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Maren Depke Acknowledgments Kidney gene expression pattern in an in vivo infection model The mouse infection model was established and performed in the setting of the DFG Sonderforschungsbereich SFB TR 34 “Pathophysiologie von Staphylokokken in der Post-Genom Ära” by Tina Schäfer and Knut Ohlsen, who also contributed to study conception and design. Marc Burian co-operated in the wet-lab-work for the second biological replicate of infected samples and in the final data analysis and interpretation. The strain S. aureus RN1HG was generated in the lab of Friedrich Götz and its isogenic sigB mutant by Jan Pané-Farré in the lab of Michael Hecker. The work was supervised by Uwe Völker. Tina Schäfer, Knut Ohlsen (Institute of Molecular Infection Biology, Julius-Maximilians University of Würzburg, Germany) Jan Pané-Farré, Susanne Engelmann, Michael Hecker (Institute of Microbiology, Ernst-Moritz-Arndt University of Greifswald, Germany) Friedrich Götz (Department of Microbial Genetics, Eberhards-Karls University of Tübingen, Germany) Marc Burian, Uwe Völker (Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, Ernst-Moritz-Arndt University of Greifswald, Germany) Gene expression pattern of bone-marrow derived macrophages after interferon-γ activation Bone-marrow derived macrophages were generated and stimulated with IFN-γ by Kathrin Breitbach. Proteome analysis was conducted by Dinh Hoang Dang Khoa. The study was performed in the setting of the DFG Sonderforschungsbereich SFB TR 34 “Pathophysiologie von Staphylokokken in der Post-Genom Ära”. The work was supervised by Uwe Völker. Kathrin Breitbach, Antje Bast, Ivo Steinmetz (Institute of Medical Microbiology, Ernst-Moritz-Arndt University of Greifswald, Germany) Dinh Hoang Dang Khoa, Lars Brinkmann, Manuela Gesell Salazar, Elke Hammer, Leif Steil, Frank Schmidt, Uwe Völker (Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, Ernst-Moritz-Arndt University of Greifswald, Germany) Host cell gene expression pattern in an in vitro infection model Infection experiments were performed in close collaboration with Melanie Gutjahr, who worked on host proteome analysis and additionally accomplished control measurements and cell culture. Petra Hildebrandt conducted FACS cell sorting. The strain S. aureus RN1HG was generated in the lab of Friedrich Götz and its GFP expressing variant RN1HG pMV158GFP by Leonard Menschner in the lab of Michael Hecker. The work was supervised by Uwe Völker. This study was performed in the setting of the DFG Sonderforschungsbereich SFB TR 34 “Pathophysiologie von Staphylokokken in der Post-Genom Ära”. Leonhard Menschner, Susanne Engelmann, Michael Hecker (Institute of Microbiology, Ernst-Moritz- Arndt University of Greifswald, Germany) Melanie Gutjahr, Petra Hildebrandt, Elke Hammer, Uwe Völker (Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, Ernst-Moritz-Arndt University of Greifswald, Germany) 238
Maren Depke Acknowledgments Pathogen gene expression profiling – growth media and in vitro infection experiment studies This study was performed in the setting of the DFG Sonderforschungsbereich SFB TR 34 “Pathophysiologie von Staphylokokken in der Post-Genom Ära” and the international cooperation EU-IP-FP6-project BaSysBio (LSHG-CT2006-037469). Infection experiments were performed in close collaboration with Melanie Gutjahr, who additionally accomplished control measurements, and Petra Hildebrandt, who conducted eukaryotic cell culture. Many thanks are given to Marc Schaffer for his valuable help during preparation of internalized staphylococci, to Ulrike Mäder for her help concerning all aspects of tiling array data, and to Marc Burian for the discussions on staphylococcal gene expression. The work was supervised by Uwe Völker. Jan Pané-Farré, Susanne Engelmann, Michael Hecker (Institute of Microbiology, Ernst-Moritz-Arndt University of Greifswald, Germany) Magda M. van der Kooi-Pol, Annette Dreisbach, Jan Maarten van Dijl (Department of Medical Microbiology, University Medical Center Groningen / UMCG, Groningen, The Netherlands; A. D. formerly: Department of Functional Genomics, Ernst-Moritz-Arndt University of Greifswald, Germany) Hanne Jarmer (Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark) Pierre Nicolas, Aurélie Leduc, Philippe Bessières (INRA, Mathématique Informatique et Génome, Jouyen-Josas, France) Melanie Gutjahr, Petra Hildebrandt, Marc Schaffer, Marc Burian, Ulrike Mäder, Uwe Völker (Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, Ernst-Moritz- Arndt University of Greifswald, Germany) FURTHER COOPERATION PARTNERS Piotr Grabarczyk, Christian A. Schmidt (Molecular Hematology, Department of Hematology and Oncology, Ernst-Moritz-Arndt University of Greifswald, Germany) FINANCIAL SUPPORT DFG-Graduiertenkolleg / Research Training Group GK840 „Wechselwirkungen zwischen Erreger und Wirt bei generalisierten bakteriellen Infektionen“/ “Host-pathogen interactions in generalized bacterial infection“ DFG Sonderforschungsbereich / Transregional Collaborative Research Center SFB TR 34 “Pathophysiologie von Staphylokokken in der Post-Genom Ära”/ „Pathophysiology of Staphylococci in the Post-Genomic Era“ 239
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G E N O M E W I D E C H A R A C T E
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Maren Depke C O N T E N T S GENOMEW
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Maren Depke Z U S A M M E N F A S S
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Maren Depke Zusammenfassung der Dis
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Maren Depke S U M M A R Y O F D I S
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Maren Depke Summary of Dissertation
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Maren Depke I N T R O D U C T I O N
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Maren Depke Introduction Besides op
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Maren Depke Introduction Extracellu
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Maren Depke Introduction with heigh
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Maren Depke Introduction 2005). SaP
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Maren Depke Introduction contains a
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Maren Depke Introduction via fibron
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Maren Depke Introduction cathelicid
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Maren Depke Introduction shock are
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Maren Depke Introduction STUDIES OF
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Maren Depke Introduction are effect
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Maren Depke Introduction cell stimu
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Maren Depke Introduction channel CF
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Maren Depke M A T E R I A L A N D M
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Maren Depke Material and Methods Li
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Maren Depke Material and Methods Ki
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Maren Depke Material and Methods GE
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Maren Depke Material and Methods Ge
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Maren Depke Material and Methods Ho
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Maren Depke Material and Methods Ho
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Maren Depke Material and Methods Pa
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corticosterone [pg/ml plasma] corti
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Maren Depke Results Liver Gene Expr
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lood glucose levels [nmol/l] resist
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LBP [ng/ml] CPR [ng/ml] Maren Depke
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Maren Depke Results Liver Gene Expr
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liver weight [g] Maren Depke Result
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infection rate cfu / 10 mg tissue c
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Maren Depke Results Kidney Gene Exp
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Table R.2.1: Genes displaying stati
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Maren Depke BR1 sign DsigB vs wt BR
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Maren Depke Results GENE EXPRESSION
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Maren Depke Results Gene Expression
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log2(ratio C57BL/6 / BALB/c) at IFN
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Maren Depke Results Host Cell Gene
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Maren Depke Results Pathogen Gene E
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S. aureus RN1HG sample conditions a
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mean normalized intensity mean norm
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mean normalized intensity Maren Dep
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log 2 (ratio) log 2 (ratio) log 2 (
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Maren Depke D I S C U S S I O N A N
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Maren Depke Discussion and Conclusi
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Page 208 and 209: Maren Depke References Athanasopoul
Page 210 and 211: Maren Depke References Byrne GI, Le
Page 212 and 213: Maren Depke References Demling R. T
Page 214 and 215: Maren Depke References Foss GS, Pry
Page 216 and 217: Maren Depke References Hagopian K,
Page 218 and 219: Maren Depke References Jin T, Bokar
Page 220 and 221: Maren Depke References Kwan T, Liu
Page 222 and 223: Maren Depke References Luster AD, U
Page 224 and 225: Maren Depke References Namiki S, Na
Page 226 and 227: Maren Depke References Puccetti P.
Page 228 and 229: Maren Depke References Siewert E, B
Page 230 and 231: Maren Depke References van den Akke
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