arabidopsis

Summary

Summary: A plant genus of the family BRASSICACEAE that contains ARABIDOPSIS PROTEINS and MADS DOMAIN PROTEINS. The species A. thaliana is used for experiments in classical plant genetics as well as molecular genetic studies in plant physiology, biochemistry, and development.

Top Publications

  1. ncbi Genome sequence of the palaeopolyploid soybean
    Jeremy Schmutz
    HudsonAlpha Genome Sequencing Center, 601 Genome Way, Huntsville, Alabama 35806, USA
    Nature 463:178-83. 2010
  2. pmc The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools
    Philippe Lamesch
    Department of Plant Biology, Carnegie Institution, 260 Panama St, Stanford, CA 94305, USA
    Nucleic Acids Res 40:D1202-10. 2012
  3. ncbi The Sorghum bicolor genome and the diversification of grasses
    Andrew H Paterson
    Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
    Nature 457:551-6. 2009
  4. ncbi microRNA-directed phasing during trans-acting siRNA biogenesis in plants
    Edwards Allen
    Center for Gene Research and Biotechnology, Oregon State University, Corvallis, Oregon 97331, USA
    Cell 121:207-21. 2005
  5. pmc WoLF PSORT: protein localization predictor
    Paul Horton
    Computational Biology Research Center, AIST, Tokyo, Japan
    Nucleic Acids Res 35:W585-7. 2007
  6. pmc Plant cis-acting regulatory DNA elements (PLACE) database: 1999
    K Higo
    Department of Genetic Resources, National Institute of Agrobiological Resources, 2 1 2 Kannondai, Tsukuba, Ibaraki 305, Japan
    Nucleic Acids Res 27:297-300. 1999
  7. pmc OrthoMCL: identification of ortholog groups for eukaryotic genomes
    Li Li
    Department of Biology and Genetics, Center for Bioinformatics, and Genomics Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
    Genome Res 13:2178-89. 2003
  8. ncbi The genome of the mesopolyploid crop species Brassica rapa
    Xiaowu Wang
    Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences IVF, CAAS, Beijing, China
    Nat Genet 43:1035-9. 2011
  9. pmc Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines
    Susanna Atwell
    Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA
    Nature 465:627-31. 2010
  10. ncbi Computational identification of plant microRNAs and their targets, including a stress-induced miRNA
    Matthew W Jones-Rhoades
    Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA
    Mol Cell 14:787-99. 2004

Detail Information

Publications310 found, 100 shown here

  1. ncbi Genome sequence of the palaeopolyploid soybean
    Jeremy Schmutz
    HudsonAlpha Genome Sequencing Center, 601 Genome Way, Huntsville, Alabama 35806, USA
    Nature 463:178-83. 2010
    ..We predict 46,430 protein-coding genes, 70% more than Arabidopsis and similar to the poplar genome which, like soybean, is an ancient polyploid (palaeopolyploid)...
  2. pmc The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools
    Philippe Lamesch
    Department of Plant Biology, Carnegie Institution, 260 Panama St, Stanford, CA 94305, USA
    Nucleic Acids Res 40:D1202-10. 2012
    The Arabidopsis Information Resource (TAIR, http://arabidopsis...
  3. ncbi The Sorghum bicolor genome and the diversification of grasses
    Andrew H Paterson
    Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
    Nature 457:551-6. 2009
    ..About 24% of genes are grass-specific and 7% are sorghum-specific. Recent gene and microRNA duplications may contribute to sorghum's drought tolerance...
  4. ncbi microRNA-directed phasing during trans-acting siRNA biogenesis in plants
    Edwards Allen
    Center for Gene Research and Biotechnology, Oregon State University, Corvallis, Oregon 97331, USA
    Cell 121:207-21. 2005
    ..An integrated approach to identify targets of Arabidopsis thaliana miRNAs and ta-siRNAs revealed several new classes of small RNA-regulated genes, including conventional ..
  5. pmc WoLF PSORT: protein localization predictor
    Paul Horton
    Computational Biology Research Center, AIST, Tokyo, Japan
    Nucleic Acids Res 35:W585-7. 2007
    ..Taken together, this information allows a user to understand the evidence (or lack thereof) behind the predictions made for particular proteins. WoLF PSORT is available at wolfpsort.org...
  6. pmc Plant cis-acting regulatory DNA elements (PLACE) database: 1999
    K Higo
    Department of Genetic Resources, National Institute of Agrobiological Resources, 2 1 2 Kannondai, Tsukuba, Ibaraki 305, Japan
    Nucleic Acids Res 27:297-300. 1999
    ..This report summarizes the present status of this database and available tools...
  7. pmc OrthoMCL: identification of ortholog groups for eukaryotic genomes
    Li Li
    Department of Biology and Genetics, Center for Bioinformatics, and Genomics Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
    Genome Res 13:2178-89. 2003
    ..has been applied to the proteome data set from seven publicly available genomes (human, fly, worm, yeast, Arabidopsis, the malaria parasite Plasmodium falciparum, and Escherichia coli)...
  8. ncbi The genome of the mesopolyploid crop species Brassica rapa
    Xiaowu Wang
    Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences IVF, CAAS, Beijing, China
    Nat Genet 43:1035-9. 2011
    ..We modeled 41,174 protein coding genes in the B. rapa genome, which has undergone genome triplication. We used Arabidopsis thaliana as an outgroup for investigating the consequences of genome triplication, such as structural and ..
  9. pmc Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines
    Susanna Atwell
    Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA
    Nature 465:627-31. 2010
    ..Here we demonstrate the power of this approach by carrying out a GWA study of 107 phenotypes in Arabidopsis thaliana, a widely distributed, predominantly self-fertilizing model plant known to harbour considerable ..
  10. ncbi Computational identification of plant microRNAs and their targets, including a stress-induced miRNA
    Matthew W Jones-Rhoades
    Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA
    Mol Cell 14:787-99. 2004
    ..comparative genomic approaches to systematically identify both miRNAs and their targets that are conserved in Arabidopsis thaliana and rice (Oryza sativa)...
  11. ncbi Prediction of plant microRNA targets
    Matthew W Rhoades
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, MA 02142, USA
    Cell 110:513-20. 2002
    We predict regulatory targets for 14 Arabidopsis microRNAs (miRNAs) by identifying mRNAs with near complementarity. Complementary sites within predicted targets are conserved in rice...
  12. ncbi Contrasting mechanisms of defense against biotrophic and necrotrophic pathogens
    Jane Glazebrook
    Department of Plant Biology, University of Minnesota, St Paul, Minnesota 55108, USA
    Annu Rev Phytopathol 43:205-27. 2005
    ..This review summarizes results from Arabidopsis-pathogen systems regarding the contributions of various defense responses to resistance to several biotrophic ..
  13. pmc Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis
    Ramanjulu Sunkar
    Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, California 92521, USA
    Plant Cell 16:2001-19. 2004
    ..In Arabidopsis thaliana, 43 miRNAs comprising 15 families have been reported thus far...
  14. ncbi MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes
    Oliver Thimm
    Max Planck Institute for Molecular Plant Physiology, Golm, Germany
    Plant J 37:914-39. 2004
    ..A first build of TRANSCRIPTSCAVENGER groups genes on the Arabidopsis Affymetrix 22K array into >200 hierarchical categories, providing a breakdown of central metabolism (for ..
  15. pmc Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis
    Tomasz Czechowski
    Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
    Plant Physiol 139:5-17. 2005
    ..to identify a new generation of reference genes with very stable expression levels in the model plant species Arabidopsis (Arabidopsis thaliana)...
  16. pmc The Arabidopsis lyrata genome sequence and the basis of rapid genome size change
    Tina T Hu
    Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA
    Nat Genet 43:476-81. 2011
    We report the 207-Mb genome sequence of the North American Arabidopsis lyrata strain MN47 based on 8.3× dideoxy sequence coverage...
  17. ncbi Whole-genome sequencing of multiple Arabidopsis thaliana populations
    Jun Cao
    Max Planck Institute for Developmental Biology, Tubingen, Germany
    Nat Genet 43:956-63. 2011
    The plant Arabidopsis thaliana occurs naturally in many different habitats throughout Eurasia...
  18. pmc Genome-wide mapping of alternative splicing in Arabidopsis thaliana
    Sergei A Filichkin
    Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331, USA
    Genome Res 20:45-58. 2010
    ..We mapped the Arabidopsis transcriptome at single-base resolution using the Illumina platform for ultrahigh-throughput RNA sequencing (..
  19. ncbi The JAZ family of repressors is the missing link in jasmonate signalling
    A Chini
    Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnologia CSIC, Campus Universidad Autonoma, 28049 Madrid, Spain
    Nature 448:666-71. 2007
    ..of JASMONATE-INSENSITIVE 3 (JAI3) and a family of related proteins named JAZ (jasmonate ZIM-domain), in Arabidopsis thaliana...
  20. ncbi Multiple reference genomes and transcriptomes for Arabidopsis thaliana
    Xiangchao Gan
    Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
    Nature 477:419-23. 2011
    Genetic differences between Arabidopsis thaliana accessions underlie the plant's extensive phenotypic variation, and until now these have been interpreted largely in the context of the annotated reference accession Col-0...
  21. pmc A gateway cloning vector set for high-throughput functional analysis of genes in planta
    Mark D Curtis
    Institute of Plant Biology and Zurich Basel Plant Science Centre, University of Zurich, Zollikerstrasse 107, Ch 8008 Zurich, Switzerland
    Plant Physiol 133:462-9. 2003
    ..In Arabidopsis, approximately 55% of genes can be assigned a putative function, however, less than 8% of these have been ..
  22. ncbi Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA
    Cesar Llave
    Center for Gene Research and Biotechnology, and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
    Science 297:2053-6. 2002
    ..Here we show that Arabidopsis thaliana miRNA 39 (also known as miR171), a 21-ribonucleotide species that accumulates predominantly in ..
  23. pmc The sequential action of miR156 and miR172 regulates developmental timing in Arabidopsis
    Gang Wu
    Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
    Cell 138:750-9. 2009
    ..Thus, like the larval-to-adult transition in Caenorhabditis elegans, the juvenile-to-adult transition in Arabidopsis is mediated by sequentially operating miRNAs...
  24. ncbi The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)
    G A Tuskan
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    Science 313:1596-604. 2006
    ..A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages...
  25. ncbi A plant miRNA contributes to antibacterial resistance by repressing auxin signaling
    Lionel Navarro
    Sainsbury Laboratory, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
    Science 312:436-9. 2006
    ..In Arabidopsis, perception of flagellin increases resistance to the bacterium Pseudomonas syringae, although the molecular ..
  26. ncbi MYB transcription factors in Arabidopsis
    Christian Dubos
    Institut Jean Pierre Bourgin, UMR1318 INRA AgroParisTech, 78026 Versailles Cedex, France
    Trends Plant Sci 15:573-81. 2010
    ..in a variety of plant-specific processes, as evidenced by their extensive functional characterization in Arabidopsis (Arabidopsis thaliana)...
  27. pmc Abscisic acid inhibits type 2C protein phosphatases via the PYR/PYL family of START proteins
    Sang Youl Park
    Department of Botany and Plant Sciences, University of California at Riverside, Riverside, CA 92521, USA
    Science 324:1068-71. 2009
    ..Our results illustrate the power of the chemical genetic approach for sidestepping genetic redundancy...
  28. ncbi miR156-regulated SPL transcription factors define an endogenous flowering pathway in Arabidopsis thaliana
    Jia wei Wang
    Department of Molecular Biology, Max Planck Institute for Developmental Biology, D 72076 Tubingen, Germany
    Cell 138:738-49. 2009
    ....
  29. ncbi A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development
    Xuemei Chen
    Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA
    Science 303:2022-5. 2004
    ..Therefore, miRNA172 likely acts in cell-fate specification as a translational repressor of APETALA2 in Arabidopsis flower development.
  30. pmc Efficient control of population structure in model organism association mapping
    Hyun Min Kang
    Department of Computer Science, University of California, Los Angeles, California 90095 1596, USA
    Genetics 178:1709-23. 2008
    ..that mixed models successfully correct for the genetic relatedness in association mapping in maize and Arabidopsis panel data sets. However, the currently available mixed-model methods suffer from computational inefficiency...
  31. ncbi Widespread translational inhibition by plant miRNAs and siRNAs
    Peter Brodersen
    Institut de Biologie Moleculaire des Plantes du CNRS, Unité Propre de Recherche 2357, 12 rue du Général Zimmer, 67084 Strasbourg Cedex, France
    Science 320:1185-90. 2008
    ..We have isolated Arabidopsis mutants defective in miRNA action...
  32. ncbi FT protein movement contributes to long-distance signaling in floral induction of Arabidopsis
    Laurent Corbesier
    Max Planck Institute for Plant Breeding Research, Carl von Linne Weg 10, D 50829 Cologne, Germany
    Science 316:1030-3. 2007
    ..The identity of the long-distance signal has yet to be determined. In Arabidopsis, activation of FLOWERING LOCUS T (FT) transcription in leaf vascular tissue (phloem) induces flowering...
  33. pmc An "Electronic Fluorescent Pictograph" browser for exploring and analyzing large-scale biological data sets
    Debbie Winter
    Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
    PLoS ONE 2:e718. 2007
    ..For the non-bioinformatics specialist, however, many of the currently available tools provide overwhelming amounts of data that are presented in a non-intuitive way...
  34. ncbi The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla
    Olivier Jaillon
    Genoscope CEA and UMR 8030 CNRS Genoscope Université d Evry, 2 rue Gaston Cremieux, BP5706, 91057 Evry, France
    Nature 449:463-7. 2007
    ..Furthermore, we explain the chronology of previously described whole-genome duplication events in the evolution of flowering plants...
  35. pmc Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome
    Charles Addo-Quaye
    Department of Computer Science and Engineering, Pennsylvania State University, University Park, PA 16802, USA
    Curr Biol 18:758-62. 2008
    ..The 5' ends of polyadenylated, uncapped mRNAs from Arabidopsis were directly sampled, resulting in an empirical snapshot of the degradome...
  36. pmc Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5' terminal nucleotide
    Shijun Mi
    National Institute of Biological Sciences, No 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
    Cell 133:116-27. 2008
    Argonaute (AGO) proteins recruit small RNAs to form the core of RNAi effector complexes. Arabidopsis encodes ten AGO proteins and a large network of small RNAs...
  37. ncbi JAZ repressor proteins are targets of the SCF(COI1) complex during jasmonate signalling
    Bryan Thines
    Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 6340, USA
    Nature 448:661-5. 2007
    ....
  38. pmc Two transcription factors, DREB1 and DREB2, with an EREBP/AP2 DNA binding domain separate two cellular signal transduction pathways in drought- and low-temperature-responsive gene expression, respectively, in Arabidopsis
    Q Liu
    Biological Resources Division, Japan International Research Center for Agricultural Sciences JIRCAS, Ministry of Agriculture, Forestry, and Fisheries, 2 1 Ohwashi, Tsukuba, Ibaraki 305 8686, Japan
    Plant Cell 10:1391-406. 1998
    ..element) plays an important role in both dehydration- and low-temperature-induced gene expression in Arabidopsis. Two cDNA clones that encode DRE binding proteins, DREB1A and DREB2A, were isolated by using the yeast one-..
  39. ncbi A multicolored set of in vivo organelle markers for co-localization studies in Arabidopsis and other plants
    Brook K Nelson
    Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996 0840, USA
    Plant J 51:1126-36. 2007
    ..In addition, the Arabidopsis organelle marker lines can also be employed in plant cell biology teaching labs to demonstrate the distribution ..
  40. ncbi Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends
    Marcelo A German
    Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA
    Nat Biotechnol 26:941-6. 2008
    ..from the 5' ends of polyadenylated products of miRNA-mediated mRNA decay, isolated from inflorescence tissue of Arabidopsis thaliana, to discover novel miRNA-target RNA pairs...
  41. ncbi Regulators of PP2C phosphatase activity function as abscisic acid sensors
    Yue Ma
    Lehrstuhl fur Botanik, Technische Universitat Munchen, Am Hochanger 4, D 85354 Freising, Germany
    Science 324:1064-8. 2009
    ..In Arabidopsis, RCARs belong to a family with 14 members that share structural similarity with class 10 pathogen-related ..
  42. pmc Evidence for a SAL1-PAP chloroplast retrograde pathway that functions in drought and high light signaling in Arabidopsis
    Gonzalo M Estavillo
    Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton, Australian Capital Territory 0200, Australia
    Plant Cell 23:3992-4012. 2011
    ..that one such signal is a phosphonucleotide (3'-phosphoadenosine 5'-phosphate [PAP]), which accumulates in Arabidopsis thaliana in response to drought and high light (HL) stress and that the enzyme SAL1 regulates its levels by ..
  43. ncbi MAP kinase signalling cascade in Arabidopsis innate immunity
    Tsuneaki Asai
    Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114, USA
    Nature 415:977-83. 2002
    ..We developed an Arabidopsis thaliana leaf cell system based on the induction of early-defence gene transcription by flagellin, a highly ..
  44. pmc Independently evolved virulence effectors converge onto hubs in a plant immune system network
    M Shahid Mukhtar
    Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
    Science 333:596-601. 2011
    ..of plant-pathogen effectors from two pathogens spanning the eukaryote-eubacteria divergence, three classes of Arabidopsis immune system proteins, and ~8000 other Arabidopsis proteins...
  45. pmc The Arabidopsis Information Resource (TAIR): gene structure and function annotation
    David Swarbreck
    Carnegie Institution, Department of Plant Biology, 260 Panama St, Stanford, CA 94305, USA
    Nucleic Acids Res 36:D1009-14. 2008
    The Arabidopsis Information Resource (TAIR, http://arabidopsis.org) is the model organism database for the fully sequenced and intensively studied model plant Arabidopsis thaliana...
  46. pmc The Arabidopsis NFYA5 transcription factor is regulated transcriptionally and posttranscriptionally to promote drought resistance
    Wen Xue Li
    Key Laboratory of Plant and Soil Interactions, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100094, China
    Plant Cell 20:2238-51. 2008
    ..We found that the Arabidopsis thaliana NFYA5 transcript is strongly induced by drought stress in an abscisic acid (ABA)-dependent manner...
  47. ncbi Arabidopsis mesophyll protoplasts: a versatile cell system for transient gene expression analysis
    Sang Dong Yoo
    Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
    Nat Protoc 2:1565-72. 2007
    The transient gene expression system using Arabidopsis mesophyll protoplasts has proven an important and versatile tool for conducting cell-based experiments using molecular, cellular, biochemical, genetic, genomic and proteomic ..
  48. ncbi The F-box protein TIR1 is an auxin receptor
    Nihal Dharmasiri
    Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
    Nature 435:441-5. 2005
    ..Finally, TIR1 synthesized in insect cells binds Aux/IAA proteins in an auxin-dependent manner. Together, these results indicate that TIR1 is an auxin receptor that mediates Aux/IAA degradation and auxin-regulated transcription...
  49. ncbi FLS2: an LRR receptor-like kinase involved in the perception of the bacterial elicitor flagellin in Arabidopsis
    L Gomez-Gomez
    Friedrich Miescher Institut, Basel, Switzerland
    Mol Cell 5:1003-11. 2000
    Flagellin, the main protein of the bacterial flagella, elicits defence responses and alters growth in Arabidopsis seedlings. Previously, we identified the FLS1 locus, which confers flagellin insensitivity in Ws-0...
  50. pmc Transgenerational epigenetic instability is a source of novel methylation variants
    Robert J Schmitz
    Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
    Science 334:369-73. 2011
    ..We examined spontaneously occurring variation in DNA methylation in Arabidopsis thaliana plants propagated by single-seed descent for 30 generations...
  51. ncbi The evolutionary fate and consequences of duplicate genes
    M Lynch
    Department of Biology, University of Oregon, Eugene, OR 97403, USA
    Science 290:1151-5. 2000
    ..Although duplicate genes may only rarely evolve new functions, the stochastic silencing of such genes may play a significant role in the passive origin of new species...
  52. ncbi Signals from chloroplasts converge to regulate nuclear gene expression
    Shai Koussevitzky
    Howard Hughes Medical Institute, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
    Science 316:715-9. 2007
    ..We propose a model in which multiple indicators of aberrant plastid function in Arabidopsis are integrated upstream of GUN1 within plastids, which leads to ABI4-mediated repression of nuclear-encoded ..
  53. ncbi Multisubunit RNA polymerases IV and V: purveyors of non-coding RNA for plant gene silencing
    Jeremy R Haag
    Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
    Nat Rev Mol Cell Biol 12:483-92. 2011
    ..However, their subunit compositions reveal that they evolved as specialized forms of RNA polymerase II, which provides the unique opportunity to study the functional diversification of a eukaryotic RNA polymerase family...
  54. pmc TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes
    V Matys
    BIOBASE GmbH, Halchtersche Strasse 33, D 38304 Wolfenbuttel, Germany
    Nucleic Acids Res 34:D108-10. 2006
    ..Drosophila transcription factor binding sites (by courtesy of the Drosophila DNase I footprint database) and of Arabidopsis factors (by courtesy of DATF, Database of Arabidopsis Transcription Factors) has to be stressed...
  55. ncbi Regulation of flowering time: all roads lead to Rome
    Anusha Srikanth
    Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 37 39 VI, Tubingen, Germany
    Cell Mol Life Sci 68:2013-37. 2011
    ..The molecular mechanisms of these pathways have been studied extensively in Arabidopsis thaliana and several other flowering plants.
  56. ncbi bZIP transcription factors in Arabidopsis
    Marc Jakoby
    MPI for Plant Breeding Research, 50829, Koln, Germany
    Trends Plant Sci 7:106-11. 2002
    ..The Arabidopsis genome sequence contains 75 distinct members of the bZIP family, of which approximately 50 are not described in ..
  57. pmc Relationship between nucleosome positioning and DNA methylation
    Ramakrishna K Chodavarapu
    Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California 90095, USA
    Nature 466:388-92. 2010
    ..Here we report a genome-wide nucleosome positioning analysis of Arabidopsis thaliana using massively parallel sequencing of mononucleosomes...
  58. ncbi Adaptation to climate across the Arabidopsis thaliana genome
    Angela M Hancock
    Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA
    Science 334:83-6. 2011
    ..We conducted a genome-wide scan to identify climate-adaptive genetic loci and pathways in the plant Arabidopsis thaliana...
  59. pmc Arabidopsis circadian clock protein, TOC1, is a DNA-binding transcription factor
    Joshua M Gendron
    Section of Cell and Developmental Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093 0130, USA
    Proc Natl Acad Sci U S A 109:3167-72. 2012
    The first described feedback loop of the Arabidopsis circadian clock is based on reciprocal regulation between Timing of CAB Expression 1 (TOC1) and Circadian Clock-associated 1 (CCA1)/late elongated hypocotyl (LHY)...
  60. ncbi Gene networks involved in drought stress response and tolerance
    Kazuo Shinozaki
    RIKEN Plant Science Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, 203 0045 Japan
    J Exp Bot 58:221-7. 2007
    ..Many drought-inducible genes with various functions have been identified by molecular and genomic analyses in Arabidopsis, rice, and other plants, including a number of transcription factors that regulate stress-inducible gene ..
  61. pmc Jasmonates: an update on biosynthesis, signal transduction and action in plant stress response, growth and development
    C Wasternack
    Department of Natural Product Biotechnology, Leibniz Institute of Plant Biochemistry, Weinberg 3, D 06120 Halle Saale, Germany
    Ann Bot 100:681-97. 2007
    ..Many of them alter gene expression positively or negatively in a regulatory network with synergistic and antagonistic effects in relation to other plant hormones such as salicylate, auxin, ethylene and abscisic acid...
  62. pmc A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana
    Ramya Rajagopalan
    Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Genes Dev 20:3407-25. 2006
    ..RNAs expressed in plants, we employed high-throughput pyrosequencing to obtain 887,000 reads corresponding to Arabidopsis thaliana small RNAs...
  63. ncbi ABA induction of miR159 controls transcript levels of two MYB factors during Arabidopsis seed germination
    Jose L Reyes
    Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Plant J 49:592-606. 2007
    ..Here, we show that, in germinating Arabidopsis thaliana seeds, ABA induces the accumulation of microRNA 159 (miR159) in an ABI3-dependent fashion, and ..
  64. ncbi Genome-wide insertional mutagenesis of Arabidopsis thaliana
    Jose M Alonso
    Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
    Science 301:653-7. 2003
    ..225,000 independent Agrobacterium transferred DNA (T-DNA) insertion events in the genome of the reference plant Arabidopsis thaliana have been created that represent near saturation of the gene space...
  65. pmc Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana
    Insuk Lee
    Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seodaemun gu, Seoul, Korea
    Nat Biotechnol 28:149-56. 2010
    ..network (AraNet) of functional associations among 19,647 (73%) genes of the reference flowering plant Arabidopsis thaliana...
  66. pmc Sequencing of natural strains of Arabidopsis thaliana with short reads
    Stephan Ossowski
    Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tubingen, Germany
    Genome Res 18:2024-33. 2008
    Whole-genome hybridization studies have suggested that the nuclear genomes of accessions (natural strains) of Arabidopsis thaliana can differ by several percent of their sequence...
  67. pmc Highly specific gene silencing by artificial microRNAs in Arabidopsis
    Rebecca Schwab
    Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
    Plant Cell 18:1121-33. 2006
    ..The design principles for amiRNAs have been generalized and integrated into a Web-based tool (http://wmd.weigelworld.org)...
  68. pmc Signatures of adaptation to obligate biotrophy in the Hyaloperonospora arabidopsidis genome
    Laura Baxter
    School of Life Sciences, Warwick University, Wellesbourne, CV35 9EF, UK
    Science 330:1549-51. 2010
    ..sequence of the oomycete Hyaloperonospora arabidopsidis (Hpa), an obligate biotroph and natural pathogen of Arabidopsis thaliana...
  69. pmc ATTED-II provides coexpressed gene networks for Arabidopsis
    Takeshi Obayashi
    Human Genome Center, Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokane dai, Minato ku, Tokyo 108 8639, Japan
    Nucleic Acids Res 37:D987-91. 2009
    ATTED-II (http://atted.jp) is a database of gene coexpression in Arabidopsis that can be used to design a wide variety of experiments, including the prioritization of genes for functional identification or for studies of regulatory ..
  70. ncbi Small silencing RNAs in plants are mobile and direct epigenetic modification in recipient cells
    Attila Molnar
    Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
    Science 328:872-5. 2010
    ..To identify the mobile RNA, we grafted Arabidopsis thaliana shoots to roots that would be a recipient for the silencing signal...
  71. ncbi Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils
    Thomas L Turner
    Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA
    Nat Genet 42:260-3. 2010
    ..To investigate whether Arabidopsis lyrata is locally adapted to serpentine soil, and to map the polymorphisms responsible for such adaptation, we ..
  72. ncbi Plant stomata function in innate immunity against bacterial invasion
    Maeli Melotto
    Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
    Cell 126:969-80. 2006
    ..Stomatal guard cells of Arabidopsis perceive bacterial surface molecules, which requires the FLS2 receptor, production of nitric oxide, and the ..
  73. ncbi Binding of brassinosteroids to the extracellular domain of plant receptor kinase BRI1
    Toshinori Kinoshita
    Howard Hughes Medical Institute and Plant Biology Laboratory, The Salk Institute for Biological Studies, 10010 N Torrey Pines Road, La Jolla, California 92037, USA
    Nature 433:167-71. 2005
    ..Our results demonstrate that brassinosteroids bind directly to the 94 amino acids comprising ID-LRR22 in the extracellular domain of BRI1, and define a new binding domain for steroid hormones...
  74. ncbi Plant ARGONAUTES
    Herve Vaucheret
    Laboratoire de Biologie Cellulaire, Institut Jean Pierre Bourgin, Institut National de la Recherche Agronomique INRA, 78026 Versailles Cedex, France
    Trends Plant Sci 13:350-8. 2008
    ..The plant model species Arabidopsis contains ten AGO proteins belonging to three phylogenetic clades...
  75. ncbi A high-resolution root spatiotemporal map reveals dominant expression patterns
    Siobhan M Brady
    Department of Biology, Duke University, Durham, NC 27708, USA
    Science 318:801-6. 2007
    ..We present microarray expression profiles of a high-resolution set of developmental time points within a single Arabidopsis root and a comprehensive map of nearly all root cell types...
  76. ncbi The AtGenExpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis and data access
    Hideki Goda
    RIKEN Plant Science Center, Tsurumi, Yokohama, Kanagawa 230 0045, Japan
    Plant J 55:526-42. 2008
    We analyzed global gene expression in Arabidopsis in response to various hormones and in related experiments as part of the AtGenExpress project...
  77. pmc An endogenous, systemic RNAi pathway in plants
    Patrice Dunoyer
    Institut de Biologie Moleculaire des Plantes du CNRS, UPR2357, Universite de Strasbourg, Strasbourg Cedex, France
    EMBO J 29:1699-712. 2010
    ..Through an exhaustive analysis performed using Arabidopsis, we provide here evidence that at least two such endogenous IRs are genetically virtually indistinguishable ..
  78. pmc Arabidopsis gene co-expression network and its functional modules
    Linyong Mao
    Virtual Reality Applications Center, Iowa State University, Ames, IA 50010, USA
    BMC Bioinformatics 10:346. 2009
    ..The organization of gene functional modules was also investigated...
  79. pmc Rank of correlation coefficient as a comparable measure for biological significance of gene coexpression
    Takeshi Obayashi
    Human Genome Center, Institute of Medical Science, The University of Tokyo, Minato ku, Tokyo, Japan
    DNA Res 16:249-60. 2009
    ..This observation was evaluated by large-scale gene expression data for four species: Arabidopsis, human, mouse and rat.
  80. pmc Comparative analysis of the receptor-like kinase family in Arabidopsis and rice
    Shin Han Shiu
    Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA
    Plant Cell 16:1220-34. 2004
    Receptor-like kinases (RLKs) belong to the large RLK/Pelle gene family, and it is known that the Arabidopsis thaliana genome contains >600 such members, which play important roles in plant growth, development, and defense responses...
  81. pmc cis-Regulatory elements and chromatin state coordinately control temporal and spatial expression of FLOWERING LOCUS T in Arabidopsis
    Jessika Adrian
    Max Planck Institute for Plant Breeding Research, Koeln, Germany
    Plant Cell 22:1425-40. 2010
    Flowering time of summer annual Arabidopsis thaliana accessions is largely determined by the timing of FLOWERING LOCUS T (FT) expression in the leaf vasculature...
  82. pmc MicroRNA control of PHABULOSA in leaf development: importance of pairing to the microRNA 5' region
    Allison C Mallory
    Whitehead Institute for Biomedical Research, Cambridge, MA 02142 1479, USA
    EMBO J 23:3356-64. 2004
    ....
  83. pmc Global analysis of gene activity during Arabidopsis seed development and identification of seed-specific transcription factors
    Brandon H Le
    Department of Molecular, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 107:8063-70. 2010
    ..specific stages of seed development, including those unique to seeds, we used Affymetrix GeneChips to profile Arabidopsis genes active in seeds from fertilization through maturation and at other times of the plant life cycle...
  84. ncbi Arabidopsis type I metacaspases control cell death
    Nuria S Coll
    Department of Biology, 108 Coker Hall, University of North Carolina UNC, CB 3280, Chapel Hill, NC 27599 3280, USA
    Science 330:1393-7. 2010
    ..demonstrated that two type I metacaspases, AtMC1 and AtMC2, antagonistically control programmed cell death in Arabidopsis. AtMC1 is a positive regulator of cell death and requires conserved caspase-like putative catalytic residues ..
  85. ncbi Genome-wide analysis of endogenous abscisic acid-mediated transcription in dry and imbibed seeds of Arabidopsis using tiling arrays
    Masanori Okamoto
    RIKEN Plant Science Center, Yokohama, Kanagawa 230 0045, Japan
    Plant J 62:39-51. 2010
    ..Bioinformatic analyses revealed that 6105 novel genes [non-Arabidopsis Genome Initiative (AGI) transcriptional units (TUs)] were expressed from unannotated regions...
  86. pmc The 1001 genomes project for Arabidopsis thaliana
    Detlef Weigel
    Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
    Genome Biol 10:107. 2009
    We advocate here a 1001 Genomes project for Arabidopsis thaliana, the workhorse of plant genetics, which will provide an enormous boost for plant research with a modest financial investment.
  87. pmc ETHYLENE RESPONSE FACTOR1 integrates signals from ethylene and jasmonate pathways in plant defense
    Oscar Lorenzo
    Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología Consejo Superior de Investigaciones Científicas, Campus Universidad Autonoma, 28049 Madrid, Spain
    Plant Cell 15:165-78. 2003
    ....
  88. pmc A conserved MYB transcription factor involved in phosphate starvation signaling both in vascular plants and in unicellular algae
    V Rubio
    Centro Nacional de Biotecnologia, Campus de Cantoblanco, 28049 Madrid, Spain
    Genes Dev 15:2122-33. 2001
    ..We prepared an EMS-mutagenized M(2) population of an Arabidopsis thaliana transgenic line harboring a reporter gene specifically responsive to Pi starvation (AtIPS1::GUS), and ..
  89. pmc High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes
    Noah Fahlgren
    Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
    PLoS ONE 2:e219. 2007
    ..we use deep sequencing and computational methods to identify, profile and analyze non-conserved MIRNA genes in Arabidopsis thaliana...
  90. pmc In vitro reconstitution of an abscisic acid signalling pathway
    Hiroaki Fujii
    Department of Botany and Plant Sciences, University of California at Riverside, Riverside, California 92521, USA
    Nature 462:660-4. 2009
    ..Our results reveal new insights into ABA signalling mechanisms and define a minimal set of core components of a complete major ABA signalling pathway...
  91. ncbi Visualization of protein interactions in living plant cells using bimolecular fluorescence complementation
    Michael Walter
    Institut fur Botanik und Botanischer Garten, Molekulare Entwicklungsbiologie der Pflanzen, Universitat Munster, Schlossplatz 4, 48149 Munster, Germany
    Plant J 40:428-38. 2004
    ..zipper (bZIP) transcription factor bZIP63 and the zinc finger protein lesion simulating disease 1 (LSD1) from Arabidopsis as well as the dimer formation of the tobacco 14-3-3 protein T14-3c...
  92. pmc Role of arabidopsis MYC and MYB homologs in drought- and abscisic acid-regulated gene expression
    H Abe
    Biological Resources Division, Japan International Research Center for Agricultural Sciences JIRCAS, Ibaraki, Japan
    Plant Cell 9:1859-68. 1997
    In Arabidopsis, the induction of a dehydration-responsive gene, rd22, is mediated by abscisic acid (ABA) and requires protein biosynthesis for ABA-dependent gene expression...
  93. pmc Multiple distinct small RNAs originate from the same microRNA precursors
    Weixiong Zhang
    Department of Computer Science and Engineering, Washington University in Saint Louis, Campus Box 1045, Saint Louis, MO 63130, USA
    Genome Biol 11:R81. 2010
    ..MicroRNAs (miRNAs), which originate from precursor transcripts with stem-loop structures, are essential gene expression regulators in eukaryotes...
  94. ncbi Small RNA duplexes function as mobile silencing signals between plant cells
    Patrice Dunoyer
    Institut de Biologie Moleculaire des Plantes du CNRS, Université de Strasbourg 12 rue du Général Zimmer, 67084 Strasbourg Cedex, France
    Science 328:912-6. 2010
    ..Cell-to-cell movement is unlikely to involve AGO1-bound siRNA single strands, but instead likely involves siRNA duplexes...
  95. ncbi Integration of plant responses to environmentally activated phytohormonal signals
    Patrick Achard
    John Innes Centre, Norwich NR4 7UJ, UK
    Science 311:91-4. 2006
    ..Here, we show that the nuclear-localized growth-repressing DELLA proteins of Arabidopsis integrate responses to independent hormonal and environmental signals of adverse conditions...
  96. ncbi A flagellin-induced complex of the receptor FLS2 and BAK1 initiates plant defence
    Delphine Chinchilla
    Zurich Basel Plant Science Center, Botanical Institute, University of Basel, Hebelstrasse 1, 4056 Basel, Switzerland
    Nature 448:497-500. 2007
    ..In Arabidopsis thaliana, the leucine-rich repeat receptor kinases flagellin-sensitive 2 (FLS2) (ref...
  97. pmc Ethylene interacts with abscisic acid to regulate endosperm rupture during germination: a comparative approach using Lepidium sativum and Arabidopsis thaliana
    Ada Linkies
    University of Freiburg, Faculty of Biology, Institute for Biology II, Botany Plant Physiology, D 79104 Freiburg, Germany
    Plant Cell 21:3803-22. 2009
    ..Here, we report on a comparative seed biology study with the close Brassicaceae relatives Lepidium sativum and Arabidopsis thaliana showing that ethylene biosynthesis and signaling regulate seed germination by a mechanism that ..
  98. pmc Evolution of Arabidopsis MIR genes generates novel microRNA classes
    Franck Vazquez
    Friedrich Miescher Institute for Biomedical Research, Novartis Research Foundation, Maulbeerstrasse 66, 4058 Basel, Switzerland
    Nucleic Acids Res 36:6429-38. 2008
    In Arabidopsis, canonical 21-nt miRNAs are generated by Dicer-like (DCL) 1 from hairpin precursors...
  99. ncbi Two novel GPCR-type G proteins are abscisic acid receptors in Arabidopsis
    Sona Pandey
    Biology Department, 208 Mueller Laboratory, Penn State University, University Park, PA 16802, USA
    Cell 136:136-48. 2009
    ..We identify and characterize two novel Arabidopsis proteins that show homology to an orphan vertebrate GPCR (GPR89) and interact with the sole Arabidopsis G ..
  100. pmc MicroRNA399 is a long-distance signal for the regulation of plant phosphate homeostasis
    Bikram Datt Pant
    Max Planck Institute for Molecular Plant Physiology, Science Park Golm, Am Muhlenberg 1, 14476 Potsdam, Germany
    Plant J 53:731-8. 2008
    ..By performing micro-grafting experiments using Arabidopsis, we further show that chimeric plants constitutively over-expressing miR399 in the shoot accumulate mature ..

Research Grants70

  1. Roles of RNA Polymerases IV and V in siRNA-mediated gene silencing
    CRAIG STUART PIKAARD; Fiscal Year: 2013
    ..Pol IV and Pol V are best understood with respect to their roles in the Arabidopsis siRNA-directed DNA methylation pathway...
  2. Dissecting the Function and Regulation of Stress-Induced SUMOylation
    ROBERT CHARLES AUGUSTINE; Fiscal Year: 2013
    ..The flowering plant Arabidopsis thaliana is well suited for understanding the role of SUMOylation during stress...
  3. Catalytic inactivation of miRNA function by customized RNase P-based ribozymes
    DANIEL R contact SCHOENBERG; Fiscal Year: 2010
    ..We have recently demonstrated the usefulness of this approach to disrupt miRNA function in Arabidopsis plants...
  4. Non-coding RNAs in the epigenetics of human centromere formation
    PETER WARBURTON; Fiscal Year: 2009
    ..Remarkably, it has been shown in S. pombe, Drosophila, Arabidopsis and mouse that assembly of centromeric heterochromatin actually requires bidirectional cis transcription of ..
  5. The Role of a New Cleavage and Polyadenylation Specificity Factor (CPSF73-II)
    Qingshun Q Li; Fiscal Year: 2010
    ..to regulate 3'- end formation of mRNAs via a combination of biochemical and molecular genetic means using Arabidopsis as the model system...
  6. Stomate-based innate immunity against bacterial infection in Arabidopsis
    Maeli Melotto; Fiscal Year: 2012
    ..RELEVANCE: This proposal describes basic research on the molecular basis of innate immunity of the model plant Arabidopsis to plant and human pathogenic bacteria...
  7. The role of host endogenous small RNAs in innate immunity
    Hailing Jin; Fiscal Year: 2013
    ..Using Arabidopsis as a model system and Illumina deep sequencing as a platform, we recently profiled the small RNA population ..
  8. Specification of alternate siRNA biogenesis pathways in Arabidopsis
    TODD LUCAS BLEVINS; Fiscal Year: 2011
    ..In the model plant Arabidopsis, protein duplication and sub-functionalization has resulted in distinct biochemical pathways that generate ..
  9. Analyses of two RNA helicases that affect intercellular transport via plasmodesma
    Patricia C Zambryski; Fiscal Year: 2012
    ..We developed a unique genetic screen that assays for altered PD mediated cell-to-cell transport during Arabidopsis embryonic development...
  10. REGULATION OF DEFENSE SIGNALING IN TOMATO
    Gregg A Howe; Fiscal Year: 2012
    ..Studies with the model plant Arabidopsis thaliana and tomato (Solanum lycopersicum) indicate that the E3 ubiquitin ligase SCFCOI1 is strictly required ..
  11. Phytochrome A: Structure/Function and Signaling Pathways
    Peter H Quail; Fiscal Year: 2013
    ..We propose to address these deficiencies here, using Arabidopsis as a model system...
  12. Regulation and Function of Active DNA Demethylation in Arabidopsis
    Daniel Zilberman; Fiscal Year: 2013
    ..Whereas most common model organisms lack DNA methylation, flowering plants, including Arabidopsis thaliana, share highly conserved methylation and demethylation pathways with mammals...
  13. The genetic basis of singlet oxygen-mediated signaling in eukaryotic cells
    Klaus Apel; Fiscal Year: 2013
    ..These problems have been alleviated in the present research project by using the conditional flu mutant of Arabidopsis. In the dark the flu mutant accumulates protochlorophyllide, a potent photosensitizer that upon illumination ..
  14. Programmed Cell Death and Disease Resistance in Arabidopsis
    Roger W Innes; Fiscal Year: 2013
    ..We have previously shown that loss-of-function mutations in the EDR1 gene of Arabidopsis confer enhanced resistance to infection by pathogens...
  15. MOLECULAR GENETICS OF NUCLEOLAR DOMINANCE
    CRAIG STUART PIKAARD; Fiscal Year: 2012
    ..In Arabidopsis suecica, the allotetraploid hybrid of A. thaliana and A. arenosa, the A...
  16. DNA Demethylation and Transcriptional Gene Silencing
    Jian Kang Zhu; Fiscal Year: 2013
    ..We have developed a unique system in the model organism Arabidopsis thaliana for dissecting active DNA demethylation and RNA-directed DNA methylation (RdDM)...
  17. Suppression of innate immunity by an ADP-ribosyltransferase type III effector
    JAMES ROBERT ALFANO; Fiscal Year: 2012
    ..An Arabidopsis mutant lacking one HopU1 substrate, AtGRP7, displayed enhanced susceptibility to P...
  18. Molecular and Genetic Dissection of Ultraviolet-B Signaling in Arabidopsis
    Zheng Hui He; Fiscal Year: 2013
    ..We have identified an Arabidopsis mutant, rus1 that is specifically hypersensitive to low- level UV-B...
  19. Genome wide views of chromatin occupancy in the control of Aquilegia development
    Levi Yant; Fiscal Year: 2013
    ..The genetic basis for this transition has been well characterized in the dicot Arabidopsis and several grass species in the monocots2-4...
  20. Signaling Mechanisms in Plant Innate Immunity
    Jen Sheen; Fiscal Year: 2012
    ..goal of this research project is to establish a regulatory framework for the convergent MAMP signaling using Arabidopsis thaliana as a model system...
  21. The role of RNA Polymerase V in RNA-directed DNA methylation
    ROSS ROLAND COCKLIN; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): Prior to publication of the Arabidopsis thaliana genome sequence in the year 2000, there were three known eukaryotic, multisubunit RNA Polymerases, abbreviated as Pol I, II and III...
  22. Glucose Signaling in Plants
    Jen Sheen; Fiscal Year: 2013
    ..Our research in the model plant Arabidopsis thaliana has provided compelling genetic and biochemical evidence that hexokinase1 (HXK1) is an evolutionarily ..
  23. FASEB SRC on Genetic Recombination and Genome Rearrangements
    JOHN HJ PETRINI; Fiscal Year: 2011
    ..studies from mammals, work concerning related proteins and mechanisms from model systems of bacteria, yeast, Arabidopsis, Drosophila, C. elegans and Xenopus will be featured...
  24. Genetics of DNA methylation patterning of arabidopsis.
    Steven E Jacobsen; Fiscal Year: 2013
    ..We are studying the mechanisms of DNA methylation control in the model plant Arabidopsis, which has methylation systems that have much in common with mammalian systems...
  25. Understanding the basis of circadian rhythms in the model system Arabidopsis
    ELAINE MUNSEY TOBIN; Fiscal Year: 2010
    ..Our long term goal is to understand in detail how the circadian clock functions in the model system Arabidopsis, and how both transcriptional and post-transcriptional processes are used to give this endogenous timekeeper a ..
  26. Novel estrogen receptor ligands from plant genomics
    John M Littleton; Fiscal Year: 2012
    ..In phase1 transgenic Arabidopsis thaliana seedlings expressing a human ERalpha/GFP construct were used to screen extracts from a native plant ..
  27. Telomere Structure and Function in Arabidopsis
    DOROTHY SHIPPEN; Fiscal Year: 2013
    ..Here we propose to exploit the many advantages of the Arabidopsis model system to investigate essential components of the telomere cap in a genetically tractable higher ..
  28. The intersection of development and innate immune system function in Arabidopsis.
    Jeffery L Dangl; Fiscal Year: 2013
    ..The experimental ease of Arabidopsis genetics, genomics, and cell biology leads to discoveries about fundamental processes shared across all ..
  29. Mechanisms governing floral stem cell maintenance and miRNA functions in Arabidop
    Xuemei Chen; Fiscal Year: 2013
    ..Flower development in the model plant Arabidopsis thaliana offers a great system to address key questions in stem cell biology...
  30. Defining the Connections between Respiratory Chain Structure and Oxidative Stress
    MATTHEW ESCOBAR; Fiscal Year: 2013
    ..the AOX gene family, the NDinternal gene family, and the NDexternal gene family in the model plant species Arabidopsis thaliana...
  31. STRESS HORMONE SIGNAL TRANSDUCTION IN ARABIDOPSIS
    Julian I Schroeder; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): Abscisic acid (ABA) is a central stress hormone in Arabidopsis that mediates rapid cellular responses, down- regulates cell proliferation and causes cell cycle arrest...
  32. Molecular analysis of the autonomous pathway
    Scott Michaels; Fiscal Year: 2013
    ..One key regulator of flowering time in Arabidopsis is FLOWERING LOCUS C (FLC), a MADS-domain-containing transcription factor that acts to delay flowering...
  33. Functional and Evolutionary Genomics of Ancient Small RNAs
    Michael J Axtell; Fiscal Year: 2012
    ..patens and the flowering plant Arabidopsis thaliana, and 3) empirically determine and compare the gene regulatory networks controlled by ancient microRNA-..
  34. Unfolded protein response in the model species Arabidopsis thaliana
    Federica Brandizzi; Fiscal Year: 2013
    ..of plant and metazoan UPR and the availability of powerful genomics and molecular tools render the model plant Arabidopsis thaliana an appealing system in which to address these questions...
  35. GENETIC ANALYSIS OF THE PLANT DEFENSE RESPONSE
    Frederick M Ausubel; Fiscal Year: 2013
    ..MAMP-activated response pathways are functionally analogous to mammalian TLR-signaling. A high throughput Arabidopsis seedling assay allowed us to make several important discoveries...
  36. Molecular Mechanism of Photoperiodic Time Measurement
    Takato Imaizumi; Fiscal Year: 2013
    ..have not yet been well described in many organisms, recent advances in the study of the model plant Arabidopsis have increased our molecular understanding of photoperiodic time measurement and have influenced the study of ..
  37. Synaptotagmin A and C in virus movement and plant development
    Asako Uchiyama; Fiscal Year: 2011
    ..to the unexpected discovery of a five-gene family of synaptotagmins (AtSYTA through AtSYTE) in the model plant Arabidopsis thaliana...
  38. Using combinatorial control to improve transgene expression specificity in plants
    Tedd D Elich; Fiscal Year: 2012
    ..elements can be used to increase the expression specificity of transcriptional promoters in the model plant Arabidopsis. As a specific product concept, Phase I research will focus on designing a root stele-specific expression ..
  39. Feedback between multiple signaling modes in control of a plant stem cell niche
    Elliot M Meyerowitz; Fiscal Year: 2013
    ..well as the remarkable regenerative abilities of plants, the shoot apical meristem (SAM) of the flowering plant Arabidopsis thaliana will be used as a model system...
  40. Genetics of Programmed Cell Death in Arabidoposis
    Jeffery L Dangl; Fiscal Year: 2010
    ..This proposal uses Arabidopsis as a genetic model with which to understand the control of HR as a paradigm for PCD in plants...
  41. Identification and Characterization of Population-Wide Epigenetic Variation
    Robert J Schmitz; Fiscal Year: 2012
    ..This proposal ims to use naturally occurring Arabidopsis thaliana strains that have been isolated from a broad range of geographically distributed regions of the planet ..
  42. The mechanism of action of a NudC domain small heat shock protein
    Nicholas J Kaplinsky; Fiscal Year: 2010
    ..The goal of this project is to understand the biological functions of BOBBER1 (BOB1), a recently identified Arabidopsis protein chaperone...
  43. Molecular Mechanisms of Steroid Hormone Perception at the Cell Surface
    Joanne Chory; Fiscal Year: 2013
    ..The strength of Arabidopsis as a genetic model has allowed the identification of dozens of mutant alleles (both gain- and loss-of-function) ..
  44. Characterization of novel subcellular structures in Arabidopsis thaliana
    Ernest Y Kwok; Fiscal Year: 2013
    ..This project will begin by looking for new organelles in the model plant Arabidopsis thaliana...
  45. A Functional Genomics Approach to Identify Regulators of Arabidopsis Clock Genes
    DAWN HEKINA NAGEL; Fiscal Year: 2012
    ..the circadian clock controls a variety of biological processes in higher plants, and furthermore, -10% of the Arabidopsis gene content is known to be circadian regulated...
  46. Structure and Function Analyses of DELLA Interacting Proteins in Arabidopsis
    Tai Ping Sun; Fiscal Year: 2013
    ..Recent studies in Arabidopsis show that DELLA directly binds to and regulates key transcription factors/regulators in several signaling ..
  47. Myosin-mediated organelle trafficking in plants
    Valerian V Dolja; Fiscal Year: 2010
    ..take advantage of the extensive genomic, bioinformatics, and cell biology resources available for a model plant Arabidopsis. Our studies into the myosin function in organelle transport, F-actin organization, polarized cell elongation, ..
  48. Regulation of cyclin-dependent kinase inhibitor p27 in cancer
    Mong Hong Lee; Fiscal Year: 2013
    ..The COP9 signalosome was originally identified from plant (Arabidopsis) mutants that mimic light-induced seedling development when grown in the dark...
  49. Identification and Characterization of Population-Wide Epigenetic Variation
    Robert J Schmitz; Fiscal Year: 2013
    ..This proposal aims to use naturally occurring Arabidopsis thaliana strains that have been isolated from a broad range of geographically distributed regions of the planet ..
  50. Epigenetic memory of plant stress response
    Se Young Kim; Fiscal Year: 2010
    ..paradigm utilized by plants to encode environmental stress, with two major aims using the model system Arabidopsis thaliana...
  51. Post-translational control mechanisms of the circadian clock
    David E Somers; Fiscal Year: 2013
    ..proposal is designed to investigate three different post-translational mechanisms of circadian clock control in Arabidopsis. The first is the role of protein phosphorylation, and the effect on activity, localization and stability of ..
  52. Molecular mechanisms in the Arabidopsis circadian clock
    Steve A Kay; Fiscal Year: 2013
    ..We propose to expand this approach on all Arabidopsis transcription factor families and validate the approach on preliminary candidates affecting the circadian ..
  53. Histone Modifications Associated w/Senescence in Arabidopsis
    JUDY ANN BRUSSLAN; Fiscal Year: 2012
    ..by applicant): The long-term objective of this project is to define the epigenome associated with senescence in Arabidopsis thaliana...
  54. Genetic characterization of phytochrome nuclear bodies in plant light signaling
    Meng Chen; Fiscal Year: 2013
    ..The long- term goal of our laboratory is to use phytochrome NBs in Arabidopsis as a genetic model to investigate general principles of NB function in eukaryotic cell signaling...
  55. The Interplay Between the Circadian Clock and Plant Immune Mechanisms
    Xinnian Dong; Fiscal Year: 2013
    ..The surprising discovery that the Arabidopsis clock component, CCA1, is a key regulator of RPP4-mediated resistance against the oomycete pathogen ..
  56. Molecular mechanisms of auxin response in Arabidopsis
    William M Gray; Fiscal Year: 2013
    ..Auxin signaling in the model plant Arabidopsis thaliana is exquisitely sensitive to perturbations in SCFTIR1 activity, and has proven to be an extremely ..
  57. Mechanisms behind Rapid Tip Growth
    Zhenbiao Yang; Fiscal Year: 2013
    ..To address these questions, the principal investigator's group has established the Arabidopsis PT as a model system...
  58. The Arabidopsis Transcription Factor ORFeome and downstream genomic application
    STEVE A contact KAY; Fiscal Year: 2010
    ..b>Arabidopsis offers some unique advantages for the development of large-scale genomic approaches for the study of TFs ..
  59. Molecular Mechanisms of Phytochrome Signaling
    JOHN CLARK LAGARIAS; Fiscal Year: 2013
    ..Phytochromes from the glaucophyte Cyanophora paradoxa, the chlorophyte Micromonas pusilla, and the land plants Arabidopsis thaliana and Triticum aestivum (wheat), will be used to examine the hypothesis that light-regulated ..
  60. Molecular analysis of circadian regulation in Arabidopsis
    Stacey L Harmer; Fiscal Year: 2013
    ..We will conduct our studies in Arabidopsis thaliana, a model plant that is uniquely well-suited for these experiments due to its compact genome, extensive ..
  61. Engineering Enhanced Plants for Arsenic Remediation
    David Lee; Fiscal Year: 2009
    ..isolated and characterized that confer fourfold increases in arsenic tolerance and uptake in the model plant Arabidopsis thaliana...
  62. Computational analysis of causality between miRNAs and antisense transcription
    CHRISTOPHER ROCK; Fiscal Year: 2009
    ..Based on computational analysis of four independent Arabidopsis transcriptome databases, it is hypothesized that miRNAs and ta-siRNAs are triggers for antisense transcription ..
  63. Genome Wide Analysis of DNA Methylation
    Joseph Ecker; Fiscal Year: 2006
    ..We will test our methods with the model plant Arabidopsis thaliana, demonstrating their usefulness for the human genome...
  64. Molecular Basis of Pathogen-Induced Cell Death in Plants
    JEAN GREENBERG; Fiscal Year: 2009
    ..by applicant): Experiments in this competing renewal combine the powerful genetic tools of the model plant Arabidopsis with cell biological and biochemical approaches to examine a major signaling pathway that controls innate ..
  65. DME-INTERACTING PROTEIN 1 REGULATES DEMETHYLATOIN AND REPRODUCTION IN ARABIDOPSIS
    Wenyan Xiao; Fiscal Year: 2009
    ..b>Arabidopsis thaliana is an excellent system to investigate epigenetic mechanisms, which are evolutionarily conserved ..
  66. TOMOGRAPHIC ANALYSIS OF CYTOKINESIS IN ARABIDOPSIS
    L Staehelin; Fiscal Year: 2002
    ..three-dimensional (3-D) structural database of the cytokinetic apparatii of somatic and syncytial types of Arabidopsis cells, tobacco BY-2 suspension cultured cells and onion epidermal cells...
  67. Arrested Development of Arabidopsis
    F Pickett; Fiscal Year: 2003
    ..the cloning and characterization of genes corresponding to the ARRESTED DEVELOPMENT (add) 1 and 3 mutations of Arabidopsis thaliana...
  68. TOMOGRAPHIC ANALYSIS OF CYTOKINESIS IN ARABIDOPSIS
    L Staehelin; Fiscal Year: 2003
    ..three-dimensional (3-D) structural database of the cytokinetic apparatii of somatic and syncytial types of Arabidopsis cells, tobacco BY-2 suspension cultured cells and onion epidermal cells...
  69. Arabidopsis basil immunity to human and plant pathogens
    Sheng He; Fiscal Year: 2004
    ..We use the model Arabidopsis-Pseudomonas syringae/enterohemorrhagic Escherichia coli (EHEC) pathosystem for this research...
  70. REGULATION OF GLYCOLYTIC GENES IN ARABIDOPSIS
    Ming Che Shih; Fiscal Year: 1993
    ..Nuclear genes encoding Arabidopsis cytosolic (GapC) and chloroplast (GapA and GapB) glyceraldehyde-3-phosphate dehydrogenase (GAPDH), will be used ..