsthe harmonization, standardization and interoperability of retinal data, protocols and clinicalpractices allowing the establishment of an effective networking systems at the Europeanlevel; (2) Identification of several novel candidate genes involved in retinal degenerationby DNA chips and proteomic analysis in dominant retinitis pigmentosa (RP) and in a severeinherited retinal disease in children(3) Retinoid dehydrogenases/reductases (RDH) catalysekey oxidation reduction reactions in the visual cycle that converts vitamin A , the chromophoreof the rod and cone photoreceptors; that the consortium has shown that mutations inRDH12, encoding a retinal dehydrogenase, result in severe and early-onset autosomal recessiveretinal dystrophy (arRD) (4) development of vectors as potential gene therapy tools.The project has already initiated a gene therapy clinical trial in a specific form of IRD.Potential Impact:EVI-GENORET will increase the scientific community’s understanding ofthe function of the retina, its cellular components, and molecular principlesas well as the mechanisms of retinal degeneration. The project aimsis to develop and validate innovative therapeutic approaches.This is a unique opportunity to implement a structured project, gatheringthe most active and experienced professional research teams on retinopathiesand basic retinal biology. The team expects will to decipheringCross-secion of the retina(microphotograph)Acknowledgement:Dr. O. Goureau, INSERM PARISFundus photograph of the humaneye Acknowledgement: Dr. S.Mohand-Saïd, INSERM, PARISFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life375

EVI-GENORETthe mechanisms underlying retinal diseases, and setting up functional assays which will contributeto advance practical development of therapeutics. EVI-GENORET has great potentialfor breakthroughs at each of the many incremental steps towards integrated system biologyas well as in the outcome measures. Thus, with the potential impact on public health, it willconvince basic and applied scientists of the importance of such concerted effort.The goal, at the completion of the project, is to help integrate a broad and in depth understandingof the function and interactions of major cells and gene networks, thereby proposingfunctional models. The unique knowledge base on molecular networks thus generatedwill facilitate identification and validation of novel therapeutic targets of broad interest.Developing stem cell culture methods and new approaches to gene and drug deliverymechanisms is expected to provide novel tools for future therapeutic interventions after testingin this privileged organ.Keywords:vision, gene expression, retinal developement, photoreceptors, age-related macular degeneration(AMD), retinal dystrophies, animal dystrophies, animal mutants, genotype-phenotype-correlationPartnersProject Coordinator:Prof. Jose-Alain SahelInstitut National de la Santé et de la RechercheMédicale (INSERM) U592Laboratoire de Physiopathologie Cellulaire etMoleculaire de la RetineInstitut de la VisionCHNO des Quinze-vingts,17 rue Moreau,75012 Paris, Francej-sahel@quinze-vingts.frProject Scientific Manager:Dr. Olivier LorentzINSERM Transfert SA7, rue Watt75013 Paris, Franceolivier.lorentz@st-antoine.inserm.frProject Administrative Manager:Dr. Thomas Wheeler-SchillingEuropean Vision Institute EEIGBrussels, BelgiumProf. Jose-Alain Sahel, Dr. Thierry Leveillard,Dr. Serge Picaud, Dr. Olivier Goureau,Dr. Josseline Kaplan, Dr. Christian Hamel,Dr. Francine Behar-Cohen, Dr.Frédéric Mascarelli,Dr. Ségolène AyméInstitut National de la Santé et de la RechercheMédicale (INSERM)Laboratoire de Physiopathologie Cellulaire etMoléculaire de la RétineParis, FranceProf. Shomi Bhattacharya, Prof. Alan Bird, Dr. Robin Ali,Dr. John Greenwood, Dr. Stephen MossUniversity College LondonInstitute of OphthalmologyLondon, UKProf. Eberhart Zrenner, Dr. Mathias Seeliger,Dr. Frank Schuettauf, Dr. Bernd Wissinger,Dr. Ulrich SchrayermeyerEberhard-Karls-Universitaet TuebingenUniversity Eye HospitalTuebingen, GermanyProf. José Cunha-VazAibili - Associação Para Investigação Biomédica EInovação Em Luz E ImagemCNTM - Centro De Novas Tecnologias Para A MedicinaAzinhaga De Santa Comba - CelasCoimbra, PortugalDr. Sandro BanfiTelethon Institute of Genetics and MedicineNaples, ItalyDr. Ronald Roepman, Dr. Frans CremersThe University Medical Centre NijmegenDepartment of Human GeneticsNijmegen, The NetherlandsDr. Theodorus Van Veen, Dr. Per Ekstroem,Dr. Maria-Theréza PerezLund UniversityDepartment of OphthalmologyWallenberg Retina CenterLund, Sweden376From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Functional genomics of the retina in health and diseaseProf. Angelo Luigi VescoviUniversity of Milano BicoccaDipartimento Di Biotecnologie E Bioscienze BtbsMilan, ItalyProf. Veronica Van Heyningen, Prof. Alan WrightMedical Research CouncilMRC Human Genetics UnitEdinburgh, UKDr. Marius UeffingGSF-Forschungszentrum Fuer Umwelt UndGesundheit GmbhInstitute of Human GeneticsNeuherberg, GermanyProf. Andreas GalUniversity Hospital Hamburg-EppendorfInstitute of Human GeneticsHamburg, GermanyDr. Christian GrimmUniversity of ZurichDepartment of OphthalmologyUniversity HospitalLab For Retinal Cell BiologyZurich, SwitzerlandDr. Pascal Dolle, Dr. Olivier PochCentre Européen pour la Recherche en Biologie etMédecine-Groupement D’Intérêt Economique(CERBM-GIE)Institut de Génétique et de Biologie Moléculaire etCellulaire (IGBMC)Illkirch, FranceDr. Kader ThiamGenowayLyon, FranceDr. Carmen AyusoFundacion Jimenez Diaz UTEDepartment of Medical GeneticsMadrid, SpainDr. Smaragda KamakariNational and Kapodistrian University of AthensSchool of Medicine, Laboratory of BiologyAthens, GreeceDr. Valeria MarigoUniversità di Modena e Reggio EmiliaDipartimento di Scienze BiomedicheModena, ItalyProf. Frank G Holz, Hendrik SchollUniversity of BonnDepartment of OphthalmologyFaculty of MedicineBonn, GermanyProf. Peter HumphriesThe Provost, Fellows and Scholars ofThe College of The Holy and Undivided Trinityof Queen ElizabethOcular Genetics UnitDublin, IrelandDr. Christina FasserRetina InternationalZurich, SwitzerlandDr. Frank MuellerResearch Centre Juelich GmbhInstitute for Biological Information ProcessingJuelich, GermanyDr. Geraoid TuohyGenable Tehnologies LtdSmurfit Institute of GeneticsTrinity College DublinDublin, IrelandProf. Usha ChakravarthyQueens University BelfastOphthalmology and Vision ScienceBelfast, UKFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life377

7.3STEMCELLSFunGenESPLURIGENESESTOOLSEuTRACC

FunGenESwww.fungenes.orgProject Type:Integrated ProjectContract number:LSHG-CT-2003-503494Starting date:1 st March 2004Duration:46 monthsEC Funding:8 500 000State-of-the-Art:Current knowledge of the genetic mechanisms regulating pluripotency and differentiation islimited. While many of the conditions that facilitate lineage commitment and differentiationare known, an in-depth understanding of the underlying genetic programmes is lacking.FunGenES aims to systematically identify genes that are involved in different aspects ofdevelopment, such as maintenance of pluripotency, formation of the three germ layers andfurther differentiation into somatic lineages. An approach of this scale has not previouslybeen attempted, and therefore there is considerable potential for advancing the field.The FunGenES consortium addresses fundamental issues of stem cell biology and functionalgenomics, pursuing an integrated strategy based on cultured mouse embryonic stem (ES)cells. Traditionally, studies in developmental genetics have used a variety of animal models.These studies are time-consuming and their results cannot be directly compared, due to theheterogeneity of methods and species used. In contrast, the FunGenES approach usingcultured murine ES cells, offers a standardised, well-characterised, in vitro model of pluripotencyand differentiation.Scientific/Technological Objectives:FunGenES will identify the gene subsets that are active at different stages of ES cell differentiation.Its major objective is to produce a gene expression atlas covering the developmentof ES cells into all three germ layers (ectoderm, mesoderm and endoderm) and the varioussomatic cell types.More specifically, the consortium has several objectives, inclusive of the following: (1) Developinga detailed understanding of ES cell self-renewal, differentiation and lineage commitment,and identifying potential novel target genes for therapeutic intervention; (2) Derivingnew molecular and cellular tools for characterising gene function in tissue-specific cellpopulations; (3) Developing new ES cell-based methods for high throughput screening ofsmall candidate molecules for therapeutic applications in human diseases.Expected Results:FunGenES expects to deliver the following results:1) A phenotypic and expression profile atlas of cell lineage commitment from the pluripotentstate (ES cells) to the three major germ lineages. Based on the information in thisatlas, the intention is to develop a detailed understanding of the following items: (i)The genetic mechanisms and extrinsic and intrinsic signalling cascades responsiblefor ES cell proliferation and self-renewal; (ii) The molecular basis of pluripotency; (iii)The processes determining fate from precursors to differentiated cells; (iv) The mechanismof mesodermal commitment, and identification of master genes, extrinsic andintrinsic signalling cascades and transcription factors involved in the determinationof cardiac cells, endothelial cells, adipocytes, osteoblasts and haematopoietic cells;(v) The mechanism of ectodermal commitment and identification of master genes,extrinsic and intrinsic signalling cascades and transcription factors involved in thedetermination of neurons and glial cells; (vi) The mechanism of endodermal commitmentand identification of master genes, extrinsic and intrinsic signalling cascades380From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Functional Genomicsin Engineered ES cellsand transcription factors involved in determination of hepatocytes and insulin producingβ-cells.2) Determination of gene expression patterns at landmark differentiation points in ESderivedsomatic cell lineages.3) Engineered ES cell lines, including physiological information on the behaviour ofthese cells.4) A set of standard operating procedures, to be used for the following purposes: (i)Use of ES cell models and differentiation protocols; (ii) Technical tools (RNA preparation,standard formatted chips for gene expression analysis, bacterial artificialchromosome methods, endoribonuclease-prepared small interfering RNA methods);(iii) Data analysis using bioinformatics and cluster gene analysis.Potential Impact:New knowledge about the genetic pathways that underlie the differentiation of ES cells tosomatic cells will contribute to novel therapeutic strategies for human diseases that are characterisedby the irreversible loss of functional cells. Potential clinical applications includetissue and cell transplantation, and new therapies for diseases such as cancer, liver disease,diabetes and cardiovascular and neurodegenerative diseases.Murine ES cells represent a valuable tool for understanding developmental processes andfor screening for embryo-toxicology without the use of animals. They are therefore expectedto have a major impact on drug development, considering that the high failure rate in thisprocess is the result of toxicity in both the early and late phases of development, includingclinical trials. These failures increase the costs of drug development dramatically, and raiseethical concerns.From Fundamental Genomics to Systems Biology: Understanding the Book of Life381

FunGenESBasic research on murine ES cells is a highly competitive field which offers the prospect ofeconomic growth in Europe, as long as technological tools, diagnostic targets and longtermdrug development are successfully translated into advances in clinical science. Growthis expected to occur in the following areas in the near future: ES cell developmental biologyand genomics tools, drug development and gene and cell therapy.Keywords: functional genomics, murine embryonic stem cells, differentiation,gene atlas, cellular, stem cellsPartnersProject Coordinator:Prof. Jürgen HeschelerUniversity of CologneInstitute of NeurophysiologyFaculty of MedicineRobert-Koch-Str. 3950931 Cologne, Germanyj.hescheler@uni-koeln.deProject Manager:Annette RingwaldARTTI58A, rue du Dessous des Berges75013 ParisFranceDr. Laurent PradierAventis Pharma Recherche-Développement,(now Sanofi-Aventis)Neurodegenerative Disease GroupGenomics DepartmentVitry sur Seine, FranceDr. Pierre SavatierInstitut National de la Santéet de la Recherche Médicale (INSERM)Unité 371 “Cerveau et vision”Bron, FranceDr. Antonis HatzopoulosGSF-Research Center for Environment and HealthGSF-Institute of Clinical Molecular Biology and TumorGenetics - Laboratory of Vascular GeneticsMunich, GermanyDr. Lesley Margaret ForresterUniversity of EdinburghJohn Hughes Bennet Laboratory / Division of OncologySchool of Molecular and Clinical MedicineWestern General HospitalEdinburgh, UK382From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Functional Genomics in Engineered ES cellsDr. Timothy E. AllsoppStem Cell Sciences LtdRoger Land BuildingEdinburgh, UKDr. Matthias AustenDeveloGen AktiengesellschaftStem Cell ResearchGoettingen, GermanyDr. Norbert Hübner, Michael BaderMax-Delbrück-Center for Molecular MedicineMolecular Biology and GeneticsBerlin, GermanyDr. Melanie J. WelhamUniversity of BathDepartment of Pharmacy and PharmacologyFaculty of Science, Laboratory of Molecular SignallingBath, UKProf. Anna M. WobusInstitute of Plant Genetics and Crop Plant ResearchCytogenetic, In vitro Differentiation GroupGatersleben, GermanyProf. Angelo Luigi Vescovi (until 31 October 2006)Fondazione Centro San Raffaele del Monte TaborDIBIT-Stem Cell Research InstituteMilan, ItalyDr. Frank BuchholzMax-Planck Institute of Molecular CellBiology and GeneticsDresden, GermanyDr. Heinz HimmelbauerMax-Planck-Institute for Molecular GeneticsDepartment of Vertebrate GenomicsAG HimmelbauerBerlin, GermanyDr. Christian Dani, Dr. Hélène BoeufCentre National de la Recherche Scientifique (CNRS)Institute of Signalling, Developmental Biologyand Cancer Research-UMR6543 (Nice)/Laboratoire Composantes innées de la réponseimmunitaire et différenciationUMR 5164 (Bordeaux)Paris, FranceProf. Domingos HenriqueInstituto e Medicina MolecularFaculdade Medicina LisboaInstituto Histologia e EmbriologiaLisbon, PortugalProf. Francis StewartTechnical University DresdenBiotec, GenomicsDresden, GermanyDr. Androniki KretsovaliFORTH, Foundation for Research & Technology HellasInstitute of Molecular Biology and BiotechnologyHeraklion, GreeceFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life383

Project Type:Specific TargetedResearch projectContract number:LSHG-CT-2005-018673Starting date:1 st January 2006Duration:36 monthsEC Funding:2 499 713PlurigenesState-of-the-Art:www.plurigenes.orgA first step towards regenerative medicine consists in finding a mean to cause controlled dedifferentiationof adult tissue. The project Plurigenes aims at achieving major breakthroughsin the discovery and understanding of the function of genes controlling pluripotency in thecentral nervous system. Plurigenes will start by identifying candidate genes in model organisms,following original approaches involving screens performed by in situ hybridisationson well-characterised neural structures or by gain-of-function analysis. Innovative technologiesof transgenesis and imaging in several model organisms will be settled to reach thisgoal. The project will first characterise the functions of candidate genes in vitro and invivo. Then, for selected genes, it will validate the possibility to restore the pluripotency ofterminally differentiated cells through transgenesis of the candidate genes. Thus, Plurigenesshould identify molecular actors and related pathways associated with pluripotency.Scientific/Technological Objectives:The overall objective of Plurigenes is to allow the dedifferentiation of differentiated neuralcells into pluripotent cells and, consequently, to improve the ability to manipulate thosecells and combat diseases, such as brain injury and/or aging. By using different animalmodels belonging to the Chordate phylum and a large panel of in vitro and in vivo methods,the project partners plan to take advantage of a multi-organism approach. In parallel,Plurigenes will improve transgenesis methods and develop novel imaging techniques inseveral model organisms.Medaka embryo hybridised witha probe for a gene signalling forcell cycle arrest (‘stop signal’)Histological section through theoptic tectum showing expressionof one gene in the arrrest zonePLURIGENES aims to identify novel (that is, so far uncharacterised) pluripotency associatedgenes in model organisms. This will be achieved through in situ hybridisation screens onfish and gain-of-function screens in ascidians on several thousands genes. It will result in30-40 genes considered as candidate regulators. The sequence identity of basal chordates’proteins with their human counterpart will allow a straightforward exploitation of the newlyisolated genes in the frame of human researches.Secondly, the consortium aims to assess the role of the latter genes in the maintenance ofpluripotency and the dedifferentiation process, using fish, mice, and human cultured cells.From the pool of 30-40 candidate genes identified, it will lead to the selection of aboutone dozen selected genes. A third objective consists of validating the physiological role ofthe selected genes in vivo. To achieve this, the expression of these genes will be perturbed(abolished, over-expressed, and mis-expressed) primarily in the nervous system of the animalmodels. The effects on the neural stem cells (NSC) and neural progenitors will also beexamined. Finally, the Plurigenes team aims to create improved methods for transgenesisand imaging in model organisms via an improvement of transgenesis. This will be achievedby using meganucleases, a very promising class of endonucleases for many applications,via the development of a novel technology for microscopy (SPIM) and the development ofhighly innovative analyses of 4D images of embryos.Expected Results:PLURIGENES aims at finding and characterising new determinants that regulate the maintenanceof the neural stem cell undifferentiated state and the reversal of differentiated neuralcells (neurons and glia) towards a neural stem cell pluripotent state. The partners predictthat several important regulators remain to be discovered, notably in the still large fractionof vertebrate predicted genes (the function of which is not presently documented), and thatthese novel actors could have many therapeutic uses. Once assayed for their dedifferentiationactivities, these newly identified genes may allow improved protocols for dedifferentia-384From Fundamental Genomics to Systems Biology: Understanding the Book of Life

tion of neural cells to be established, sole or in combination with already known factors.Other important enhancements expected from this project concern the development of newmethodologies, in particular the manipulation of gene expression (transgenesis) in modelorganisms, and innovative microscopy methods for in vivo imaging of the fate of dedifferentiatedcells.Potential Impact:Pluripotency Associated Genesto Dedifferentiate Neural Cellsinto Pluripotent CellsPLURIGENES constitutes a unique opportunity to bring together specialists in developmentalgenetics of model organisms, cellular biology of human NSC, and oncology. Comparedto programmes underway in non-European countries, the project focuses on a competitivearea. The ability to isolate and transplant NSC in vivo from differentiated cells should simplifythe development of stem cell-based therapies for a range of neurological disorders.Pathways that regulate self-renewal of normal stem cells are deregulated in cancer stemcells, resulting in the continuous expansion of cancer cells. Therefore, finding of new genefamilies involved in pluripotency should have a significant impact on pharmaceutical companiesby allowing novel strategies of anti-tumour drug design.Keywords: de-differentiation, pluripotency, transgenesis, central nervous system,regenerative medecine, model organisms, embryosPartnersProject Coordinator:Dr. Jean-Stéphane JolyInstitut National de laRecherche Agronomique (INRA)Physiologie animale etsystèmes d’élevage (PHASE)UNIT 1126. DEPSN-bt32-33 Avenue de la Terrasse91198 Gif-sur-Yvette, Francejoly@iaf.cnrs-gif.frDr. Jochen WittbrodtEuropean MolecularBiology Laboratory (EMBL)Developmental Biology UnitHeidelberg, GermanyDr. Patrick LemaireCentre National de laRecherche Scientifique (CNRS)Genetics and PhysiologyDevelopment LaboratoryMarseille, FranceDr. Filomena RistoratoreStazione Zoologica Anton DorhnNaples, ItalyProf. Manfred SchartlUniversity of WurzburgDepartment ofPhysiological ChemistryWurzburg, GermanyDr. Philippe GennesONCODESIGNDijon, FranceDr. François GuillemotMedical Research CouncilMolecular NeurobiologyLondon, UKProf. Angelo VescoviUniversity of Milano BicoccaIstituto di Ricerca per leCellule StaminaliMilan, ItalyFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life385

ESTOOLSwww.estools.euProject Type:Integrated ProjectContract number:LSHG-CT-2006-018739Starting date:1 st August 2006Duration:48 monthsEC Funding:12 000 000State-of-the-Art:ESTOOLS will significantly advance the fundamental understanding that will underpin biomedicalapplication of human embryonic stem (hES) cells. Pluripotent hES cells present aunique opportunity to study human cellular differentiation and pathogenesis. hES cells alsooffer a new resource for cellular transplantation in human degenerative disease and apowerful platform for pharmaceutical and toxicology screening. The promise of hES cellsrests largely on unlimited expansion in stem cell numbers without genetic or epigenetic compromise,and on directing differentiation with absolute phenotypic fidelity. Success entailsunderstanding the mechanisms controlling the choice between (a) proliferation and selfrenewal, and (b) apoptosis or commitment to differentiation.Genetic intervention is a key tool for delineating the molecular circuitry of hES cells. ES-TOOLS will develop the tools needed to elucidate the genetic and molecular networksthat control the self renewal, commitment and terminal differentiation of hES cells. Neuralcommitment provides a paradigm for understanding the mechanisms by which embryonicstem cells choose between self renewal and lineage commitment. Neuronal and glial differentiationof hES cells offer major new experimental avenues for cellular neurobiologyand pathogenesis, with potential eventual application in bio-industry and medicine viapharmaceutical and toxicological screening and cell replacement therapies. By characterisingprogression from embryonic stem cell through naive neuroectodermal precursors tofunctionally differentiated neuronal and glial sub-types and establishing conditions for thequantitative production of neurons and glia, ESTOOLS will provide vital new experimentalavenues for study of cellular neurobiology and neuropathogenesis. In parallel, an ethicsteam will research ethical issues pertinent to the derivation and use (including commercial)of hES cells and will engage with scientists in ESTOOLS and with stakeholders.Scientific/Technological Objectives:The overall goal of ESTOOLS is to standardise and optimise protocols for the culture of humanembryonic stem cells, to ensure their genotypic and phenotypic stability and to establishtechniques and understanding to allow their robust differentiation into functional cells ofthe neural lineage. Other objectives include:1) developing optimised culture conditions to enable standardised propagation of humanembryonic stem cells;2) permitting the use of reliable, defined serum-free culture protocols and automated cellculture systems;3) providing a toolkit of protocols and reagents for routine genetic manipulation of humanembryonic stem cells, to establish them as a genetically tractable system comparablewith mouse embryonic stem cells;4) determining mechanisms that control self renewal and commitment to differentiationof human embryonic stem cells, allowing: (a) improved techniques to monitor the geneticand epigenetic integrity of human embryonic stem cell cultures (b) developmentof culture methods that minimise the genetic instability of human embryonic stem cells(c) definition of the key parameters of epigenetic stability and variability in humanembryonic stem cells (d) development of methods to maintain human embryonic stemcells in an undifferentiated state and prevent unwanted spontaneous differentiation;5) establishing models of fate, choice and pathogenesis for the human central nervoussystem and elucidation of the molecular mechanisms, regulatory networks and key386From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Platforms for biomedical discoverywith human ES cellsNeuronal cells differentiatedfrom hES derived neural stemcells stained with beta-III tubulinpositive (green) and Hoechst33342 (blue) University ofSheffield (UK) Centre for StemCell Biology, 2006signalling pathways that govern choice between self-renewal and lineage commitment,allowing: (a) development of protocols to promote the differentiation of humanembryonic stem cells to the neuroectodermal lineage; (b) delineation of the epigeneticcontribution to lineage commitment; (c) development of new tools for geneticallymonitoring specific states of the cells from ‘undifferentiated’ to ‘lineage committedand ‘terminally differentiated’; (d) identification of conditions for the robust productionof functionally validated, mature neuronal phenotypes;6) promoting bio-industry exploitation of human embryonic stem cell biology throughsmall to medium sized enterprise (SME) partners and the biopharmaceutical sectorby developing: (a) procedures to automate biomanufacturing of human embryonicstem cells and their differentiated progeny; (b) novel monoclonal antibodies to cellsurface markers for the identification of undifferentiated human embryonic stem cellsand for monitoring their differentiation; (c) tools for neurodegeneration.Expected Results:By the end of its fourth year ESTOOLS will have established that human embryonic stemcells provide a genetically tractable system, comparable with mouse embryonic stem cells,facilitating realisation of the potential benefits that these cells offer to human health care. Thefollowing expected achievements will provide evidence for these conclusions:1) a refinement, standardisation and optimisation of the culture conditions needed topropagate human embryonic stem cells with phenotypic and genotypic fidelity and tocreate associated user-friendly and reliable protocols;2) the ability to monitor multiparametrically the genotypic and epigenotypic integrity ofhuman embryonic stem cell cultures;3) a toolkit of protocols and reagents for the routine genetic manipulation of humanembryonic stem cells;4) an understanding of the molecular mechanisms and regulatory networks that governa stem cell’s choice of self-renewal or lineage commitment;From Fundamental Genomics to Systems Biology: Understanding the Book of Life387

ESTOOLS5) a definition of the key parameters of epigenetic stability and variability in the humanembryonic stem cells;6) an understanding of the molecular process and mechanism of lineage commitment;7) a delineation of the epigenetic contribution to lineage commitment;8) an ability to direct neuroectodermal lineage choice to 90% efficiency;9) a description of the necessary conditions for robust production of functionally validatedmature neuronal phenotypes and the generation of specific classes of neuronaland glial progenitors;10) the initiation of neuro-degeneration modelling and of neuro-modulatory drugscreens;11) the introduction of quality-controlled ‘good manufacturing processes’ for human embryonicstem cells;12) procedures to automate the bio-manufacturing of human embryonic stem cells andtheir differentiated progeny.Potential Impact:Human embryonic stem cellbiology provides new tools forapplications in a wide range offields from understanding humandevelopment and diseaseprocesses to drug discoveryand toxicology and, eventually,to regenerative medicine.ESTOOLS will help realise thispotential by widening anddeepening the range of skillsand experience in human embryonicstem cell researchacross Europe. The project willplay a significant role in thedevelopment of standardisedtechniques, protocols and reagents,permitting standardisationof research with humanembryonic stem cells in Europe,and throughout the world, through the close relationship between ESTOOLS and theInternational Stem Cell Initiative. The SME partners in ESTOOLS will be the springboardfor bio-industrial exploitation of the project’s results. Future research into the mechanismsof human embryonic stem cell lineage commitment and differentiation, and developmentof biopharmaceutical industry applications - eventually for regenerative medicine - requiresthese cells to be genetically manipulated robustly in well-defined ways. Thus ESTOOLS willdevelop a genetic ‘toolkit’ to help realise the potential of human embryonic stem cell researchin Europe. ESTOOLS will contribute to the social sustainability of continuing researchand application of knowledge outputs by analysis of the ethical issues surrounding use ofhuman embryos and their stem cells in the different social contexts of European countries.Keywords:differentiation, self-renewal, neural, stem cells, human embryonic stem cells388From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Platforms for biomedical discovery with human ES cellsPartnersProject Coordinator:Prof. Peter W AndrewsUniversity of SheffieldCentre for Stem Cell BiologyDepartment of Biomedical SciencesWestern BankSheffield, S10 2TN, UKp.w.andrews@sheffield.ac.ukProject Manager:Andrew SmithESTOOLS Project Officec/o University of Sheffield - BMSWestern BankSheffield, S10 2TN, UKasmith@estools.euDr. Tim AllsoppStem Cell Sciences UK LtdCambridge, UKProf. Yves-Alain BardeUniversity of BaselBiozentrumBasel, SwitzerlandProf. Nissim BenvenistyHebrew University of JerusalemDepartment of GeneticsInstitute of Life SciencesJerusalem, IsraelProf. Riitta LahesmaaUniversity of TurkuTurku Centre for BiotechnologyTurku, FinlandDr. Jim WalshAxordia LtdSheffield, UKDr. Petr DvorakInstitute of Experimental MedicineAcademy of Sciences of the Czech RepublicPrague, Czech RepublicProf. Goran HermerenLund UniversityFaculty of MedicineLund, SwedenProf. Outi HovattaKarolinska InstitutetDepartment of Clinical ScienceIntervention and TechnologyStockholm, SwedenDr. Maarten van LohuizenNetherlands Cancer InstituteDivision of Molecular GeneticsAmsterdam, The NetherlandsProf. Timo OtonkoskiUniversity of HelsinkiBiomedicum Stem Cell CenterHelsinki, FinlandDr. Danny KitsbergSCT Stem Cell Technologies LtdJerusalem, IsraelDr. Andrew SmithUniversity of EdinburghInstitute for Stem Cell ResearchEdinburgh, UKDr. Konstantinos AnastassiadisTechnische Universität DresdenBIOTECDresden, GermanyProf. Austin SmithUniversity of CambridgeSchool of the BiologicalSciencesWellcome Trust Centrefor Stem Cell ResearchCambridge, UKDr. Meng LiImperial College of ScienceTechnology and MedicineLondonMRC Clinical Sciences CentreLondon, UKProf. Oliver BrustleRheinische Friedrich-Wilhelms-Universität BonnInstitute of Reconstructive NeurobiologyBonn, GermanyProf. Elena CattaneoUniversita Degli Studi di MilanoDepartment of Pharmacological SciencesMilan, ItalyProf. Tariq EnverMedical Research CouncilWeatherall Institute of Molecular MedicineOxford, UKDr. Manuel EstellerCentro Nacional de Investigaciones OncológicasGrupo de Epigenética del CáncerMadrid, SpainFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life389

EuTRACCwww.eutracc.euProject Type:Integrated ProjectContract number:LSHG-CT-2007-037445Starting date:1 st April 2007Duration:48 monthsEC Funding:12 000 000State-of-the-Art:The EuTRACC consortium proposes to determine the regulation of the genome by mappingthe regulatory pathways and networks of transcription factors (TFs) that control cellularfunctions. EuTRACC will be part of and work in close collaboration with the InternationalRegulome Consortium (IRC), a worldwide network that will address the regulation of genomefunction at a higher level by mapping the genetic regulatory nodes and networksthat control the activity of embryonic stem cells and the process of differentiation to specificcell types. It will focus on mapping the genetic circuitry that controls the formation of neuraltissues and the blood system. The project will utilise genetics, proteomics and genomicstools in the mouse, zebrafish and Xenopus model organisms. These approaches will allowthe characterisation of transcription factor complexes and the genome-wide identificationof binding sites for these TFs in undifferentiated and differentiated ES cells or differentiatedtissues (blood and neuronal system). It will systematically identify TF complexes and TFbinding sites in vertebrate genomes required for the differentiation into haematopoietic andneural cells. The bio-informaticians will develop novel algorithms to extract and interpret thedata and viewers to integrate the information in the ENSEMBL database. Data will be madeavailable publicly through web based platforms and tools. Databases will be constructedthat will include annotated TFs, TF-DNA interactions, protein- and RNA TF interactions andcellular regulation (gene, effect, cell type, cell state). The project databases will be interfacedwith existing micro-array databases as well as other public databases. The projectwill provide new insights into the regulation of cell function that stimulate translational research,which is critical for developing novel therapies, particularly in the areas of stem celltransplantation and tissue engineering.Scientific/Technological Objectives:1) to ensure a substantial contribution of EU based science to the field of transcriptionalregulation of differentiation and development;2) to provide strong input from the EU to the International Regulome Consortium (IRC),a worldwide consortium that represents a third generation genomics project addressingthe regulation of genome function at a higher level by mapping the geneticregulatory nodes and networks;3) to identify protein complexes of basic, general and tissue-specific TFs and interactingpartners expressed in neuronal and haematopoietic cell types;4) to use bioinformatic methods to correctly annotate mouse genes that encode bonafide TFs and interacting proteins. Microarray data will be analysed to identify TFcomplexes expressed in the selected cell types;5) to validate interactions by IPs and/or BiFC;6) to determine intracellular localisation of TFs and/or associated proteins;7) to identify target genes of the different TF complexes;8) to functionally analyse TFs and selected interacting proteins by morpholino injectionsin zebrafish and Xenopus embryos;9) to create computational procedures and models that describe the mechanism ofregulation of gene transcription in order to differentiate embryonic stem cells fromneuronal or haematopoietic cells. Specific databases and tools will be developed tofacilitate the collection, curation and analysis of the data, as well as for the publicdissemination of findings.390From Fundamental Genomics to Systems Biology: Understanding the Book of Life

European Transcriptome, Regulome &Cellular Commitment ConsortiumTechnical objectives for this application are:1) to generate 100 knock-ins of protein tags for affinity purification of TF complexes andconcurrently generate conditional TF KOs in ES cells;2) to generate homozygous null mutations in key TFs in ES cells and mice;3) to culture and differentiate TF tagged ES cells in vitro and isolate the relevant tissuesfrom ES generated mice for genomic and proteomic analyses;4) to characterise the protein components of transcriptional complexes containing thetagged TFs in selected cell and tissue types;5) to purify and identify TF binding sites in selected cell types by two approaches -chromatin affinity purification, followed by DNA amplification, and hybridisation togenome wide microarrays (Affymetrix, Agilent or Nimblegen). Fine mapping, whenrequired, will be done by in vivo footprinting.6) to repeat cycles of tagging knock-ins for affinity purification etc. by tagging selectedinteraction partners from the previous screen.Expected Results:The development of methodology to set up a ‘pipeline’ that allows:1) the tagging of the N- or C-terminus of protein via homologous recombination in EScells (and/or other cell lines) of the gene coding for the protein of interest;2) rapid affinity-based purification of proteins of interest;3) concomitant generation of conditional KO alleles of the gene coding for the protein ofinterest by inclusion of loxP sites for Cre mediated recombination in vivo or in vitro;4) two rounds of affinity purification and protease mediated release to rapidly obtainhighly purified protein complexes that can be used for a variety of functional andstructural studies;From Fundamental Genomics to Systems Biology: Understanding the Book of Life391

EUTRACC5) rapid identification of transcription factor binding sites in vivo, using the proteintags;6) rapid functional analysis using morpholinos to functionally identify the key proteinsin a TF complex;7) the generation of databases of transcription factors and interacting partners forstem cells, haematopoietic cells and neuronal cells. This will also help to improvethe predictive power of in silico prediction methods;8) the generation of algorithms to model transcription factor networks in collaborationwith IRC.Potential Impact:EuTRACC will focus on mapping the transcriptional circuitry on the molecular level and howit controls the formation of neural tissue and the blood system. Understanding the regulatorynetwork is one of the big challenges for biology in the next decade. It will provide much betterinsight into the normal and abnormal formation of stem cells and tissues and into diseaseprocesses and be an essential part of future developments in medicine and biotechnology,in particular those areas that are concerned with stem cell biology. EuTRACC will providea substantial impetus to fundamental and translational research by making its data publiclyavailable and seeking new collaborations and alliances where appropriate. The expectationis therefore that it will substantially contribute to the development of novel therapies andimproved health benefits for society. EuTRACC provides an excellent opportunity for the EUto strengthen its competitive position in this area by bringing together a group of excellentresearchers with a high level of expertise in the different areas required for a successful,comprehensive and integrated approach. Genomic research is an essential component ofan innovation-based economy, generating Intellectual Property, leading to the developmentof new technologies, providing the basis for new companies and stimulating employmentin new industries.Keywords:transcriptome, regulome, cellular commitment, transcription factors, neurobiology, hematopoiesis,embryonal developmentPartnersProject Coordinator:Prof. Dr. Frank GrosveldErasmus MC University Medical CenterDepartment of Cell Biology and GeneticsP.O. Box 20403000 CA Rotterdam, The Netherlandsf.grosveld@erasmusmc.nlProject Manager:Dr. Rini de CromErasmus MC University Medical CenterDepartment of Cell Biology and GeneticsP.O. Box 20403000 CA Rotterdam, The Netherlandseutracc@erasmusmc.nlProf A. Francis StewartBiotec, GenomicsDresden, GermanyDr. Irwin Davidson, Dr. Laszlo ToraCERBM-GIE (IGBMC)Illkirch, FranceProf. Dr. Meinrad BusslingerResearch Institute of Molecular Pathology GmbHVienna, AustriaProf. Dr. Yves-Alain BardeUniversity of BaselDepartment of NeurobiologyBasel, Switzerland392From Fundamental Genomics to Systems Biology: Understanding the Book of Life

European Transcriptome, Regulome & Cellular Commitment ConsortiumProf. Dr. Uwe StraehleInstitute of Toxicology and GeneticsForschungszentrum KarlsruheKarlsruhe, GermanyProf. Dr. Magdalena Goetz, Prof. Dr. Wolfgang WurstHelmhotz Zentrum MünchenDeutsches Forschungszentrum fürGesundheit und Umwelt GmbHNeuherberg, GermanyDr. W. SkarnesGenome Research LtdWellcome Trust Sanger InstituteHinxton, UKDr. Michael RudnickiOttawa Health Research InstituteOttawa, CanadaDr. Ferenc MüllerUniversity of BirminghamInstitute of Biomedical Research, Medical SchoolBirmingham, UKProf. Dr. Michael MeisterernstUniversity of MünsterDepartment of Medicine, Tumor BiologyMünster, GermanyProf. Dr. H. Th. M. TimmersUniversity Medical Centre UtrechtDepartment of Physiological ChemistryUtrecht, The NetherlandsProf. R. PatientUniversity of OxfordWeatherall Institute of Molecular MedicineJohn Radcliffe HospitalOxford, UKProf. J. SmithWellcome Trust/Cancer Research UK Gurdon InstituteCambridge, UKProf. C. BoniferUniversity of LeedsDivision of Experimental HaematologyLeeds Institute for Molecular MedicineWellcome Trust Brenner BuildingSt. James’ University HospitalLeeds, UKProf. Dr. M. VingronMax-Planck Institute for Molecular GeneticsDepartment of Computational Molecular BiologyBerlin, GermanyProf. Dr. R. Aasland, Dr. Boris LenhardUniversity of BergenBergen, NorwayProf. A. SimeoneCEINGE Biotecnologie Avanzate s.c.a.r.l.Naples, ItalyProf. R. Di LauroInstituto Ricerche Genetiche Gaetano SalvatoreAriano Irpino (Av), ItalyFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life393

7.4RNABIOLOGYRIBOREGFOSRAKCallimirEURASNETBACRNAsRNABIOSIROCCO

Project Type:Specific TargetedResearch ProjectContract number:LSHG-CT-2003-503022Starting date:1 st February 2004Duration:36 monthsEC Funding:2 400 000In situ hybridization of miRNAsin flower tissues ofarabidopsis thaliana usingdifferent LNA probes.RIBOREGwww.isv.cnrs-gif.fr/mc/riboregState-of-the-Art:The post-genomic era is yielding tremendous amounts of data about plant and animalgenomes and their expression. In order to exploit and understand this data it will be necessaryto determine the mechanisms leading to patterns of gene expression in differentiationprocesses. The ability to understand how gene expression varies and how cytoplasmicprocesses communicate with the nucleus to establish an overall RNA-mediated regulation isof key importance in the post-genomics phase.Riboregulators can be separated into three major classes, namely, the small (21-25nt) si/miRNAs, the long non-protein coding RNAs produced by RNA polymerase II (npc-mRNAs)and the ncRNAs produced by RNA polymerase III or pol III riboregulators (e.g. snoRNAs,SINE elements). The RIBOREG project concentrates on the identification of novel riboregulatorsinvolving all three types of riboregulators, in plants and animals.Scientific/Technological Objectives:RIBOREG aims to identify novel non-coding RNA (ncR-NA) genes linked to cell differentiation and diseaseand analyse their mechanisms of action by developinga multidisciplinary approach integrating bioinformatics,cell biology, genetics and genomic strategies.RIBOREG’s key objectives were to develop bioinformaticstools for gene mining; isolate novel regulatoryncRNAs; utilise genomics approaches to characteriseexpression patterns for these genes; identify cellulartargets of ncRNAs by screening and/or preparingmutants affected in their function in model organisms;dissect cellular mechanisms involving selected RNAsin differentiation and disease; establish cell biologicalapproaches for monitoring in vivo RNA-proteininteractions; and to validate innovative technologyfor functional and structural analysis of ncRNAs. RI-BOREG also aimed to integrate the results obtainedin different systems on the function of riboregulators. The project was therefore of extremeimportance for SMEs concerned with developing and validating tools for the analysis of thisnovel area of gene regulation. The project gave European biotechnology a lead in exploringthe potential of genome information in relation to human health.Expected Results:The main expected results were: C. elegans and A. Thaliana; Throughout the project RIBOREG published its results in scientific journals (approximately30 scientific publications with several in high-impact journals such as Molecular Cell, NatureGenetics and Science). Technological developments in the project also resulted in twopatents that were applied for in Spain by an SME partner (Biomedal); one was undertakenin collaboration with a University partner (ABC, Hungary) and the other with the SpanishNational Research Council partner (CSIC).Finally, collaboration within the RIBOREG project has led to the acceleration of the developmentof Locked Nucleic Acid (LNA) probe technology, which has allowed RIBOREG’spartner, Exiqon, to commercialise a number of products based on this technology.396From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Potential Impact:Novel non-coding RNAsin differentiation and diseaseRIBOREG’s work proves tremendously beneficial to researchers interested in genome miningand novel regulatory mechanisms, biotechnologists dealing with RNA-based productdevelopment in plants and animals, and clinicians interested in new RNA-based therapies.The project also aims to integrate the results obtained in different systems on the function ofriboregulators. In this sense, RIBOREG helps SMEs concerned with developing and validatingtools for the analysis of this novel area of gene regulation.In general, the dissemination of project achievements, combined with a possible pooling ofresources and an active networking approach contributes to the development of skills andknow-how throughout the European industrial and scientific community. The technologicalprogress stimulated by RIBOREG’s innovative solutions also provides the foundation for enhancedcooperation between SMEs and public institutions. In particular, SMEs are able tocompare their genomic approaches for the study of non-coding RNAs, and develop marketableproducts specifically suited for this purpose (as was notably the case for Exiqon andthe LNA technology and for BIOMEDAL and the c-LYTAG system). The validation of thesetechnologies is an area of considerable interest for SMEs.Keywords: non-coding RNAs, riboregulator, differentiation, diseasePartnersProject Coordinator:Dr. Martin CrespiCentre National de la RechercheScientifique (CNRS)Institut des Sciences duVégétal (UPR no 2355)Avenue de la Terrasse 191198 Gif-sur-Yvette, Francecrespi@isv.cnrs-gif.frProf. Jürgen BrosiusWestfaelische Wilhelms – UniversitaetInstitute of ExperimentalPathology ZMBEMünster, GermanyDr. Erik Antonie Cornelis WeimerErasmus Medical Center RotterdamDepartment of Medical OncologyJosephine Nefkens InstituteRMB420Rotterdam, The NetherlandsDr. Jean-Marc Deragon,Dr. Claude ThermesCentre National de la RechercheScientifique (CNRS)Gif–sur-Yvette, FranceDr. Jozsef BurgyanAgricultural BiotechnologyCentre (ABC)Plant Biology InstituteGodollo, HungaryDr. Hervé VaucheretInstitut National de laRecherche Agronomique (INRA)Unité de Biologie CellulaireVersailles, FranceDr. Peter MouritzenExiqon A/SDepartment of Functional GenomicsVedbaek, DenmarkDr. Palmiro PoltronieriBIOTECGEN SrlNovoli, ItalyDr. Angel Cebolla RamirezBIOMEDAL S.L.Sevilla, SpainProf. Javier Paz-Ares RodriguezConsejo Superior deInvestigaciones Cientificas (CSIC)Centro Nacional de BiotecnologiaMadrid, SpainFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life397

Project Type:Specific TargetedResearch ProjectContract number:LSHG-CT-2004-005120Starting date:1 st January 2005Duration:36 monthsEC Funding:1 442 000FOSRAKState-of-the-Art:www.fosrak.orgTraditionally, the focus of molecular biology and biochemistry has been on DNA and proteins.However, important findings over the last 15 years or so, suggest that the role of smallRNAs (sRNAs) in the life sciences has been significantly underestimated. In eukaryotes,sRNAs of approximately 20-25 nucleotides in length — so-called small interfering RNAs(siRNAs), and micro RNAs (miRNAs) — either induce degradation of homologous targetmessenger RNAs (mRNAs) by RNA interference, or inhibit their translation.A second, important class of non-coding RNAs, involved primarily in the modification ofribosomal RNAs (rRNAs) and small nuclear RNAs (snRNAs), is the small nucleolar RNAs(snoRNAs) of eukaryotes and archaea. There are indications that some snoRNAs act onhitherto unidentified cellular mRNAs. Equally of interest, is the high prevalence of regulatoryRNAs in bacteria. Bacterial sRNAs regulate specific functions in plasmids, phages andtransposons. Bacterial chromosomes encode many non-coding RNAs, most of which appearto regulate target genes by antisense mechanisms. In Escherichia coli, sRNAs controlstress responses, while in Staphylococcus aureus they control virulence.Spontaneous systemicspreading of silencingof a GFP (greenfluorescent protein)transgene in aNicotiana benthamianaleaf. Red areasindicate loss of GFPexpression.RNAs act as regulators of gene expression and also perform other activities, often aided byproteins. Creating a division between bacterial and eukaryotic systems can be detrimental forthe development of a profound understanding of RNA biology. By contrast, it proves extremelyfruitful to bridge the gap between different experimental systems, organismic backgroundsand scientific cultures. FOSRAK aims to develop an understanding of the peculiarities of eachsystem. Furthermore, the team plans to ascertain what the fundamental similarities are betweenthe functions of regulatory RNAs across kingdoms. Europe is currently lagging behindin the field of RNA biology, and FOSRAK intends to make headway in closing that gap.Scientific/Technological Objectives:FOSRAK addresses the recently recognised importance of sRNAs in organisms acrosskingdoms, and the mechanisms of gene regulation by which they control physiologicalresponses, developmental checkpoints and virulence in several human pathogens. The generalobjective is to advance knowledge of sRNAs beyond the state-of-the-art, but also, morespecifically, to explore their potential for application in the prevention or treatment of humandiseases.The project has several specific aims, summarised below: (1) Identification of moleculartargets for various RNAs acting in gene regulation (regulatory RNAs); (2) Characterisationof protein components that are part of the cellular machinery, and are involved in thefunctionality of small regulatory RNAs; (3) Understanding the mechanisms by which smallregulatory RNAs recognise and interact with their cognate molecular targets; and (4) Decipheringthe biological role of different classes of small regulatory RNAs and their generalfunctional significance in regulating gene expression.Expected Results:Elucidation of the major aspects of RNA biology across kingdoms, and understanding thesimilarities and differences in RNA-mediated molecular mechanisms between organisms,are among the expected results of FOSRAK. During the first stage of the project, tremendousprogress was made relating to the identification of experimentally validated or strongly predictedtargets for miRNAs, imprinted miRNAs and regulatory RNAs in protists and bacteria(non-pathogenic and pathogenic). The enzymology of proteins associated with, or requiredfor, the functioning of regulatory RNAs, has been another focus of the project so far. Forinstance, the role of the Hfq protein in bacteria, the roles of Dcr, helicases, RDRs and Agoproteins in RNAi/miRNA-dependent regulation, and the role of ribonucleases in RNA metabolismand regulation, have proved fruitful areas of investigation.398From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Function of small RNAs across kingdomsPotential Impact:The identification of the targets of regulatory RNAs and mechanistic studies,will have critical implications for our understanding of cellular gene expression.The project also deals with the potential role of small regulatory RNAs inhuman diseases, research that may influence the development of RNA-basedtherapeutics.FOSRAK will contribute to conceptual and technological advances, such as thedevelopment of a bioinformatics platform for the prediction of sRNA targets,and the use of sophisticated instruments (e.g. scanning force microscopy andbiosensors), which are not yet being used as standard methods for the analysisof RNA-RNA and RNA-protein interactions.Keywords: regulatory RNA, non-transcriptional gene regulation,Dicer, non-coding RNA, bioinformatics, fundamental genomics, functionalgenomics, gene expression, structure analysis, miRNA, snoRNAPartnersProject Coordinator:Prof. E.Gerhart WagnerUppsala UniversityDepartment of Cell andMolecular BiologyBiomedical CenterHusargatan 575124 Uppsala, SwedenGerhart.Wagner@ICM.UU.SEProf. Wolfgang Nellen,Christian HammannUniversität KasselFaculty of Natural SciencesInstitute of BiologyLaboratory of GeneticsKassel, GermanyDr. Martina PaulsenUniversität des SaarlandesFR 8.3 BiowissenschaftenGenetik / EpigenetikSaarbrücken, GermanyProf. Martin Tabler †, Dr. Kriton KalantidisFoundation for Researchand Technology - HellasRNA laboratoryHeraklion, GreeceDr. Michael WasseneggerRLP AgroScience GmbH,AIPlanta-Institute for Plant ResearchGene Silencing and EpigeneticsNeustadt/Weinstrasse, GermanyProf. Witold FilipowiczFriedrich Miescher Institute forBiomedical ResearchBasel, SwitzerlandDr. Bastian ZimmermannBiaffin GmbH & Co KGFaculty of Natural SciencesInstitute of BiologyKassel, GermanyUpper left: Electron microscopypicture of Escherichia coli cells(artificially colored)Upper right: 3D model of thecatalytically active hammerheadribozymes in Arabidopsis thaliana(acc. to Przybilski et al., 2005,Plant Cell). The catalytic centreis shown in green and orange,and the tertiary interacting apicalloops are in magenta.Lower left: Schematic model ofantisense RNA inhibition of ribosome“standby” in control of abacterial toxin (acc. to Darfeuilleet al., 2007, Mol. Cell).Lower right: Example of a lead(II)probing experiment; binding of acomplementary RNA to its targetsite results in a “footprint” onthe 5’-end-labeled mRNA (tworight-hand lanes).Dr. Pascale RombyCentre National de la Recherche Scientifique (CNRS)UPR 9002 CNRS-SMBMR “Structure desMacromolecules et Mecanismes deReconnaissance Moleculaire”Institut de Biologie Moleculaire et CellulaireStrasbourg, FranceDr. Fredrik SöderbomSwedish University of Agricultural SciencesDepartment of Molecular BiologyUppsala, SwedenFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life399

Callimirwww.fmv.ulg.ac.be/genmol/Callimir_Page/Callimir_home.htmProject Type:Specific TargetedResearch ProjectContract number:LSHG-CT-2004-005255Starting date:1 st January 2005Duration:36 monthsEC Funding:958 849State-of-the-Art:Schematic representation of the Dlk1-Gtl2 imprinted domain:Key elements are depicted: paternally expressed genes inblue, maternally expressed non coding RNA, including clustersof snoRNA and miRNA in red, localization of two regulatoryelements, the callipyge mutation (yellow dot) and the intergenicdifferentially methylated region (IG-DMR, black dot whenmethylated, white dot when unmethylated).Brackets and numbers represent animal models currentlyanalysed: [1] the callipyge sheep (left picture) and twotransgenic mice lines for this mutation; [2] amouse model with a deletion of the IG-DMR; [3]several mouse models targeting each miRNA ofthe antiPeg11 gene as well as introducing a stopcodon in the Rtl1/Peg11 gene; [4] a mouse modelcarrying a conditional deletion of the entire miRNAcluster in Mirg.In addition to the protein-encoding messenger RNA (mRNA), genome transcription generatesa flurry of so-called non-coding RNA genes, including ribosomal RNAs, transfer RNAs,small nuclear and small nucleolar RNAs (snRNAs and snoRNAs respectively). This familyhas recently witnessed a spectacular expansion, with the discovery of a multitude of smallRNA species that are involved in RNA interference-related biology (including micro RNAs,or miRNAs), and long, non-coding RNA species of unknown function.The aim of Callimir is to decipher the biological role of non-coding RNA genes by studyingthe imprinted Dlk1-Gtl2 domain, due to this domain possessing one of the highest densitiesof miRNAs in the mammalian genome. The region contains several long, non-coding RNAgenes exclusively expressed by the maternal allele, which are the hosts of a very largenumber of snoRNAs and miRNAs. A series of unique genetic mutants will permit the studyof these non-coding RNAs.Scientific/Technological Objectives:The Dlk1-Gtl2 domain is an evolutionarily conserved,1 megabase cluster of imprinted genes thatcontains at least three protein-encoding genes expressedby the paternal allele (Dlk1, Rtl1, Dio3), aseries of non-coding RNA genes expressed by thematernal allele (Gtl2, Meg8, Mirg), and multiple,small, non-coding RNA genes. The latter includea pair of miRNA genes (mir127 and mir136) thatare antisense to Rtl1, a cluster of snoRNA genesprocessed from the introns of Meg8, and a clusterof miRNA genes processed from a large precursortranscript (Mirg). Callimir intends to analyse thebiological function of miRNA in Mirg, and the roleof Mirg miRNAs in mediating the CLPG trans effect.Callimir aims to elucidate the function and modeof action of these miRNA genes, by studying thenature of their interaction and the consequences oftheir elimination. Due to an existing battery of unique reagentsalready available or generated as part of the project, the consortiumis well-equipped to determine the role of mir127 andmir136 in regulating the expression of Rtl1, and to analyse thedevelopmental roles of Rtl1 and mir127/136.Expected Results:There have been several major achievements within the project’sfirst year:1) For the first time, there has been demonstration of the roleof miRNA-mediated RNA interference in regulating imprintedgenes.2) Using multicolour RNA FISH at the single nucleus level, therehas been demonstration that non-coding RNAs transcribedfrom the Dlk1-Gtl2 domain form large elongated ‘nucleartrack’ structures, and accumulate as single-molecule nuclearRNA foci within the interchromatin space.400From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Studying the biological role of microRNAsin the Dlk1-Gtl2 imprinted domain3) A comparative evolutionary analysis identified the origin and identity of membersof the Rtl1/Peg11 gene family in the mammalian genome. The hypothesis that thisretrotransposon-like gene plays a role in conferring imprinting was tested and disproved.4) By studying a muscular hypertrophy in sheep, the Callimir consortium has identified animportant novel class of mutations that affect the interaction between miRNAs and theirtargets. Bioinformatics analyses of SNPs databases for human and mice has demonstratedthat mutations creating or destroying putative miRNA target sites are abundant, andmight be important effectors of phenotypic variation. A publicly accessible databasewith this information compiled on it, has been created - http://www.patrocles.org/Potential Impact:Callimir is studying fundamental biological mechanisms related to the role and mode ofaction of miRNAs. It has been demonstrated recently that miRNAs regulate as much as athird of our genes, if not more. Hence miRNAs play a key role in orchestrating and finetuningmammalian gene expression, and perturbation of miRNA-mediated gene regulationcontributes to disease.The Callimir consortium has unique genetic models, either created by genetic engineeringor discovered as naturally-occurring oddities, which express mutations that perturb miRNAmediatedgene regulation, causing complex phenotypes. These models will allow the studyof the mechanisms of miRNA-mediated gene regulation in vivo. In addition, the Patroclesdatabase, which compiles mutations that have the potential to perturb miRNA-target interactionsand hence gene regulation, in a variety of species including man and mouse, will beof benefit to the genetics community at large.Keywords: micro RNA, sno RNA, imprinting, callipygePartnersProject Co-Coordinators:Dr. Michel Georges,Dr. Carole CharlierUniversity of LiègeUnit of Animal GenomicsFaculty of Veterinary Medicine1 Avenue de l’Hôpital4000 Liège, Belgiummichel.georges@ulg.ac.becarole.charlier@ulg.ac.beDr. Jérôme CavailléCentre National de la RechercheScientifique (CNRS)Laboratoire de Biologie Moléculairedes EucaryotesUMR 5099Toulouse, FranceProf. Anne Ferguson-SmithUniversity of CambridgeDepartment of PhysiologyDevelopment & NeuroscienceCambridge, UKFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life401

EURASNETwww.eurasnet.euProject Type:Network of ExcellenceContract number:LSHG-CT-2005-518238Starting date:1 st January 2006Duration:60 monthsEC Funding:10 000 000State-of-the-Art:The rationale behind the sequencing of the human genome and that of other model organismsstemmed from the assumption that, by knowing the content of the genetic material, itwould be possible to understand the processes that control development and reproductionin living organisms. This would consequently lead to better insights into how these processesare altered in disease.The concept of the gene is central for the understanding of these issues. The “dogma” ofmolecular biology has classically treated a gene, as a genetic unit directing the synthesis ofa single protein product. From this perspective, the genetic program of an organism is dictatedby the subset of genes transcribed into RNA and translated into protein in a particularcell or at a particular time during development.Schematic overview of the geneexpressionpathway in eukaryoticorganisms. The genome islocated in the cellular nucleuswhere it is transcribed and thepre-mRNA is formed. Afterseveral RNA processing steps(including splicing) the maturemRNA is transported to thecytoplasm where protein productionproceeds (translation).One of the most surprising results of the human genome project and of similar projects onother metazoan genomes was the surprisingly low number of protein-coding genes found.A dramatic gap was noted between the possibly only 25 000 protein-coding genes andthe observed huge diversity of the human proteome, that is, the complete spectrum of allexpressed protein forms in the cell. This figure has to be placed at least in the order of100 000 proteins. The “missing diversity” on the DNA level is compensated for by thealternative mRNA-splicing mechanism. This posttranscriptional event affects most humangenes and is responsible for the creation of potentially thousands of distinct proteins froma single gene.A eukaryotic gene encoding the message used for the production of a protein during translationis composed of various DNA segments: protein coding exons alternate with DNAsequences that do not carry a protein coding function (introns). During the first step of geneexpression, DNA is transcribed into messenger RNA (mRNA). While the primary RNA tran-402From Fundamental Genomics to Systems Biology: Understanding the Book of Life

European Alternative SplicingNetwork of Excellencescript still contains both the exonic and the intronicsequences, only a mature mRNA without intronicsequences can serve as a template for ribosomalprotein synthesis. The process which removes theintrons from the primary mRNA transcript is calledpre-mRNA splicing. Introns are excised and theremaining exons are joined to form a continuousstretch of protein-coding sequence.Pre-mRNA splicing not merely removes introns, italso serves as a unique mechanism to create proteindiversity. During the splicing process not all ofthe exons are retained in the mature mRNA, someexons are either included or excluded, the inclusionof exons can be mutually exclusive, and forother exons there exists a large set of variants of which only one is selected for inclusion. Byemploying such a combinatorial approach, alternative splicing creates a variety of distinctproteins from one single gene. Protein variants (isoforms) thus created often have distinctand often antagonistic functions.Consequently, alternative splicing can greatly expand the information content of genomes,and understanding the mechanisms that lead to alternatively spliced transcripts willbe essential for a functional interpretation of genomic sequences. We will not be ableto decipher the genetic program of a higher eukaryotic genome unless we understandthe rules leading to the generation of alternatively spliced transcripts and the functionaldiversity they provide.The splicing reaction is catalyzed in the cell nucleus by a highly complex molecular machine,the spliceosome. The spliceosome is an RNP (for ribonucleoprotein) machine composedof several RNAs and numerous proteins organized in several distinct subcomplexeswhich are themselves RNP particles. A plethora of highly dynamic RNA-RNA, RNA-proteinand protein-protein interactions holds together this intricate mechanism. The recognitionand selection of the intron-exon borders (that is the substrates of the splicing reaction), theassembly of the spliceosome and the structural and functional remodelling the spliceosomeundergoes during the course of the splicing reaction, are all part of an extraordinarily complicatedprocess.It is therefore not surprising that alternative splicing during recent years has been increasinglyrecognized as the causative agent or as a severity modifier behind an everincreasing number of human pathologies, including cancer, neurodegenerative diseases,viral infection and inflammatory responses. Current conservative estimates assume thatmore than 15% of genetic diseases are caused by aberrant splice events. Our currentunderstanding of alternative splice events still lacks sufficient insight into the molecularmechanisms of the combinatorial action of multiple regulators that govern splice site selection.Also the interplay between alternative splicing and other cellular processes requiresenhanced research efforts.Thirty leading laboratories in the field of pre-mRNA splicing and splicing regulation havejoined efforts to create a Network of Excellence. These groups cover a wide range ofcomplementary expertise including computational, biochemical, proteomic, genomic, cellbiologicaland organism-biological approaches to the study of post-transcriptional generegulation and its alterations in disease.Alternative splicing dramaticallyincreases the complexityof the proteome.From Fundamental Genomics to Systems Biology: Understanding the Book of Life403

EURASNETThe primary purpose of this network will be to develop an integrated approach to the studyof alternative splicing that will (1) provide durable structures that will change the way researchin this research topic is carried out in Europe, (2) establish an ambitious, innovativeand multidisciplinary program of joint research activities with high impact, and (3) spreadexcellence within Europe, disseminate knowledge about alternative splicing in the molecularbiology and medical communities, and foster public awareness of genomics and RNAresearch and their applications.Scientific/Technological Objectives:EURASNET aims not only to improve our knowledge of alternative splicing but also to raiseawareness on alternative splicing related issues, particularly in the health science community.Mis-splicing and disease:The Joint Program of Research has a strong focus on alternative splicing events and regulatorymechanisms related to genetic disease or influencing disease progression. Our understandingof signals involved in the mis-regulation of splice events is incomplete. Moreover, theiroften elusive nature as mutations not resulting in obvious amino acid changes complicatesdiagnostics and therapeutic strategies of aberrant splicing. Regulatory splicing factors andtheir disease-dependent changes in abundance and tissue-specific concentration will be scrutinized.Data on particular diseases is still too sparse and, in order to establish the concept of “RNAand Disease”, a wide range of diseases needs to be surveyed. Deciphering the regulatorynetworks of cell-type specific alternative splicing, governed by expression and regulation ofsplicing factors and their isoforms associated with a particular pathology, poses a problemaddressable through the concepts and tools of systems biology. In parallel therapeutic strategiesto correct splicing defects will be developed.Development of High-Throughput-Enabling Technologies:Another important Network activity comprises development and application of High-Throughput-EnablingTechnologies for the study of alternative splicing, in particular of microarraysfor the detection of alternative splice forms and the screening of small chemical compoundlibraries. Most of the currently available microarray designs ignore the fact that the majorityof genes in higher eukaryotes generates multiple mRNAs that encode proteins with distinct,sometimes opposite functions. Therefore results from such designs are at best incomplete, ifnot misleading. Analyzing the full complement of cellular transcripts under different biologicalor pathological conditions requires microarray platforms able to distinguish between alternativelyspliced mRNAs. EURASNET envisions the task of establishing these microarrays as oneof the key contributions of EURASNET to European scientists, regardless of whether they arein the splicing field or not, and to the clinicians.A second Network effort is directed towards high-throughput identification of compounds thatinhibit or modulate specifically the splicing reaction. An initial explorative phase will comprisethe development of an assay with suitable fluorescence readout for screening purposes andthe screening of small to medium-sized chemical libraries. Selecting appropriate target reactionsand the right class of chemical compound are then preconditions for large-scale screening.While exhaustive screens for compounds useful as therapeutic agent for specific splicingdefects associated with a human disease are clearly beyond the scope of this Network, thevalidation of the general screening strategy will help to raise interest among potential commercialpartners to engage in further collaborative studies.The alternative splicing databaseEURASNET research requires close communication and joint activities between computerbiologists and experimentalists. The mere task of accurate intron identification in eukaryotic404From Fundamental Genomics to Systems Biology: Understanding the Book of Life

European Alternative Splicing Network of Excellencegenomes still poses a considerable challenge. Even more so the prediction, which potentiallyalternatively spliced mRNA will appear in which tissue and under what conditions. The explodingnumber of mRNA and EST sequences and high-throughput enabling technologiesproducing large data sets of transcripts, their structure, abundance, tissue distribution anddevelopmental specificity, require a strong bioinformatics infrastructure to secure the acquisitionof quality data in user-friendly databases and to ensure efficient data analysis which inthe long run wants to become a highly predictive analysis of splice signals and regulatoryelements.The Young Investigator ProgramAs part of the Network’s integration activities, young investigators and their research will beintegrated.Expected Results:As the outcome of EURASNET research activities the team expects: i) a significant numberof important publications (estimated 150 publications in the five years period) ii) a severalfoldincrease in high impact joint publications by members of the network iii) the developmentand optimization of experimental designs and technological platforms applicable tostudies of alternative splicing in a variety experimental systems. In particular, standards forHigh-Throughput technologies like microarrays and small-compound screening will be developed.iv) the development of user-friendly software of high predictive power to supportthe experimental design of experimentalists.Potential Impact:The ambitious, innovative and multidisciplinary Joint Programme of activities of EURASNETwill give a massive impetus to progress in elucidating the mechanisms of alternative splicingand will thus greatly enhance the scientific community’s understanding of one of themost important steps in the expression of genetic information. Insights into this process area prerequisite for allowing us to decipher, and ultimately to predict, the genetic programof eukaryotic genomes. EURASNET and its Young Investigator Program (YIP) will also playan important role in making Europe attractive for young and talented scientists in the field.Moreover, it will ensure their integration into the “alternative splicing” community and, onaccount of the importance of this field today, it will in turn make a significant contribution tothe spread of sustained excellence within European life sciences.The information generated from the activities of this NoE canrealistically be expected to have a significant impact, not onlyon the academic research community, but also on the industrialresearch and medical communities. Further, developmentsresulting from the information generated by EURASNET willform an important knowledge base that ultimately will aidpublic policy makers in making decisions that will shape thesocio-economic future of our society. Efforts by EURASNETwill also contribute to the enhancement of public awarenessof genomics and RNA research, with corresponding indirectbenefits to society as a whole. EURASNET represents a consortiumof many of the world’s best laboratories investigatingthe process of alternative splicing and its implications for humanhealth.Transcribed genes localize in closeproximity two nuclear specklesKeywords: alternative RNA splicing, RNA splicingFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life405

EURASNETPartnersProject Coordinator:Prof. Reinhard LührmannMax-Planck Institute for Biophysical ChemistryDepartment of Cellular BiochemistryAm Fassberg 1137077 Göttingen, GermanyReinhard.Luehrmann@mpi-bpc.mpg.deProject Manager:Dr. Reinhard RauhutMax-Planck Institute for Biophysical ChemistryDepartment of Cellular BiochemistryAm Fassberg 1137077 Göttingen, GermanyReinhard.Rauhut@mpi-bpc.mpg.deDr. Karla NeugebauerMax-Planck Institute of MolecularCell Biology and GeneticsDresden, GermanyDr. Henning UrlaubMax-Planck Institute for Biophysical ChemistryGöttingen, GermanyDr. Juan ValcárcelCentre de Regulació GenòmicaRegulation of Alternative Pre-mRNA SplicingBarcelona, SpainProf. Stefan StammFriedrich-Alexander-Universität Erlangen-NürnbergInstitute for BiochemistryErlangen, GermanyProf. Göran AkusjärviUppsala UniversityDepartment of Medical Biochemistryand Microbiology (IMBIM)Faculties of Medicine and PharmacologyUppsala, SwedenDr. Peer BorkEuropean Molecular Biology Laboratory (EMBL)Structural and Computational Biology ProgrammeHeidelberg, GermanyDr. Rolf Apweiler,European Molecular Biology Laboratory (EMBL)European Bioinformatics Institute (EBI)Sequence Database GroupHinxton, UKDr. Gil AstTel Aviv UniversityDepartment of Human GeneticsTel Aviv, IsraelProf. Francisco E. BaralleInternational Centre for Genetic Engineeringand BiotechnologyMolecular Pathology GroupTrieste, ItalyProf. Andrea BartaMedical University ViennaDepartment of Medical BiochemistryVienna, AustriaProf. Jean BeggsUniversity of EdinburghInstitute of Cell BiologyEdinburgh, UKDr. Giuseppe BiamontiConsiglio Nazionale delle Ricerche (CNR)Istituto di Genetica MolecolarePavia, ItalyProf. Glauco Tocchini-ValentiniConsiglio Nazionale delle Ricerche (CNR)Istituto di Biologia CellulareMonterotondo Scalo, ItalyProf. Albrecht BindereifJustus Liebig Universität GiessenInstitut für BiochemieGiessen, GermanyProf. Jamal Tazi, Dr. Edouard BertrandCentre National de la Recherche Scientifique (CNRS)Institut de Genetique Moleculaire(JRU 5535 CNRS-UMII)Montpellier, FranceDr. Bertrand SéraphinCentre National de la Recherche Scientifique (CNRS)Centre de Genetique Moleculaire (CGM), UPR2167Gif-sur-Yvette, FranceDr. Christiane BranlantCentre National de la Recherche Scientifique (CNRS)UMR 7567 CNRS-UHPMaturation des ARN et Enzymologie Moléculaire MAEMVandoeuvre les Nancy, FranceProf. Daniel SchümperliUniversität BernInstitut für ZellbiologieBern, Switzerland406From Fundamental Genomics to Systems Biology: Understanding the Book of Life

European Alternative Splicing Network of ExcellenceDr. John W.S. BrownScottish Crop Research InstituteGene Expression Programme - RNA Processing LabDundee, UKDr. Javier Fernando CáceresMedical Research CouncilMRC Human Genetics UnitEdinburgh, UKProf. Maria Carmo-FonsecaInstituto de Medicina MolecularCell Biology UnitLisbon, PortugalProf. Ian EperonUniversity of LeicesterDepartment of BiochemistryLeicester, UKProf. Artur JarmolowskiAdam Mickiewicz University in PoznanDepartment of Gene Expression / Institute ofMolecular Biology and Biotechnology (IMBB)Poznan, PolandProf. Jørgen KjemsUniversity of AarhusDepartment of Molecular BiologyAarhus, DenmarkProf. Hermona SoreqHebrew University of JerusalemDepartment of Biological ChemistryInstitute of Life SciencesJerusalem, IsraelDr. James StéveninCentre Européen de Recherche enBiologie et Médecine – GIEInstitut de Génétique et de BiologieMoléculaire et Cellulaire (IGBMC)Illkirch, FranceDr. Didier AuboeufInstitut National de la Santé etde la Recherche (INSERM)AVENIR/Inserm U685Centre Hayem-Hôpital Saint LouisParis, FranceDr. Davide GabelliniFondazione Centro San Raffaele del Monte TaborMilan, ItalyDr. Mihaela ZavolanBiozentrum, University of BaselISB-SIB RNA Regulatory Networks GroupBasel, SwitzerlandProf. Alberto R. KornblihttUniversidad de Buenos AiresDepartamento de FisiolgíaBiología Molecular y CelularBuenos Aires, ArgentinaProf. Angela KrämerUniversité de GenèveDépartement de Biologie CellulaireGeneva 4, SwitzerlandProf. Angus LamondUniversity of DundeeDivision of Gene Regulation & ExpressionSchool of Life SciencesDundee, UKDr. Christopher SmithUniversity of CambridgeDepartment of BiochemistryCambridge, UKFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life407

BACRNAsProject Type:Specific TargetedResearch projectContract number:LSHG-CT-2005-018618Starting date:1 st February 2006Duration:36 monthsEC Funding:2 599 988State-of-the-Art:From being regarded as a minor class of RNAs, non-coding RNAs (ncRNAs - mostly antisenseRNAs) have recently emerged as ubiquitous players in important life processes inanimals, plants, fungi and metazoans. Similarly, over 85 small ncRNAs, encoded by theEscherichia coli genome, have recently been identified, while others are being discoveredin many bacterial species. Many of these RNAs play key roles in global regulatory networks.The BACRNAs consortium investigates novel ncRNAs and their targets (messengerRNA (mRNA) and proteins) in several representative pathogens and analyses their roles inthe establishment of bacterial pathogenicity. Infection studies using cell cultures will allowthe validation of ncRNAs and their targets in virulence. Exploration of structural and mechanisticaspects of ncRNAs will elucidate how they interact with those targets. This researchwill lead to an understanding of how regulatory ncRNAs are integrated into the generalnetwork that controls stress responses, host adaptation and bacterial virulence.Scientific/Technological Objectives:1) Many non-coding RNAs act as antisense RNAs, via a base-pairing mechanism, whereassensor elements, mostly located in the 5’ untranslated region (UTR) of mRNA, canact as ‘riboswitches’. The consortium focuses mainly on ncRNAs that belong to thesetwo classes, and that are implicated in the regulatory networks controlling bacterialpathogenicity. It develops tools for the identification, characterisation and structuralanalysis of ncRNAs in pathogenic bacteria, as well as for the identification and validationof targets (virulence factors) controlled by ncRNAs involved in virulence.2) Current studies have reported a growing number of small RNAs, including ncRNAsthat play key roles in the regulation of fundamental adaptive processes such ascell-to-cell communication (quorum sensing), transition to the stationary phase, ironhomeostasis and bacterial virulence. The BACRNAs project aims to elucidate howregulatory RNAs are integrated into the general network of pathogenesis controlwhilst also taking into account other mechanisms such as response and adaptation tobacterial stress or changing environment.3) The determination of the most relevant virulence factors amenable to drug developmentis the concluding step within the present BACRNAs project. The relevance todrug development is determined by the ability of small molecules to bind virulencefactors. These small molecules (compounds) on one hand are needed to verify thefunctionality and on the other the modification ability of identified virulence factors.The outcome describes the prove-of-concept and builds the basis for further drugdevelopment by the pharmaceutical industry. Therefore the analysis of the virulencemechanism that is triggered by ncRNAs, as well as the expression/regulation ofvirulence factor and its influence to pathogenicity needs to be investigated by theconsortium. Further information on drug design will be guided by structural informationprovided by nuclear magnetic resonance techniques.Expected Results:The consortium expects to see the following results: (1) Development of tools for the identification/analysisof ncRNAs involved in bacterial pathogenicity; (2) Identification of ncRNAs408From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Non-coding RNAsin Bacterial Pathogenicityinvolved in bacterial pathogenicity; (3) Identification of targets (virulence factors) controlledby ncRNAs involved in virulence; (4) Identification of the structure of the ncRNAs as well asthe regulatory mechanisms of ncRNAs involved in bacterial pathogenicity and (5) Validationof novel targets for therapy and initial identification of compounds that interfere withthe function of those targets.Potential Impact:The project has set its sights on facilitating the establishment of European leadership in theinnovative field of regulatory RNAs. It aims to generate fundamental knowledge that can betranslated directly into new therapeutic strategies. The identification of novel drug targetsbuilds the basis to develop new drugs and thus to combat widespread bacterial infections.Keywords: antisense RNA, non-coding RNA, biochemistry, antimicrobial agents,regulatory networks, bacterial virulencePartnersProject Coordinator:Prof. Renée SchroederUniversity of ViennaDepartment of Biochemistry“Max F. Perutz Laboratories”Dr Bohr Gasse 9/51010 Vienna, Austriarenee.schroeder@univie.ac.atDr. Pascale RombyCentre National de la RechercheScientifique (CNRS)UPR 9002 CNRS-ARN“Architecture et réactivité des ARN”Strasbourg, FranceProf. Pascale CossartInstitut PasteurUnité des Interactions Bactéries-CellulesParis, FranceProf. Gerhart WagnerUppsala UniversityDepartment of Cell and MolecularBiology (ICM), Biomedical CenterUppsala, SwedenDr. Jörgen JohanssonUmeå UniversityDepartment of Molecular BiologyUmeå, SwedenDr. Shoshy AltuviaHebrew Universityof JerusalemInstitute for MicrobiologyJerusalem, IsraelMs Brigitte RohnerBrigitte Rohner punktVienna, AustriaFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life409

RNABIOProject Type:Specific Support ActionContract number:LSSG-CT-2006-037604Starting date:1 st July 2006Duration:4 monthsEC Funding:22 500State-of-the-Art:RNA molecules such as microRNAs, riboswitches, or regulatory RNAs in bacteria (broadlycalled noncoding RNAs or ncRNAs) have become extremely active areas of research inbasic science such as cell development, cancer and therapeutic research. The prediction ofthe secondary structure of an RNA molecule is the most extensively studied aspect in computationalmethods for ncRNAs. Despite this, the accuracy in predicting secondary structureis limited (56 to 76 percent). Alternatives to standard models are probabilistic models, thesystematic use of comparative analysis, and the incorporation of known 3D structures. RNAbioinformatics is now following two paths.The first is structure-based analyses in which three-dimensional structures are central. Thesecond is sequence-based analyses in which sequence and sequence recognition dominatethe analysis. These two paths are running parallel courses at the moment, but they willsoon converge. This must occur if scientists are to fully understand RNA evolution and therelationships between sequence, structural folding and reactivity. Science is now facingnew challenges in trying to identify the function of these ncRNAs. For this to happen, it isnecessary to refine the algorithms involved so that structures can be systematically searchedin genomes and reliably predicted. The result will be that homology searches for ncRNAscan take into account the overall structure, alignment algorithms for RNA structure and willbe fast enough to search whole databases.Scientific/Technological Objectives:A workshop entitled ``Computational approaches to noncoding RNAs’’ and organizedby Elena Rivas (Washington University, USA) and Eric Westhof (University Louis Pasteur,France) was held in Benasque (Spain) from the 16th of July to the 28th of July 2006. It gathereda group of 55 researchers mostly theoreticians and computational scientists workingon problems related to the computational analysis of functional and regulatory RNAs.The main objectives of the RNABIO workshop were:1) To present and discuss the state of RNA computational biology, to identify the needsand to propose new developments for the identification, annotation and the computationalanalysis of functional and regulatory RNAs present in genomes.2) To try to identify the function of ncRNAs. In order to do this it is necessary to refine algorithmsin order to perform structure predictions reliably and do research on ncRNAsthat take into account the structure and alignment algorithms for RNA structures andare fast enough to search whole databases. This permits, for instance, the alignmentof thousands of ribosomal RNA molecules.3) To identify new ncRNAs, which may lead to novel regulator mechanisms.4) For biologists working on RNA to make reliable annotations of eukaryotic genomes.5) To make grammatical models to describe RNAs, to provide more information on theparameters of the models, along with more complex objective functions to describethe nature of a functional RNA.6) The development of improved methods for the efficient classification of short RNAs(using techniques such as support vector machines).7) To create statistical modelling of new high throughput data in the RNA context.8) To relate genome location of small RNAs to RNA type (eg through characterisingclustering behaviour).410From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Expected Results:One major problem with ncRNA prediction has been that they require substantially more computertime than the methods employed for more traditional protein coding gene finding, whichcan exploit much more regular search patterns. However, the recent progress in ncRNA genediscovery promises to reduce search time significantly.Secondary structures predicted by various methods are at variance with the fact that RNAs arethree-dimensional molecules. Thus, basepairing can be impossible due to steric clashes. An attemptto approach this problem is currently being planned. The result will be the incorporation ofa model for the RNA backbone, using directional statistics, into the secondary structure prediction.This should weed out impossible structures and could, in time, be extended to do ab initio3D prediction of RNA structures.The data produced on RNA is made freely available without restrictions through web pages anddatabase downloads. The computational RNA community already makes heavy use of Rfamdata as training and testing sets for developing algorithms. Both RNA databases, Rfam andmiRBase are heavily used by genome annotation projects, and miRBase is central to the rapidgrowth and progress of microRNA research. One of the expected results of the project is to makesuch resources far more community oriented by hosting diverse data types on the database. TheRNA bioinformatics community are immensely supportive and the RNABIO workshop proved tobe very efficient at generating and maintaining ideas and collaborations to this end.Potential Impact:Computational approachesto non-coding RNAsNow, several groups, especially in Europe, have been involved in developingcomputational methods which seek simultaneously to align and fold two or moreRNA sequences while screening - eg two genomes or matching up regions withlow sequence similarity.The major outcome was to valuate the state of RNA computational biology,to identify the needs, and to propose new developments for the identification,annotation, and the computational analysis of functional andregulatory RNAs present in genomes. The long- term goal of applyingsuch methods is to help identify ncRNA genes or structural elements,which will have an important impact on phenotypes,diseases and production traits in domestic animals.Keywords: microRNAs, riboswitches,noncoding RNAsPartnersProject Coordinator:Prof Eric WesthofCentre National De La Recherche Scientifique (CNRS)Université Louis PasteurInstitut de biologie moléculaire et cellulaireARN ‘Architecture et Réactivité de l’ARN’15 Rue Rene DescartesF-67084 Strasbourg, Francee.westhof@ibmc.u-strasbg.frFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life411

Siroccowww.sirocco-project.euProject Type:Integrated ProjectContract number:LSHG-CT-2006-037900Starting date:1 st January 2007Duration:48 monthsEC Funding:11 781 445Secondary siRNA production inplants and animals. BaulcombeDC Amplified silencing Science2007 Jan 12;315(5809):199-200.State-of-the-Art:RNA silencing is the natural ability of a cell to turn off genes. Only a few years ago it wasunknown, but now RNA silencing is one of the most powerful tools available to researchers.Recent discoveries have revealed a previously unknown role for RNA (ribonucleic acid). Theyhave shown how, in addition to the previously understood role as a cellular messenger thatdirects protein synthesis, RNA can also silence expression of genes. By introducing specificsilencing RNAs into an organism, the expression of genes can be turned down in a controlledway. The phenomenon of RNA silencing is thought to have evolved as a defence mechanismagainst viruses. In primitive cells it was a type of immune system that could recognize and thensilence viral genes. Later in evolution the silencing mechanism was recruited for switching offgenes involved in normal growth of cells and responses to stress. Small regulatory RNAs (sR-NAs) are the mediators ofRNA silencing and areimportant integrators ofgenetic, epigenetic andother regulatory systems.They are the focus of theSIROCCO programme.sRNAs have been referredto as the dark matter of genetics:a recently discoveredmass of moleculesthat crucially affect thebehaviour of the geneticuniverse through interactionsat the RNA level.The exploitation of sRNAsoffers many opportunitiesfor improving the diagnosisand therapy of humandisease and for advancesin biotechnology.sRNAs fall into two major classes: i) short interfering RNAs (siRNAs) which are 21-24 nucleotideRNAs derived from long double-stranded RNA and ii)microRNAs (miRNAs) which arederived from transcripts containing partially double-stranded stem-loop “hairpin” structuresabout 70 nucleotides long. Both are cleaved from their precursor RNA by double strandedRNA-specific endonucleases. One strand of the resulting small RNA is loaded into RNAinducedsilencing complex (RISC) that also contains Argonaute (AGO) proteins. Binding tothe correct Argonaute protein is necessary for cleavage of the target messenger RNA. siRNAsand miRNAs have been found in a variety of organisms including plants, fruit flies, zebrafish,mice, and humans. sRNAs are also a useful tool in the laboratory, where they can be used tosilence gene expression (RNA interference).Scientific/Technological Objectives:The overall objectives of the SIROCCO project are:1) Create catalogues of sRNAs from healthy and diseased cells. Novel sRNAs will412From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Silencing RNAs:organisers and coordinatorsof complexity in eukaryotic organismsbe identified through using a combinationof bioinformatics and high throughput sequencing.2) Determine the tissue- and cell-type pattern ofmiRNA expression using microarray, RNAblot and in situ hybridisation methods3) Fully refine methods for sRNA detection.These detection methods will be enhancedusing locked nucleic acid-containing andother oligonucleotide probes, and by modifiedPCR methods.4) Characterise proteins and subcellular compartmentsrequired for sRNA processing andactivity. At present, there is a foundation ofknowledge about miRNAs, but very little isknown about siRNAs. Genetic, biochemicaland imaging approaches will be usedto fully characterise the molecular machinesresponsible for both miRNA and siRNA biogenesis5) Dissect sRNA regulatory networks. It isknown that miRNAs may affect particulartarget mRNAs but how their activity fits intomore complex regulatory networks is poorlyunderstood. Developing this understandingis one of the major objectives of the SIROC-CO programme.6) Identify rules for sRNA efficiency and specificity.The RNA-silencing efficiency of sR-NAs will be determined by assay of sRNAs,their precursors or their DNA in transgenicorganisms, in cell cultures or in vitro7) Explore delivery methods for sRNAs or sRNA precursors.Fig.1Fig.2FIGURE 1: Somite-specificexpression of miR-206. Mouseembryo (E10.5) was hybridisedto an LNA oligonucleotidescomplementary to miR-206.The blue staining indicates thevery specific accumulation ofmiR-206 in the somites.Wheeler G, Valoczi A, HaveldaZ, Dalmay T. In situ detection ofanimal and plant microRNAs.DNACell Biol. 2007 Apr;26(4):251-5.FIGURE 2: RNA silencing of agreen fluorescent protein.The red areas illustrate how asignal of silencing is spreadingout of the veins in a leafof Nicotiana benthamiana.Eventually the signal spreadsthroughout the plant.Efficient use of sRNAs as pharmaceuticals will depend on the development of methods fortheir efficient delivery into cells and animals. Current technology uses modified viruses tointroduce siRNAs into cells to reduce expression of a target gene. In the later stages of theproject, the SIROCCO consortium will initiate research into the suppression of genes implicatedin various diseases.The mechanism of RNA silencing must be thoroughly understood in order to use RNA as adrug without side effects. It is also necessary to understand more about the role of silencingRNAs in normal growth and development. That information will then allow us to use thepresence of silencing RNAs to diagnose disease states in a cell.Expected Results:The SIROCCO consortium will investigate the stages in growth, development and diseasethat are influenced by sRNAs. The project can be considered to have three overlappingphases. The first is descriptive and will continue throughout the programme. This phaseaims to describe the full complement of sRNAs in a range of organisms and cell types andFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life413

SIROCCOcorrespondingly to develop a complete understanding of the proteins that act as enzymes,co-factors and structural components of the sRNA machinery.The second phase involves testing the function of sRNAs and sRNA-related proteins inthe basic sRNA mechanisms, and eventually establishing their role in regulatory networksthrough experimental intervention. Genetic and molecular methods will be used to manipulatethe expression of these components, while biological assays and molecular profiling ofRNA will be used to assess the role of the targeting components.In the third, predictive phase of the programme, the aim will be to develop rules to describethe behaviour of sRNA systems as isolated regulatory modules and as part of complexregulatory networks. Component activities in this phase will involve the computation of rulesand their validation by experimentation. It will be possible from this phase to design sRNAmimics of natural sRNAs, and to predict their effects in cells and organisms. It will also bepossible to predict the behaviour of cells or organisms in which the sRNA machinery isregulated by developmental or external stimuli.Potential Impact:RNA silencing technology has enormous potential for use as a therapeutic agent in thetreatment of infectious diseases and for any condition involving the mis-regulation of geneexpression. It is known that different microRNAs can function as tumour suppressors or oncogenesand that their expression levels have diagnostic and prognostic significance. Therole of small RNAs in complex neuropathological disorders such as schizophrenia and inneurodegenerative conditions such as Alzheimer’s Disease is being investigated by membersof the SIROCCO consortium. Diagnostic or therapeutic advances in these areas wouldhave powerful public health implications.The SIROCCO consortium aims to understand and exploit the diversity of sRNA mechanisms.The elucidation of the genomics of sRNA and of sRNA-based regulation will leadto novel and fundamental insights into the composite genetic networks that underlie normaland diseased growth and development. Achieving these aims will reinforce Europeancompetitiveness in fundamental research and innovation and will solve important societalproblems relating to public health by improving diagnosis and treatment of diseases.Keywords:RNA silencing, microRNA, RNA interference, short interfering RNA, developmental biology,molecular biology, gene expressionPartnersProject Coordinator:Prof. David BaulcombeThe Sainsbury LaboratoryJohn Innes CentreNorwich, NR4 7UH, UKdavid.baulcombe@sainsbury-laboratory.ac.ukProject Manager:Dr. Aileen HoganThe Sainsbury LaboratoryJohn Innes CentreNorwich, NR4 7UH, UKaileen.hogan@sainsbury-laboratory.ac.ukDr. József BurgyánAgricultural Biotechnology CentreInstitute of Plant Biology, Molecular Virology GroupGodollo, Hungary414From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Silencing RNAs: organisers and coordinators ofcomplexity in eukaryotic organismsDr. Annick Harel-BellanCentre National de la Recherche Scientifique (CNRS)FRE 2944 - Epigenetique et cancerInstitut André LwoffVillejuif, FranceDr. Olivier VoinnetCentre National de la Recherche Scientifique (CNRS)UPR 2357Institut de Biologie Moléculaire des PlantesStrasbourg, FranceProf. Witold FilipowiczFriedrich Miescher Institute for Biomedical ResearchBasel, SwitzerlandDr. René KettingNetherlands Institute for Developmental BiologyHubrecht LaboratoryUtrecht, The NetherlandsDr. Detlef Weigel, Dr. Elisa IzaurraldeMax-Planck Institute for Developmental BiologyTübingen, GermanyDr. Gunter MeisterMax-Planck Institute for BiochemistryLaboratory for RNA BiologyMartinsried, GermanyProf. Jørgen KjemsUniversity of AarhusDepartment of Molecular BiologyAarhus, DenmarkProf. Xavier EstivillCenter for Genomic Regulation (CRG)Genes and Disease ProgramBarcelona, SpainProf. Caroline DeanJohn Innes Centre, Norwich Research ParkDepartment of Cell & Developmental BiologyNorwich, UKDr. Michael WasseneggerAlPlanta-Institute for Plant ResearchNeustadt, GermanyDr. Peter MouritzenExiqon A/SResearch and DevelopmentVedbaek, DenmarkDr. Stephen CohenTemasek Life Sciences Laboratory LtdNational University of SingaporeSingapore, Republic of SingaporeProf. Thomas MeyerMax-Planck Institute for Infection BiologyBerlin, GermanyDr. Gyorgy Hutvagner, Dr. Simon ArthurUniversity of DundeeDundee, UKDr. Tamas DalmayUniversity of East AngliaSchool of Biological SciencesNorwich, UKProf. Irene Bozzoni. Prof Giuseppe MacinoUniversity of Rome ‘La Sapienza’Rome, ItalyDr. Eric MiskaUniversity of CambridgeWellcome Trust/Cancer Research UK Gurdon InstituteCambridge, UKProf. Roberto Di LauroBIOGEM Biotecnologie Avanzate s.c.a r.l.Laboratory of Animal GeneticsNaples, ItalyFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life415

7.5CHRONOBIOLOGYEUCLOCKTEMPO

Project Type:Integrated ProjectContract number:LSHG-CT-2006-018741Starting date:1 st January 2006Duration:60 monthsEC Funding:12 299 389EUCLOCKState-of-the-Art:www.euclock.euBehaviour, physiology and biochemistry are temporally structured, and therefore generatedaily oscillations. These cycles are not driven simply by external changes (such as thechanges of light/dark or warm/cold), but are controlled by an endogenous clock that existsin the most diverse organisms, from cyanobacteria to humans. In real life, this circadianclock is synchronised with the outside world by rhythmic environmental signals, called ‘zeitgebers’,through a process called entrainment. Circadian rhythms exist at all levels of biology.They are present, for example, in rest, arousal or vigilance activities; in temperature,urinary output, blood pressure or heart rate; in enzyme activity, hormone concentrations orgene expression. Previous experiments have shown that circadian rhythms continue even inthe absence of environmental time cues. This internal ‘day’ is self-sufficient but not entirelyindependent from the external day. A critical feature of the clock is its synchronisation withthe external day. This so-called entrainment is the key to understanding the circadian clockand its control mechanisms. Human beings rarely experience constant conditions and, as aconsequence, any research on humans entails concentrating on the entrained state.EUCLOCK, a large research network, was launched in January 2006. Its main aim is toinvestigate the circadian clock in different organisms, from cells to humans. More specifically,the project seeks to understand how circadian clocks synchronise with their cyclicenvironment.Scientific/Technological Objectives:Within this field of research, EUCLOCK investigates the circadian clock in the context ofentrainment. The project aims to understand, for example, the misalignment between internaland external time, as a consequence of shift-work, as well as insufficient entrainmentowing to age-related changes, both elements which can have a strong impact on health andwell-being. A major objective of EUCLOCK is to enable large-scale, non-invasive studies(the CLOCK-watcher device) that can prove or disprove the efficacy of medical treatmentof pathologies, ranging from heart diseases to cancer, using 24-hour monitoring of impactof these treatments.Expected Results:In EUCLOCK, European researchers join forces to investigate the circadian clock under entrainment.Utilising the most advanced methods of functional genomics and phenomics, theteam will compare genetic model organisms and humans. Important findings, such as theprerequisites for large-scale, non-invasive research on human entrainment as well as the firstanimal models for shift-work, will be developed. As with 20% of the human working population,flies and mice will likewise be exposed to ‘shift work’ schedules, i.e. will be active andfeed out of phase, with respect to their natural rhythms. The ensuing ‘dys-entrainment’ willbe investigated at different levels, from genes to behaviour, so as to provide insights intothe prevention of negative consequences of human shift-work.New genetic components that control the circadian clock and its entrainment will be identified(both in animals and humans). Moreover, new tools will be developed and new circadianmodel organisms will be explored. These findings will enable the field of chronobiologyto exploit the advantages of systems’ biology research on circadian timing, and to performand integrate the findings at the level of the genome, the proteome, and the metabolome.The innovations of EUCLOCK are predestined to shape the future of circadian research.418From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Entrainment of the Circadian ClockPotential Impact:Contributions to standardsThis IP uses an entirely novel approach tounderstanding entrainment of the circadianclock. It will, therefore, establish standardson several levels.A tissue bank from EUCLOCK lab subjectswill be established. The EUCLOCK websitewill compile the accumulating data ontissue-specific clock gene expression underdifferent entrainment of dys-entrainmentprotocols. The integrated use of many differententrainment protocols will producestandard operating procedures, for means of investigating the effects of clock genepolymorphisms on the endogenous daily programme, from behaviour, to physiology,and to molecules. The first-time use of dawn and dusk simulation in entrainment will havewide-ranging consequences on how entrainment will be investigated in all circadianmodel systems.The first-time use of forced dys-entrainment protocols will set new standards for animalmodels for shift work research. The development of a “Real Life Routine” (CLOCK-watcher),will provide researchers of the human clock with a standard set of parameters thatare useful and meaningful, when the daily programme of humans is investigated in fieldexperiments (e.g. in shift workers).Our results concerning circadianly effective light environments will be shared (via anadvisory committee) with the European lighting industry.Impact on European scienceThe circadian clock was discovered in Europe. With the advent of molecular genetics,the centre of gravity in circadian biology shifted from Europe to the USA. This IP nowsupports a developing area of European scientific expertise (the accumulative impactfactor of EUCLOCK’s scientists is well over 11,000, with an average of 420), andimportantly lends financial support in an area where dedicated financial funding in allEuropean countries cannot match corresponding funding in the USA.Impact on European healthcareEUCLOCK will contribute significantly to the understanding of how the different partsof the circadian clock come together to form an entrained system, from molecules tobehaviour. These insights will form an essential basis for understanding all temporalaspects of normal physiology and of pathology. They will also contribute to developingchrono-pharmacological interventions.Impact on Europe’s societal problems and economyModern society creates conditions which frequently challenge the optimal function of thecircadian clock. For example, approximately 20% of employees have shift- or night-workschedules; this creates enormous societal problems. Any measure intended to counteractthe detrimental effects of shift-work, must encompass both health and sociological issues(e.g. who undertakes the responsibility of childcare while one of the parents is workingnight shifts?). In order to solve these problems (e.g. through the development of bettershift schedules) the bio-medical sciences need to strongly communicate with the socialsciences. The management of EUCLOCK will facilitate bridges between its own basicscience approaches, and the approaches of other networks which deal with the cognitiveand social aspects of daily work (e.g. the Daimler-Benz-network, “Optimising thedaily structure of work”).Due to their ‘mal-entrained’ circadian clocks, shift-workers show reduced vigilance (bothin night and other shifts), and suffer from health problems. The consequences are farreaching,in terms of both societal and economic costs, due to reduced productivity, faultyFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life419

EUCLOCKworkmanship, absenteeism and increasedhealth problems upon retirement, not tomention mistakes and accident rates. Theresults of EUCLOCK could therefore vitallyimpact on work productivity.EUCLOCK will also increase the potentialfor development and optimisation ofindustrial products. For example, lightingconditions have profound effects on circadianentrainment in particular, and onhuman health in general. By developingthe potential for measuring the humanclock in real life, we enable scientific approachesto test new products, which aimto improve entrainment.Added value in carrying out the work at aEuropean levelAt the end of the last century, attentionin the field was focused on the searchfor the molecules and intracellular regulatorymechanisms of the circadian clock— with great success. As a consequence,a consortium of US universities (the NSFCenter for Biological Timing) was established,which has now completed operations,concluding 10 years of success.The next critical step will be EU-based.EUCLOCK is poised to become the preeminentchronobiological ‘power’ of thenew century.The objectives and aims of EUCLOCK canonly be implemented if many laboratories,specialising in different circadian aspectsand methods, cooperate with clearly definedSOPs. This can work only if resources aredrawn Europe-wide.Keywords:Triangle plot of the NPAS2 gene variants.circadian clock, shift work models, light, entrainment,chronobiology, animal modelsPartnersProject Coordinator:Prof. Till RoennebergLudwig Maximilians UniversityInstitute for Medical PsychologyGoethstr. 31Munich, Germanyroenneberg@lmu.deProf. Urs AlbrechtUniversity of FribourgDepartment of MedicineFribourg, SwitzerlandDr. Howard CooperInstitut National de la Santé et de laRecherche Médicale (INSERM)Unite 371, Cerveau et VisionBron, FranceProf. Rodolfo CostaUniversity of PaduaDipartimento di BiologiaPadova, ItalyProf. Dominicus G.M. BeersmaUniversity of GroningenDepartment of ChronobiologyGroningen, The NetherlandsProf. Charlotte FörsterUniversity of RegensburgInstitut für Zoologie/Entwicklungsbiologieund ChronobiologieRegensburg, GermanyProf. Russel FosterUniversity of OxfordNuffield Laboratory of OphthalmologyCircadian and Visual Neuroscience GroupOxford, UKProf. Achim KramerCharité Universitatsmedizin BerlinInstitute of Medical ImmunologyBerlin, GermanyProf. Charalambos KyriacouUniversity of Leicester,Department of GeneticsLeicester, UKDr. Johanna MeijerLeiden University Medical CenterDepartment of NeurophysiologyLeiden, The Netherlands420From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Entrainment of the Circadian ClockProf. Thomas MeitingerGSF Institute of Human GeneticsGSF Nat. Res. CentreNeuherberg, GermanyProf. Andres MetspaluEstonian BiocentreGene Technology LaboratoryTartu, EstoniaProf. Dr. Andrew MillarUniversity of EdinburghInstitute of Molecular Plant ScienceEdinburgh, UKProf. Ferenc NagyPlant Biology InstituteBiological Research CenterSzeged, HungaryDr. Pat NolanMedical Research CouncilMammalian Genetics UnitNeurobehavioural GeneticsOxfordshire, UKDr. François RouyerCentre National de la Recherche Scientifique (CNRS)Institute de Neurobiologie Alfred FessardGif-sur-Yvette Cedex, FranceProf. Ueli SchiblerUniversity of GenevaDepartment of Molecular BiologyGeneva, SwitzerlandProf. Debra SkeneUniversity of SurreyNeuroendocrinology GroupGuildford, UKDr. Konstantin DanilenkoChronobiology CentreInstitute of Internal Medicine SB RAMSNovosibirsk, RussiaDr. Emma PerfectLUX BiotechResearch and Development DepartmentEdinburgh, UKUwe StrobelTechnical Light Control DevelopmentLichtblickBonstetten, GermanyProf. Hans-Peter LippNewBehavior AGZurich, SwitzerlandAnand KumarPersonal Health InstInt. VOFAmsterdam, The Netherlands,Dr. Juha HintsaSowoon TechnologiesLausanne, SwitzerlandDr, Jakob WeberBuehlmann Laboratories AGSchonenbuch, SwitzerlandProf. Ralf StanewskyQueen Mary, University of LondonSchool of Biological andChemical SciencesLondon, UKDr. Alena SumovaThe Academy of Sciences of the Czech RepublicInstitute of PhysiologyDepartment of Neurohumoral RegulationsPrague, Czech RepublicDr. G.T.J. van der HorstErasmus MC-RotterdamDepartment of Cell Biology and GeneticsRotterdam, The NetherlandsProf. Dr. Anna Wirz-JusticeUniversity of BaselUniversity Psychiatric Clinics / Centre for ChronobiologyBasel, SwitzerlandFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life421

TEMPOwww.chrono-tempo.orgProject Type:SME- Specific TargetedResearch ProjectContract number:LSHG-CT-2006-037543Starting date:1 st October 2006Duration:36 monthsEC Funding:2 086 720State-of-the-Art:Non-communicable, chronic diseases represent the bulk of morbidity, disability and prematuredeaths in Europe, and account for 75 per cent of disability-adjusted life years. Amongthose diseases, cancer is the second most important cause of morbidity and mortality. Differencesin the molecular characteristics of tumour cells, as well as differences in patients’genetic make-up, gender, age, lifestyle and circadian rhythms, account for large variabilityin the time-course of cancer and in patients’ responses to treatment.Scientific/Technological Objectives:The general objective of TEMPO is to design mouseand in silico models that reflect this variability andallow the prediction of optimal chronotherapeuticdelivery patterns for anti-cancer drugs.Schematic representation ofcellular circadian rhythms.Expected Results:TEMPO combines functional genomics, proteomics,cell signalling, systems biology and pharmacokineticsto optimise the therapeutic index in patients.This index in turn determines the chronotherapeutics schedules, according to whichtemporal delivery patterns of the same anticancer drug vary. Each schedule is adjustedto a different dynamic class of temporal genomics and phenomics parameters, relating tointerwoven circadian and cell division cycles as well as drug metabolism. The multidisciplinarynature of the consortium means that in vivo, in vitro and in silico approaches will beintegrated to achieve this end.Potential Impact:TEMPO epitomises the translationof basic research findingsinto useful clinical applications.Through the identification ofnodes in the interplay betweenthe circadian timing system,the cell division cycle and drugpharmacology parameters, itwill provide critically importantinformation for the targeted developmentof new anti-cancerdrugs.Programmable in time drugdelivery pump.Keywords:cell cycle, circadian clock422From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Temporal Genomicsfor Tailored ChronotherapeuticsPartnersProject Coordinator:Dr. Francis LéviInstitut National de la Santé et de laRecherche Médicale (INSERM)U776 - Rythmes biologiques et cancersHôpital Paul BrousseAvenue Paul-Vaillant Couturier 1494807 Villejuif, Francelevi-m@vjf.inserm.frProject Manager:Dr. Isabelle GeahelINSERM - Transfert SAEuropean Project Management DepartmentRue de Tolbiac 10175654 Paris, FranceProf. Franck DelaunayCentre National de la Recherche Scientifique (CNRS)Université de Nice - CNRS UMR 6348Bâtiment de Sciences NaturellesPhysiologie cellulaire et moléculaire dessystèmes intègresNice, FranceProf. Laurent MeijerCentre National de la Recherche Scientifique (CNRS)Laboratoire Mer et Sante UMR7150Station Biologique - Amyloïds and Cell Division CycleRoscoff, FranceDr. Jean ClairambaultInstitut National de Recherché en Informatiqueet Automatique (INRIA)Rocquencourt Research Unit -Teams Bang and ContraintesLe Chesnay, FranceProf. Stefano IacobelliConsorzio Interuniversitario Nazionaleper la Bio-oncologiaLaboratory of molecular oncology center ofexcellence on aging Ce. S.I.Chieti, ItalyDr. Marco PirovanoH.S. Hospital Services S.p.A.Therapeutic deliveryAprilia (Latina), ItalyDr. Todor VujasinovicHelios Biosciences SarlCréteil, FranceDr. Christophe ChassagnolePhysiomics PlcThe Magdalen CentreOxford, UKCircadian rhythms in cellularproliferation in humans.From Fundamental Genomics to Systems Biology: Understanding the Book of Life423

7.6BIOLOGY OF PROKARYOTESAND OTHER ORGANISMSBACELL HEALTHDIATOMICS

BACELL HEALTHProject Type:Specific TargetedResearch ProjectContract number:LSHG-CT-2004-503468Starting date:1 st March 2004Duration:48 monthsEC Funding:2 000 000State-of-the-art:Pre-genomic research in cell biology has yielded a wealth of knowledge about individualregulatory pathways and metabolic processes that are obligatory for the survival of pathogensin their host, and for the productivity of microbes in industrial bioprocesses. The majorchallenge for the BACELL HEALTH consortium, using state-of-the-art post-genomic technologies,is to understand how individual regulatory pathways are networked to maintain cellularhomeostasis. The networking of individual regulatory pathways ensures that the cellprovides a balanced response to stress, sensing both the magnitude of the stress, and theeffectiveness of the response. In the case of pathogens, the identification of key nodes inthese regulatory networks will provide new targets for the development of antimicrobialcompounds that perturb or disrupt the cell stress management system. For industrial productionstrains, the inactivation of stress-induced processes that limit the production of heterologousproteins will lead to the development of a new generation of host/vector systems forthe production of pharmaceutically-active proteins.Scientific/Technological objectives:The BACELL HEALTH consortium aims to unravel the integrative cell stress-management systemsand stress-resistance processes required to sustain a bacterial cell when exposed tothe types of environmental insults that are encountered in two very specific environments —macrophages and industrial fermentors. Although both of these environments induce genericstress responses, they also induce non-overlapping specific stress responses (eg. pH, iron andoxidative stress in the case of macrophages, protein synthesis, secretion and nutrient stressin the case of industrial fermentations). A specific scientific objective is to determine howthe induced responses function to relieve the applied stress. In the case of pathogens, theconsortium has identified key elements in stress-resistance mechanisms, and their signallingpathways, for development as potential drug targets. With respectto bio-production strains, the consortium has identified stress pathwaysthat specifically limit product formation and have constructedprototype production strains. Previous EU-funded studies (BACELLNETWORK) have demonstrated regulatory crosstalk between generaland specific stress responses. A further specific scientific objectiveis to develop a model for the regulatory interactions that occurwithin the cell’s stress management system. The scientific objectiveswere therefore aimed at improving European competitiveness andhelping to meet the health needs of society.Expected results:Detail of a non ribosomalpeptide synthetase asa novel drug targetBACELL HEALTH has built on the technological knowledge and industrialbase developed in Europe by focusing on aspects that directly influence humanhealth, namely the establishment of novel targets for anti-infective agents and the improvedproduction of pharmaceutically-active proteins. The added-value nature of this project wasconfirmed by the participation of three European companies and the support of the BacillusIndustrial Platform (BACIP). The realised deliverables included knowledge of fundamentalbiological systems, the identification of novel targets for the development of broad-spectrumand/or Gram-selective drugs, an improved understanding of microbial virulence and theregulatory response of bacteria to host-mediated stress responses, prototypes of productionstrains and new protein functions. In addition, the consortium trained a group of young Europeanscientists, and disseminated its knowledge via European and international meetingsand publications.426From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Bacterial stress management relevant toinfectious disease and biopharmaceuticalsPotential impact:European research groups and industries are global leaders in the development of Bacillustechnology and the commercial exploitation of bacilli. A direct industrial benefit of BACELLHEALTH will therefore be to help maintain Europe’s competitive market position in the faceof competition from the US and the Far East. The project will impact on human health byproviding knowledge of the mechanisms bacteria use to avoid the immune response.Keywords:bacterial pathogens, drug targets, comparative genomics, proteome, transcriptome, ironhomeostasis, infectious diseases, biopharmaceuticalsPartnersProject Coordinator:Prof. Colin R HarwoodNewcastle UniversityMolecular Microbiology GroupInstitute for Cell andMolecular Biosciences6 Kensington TerraceNewcastle upon Tyne, NE1 7RU, UKcolin.harwood@ncl.ac.ukProject Manager:Dr. Sierd BronUniversity of GroningenDepartment of GeneticsHaren, The Netherlandss.bron@rug.nlProf. Kevin DevineTrinity College DublinDepartment of GeneticsDublin, IrelandProf. Mohamed MarahielMarburg UniversityFach Bereich ChemieMarburg, GermanyProf. Wolfgang SchumannBayreuth UniversityInstitute of GeneticsBayreuth, GermanyDr. Tarek. MsadekInstitute PasteurUnit de Biochimie MicrobienneParis, FranceProf. Michael HeckerGreifswald UniversityInstitut for MikrobiologieGreifswald, GermanyDr. Rocky CranenburghCobra BiomanufacturingStephenson BuildingThe Science ParkKeele, UKProf. Jan Maarten van DijlGroningen UniversityDepartment ofMedical MicrobiologyLaboratory ofMolecular BacteriologyGroningen, The NetherlandsProf. Oscar KuipersGroningen UniversityDepartment of GeneticsGroningen, The NetherlandsDr. Marc KolkmanR&D Genencor International BVLeiden, The NetherlandsDr. Michael Dolberg RasmussenBacterial Gene TechnologyBagsvaerd, DenmarkFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life427

Project Type:Specific TargetedResearch projectContract number:LSHG-CT-2004-512035Starting date:1 st January 2005Duration:36 monthsEC Funding:1 800 000Pictures of fusiform, oval,triradiate cells respectively.There is a big difference in shapebetween the morphotypes.DIATOMICSwww.biologie.ens.fr/diatomicsState-of-the-Art:The world’s oceans cover 70 percent of the Earth’s surface and are the largest ecosystemon our planet. This ecosystem is formed by more than 5,000 species of marine phytoplankton,but only a few taxonomic groups of phytoplankton are responsible for most ofthe system’s primary production and subsequent energy transfer to higher trophic levels aswell as vertical export to the deep ocean. The most significant phytoplankton are diatoms,which contribute around 40 percent of marine primary production, thereby providingclose to one fifth of the oxygen we breathe. Diatoms are therefore central to all life onEarth, although to date, remarkably little is known about their basic biology and how it isaffected by environmental change.The challenge for marine biologists in the genomics era is to exploit genomics technologiesfor all the potential they have, whilst maintaining the holistic view necessary for understandingmarine ecosystem function. For diatom researchers, this is especially difficult because thereare more than 100,000 extant species occupying widely varying habitats, from temperate topolar waters, and so it has been extremely difficult to derive a consensus ‘model’ species.Scientific/Technological Objectives:DIATOMICS will make use of whole genome sequences from diatoms to provide informationabout gene function and its relationship to ecology and evolution. Four scientific workpackages will deal with aspects of diatom biology that are ecologically relevant and criticalfor diatom success and survival. Important topics that will be addressed include carbonconcentratingmechanisms, nutrient acquisition, the rise and fall of blooms and adhesion.Investigations into these areas will be carried out through the following steps: (1) The studyof gene expression profiles in response to a range of ecologically relevantstimuli, such as nutrients and stress; (2) The manipulation of the expression ofkey candidate genes in Phaeodactylum tricornutum, by reverse genetics; (3) Thestudy of the phylogenetic histories and ecological significance of these genes ina range of diatoms. A fifth work package is designed to utilise the knowledgegenerated from the other four work packages for the development of non-neutralprobes for assessing diatom physiology in the natural environment.Expected Results:The DIATOMICS project is divided into five scientific work packages, plus onework package dealing with project management. Four of the scientific workpackages will deal with an aspect of diatom biology that is ecologically relevantand critical for diatom success and survival. Important topics that will be addressedinclude carbon-concentrating mechanisms, nutrient acquisition, the rise and fall ofblooms, and biofouling. A fifth work package is designed to utilise the knowledge generatedfrom these other four work packages for the development of non-neutral probes for assessingdiatom physiology in the natural environment.Potential Impact:Climate change is occurring on a global scale and it is of major concern. It is therefore essentialthat the secrets of diatom biology be discovered so as to increase our knowledge of therole they play in global biogeochemical cycles, and to understand how they are influenced byenvironmental change. These issues are being addressed in DIATOMICS using post-genomicstools. Furthermore, the SME partner in DIATOMICS is interested in transferring diatom genesinto rice, in order to reduce fertiliser inputs, to increase stress tolerance and to improve theircarbon sequestering capabilities.428From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Understanding Diatom Biology byFunctional Genomics ApproachesAn improved understanding of diatom biology can lead to advances in human health careand well being, due to the phylogenetic relatedness of diatoms to important human pathogens,eg ciliates and apicomplexans, and to the potential biomedical applications of diatomsilica nanofabrication. In summary, DIATOMICS is stimulating multidisciplinary basic researchin Europe to exploit the full potential of diatom genome sequences to underpin applications ofrelevance for human health, and for predicting and monitoring global climate change.Keywords: cell biology, diatoms, genomics, reverse geneticsPartnersProject Coordinator:Dr. Chris BowlerStazione Zoologica Anton DohrnCell Signalling LaboratoryVilla Comunale80121 Naples, Italychris@szn.itProf. Colin BrownleeMarine Biological Associationof the UKThe Laboratory, Citadel HillPlymouth, UKProf. Veronique Martin-JezequelUniversity of NantesFaculty of Sciences ISOMerEA 2663Nantes, FranceProf. James A CallowUniversity of BirminghamSchool of BiosciencesBirmingham, UKProf. Julie La RocheLeibniz Institut fuerMeereswissenschaffenDepartment of MarineBiogeochemistryKiel, GermanyProf. Aaron KaplanHebrew University of JerusalemDepartment of Plant SciencesInstitute of Life SciencesJerusalem, IsraelDr. Chris BowlerCentre National dela Recherche Scientifique(CNRS) UMR 8186Biologie Moléculairedes OrganismesPhotosynthétiquesEcole Normale SupérieureParis, FranceProf. Linda Karen MedlinStiftung AlfredWegener Institut fur Polarund MeereschforschungDepartment of BiologicalOceanographyBremerhaven, GermanyDr. Leszek RychlewskiBioInfoBank InstituteBioinformatics LaboratoryPoznan, PolandProf. Valerie FrankardCropdesign NVTechnology ManagementGroupZwijnaarde, BelgiumProf. Wim VyvermanUniversity of GhentLaboratory of Protistology andAquatic EcologyGhent, BelgiumDr. Richard WetherbeeUniversity of MelbourneSchool of BotanyParkville, AustraliaFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life429

8. SYSTEMS BIOLOGY

8.SYSTEMSBIOLOGYEUSYSBIOSYMBIONICEMI-CDQUASICOMBIOCOSBICSDIAMONDSEU-US WorkshopELIfeESBIC-DYSBNAMPKINRIBOSYSEUROBIOFUNDVALAPODYNAGRON-OMICSBaSysBioBioBridgeSYSBIOMEDSysProtStreptomicsSYSCOProust

EUSYSBIOwww.eusysbio.org/index.htmProject Type:Specific Support ActionContract number:LSSG-CT-2003-503218Starting date:1 st November 2003Duration:24 monthsEC Funding:500 000State-of-the-Art:Systems biology (SB) covers research into in silico simulation of complex life processes,combining concepts from molecular biology, engineering sciences, mathematics and IT in aholistic approach to complex biological systems such as living cells. SB is currently receivingwidespread attention in Japan and the USA and is being intensively researched andpromoted. Europe is lagging behind in systems biology research and EUSYSBIO was set upwith the aim of bringing together research groups to create a future research network.Scientific/Technical Objectives:A survey carried out by the EUSYSBIO team indicated that the training of young scientistsis essential to the creation of a European systems biology network and also universitytraining programmes in interdisciplinary subjects. The consortium therefore set up trainingactivities, including a series of lectures in Austria. They also began a search for researchnetworks outside Europe to make links with groups for future cooperative research projects.The team carried out the task of identifying the strengths and weaknesses in the Europeansystems biology field and consequently began the task of forming a research network thatcan compete worldwide.Expected Results:The project laid the foundations of the successful start of European systems biology researchand will form the foundation of further SB research activities. Researchers met in Germanyin 2004 to discuss how to establish standards for cooperation and data exchange acrossEurope and beyond. EUSYSBIO also set up a website and database to contact potentialresearch collaborators and advertise vacancies in the field of SB.Potential Impact:European SMEs have the necessary knowledge to use opportunities given by the commercialisationof SB results. If Europe exploits this competitive advantage it can move into aleading position in the field of international SB research.Keywords:systems biology, research policies434From Fundamental Genomics to Systems Biology: Understanding the Book of Life

The Take-off of European Systems BiologyPartnersProject Coordinator:Dr. Petra WolffForschungszentrum Juelich GmbHProject Management Juelich (Ptj)Leo-Brandt-Strasse52425 Juelich, Germanyp.wolff@fz-juelich.deDr. Thomas ReissFraunhofer Institute for Systems andInnovation Research (Isi)Munich, GermanyProf. Hans Victor WesterhoffVrije Universiteit AmsterdamFaculty of Earth and Life SciencesDepartment of Molecular Cell PhysiologyAmsterdam, The NetherlandsProf. Karl KuchlerUniversity of ViennaDivision of Molecular GeneticsVienna, AustriaDr. Roland EilsDeutsches KrebsforschungszentrumTheoretical BioinformaticsHeidelberg, GermanyDr. Barbara StreicherDialog GentechnikVienna, AustriaDr. Rudiger MarquardtDechema Gesellschaft Fuer ChemischeTechnik Und Biotechnologie E.V.Vbu Vereinigung Deutscher Biotechnologie-Unternehmen (Vbu)Frankfurt, GermanyDr. Sirpa NuotioAcademy of FinlandHealth Research UnitHelsinki, FinlandFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life435

SYMBIONICwww.symbionicproject.orgProject Type:Specific Support ActionContract number:LSHG-CT-2003-503477Starting date:1 st November 2003Duration:24 monthsEC Funding:200 000State-of-the-Art:In the next few years, systematic data from proteomics and genomics will allow the designof an in silico virtual cell, a model that will have an enormous impact on biomedical andpharmaceutical areas, as it will contribute to a rational design of treatments for human neurodegenerativediseases. Hence, there is a pressing need to start a European-wide initiativeon the systems biology (SB) of neuronal cells and synapses. The SYMBIONIC project aimsat putting the issue of a systems biology approach in the field of neuronal cell study at thecentre of interest for a wide scientific community, from cell and molecular neurobiologyand neurophysiology to functional genomics, proteomics, bioinformatics, biophysics andcomputational biology.Scientific/Technological Objectives:The SYMBIONIC project was designed to capitalise on the enormous scientific potential inEurope and fill a significant void in the international scientific arena. Its long-term aim is tobe the driving force for a future set-up of a European-based exhaustive and reliable computationalmodel of the neuron. The activity of the SYMBIONIC project was mainly focusedon training and dissemination and on the coordination of the project with other Europeaninitiatives in the SB field. Further objectives were: tionaland experimental fields ences about the great potential of neuronal cells and technological projectsExpected Results:The SYMBIONIC project helped to integrate knowledge and expertise, provided a generalassessment of the existing data and know-how in several different scientific domains (fromneurophysiology to computer science), triggered the growth of a consensus on the initiativefrom pharmaceutical, biotechnological and computing industries and found new strategiesfor fundraising. Furthermore, it helped to integrate and coordinate the ongoing Europeanwideinitiatives on different aspects of systems biology. The project organized workshops,conferences and training courses on the scientific and technological themes involved for thegrowth of a future generation of scientists.Potential Impact:SYMBIONIC is creating a broad European network of research institutions and industrieswith interdisciplinary expertise in the SB field, which will be a driving force for future ambitiousinitiatives in neuronal cell modelling. Through its workshops and conferences theproject is contributing to the training of young scientists and to making the pharmaceutical436From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Towards European Neuronal Cell Simulation:a European consortium to integratethe scientific activities for the creationof a European Alliance devoted tothe complete in-silico model of Neuronal Celland biotechnology industries more aware of the opportunities offered by SB and its hugepotential impact on the economy, The European network of scientists and research groupscreated through SYMBIONIC activities are now likely to generate new and more ambitiousresearch projects in the area of SB.Keywords:protein-protein interaction, simulation, neuron, protein network, signaling pathway, synapse,computational systems biology, in silico models, research policiesPartnersProject Coordinator:Dr. Ivan ArisiLay Line Genomics SpA.c/o San Raffaele Scientific ParkBuilding B, Floor 4Via di Castel Romano 10000128 Rome, Italyi.arisi@laylinegenomics.comProf. Antonio CattaneoScuola Internazionale Superiore Di Studi AvanzatiDepartment of BiophysicsTrieste, ItalyDr. Christopher SandersonMedical Research CouncilMRC Human Genome Mapping ProjectLondon, UKProf. Marta CascanteUniversitat de BarcelonaDepartament de Bioquimica i Biologia MolecularBarcelona, SpainFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life437

EMI-CDhttp://pybios.molgen.mpg.de/EMICDProject Type:Specific TargetedResearch ProjectContract number:LSHG-CT-2003-503269Starting date:1 st January 2004Duration:42 monthsEC Funding:1 905 772State-of-the-Art:The main sociological and economical impact of genome research lies in the molecular understandingof major human diseases, and the development of new therapies. However, despitesignificant increases in pharmaceutical R&D spending, the number of new approvedmedicines has remained fairly constant. One possible reason for this development might bethe fact that analytical methods and tools are not yet significantly installed in the drug developmentprocess. While bioinformatics are used in drug target discovery, this is not the case forthe later stages. In particular, the simulation and modelling of biological processes, such asdisease-relevant signalling pathways and metabolic processes, are underdeveloped in drugtarget validation. experiments could be the basis for successful screening, and the entiredrug development process should be accompanied by bioinformatics and systems biologyapproaches, especially through the introduction of simulation techniques and experimentaldesign at all phases of the process. Furthermore, the need for integration of rules and methodsis fundamental in current functional genomics research. Multiple databases exist already, a varietyof experimental techniques have produced gene and proteome expression data from varioustissues and samples, and important disease-relevant pathways have been investigated.Scientific/Technological Objectives:The analysis of the processes involved in the course of multigenic diseases, necessitates copingwith data from diverse experimental platforms. Consequently, important elements of the EMI-CD software platform target data integration, as well as data standardisation. In particular,the EMI-CD platform is designed in a modular way. The main modules are set out below:Database integration: The role of several partners (BioWisdomSRS, EBI and MicroDiscovery)in the EMI-CD project is to provide an information layer on the biological objects needed bythe modelling software (Max Planck Institute for Molecular Genetics), and is therefore of keyimportance to the project, due to it providing a central repository for the data sources usedby the project.Experimental data integration: Due to limitations of the current state-of-the-art in data integration,there is an essential need for a computer application. Even more crucial for the EMI-CDproject is access to data of high quality, indispensable for modelling and simulation tasks.Modelling of high-throughput data: Computational methodologies are expected to directbiological discovery, by enabling formalisation of the current biological knowledge into aformal model, and improving our knowledge, by refining the model systematically, accordingto the high-throughput data. Tel-Aviv University has introduced an extended computationalframework for studying biological systems. The approach combines formalisation of existingqualitative models that are in wide but informal use today, with probabilistic modelling andintegration of high throughput screening.Expected Results:The main purpose of EMI-CD is to provide a software platform complex enough to cope withvarious experimental techniques, aimed at discovering the gene function, and at understandingdisease processes. Another important issue is the tight cooperation with experimentalprojects, on the design of experiments for combined strategies to combat human diseases(such as cancer and diabetes). Compatibility with other systems is also an issue, but by usingSBML, models can be interchanged between different systems. A further issue stems from scalingof the platform to large systems (i.e. whole cell models). At the current stage, systems witha few thousand reactions are computationally feasible. EMI-CD will be an open system for theintegration of advanced analysis tools and other database systems.438From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Potential Impact:European Modelling Initiativecombating complex diseasesIn silico modelling approacheswill have an increasingimpact on Life Scienceand Health programs.More specifically, they willcreate immense potentialfor improving the qualityof life, through their creationof highly skilled jobs inthe health sector, improvedcompetitiveness and economicgrowth in Europe,and better healthcare andnew tools to address thediverse and important challengesof the European Community. In terms of health care, the post-genomics era willenable the invention and production of new diagnostic and analysis tools. A revolution inhealth care is anticipated with the move towards personalised medical treatments, bymeans of genetic medicine and the modelling of patient-specific therapy. This isbound to have an important impact on the future health status and quality of lifeof European citizens, and also to affect the cost implications for the population.PyBioS database interface.The PyBioS system is linkedto the other platforms of theEMI-CD project that are providingtopological data on cellularreaction systemsand experimental data viaspecific interfaces.Keywords: bioinformatics, modelling complex diseases,network analysis, complex diseasesPartnersProject Coordinator:Dr. Ralf HerwigMax Planck Institute for Molecular GeneticsVertebrate GenomicsIhnestr. 7314195 Berlin, Germanyherwig@molgen.mpg.deProf. Dr. Ron ShamirTel Aviv UniversitySchool of Computer ScienceTel Aviv, IsraelDr. Ewan BirneyEuropean Moleculer Biology Laboratory (EMBL)European Bioinformatics Institute (EBI)Hinxton, UKDr. Chris HodkinsonBioWisdom LtdCambridge, UKDr. Arif MalikMicroDiscovery GmbHBerlin, GermanyFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life439

Project Type:Specific TargetedResearch ProjectContract number:LSHG-CT-2003-503 230Starting date:1 st January 2004Duration:42 monthsEC Funding:1 920 410QUASIState-of-the-art:www.idp.mdh.se/quasiPresent understanding of cellular signal transduction is restricted, at best, to the wiringschemes of signalling pathways. Little is known about the details of their dynamic operationand the importance of quantitative, spatial and time-dependent parameters for signallingoutput. These are, however, crucially important for drug discovery and application.QUASI is a multidisciplinary project which aims at obtaining a coherent and detailed pictureof the dynamic operation of a model signalling transduction network. The signallingpathways contain the evolutionarily conserved MAP kinase cascade module, which is ofcentral importance for signalling in human cells and is implicated in human diseases suchas cancer and inflammatory disorders. MAP kinase pathways are currently being exploredas drug targets. A better understanding of the dynamic operation of these pathways offersnew opportunities for drug discovery and for efficient individualised treatment based on thegenetic makeup of the patient (pharmacogenomics).Scientific/Technological objectives:The overall objective of QUASI is to assess the dynamic and quantitative operation of signaltransduction pathways and to elucidate relevant paradigms. The individual scientific,technical and innovation objectives of the project are:1. To monitor activated protein kinases in the cell. A range of immunoreagents is beingused to quantify key phosphorylation events.2. To determine dynamic signalling events in single living cells using advanced microscopicand optic tools. These methods aim at the determination of protein movementswithin the living cell.3. To specifically, rapidly and temporarily inhibit signalling components in the livingcell. For this purpose, the team will design functional protein kinase variants that aresensitive to highly specific inhibitory compounds. In addition, QUASI is initiatingdevelopment of inhibitors based on protein kinase target structure.4. To identify direct protein kinase targets and quantify kinase-substrate reactions. In orderfor QUASI to reach its objective the team will develop and verify ATP analoguesrecognised by specific, modified protein kinases.5. To follow protein complex formation dynamics in the living cell. More specifically, theteam is employing protein tags that allow the use of specific cross-linking reagents forprotein complexes in solutions as well as on DNA templates in the cell. In addition,activatable Green Fluorescent Protein (GFP) variants and advanced microscopy/opticsare also being used to determine cellular movement and assembly of individualsubunits and protein complexes.Yeast cells stained for cell wallusinf calcofluor white (top) andplasma membrane Using anAqy2-GFP fusion (bottom). Thediameter of the cell is about 5micrometer. Yeast cells activelycontrol their volume via conservedsignalling systems thatare Studied in QUASI using asystems biology approach.Expected results:1. A better understanding of the importance and role of quantitative aspects of signaltransduction. Particular attention will be given to the signal amplitude and period forthe quality and intensity of different responses. This is vital for improved concepts indrug development and in drug applications such as personalised medication.2. A better understanding of the signalling of protein complex formation and proteinmovement as possible targets for pharmacological intervention.3. Identification of overriding rules of signalling pathway control including feed-forwardand feed-back control principles and robustness.4. A better understanding of how pathway specificity is achieved and maintained duringsignal transduction and how cross-talk between pathways is regulated.5. A set of optimised tools and approaches of general applicability.6. Mathematical models, which could be applied with adjusted parameters to MAP440From Fundamental Genomics to Systems Biology: Understanding the Book of Life

kinase pathways from any system.7. Information design and visualisation tools of wide applicability for the communicationof signalling and other dynamic events.Potential impact:Quantifying signal transductionQUASI is a project at the frontline of fundamental biomedical research. The results obtainedwill have a direct impact on drug development and drug application in diseases associatedwith altered MAP kinase signalling, and therefore can potentially contribute to givingEurope a competitive advantage in signal transduction research.Diseases such as cancer, and chronic inflammatory diseases such as rheumatoid arthritis,asthma and autoimmunity affect many millions of Europeans; they are either life-threateningor affect a person’s quality of life for many years. Because of this they require treatmentover long periods of time and are a huge financial burden on society. Hence, QUASI hasthe potential to open new avenues leading to better treatment of these diseases, therebycontributing to disease prevention in Europe and cost reductions for health services.Keywords: signal transduction, MAP kinases, cellular dynamics, mathematicalmodelsPartnersProject Coordinator:Prof. Stefan HohmannGothenburg UniversityDepartment of Celland Molecular BiologyBox 462 (Medicinaregatan 9E)405 30 Gothenburg, Swedenstefan.hohmann@hu.seDr. Per Sunnerhagen,Dr. Markus TamasDr. Morten GrötliGothenburg UniversityDepartment of Cell andMolecular Biologyand Department of ChemistryGothenburg, SwedenProf. Francesc PosasUniversitat Pompeu Fabra (UPF)Cell Signalling UnitDepartment de CiènciesExperimentals i de la SalutBarcelona, SpainDr. Gustav AmmererUniversity of ViennaInstitute of Biochemistryand Molecular Cell BiologyVienna BiocenterVienna, AustriaProf. Matthias PeterSwiss Federal Institute ofTechnology Zurich (ETH Zurich)Institute of BiochemistryZurich, SwitzerlandDr. Edda KlippMax-Planck Institute forMolecular GeneticsDepartment of Vertebrate GenomicsBerlin Centre for GenomeBased Bioinformatics (BCB)Berlin, GermanyDr. Rune PetterssonMälardalens HögskolaInstitutionen för InnovationDesign och ProduktutvecklingEskilstuna, SwedenFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life441

COMBIOProject Type:Specific TargetedResearch ProjectContract number:LSHG-CT-2004-503568Starting date:1 st March 2004Duration:36 monthsEC Funding:1 998 000Prolonged oscillations in thenuclear levels of fluorescentlytaggedp53 and Mdm2 inindividual MCF7 cells followinggamma irradiation.State-of-the-Art:It is increasingly becoming recognised that progress in biology depends on an understandingof the interactions between genes and proteins, and the functional systems they generate.Given the complexity of even the most primitive living organism, and the fact that ourknowledge of these interacting networks is still very limited, it is unreasonable to expect thatwe might achieve such understanding at the level of the cell in the near future. However, significantprogress towards a system-level understanding should be achievable by applyingan integrated approach to the analysis of a set of well-defined and biologically importantcellular processes.By combining experimental, simulation and bioinformatics approaches, COMBIO aims toincrease understanding of two biologically important systems: the first is the p53-Mdm2regulatory network, in which the oncoprotein Mdm2 controls the activity of the tumour suppressor‘gatekeeper’ protein p53, via a negative feedback loop, and the second is the selforganisationprocess whereby chromatin controls microtubule nucleation and organisationduring spindle formation. These two systems have been selected because they representtwo important and different kinds of biological system — one which can be describedapproximately as a network of free components, and the other in which localisation, selforganisationand gradients play an important role.Scientific/Technological Objectives:The general objective of COMBIO is to benchmark the ability of current modelling andsimulation methods to generate useful hypotheses for experimentalists, and to provide newinsights into complex biological processes.In both systems COMBIO has selected to study — the p53-Mdm2 regulatory network, and thedynamics of spindle assembly — the consortium will use different approaches to obtain quantitativedata, as well as data regarding localisation and the dynamics of the system. Three ofthe consortium’s partners are leaders in the field of database construction and display. Workingin close collaboration with experimentalists, they will develop databases that are adaptedto experimental work and computer modelling. Data will be stored in such a way that theywill be accessible to various simulation packages, and will be displayed in such a way thatnon-experts will be able to make sense of them. This aspect of the project will require significanttechnological innovation. Two of the groups in COMBIO develop modelling approximationswhile simultaneously conducting experiments to validate the models’ predictions. Thesegroups will act as a kind of bridge between the dry and wet labs in the consortium. The differentmodelling tools will be assessed and a handbook drawn up, which will allow the rapiddissemination of these tools to the broader experimental community.Expected Results:It is the ambition of the COMBIO consortium to create a truly interdisciplinary environment,in which a range of theoretical and experimental approaches that were hitherto consideredseparate areas of research, will be integrated and applied to the understanding of complexbiological systems. In so doing, it hopes to make an important contribution to functionalgenomics, and to provide means for elucidating the mechanisms of action of pharmacologicalcompounds.Potential Impact:Systems biology recognises the importance of wholeness, acknowledging that systems cannotbe understood by investigation of their parts in isolation. Today, systems biology bringsmathematics, engineering, physics and computer science expertise to the exploration ofcomplex biological systems and their regulation.The current emphasis on systems in biology is the result of recent developments in molecular442From Fundamental Genomics to Systems Biology: Understanding the Book of Life

An integrative approachto cellular signalling and control processes:Bringing computational biology to the benchbiology and biochemistry, which have enabled researchers to collect comprehensive datasets on the performance of systems, and to acquire information about their molecular substrates.These developments have implications for medicine and drug development.Humandisease phenotypes are controlled not only by individual genes and their products, but alsoby networks of interactions that exist between those genes and their products, and the systemwidedynamic behaviour that they display. The networks range from metabolic pathways tosignalling pathways that regulate hormone action. Study of the dynamics of these networks,using approaches such as metabolic control analysis (for metabolic networks), or stochastic orlogical approaches (for gene regulation networks), may provide new insights into the pathogenesisand treatment of complex diseases such as cancer.Keywords: systems biology, computer modelling, gene & protein networks, gradients,software evaluation, network design, computational biology,signallingPartnersProject Coordinator:Prof.. Luis SerranoCRG - Centre de Regulació GenòmicaSystems Biology Research UnitDr. Aiguader 8808003 Barcelona, Spainluis.serrano@crg.esDr. Francois NedelecEuropean Molecular BiologyLaboratory (EMBL)Cell Biology and Biophysics UnitHeidelberg, GermanyDr. Olga Kel-MargoulisProf. Edgar WingenderBIOBASE Pathway DatabasesWolfenbüttel, GermanyDr. Uri AlonWeizmann Institute of ScienceDepartment of Molecular Cell BiologyRehovot, IsraelDr. Marcelle KaufmanUniversité Libre de BruxellesCentre for Nonlinear Phenomenaand Complex SystemsBrussels, BelgiumDr. Amancio CarneroCentro Nacional deInvestigaciones OncológicasMadrid, SpainProf. Edgar WingenderUniversity of GöttingenDepartment of BioinformaticsGöttingen, GermanyProf. Béla NovákTechnical University of BudapestMolecular Network DynamicsResearch GroupBudapest, HungaryProf. Alfonso ValenciaNational Centre for BiotechnologyProtein Design GroupMadrid, SpainDr. Cayetano GonzalesInstitute of BiomedicalResearchCell Division LaboratoryBarcelona, SpainDr. Isabelle VernosCentre for GenomicRegulation (CRG)Barcelona, SpainFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life443

COSBICSProject Type:Specific TargetedResearch ProjectContract number:LSHG-CT-2004-512060Starting date:1 st January 2005Duration:39 monthsEC Funding:1 684 159State-of-the-Art:Cancer can be considered a disease of communication at molecular level. The area of cellsignalling investigates the transmission of information from receptors to gene activation bymeans of biochemical reaction pathways, which form complex signalling networks andimpinge on the development and health of organisms. COSBICS will establish and applya novel computational framework in which it will investigate dynamic interactions of moleculeswithin cells. Instead of simply mapping proteins in a pathway, COSBICS is concernedwith ‘dynamic pathway modelling’. Dynamic pathway modelling establishes mathematicalmodels to predict quantitatively the spatial-temporal response of signalling pathways andsubsequent target gene expression. This project considers two important systems: the Ras/Raf/MEK/ERK and the JAK-STAT pathways. With these pathways, COSBICS will investigatethe heart of the intracellular communication network that governs cell growth, differentiationand survival.Scientific/Technological Objectives:COSBICS’ main goals are to identify and quantify dynamic interactions of signalling pathwaysusing system- and signal-orientated approaches, and to develop methodologies thatare applicable to the dynamic and predictive analysis of signalling networks in general. Asparadigms, we consider two important systems at the heart of the intracellular communicationnetwork that govern cell growth and survival: the Ras/Raf/MEK/ERK pathway and theJAK-STAT pathway. COSBICS combines mathematical modelling with biological knowledgeto improve our understanding of how these two central communication networks are subvertedin tumour cells.JAK2-STAT5pathway mapExpected Results:The COSBICS project will develop two complete mathematical models of the JAK2-STAT5and Ras/Raf1/MEK/ERK pathways. The structure and parameter values of these modelsare based on quantitative time series data generated by the consortium. The consortium444From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Computational Systems Biologyof Cell Signallingwill develop mathematical and computational methods that are generic and should beapplicable to a wide range of cell signalling systems. The ultimate biological goal is anunderstanding of the two signalling pathways that play an important role in cell differentiationand proliferation. We are hoping that our models and experiments will reveal generalprinciples by which cells decide upon cell growth and development.Potential Impact:The tools we are developing for the mathematical analysis of nonlinear signal transductionpathway models are generic and can be applied to other systems biology projects as well.We aim to develop models that can predict the biochemical behaviour of pathways in responseto perturbations, which will be experimentally tested. We also will use this informationto help in the design of biological experiments, for example, by determining how manymeasurements need to be taken at what time intervals for a robust result to be obtained.Both applications will be useful for academic as well as industrial research mainly throughminimising the ‘wet’ experimental load, which is very expensive and time-consuming.Keywords: dynamic modelling of signal transduction pathwaysPartnersProject Coordinator:Prof. Olaf WolkenhauerUniversität RostockDepartment of Computer ScienceUniversitätsplatz 118051 Rostock, Germanywolkenhauer@informatik.uni-rostock.deDr. Ursula KlingmullerDeutsches KrebsforschungszentrumTheodor Boveri Nachwuchsgruppe:Systembiologie der SignaltransduktionHeidelberg, GermanyProf. Walter KolchBeatson Institute for Cancer ResearchGlasgow, UKDr. Julio Rodriguez BangaInstituto de Investigaciones Marinas delConsejo Superior de Investigaciones CientificasProcess Engineering GroupMadrid, SpainProf. Valko PetrovBulgarian Academy of SciencesInstitute of Mechanics and BiomechanicsLaboratory of Biodynamics and BiorheologySofia, BulgariaDr. Jens TimmerAlbert-Ludwigs-Universität FreiburgFreiburger Zentrum fürDatenanalyse und ModellbildungFreiburg, GermanyFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life445

Project Type:Specific TargetedResearch ProjectContract number:LSHG-CT-2004-512143Starting date:1 st January 2005Duration:42 monthsEC Funding:2 500 000DIAMONDSwww.SBcellcycle.orgState-of-the-Art:The field of systems biology aims to build on the success of novel functional genomics technologies,by improving data extraction and data modelling in order to get an understandingof biological processes as ‘control systems’. Essential to systems biology is the mathematicalmodelling of biological processes, and its use to build hypotheses and to carryout subsequent experimental validation. The complexity of biological processes is such thatwithout modelling and simulation its dynamics cannot be fully understood. Systems biologyrequires strong skills in biology and in computational analysis. Within DIAMONDS we wishto set in motion a multinational systems biology effort to study and model cell cycle controlin baker’s and fission yeast, and in and human cells.Scientific/Technological Objectives:The overarching objective is to demonstrate the power of a systems biology approachto study fundamental biological processes. We focus on eukaryotic cell cycle regulation,and will develop and implement a computational model that will function as a hypothesisgeneratingengine in a systems biology ‘wet lab’ environment. To reach this we set out todevelop two parts: a cell cycle knowledge base and an integrated platform of data mining,modelling and simulation tools. This will allow the integrated analysis of that data in a systemsbiology approach: the development of a basic model, the use of this model to designnew experiments, the production and analysis of novel data and the integration of theseinto a refined model.The major means of reaching this target is to harvest and/or produce a large body of cellcycle-related biological knowledge. This will function as the central resource for the modellingand simulation environment that will be developed. The project will showcase the factthat a systems biology approach toward analysis of a fundamental biological process canin fact become mature today, and hinges on an integrated data analysis pipeline, extendedwith modelling and simulation tools.Expected Results:At the end of the project we will have an integrated toolbox forthe analysis of functional genomics data, and the modelling ofcell cycle information for simulation purposes. We will also delivera knowledge base (GIN-db) containing detailed informationabout core cell cycle genes. The project is in its final year. Wehave begun concrete experiments to synchronise cells in culture inorder to study the dynamics of expression with microarrays andproteomics approaches. We have also finished the design of thedata analysis platform and will deliver the first working versionby early 2008.Potential Impact:The project will allow extensive data integration and modelling,and will deliver new insights in cell cycle regulation and themechanisms that prevent the uncontrolled proliferation of cells,opening the way to novel anti-tumour drugs and strategies. The potential for applications oflife sciences and biotechnology promises to be a growing source of wealth creation in thefuture, leading to the creation of jobs, particularly in the areas of highly skilled labour, andnew opportunities for investment in further research.446From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Keywords:Dedicated Integration and Modellingof Novel Data and Prior Knowledgeto Enable Systems Biologyfunctional genomics, systems biology, cancer, regulatory networks, dynamical modellingPartnersProject Coordinator:Prof. Martin KuiperFlanders Interuniversity Institutefor BiotechnologyDepartment of Plant Systems BiologyComputational Biology GroupTechnologiepark 9279052 Ghent, Belgiummakui@psb.ugent.beDr. Kristian HelinUniversity of CopenhagenBiotech Research and Innovation CentreCopenhagen K, DenmarkMarta AciluNoray Bioinformatics, S.L.Derio, SpainDr. Jürg BählerGenome Research LtdWellcome Trust Sanger InstituteCambridge, UKProf. Alfonso ValenciaFundación Centro Nacional DeInvestigaciones Oncológicas Carlos IiiStructural Biology And Biocomputing ProgrammeMadrid, SpainProf. Denis ThieffryUniversité de la MéditerranéeTechnologies Avancées pour leGénome et la Clinique (TAGC)Faculté des Sciences de LuminyMarseille, FranceProf. Søren BrunakTechnical University of DenmarkCenter for Biological SequenceAnalysis (CBS), BioCentrum, DTUKgs. Lyngby, DenmarkDr. Alvis BrazmaEuropean Molecular BiologyLaboratory (EMBL)European Bioinformatics Institute (EBI)Hinxton, UKProf. Michal LinialHebrew University of JerusalemDepartment of Biological ChemistryInstitute of Life Sciences, Faculty of ScienceJerusalem, IsraelDr. Tor-Kristian JenssenPubGene ASOslo, NorwayFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life447

EU-US WorkshopProject Type:Specific Support ActionContract number:LSSG-CT-2004-013079Starting date:1 st September 2004Duration:18 monthsEC Funding:60 000State-of-the-Art:DNA is under constant attack from physical and chemical agents that weaken and compromiseit. This means there is a potential risk for cancer and other health problems. Largenumbers of chemicals in our food and in the environment have a potentially harmful affecton our DNA under conditions in which its repair capacity is lowered. More research isneeded to increase our knowledge of DNA repair pathways and interacting processes andto obtain a better understanding of DNA responses at cellular level. As a response to thisthe Systems Biology of DNA-Damage-Induced Stress Responses workshop was organisedas a follow up to the Molecular Signature of DNA Damage Induced Stress Responses workshopthat was held in 2003.Scientific/Technological Objectives:The main objective was to provide unique opportunities for interactions between Americanand European researchers in DNA repair and systems biology and to discuss a future visionfor this series of workshops.Expected Results: researchers that will be of great benefit to both. DNA repair (possibly NIH-EU co-funded). shops. combines approaches represented by CEBS, the Reactome Database and Fabio Piano’sC. elegans developmental phenotype database.The Workshop was held inVermont and had about 70participants both from the EUand the USA. The relativelysmall size of the group andopen mindedness allowed forvery fruitful discussions on thestate of the art in the field of“Systems level understanding ofDNA damage responses” and anassessment of future possibiltiesand collaborations.Potential Impact:It is hoped that the workshop will lead to an invigorating effect on the international scientificcommunity, particularly scientists researching DNA repair pathways, and it was agreed thatparticipants of the workshop would make a point of researching into specific collaborationsthat have been organised as a direct result of the previous workshop.448From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Workshop on “Systems biology ofDNA-damage-induced stress responses”Y2H and literature–curatedinteractions. This figure showsthe human protein interactomededuced from yeast-two-hybrid(Y2H) data (red edges) or fromliterature–curated (LC) data (blueedges). The overlap is relativelylow (2.3% of all LC interactionsand 8.4% of the most highlyconserved LC hypercoreinteractions), suggestingrelatively strong sociologicalor technical bias for literaturebasedor Y2H-based interactomemapping, respectively.Keywords:systems biology, DNA damage, stress response, EU-US collaboration, genome wide transcriptionalprofilingPartnersProject Coordinator:Dr. Harry VrielingLeiden University Medical CenterAlbinusdreef 22300 Leiden, The Netherlandsh.vrieling@lumc.nlFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life449

ELIfewww.lipidomics.netProject Type:Specific Support ActionContract number:LSSG-CT-2004-013032Starting date:1 st January 2005Duration:30 monthsEC Funding:487 200State-of-the-Art:Research dealing with the molecular constituents of cells is referred to as genomics forgenes and nucleic acids, proteomics for proteins and glycomics for carbohydrates. Whathas been missing in the ‘-omics’ realm to date has been lipidomics. Since both carbohydratesand lipids are cellular metabolites, glycomics and lipidomics represent sub-divisionsof metabolomics.Lipids are essential constituents of cell membranes, where multiple cellular machines andsignalling systems carry out their functions. An imbalance in lipid metabolism results in variousdiseases, such as obesity, cardiovascular disease, stroke and Type 2 diabetes, whichpose a serious human and economic burden on the developed world. Lack of technologyhas hampered the analysis of lipids. However, new, fast and sensitive mass spectrometrymethods are now revolutionising the field, and are on the verge of being applied to diseasesrelated to the lipidome.Cholesterol monohydrate crystalsin murine gallbladder bile at thepolarizing light microscopy.Scientific/Technological Objectives:The aim of ELIfe was to mobilise and organise key stakeholders in the field of metabolomics,especially in lipidomics research. Its objectives were as follows:1) Encourage the formation of alliances between stakeholders in the metabolomics field,including academic research groups and representatives of the healthcare professionand industry;2) Link metabolomics initiatives with genomics and proteomics initiatives, and to adaptbioinformatics tools used in the latter for metabolomics;3) Define a strategy for metabolomics research, using lipidomics as an example;4) Establish a Lipidomics Expertise Platform as a first step towards mobilising the field.This virtual platform should be linked to the European Federation for the Science andTechnology of Lipids (Euro Fed Lipids) and was to act as a test centre for benchmarkingnew lipidomics technology;5) Hold both science-related and policy meetings.Expected Results:The ELIfe consortium was to make significant contributions towards the development of acomprehensive classification system for lipids. In addition to this, it expected to producethe following two results: 1) The Lipidomics Expertise Platform (http://www.lipidomics-expertise.de),based on a survey of lipidomics expertise and infrastructure in Europe and 2)The organisation of, and contribution to, multiple workshops and conferences (http://www.lipidomics.net).Potential Impact:ELIfe brought together and co-ordinated European expertise in metabolomics and lipidomics,drawing attention to these fields and establishing strategic alliances that should resultin the translation of basic research findings into medical and commercial applications.The project will help shape European and national policies and activities in relation to appliedand fundamental research. The improvements in analysis of lipid patterns in diseasedand healthy people that it aims to generate, will yield insights into the potential effects ofdifferent types of (lipid) nutrition on human health.450From Fundamental Genomics to Systems Biology: Understanding the Book of Life

The European Lipidomics Initiative:Shaping the life sciencesKeywords: lipidomics, metabolomics, clinical application of lipidsPartnersProject Coordinator:Prof. Gerrit van MeerUtrecht UniversityBijvoet Center andInstitute of BiomembranesUtrecht, The Netherlandsg.vanmeer@uu.nlProf. Gerd SchmitzUniversity Hospital RegensburgInstitute for Clinical Chemistryand Laboratory MedicineRegensburg, GermanyProf. Kai SimonsMax-Planck Institute of MolecularCell Biology and Genetics:MPI-CBGDresden, GermanyProf. Elina IkonenUniversity of HelsinkiInstitute of BiomedicineHelsinki, FinlandProf. Michel LagardeInstitut National des SciencesAppliquées de LyonPathophysiology of Lipidsand Membranes (PLM)Villeurbanne, FranceProf. Konrad SandhoffRheinische Friedrich-WilhelmsUniversität BonnKekulé-Institut für OrganischeChemie und BiochemieBonn, GermanyProf. Friedrich SpenerUniversität GrazDepartment ofMolecular BiosciencesGraz, AustriaProf. Sandro SonninoUniversity of MilanDepartment Medical ChemistryBiochemistry and BiotechnologySegrate, ItalyProf. Gerd UtermannMedical University InnsbruckInstitute for Medical Biologyand Human GeneticsInnsbruck, AustriaDe P4-ATPase structure is from:Lenoir, G. & Holthuis, J. C. Theelusive flippases Curr Biol 14,R912-913 (2004).Prof. Jürgen BorlakFraunhofer-Gesellschaft zurFörderung der angewandtenForschung e.V.Fraunhofer Institut fürToxikologie undExperimentelle MedizinHannover, GermanyProf. Raymond DwekUniversity of OxfordGlycobiology InstituteOxford, UKProf. Pam FredmanGothenburg UniversityInstitute of Neuroscienceand PhysiologyMölndal, SwedenProf. Balázs SarkadiNational Medical CenterInstitute of Haematologyand ImmunologyDepartment of MolecularCell BiologyBudapest, HungaryProf. Félix M. GoñiUniversidad del País Vasco/Euskal Herriko UnibertsitateaDepartment of Biochemistry andMolecular BiologyLeioa (Bizkaia), SpainFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life451

ESBIC-DProject Type:Co-ordination ActionContract number:LSHG-CT-2005-518192Starting date:1 st November 2005Duration:24 monthsEC Funding:350 000State-of-the-Art:Activities to combat multigenic complex diseases such as cancer, diabetes, obesity, heartdiseases and diseases of the nervous system are primary targets of the Sixth FrameworkProgramme. After decades of research, cancer remains a devastating disease, responsiblefor roughly one quarter of the deaths in Europe.Essentially, there are three main causes of cancer: infection, environmental influence andgenetic predisposition. However, on a more analytical and molecular level, the ontogenyof cancer is less evident and both clinical as well as basic research suggests that cancer isthe result of an accumulation of many factors that promote growth and metastasis (Hanahanand Weinberg, 2000). Consequently, it is not clear whether much of the current cancerresearch, especially the research focussed on analysing subprocesses which involve atmost a few genes or gene products at a time, will ever be able to “understand” such acomplex phenomenon and form the basis for dramatic improvements in cancer treatment.It is also clear that, in spite of all the successes in some specific areas, the current researchapproaches have not resulted in any dramatic increase of the rates of cure for the mostcommon cancers. Within this context, it is the goal of the project’s Coordination Action (CA)to establish a European framework for a systems’ biology approach to combat complexdiseases using cancer as a prototypical problem. The project’s Coordination Action will befundamentally based on existing resources of leading research groups in Europe. It unitesgroups with a strong clinical focus, with experience in high throughput functional genomics,as well as with computational and systems biology resources. Moreover, it brings togethergroups from some of the largest European cancer research organisations and centres.Scientific/Technological Objectives:ESBIC-D will set up a cancer-relevant model repository consisting of known pathways andgene regulatory networks associated with cancer, the role of specific mutations or otherchanges in key genes/gene products in these pathways, and, as far as available, detailedclinical data with special emphasis on the influence of different anti-cancer drugs on thesepathways. In this CA, important test cases that combine experimental and clinical data withtheoretical models and which will guide further analyses and approaches of the participatinggroups, will be identified. Attention will be given to in silico models of cancer-related(e.g. signalling) pathways, which analyse the feedback of theoretical models and experimentaldata as well as the construction of a complete human metabolic network in order totest responses to drugs and chemical treatments.Moreover, the ESBIC-D project aims to create a network of leading groups in the fields ofcancer research, genomics, proteomics and computational biology and to strengthen theexpertise and research infrastructure in Europe.Expected Results:DNA microarrays. Andre Nantel©Shutterstock,20071) Change and dissemination of information by combining leading EU wide resources;2) Performance of joint studies and analyses by bridging experiment and model;3) Performance of benchmarking exercises by defining test cases for systems biology approachesin Cancer;4) Organisation and management by setting up an expert group for a European widesystems approach towards the combat of complex diseases (cancer).The major added-value of ESBIC-D to the European scientific community is the provision ofthe necessary groundwork for the integration and dissemination of essential parts of systemsbiology initiatives to tackle cancer.452From Fundamental Genomics to Systems Biology: Understanding the Book of Life

European Systems Biology Initiative forCombating Complex DiseasesPotential Impact:Systems biology approaches will have an increasing impact on Life Science and Healthprogrammes in general and on anticancer drug development in particular. They provide ahuge potential for improving the quality of life through the creation of highly skilled jobs,improved competitiveness and economic growth in Europe, better healthcare and new toolsto address different important challenges of the European Community.In health care, the post genomics era will enable the invention and production of new diagnostictools and analysis tools. A revolution in health care is anticipated through a move towardspersonalised medical treatments by means of genetic medicine and the modelling ofpatient-specific therapy. This will represent an impact on the future health status and qualityof life of European citizens as well as on the cost implications. The technical progress withinthe health care sector will make many new or improved, but costly, medical treatments possible.However, in the long run this is expected to change as there will be a direct positiveeffect on the exploding health budgets throughout Europe.Keywords: systems biology, complex diseases, mathematical modelling,bioinformaticsPartnersProject Coordinator:Prof. Dr. Hans LehrachMax-Planck Institute for Molecular GeneticsVertebrate GenomicsIhnestr. 7314195 Berlin, GermanyE-mail: lehrach@molgen.mpg.deProf. Dr. Annemarie PoustkaGerman Cancer Research Center (DKFZ)Molecular Genome AnalysisHeidelberg, GermanyDr. Jean-Philippe VertEcole des Mines de ParisComputational Biology GroupParis, FranceProf. Dr. Ron ShamirTel Aviv UniversitySchool of Computer ScienceTel Aviv, IsraelDr. Crispin MillerUniversity of ManchesterPaterson Institute for Cancer ResearchManchester, UKDr. Emmanuel BarillotInstitut CurieBioinformatics GroupParis, FranceProf. Dr. Kurt ZatloukalMedical University GrazInstitute for PathologyGraz, AustriaFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life453

Project Type:Co-ordination ActionContract number:LSHG-CT-2005-018942Starting date:1 st November 2005Duration:36 monthsEC Funding:1 300 000YSBNState-of-the-Art:www.ysbn.euThe field of systems biology is expected to significantly affect biological and medical research.It aims to develop a systems-level understanding of biological processes, by employingmathematical analyses and computational tools, so as to integrate the informationcontent obtained in experimental biology. Gaining insight into the complete behaviour ofthe cell will assist in the understanding of specific cellular processes and human diseases.Systems biology will also be used for biotechnological production of pharmaceuticals, foodingredients, fuels and chemicals.The Yeast Systems Biology Network (YSBN) project uses the yeast Saccharomyces cerevisiaeas a model system, in order to advance the understanding of cellular systems. Thecentral focus of YSBN is on facilitating cooperation between experimental and theoreticalyeast researchers, thus exploiting the interdisciplinary characteristics of a systems biologyapproach.Scientific/Technological Objectives:The YSBN project aims to provide a platform that will integrate data acquisition, datageneration, modelling and recursive model optimisation. The achievement of the overallobjectives of YSBN involves meeting the following targets: metabolome, interactome, locasome and fluxome data; Saccharomyces cerevisiae, allowingfor queries about experimental conditions and data from miscellaneous sources; ablemodel development; tionas a port, allowing the entire international community to access the tools producedby YSBN; biology in Europe; for the production of fuels and chemicals.Expected Results:The YSBN collaboration action is expected to: generating new ideas for future projects and collaborations; mentationand mathematical model development; biology; take place in Helsinki, in June 2006 (http://issy25.vtt.fi); be collected, maintained and queried, also allowing for links to information containedin other databases; a dissemination site for the tools generated by the project, and as an interface for thecommunication between experimental and theoretical scientists 454From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Potential Impact:Yeast Systems Biology NetworkYSBN is expected to have a powerful impact upon the scientific community; by settingstandards and providing a template for a focussed systems biology initiative, the projectwill decrease fragmentation in European research, consequently benefiting systems biologyof other organisms. More specifically, the positive effects of YSBN will be noted in drug discovery(directly connected to human health), in the development of new biotech processes(which influence society), and also in education and training.Within YSBN, there are two SMEs that will further improve the competitiveness of the EuropeanBiotechnology industry, by providing a new software platform for model simulations,and by developing biotechnological processes based on cell factories.Keywords: systems biology, Saccharomyces cerevisiae, bioinformatics,mathematical modellingPartnersProject Coordinator:Prof. Jens NielsenTechnical University of DenmarkCentre for Microbial BiotechnologyBiocentrumLyngby, Denmarkjn@biocentrum.dtu.dkProf. Stefan HohmannUniversity of GothenburgDepartment of Cell andMolecular Biology/MicrobiologyGothenburg, SwedenProf. Stephen OliverUniversity of ManchesterSchool of Biological SciencesManchester, UKProf. Hans WesterhoffFree University of AmsterdamBiocentrumAmsterdam, The NetherlandsProf. Karl KuchlerMedical University of ViennaDivision of Molecular GeneticsMedical BiochemistryVienna, AustriaProf. Peter PhilippsenUniversity of Basel0BiocentrumBasel SwitzerlandProf. Matthias ReussUniversity of StuttgartInstitute of Biochemical EngineeringStuttgart, GermanyProf. Jack PronkTechnical University of DelftDelft, The NetherlandsProf. Merja PenttiläVTT BiotechnologyEspoo, FinlandDr. Edda KlippMax-Plank Institute forMolecular GeneticsDepartment of Vertebrate GenomicsBerlin, GermanyProf. Bela NovakBudapest University ofTechnology and EconomicsBudapest, HungaryProf. Lilia AlberghinaUniversity of MilanBicocca, ItalyDr. Uwe SauerSwiss Federal Institute of TechnologyInstitute of MolecularSystems BiologyZurich, SwitzerlandDr. Bärbel Hahn-HägerdalUniversity of LundLund, SwedenDr. Jochen FörsterFluxome Sciences A/SCopenhagen, DenmarkDr Johan GunnarssonInNetics ABLinköping, SwedenDr. Macha NikolskiUniversity BordeauxBordeaux, FranceProf. Betul KirdarBogazici UniversityIstanbul, TurkeyFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life455

Project Type:Specific TargetedResearch ProjectContract number:LSHG-CT-2005-518181Starting date:1 st January 2006Duration:42 monthsEC Funding:2 106 593AMPKINwww.sbi.uni-rostock.de/projects_ampkin.htmlState-of-the-Art:Systems Biology aims at understanding design principles and dynamic operation of cellularmodules, entire cells, and organisms. The quantitative approach to biological systems isdriven by technological advances and close collaboration between different disciplines. Abetter understanding of the properties of biological systems is vital for drug development,treatment of diseases and for the improvement of bioprocesses.In the AMPKIN project, experimental and theoretical studies will be integrated to achievean advanced understanding of the dynamic operation of the AMP-activated protein kinase(AMPK) signalling pathway. This pathway plays a central role in monitoring the cellular energystatus and controlling energy production and consumption. The main objective of theproject is to generate predictive kinetic mathematical descriptions of pathway activation/deactivation in yeast and mammalian cells and thereby to identify potential drug targets totreat human metabolic diseases.Scientific/Technological Objectives:The main technological and scientific objectives of the AMPKIN project are the following:1. Establish and critically compare the network structures of the AMPK pathway from activationto response in yeast and mammalian cells by using existing data and knowledgefrom literature, databases and own research;2. Generate, optimise and verify assay systems for as many different steps as possible inthe AMPK pathway of yeast and mammalian cells in order to generate quantitative dataand maximise the use of real data in modelling;3. Generate reference quantitative dynamic datasets following activation and deactivationof the AMPK pathway in yeast and mammalian cells. This reference data set will beused for generating dynamic models of the pathways and to optimise parameters thatcan not be determined experimentally;4. Generate and critically compare dynamic models for the yeast and mammalian AMPKpathway. In addition, the project aims to use information from the yeast model to complementgaps in the mathematical description of the mammalian model;5. Produce tools for system perturbation, which will be used to generate data for modeltesting, iterative model improvement, and for the potential development of drug screeningapproaches;6. Provide ‘dynamic’ datasets from experiments, employing a range of defined systemperturbations in both yeast and mammalian cells with the aim of testing and iterativelyimproving the models and of optimising the underlying parameters;7. Generate iteratively improved mathematical models in order to determine system propertiesand to provide an assessment of similarities and dissimilarities of the models inyeast and mammalian cells. As a consequence, to establish the significance and thelimitations of the approach of comparative modelling from experimental and theoreticalperspectives;8. Predict the result of pharmacological system perturbations and, where possible, to assessthese experimentally, thereby implementing the models in drug screening programmes.Expected Results:The AMPK pathway plays a central role in yeasts, fungi, plants, animals and humans in thecontrol of the energy balance, and therefore it is crucial for life. The overall objective of thisproject is to generate mathematical models, that is, computational replicas of the AMPKpathway that will be used in drug target identification and drug screening. The results havemajor potential for tackling some of the most rapidly advancing diseases in the modern456From Fundamental Genomics to Systems Biology: Understanding the Book of Life

world, such as obesity and type-2 diabetes. The project will result in a case study for employingsystems biology in drug target identification and in drug development. Moreover, itwill produce results exploitable for engineering of microbial metabolism and systems biologysoftware development.Potential Impact:Innovation: the project is at the frontline of post-genomic research.Competitiveness: the project strengthens the European research base in an emerging fieldand it helps European companies to develop and optimise products for worldwide markets.Exploitation: the results will be exploited by SMEs’ in different sectors of the European bioindustries.Dissemination: the results will be made widely visible to different audiences.Solving societal problems: AMPKIN supports the development of treatments for emergingdiseases, such as obesity and type-2 diabetes.Integration of research activities: the project uses EC funding to mobilise national resources. Itmakes use of the results obtained in other EC-funded projects and is linked to other Europeaninitiatives.Training of the work force: the project will contribute to training and life-long learning of thepeople employed by the project.European added value: in order to tackle the project, AMPKIN brings together strong andunique European expertise that cannot be found in a single country.Keywords:signal transduction, matabolism, mathematical models, drug development, diabetes,protein kinase, systems biologyPartnersSystems biology of the AMP-activatedprotein kinase pathwayProject Coordinator:Prof. Stefan HohmannGothenburg UniversityDepartment of Cell andMolecular BiologyBox 462 (Medicinaregatan 9E)40530 Gothenburg, Swedenstefan.hohmann@gu.seProf. Olaf WolkenhauerUniversity of RostockSystems Biology &BioinformaticsRostock, GermanyProf. David CarlingImperial College LondonMRC Clinical Sciences CentreCellular Stress GroupHammersmith Hospital CampusLondon, UKProf. Jens NielsenTechnical Universityof DenmarkCenter for MicrobialBiotechnologyBioCentrum-DTUKgs. Lyngby, DenmarkDr. Thomas SvenssonArexis AB (Biovitrum AB)BioinformaticsStockholm, SwedenFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life457

RIBOSYSProject Type:Specific TargetedResearch ProjectContract number:LSHG-CT-2005-518280Starting date:1 st January 2006Duration:48 monthsEC Funding:2 400 000This figure shows the use offluorescence to detect thelocalisation of molecules in yeastcells. Red represents protein; bluerepresents nuclear DNA. Shownare RNA-associated proteinsthat are present A) exclusivelyin the nucleus, B) throughoutthe whole cells, C) exclusivelyin the cytoplasm. The cellularlocalisations of these proteinsreflect where they function inRNA metabolism.State-of-the-Art:The RIBOSYS project will use systems biology approaches to model RNA metabolism inyeast. In order to develop kinetic models, we will quantify RNA precursors and determinetheir rates of production, their processing and degradation through the various post-transcriptionalpathways. Starting with ab-initio models describing the processing and degradationof yeast pre-messenger RNAs and pre-ribosomal RNAs, we will produce twocomparable mathematical representations and populate the parameters using quantitativeexperimental data. Manipulation of the parameters will permit predictions to be made aboutthe behaviour of the systems. These will be tested experimentally, using yeast mutants thatblock specific steps. Imaging techniques will be refined to visualise individual transcripts todetermine whether the population data reflect the situation in individual cells. Comparisonof the performance of the two models should provide further insights and enrich our understandingof both pathways.Scientific/Technological Objectives: optimised experimental protocols (standard operating procedures) for quantitativeanalyses of in vivo RNA processing models with each other and with data existing in the literature a mathematical representation and populate it with parameters from the experimentaldata; perturb model parameters and make qualitative predictions about systembehaviour and verify against other experimental data scriptsas normalisation standards for evaluation of processing defects observed inmutants affecting downstream processing/degradation events wide mRNA polyadenylation status using microarrays degradation factors on rates of pre-mRNA transcription, processing and degradation matesfor levels of their degradation. Development of a quantitative model for the fluxthrough the pathway. Testing and refinement of the model by analyses of the effectsof different growth conditions and mutations in the ribosome synthesis machineryand in the rRNA precursors of gene expression, using yeast tiling arrays and wild-type or mutant strains grownunder different conditions thereby test and refine the RNA processing modelsExpected Results:A notation for RNAA notation system is needed that permits RNA molecules to be described in a universalformat, comparable between species/organisms, which are also compatible with a mathematicaldescription.Enhanced mechanistic understandingQuantitative analyses will allow us to understand better the relationships between different458From Fundamental Genomics to Systems Biology: Understanding the Book of Life

steps, activities and factors in the pathway than has been achieved by qualitative analysesand intuitive interpretations. This will lead to fresh insights into, for example, the key stepsat which regulation would most likely be exerted, and should lead to testable hypotheses,which would be addressed experimentally.Enhanced insight across systemsComparison of the pre-mRNA and pre-rRNA models will enrich our understanding of eachpathway, providing further insights. This should illuminate equivalent pathways in humancells which are less amenable to direct experimentation, enhancing understanding of humangenetic disorders.Potential Impact:Systems Biology ofRNA Metabolism in YeastThis project will provide valuable new biochemical and genetic tools for the community andwill set experimental standards for a variety of other RNA studies.Modelling precursor RNA processing in yeast will be of great benefit for understandingthese pathways in human cells, which are less amenable to direct experimentation, andtheir significance for human genetic disorders.This collaboration will bring together experimental biologists, mathematicians and computerscientists and promote better understanding across these disciplines.Keywords: modelling, yeast, RNA metabolismPartnersProject Coordinator:Prof. Jean BeggsUniversity of Edinburgh,The Wellcome Trust Centre for Cell BiologyThe Kings Buildings, Mayfield Road EH9 3JREdinburgh, UKJ.Beggs@ed.ac.ukDr. Edouard BertrandCentre National de laRecherche Scientifique (CNRS)Universite Montpellier IIInstitut de GénétiqueMoléculaire de MontpellierMontpellier, FranceZipi Fligelman-ShaqedCompugen LtdComputational Life-SciencesTel Aviv, IsraelProf. Bernhard DichtlUniversität Zürich-IrchelInstitut fur MolekularbiologieZurich, SwitzerlandDr. Joanna KufelWarsaw UniversityDepartment of GeneticsBotany FacultyWarsaw, PolandDr. Oleg DeminInstitute for Systems BiologySPb Company LtdDepartment of BioenergeticsSaint Petersburg, RussiaFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life459

EuroBioFundProject Type:Specific Support ActionContract number:LSSG-CT-2005-019009Starting date:1 st January 2006Duration:36 monthsEC Funding:907 790State-of-the-Art:Life sciences and biotechnology have become extremely important in our knowledge-basedeconomy. However, they have also undergone a revolution in terms of research approaches,infrastructure, technology developments, and costs. The EuroBioFund project will addressthese challenges by combining expertise and resources in an organized and coordinatedmanner. Currently, the lack of coordination at the European level is a major obstacle toachieving EuroBioFund’s objectives and is jeopardizing Europe’s position on the globalscene. Against this background new strategies are needed to help match research dynamicsand funding opportunities.Scientific/Technological Objectives:The EuroBioFund project has been created to foster dialogue and coordination betweenfunding organizations and to promote and coordinate interaction among European life sciencesresearchers and funders. Other important objectives are: i) to provide a platform forfunding organisations and life science researchers to foster joint research initiatives throughnetworking; ii) to help organise research communities and facilitate Europe-wide researchprogrammes; iii) to develop a new funding process in Europe by helping to develop jointinvestments and funding of life sciences research. The project also aims to identify futurechallenges in the life sciences which require a coordinated European approach for theirfinancing and implementation. Identification of these topics will be based on ideas putforward by the scientific community in line with the strategic goals of public and privatefunding organisations across Europe.Expected Results:EuroBioFund will formulate answers to some of the numerous challenges faced by the lifesciences in Europe. It will provide a platform for funding organizations and life sciencesresearchers to create joint research initiatives through networking. It will also organise researchcommunities and facilitate research programmes of European scale and scope andpromote information exchanges and discussions of research policies. All of the above willbe crystallized through an annual conference, consisting of national agencies, intergovernmentalorganisations, private foundations, charities and industry. The conference willprovide a framework for dialogue between the various bodies funding the life sciences andhelp achieve better programme and policy coordination.Potential Impact:EuroBioFund will help to establish an invigorating new approach to life sciences in Europethrough new methods of funding and research, joint investments and information exchanges,creating a single European market for research. The project will have an impact onEuropean science by bringing together leading scientists and research funding agencies todebate, plan and implement initiatives, resulting in European life sciences becoming muchmore dynamic and competitive.460From Fundamental Genomics to Systems Biology: Understanding the Book of Life

A Strategic Forum for the Dialogue andCoordination of European Life Sciences,Funders and PerformersKeywords:life sciences, networking,research initiativesPartnersProject Coordinator:Prof. Marja MakarowEuropean Science Foundation (ESF)1 quai Lezay-Marnésia67080 Strasbourg, Franceceo@esf.orgProject Manager:Dr. Wouter SpekEuropean Science Foundation (ESF)1 quai Lezay-Marnésia67080 Strasbourg, Francewspek@esf.orgFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life461

Project Type:SME-Specific TargetedResearch ProjectContract number:LSHG-CT-2006-037277Starting date:1 st October 2006Duration:36 monthsEC Funding:1 488 560VALAPODYNwww.valapodyn.euState-of-the-Art:Mathematical modelling is generally based on (1) the understanding or theory of the waythe modelled system behaves, and (2) experimental data (e.g. measures) of elements ofthe system, and how it reacts under certain conditions. Genetic regulatory networks (orMINs) are very robust; it is therefore possible to model them, although this means thata vast amount of data (thousands of genes and proteins) needs to be considered, withhighly redundant interactions. Moreover, the different networks behave with non-linear andnon-additive responses. All these characteristics therefore necessitate the development of alarge-scale MIN modelling method, allowing one to rationally address the physiopathologyof many diseases.Scientific/Technological Objectives:The overall aim is to develop an innovative systems biology approach, in order to model thedynamics of Molecular Interaction Networks (MINs) related to cell death and survival in theorganism. The aim of the VALAPODYN project is to set up the scientific and technologicalbasis, for tasks within the following areas:ACell loss and plasticity observed inthe hippocampus in a mouse modelof mesiotemporal lobe epilepsy(A) compared to controls (B) functional annotation of genes and proteins, investigation ofstructure and dynamics of signal transduction and transcription regulatory networks. use of innovativebiomathematics / bioinformatics to integrate experimental MIN data with biologicaltissue and pathological states data obtained through the use of transcriptomic andproteomic approaches. establishment of a highly specialised database on the genomics andproteomics of MIN modelling. analysis of validated animal models of brainpathologies to evaluate gene/protein expression during initial cell death. extensive multi-level global gene expression profiling using the Affimetrixplatform. application of advanced quantitative proteomics technologies (MALDI,ICAT, 2-DPAGE, Heavy Peptides isotopic dilution) for large-scale proteomescreening. characterization of molecules in the MIN of celldeath, the modulation of which should improve or cureneurodegenerative brain disease.BExpected Results:The VALAPODYN network is composed of leading authoritiesin the fields of genomics, proteomics, bioinformatics andneuroscience in Europe. They have decided to join their effortsto develop a new innovative System Biology approachto model the dynamics of Molecular Interaction Networks (MIN) related to cell death andsurvival in the brain.This model will be dedicated to the selection of drug targets for human brain. The projectwill first validate dynamic models for cell death through the characterisation of new potentialdrug targets in an animal model for epilepsy where neurodegeneration is the initial stepof the development of epileptic seizures.462From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Validated Predictive Dynamic Modelof Complex Intracellular Pathways relatedto cell death and survivalPotential Impact:The development of new and unique dynamic modellingtools will allow the Consortium to participate in theprocess of applying integrative biology to pathologyresearch. This should significantly improve the qualityof life for EU citizens, by advancing the identificationof new generations of more efficient drug targets;these drugs will be used to treat numerous diseasesaccounting for mortality and several serious illnessesin the EU, such as cancer, cardiovascular diseases,neurological diseases, etc. Dynamic models will formthe basis for the next generation of biological validationsfor novel therapeutic targets, instead of themethods currently in use. VALAPODYN will also havea significant impact on the ERA, by creating a newfoundation for the exchange of fundamental research and knowledge. The development ofthe international R&D network of SMEs in the biotechnology sector (HELIOS, BIOBASE andSynapCell through INSERM during the project) will accelerate the emergence of the EU asa powerful contender in the global technological market. The VALAPODYN consortium willalso allow for optimal use of the available EU resources and human potential.Keywords: predictive dynamic models, systems biology, molecularinteraction networks, cell death and survival,neurodegenerationPartnersProject Coordinator:Dr. Antoine DepaulisGrenoble – Institut desNeurosciencesCentre de Recherche INSERM U 836Université Joseph FourierBP 17038042 Grenoble, FranceDr. Olga Kel-Margoulis,Prof. Edgar WingenderBIOBASE, GmbHWolfenbuettel, GermanyDr. Todor VujasinovicHELIOS BiosciencesCreteil, FranceDr. Despina SanoudouFoundation of Biomedical Researchof the Academy of Athens (FBRAA)Molecular Biology DivisionCenter for Basic ResearchAthens, GreeceProf. Edwin de PauwUniversity of LiegeDepartment of ChemistryMass Spectrometry LaboratoryLiege, BelgiumProf. Hermona SoreqHebrew University ofJerusalemDepartment ofBiological ChemistryInstitute of Life SciencesJerusalem, IsraelDr. Raffaella CatenaAlma Consulting Group ALMALevallois Perret Cédex, FranceFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life463

Project Type:Integrated ProjectContract number:LSHG-CT-2006-037704Starting date:1 st November 2006Duration:60 monthsEC Funding:12 000 000AGRON-OMICSwww.agron-omics.euState-of-the-Art:Agriculture is crucial to humankind. Crops supply food, animal feed, chemicals, pharmaceuticalsand renewable sources of materials and energy. Plant growth results in biomassaccumulation, which, in turn, is the major determinant of crop yield. Despite its importanceand complexity, plant growth is, however, a poorly understood trait. Plants evolved multicellularbodies independently from animals and fungi. This evolutionary step, coupled withthe unique photosynthetic lifestyle, explains why plants rely on mechanisms for growth anddevelopment that are unique. It is therefore crucial to investigate how these mechanismsfunction in plants in order to forge novel technological tools for tomorrow’s agriculture.At the present time, Arabidopsis thaliana is the only plant species for which the necessaryresources are accessible for studying complex traits. The typical growth and developmentof Arabidopsis has been accurately described, providing a solid platform on which tobase experimental studies of growth processes. Arabidopsis also has unparalleled genomicsresources, including high quality genome sequence and annotation comprising over30,000 genes of which 26,000code for proteins; tagged mutantalleles for 73 percent of thesegenes; a choice of DNA arraysto investigate genome transcription;modification and polymorphisms;comprehensive transcriptome,proteome and metabolomeatlases; cloned repertoires forfunctional proteomics; and RNAinterference. Furthermore, haplotypemaps of unprecedented densityfor any eukaryote, includinghumans, will soon be released for20 Arabidopsis ecotypes, helpingassociation mapping. Finally, thegenome sequencing of close relatives(Arabidopsis lyrata, Capsellarubella) has been launched andwill help to improve the accuracyof comparative genome analyses.Growth results from a complexnetwork of processes occurringat different organisational levels(whole plant, organ, cell, molecularmodule, molecule). Some ofthe key factors involved in theseprocesses have been identified inthe past decades via (eco)physiology,cell biology and moleculargenetics but many more still haveto be found. The major challengesare the elucidation of the interactionnetworks (eg macromolecularcomplexes, cell-to-cell signallingetc) that constitute each of the differentlevels of organisation, andthe understanding of how these464From Fundamental Genomics to Systems Biology: Understanding the Book of Life

different levels are linked. For example, plant growth regulators such as auxin and cytokinin,which coordinates the integration of growth at the cell-organ and organ-whole plantinterfaces, have been extensively studied in plants for many years. However, although afew components of their biosynthetic and signalling networks have been uncovered, verylittle is known about how they impinge on the machinery underlying cell expansion andcell division.Scientific/Technological Objectives:The main research goals of the project are: (i) to investigate systematically the componentscontrolling growth processes in plant cells (genome sequences, proteins, metabolites); (ii) tounderstand how they coordinate their action; (iii) to explain quantitative growth phenotypesat the molecular level. The growth process will be studied within a common research frameworkof five work packages (WP). In particular, the project will generate high-throughput(HTP) quantitative data defining growth variables, genetic components of growth, the molecularcomposition of leaves at successive stages of development, molecular interactionnetworks and small molecules affecting growth (WP1-5). Finally, mathematical and statisticalmethods to model and predict leaf processes will be developed and tested in closecollaboration with computer scientists, statisticians and experimentalists (WP7). The suite ofanalytical tools will be exhaustively tested and modified before being made available as apackage of integrated systems biology applications and as web services.The technology platforms at the core of the research programme have been selected toprovide quantitative information at all relevant levels of organisation: growth variables recordedat the level of whole plant, organ and cell; profiling of the genome, transcriptome,proteome and metabolome; protein-protein and protein-DNA interaction networks. Theycan be ranked in four classes:1) Well-established methods, but only exceptionally applied at this scale to study a singlebiological system in an integrative framework, requiring standardisation of existingprotocols and datasets; they include microarray transcript profiling, HTP real time RT-PCR, flow cytometry, large-scale recombinational cloning methods, GFP-fusion subcellularlocalisation, yeast two-hybrid, tandem affinity purification, mass spectrometry,chromatin immunoprecipitation.2) More advanced profiling techniques; they include large-scale SNP genotyping, systematicenzyme profiling (>40 activities) of identical samples, ITRAQ for relative proteinquantification, cell flow sorting, FT-IR microspectroscopy, bimolecular fluorescencecomplementation.3) Novel HTP techniques requiring extensive development and aimed at taking full advantageof Arabidopsis as a model species; they include automated leaf structureanalysis at cell-level resolution, in planta two-hybrid based on antibiotic selection,Arabidopsis cell-based assays and high content screening to study systematically theresults of genetic (genome scale) or chemical (library scale) perturbations.4) Software tools enabling data integration and biological system modelling.Expected Results:Arabidopsis growth networkintegrating OMICS technologiesAGRON-OMICS will yield four types of results:1) Novel analytical pipelines will be developed to measure cellular processes acrossmultiple levels, including mass spectrometry, remote macroscopic and microscopicimaging and environmental control. These research efforts require the generationFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life465

AGRON-OMICSof specific informatics infrastructure, common data standards and analytical toolsrequired to capture, store, distribute and analyse high-throughput data. The resultingknowledge and equipments will be accessible to the participant’s laboratories andthe know-how will be propagated further through training programmes and scientificexchanges.2) Novel well-documented integrated software applications will form the basis for a“plant systems biology toolbox”. These applications will be constructed to allowadaptability and integration with pre-existing software, and will be made freelyavailable to other scientists working in systems biology.3) Transgenic lines, genetic stocks and constructs created or characterised in theproject’s framework will be disseminated via stock centres.4) AGRON-OMICS will generate primary data and biological knowledge includingthe identification of genes/loci and molecules that control growth, and the constructionof models that explain how these components interact and function across pathwaysand processes. The information relative to leaf growth control networks will beexploited to postulate how best to combine inputs to increase plant biomass productionvia improved germplasm and the use of growth regulators. AGRON-OMICSresults will be published as soon as practicable both in peer-reviewed articles andvia online databases. Unlike most data produced in biological investigations, dataobtained in this project will be represented according to standard formats, in thecontext of networks, and supported by ontology.Potential Impact:AGRON-OMICS will have a significant impact in several research areas.Firstly, the consortium is pioneering systems biology approachesin order to understand biological complexity in the context of a multicellularorganism, and across multiple levels of organisation (cells,tissue, and whole organism). The tools, techniques and expertise builtup in the course of the project may be used to inform research onthe complex mechanisms involved in human disease, which resultin alteration of cell growth and development. In particular, currentknowledge shows that core molecular processes regulating cell proliferationand cytoplasmic growth are conserved between plants andanimal cells. Secondly, progress in the mechanistic analysis of thesemolecular pathways in plants may contribute fundamental insight intothe biology of human cancers. In addition, in-depth knowledge andmodelling of specific molecular pathways may result in the potentialto develop translational research projects for biomedical purposes(eg production of natural compounds for therapeutic use, and productionof vaccines against human diseases in plants). Thirdly, growthprocesses are difficult to characterise in mammalian species at ascale comparable to the one which is the target of AGRON-OMICS,or without breaching ethical barriers. In this respect, the ability tosystematically genotype, phenotype and profile at the molecular levelthousands of individual plants in a unique asset of this project and willbe of great value in developing similar system level research in mammals.Fourthly, AGRON-OMICS may help to reduce the environmentalimpact of agriculture. Agricultural practices withdraw about 70 percent of groundwaterresources worldwide. In the long-term, irrigation increases soil salinity and leads to thepermanent destruction of otherwise fertile soils. Using plants that have improved water useefficiency will help contain the amount of water consumed by agriculture and mitigate theimpacts of irrigation. Finally, a major goal in plant science is the development of crops as asource of renewable resources and industrial feedstock. In the coming years, 20 percent oftransport energy will hopefully come from renewable resources. As leaves are the primaryharvesters of energy, the integrated knowledge of mechanisms controlling metabolism,466From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Arabidopsis growth network integrating OMICS technologiesgrowth and environmental responses developed in this project will provide a strong foundationfor future work in this area.Keywords: Arabidopsis, plant, leaf, functional genomics, growth, integrativebiology, systems biologyPartnersProject Coordinator:Dr. Pierre HilsonGhent UniversityFlanders Institute for Biotechnolgy (VIB)VIB Department of Plant Systems BiologyTechnologiepark 9279052 Ghent, Belgiumpierre.hilson@psb.ugent.beProject Manager:Dr. Fabio FioraniGhent UniversityVIB Department ofPlant Systems BiologyTechnologiepark 9279052 Ghent, BelgiumFabio.fiorani@psb.ugent.beProf. George CouplandMax-Planck Institute forPlant Breeding ResearchCologne, GermanyProf. Wilhelm GruissemETH ZurichSwiss Federal Institute of TechnologyInstitute of Plant SciencesZurich, SwitzerlandProf. John DoonanJohn Innes CenterNorwich Research ParkDepartment of Cell andDevelopmental BiologyNorwich, UKProf. Sean MayEuropean ArabidopsisStock Centre (NASC)University of NottinghamLoughborough, UKProf. Gerco AngenentPlant ResearchInternational (PRI)BioscienceWageningen, The NetherlandsProf. José Luis MicolUniversidad Miguel HernándezInsituto de BioingenieríaDivisión de GenéticaElche, Alicante, SpainProf. Herman HöfteInstitut National de laRecherche Agronomique (INRA)Institut Jean-Pierre Bourgin (IJPB)Versailles, FranceDr. Christine GranierInstitut National de laRecherche Agronomique (INRA)Laboratoire d’Ecophysiologie desPlantes sous Stress Environnementaux (LEPSE)Montpellier, FranceDr. Claire LurinInstitut National de laRecherche Agronomique (INRA)Unité de Recherche enGénomique Végétale (URGV)Evry, FranceProf. Lothar WillmitzerMax-Planck Institute ofMolecular Plant PhysiologyPotsdamGolm, GermanyProf. Detlef WeigelMax-Planck Institute forDevelopmental BiologyDepartment of Molecular BiologyTübingen, GermanyDr. Vicky Buchanan WollastonUniversity of WarwickWarwick Systems Biology CenterWarwick, UKDr. Johan GeysenMaia ScientificGeel, BelgiumFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life467

BaSysBioProject Type:Integrated ProjectContract number:LSHG-CT-2006-037469Starting date:1 st November 2006Duration:48 monthsEC Funding:12 029 619State-of-the-Art:BaSysBio aims to achieve major breakthroughs in the understanding of the regulation ofgene transcription in bacteria, on a global scale. The highly dynamic gene regulation is mediatedby transcription factors (TFs), which trigger or repress the expression of their targetgenes. Transcription control is embedded into a hierarchical flow of information from genesto phenotype, in which many regulatory steps can occur.BaSysBio adopts a systems biology approach, in which quantitative experimental datawill be generated for each step of the information flow, and will fuel computational modelling.High-throughput technologies (such as living cell arrays, tiling DNA microarrays,multidimensional liquid chromatography proteomics and quantitative metabolomics) will bedeveloped, in conjunction with new computational modelling concepts, so as to facilitatethe understanding of biological complexity. In addition, models will simulate the cellulartranscriptional responses to environmental changes, and their impact on metabolism andproteome dynamics. The iterative process of simulations and model-driven targeted experimentswill generate novel hypotheses about the mechanistic nature of dynamic cellular responses,unravel emerging systems properties and ultimately provide an efficient roadmapto assist in tackling novel, pathogenic organisms.This system-based strategy will enable BaSysBio not only to understand how transcriptionalregulation and metabolism are quantitatively integrated at a global level, but also to understandcellular transcriptional responses in conditions mimicking pathogenesis. Finally, theproject will validate the general applicability of the findings, and integrate the modellingexperimentalstrategy developed in the highly tractable B. subtilis model, towards an understandingof regulatory networks controlling pathogenesis in disease-causing bacteria.BaSysBio will make a significant contribution towards overcoming the structural obstaclesthat hinder the development of systems biology in Europe.Scientific/Technological Objectives:The overall objective of BaSysBio is to generate quantitative data about the network componentsat all the levels of the information flow, in order to understand, at the system’s level,the global regulation of gene transcription in bacteria. To achieve this objective, BaSysBiowill focus on developing and adapting high-throughput technologies to facilitate quantitativemeasurements, in conjunction with developing and validating computational systemsbiology methodologies; this will enable quantitative interpretation of the data and unravelthe underlying principles of regulatory network interactions.At a technological level, BaSysBio aims to develop and adapt high throughput technologiesfor the quantitative determination of the cellular transcriptional responses to standardisedgenetic and environmental perturbations, as a function of time. In addition, the project willdevelop new concepts in computational modelling and simulation of regulatory networks.More specifically, the project involves the following activities:1) Using a novel multi-purpose DNA tiling microarray to identify, in a systematic andunbiased way, all the RNA transcripts (mRNAs and small RNAs) produced in the B.subtilis cells, and to facilitate a comprehensive inventory of the cis-acting regulatorysequences bound by transcription factors;2) Bridging technological gaps by developing living cell arrays which allow the ge-468From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Towards an understandingof dynamic transcriptional regulationat global scale in bacteria:a systems biology approachnome-wide determination of promoter activities as a function of time during the cellresponses;3) Exploiting the latest developments in mass spectrometry and non-gel-based proteinseparation techniques, to quantify proteins and determine their modifications in responseto perturbations;4) Developing methods for quantitative high-throughput metabolomics, using complementarymass spectrometry-based approaches (e.g. GC-TOF, LC (CE)-ESI-TOF andLC-MS/MS), to analyse the vast chemical diversity of intracellular metabolites inresponse to perturbations;5) Extending the use of parallel 13C-flux analyses to novel substrates;6) Developing chromosome engineering tools, based on the recombination systems ofprophages of Gram-positive bacteria, to facilitate high throughput tagging of genesin Bacillus subtilis and related pathogens;7) Developing new concepts and methodologies to improve modelling and simulationof regulatory networks. This includes standardised and unequivocal representationof networks basic components and interactions to be modelled; hybrid mathematicalmodels combining constraint-based approaches and detailed dynamic modelling.Expected Results:In contrast to the present large-scale and mostly descriptive studies on genome-wide datasets, BaSysBio’s systems biology approach relies on iterative cycles of model prediction,system perturbations and system response monitoring, which will incrementally refine themodels, thereby generating quantitative understanding of the in vivo operation of complexregulatory networks. This system-based approach will combine an unprecedented numberof different experimental approaches, to generate data in a limited number of standardisedconditions for two biological processes, thus considerably reducing the need to makehypotheses.BaSysBio has made several technological contributions: 1) B. subtilis living cell arrays tostudy the temporal regulation and the design principles of the transcription networks thatcontrol the timing of gene expression; 2) efficient chromosomal engineering techniques forGram-positive bacteria, including the pathogens B. anthracis and S. aureus; 3) parallelflux analysis based on 13C-labelling experiments in microtiter plates; and 4) adaptationand improvement of existing high throughput technologies for the specific project needs.Significantly, the developed methodologies will have additional benefits beyond the scopeof this project. The novel conceptual aspect of BaSysBio is the development of a theoreticalframework for comprehensive, system-widedata interpretation. This differs from the current focusof much of systems biology, which concentratesProteomic analysis of mutants of Bacillus anthracis to oxidative stress.The ability of Bacillus anthracis to resist oxidative stress is a key componentof this bacterium’s ability to resist the innate immune response and to causeinfection. To determine the relative contributions of two genes, hemH2 encodinga ferrochelatase and katB encoding a catalase to combating oxidative stress,mutant cells were grown in the presence or absence of the oxidising agenthydrogen peroxide and the resulting protein profiles determined by twodimensionalgel electrophoresis. The resulting images were false-coloured(untreated = green; treated = red), superimposed on each other and warpedso that corresponding proteins were coincident on the resulting image.Proteins whose expression was up- regulated in the mutant in responseto oxidative stress appear as red spots. (Dr. Susanne Pohl, University ofNewcastle upon Tyne, UK)From Fundamental Genomics to Systems Biology: Understanding the Book of Life469

BaSysBioSubtilis scanning – ElectronMicroscopeon signalling networks andmetabolic networks reconstructedthrough comparativegenomics. It extendsconceptually beyond dataacquisition and interpretationapproaches, throughquantitative interpretationwith the mathematical rigorof computational models.By integrating the multipleregulatory levels in a biologicalsystem, models willhave high potential to simulatethem accurately, to predict novel systems properties and properties of uncharacterisedsystems components, and to drive mechanistic understanding of the global regulation of B.subtilis metabolism, and of the adaptive transcriptional responses to stresses encounteredby cells during pathogenesis.Potential Impact:BaSysBio embraces the broad issues of the integration of transcriptional regulation and metabolismat a global level in cells. It thereby has the ambition to understand the general principles,as well as the mechanistic details of regulatory networks, and to drive key discoveriesand applications in systems biology. An important element that is critical for the successof BaSysBio, is the integration effect generated by concentrating resources in European research.The common development and use of standardised methodologies, procedures and tools willgenerate a large and unique body of data that will potentially allow a genuinely global understandingof genetic control in bacteria. The BaSysBio iterative theoretical-experimental strategy,which provides quantitative data about the regulatory steps in the information flow fromDNA to phenotype, will become applicable to multiple cellular processes. This will open theway to the construction of mechanistic models integrating basic regulatory components andtheir combined interactions at a global scale, potentially leading to in silico models simulatingthe dynamic behaviour of the whole cell. By elaborating on new concepts in computationalmodelling, BaSysBio will provide new ways to grasp biological complexity, and will revealas yet unknown properties of dynamic biological systems. This will open entirely new fields ofinvestigation to experimental biology.The new knowledge and the integrated modelling/experiments strategy developed by BaSys-Bio will be applicable to other micro-organisms, and will promote understanding of the globalcontrol of pathogenesis, thus leading to potential new strategies to combat disease-causingbacteria. The research in BaSysBio will yield a wealth of detailed knowledge about the keyprocesses that lead to a bacterial cell ‘fit for pathogenesis’, and will also help translate gainedknowledge into practical applications for the control of infectious diseases. Along the samelines, BaSysBio will facilitate the exploitation of the beneficial capabilities of microbes.Keywords:transcriptomics, metabolomics, fluxomics, proteomics, quantitative biology, modelling, bioinformatics,living cell array, DNA tiling microarrays, chromosome engineering, Bacillus,Staphylococcus470From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Towards an understanding of dynamic transcriptional regulation at globalscale in bacteria: a systems biology approachPartnersProject Coordinator:Dr. Philippe NoirotInstitut National de la Recherche Agronomique (INRA)147 rue de l Université75338 Paris, Francephilippe.noirot@jouy.inra.frProject Manager:Caroline SautotINRA Transfert10 rue Vivienne75002 Paris, Francecaroline.sautot@paris.inra.frDr. Alexander JungApplera Deutschland GmbHDarmstadt, GermanyDr. Franck MolinaCentre National de la Recherche Scientifique (CNRS)Faculté de Pharmacie CPBS-CNRS UMR5160Montpellier, FranceDr. Julio R. BangaConsejo Superior de Inestigaciones CientificasMadrid, SpainProf. Kevin DevineTrinity College DublinSmurfit Institute of GeneticsDublin 2, IrelandDr. Hanne Ø. JarmerTechnical University of DenmarkCenter for Biological Sequence analysisLyngby, DenmarkProf. Colin HarwoodUniversity of Newcastle upon TyneDepartment of Cell and Molecular BiosciencesNewcastle upon Tyne, UKProf. Anthony WilkinsonUniversity of YorkDepartment of ChemistryYork, UKDr. Peter J. LewisUniversity of Newcastle of AustraliaSchool of Environmental and Life SciencesCallaghan, AutsraliaProf. Michael HeckerErnst-Moritz-Arndt Universität GreifswaldInstitut fur MikrobiologieGreifswald, GermanyProf. Uwe SauerSwiss Federal Institute of Technology (ETH Zurich)Department of BiologyInstitute of Molecular Systems BiologyZurich, SwitzerlandDr. Othmar PfannesGenedata AGBasel, SwitzerlandDr. Benno SchwikowskiInstitut PasteurDepartment of MicrobiologyParis, FranceDr. Edda KlippMax-Planck Institute for Molecular GeneticsBerlin, GermanyProf. Jan Maarten Van DijlUniversity Hospital GroningenDepartment of Medical MicrobiologyGroningen, The NetherlandsFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life471

BioBridgeProject Type:SME- Specific TargetedResearch ProjectContract number:LSHG-CT-2006-037939Starting date:1 st December 2006Duration:30 monthsEC Funding:1 800 000State-of-the-Art:Chronic diseases are usually the result of interactions between individual susceptibility anddifferent environmental and/or lifestyle factors, and are often modulated by multiple genes.The interplay between these factors determines disease phenotype and hence, the prognosticand therapeutic implications of the disease. This interplay between genetically predeterminedsusceptibility and disease phenotype, can in turn be revealed by computer analysisintegrating clinical and biomedical data. Some examples of the application of computeranalysis to clinical practice are the classification and prognosis of ovarian cancer (Wu et al,2003), the analysis of myocardial perfusion images and cardiograms (Fletcher et al, 1978)and the development of a screening device for the diagnosis of heart murmurs (Bhatikar etal, 2005). In addition, several projects in the European Union are implementing informationtechnology-based services for diabetes management (Bellazzi et al, 2004). However, all theapproaches currently implemented in clinical practice use very limited datasets, despite theavailability of vast amounts of data from various life science disciplines since the “-omics”revolution. Only by integrating genomic, proteomic and metabolomic data can knowledgethat is useful for the understanding and treatment of complex human pathologies, begin tobe obtained. This is the goal of the BioBridge project.Scientific/Technological Objectives:BioBridge will focus on the application of simulation techniques on top of multilevel data,in order to create models for understanding, how molecular mechanisms are dynamicallyrelated to complex diseases at the systemic level.The BioBridge objectives are twofold. Firstly, a bioinformatic aspect will involve the developmentof software for integrated genomic, proteomic, metabolomic and kinetic dataanalysis, in order to build a bridge between basic science and clinical practice. Secondly,a biomedical aspect will focus on understanding the distortion of cellular metabolism thatis associated with certain target diseases. The diseases in question are congestive heartfailure (CHF), chronic obstructive pulmonary disease (COPD) and type II diabetes. Theavailable facts strongly indicate that these diseases comprise a cluster of chronic conditions,all of which are associated with nitroso-redox imbalance. The integration of data into adynamic framework will enable the development of the first kinetic model of the metabolismshared by COPD, CHF and type II diabetes, thereby revealing the common and individualtraits of these three complex diseases.Expected Results:After 30 months, BioBridge will have achieved the following goals:1) Creation of a structured database for the collection of clinical information relating toCOPD, CHF and type II diabetes;2) Identification of the metabolic pathways implicated in the target diseases;3) Recording of genomic, proteomic, metabolomic and kinetic information into the relevantstructured databases;4) Development of a software product designed for specific disease-related data searching;5) Development of standards for the different levels of data, which will be useful for theirintegration from genomic and metabolomic databases, and from specific proteomicsand metabolomics profiling experiments, including microarray analysis and stableisotope tracer data.;6) Development of protocols for transferring data from the structured databases intodynamic models;7) Using a differential equation approach, the design and development of an innova-472From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Integrative Genomics andChronic Disease Phenotypes:modelling and simulation tools forclinicianstive simulation environment that will accommodate the dynamic behaviour of complexnetworks, and in particular the metabolic pathways that are altered by the targetdiseases;8) Development of generic tools that will be clinically useful beyond the target diseasesaddressed during the lifetime of the project.Potential Impact:The main outcome of the project will be a protocol for organising multilevel data relatedto the target diseases into a convenient form for use in the construction and refinement ofkinetic models of intracellular metabolic pathways. The software developed will be applicableto more general cases of multilevel data integration. In helping to provide insights intothe key molecular mechanisms that determine poor prognosis in the CHF/COPD/type II diabetesdisease cluster, BioBridge will generate novel strategies for personalised preventionand enhanced delivery of patient care. Existing computational models have already provedpowerful in this context. For example, one of the BioBridge partners has recently developeda statistical framework for analysis of multivariate models from large-scale datasets. Thissoftware environment (GALGO) uses a genetic algorithm search procedure, coupled withstatistical modelling methods, for supervised classification and regression. BioBridge willbuild on and improve this and other computational models.Keywords: diabetes, chronic obstructive pulmonary diseases, COPD, chronicheart failure, systemic effects, genomics, proteomics, metabolomics,modellingPartnersProject Coordinator:Josep RocaInstitut d’InvestigacionsBiomèdiques August Pi iSunyer (IDIBAPS)Villarroel 17008036 Barcelona, Spainjroca@clinic.ub.esDr. Marta CascanteUniversity of BarcelonaInstitut d’InvestigacionsBiomèdiques August Pi iSunyer (IDIBAPS)Barcelona, SpainPeter AronssonMathCore Engineering ABLinköping, SwedenDieter MaierBiomax Informatics AGMartinsried, GermanyDr. Jordi Villa i FreixaUniversitat Pompeu FabraComputational Biochemistryand Biophysics LaboratoryBarcelona, SpainDr. Pranav SinhaInstitut für Medizinische undChemische LabordiagnostikLandeskrankenhaus KlagenfurtKlagenfurt, AustriaJohn BrozekGenfit LaboratoriesGenfit SALoos, FranceDr. Francesco FalcianiUniversity of BirminghamSchool of BiosciencesBirmingham, UKFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life473

SYSBIOMEDProject Type:Specific Support ActionContract number:LSHG-CT-2006-037673Starting date:1 st December 2006Duration:25 monthsEC Funding:362 500State-of-the-Art:The goal of systems biology (SB), or ‘integrative biology’, is to progress from a qualitative,static description of the constituents of living cells, to a quantitative, dynamic understanding oftheir systemic and functional properties. It is an interdisciplinary endeavour that has emergedfrom the fields of genomics and bioinformatics. The obvious value of predictive SB models forthe elucidation of pathological processes beyond the cellular level, calls for closer investigationof the potential applications of such models to medical research. Medical SB (MSB) mustdemonstrate the ability to cross levels: from cells to organs and organisms, from cell functionto physiological phenomena, and from model organisms to human diseases.Pioneering studies in the modelling of whole organ function have already demonstrated thatmodels can correctly predict certain physiological and pathological functions of the heart,for example. However, SB as a field is in its infancy and this, combined with its emphasison basic research, its focus on model organisms and individual intracellular pathway, are allobstacles to the application of SB to medical research. Although many SB groups are workingon disease-related models and pathways, there is little crossover between this basic researchand clinical research. Europe urgently needs to build capacity, both in terms of knowledgeand in terms of personnel trained to bridge the gap between the two disciplines, so that thefield of MSB can be launched in a correct and timely fashion.Scientific/Technological Objectives:SYSBIOMED seeks to explore the potential application of SB to medical research, includingthe development of drugs and other therapies. It will do this through a series of workshopsfocusing on topics at the cutting edge of SB and physiology, which will be organised by acore group of young scientists working in relevant areas.The workshops will explore how SB can be applied to research in major disease areasidentified by the World Health Organization (infectious, neurodegenerative, metabolic andcardiovascular diseases and cancer). They will promote the formation of collaborations,teams and research programmes, and they should also contribute to the breaking downof barriers — between theoreticians and clinicians, between basic researchers and thoseinterested in medical applications/drug development, and between newcomers and establishedgroups. These workshops will provide valuable opportunities for young academicsto enter the SB field, for theoreticians to meet experimentalists, and for representatives ofindustry to meet academic researchers. Scientists from industrial enterprises are especiallyencouraged to participate, so that they may assess the potential outcomes of applying SBto medicine as early as possible.Expected Results:SYSBIOMED intends to provide an appropriate and timely response to the imminent challengeof applying SB to medical research. The field of MSB has potential for getting offto a promising start, provided that Europe’s strengths are exploited wisely. Translationalby nature, it is expected to accelerate progress in medicine, in particular by opening upnew avenues to personalised medicine and to the development of multi-drug therapies.The potential translation of MSB results into new markets will have a positive impact onboth large and small enterprises.SYSBIOMED will supply decision-makers with useful information on the potential challengesand opportunities for action in the MSB field. The multidisciplinary nature of theconsortium means that it is well-placed to achieve its primary goal, which is to build anetwork of talented young researchers who will drive SB towards medical applications.SYSBIOMED will also benefit from an earlier, successful SSA, EUSYSBIO, when buildingits network of experts.474From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Systems Biology for Medical ApplicationsThe involvement of scientific journals in the SYSBIOMED consortium will be valuable forinforming non-specialists about MSB, for attracting young scientists (including theoreticiansand medical researchers) to the field, and for alerting ‘scouts’ from the biotechnology andpharmaceutical industries to new advances. To this end, SYSBIOMED is pleased to have thesupport of the journals The Scientist, Nature Biotechnology and IEE Proceedings SystemsBiology. The participating media will also prove extremely useful for disseminating SYSBI-OMED’s results.Potential Impact:SYSBIOMED complements both ongoing and planned European SB initiatives. A first steptowards the establishment of MSB as a new discipline, has recently been taken by the EuropeanMolecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), whichorganised a workshop on the therapeutic applications of computational biology (TACB).Although this workshop emerged from a bioinformatics background, SYSBIOMED will considerits main findings and extend them, placing a stronger emphasis on the practical translationof SB-related research into clinical applications, and identifying the disease areaswhich stand to benefit most from a coordinated SB approach. A representative of EMBL-EBIis a member of the SYSBIOMED core group, and TACB workshop organisers will be invitedto join the consortium’s advisory board.Regarded as a branch of translational research, MSB is likely to benefit from the spirit ofthe younger generation of European SB experts. The success of SYSBIOMED will dependon the efficient cooperation of this still-small community, but the consortium is also committedto joining forces with all relevant partners, including industry (both big pharma andSMEs). The project could lead to strategy adjustments in the healthcare sector, with respectto identifying the most promising therapies and technologies emerging from this branchof biomedical research. It is intended that the young scientists’ network should provide aconsulting service beyond SYSBIOMED’s lifetime.Keywords: systems biology, medicine, postgenomicsPartnersProject Coordinator:Dr. Karsten SchürrleDECHEMA e.V.Theodor-Heuss-Allee60486 Frankfurt am Main, Germanyschuerrle@dechema.deProf. Olaf WolkenhauerRostock UniversitySystems Biology and BioinformaticsRostock, GermanyCarole Moquin-PatteyEuropean Science Foundation (ESF)European Medical Research CouncilsStrasbourg, FranceFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life475

Project Type:SME- Specific TargetedResearch ProjectContract number:LSHG-CT-2006-037457Starting date:1 st January 2007Duration:36 monthsEC Funding:2 097 268Mouse model (left NZO mousein comparison to a C57BL/6mouse) used in SysProt for theanalysis of obesity induced type-2 diabetes. C57BL/6J mice serveas control strain.SysProtState-of-the-Art:Bioinformatics methods for diagnostic screening are a bottleneck in current biomedicalresearch. While exploratory methods – such as statistical hypotheses testing, clustering ofgene expression profiles and classification methods – have been successful in the detectionof molecular markers for interesting diseases, these techniques fail to validate these markersin their gene regulatory context and to integrate other data sources relevant for diagnosticpurposes. For these tasks, novel modelling techniques, network analyses, and data integrationmethods are indispensable. The analysis of processes involved in the course of complexpolygenic diseases, such as obesity and type-2 diabetes, is in fact a multi-step procedurethat has to cope with data from diverse experimental functional genomics platforms (geneand protein expression), physiological data, environmental factors, and others.Scientific/Technological Objectives:The project SysProt aims to develop a new paradigm for the integration of proteomics datainto systems biology. The goal is to gain relevant knowledge on the biological processesthat are important for human health and to use this knowledge for the purpose of diseasemodelling.In order to achieve this objective, an innovative, explorative biological systems approach(on both the molecular and the physiological level) will be adopted, with a strong focus onprotein function and modification. SysProt will produce proteomics data, indispensable forthe identification of novel circulating protein factors, and post-translational protein modificationsthat are important for the onset, dynamics, and progression of complex diseases.Data generation will be complemented by the development of computational analysis methodsfor these novel data types and the creation of adequate modelling technology. Theproject will benefit from the utilisation of established mousedisease models, existing benchmarking modules for computationalanalysis, and the functional genomics platforms developedby and accessible to the partners. In particular, theconsortium aims to demonstrate newly developed technologiesin a proof-of-principle study within an obesity-induced type-2diabetes mouse model.The project consortium is headed by an SME and includesfour academic partners from three European countries. Thiscomposition of commercial and academic interests guaranteeshigh-level scientific research, as well as a strong focus on thecommercial relevance and exploitation of the project’s results.Expected Results:www.sysprot.euAn important feature of the project’s approach will be the integration of phenotypic andphysiological parameters with proteomics data and expression profiles from time courseseries representing the onset and progression of insulin resistance of type-2 diabetes. Theexpected results of this project are:1) Model the knowledge about biological objects (genes, proteins and protein complexes)in the context of nutrition and type-2 diabetes in equivalent computer objects;2) Integrate heterogeneous data types from proteomics and functional genomics approaches;3) Develop and use a prototype framework for the automatic detection and localisationof protein modifications on high-accuracy mass spectrometry data;4) Generate specific proteomics and functional genomics data providing the necessaryinformation for disease model generation with an appropriate animal model;476From Fundamental Genomics to Systems Biology: Understanding the Book of Life

System-wide analysis and modellingof protein modification5) Gain new knowledge on the pathways and marker genes relevant for obesity-inducedtype-2 diabetes disease progression that will lead to the discovery of noveldiagnostic biomarkers for disease susceptibility;6) Simulate perturbations of the disease-relevant pathways;7) Develop tools and methods for the correlation of phenotype and genotype;8) Accelerate the identification and positional cloning of disease candidate genes bycombining gene expression, proteomics, genotype, and clinical data;9) Set up a knowledge base that integrates all available data and methodology as anexploitable product for disease modelling.The main result of the project will be an exploitable prototype that allows medical researchersto draw predictions on disease-relevant pathways.Potential Impact:Systems biology approaches will increasingly have an impact on Life Science and Health programmesin general and on drug development in particular. They provide a huge potential forimproving the European competitiveness. Through the application and broadening of systemsbiology approaches, the SysProt project is likely to impact on the scientific understanding ofbiological processes, with particular relevance to improving human health and wellbeing.Keywords: systems biology, fundamental biological processes, proteomics,bioinformaticsPartnersProject Coordinator:Dr. Arif MalikMicroDiscovery GmbHNutriSystemicsMarienburger Str.110405 Berlin, Germanyarif.malik@microdiscovery.deDr. Hadi Al-HasaniDeutsches Institut fuer ErnaehrungsforschungDepartment of PharmacologyNuthetal (OT Bergholz-Rehbruecke), GermanyDr. Ralph SchlapbachEidgenössische Technische Hochschule, ZürichFunctional Genomics Center ZurichZurich, SwitzerlandProf. Rainer CramerThe University of ReadingThe BiocentreReading, UKDr. Ralf HerwigMax-Planck Institute for Molecular GeneticsDepartment Vertebrate GenomicsBerlin, GermanyFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life477

Streptomicswww.streptomics.orgProject Type:SME- Specific TargetedResearch ProjectContract number:LSHG-CT-2006-037586Starting date:1 st January 2007Duration:36 monthsEC Funding:2 850 851State-of-the-Art:The biotechnology industry is constantly searching for better hosts for the production of biopharmaceuticalsand enzymes of diverse origin. The Gram-positive soil bacterium STREPtomyceshas already proved an invaluable host for this purpose, since it can secrete severalheterologous proteins in satisfactory amounts. However, in order to optimise strain selection,knowledge is required, concerning the following points: (1) How protein secretionprocesses are integrated within the metabolome, and how they interact; (2) How heterologousprotein secretion stresses the metabolome and induces negative cellular cascades.*Automated proteinengineering:* A precisionrobot arm retrieves a custommanufactured 1536-well platein one corner of a room full ofrobotics-compatible equipmentincluding nano-litervolume liquidhandlers,single cell sorters,humidified incubators, heatingand cooling blocks, centrifuges,confocal laser-based platereaders and other equipmentintegrated for fully automatedhigh throughput proteinengineering at Direvo BiotechAG in Cologne, Germany.Systems biology, the science of analysing and modelling genetic, macromolecular andmetabolic networks, provides the means to address these questions. By combining biochemicalinformation with genetic and molecular data, the Streptomics consortium hopes togain novel insights into the functions of genes related to protein secretion, as well as howthat protein secretion mechanism responds to external and internal stimuli. With a betterunderstanding of this mechanism at the cellular level, it should be possible to optimise proteinsecretion.478From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Systems biology strategiesand metabolome engineering forthe enhanced production ofrecombinant proteins in StreptomycesScientific/Technological Objectives:Streptomics aims to enhance the production of heterologous proteins, using Streptomycesas a host. More specifically, it has the following goals:1) To evaluate Streptomyces lividans as a cell factory for the production of heterologousproteins of interest;2) To investigate the transcriptome and proteome of the host strain under different growthconditions, with different expression/secretion vectors, and using different fermentationstrategies, in order to identify the genes important for optimal cell performance,with respect to heterologous protein secretion;3) To analyse metabolic flux control and flux balance with a view to engineering metabolicpathways found in a Streptomyces background, and hence to exploit cellularpathways which provide improved energy transduction, balanced growth and supramolecularassembly;4) To engineer better production/secretion strains of Streptomyces based on the above,and based on information about secretion bottlenecks that will be identified throughthe production of muteins, either via direct mutation of specific amino acids, or bydirected evolution;5) To optimise the protein production process.Fig. 1 Fig. 24. The secretome Platform1. Heterologous genes clonedSecA optimization• Rational mutagenesis• Directed evolutionSPase bindingPMF and PspA5. Strain engineering Platform3. MetabolomicsPlatform2. Analytical Platform4. Bioinformatics Platform2.1 TranscriptomicsFlux analysisIn silicoIn vitroIn vivo2.2. Proteomics6. Production process optimizationImproved production process forprotein of interestFig. 1: The secretome Platform:Production process optimizationFig. 2: Long oligo based/S. coelicolor /microarray(courtesy of Eurogentec)From Fundamental Genomics to Systems Biology: Understanding the Book of Life479

StreptomicsFig. 3 Fig. 4Fig. 3: *Modern fermentationcapabilities:* Up to 100 literfermentors and downstreamprotein purification andcharacterization allowpreparation of engineered“optimized” protein variantsfor injectable or ingestibleanimal trials, biorefining andother industrial or pharmaceticalbiotechnology applications atDirevo Biotech AG inCologne, Germany.Fig. 4: EM photograph ofbranching and sporulating /Streptomyces coelicolor(courtesy of John Innes Institute,Norwich, UK)Expected Results:Based on a better understanding of metabolome-secretome interplay, strategies for improvedprotein secretion will be designed. These will combine better energy generationand directed energy consumption for either cell mass production or heterologous proteinsecretion. Ultimately, a “toolbox” of Streptomyces strains will be engineered and refined,which optimally over-secrete proteins of interest during fermentation.Consequently, Streptomics will generate knowledge which will assist SMEs in the biotechnologyand other industries to develop new and more efficient systems for the industrialproduction of heterologous proteins, using S. lividans as a cell factory. These systems willbe useful in both red (medical) and white (industrial) areas of biotechnology.Potential Impact:This project aims to increase the number of efficient cell factory platforms for the productionof heterologous proteins important in health, biocatalysis and the environment, using Streptomycesas a host. It will therefore contribute to a competitive, knowledge-based economyand sustainable development in Europe, by serving the needs of a research-intensive industrialsector in which many SMEs have traditionally been involved.Keywords: systems biology, Streptomyces, protein secretion, enzymes, biopharmaceuticals,directed evolution, metabolomics, transcriptomics,proteomics480From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Systems biology strategies and metabolome engineering for the enhancedproduction of recombinant proteins in StreptomycesPartnersProject Coordinator:Prof. Jozef AnnéCatholic University of LeuvenLaboratory of BacteriologyRega InstituteMinderbroedersstraat 10B-3000 Leuven, Belgiumjozef.anne@rega.kuleuven.beProf. Michael HeckerErnst-Moritz-Arndt-UniversityInstitute for MicrobiologyGreifswald, GermanyDr. Wayne M. CocoDirevo Biotech AGCologne, GermanyProf. Anastassios EconomouFoundation of Research and TechnologyInstitute of Molecular Biology and BiotechnologyHeraklion, GreeceDr. Marc DaukandtEurogentecDNA MicroArray DepartmentSeraing, BelgiumProf. Jakob KristjánssonProkaria LtdReykjavik, IcelandDr. Benjamin DamienBioXprNamur, BelgiumProf. Roy GoodacreUniversity of ManchesterSchool of ChemistryManchester, UKProf. Anna Eliasson LantzTechnical University of DenmarkCentre for Microbial BiotechnologyLyngby, DenmarkFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life481

SYSCOProject Type:SME- Specific TargetedResearch ProjectContract number:LSHG-CT-2006-037231Starting date:1 st September 2007Duration:36 monthsEC Funding:1 840 719State-of-the-Art:A study conducted by an international expert panel for the University of Toronto, ranked thecomputational examination of host-pathogen interactions among the top 10 biotechnologiesmost likely to improve global health in the next 10 years (Daar et al, 2002). However,information about fundamental aspects of the cellular machinery involved in the interactionsbetween macrophages and intracellular pathogens has not yet been sufficiently categorised,particularly with regard to macrophage function, and there is a need for a systematicand integrative approach to the identification of interconnected functional modules andsalient modifications triggered by intracellular parasitism.Scientific/Technological Objectives:The overall objective of the SYSCO project is to decipher the intracellular biological pathwaysand basic cellular processes that act in physiological conditions as well as in thecontext of intracellular parasitism, in order to highlight the alteration in gene expressionthat stems from the conflict between the host and pathogen genomes. More specifically,the project will use human and mouse macrophages as cellular targets, and the Leishmaniaparasite as a prototype for intracellular pathogens. Leishmania is one of the most intensivelystudied biological models in terms of parasite, host immune response and genetics.SYSCO will decipher and modularise the cascade of intracellular events generated byparasite-cell interactions, and also how they result in either parasite elimination or infectionin humans. A comparative analysis with mouse strains expressing differing susceptibilitieswill help identify key determinants of natural resistance or susceptibility to parasites actingat the macrophage level.In a combined strategy of experimental and theoretical work, the SYSCO consortium willsystematically capture data at different levels of cellular information, using state-of-the-art,multi-parametric molecular technologies (both in human and in mouse). These data will beused to identify regulatory motifs through systematic promoter analysis, and to populatecomputer models with the relevant motifs and associated signalling pathways. The computermodels will be designed as independent modules covering gene regulation, geneexpression, protein interactions and signalling. This modular approach will be used tomimic different types of innate macrophage responses, and to map theoretical predictionsto experimental data.Expected Results:After 36 months, SYSCO will have achieved the following aims:1) Development of a hybrid, in silico model for the innate response of macrophages toan intracellular pathogen, based on the composition of interconnected modules thatmimic different cellular events;2) Development of a comprehensive systems ontology;3) Experimental investigation and categorisation of four different modules, namely generegulation, gene and protein expression and signal transduction;4) Complementary high throughput analysis of the macrophage transcriptome by Affymetrixoligonucleotide arrays and serial analysis of gene expression, both in parasite-infectedand in non-infected cells;5) Prediction and validation of the regulatory networks in macrophages;482From Fundamental Genomics to Systems Biology: Understanding the Book of Life

Systematic Functional analysisof Intracellular Parasitismas a model of genomes conflict6) Experimental determination of cell regulation by quantitative transcription factor assaysand by RNA interference.Potential Impact:Leishmaniasis is one of the world’s major parasitic diseases, but there is no vaccine for it asyet, and the drugs currently prescribed to treat it are fairly toxic. Millions of people living indeveloping countries, mainly in southern and eastern Mediterranean regions and in centraland South America, are exposed to leishmaniasis. The Leishmania parasite is also a majorco-pathogen in the context of HIV infection in southern Europe. The results of this project willbe significant, not only in the context of leishmaniasis, but also for the understanding andtreatment of infection by other intracellular pathogens, such as Mycobacterium tuberculosis,the bacterium which causes tuberculosis.PartnersProject Coordinator:Dr. Alexander KelBIOBASE GmbHDepartment of Research and DevelopmentHalchtersche strasse 3334090 Wolfenbüttel, GermanyAlexander.kel@biobase-international.comDr. David PiquemalSARL Skuld-TechMontpellier, FranceProf. Winston HideUniversity of the Western CapeSouth African National Bioinformatics InstituteBellville, South AfricaDr. Pierre-Andre CazenaveUniversité Pierre et Marie Curie-Paris VI,Laboratoire d’ImmunophysiopathologieInfectieuse – URA 1961Paris, FranceDr. Ralf HerwigMax-Planck Institute forMolecular GeneticsBerlin, GermanyDr. Béatrice RegnaultInstitut PasteurPlate-forme Puce à ADN – Genopole PasteurParis, FranceProf. Patricia RenardFacultés Universitaires Notre-Dame de la PaixUnite de Recherche en Biologie CellulaireNamur, BelgiumProf. Koussay DellagiInstitut Pasteur de TunisLaboratoire d’ImmunopathologieVaccinologie et Genetique Moleculaire (LIVGM)Tunis, TunisiaFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life483

ProustProject Type:Specific Support ActionContract number:LSHG-CT-2006-037654Starting date:1 st January 2007Duration:24 monthsEC Funding:250 000Picture taken at the Proustproject first course, entitled“The dimension of time and genefunctioning: focus on the nervoussystem” which was held at theKristineberg Marine Station inSweden from June 7 to June 12.State-of-the-Art:Knowledge about how regulatory genes and their mechanisms of expression change overtime is expanding rapidly, and it is now clear that this temporal dimension is a commondenominator of experimental systems studied in different life science disciplines. In thepost-genomic era, the focus of research has shifted from the identification of genes to understandingtheir function.Some fundamental aspects of gene function cannot be captured without taking into accountthe complex dynamics of interactions between genes, both in space and in time. A completeunderstanding of gene function therefore requires the development of novel tools forthe analysis of those dynamics, particularly in the temporal domain. Given the complexityof known genetic networks, it seems inevitable that a purely deterministic approach will notgenerate realistic descriptions of cell function.Scientific/Technological Objectives:The overall objectives of PROUSTare as follows: to bring togetherscientists from different disciplinesor fields of research, to establishgenuinely leading-edge projectson gene and protein networkswhich focus on the temporal dimension,and to standardise toolsfor the investigation of timescalesin functional genomics.Furthermore, PROUST plans tocoordinate knowledge on thetemporal dimension of intracellularand intercellular signallingpathways, in order to define theirrole at the molecular, cellular, tissueand organism levels.The above will be crucial for the identification of therapeutic targets with time-dependent susceptibilities.The last general objective for PROUST is to foster and disseminate knowledge onthe temporal dimension of biological processes not only among students and scientists workingin different disciplines, but also among other stakeholders in society. More specifically, thehighly interdisciplinary PROUST consortium will address the following topics:1) Oscillation in gene expression, and the development of tools for investigating dynamicparameters, including rhythmic expression of genes, rhythmic post-transcriptional regulation,regulation of the cell cycle, timing in microRNAs, timing by natural antisensetranscripts, modelling of the timing factors in biological systems, and modelling ofintracellular signalling pathways for therapeutic targeting;2) The implications of the above on human disease, including cardiovascular, neurologicaland psychiatric diseases, abnormal cell proliferation and cancer, nutrition and metabolism,infections and immunity;3) The implications of the above across the human lifespan, from childhood to oldage, in males and females, as well as a focus on issues relating to reproduction andpregnancy;484From Fundamental Genomics to Systems Biology: Understanding the Book of Life

4) The implications of the above across populations and species. This aspect of the consortium’sresearch will draw on the disciplines of population genetics and comparativegenomics, focusing on genes that are conserved throughout evolution, as well as onthe issue of time and population history.Expected Results:PROUST plans to organise workshops and two training courses, ultimately delivering aposition paper on the temporal dimension in functional genomics. The expected output ofPROUST will contribute firstly to the standardisation of approaches to gene expression analyseswhich take into account the temporal dimension as a stochastic variable. Secondly, itwill assist in narrowing the gap between clinically correlative data and causative data forcomplex diseases such as cardiovascular and neurological diseases and cancer, as well asfor the regulation of normal lifetime events (e.g. pregnancy).The mathematical and modelling approaches, whose development PROUST will further,such as false discovery rate (FDR)-based methods for analysing time-course microarraydata, are of particular interest: they can be applied to typical comparisons and samplingschemes or chaotic dynamics in neural networks.Potential Impact:The temporal dimensionin functional genomicsPROUST offers European scientists a unique opportunity to interact in an innovative andmultidisciplinary field of research, providing them with a forum in which they can exchangescientific information relevant to developments in biomedical technology. In particular,PROUST will focus on common denominators (e.g. common genes, gene products and signaltransduction pathways) in functional genomics, in relation to time. Such a coordinatedresearch effort will provide the European Research Area with an obvious strategic advantagein relation to drug discovery, drug delivery, disease prevention, disease therapy andthe general wellbeing of the ageing European population.Keywords: functional genomics, temporal dimensionPartnersProject Coordinator:Prof Marina BentivoglioUniversity of VeronaDepartment of Morphological Biomedical SciencesStrada Le Grazie 837134 Verona, Italymarina.bentivoglio@univr.itDr. Maris LaanEstonian BiocentreFunctional Genomics WorkgroupTartu, EstoniaProf. Krister KristenssonKarolinska InstituetDepartment of NeuroscienceStockholm, SwedenProf. Francis LéviInstitut National dela Recherche Medicale (INSERM)U776 Chronotherapie des cancersHôpital Paul BrousseVillejuif, FranceFrom Fundamental Genomics to Systems Biology: Understanding the Book of Life485

INDEXES

PROJECTS INDEX03D-EM New Electron Microscopy Approaches for Studying Protein Complexesand Cellular Supramolecular Architecture //////////////////////////// 1703DGENOME 3D Genome Structure and Function //////////////////////////////// 1643D-Repertoire A Multidisciplinary Approach to Determine the Structures of ProteinComplexes in a Model Organism ////////////////////////////////// 190AAGRON-OMICS Arabidopsis growth network integrating OMICS technologies ///////////// 464AMPKIN Systems biology of the AMP-activated protein kinase pathway //////////// 456AnEUploidy AnEUploidy: understanding gene dosage imbalance in human healthusing genetics, functional genomics and systems biology //////////////// 350ATD The Alternate Transcript Diversity Project ///////////////////////////// 300Autoscreen AUTOSCREEN for Cell Based High-throughput and High-content GeneFunction Analysis and Drug Discovery Screens ///////////////////////// 98BBACELL HEALTH Bacterial stress management relevant to infectious diseaseand biopharmaceuticals ///////////////////////////////////////// 426BACRNAs Non-coding RNAs in Bacterial Pathogenicity ////////////////////////// 408BaSysBio Towards an understanding of dynamic transcriptional regulationat global scale in bacteria: a systems biology approach ///////////////// 468BioBridge Integrative Genomics and Chronic Disease Phenotypes: modellingand simulation tools for clinicians ////////////////////////////////// 472BIOSAPIENS A European Network for Integrated Genome Annotation //////////////// 296BIOXHIT Bio-Crystallography on a Highly Integrated Technology Platformfor European Structural Genomics ////////////////////////////////// 166CCallimir Studying the biological role of microRNAs in the Dlk1-Gtl2 imprinteddomain ///////////////////////////////////////////////////// 400CAMP Chemical Genomics by Activity Monitoring of Proteases ///////////////// 114CASIMIR Co-ordination And Sustainability of International Mouse InformaticsResources //////////////////////////////////////////////////// 238ChILL Chromatin Immuno-linked ligation: A novel generation of biotechnologicaltools for research and diagnosis /////////////////////////////////// 156COMBIO An integrative approach to cellular signalling and control processes:Bringing computational biology to the bench ///////////////////////// 442COMPUTIS Molecular Imaging in Tissue and Cells by Computer-Assisted InnovativeMultimode Mass Spectrometry //////////////////////////////////// 126COSBICS Computational Systems Biology of Cell Signalling ////////////////////// 444488 From Fundamental Genomics to Systems Biology: Understanding the Book of Life

DDanuBiobank The Danubian Biobank Initiative - Towards Information-based Medicine ///// 286DIAMONDS Dedicated Integration and Modelling of Novel Data and Prior Knowledgeto Enable Systems Biology /////////////////////////////////////// 446DIATOMICS Understanding Diatom Biology by Functional Genomics Approaches /////// 428DNA REPAIR DNA Damage Response and Repair Mechanisms ////////////////////// 334EELIfe The European Lipidomics Initiative: Shaping the life sciences ////////////// 450EMBRACE A European Model for Bioinformatics Research and Community Education /// 302E-MeP The European Membrane Protein Consortium ///////////////////////// 176E-MeP-Lab E-MeP-Lab Training events in membrane protein structural biology ////////// 196EMERALD Empowering the Microarray-Based European Research Area to Takea Lead in Development and Exploitation ////////////////////////////// 96EMI-CD European Modelling Initiative combating complex diseases ////////////// 438EndoTrack Tracking the Endocytic Routes of Growth Factor Receptor Complexesand their Modulatory Role on Signalling ///////////////////////////// 346ENFIN An Experimental Network for Functional Integration //////////////////// 306EpiGenChlamydia Contribution of molecular epidemiology and host-pathogen genomicsto understand Chlamydia trachomatis disease //////////////////////// 290ESBIC-D European Systems Biology Initiative for Combating Complex Diseases ////// 452ESTOOLS Platforms for biomedical discovery with human ES cells ///////////////// 386EUCLOCK Entrainment of the Circadian Clock ///////////////////////////////// 418EUCOMM The European Conditional Mouse Mutagenesis Programme ////////////// 230EUHEALTHGEN Harnessing the Potential of Human Population Genetics Researchto Improve the Quality of the EU Citizen ///////////////////////////// 280EUMODIC The European Mouse Disease Clinic:A distributed phenotyping resource for studying human disease /////////// 234Eurasnet European Alternative Splicing Network of Excellence /////////////////// 402EURATools European Rat Tools for Functional Genomics ////////////////////////// 244EuReGene European Renal Genome Project ////////////////////////////////// 370EURExpress A European Consortium to Generate a Web-Based Gene Expression Atlasby RNA in situ Hybridisation ///////////////////////////////////// 218EUROBIOFUND A Strategic Forum for the Dialogue and Coordinationof European Life Sciences, Funders and Performers ///////////////////// 460EUROFUNGBASE Strategy to build up and maintain an integrated sustainable European fungalgenomic database required for innovative genomics research on filamentousfungi, important for biotechnology and human health /////////////////// 310EuroHear Advances in hearing science: from functional genomics to therapies //////// 362EUROSPAN EUROpean Special Populations Research Network: Quantifyingand Harnessing Genetic Variation for Gene Discovery ////////////////// 284EUSYSBIO The Take-off of European Systems Biology //////////////////////////// 434EuTRAC European Transcriptome, Regulome & Cellular Commitment Consortium ///// 390EU-US Workshop Workshop on “Systems biology of DNA damage-induced stress responses /// 448EVI-GENORET Functional genomics of the retina in health and disease ///////////////// 374Extend-NMR Extending NMR for Functional and Structural Genomics ///////////////// 202FFESP Forum for European Structural Proteomics //////////////////////////// 194FGENTCARD Functional GENomic diagnostic Tools for Coronary Artery Disease ///////// 102FLPFLEX A Flexible Toolkit for Controlling Gene Expression in the Mouse /////////// 228FOSRAK Function of small RNAs across kingdoms //////////////////////////// 398FSG-V-RNA Functional and Structural Genomics of Viral RNA ////////////////////// 180FunGenEs Functional Genomics in Engineered ES cells ////////////////////////// 380From Fundamental Genomics to Systems Biology: Understanding the Book of Life 489

PROJECTS INDEXGGeneFun In-Silico Prediction of gene function///////////////////////////////// 174GENINTEG Controlled gene integration:a requisite for genome analysis and gene therapy ///////////////////// 130GENOSEPT Genetics of Sepsis in Europe ///////////////////////////////////// 276HHEROIC High-Throughput Epigenetic Regulatory Organisation in Chromatin ///////// 152HT3DEM High throughput Three-dimensional Electron Microscopy ///////////////// 198HUMGERI Human Genomic Research Integration ////////////////////////////// 270IImpacts Archive Tissues: Improving Molecular Medicine Researchand Clinical Practice /////////////////////////////////////////// 288IMPS Innovative tools for membrane structural Proteomics //////////////////// 204INTERACTION PROTEOME Functional Proteomics: Towards defining the interaction proteome ////////// 108LLYMPHANGIOGENOMICS Genome-Wide Discovery and Functional Analysisof Novel Genes in Lymphangiogenesis ////////////////////////////// 358MMAIN Targeting Cell Migration in Chronic Inflammation ////////////////////// 316Med-Rat New Tools to Generate Transgenic and Knock-out Mouse and Rat Models /// 248MEGATOOLS New tools for Functional Genomics based on homologous recombinationinduced by double-strand break and specific meganucleases ///////////// 136MICROSAT workshop Microsatellites and VNTRs: workshop on bioinformatics,genomics and functionality /////////////////////////////////////// 278MITOCHECK Regulation of Mitosis by Phosphorylation - A Combined FunctionalGenomics, Proteomics and Chemical Biology Approach ///////////////// 322MODEST Modular Devices for Ultrahigh-throughput and Small-volume Transfection //// 104MOLECULAR IMAGING Integrated Technologies for In Vivo Molecular Imaging ////////////////// 120MolPAGE Molecular Phenotyping to Accelerate Genomic Epidemiology ///////////// 272MolTools Advanced Molecular Tools for Array-Based Analyses of Genomes,Transcriptomes, Proteomes and Cells //////////////////////////////// 86MUGEN Integrated Functional Genomics in Mutant Mouse Models as Toolsto Investigate the Complexity of Human Immunological Disease /////////// 222MYORES Multiorganismic Approach to Study Normal and Aberrant MuscleDevelopment, Function and Repair ///////////////////////////////// 366NNDDP NMR Tools for Drug Design Validated on Phosphatases ///////////////// 188NemaGENETAG Nematode Gene-Tagging Tools and Resources //////////////////////// 260NEUPROCF Development of New Methodologies for Low Abundance Proteomics:Application to Cystic Fibrosis ///////////////////////////////////// 112NFG Functional Genomics of the Adult and Developing Brain ///////////////// 356NMR-Life Focusing NMR on the Machinery of Life ///////////////////////////// 200490 From Fundamental Genomics to Systems Biology: Understanding the Book of Life

PROJECTS INDEXOOptiCryst Optimisation of Protein Crystallisation for European Structural Genomics //// 210PPEROXISOMES Integrated Project to decipher the biological function of peroxisomesin health and disease /////////////////////////////////////////// 330PHOEBE Promoting harmonisation of epidemiological biobanks in Europe ////////// 282PLASTOMICS Mechanisms of transgene integration and expression in crop plant plastids,underpinning a technology for improving human health ///////////////// 132PLURIGENES Pluripotency Associated Genes to Dedifferentiate Neural Cellsinto Pluripotent Cells //////////////////////////////////////////// 384PRIME Priorities for mouse functional genomics research across Europe:integrating and strengthening research in Europe ////////////////////// 226ProDac Proteomics Data Collection /////////////////////////////////////// 116Proust The temporal dimension in functional genomics /////////////////////// 484QQUASI Quantifying signal transduction /////////////////////////////////// 440RREGULATORY GENOMICS Advanced Genomics Instruments, Technology and Methods forDetermination of Transcription Factor Binding Specificities:Applications for Identification of Genes Predisposing to Colorectal Cancer //// 90RIBOREG Novel non-coding RNAs in differentiation and disease ////////////////// 396RIBOSYS Systems Biology of RNA Metabolism in Yeast ///////////////////////// 458RNABIO Computational approaches to non-coding RNAs /////////////////////// 410RUBICON Role of Ubiquitin and Ubiquitin-like Modifiers in Cellular Regulation //////// 342SSIGNALLING & TRAFFIC Signalling and Membrane Trafficking in Transformation and Differentiation /// 326Sirocco Silencing RNAs: organisers and coordinatorsof complexity in eukaryotic organisms ////////////////////////////// 412SMARTER Development of small modulators of gene activationand repression by targeting epigenetic regulators ////////////////////// 158SPINE2-COMPLEXES From Receptor to Gene: Structures of Complexesfrom Signalling Pathways linking Immunology, Neurobiology and Cancer //// 206STAR A SNP and Haplotype Map for the Rat ////////////////////////////// 242STEROLTALK Functional Genomics of Complex Regulatory Networks from Yeastto Human: Cross-Talk of Sterol Homeostasis and Drug Metabolism ///////// 338Streptomics Systems biology strategies and metabolome engineering for the enhancedproduction of recombinant proteins in Streptomyces //////////////////// 478SYSBIOMED Systems Biology for Medical Applications //////////////////////////// 474SYMBIONIC Towards European Neuromal Cell Simulation: a European consortiumto integrate the scientific activities for the creation of a European Alliancedevoted to the complete in-silico model of Neuronal Cell //////////////// 436SYSCO Systematic Functional analysis of Intracellular Parasitism asa model of genomes conflict ////////////////////////////////////// 482SysProt System-wide analysis and modelling of protein modification ////////////// 476From Fundamental Genomics to Systems Biology: Understanding the Book of Life 491

PROJECTS INDEXTTAGIP Targeted Gene Integration in Plants: Vectors, Mechanismsand Applications for Protein Production ///////////////////////////// 134TargetHerpes Molecular intervention strategies targeting latentand lytic herpesvirus infections //////////////////////////////////// 100Tat machine Functional genomic characterisation of the bacterial Tat complexas a nanomachine for biopharmaceutical production anda target for novel anti-infectives //////////////////////////////////// 92TEACH-SG Training and Education in High Volume and High Value Structural Genomics / 212TEMPO Temporal Genomics for Tailored Chronotherapeutics //////////////////// 422THE EPIGENOME Epigenetic plasticity of the genome ///////////////////////////////// 148Tips4Cells Scanning Probe Microscopy techniques for real time, high resolutionimaging and molecular recognition in functional and structural genomics //// 124TP Plants and Health The European Technology Platform on Plant Genomics and Biotechnology:Plants for healthy lifestyles and for sustainable development ////////////// 262TransCode Novel Tool for High-Throughput Characterisationof Genomic Elements Regulating Gene Expression in Chordates //////////// 94TransDeath Programmed cell death across the eukaryotic kingdom ////////////////// 328TRANS-REG Transcription Complex Dynamics Controlling SpecificGene Expression Programmes //////////////////////////////////// 142UUPMAN Understanding Protein Misfolding and Aggregation by NMR ///////////// 186VVALAPODYN Validated Predictive Dynamic Model of Complex Intracellular Pathwaysrelated to cell death and survival ////////////////////////////////// 462VIZIER Comparative structural genomics on viral enzymes involved in replication //// 182WWOUND A multi-organism functional genomics approachto study signalling pathways in epithelial fusion/wound healing /////////// 320XX-OMICS Xenopus Comparative Genomics: Coordinating Integrated and ComparativeFunctional Genomics for Understanding Normal and Pathologic Development 264X-TRA-NET ChIP-Chip to Decipher Transcription Networks of RXR and Partners ///////// 144YYSBN Yeast Systems Biology Network /////////////////////////////////// 454ZZF-MODELS Zebrafish Models for Human Development and Disease ///////////////// 252ZF-TOOLS High-throughput Tools for Biomedical Screens in Zebrafish /////////////// 256492 From Fundamental Genomics to Systems Biology: Understanding the Book of Life

INSTITUTION ANDCOORDINATOR INDEXA■ Amaxa AG, Dr. Birgit Nelsen-Salz, MODEST //////////////////////////////////////////// 105■ Agricultural Biotechnology Center, Genetic Reprogramming Group, Dr. Andras Dinnyes, Med-Rat ///// 249■ Aston University, Department of Life and Health Sciences, Dr. Roslyn Bill, E-MeP ////////////////// 178■ Aston University, Department of Life and Health Sciences, Dr. Roslyn Bill, E-MeP-Lab /////////////// 197■ Aston University, Department of Life and Health Sciences, Dr. Roslyn Bill, OptiCryst //////////////// 211B■ BIOBASE GmbH, Department of Research and Development, Dr. Alexander Kel, SYSCO /////////// 483■ Biomedical Sciences Research Center, Dr. George Kollias, MUGEN /////////////////////////// 224C■ Catholic University of Leuven, Laboratory of Bacteriology, Rega Institute,Prof. Jozef Anné, Streptomics /////////////////////////////////////////////////////////481■ CELLECTIS SA, Dr. Frédéric Pâques, MEGATOOLS //////////////////////////////////////// 137■ Centre de Regulació Genòmica (CRG), Systems Biology Laboratory,Prof. Luis Serrano, 3D repertoire ////////////////////////////////////////////////////// 192■ Centre for Brain Research, Medical University of Vienna, Prof. Johannes Berger, Peroxisomes //////// 333■■■Centre National de la Recherche Scientifique (CNRS), Institut des Sciences du Végétal(UPR no 2355), RIBOREG /////////////////////////////////////////////////////////// 397Centre National de la Recherche Scientifique (CNRS), UMR 8080 Développement et Evolution,Dr. Andre Mazabraud, X-OMICS ///////////////////////////////////////////////////// 265Centre National De La Recherche Scientifique (CNRS), Université Louis Pasteur, Institut de biologiemoléculaire et cellulaire, ARN ‘Architecture et Réactivité de l’ARN’, Prof. Eric Westhof, RNABIO ////// 411■ Centre National de la Recherche Scientifique (CNRS)/Université Paris-7 UMR 7099,Institut de Biologie Physico-Chimique, IMPS ////////////////////////////////////////////// 205■■Commissariat à l’Energie Atomique CEA), LIST/DETECS, Dr Haan Serge,Dr Robbe Marie-France, COMPUTIS /////////////////////////////////////////////////// 127Consejo Superior de Investigaciones Cientificas (CSIC), Instituto de Biologia Molecularde Barcelona, Dr. Enrique Martin-Blanco, WOUND /////////////////////////////////////// 321■ Consorzio Interuniversitario di Risonanze Magnetiche di Metalloproteine Paramagnetiche,Magnetic Resonance Center (CERM), Prof. Ivano Bertini, NMR-Life //////////////////////////// 201■ CRG - Centre de Regulació Genòmica, Systems Biology Research Unit, Prof. Luis Serrano, COMBIO // 443D■ DECHEMA e.V., Dr. Karsten Schürrle, SYSBIOMED //////////////////////////////////////// 475■ Diagenode SA, Didier Allaer, ChILL //////////////////////////////////////////////////// 157E■■Erasmus MC University Medical Center, Department of Cell Biology and Genetics,Prof. Dr. Frank Grosveld, EuTRACC //////////////////////////////////////////////////// 392Erasmus Universitair Medisch, Centrum Rotterdam, Dept. of Cell Biology and Genetics,Prof. Jan Hoeijmakers, DNA Repair /////////////////////////////////////////////////// 336From Fundamental Genomics to Systems Biology: Understanding the Book of Life 493

INSTITUTION AND COORDINATOR INDEX■■■■■ERM-0206 TAGC, Institut National de la Santé et de la Recherche Médicale (INSERM),Prof. Daniel Gautheret, ATD ///////////////////////////////////////////////////////// 301European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EBI),Wellcome Trust Genome Campus, Dr. Graham Cameron, EMBRACE ////////////////////////// 304European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EBI),Wellcome Trust Genome Campus, Prof. Ewan Birney, ENFIN //////////////////////////////// 308European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute (EBI),Wellcome Trust Genome Campus, Prof. Janet Thornton, BioSapiens //////////////////////////// 298European Molecular Biology Laboratory (EMBL), Mouse Biology Unit, Monterotondo Outstation,Prof. Nadia Rosenthal, FLPFLEX /////////////////////////////////////////////////////// 229■ European Molecular Biology Laboratory (EMBL), Outstation Hamburg,Macromolecular Crystallography, Dr. Victor Lamzin, BIOXHIT //////////////////////////////// 168■ European Plant Science Organisation, Dr. Karin Metzlaff, TP Plants and Health /////////////////// 263■ European Science Foundation (ESF), Prof. Marja Makarow, EuroBioFund /////////////////////// 461■F■■■European Society of Intensive Care Medicine, Research Activities, Prof. Julian Bion,Dr. Nathalie Mathy, GenOSept /////////////////////////////////////////////////////// 277Flanders Interuniversity Institute for Biotechnology, Department of Plant Systems Biology,Computational Biology Group, Prof. Martin Kuiper, DIAMONDS ///////////////////////////// 447Fondazione Centro San Raffaele Del Monte Tabor, Department of Molecular Biologyand Functional Genomics, Prof. Ruggero Pardi, MAIN ///////////////////////////////////// 319Fondazione Telethon, Telethon Institute of Genetics and Medicine, Molecular Biology Unit,Dr. Sandro Banfi, TransCode ////////////////////////////////////////////////////////// 95■ Fondazione Telethon, TIGEM-Telethon Institute of Genetics and Medicine,Prof. Andrea Ballabio, EURExpress //////////////////////////////////////////////////// 221■ Forschungsinstitut für Molekulare Pathologie GmbH, Dr. Jan-Michael Peters, MitoCheck ///////////// 325■ Forschungszentrum Juelich GmbH, Project Management Juelich (Ptj), Dr. Petra Wolff, EUSYSBIO ////// 435■■■G■Foundation for Research and Technology – Hellas, Institute of Electronic Structureand Laser (IESL), Institute of molecular biology and biotechnology (IMBB),Prof. Eleftherios Economou, MOLECULAR IMAGING /////////////////////////////////////// 122Foundation for Research and Technology – Hellas, Institute of Molecular Biology and Biotechnology,Dr. Nektarios Tavernarakis, NemaGENETAG //////////////////////////////////////////// 261Foundation for Research and Technology – Hellas, Institute of Molecular Biology and Biotechnology,Prof. Iannis Talianidis, TRANS-REG //////////////////////////////////////////////////// 143Ghent University/Flanders Interuniversity Institute for Biotechnology, Department of Plant SystemsBiology, Computational Biology group, Prof. Martin Kuiper, EMERALD ////////////////////////// 97■ Ghent University, Flanders Institute for Biotechnolgy (VIB), Department of Plant Systems Biology,Dr. Pierre Hilson, AGRON-OMICS //////////////////////////////////////////////////// 467■ Gothenburg University, Department of Cell and Molecular Biology, Prof. Stefan Hohmann, AMPKIN /// 457■ Gothenburg University, Department of Cell and Molecular Biology, Prof. Stefan Hohmann, QUASI //// 441■ Grenoble – Institut des Neurosciences Centre de Recherche INSERM U 836,Université Joseph Fourier, Dr. Antoine Depaulis, VALAPODYN //////////////////////////////// 463■GSF-Forschungszentrum fur Umwelt und Gesundheit GmbH, Institute of Molecular Radiation Biology,Prof. Dr. Jean-Marie Buerstedde, GENINTEG //////////////////////////////////////////// 131H■Helmholtz Zentrum München, German Research Center for Environmental Health GmbH,Institute of Developmental Genetics, Prof. Wolfgang Wurst, EUCOMM ///////////////////////// 233I■ Institut d’Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Josep Roca, BioBridge /////////// 473494 From Fundamental Genomics to Systems Biology: Understanding the Book of Life

INSTITUTION AND COORDINATOR INDEX■ Institut Jacques Monod, Team ‘Avenir’ INSERM, Prof. Thierry Galli, SIGNALLING & TRAFFIC///////// 327■ Institut National de la Recherche Agronomique (INRA), Dr. Philippe Noirot, BaSysBio ////////////// 471■■Institut National de la Recherche Agronomique (INRA), Physiologie animaleet systèmes d’élevage (PHASE), Dr. Jean-Stéphane Joly, Plurigenes //////////////////////////// 385Institut National de la Santé et de la Recherche Médicale, Faculte de Medecine Necker InsermU467, Dr. Aleksander Edelman, NEUPROCF //////////////////////////////////////////// 113■ Institut National de la Santé et de la Recherche Médicale (INSERM), U384,Dr. Krzysztof Jagla, MYORES //////////////////////////////////////////////////////// 368■ Institut National de la Santé et de la Recherche Médicale (INSERM) U592,Laboratoire de Physiopathologie Cellulaire et Moleculaire de la Retine, Institut de la Vision,Prof. Jose-Alain Sahel, EVI-GENORET ////////////////////////////////////////////////// 376■■Institut National de la Santé et de la Recherche Médicale (INSERM), U776Rythmes biologiques et cancers ,Hôpital Paul Brousse, Dr. Francis Lévi, TEMPO /////////////////// 423Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS 587- Institut Pasteur,Unité de Génétique et Physiologie de l’Audition, Prof. Christine Petit, EuroHear /////////////////// 364J■Johann Wolfgang Goethe-Universität, Center for Biomolecular Magnetic Resonance,Institute for Organic Chemistry and Chemical Biology, Prof. Harald Schwalbe, UPMAN //////////// 187K■ Karolinska Institutet, Department of Cell and Molecular Biology, Prof. Maria Masucci, RUBICON ///// 345■LKing’s College, University of London, Department of Social Genetic and Developmental Psychiatry,Institute of Psychiatry, Prof. David Collier, MICROSAT workshop ////////////////////////////// 279■ Lay Line Genomics SpA, c/o San Raffaele Scientific Park, Dr. Ivan Arisi, SYMBIONIC ////////////// 437■ Leiden Institute of Physics, Leiden University, Dr. Tjerk Oosterkamp, Tips4Cells //////////////////// 125■ Leiden University, Clusius Laboratory, Prof. Cees van den Hondel, EUROFUNGBASE ////////////// 311■ Leiden University, Institute of Biology, Molecular Cell Biology, Dr. Annemarie H. Meijer, ZF-TOOLS //// 257■ Leiden University Medical Center, Dr. Harry Vrieling, EU-US Workshop ///////////////////////// 448■ Ludwig Maximilians University of Munich, Adolf-Butenandt Institute, Histone Modifications Group,Protein Analysis Core Facility, Prof. Axel Imhof, SMARTER /////////////////////////////////// 159■ Ludwig Maximilians University, Institute for Medical Psychology, Prof. Till Roenneberg, EUCLOCK ///// 420M■■■■Max-Delbrück-Center for Molecular Medicine, Cardiovascular Research Centre, Departmentof Cardiovascular Research, Lipids and Experimental Gene Therapy, Thomas Willnow, EuReGene //// 373Max-Delbrück-Center for Molecular Medicine, Experimental Geneticsof Cardiovascular Diseases, Dr. Norbert Hübner,STAR ///////////////////////////////////// 243Max-Planck-Institute of Biochemistry, Department of Cellular Biochemistry,Prof. F. Ulrich Hartl, INTERACTION PROTEOME ////////////////////////////////////////// 111Max-Planck Institute for Biophysical Chemistry, Department of Cellular Biochemistry,Prof. Reinhard Lührmann, Eurasnet //////////////////////////////////////////////////// 406■ Max Planck Institute for Developmental Biology, Department of Genetics,Dr. Robert Geisler, ZF-MODELS /////////////////////////////////////////////////////// 254■ Max-Planck Institute of Molecular Cell Biology and Genetics, Prof. Marino Zerial, EndoTrack///////// 349■ Max Planck Institute for Molecular Genetics, Vertebrate Genomics, Dr. Ralf Herwig, EMI-CD ///////// 439■ Max-Planck Institute for Molecular Genetics, Vertebrate Genomics, Prof. Dr. Hans Lehrach, ESBIC-D /// 453■ Medical Research Council, Mammalian Genetics Unit, MRC Harwell, Prof. Steve Brown, PRIME ////// 227■ Medical Research Council, Mammalian Genetics Unit, MRC Harwell, Prof. Steve Brown, EUMODIC /// 236■Medical Research Council, Physiological Genomics and Medicine, MRC Clinical Sciences Centre,Prof. Timothy J. Aitman, EURATools //////////////////////////////////////////////////// 246From Fundamental Genomics to Systems Biology: Understanding the Book of Life 495

INSTITUTION AND COORDINATOR INDEX■ MicroDiscovery GmbH, NutriSystemics, Dr. Arif Malik, SysProt /////////////////////////////// 477N■ Newcastle University, Molecular Microbiology Group, Institute for Cell and Molecular Biosciences,Prof. Colin R Harwood, BACELL HEALTH //////////////////////////////////////////////// 427■ Norwegian Institute of Public Health, Division of Epidemiology, Dr. Jennifer Harris, PHOEBE ///////// 283R■ Radboud University Nijmegen, IMM/Faculty of Science, Mathematics and Informatics,Prof. Sybren Wijmenga,FSG-V-RNA /////////////////////////////////////////////////// 181■ Research Institute for Molecular Pathology (IMP), Prof. Thomas Jenuwein, THE EPIGENOME ///////// 150■ Ruhr-Universitaet Bochum, Medizinisches Proteom-Center, Prof. Helmut E. Meyer, ProDac /////////// 117S■ Saarland University, Department of Biochemistry, Prof. Rita Bernhardt, STEROLTALK //////////////// 341■ SISSA (Scuola Internazionale Superiore di Studi Avanzati / International School for AdvancedStudies), Neurobiology Sector, Prof. Anna Menini, NFG //////////////////////////////////// 357■ Stazione Zoologica Anton Dohrn, Cell Signalling Laboratory, Dr. Chris Bowler, DIATOMICS ///////// 429■ Stichting Katholieke Universiteit, Department of Molecular Biology, Prof. Henk Stunnenberg, HEROIC // 155T■ Technical University of Denmark, Centre for Microbial Biotechnology Biocentrum,Prof. Jens Nielsen, YSBN /////////////////////////////////////////////////////////// 454■ The Sainsbury Laboratory, John Innes Centre, Prof. David Baulcombe, Sirocco /////////////////// 414■The Wellcome Trust, Department of Biomedical Resources and Functional Genomics,Dr. Alan Doyle, EUHEALTHGEN ////////////////////////////////////////////////////// 281U■ Universitat Autonoma de Barcelona, Institut de Biotecnologia i de Biomedicina,Protein Engineering and Enzymology Unit, Prof. Francesc Xavier Aviles, CAMP /////////////////// 115■ Universität Rostock, Department of Computer Science, Prof. Olaf Wolkenhauer, COSBICS ////////// 445■■■■■■■Universiteit van Amsterdam, Science Faculty, Swammerdam Institute for Life Sciences,Prof. Roeland Van Driel, 3DGENOME ///////////////////////////////////////////////// 165Université de la Méditerranée, Centre National de la Recherche Scientifique (CNRS), LaboratoireArchitecture et Fonction des Macromolecules Biologiques UMR 6098, Dr. Bruno Canard, VIZIER////// 184Université Libre de Bruxelles, Service de Conformation de Macromolecules Biolgiqueset Bioinformatique, Biologie Moleculaire, Prof. Shoshana Wodak, GeneFun ///////////////////// 175University Hospital Regensburg, Institute of Clinical Chemistry and Laboratory Medicine,Prof. Gerd Schmitz, DanuBiobank ///////////////////////////////////////////////////// 287University Medical Center Groningen, Department of Medical Microbiology,Prof. Jan Maarten van Dijl, Tat machine ///////////////////////////////////////////////// 93University of Basel, M.E. Miller Institute for Structural Biology, Biozentrum,Prof. Andreas Engel, 3D-EM ///////////////////////////////////////////////////////// 173University of Basel, M E Mueller Institute for Structural Biology, Biozentrum,Prof. Andreas Engel, HT3DEM /////////////////////////////////////////////////////// 199■ University of Bologna, Centro Interdipartimentale Galvani (CIG),Prof. Gabriella Campadelli-Fiume,TargetHerpes ////////////////////////////////////////// 101■ University of Cambridge, Professor Ernest D. Laue, Extend-NMR ////////////////////////////// 203■ University of Cambridge, Department of Plant Sciences, Prof. John Gray, PLASTOMICS ///////////// 133■■University of Cambridge, Department of Physiology, Development and Neuroscience,Dr. Paul Schofield, CASIMIR ///////////////////////////////////////////////////////// 239University of Cologne, Institute of Neurophysiology, Faculty of Medicine,Prof. Jürgen Hescheler, FunGenES ///////////////////////////////////////////////////// 382496 From Fundamental Genomics to Systems Biology: Understanding the Book of Life

INSTITUTION AND COORDINATOR INDEX■ University of Copenhagen, Institute of Molecular Biology, Prof. John Mundy, TransDeath //////////// 329■ University of Debrecen, Medical and Health Science Center, Department of Biochemistryand Molecular Biology, Dr. László Fésüs, HUMGERI /////////////////////////////////////// 271■ University of Edinburgh, Public Health Sciences, Prof. Harry Campbell, EUROSPAN /////////////// 285■ University of Edinburgh, The Wellcome Trust Centre for Cell Biology, Prof. Jean Beggs, RIBOSYS ////// 459■■■■■University of Freiburg, Institute for Biology II, Faculty of Biology, Center for Applied Biosciences,Prof. Dr. Klaus Palme, Autoscreen ////////////////////////////////////////////////////// 99University of Geneva, Faculty of Medicine, Department of Genetic Medicine and Development,Prof. Stylianos Antonarakis, AnEUploidy //////////////////////////////////////////////// 353University of Helsinki, Faculty of Medicine, Biomedicum Helsinki, Molecular Cancer BiologyProgram, Prof. Kari Alitalo, LYMPHANGIOGENOMICS //////////////////////////////////// 361University of Helsinki, Faculty of Medicine, Genome-Scale Biology Research Programme,Prof. Jussi Taipale, REGULATORY GENOMICS //////////////////////////////////////////// 91University of Liège, Unit of Animal Genomics, Faculty of Veterinary Medicine,Dr. Michel Georges, Dr. Carole Charlier, Callimir ///////////////////////////////////////// 401■ University of Oxford, Oxford Centre for Diabetes, Endocrinology and Metabolism (OCDEM),Prof. Mark McCarthy, MolPAGE ////////////////////////////////////////////////////// 275■ University of Oxford, Prof. John Bell, MolPAGE /////////////////////////////////////////// 275■■■■■■■University of Oxford, Wellcome Trust Centre for Human Genetics,Dr. Dominique Gauguier, FGENTCARD ///////////////////////////////////////////////// 103University of Oxford, Wellcome Trust Centre for Human Genetics, Division of Structural Biology,Prof. David Stuart, TEACH-SG //////////////////////////////////////////////////////// 213University of Sheffield, Centre for Stem Cell Biology, Department of Biomedical Sciences,Prof. Peter W Andrews, ESTOOLS///////////////////////////////////////////////////// 389University of Southern Denmark, Department of Biochemistry and Molecular Biology,Prof. Susanne Mandrup, X-TRA-NET /////////////////////////////////////////////////// 145University of Trieste, Department of Clinical Morphological and Technological Sciences,International Centre for Genetic Engineering and Biotechnology, Molecular HistopathologyLaboratory, Prof. Giorgio Stanta, Impacts /////////////////////////////////////////////// 289University of Verona, Department of Morphological Biomedical Sciences,Prof. Marina Bentivoglio, Proust ////////////////////////////////////////////////////// 485University of Vienna, Department of Biochemistry, “Max F. Perutz Laboratories”,Prof. Renée Schroeder, BACRNAs ///////////////////////////////////////////////////// 409■ Uppsala University, Department of Cell and Molecular Biology, Biomedical Center,Prof. E. Gerhart Wagner, FOSRAK //////////////////////////////////////////////////// 399■ Uppsala University, Department of Genetics and Pathology, Prof. Ulf Landegren, MolTools /////////// 89■ Utrecht University, Bijvoet Center for Biomolecular Research, Faculty of Sciences,Prof. Rolf Boelens, NDDP /////////////////////////////////////////////////////////// 189■ Utrecht University, Bijvoet Center and Institute of Biomembranes, Prof. Gerrit van Meer, ELIfe ///////// 451V■VU University Medical Center, Immunogenetics of Infectious Diseases, Department of Pathology,Laboratory of Immunogenetics, Dr. Servaas A. Morré, EpiGenChlamydia /////////////////////// 291W■ Weizmann Institute of Science, Department of Structural Biology, Prof. Joel L. Sussman, FESP ///////// 195■■Weizmann Institute of Science, Faculty of Biochemistry, Department of Plant Sciences,Prof. Avi Levy, TAGIP /////////////////////////////////////////////////////////////// 135Wellcome Trust Centre for Human Genetics, Division of Structural Biology,Prof. David Stuart, SPINE2-COMPLEXES //////////////////////////////////////////////// 208From Fundamental Genomics to Systems Biology: Understanding the Book of Life 497

KEYWORDS INDEX02D crystallisation: ................................................................................................1993D electron microscopy: .......................................................................................1723D structure: ..................................................................................................165, 1783D-electron microscopy: ........................................................................................192Aadult stem cells: ...................................................................................................105ageing disorder: ..................................................................................................286ageing: ...............................................................................................................336age-related macular degeneration (AMD):...............................................................376alternative RNA splicing: ......................................................................................405amphipols: ..........................................................................................................205Aneuploidy: ........................................................................................................352animal dystrophies: ..............................................................................................376animal immunology: .............................................................................................224animal models: ................................................ 224, 227, 228, 236, 239, 249, 254, 257, 372, 420animal mutants: ...................................................................................................376anti-infectives: .......................................................................................................93antimicrobial agents: ............................................................................................409antisense RNA: ....................................................................................................409anti-tumor drug discovery: .....................................................................................257antiviral drugs: ....................................................................................................184apoptosis: .....................................................................................................105, 329applied optics: .....................................................................................................122Arabidopsis: ..................................................................................................135, 467association: .........................................................................................................279automated RNA ISH system: ..................................................................................220automation techniques: .........................................................................................168BBacillus, E. coli: .....................................................................................................93Bacillus: ..............................................................................................................470bacterial factors: ..................................................................................................290bacterial pathogens: .............................................................................................427bacterial virulence: ...............................................................................................409basic biological processes:....................................................................................301bioanalytical chemistry: ........................................................................................127biobank: .............................................................................................................286biobanks: ................................................................................................ 281, 283, 289biochemistry: .......................................................................................................409bioethics: ............................................................................................................283bioinformatics algorithms: ......................................................................................95bioinformatics: .............................. 93, 184, 192, 239, 254, 265, 303, 329, 399, 439, 453, 455, 470, 477498From Fundamental Genomics to Systems Biology: Understanding the Book of Life

iomolecular complexes: .......................................................................................203biopharmaceuticals: ...................................................................................93, 427, 480biotechnology: .....................................................................................................131brain: .................................................................................................................357CCaenorhabditis elegans: .......................................................................................261callipyge: ............................................................................................................401cancer metastasis: ................................................................................................348cancer: ................................................................................... 91, 325, 329, 336, 360, 447cardiovascular disease: ........................................................................................103cardiovascular diseases: .......................................................................................372cell adhesion: ......................................................................................................327cell biology: ........................................................................................................429cell cycle: ......................................................................................................325, 422cell death and survival: .........................................................................................463cell division: ........................................................................................................327cell fate determination: .........................................................................................150cell migration: ...............................................................................................318, 327cell physiology: ....................................................................................................364cellular commitment: .............................................................................................392cellular dynamics: ................................................................................................441cellular: ..............................................................................................................382central nervous system: .........................................................................................385chemical biology: ................................................................................................325chemical inhibitors: ..............................................................................................325chemiotherapeutics: ..............................................................................................101chemogenomics: ..................................................................................................115chemoproteomics: ................................................................................................115ChIP assay: .........................................................................................................157ChIP-chip: ...........................................................................................................145Chlamydia: .........................................................................................................290chromatin modification: ........................................................................................150chromatin remodelling: .........................................................................................157chromatin: ...........................................................................................................154chromatin-IP: ........................................................................................................145chromosome engineering: .....................................................................................470chronic heart failure: ............................................................................................473chronic obstructive pulmonary diseases: .................................................................473chronobiology: ....................................................................................................420circadian clock: .............................................................................................420, 422clinical application of lipids: ..................................................................................451co-factors: ...........................................................................................................145COGENE: ...........................................................................................................283comparative genomics: .................................................................................... 95, 427comparative: .................................................................................................249, 279complex disease: .................................................................................................283complex diseases: ..........................................................................................439, 453complex genetics: ................................................................................................372complex traits: .....................................................................................................246complex-complex interactions: ...............................................................................143computational biology: .........................................................................................443computational predictions: ....................................................................................308computational systems biology: ..............................................................................437computer modelling: .............................................................................................443conditionally mutated mouse ES cell library: ............................................................232From Fundamental Genomics to Systems Biology: Understanding the Book of Life499

KEYWORDS INDEXconserved genes: ...........................................................................................265, 321conserved non-genic sequences: .............................................................................95COPD: ................................................................................................................473copy number polymorphisms: ................................................................................352coronary artery:...................................................................................................103cryoelectron microscopy: ......................................................................................172crystal structure: ...................................................................................................184crystallization: .....................................................................................................205crystallography: .............................................................................................208, 213cystic fibrosis: ......................................................................................................113Ddata integration: ..................................................................................................298data management: ...............................................................................................283data modelling: ....................................................................................................97databases: .............................................................................................. 117, 239, 298datawarehouse development: ................................................................................290de-differentiation: .................................................................................................385degenerative diseases: .........................................................................................368development: .......................................................................................................357developmental biology: ..................................................................................368, 414developmental genetics: ........................................................................................265diabetes: .......................................................................................................457, 473diagnosis: .....................................................................................................301, 332diagnostics: .................................................................................................... 88, 103diatoms: ..............................................................................................................429Dicer: .................................................................................................................399differentiation: ......................................................................................... 382, 388, 397directed evolution: ................................................................................................480disease markers: ..................................................................................................301disease mechanisms: ......................................................................................246, 254disease: ..............................................................................................................397disorders: ............................................................................................................187diversification of muscle fibres: ..............................................................................368DNA chips: .........................................................................................................357DNA damage: ...............................................................................................336, 449DNA methylation: ................................................................................................157DNA repair mechanisms: ......................................................................................336DNA tiling microarrays: ........................................................................................470Drosophila: .........................................................................................................205drug design: ........................................................................................................189drug development: .........................................................................................246, 457drug screening: .....................................................................................................99drug targets: ..............................................................................................93, 254, 427dynamic modelling of signal transduction pathways: ................................................445dynamical modelling: ...........................................................................................447Eelectron microscopy techniques: .............................................................................172electron tomography:......................................................................................172, 192embryonal development: .......................................................................................392embryos:.............................................................................................................385endocytosis: ........................................................................................................348endophenotypes: .................................................................................................285entrainment: ........................................................................................................420500 From Fundamental Genomics to Systems Biology: Understanding the Book of Life

KEYWORDS INDEXenvironmental factors: ...........................................................................................290enzymes: ............................................................................................................480epidemiology: ......................................................................................... 274, 277, 283epigenetic code: ..................................................................................................150epigenetics: ............................................................................................. 154, 157, 159ethics in health sciences: .......................................................................................289European technology platform: ..............................................................................263EU-US collaboration: ............................................................................................449exploratory drug discovery: ..................................................................................224expression profiling: .............................................................................................257Ffluorescence: .......................................................................................................122fluorescent in situ hybridization: .............................................................................165fluxomics: ............................................................................................................470Function prediction: ..............................................................................................175function: ..............................................................................................................181functional analysis of the mouse genome: ................................................................232functional biology: ...............................................................................................224functional genomics: ......................................... 122, 135, 137, 203, 220, 224, 249, 254, 261, 289308, 325, 340, 357, 364, 382, 399, 447, 467, 485functional in vivo studies: ......................................................................................265functional probing: ...............................................................................................115functions of muscle-specific proteins: .......................................................................368fundamental biological processes: ..........................................................................477fundamental genomics: .........................................................................................399fungal health applications: ....................................................................................311fungal pathogenicity: ............................................................................................311fusion; glycoproteins: ............................................................................................101Ggene & protein networks: ......................................................................................443gene atlas: ..........................................................................................................382gene discovery: ...................................................................................................285gene dosage imbalance: ......................................................................................352gene expression analysis: .....................................................................................220gene expression regulation: .............................................................................. 95, 301gene expression: ............................................................... 133, 143, 165, 352, 376, 399, 414gene integration:..................................................................................................133gene knock-out: ...................................................................................................261gene regulation: ............................................................................................154, 159gene silencing/knockdown: ..................................................................................105gene targeting: .................................................................................. 135, 137, 246, 249gene: ..................................................................................................................131general pathology: ...............................................................................................318genetic engineering: .......................................................................................122, 228genetic epidemiology and standardisation: .............................................................290genetic epidemiology: ..........................................................................................283genetic isolate: ....................................................................................................285genetic predisposition: ..........................................................................................277genetic testing: ....................................................................................................277genetic variation: ...........................................................................................243, 285genetics: .......................................................................................................279, 357genome (in)stability: .............................................................................................336genome annotation: .............................................................................................298From Fundamental Genomics to Systems Biology: Understanding the Book of Life 501

KEYWORDS INDEXgenome engineering: ...........................................................................................137genome structure and maintenance: .......................................................................135genome wide transcriptional profiling: ....................................................................449GenomEUtwin: ....................................................................................................283genomic databases: .............................................................................................311genomic function: .................................................................................................131genomics: .....................................88, 91, 99, 181, 184, 263, 265, 274, 285, 332, 336, 360, 429, 473genotype-phenotype-correlation: ............................................................................376genotyping: .........................................................................................................283global target site array: ........................................................................................145gradients: ...........................................................................................................443growth: ...............................................................................................................467Hhair bundle: ........................................................................................................364haplotype map: ...................................................................................................243hard-to-transfect cell lines: .....................................................................................105hardware and software pipeline: ...........................................................................168HBV: ..................................................................................................................181HCV: ..................................................................................................................181health sciences: ...................................................................................................281hearing impairment: .............................................................................................364hematopoiesis: ....................................................................................................392herpes simplex virus: ............................................................................................101herpesvirus: .........................................................................................................101heterologous transposition: ....................................................................................261high resolution: ....................................................................................................125high throughput: ............................................................................................199, 211high-throughput imaging analysis: ..........................................................................165high-throughput screen: .........................................................................................348high-throughput screening: ....................................................................................184high-throughput techniques: ..................................................99, 145, 154, 203, 208, 257, 348Histones: ............................................................................................................157:HIV: ....................................................................................................................181homologous recombination: ...................................................................... 131, 135, 137host factors: .........................................................................................................290host response: .....................................................................................................101human cytomegalovirus: .......................................................................................101human development: ............................................................................................254human disease models: .........................................................................................236human disease:....................................................................................................336human diseases: ..................................................................................................332human embryonic stem cells: .................................................................................388human genetics: ...................................................................................................281human genomics: .................................................................................................271human health: .......................................................................................................93human herpesvirus 8: ...........................................................................................101IIFN: ...................................................................................................................101imaging techniques: .............................................................................................125imaging: ........................................................................................................ 99, 172immobilised proteins: ............................................................................................201immune response markers: ....................................................................................257immunology: .......................................................................................................318502 From Fundamental Genomics to Systems Biology: Understanding the Book of Life

KEYWORDS INDEXimprinting: ..........................................................................................................401improved human health: .......................................................................................340in silico models: ...................................................................................................437infectious diseases: ...............................................................................................427inflammation: ......................................................................................................318inflammatory diseases: .........................................................................................360informatics: .........................................................................................................246infrastructures: .....................................................................................................227innate immunity: ..................................................................................................101inner ear: ............................................................................................................364integrating research: ............................................................................................227integration: .........................................................................................................303integrative biology: ..............................................................................................467intensive care medicine: ........................................................................................277interaction networks: ............................................................................................175interactive databases: ...........................................................................................265inverse problem: ..................................................................................................122iron homeostasis: .................................................................................................427isolated populations: ............................................................................................283KK+ homeostasis: ...................................................................................................364kidney diseases: ..................................................................................................372Llabelling, synthesis:...............................................................................................181lead: ..................................................................................................................105leaf: ...................................................................................................................467life sciences: ........................................................................................................461ligand interfaces: .................................................................................................208ligand specific effects: ..........................................................................................145light: ...................................................................................................................420linkage: ..............................................................................................................279lipid cubic phases: ...............................................................................................205lipidomics: ..........................................................................................................451living cell array: ...................................................................................................470low abundance proteins: .......................................................................................113lymphangiogenesis: ..............................................................................................360lymphoedema: .....................................................................................................360MMAP kinases: ......................................................................................................441mapping: ............................................................................................................279mass spectrometry: .........................................................................................127, 325massive data processing and information treatment: .................................................127mathematical modelling: .................................................................................453, 455mathematical models: .....................................................................................441, 457medical genetics: .................................................................................................228medical pathway modelling: .................................................................................340medicine: ......................................................................................................318, 475meganucleases: ...................................................................................................137membrane proteins:............................................................................ 178, 199, 201, 205membrane trafficking: ...........................................................................................327metabolic disorder: ..............................................................................................286From Fundamental Genomics to Systems Biology: Understanding the Book of Life 503

KEYWORDS INDEXmetabolism: .........................................................................................................457metabolomics: ..............................................................................103, 451, 470, 473, 480micro RNA: .........................................................................................................401microarray technology: ..........................................................................................97microarrays: ........................................................................................................301microcrystallography: ...........................................................................................205microRNA: ..........................................................................................................414microRNAs: .........................................................................................................411microsatellite: ......................................................................................................279microscopy: .........................................................................................................122miRNA: ..............................................................................................................399mitosis: ...............................................................................................................325model organisms: ..................................................................................... 135, 254, 385modelling complex diseases: .................................................................................439modelling: ............................................................................................... 459, 470, 473molecular biology: ........................................................................289, 336, 360, 368, 414molecular chemistry: .............................................................................................122molecular evolution: .............................................................................................187molecular genetics: ....................................................................................91, 224, 228molecular interaction networks: ..............................................................................463molecular medicine: .............................................................................................289molecular pathways: ............................................................................................224molecular phenotyping: ........................................................................................274molecular recognition: ..........................................................................................125monosomy: .........................................................................................................352morphogenesis: ...................................................................................................321mortality: ............................................................................................................277mouse disease models: ...................................................................................232, 236mouse functional genomics: ...................................................................................227mouse models: .....................................................................................................332mouse transgenesis: .............................................................................................352mouse: .........................................................................................220, 239, 249, 265, 372murine embryonic stem cells: .................................................................................382muscle differentiation: ...........................................................................................368muscle patterning: ................................................................................................368muscle regeneration: ............................................................................................368muscle stem cells: .................................................................................................368mutation genetics: ................................................................................................187Mycobacterium: ....................................................................................................93myoblasts fusion:..................................................................................................368myogenic specification: ........................................................................................368Nnanodrop technology: ..........................................................................................208nanomachines: .....................................................................................................93nematode: ...........................................................................................................261network analysis: .................................................................................................439network design: ...................................................................................................443networking: ...................................................................................................213, 461neural: ................................................................................................................388neurobiology: ......................................................................................................392neurodegeneration: ..............................................................................................463neuro-degenerative disorder: .................................................................................286neuron: ...............................................................................................................437neuronal cells: .....................................................................................................105NMR spectroscopy: ..............................................................................................189504 From Fundamental Genomics to Systems Biology: Understanding the Book of Life

KEYWORDS INDEXNMR: ..................................................................................................... 181, 201, 203non-coding RNA: ...........................................................................................399, 409non-coding RNAs: ..........................................................................................397, 411non-transcriptional gene regulation: ........................................................................399novel surfactants: .................................................................................................205nuclear magnetic resonance: .................................................................................203nuclear receptors: ................................................................................................145nuclear replacement: ............................................................................................249nucleation: ..........................................................................................................211nucleofection: ......................................................................................................105Ooncogenic cell implants: ........................................................................................257Organogenesis: ...................................................................................................372overexpression:....................................................................................................205PP3G: ..................................................................................................................283pathological anatomy: ..........................................................................................289pathways: ...........................................................................................................308peroxisome: ........................................................................................................332personalised medicine: .........................................................................................289pharmacogenomics: .............................................................................................145phase diagrams: ..................................................................................................211phenotyping: ................................................................................122, 236, 243, 274, 283Phosphatises: .......................................................................................................189phosphorylation: ..................................................................................................325photoreceptors: ....................................................................................................376plant models: .................................................................................................133, 263plant technologies: ...............................................................................................135plant: ..................................................................................................................467plastid transformation: ..........................................................................................133pluripotency: .......................................................................................................385policy recommendations: ......................................................................................263population genetics: .............................................................................................281population:..........................................................................................................279population-based cohorts: .....................................................................................283positional cloning: ................................................................................................243postgenomics: .....................................................................................................475predictive dynamic models: ...................................................................................463primary cells:.......................................................................................................105protein complexes: ................................................................................... 172, 192, 208protein crystallisation: .....................................................................................168, 211protein degradation: ............................................................................................133protein deposition: ...............................................................................................187protein engineering: .............................................................................................137protein expression: ...............................................................................................208protein interactions: ..............................................................................................201protein kinase: .....................................................................................................457protein ligand interactions: ....................................................................................201protein network: ...................................................................................................437protein production: ................................................................................... 135, 178, 184protein secretion: .................................................................................................480protein structure: ............................................................................................175, 208protein-protein interaction:...............................................................................110, 437From Fundamental Genomics to Systems Biology: Understanding the Book of Life 505

KEYWORDS INDEXprotein-protein interactions: ...................................................................................175proteolytic enzymes: .............................................................................................115proteome: .....................................................................................................110, 427proteomics: .............................................88, 99, 113, 117, 133, 325, 332, 336, 470, 473, 477, 480QQTL mapping: .....................................................................................................372quality assurance: .................................................................................................97quality control: ......................................................................................................97quantitative biology: .............................................................................................470quantitative genetics: ............................................................................................103quantitative traits: .................................................................................................285Rrat model: ...........................................................................................................243rat: .....................................................................................................................249receptor trafficking: ..............................................................................................348regenerative medicine: .........................................................................................385regulation: ..........................................................................................................325regulatory networks: .......................................................................................409, 447regulatory RNA: ..................................................................................................399regulome: ...........................................................................................................392renal pathogenesis: ..............................................................................................372reporter cell lines: ................................................................................................257reprogramming: ...................................................................................................150research initiatives:...............................................................................................461research policies: .................................................................... 195, 197, 227, 271, 434, 437Research Projecttomyces: .......................................................................................93resources: ...........................................................................................................227retinal development: .............................................................................................376retinal dystrophies: ...............................................................................................376reverse genetics: ..................................................................................................429riboregulator: ......................................................................................................397riboswitches: .......................................................................................................411RNA in situ hybridisation: .....................................................................................220RNA interference: ................................................................................................414RNA metabolism: .................................................................................................459RNA polymerase-II: ..............................................................................................143RNA silencing:...............................................................................................150, 414RNA splicing: ......................................................................................................405RNA structure: .....................................................................................................181RNA viruses: .................................................................................................181, 184RNA: ..................................................................................................................181RNAi: ..................................................................................................... 105, 181, 325robotics: .......................................................................................................168, 211SSaccharomyces cerevisiae: ....................................................................................455sample collections: ...............................................................................................290scanning force microscopy: ...................................................................................125screening: .................................................................................................99, 105, 181screening-cohorts: ................................................................................................290screens: ..............................................................................................................257self-renewal: ........................................................................................................388506 From Fundamental Genomics to Systems Biology: Understanding the Book of Life

KEYWORDS INDEXsepsis: ................................................................................................................277shift work models: ................................................................................................420short interfering RNA: ...........................................................................................414signal transduction: ............................................................................ 143, 318, 441, 457signalling network: ...............................................................................................110signalling pathway: ..............................................................................................437signalling pathways:.......................................................................................208, 321signalling: ............................................................................................... 327, 348, 443simulation: ..........................................................................................................437single particle: .....................................................................................................172siRNA: ...........................................................................................................101,105site-specific, integration: ........................................................................................131skin: ...................................................................................................................321small molecules: ...................................................................................................159snoRNA: .......................................................................................................399, 401SNP: ..................................................................................................................243SNP-Chip: ...........................................................................................................290software evaluation: .............................................................................................443solute carrier: ......................................................................................................372somatic cell: ........................................................................................................249Specific Targeted: .................................................................................................93spectrum assignment:............................................................................................203splicing: ..............................................................................................................301stabilization: ........................................................................................................205stakeholder forum: ...............................................................................................263standardisation: .............................................................................................117, 168standards: ...........................................................................................................303Staphylococcus: .............................................................................................. 93, 470stem cells: ............................................................................................... 360, 382, 388Streptomyces: ......................................................................................................480stress response: ....................................................................................................449structural biology: ................................................................................................172structural genomics: ................................. 93, 168, 175, 178, 184, 189, 192,195, 197, 203, 208, 211structural proteomics: ................................................................................ 195, 197, 213structure analysis: .................................................................................................399structure calculation: .............................................................................................203structure determination: ...................................................................................178, 213synapse: .......................................................................................................364, 437synchrotrons: .......................................................................................................168systematic high-throughput gene expression studies: .................................................265systemic effects: ...................................................................................................473systems biology: ......................... 97, 308, 434, 443, 447, 449, 453, 455, 457, 463, 467, 475, 477, 480Ttandem repeat: ....................................................................................................279targeted mutagenesis: ...........................................................................................224technology development: .......................................................................................97technology platform: .............................................................................................168temporal dimension: .............................................................................................485therapy: ........................................................................................................332, 364three-dimensional electron microscopy: ...................................................................199tomography: ........................................................................................................122tools and technologies: .........................................................................................137Trachomatis: ........................................................................................................290training: ..............................................................................................................213transcript: ............................................................................................................301From Fundamental Genomics to Systems Biology: Understanding the Book of Life 507

KEYWORDS INDEXtranscription factors: .............................................................................91, 143, 145, 392transcription regulation: ..................................................................................143, 157transcription: .......................................................................................................143transcriptome analysis: .........................................................................................372transcriptome atlas: ..............................................................................................220transcriptome: .................................................................................... 301, 352, 392, 427transcriptomics: ..............................................................................................470, 480transformation: ....................................................................................................131transgenes:..........................................................................................................131transgenesis: .......................................................................................................385transgenic animals: ..............................................................................................372transposable elements: ..........................................................................................261transposon-mediated mutagenesis: .........................................................................261transposontagged mutants: ....................................................................................261trisomy: ...............................................................................................................352tumor markers: .....................................................................................................257twin-arginine translocation: ....................................................................................93Uultra high throughput transfection: ..........................................................................105Vvascular biology: .................................................................................................360vascular disease: ...........................................................................................286, 360vertebrate models:................................................................................................265vision: ................................................................................................................376VNTR:.................................................................................................................279Wweb services: ......................................................................................................303web-based virtual microscope: ...............................................................................220web-linked gene expression database: ...................................................................220website: ..............................................................................................................213workshops: ..........................................................................................................213wound healing: ....................................................................................................321XXenopus: .......................................................................................................265, 372X-ray crystallography: ............................................................................... 168, 178, 192Yyeast engineering:................................................................................................340yeast: ..................................................................................................... 192, 205, 459Zzebrafish embryo model: ......................................................................................257zebrafish: .......................................................................................... 254, 257, 265, 372508 From Fundamental Genomics to Systems Biology: Understanding the Book of Life

European CommissionEUR 23132 — From Fundamental Genomics to Systems Biology: UNDERSTANDING THE BOOK OF LIFELuxembourg: Office for Official Publications of the European Communities2008 —512 pp. — 21.0 x 29.7 cmISBN 978-92-79-08004-3ISSN 1018-5593DOI 10.2777/49314Price (excluding VAT) in Luxembourg: EUR 40

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KI-NA-23132-EN-CThe sequencing of the human genome and many other genomes heralded a new age in human biology, offeringunprecedented opportunities to improve human health and to stimulate industrial and economic activity. The globalunderstanding of the complete function of approximately 22 000 human genes constitutes a major challengefor understanding normal and pathological situations. To tackle this challenge, the European Commission madefundamental genomics research a priority in the Sixth Framework Programme for RTD (FP6) (2002-2006).The European Commission has allocated approximately 594 million in FP6 to fundamental genomics researchactivities with the overall aim of fostering the basic understanding of genomic information by developing theknowledge base, tools and resources needed to decipher the function of genes and gene products relevant tohuman health, and to explore their interactions with each other and with their environment.The present publication provides a brief description of the goals, expected results, achievements and expectedimpact of all the projects supported during FP6 in the fundamental genomics priority area in the following scientificsub-areas: the development of tools and technologies for functional genomics; regulation of gene expression;structural genomics and proteomics; comparative genomics and model organisms; population genetics andbiobanks; bioinformatics; multidisciplinary fundamental genomics research for understanding basic biologicalprocesses in health and disease; and the emerging area of systems biology.During FP6, the European Commission has supported several systems biology initiatives which paved the way forfurther developing the genomics and systems biology programme in the Seventh Framework Programme for RTD(FP7) (2007-2013). The introduction provides an overview of the FP6 research policies and the steps taken tostrengthen the European Research Area in each of the scientific sub-areas, as well as the FP7 vision in genomicsand systems biology collaborative research.