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The Multinational Coordinated Arabidopsis thaliana
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The Multinational Coordinated, Arabidopsis thaliana. Functional Genomics Project, Annual Report 2004, 2nd Edition. Thomas Altmann altmann mpimp golm mpg de, Philip Benfey philip benfey duke edu. Jorge Casal casal ifeva edu ar, Bill Crosby bcrosby cs usask ca. Ian Furner ijf mole bio cam ac uk, Mary Lou Guerinot Mary Lou Guerinot Dartmouth edu.
Pierre Hilson pierre hilson gengenp rug ac be, Heribert Hirt HEHI gem univie ac at. Gerd J rgens gerd juergens uni tuebingen de, Jaakko Kangasj rvi jaakko kangasjarvi helsinki fi. Maarten Koornneef maarten koornneef wur nl, Ottoline Leyser hmol1 york ac uk. Keith Lindsey keith lindsey durham ac uk, Sean May arabidopsis nottingham ac uk. Peter McCourt mccourt botany utoronto ca, Javier Paz Ares jpazares samba cnb uam es.
Kazuo Shinozaki sinozaki rtc riken go jp, Willem Stiekema w j stiekema plant wag ur nl. Ian Small small evry inra fr, Paola Vittorioso paola vittorioso uniroma1 it. Geoffrey Wasteneys geoffw rsbs anu edu au, Jianru Zuo jrzuo genetics ac cn. Isabell Witt witt mpimp golm mpg de, Executive Secretary and Coordinator. The Multinational Arabidopsis Steering Committee July 2004. Table of Content, Foreword to the Report 7, Executive Summary 8.
Analysis and Recommendations 9, Current status of the program. Recommendations, A brief history of Arabidopsis research and its value as a model system 12. How Arabidopsis became a model, Best understood biological processes in Arabidopsis. Testing Arabidopsis genes in crops, Synteny and colinearity between Arabidopsis and other plants. Transfer of knowledge from Arabidopsis to crops, Why are model plants essential for our survival.
Progress and Activities of the Multinational Arabidopsis Steering Committee MASC 16. Highlights of the past year, Measuring the gene function knowledge. Reports of the MASC Subcommittees 20, Bioinformatics. cDNAs and Clone Based Functional Proteomics ORFeomics. Multiparallel Analytical Tools Phenotype Analyses, Forward and Reverse Genetics Stocks. The International Arabidopsis Functional Genomics Community 28. Australia and New Zealand, Eastern European Arabidopsis Activity. European Union, The Netherlands, Nordic Arabidopsis Network.
United Kingdom, United States, Members of the Multinational Arabidopsis Steering Committee 44. Members of the MASC Subcommittees 45, Foreword to the Report. This is the third annual report of the Multinational Arabi theless a new goal emerged To uncover the mechanisms and pro. dopsis Steering Committee MASC on the status of the cesses underlying the spatial temporal and conditional control of. Multinational Coordinated Arabidopsis thaliana Functio the activity of the genes the identity function and localization of. nal Genomics Project This 10 year program initiated in 2001 gene products and their interactions in the cellular context which. was described in a long range plan for this new phase of the Ara are the basis of the multitude of cellular physiological and develop. bidopsis Genome Research Program in the 2002 MASC report mental processes of plant life To accomplish this goal requires the. The goals of this project are to determine the function of every use of newly developed high throughput technologies novel exper. Arabidopsis gene and obtain a detailed and comprehensive under imental tools and comprehensive collections of plant resources as. standing of the molecular processes underlying the development well as powerful procedures for data analysis storage and display. metabolism and interaction with the environment of a flowering Arabidopsis research has provided the cutting edge in gener. plant The intent is that the knowledge gained on this experimental ating resources and analytical tools providing an example for the. model organism will serve as the central reference and conceptual investigation of other plant species One of the most important de. framework for all of plant biology Arabidopsis is uniquely situated terminants of the success of the Arabidopsis Functional Genomics. to play this role for a number of reasons 1 Its genome is the best Project is the integration of worldwide efforts The nature and vol. characterized among plants 2 It has the most comprehensive re ume of the proposed work necessitates the marshalling of all re. verse and forward genetic tools and resources 3 The international sources to attain a maximum level of synergy as well as the avoi. research community that uses these tools and resources is among dance of duplication of effort to enable the Arabidopsis community. the most active and co operative and 4 The solution of most prob to achieve its ambitious goals The Multinational Arabidopsis. lems in plant biology whether applied or basic can be achieved ra Steering Committee plays a key role in supporting this international. pidly and in a cost effective manner through the use of Arabidopsis coordination by collecting and disseminating information from the. The results generated by the Arabidopsis Functional Genomics various initiatives and projects on technology development and. Project which are made publicly available through central data functional analyses and by giving specific recommendations for fur. bases not only provide unprecedented insight into plant function by ther directions. uncovering basic biological concepts but also greatly advance our As is outlined in this report the high level of cooperation and. knowledge of the genetic determinants of important traits in crop widespread willingness to share data throughout the Arabidopsis. plants Studies comparing the physiology biochemistry and devel community as well as the support by the funding agencies has. opment of Arabidopsis with that of other plant taxa and with eco yielded important and exciting results These favorable develop. nomically important agricultural species will be of increasing impor ments indicate that the ambitious goal of understanding. tance the function of all Arabidopsis genes as a first step to. The availability of the complete genome sequence of Arabidop ward an in depth understanding of the biology of higher. sis thaliana the ultimate accomplishment of the previous phase of plants to the benefit of our society can be achieved if. the Multinational Coordinated Arabidopsis thaliana Genome sufficient and sustainable research funding is secured. Research Project provided a quantum leap in the information biological materials and services are made available. base for plant molecular biological research On the one hand this around the world and human resources are further deve. information allowed the Arabidopsis research community to develop loped. new approaches and research tools On the other hand it high. lighted the enormous complexity of the plant biological system and The Multinational Arabidopsis Steering Committee. the difficulty of deciphering the function of every gene Never July 2004. Executive Summary, After completion of the genome sequence of Arabidopsis The available resources and their widespread use and the. thaliana in the year 2000 the Arabidopsis research community put strong support of individual projects devoted to gene function analy. forward the goal of elucidating the function of all genes of the Ara sis has resulted in an increase of the fraction of experimen. bidopsis thaliana model organism to provide the basis for achieving tally studied genes functionally characterized to various. full understanding of the biology of a flowering plant Arabidopsis extents from 9 in the year 2000 to a current 20. not only serves as a plant model but it has proven to be a key sys There are a few areas that are lagging behind original plans or. tem for uncovering basic biological processes Arabidopsis there are currently underrepresented particularly proteomics and. fore plays an indispensable and unique role as an experimentally ORFeome work Several projects that have recently been initiated to. tractable system for the advance of basic science Moreover due to move this field forward should be given further emphasis Urgently. the dependency on plants of all human and animal life the results needed by the Arabidopsis research community are complete col. of research on Arabidopsis and their application to crop science are lections of full length cDNAs ORF clones and a further develop. of central relevance to our global society ment of a comprehensive microarray repository suitable for data. The major aim of the 10 year Multinational Coordinated Arabi mining as well as several other resources including protein function. dopsis thaliana Functional Genomics Project is the elucidation of the analysis tools comparative genomics improved access to metabo. function of every Arabidopsis gene in its cellular organismal and lomics technology and means for facile access to genomic data. evolutionary context ultimately leading to a comprehensive under Another area in need of development is the large scale gener. standing of the biology of a flowering plant The research program ation of standardized molecular transcriptome proteome metabo. has been broken down into short mid and long term goals Of the lome etc and phenotype information One way of providing this. short term goals most have already been achieved including type of information is through genome technology centers that carry. Genome annotation has been dramatically improved through out large scale high throughput analysis programs place high. the use of information on expressed sequences and expert quality data freely accessible into the public domain and provide. knowledge service to individual labs as well as education through courses and. Comprehensive sets of sequence indexed mutants have been workshops. created and are widely used for gene function determination Several developments highlighted by multinational co opera. Genome wide sets of gene specific probes have been created tion projects such as AtGenExpress and the interaction of funding. and are in widespread use for expression analysis agencies such as the NSF DFG co operation indicate that the inter. Full length cDNA sequences have been defined for more than national Arabidopsis community is ready to move towards a global. 60 of all Arabidopsis genes research strategy composed of multinational large scale projects. Methods for global metabolic profiling have been established and numerous individual expert knowledge driven projects Given. Databases have been dramatically expanded providing access that this transition receives sufficient support the Multinational. to large functional data sets Arabidopsis Functional Genomics Project will meet its goal of eluci. Of particular note are the availability of full length cDNA sequences dating the function of every Arabidopsis gene. of ca 16 000 genes knowledge of expression for ca 21 000 80. of all genes the identification of T DNA or transposon insertions in. 22 400 genes ca 85 and the establishment of a freely acces. sible transcriptome reference data set, Analysis and. Recommendations, After completion of its third year the Multinational Coordinated 4 The production of genome wide sets of gene specific probes for.
Arabidopsis thaliana Functional Genomics Project has moved for expression analysis 5 Isolation of full length cDNAs for more than. ward tremendously with unprecedented increase in publicly acces 60 of the genes facilitating genome annotation and protein analy. sible information Expression profiling is an example of the drama ses 6 Establishment of methods for global metabolic profiling and. tic change of paradigms that Arabidopsis research is undergoing 7 The establishment of MASC with a full time coordinator to fos. Very few years ago gene expression profiling technology was avail ter information flow international collaboration and coordination. able in only a few labs and limited to a fraction of the genome and to monitor progress of the program. Today although still costly genome wide array analyses are acces The improved genome annotation i e identification of genes. sible in principle to every researcher A hallmark of this technique is is one of the most notable recent achievements Of critical impor. that the researcher who carries out the experiment will usually use tance was information from full length cDNA sequences and from. only a minor fraction of the information generated allowing a large full genome tiling chip hybridizations The current release lists a. number of colleagues to benefit from access to the complete data total of 26 207 genes not including 2 355 transposons and 1 652. set To make use of this new opportunity of creating synergy and of non transposon pseudogenes of which 16 138 are represented by. further accelerating our gain of knowledge the research communi a full length cDNA and 20 901 ca 80 have been shown to be. ty needs to move to a new level of co operation and further increase expressed Resources for the characterization of the biochemical. its willingness to share data Building on its history of cultivating a functions of the gene products have been vastly expanded Full. strong spirit of collaboration and free exchange the Arabidopsis length cDNA clones of ca 13 000 genes are being distributed and. community is well prepared to meet this challenge This report con almost 12 000 ORF clones useful for recombination cloning have. tains numerous examples of sharing of materials resources and been created and deposited at the Arabidopsis Biological Resource. After completion of its third year the Multinational Coordinated Arabidopsis thaliana Functional Genomics Project has moved for ward tremendously with unprecedented increase in publicly acces sible information Expression profiling is an example of the drama tic change of paradigms that Arabidopsis research is undergoing

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