75 Integrating Membrane Transport with Male Gametophyte ... - TAIR

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97 Applications of Plant Ontologies for Describing and Comparing Phenotypes and Gene Expression in Plant Databases Katica Ilic 1 , Elizabeth Kellogg 2 , Peter Stevens 3 , Felipe Zapata 3 , Pankaj Jaiswal 4 , Anuradha Pujar 4 , Shulamit Avraham 5 , Leszek Vincent 6 , Leonore Reiser 1 , Marty Sachs 7 , Susan McCouch 4 , Mary Schaeffer 6 , Doreen Ware 5 , Lincoln Stein 5 , Seung Rhee 1 1 TAIR, Carnegie Institution, Department of Plant Biology, Stanford, CA, 2 Department of Biology, University of Missouri-St. Louis, MO, 3 Botanical Garden, University of Missouri - St. Louis, MO, 4 Gramene, Deptartment of Plant Breeding, Cornell University, Ithaca, NY, 5 Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 6 MaizeGDB, University of Missouri - Columbia, MO, 7 Maize Genetics Cooperation - Stock Center & Department of Crop Sciences, University of Illinois, Urbana, IL The Plant Ontology Consortium (POC) was established as a collaboration among several plant databases and experts in plant systematics, botany and genomics. The primary goal of POC was to create a semantic framework for meaningful cross-species queries across plant databases and to facilitate and accommodate functional annotation efforts in plant databases and by the plant research community at large. Thus, the POC has created controlled vocabularies (ontologies) which describe morphology, anatomy, growth and developmental stages of a flowering plant. Plant Ontology (PO) has two aspects: 1) Plant Structure Ontology, with terms describing organs, organ systems, tissues, and cell types; and 2) Plant Growth and Developmental Stage Ontology, with terms describing spatial-temporal growth stages of a whole plant and developmental stages of organs and organ systems. The initial releases of Plant Ontology included integration of existing ontologies for Arabidopsis, maize and rice, thus spanning the eudicot-monocot divide. Recently, we have expanded PO to encompass Fabaceae, Solanaceae and other cereal crops. Consistent use of these ontologies potentially reduces the problem of heterogeneity of terminology used to describe comparable object types in plant databases - an obvious obstacle for conducting queries for multiple species across plant genomic databases. As a part of ongoing functional annotation efforts, participating databases, such as TAIR, NASC, Gramene, MaizeGDB and SOL Genomics Network, have been using PO to describe expression patterns of genes and phenotypes of mutants and natural variants. Close to 10,000 gene annotations and phenotype descriptions from several species-specific databases can now be queried and retrieved using the Plant Ontology browser. A summary of the organizing principles and rules followed in developing PO will be presented, as well as the annotation examples from member databases using PO terms. The PO and gene and phenotype associations contributed from member databases can be obtained at www.plantontology.org. 98 Report on plant resource project in RIKEN BRC Masatomo Kobayashi, Hiroshi Abe, Satoshi Iuchi, Toshihiro Kobayashi RIKEN BRC RIKEN BRC preserves and distribute plant resources such as seeds for Arabidopsis transposon-tagged lines (KOline) and Arabidopsis full-length cDNA (RAFL) clones that have been developed in Japan. During last year, RIKEN BRC almost finished the preparation of these important materials for distribution. We are now establishing homozygous seed stocks of the transposon-tagged lines that will be partially available within the end of this year. Now approximately 366,000 materials are preserved in RIKEN BRC, and more than 18,000 materials have been shipped to world research community. Our stock include Arabidopsis transposon-tagged and activation (T-DNA)- tagged lines, seed lines for natural accessions, RAFL clones and full-length clones of some model plant species such as Physcomitrella patens (model moss) and Populus nigra (model tree). The detail information is available from our web site: http://www.brc.riken.jp/lab/epd/Eng/.
99 ReIN: an interactive tool to create and visualize regulatory networks in Arabidopsis thaliana Saranyan Palaniswamy, Sarat Subramaniam, Rebecca Lamb, Ramana Davuluri, Erich Grotewold The Ohio State University ReIN is a web-based software tool for creating, visualizing and identifying regulatory networks in Arabidopsis thaliana. Regulatory motifs represent the simplest units of the overall regulatory network of an organism. A simple graphical interface tool like ReIN will facilitate biologists a fast and easy way to visualize networks of interactions in Arabidopsis with the potential to be extended to other organisms. The identification of the direct targets for TFs is a first step in establishing the regulatory motifs in which particular TFs are involved. Arabidopsis is a small dicotyledoneous plant for which the entire genome is available. The Arabidopsis Gene Regulatory Information Server (AGRIS, http:// arabidopsis.med.ohio-state.edu) provides a comprehensive collection of all known Arabidopsis TFs, the promoters, and known and predicted interactions between the TFs and the corresponding promoters. For a complete understanding of the intricate behavior of these gene regulatory networks, the development of web-based computational tools becomes essential (Blais and Dynlacht, 2005). The visualization of a network of regulatory interactions between different TFs and genes consists of translating interaction data into 2D images where different participants in the regulatory chain are represented by different geometric entities. The visualization process may therefore be divided into three steps or models: extracting information from a database consisting of TF or gene interactions; mapping these data into various geometrical shapes and arrows, representing the interactions; and finally, laying out and drawing these shapes while providing the user ability to control and interact with the drawn network in various ways. ReIN is a web-based application with a multitier architecture based on J2EE technology. The application is available to the user as a Java applet embedded in JSP which provides the user the ability to search for TFs or genes in the Arabidopsis thaliana Regulatory Network Database (AtRegNet). ReIN uses java servlets to retrieve information and allows the user to upload input (network) data as a file and download the network visualization as an image. This process allows a large number of users to simultaneously interact with the database without a noticeable impact on performance http://arabidopsis.med.ohio-state.edu/REIN. 100 ARGOS, a simple and one-step SSR finder for supporting molecular marker development in plant researches Kyu-Won Kim 1 , Jae-Woong Yu 2 , Hun-Ki Chung 3 , Kyung-Ho Ma 3 , Tae-San Kim 3 , V. Ramanatha Rao 4 , Yong-Jin Park 4 1 Qube Soft Inc., 2 Seoul National University, Seoul, R. Korea, 3 National Institute of Agricultural Biotechnology, Suwon, R. Korea, 4 International Plant Genetic Resources Institute (IPGRI-APO), Serdang, Malaysia SSR marker system technology is useful for comparing genetic characteristic of subspecies and finding markers related to phenotypes of economic importance and mapping genes through construction of linkage map. Since computer power can help searching simple sequence repeats (SSRs) quickly in the sequence data read from the mass DNA fragments, there are many algorithms developed for helping that. But it is very complicated to modify output results obtained from one program to input format of another program. This situation would be more serious when handling many clone sequences, at a time and this is very hard work to manage mass data read from DNA fragment sequences and their data output after analysis. Therefore, I developed one step computer program for rapid identification of simple sequence repeats and primer design which is coded with C# and Microsoft Visual Studio.NET. Distant parser sorts the SSR motifs from local N repeat parser and merges neighboring SSRs to same motif for primer design. We compared this program with 4 other SSR finding programs (Mreps, SSRIT, Sputnik, Troll) with 320 clone sequences of 8 different plant species. We found increased accuracy and outstanding outputs of this program, compared with other currently used programs. This research was conducted through IPGRI and RDA (Rural Development Administration, R. Korea) collaboration, supported by BioGreen 21 Program.
Page 1 and 2: 75 Integrating Membrane Transport w
Page 3 and 4: 79 PREP: Partnership for Research a
Page 5 and 6: 83 Characterization of Orthologous
Page 7 and 8: 87 High-density Arabidopsis Protein
Page 9 and 10: 91 Approaches to Study Homologous R
Page 11: 95 Predicting the Redundome: A Geno
Page 15 and 16: 103 Proteomic services at the Europ
Page 17 and 18: 107 Ubiquitin Lys 63 Chain Forming
Page 19 and 20: 111 Characterization of the Anti-mi
Page 21 and 22: 115 Molecular Genetic Analysis of P
Page 23 and 24: 119 CLB19, a Novel Pentatricopeptid
Page 25 and 26: 123 The Arabidopsis CDC48 Adapter P
Page 27 and 28: 127 AtCKT1, a Novel Transporter for
Page 29 and 30: 131 Sub-Cellular Localization of DR
Page 31 and 32: 135 Discovering the function of WAV
Page 33 and 34: 139 WRINKLED1, an AP2/EREBP Class T
Page 35 and 36: 143 The Ubiquitin-Specific Protease
Page 37 and 38: 147 Systemic signal transduction of
Page 39 and 40: 151 Dissection of Flowering Pathway
Page 41 and 42: 155 Dissecting genetic pathways und
Page 43 and 44: 159 HANABA TARANU (HAN) Organizes A
Page 45 and 46: 163 What are SCAMPS doing in plants
Page 47 and 48: 167 Analysis of DNA methylation and
Page 49 and 50: 171 Identification of TIA as a Myb-
Page 51 and 52: 175 DEMETER DNA Glycosylase Regulat
Page 53 and 54: 179 Investigation Of The Connection
Page 55 and 56: 183 Genetic Analysis of Vascular Pa
Page 57 and 58: 187 Arabidopsis BRANCHED genes are
Page 59 and 60: 191 Regulation Of BDL Gene Expressi
Page 61 and 62: 195 ARROW1 (ARO1), a Novel Regulato
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199 The Trichome Pock Phenotype of
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203 Control of Leaf Vascular Patter
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207 FAMA Controls The Switch Betwee
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211 Subtilisin-like serine protease
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215 TRIDENT and VARICOSE encode com
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219 Analysis of a Mutant, #1-63, wh
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223 Quantitative Trait Analysis of
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227 LEAFY and the Evolution of Rose
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231 Overexpression of Arabidopsis S
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235 Ethylene Signaling Components A
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239 Accumulation of Reactive Oxygen
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243 Intracellular Production Of Rea
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247 Large-Scale Screen and Isolatio
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251 Ontogeny of the Arabidopsis Cir
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255 Cell type-specific expression a
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259 Characterization of Flowering T
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263 Involvement of Cytokinins and T
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267 Identification of new actors of
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271 Scarecrow-like Protein SCL14 In
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275 Protein Prenylation Is Required
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279 Mechanisms controlling coordina
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283 GLZ1, a member of family 8 glyc
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287 Arabidopsis as a Model System t
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291 The NIMIN-NPR1 Connection: A Mo
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295 A Search for Transcriptional Re
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299 Identification of genes contrib
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303 Regulation of AGAMOUS Expressio
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307 Genetic Control of the Interplo
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311 Centromeric Retrotransposons: P
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315 Finding Intron Sequences That E
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319 Biochemical Characterization Of
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323 Fluorescent amino acid sensors
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327 The Role of Tryptophan Metaboli
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331 A Putative Bifunctional Wax Est
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335 Analysis of the Complex BIO3 /
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339 Exploring of Arabidopsis non-ho
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343 A Yeast-2-Hybrid Assay Reveals
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347 Genetic Mechanisms of Glucosino
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351 Potent Induction of flowering b
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355 Phylogenetic Analysis of Arabid
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359 eQTL-mapping reveals AMP2A, a c
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363 Progress Towards the Cloning of
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367 Natural Variation in Infloresce
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371 Natural Variation for Seed Dorm
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375 Natural genetic and epigenetic
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379 SPIKE1 is a guanine nucleotide
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383 The RAD23 Family of Ubiquitin-L
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387 Molecular Functions of ARL2 and
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391 Characterization of the Sugar-I
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395 Functional analysis of phosphat
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399 Identification and Characteriza
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403 Association and Localization of
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407 Functional Requirements for PIF
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411 Using High-throughput Chemical
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415 The F-box Protein PPS Functions
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419 Round The Clock - The Molecular
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423 Protein Prenylation Process Neg
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427 Integration of light and abscis
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431 Functional analysis of ROP10 sm
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435 The Importance Of RecQ Like Hel
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439 A Comparison of Full Versus Par
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