Databases  |   Analysis  |   Knockout Info  |   Stress  |   Plant Info Databases The Arabidopsis Ionomics Database -We describe here the use of mineral nutrient and trace element profiling as a new tool to determine the biological significance of connections between a plants genome and its elemental-profile. Using inductively-coupled plasma mass spectrometry (ICP-MS) we have quantified Li, Na, Mg, P, K, Ca, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Se, Mo, Cd and Pb in shoots of 8,300 fast neutron mutagenized Arabidopsis thaliana plants consisting of 4747 M2 plants (representing 2373 M1 parental lines) and 320 M3 families selected in the M2 generation for their modified elemental-profiles. All elemental-profile data for both the M2 and M3 plants is available in a searchable database format and seed from each M3 family will be available at the ABRC. Including the database the research group at UCSD has supplemental information to accompany this database. Arabidopsis Membrane Protein Database -ARAMEMNON is a database about membrane proteins of thale cress (Arabidopsis thaliana). It stores data about sequences, similarities between different proteins, transmembrane protein predictions and signal peptide predictions of Arabidopsis thaliana membrane proteins. A basic idea behind this database is to compare several prediction data. Currently it contains the data of seven transmembrane protein predictions and of eight signal peptide predictions. A P-Type ATPase Database -Kristian Axelsen P-Type ATPase Database is a collection of various P-Type ATPases present in various species. There are crystal structures, phylogenetic trees and a classification of subfamilies. Transport Classification Overview -Milton Saier Transport Classification site is the one stop shop for descriptions and references to various transporters throughout any species. His classification system has just been accepted and it's the same classification system we use for PlantsT. He has just set up a database for these transporters called TCDB. You can reach it from his site. TAIR gene families -This site contains information on Arabidopsis Gene Families. The information provided here has been compiled from the Arabidopsis Genome Initiative, Anton Sanderfoot's Arabidopsis Syntaxins, SNAREs and associated proteins website, Todd Richmond'sPlant Cell Wall Biosynthesis website, Meagher Lab website, Soren Bak's The Arabidopsis P450, cytochrome b5, P450 reductase, and Glycosyltransferase Family 1 Site at PlaCe, Dr. David Nelson's Cytochrome P450 website , Arabidopsis Membrane Protein Library, Daniel Cosgrove's Expansin Genes website, Browning Research Group Protein Synthesis Genomic Database, CAZy- Carbohydrate-Active enZymes server, Barbara Leyman's Trehalose Biosynthesis Gene Families and Lutz Nover's Heat shock transcription factors (Hsfs) of Arabidopsis thaliana. Analysis The Arabidopsis Membrane Protein Library -John Ward's Arabidopsis membrane protein library is a collection of polytopic membrane protein sequences (containing two or more predicted membrane spanning domains) from the model plant Arabidopsis thaliana. The protein sequences have been clustered into families based on sequence homology and the families have been assigned to functional categories. Targeting Analysis -TargetP predicts the subcellular location of eukaryotic protein sequences. The subcellular location assignment is based on the predicted presence of any of the N-terminal presequences chloroplast transit peptide (cTP), mitochondrial targeting peptide (mTP) or secretory pathway signal peptide (SP). Transport Protein Analysis -Ian Paulsen has set up a website to analyze different transporters and predicts their function. This page provides a comparison of the cytoplasmic membrane transport sustems identified in organisms for which a complete genome sequence are available. Each transporter found will be listed with its known or putative function and classified into families according to Saier's TC system. Knockout Information GENE KO -This is a sequence indexed library of insertion mutations in the Arabidopsis genomoe. The goal of this program is to create a sequence-indexed library of mutations in the Arabidopsis genome. The Salk Institute Genome Analysis Laboratory (SIGnAL) will use high-throughput genome sequencing methods to identify the sites of insertion of Agrobacterium T-DNA in the Arabidopsis genome. T-DNA transformed plants from the Alonso/Crosby/Ecker collection will be grown, genomic DNA will be prepared, T-DNA flanking plant DNA will be recovered and sequenced. Wisconsin KO facility -UWBC has established a UW-Madison user-fee service facility to provide "knock-out" Arabidopsis mutant plants for the research community. This web site gives you all of the information you need to interact with the facility. Insert Watch -Submit sequences to be searched against sequenced inserts as soon as they are released. When a match is found you will be notified by email with links into the catalogue to facilitate ordering the stocks. Yeast Deletion Strains -Search for strains made by the Saccharomyces Deletion Project available from Research Genetics and from American Type Culture Collection. Stress Plant Stress -The PlantStress web site presents concise and updated discussions of the main stresses: Drought, Heat, Cold (chilling and freezing), Salinity, Soil Mineral Deficiency and Soil Mineral Toxicity (mainly aluminum and acid soil). Each discussion is divided into two parts: - The Impact of stress - The Mitigation of the effect of stress Salt Stress -George Brown Jr. has set up a site that conducts research on salt stress in plants. Part of the mission statement from their grant includes conducting Research on the effects of salts on physiology and development, and the integration of physical and chemical factors associated with the environment and management are being combined to develop comprehensive approaches for dealing with the salinity problems in agriculture. Plant Information Center for Molecular Agriculture -The San Diego Center for Molecular Agriculture (SDCMA) is an interdepartmental and interinstitutional research center that comprises scientists from the University of California San Diego (UCSD) and The Salk Institute for Biological Studies. It provides a focal point for studies on the molecular improvement of crop improvement and crop protection. Functional Genomics -This is Science magazine's section for papers that involve functional genomics research. WHO, human nutrition -WHO includes information on collaborating organizations; databases for breastfeeding, micronutrients, obesity & body mass index (BMI) in adults, and national nutrition policies & programmes; meetings; project information; publications; and research. Crop Nutrition -This site offers recommendations and various information on essiential plant nutrients, types of fertilizers, soil testing, and plant tissue analysis. Bioremediation Resources -This site is mainly a link site to various web pages that deal with Bioremediation. There are resources from the government and disscussion groups one can join.