Arabidopsis Protocols

<p>Part I. Growing Arabidopsis</p><p> </p><p>1. Handling Arabidopsis Plants: Growth, Preservation of Seeds, Transformation and Genetic Crosses</p><p>Luz Rivero, Randy Scholl, Nicholas Holomuzki, Deborah Crist, Erich Grotewold, and Jelena Brkljacic</p><p> </p><p>2. Using Arabidopsis Related Model Species (ARMS): Growth, Genetic Transformation and Comparative Genomics</p><p>Giorgia Batelli, Dong-Ha Oh, Matilde Paino D’Urzo, Francesco Orsini, Maheshi Dassanayake, Jian-Kang Zhu,  Hans J. Bohnert, Ray A. Bressan and Albino Maggio</p><p> </p><p>3. Growing Arabidopsis in vitro: Cell Suspensions, in vitro Culture, and Regeneration</p><p>Bronwyn J. Barkla, Rosario Vera-Estrella, and Omar Pantoja</p><p> </p><p> </p><p>Part II. Arabidopsis resources</p><p> </p><p>4. Arabidopsis Database and Stock Resources</p><p>Donghui Li, Kate Dreher, Emma Knee, Jelena Brkljacic, Erich Grotewold, Tanya Z. Berardini, Philippe Lamesch, Margarita Garcia-Hernandez, Leonore Reiser and Eva Huala</p><p> </p><p>5. Bioinformatic Tools in Arabidopsis Research</p><p>Miguel de Lucas, Nicholas J. Provart, and Siobhan Brady</p><p> </p><p>Part III. Genetic techniques</p><p> </p><p>6. Exploiting Natural Variation in Arabidopsis</p><p>Johanna A. Molenaar and Joost J. B. Keurentjes</p><p> </p><p>7. Grafting in Arabidopsis</p><p>Katherine Bainbridge, Tom Bennett, Peter Crisp, Ottoline Leyser, and Colin Turnbull</p><p> </p><p>8. Agrobacterium tumefaciens Mediated Transient Transformation of Arabidopsis thaliana Leaves</p><p>Silvina Mangano, Cintia Daniela González, and Silvana Petruccelli</p><p> </p><p>9. iTilling: Personalized Mutation Screen</p><p>Susan M. Bush and Patrick J. Krysan</p><p> </p><p>10. Tailor Made Mutations in Arabidopsis Using Zinc-Finger Nucleases</p><p>Yiping Qi, Colby G. Starker, Feng Zhang, Nicholas J. Baltes, and Daniel F. Voytas</p><p> </p><p>11. The Use of Artificial Micro RNA Technology to Control Gene Expression in Arabidopsis thaliana</p><p>Andrew L. Eamens, Marcus McHale, and Peter M. Waterhouse</p><p> </p><p>12. Generation and Identification of Arabidopsis EMS Mutants</p><p>Li-Jia Qu and Gengi Qin</p><p> </p><p>13. Generation and Identification of Arabidopsis T-DNA Insertion Mutants</p><p>Li-Jia Qu and Gengi Qin</p><p> </p><p>14. Identification of EMS-induced Causal Mutations in Arabidopsis thaliana by Next-Generation Sequencing</p><p>Naoyuki Uchida, Tomoaki Sakamoto, Masao Tasaka, and Tetsuya Kurata</p><p> </p><p>15. Arabidopsis Transformation with Large Bacterial Artificial Chromosomes </p><p>Jose M. Alonso and Anna N. Stepanova</p><p> </p><p>16. Global DNA Methylation Analysis Using Methyl-Sensitive Amplification Polymorphism (MSAP)</p><p>Mahmoud W. Yaish, Mingsheng Peng, and Steven J. Rothstein</p><p> </p><p>Part IV. Molecular biological techniques</p><p> </p><p>17. Next Generation Mapping of Genetic Mutations Using Bulk Population Sequencing</p><p>Ryan S. Austin, Steven P. Chatfield, Darrell Desveaux, and David S. Guttman</p><p> </p><p>18. Chemical Fingerprinting of Arabidopsis Using Fourier-transform Infrared (FT-IR) Spectroscopic Approaches </p><p>András Gorzsás and Björn Sundberg</p><p> </p><p>19. A Pipeline for 15N Metabolic Labeling and Phosphoproteome Analysis in Arabidopsis thaliana</p><p>Benjamin B. Minkoff, Heather L. Burch, and Michael R. Sussman</p><p> </p><p>20. Gene Expression Profiling Using DNA Microarrays</p><p>Kionoshin Maruyama, Kazuko Yamaguchi-Shinozaki, and Kazuo Shinozaki</p><p> </p><p>21. Forward Chemical Genetic Screening </p><p>Hyunmo Choi, Jun-Young Kim, Young Tae Chang, and Hong Gil Nam</p><p> </p><p>22. Highly-Reproducible ChIP-On-Chip Analysis to Identify Genome-Wide Protein Binding and Chromatin Status in Arabidopsis thaliana</p><p>Jong-Myong Kim, Taiko Kim To, Maho Tanaka, Takaho A. Endo, Akihiro Matsui, Junko Ishida, Fiona C. Robertson, Tetsuro Toyoda, and Motoaki Seki</p><p> </p><p> </p><p>Part V. Cell biological techniques</p><p> </p><p>23. Fluorescence Microscopy</p><p>Sebastien Peter, Klaus Harter, and Frank Schleifenbaum</p><p> </p><p>24. Immunocytochemical Fluorescent In Situ Visualization of Proteins in Arabidopsis </p><p>Yohann Boutté and Markus Grebe</p><p> </p><p>25. High Pressure Freezing and Freeze Substitution of Arabidopsis For Electron Microscopy</p><p>Jotham R. Austin, II.</p><p> </p><p>26. Applications of Fluorescent Marker Proteins in Plant Cell Biology</p><p>Michael R. Blatt and Christopher Grefen</p><p> </p><p>27. Flow Cytometry and Sorting in Arabidopsis</p><p>David W. Galbraith</p><p> </p><p>28. Live Imaging of Arabidopsis Development </p><p>Daniel von Wangenheim, Gabor Daum, Jan U. Lohmann , Ernst K. Stelzer, and Alexis Maizel</p><p> </p><p>29. Arabidopsis Organelle Isolation and Characterisation</p><p>Nicolas L. Taylor, Elke Ströher, and A. Harvey Millar</p><p> </p><p>Part VI. Biochemical and physiological techniques</p><p> </p><p>30. Analysis of Subcellular Metabolite Distributions within Arabidopsis thaliana Leaf Tissue: A Primer for Subcellular Metabolomics</p><p>Stephan Krueger, Dirk Steinhauser, Jan Lisec, and Patrick Giavalisco</p><p> </p><p>31. Hormone Profiling</p><p>Gaetan Glauser, Armelle Vallat, and Dirk Balmer</p><p> </p><p>32. Purification of Protein Complexes and Characterization of Protein-Protein Interactions</p><p>Kirby N. Swatek, Chris B. Lee, and Jay J. Thelen</p><p> </p><p>33. Protein Fragment Bimolecular Fluorescence Complementation Analysis for the In vivo Study of Protein-Protein Interactions and Cellular Protein Complex Localizations</p><p>Rainer Waadt, Kathrin Schlükling, Julian I. Schroeder, and Jörg Kudla</p><p> </p><p>34. The Split Ubiquitin System for the Analysis of Three-Component Interactions</p><p>Christopher Grefen</p><p> </p><p>35. RNA-Binding Protein Immunoprecipitation from Whole Cell Extracts</p><p>Tino Köster and Dorothee Staiger</p><p> </p><p>36. High Throughput Analysis of Protein-DNA Binding Affinity</p><p>José M. Franco-Zorrilla and Roberto Solano</p>