Description
Arabidopsis Protocols, Third Edition compiles some of the most recent methodologies developed to exploit the Arabidopsis genome. These methodologies cover from the guided access to public resources, to genetic, cell biology, biochemical and physiological techniques, including both those that are widely used as well as those novel techniques likely to open up new avenues of knowledge in the future. In addition, considering the recent unparalleled progress of the “omics” tools in Arabidopsis, leading experts have contributed sections on genome, transcriptome, proteome, metabolome and other whole-system approaches. Arabidopsis thaliana is acknowledged as the most important plant model system by the scientific community and Arabidopsis research has fundamentally influenced our understanding of the basic biology and ecology of plants. Written in the successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Arabidopsis Protocols, Third Edition seeks to serve both experienced researchers and beginners with its detailed methodologies on this burgeoning scientific field. Part I. Growing Arabidopsis 1. Handling Arabidopsis Plants: Growth, Preservation of Seeds, Transformation and Genetic Crosses Luz Rivero, Randy Scholl, Nicholas Holomuzki, Deborah Crist, Erich Grotewold, and Jelena Brkljacic 2. Using Arabidopsis Related Model Species (ARMS): Growth, Genetic Transformation and Comparative Genomics 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 3. Growing Arabidopsis in vitro: Cell Suspensions, in vitro Culture, and Regeneration Bronwyn J. Barkla, Rosario Vera-Estrella, and Omar Pantoja Part II. Arabidopsis resources 4. Arabidopsis Database and Stock Resources Donghui Li, Kate Dreher, Emma Knee, Jelena Brkljacic, Erich Grotewold, Tanya Z. Berardini, Philippe Lamesch, Margarita Garcia-Hernandez, Leonore Reiser and Eva Huala 5. Bioinformatic Tools in Arabidopsis Research Miguel de Lucas, Nicholas J. Provart, and Siobhan Brady Part III. Genetic techniques 6. Exploiting Natural Variation in Arabidopsis Johanna A. Molenaar and Joost J. B. Keurentjes 7. Grafting in Arabidopsis Katherine Bainbridge, Tom Bennett, Peter Crisp, Ottoline Leyser, and Colin Turnbull 8. Agrobacterium tumefaciens Mediated Transient Transformation of Arabidopsis thaliana Leaves Silvina Mangano, Cintia Daniela Gonzlez, and Silvana Petruccelli 9. iTilling: Personalized Mutation Screen Susan M. Bush and Patrick J. Krysan 10. Tailor Made Mutations in Arabidopsis Using Zinc-Finger Nucleases Yiping Qi, Colby G. Starker, Feng Zhang, Nicholas J. Baltes, and Daniel F. Voytas 11. The Use of Artificial Micro RNA Technology to Control Gene Expression in Arabidopsis thaliana Andrew L. Eamens, Marcus McHale, and Peter M. Waterhouse 12. Generation and Identification of Arabidopsis EMS Mutants Li-Jia Qu and Gengi Qin 13. Generation and Identification of Arabidopsis T-DNA Insertion Mutants Li-Jia Qu and Gengi Qin 14. Identification of EMS-induced Causal Mutations in Arabidopsis thaliana by Next-Generation Sequencing Naoyuki Uchida, Tomoaki Sakamoto, Masao Tasaka, and Tetsuya Kurata 15. Arabidopsis Transformation with Large Bacterial Artificial Chromosomes Jose M. Alonso and Anna N. Stepanova 16. Global DNA Methylation Analysis Using Methyl-Sensitive Amplification Polymorphism (MSAP) Mahmoud W. Yaish, Mingsheng Peng, and Steven J. Rothstein Part IV. Molecular biological techniques 17. Next Generation Mapping of Genetic Mutations Using Bulk Population Sequencing Ryan S. Austin, Steven P. Chatfield, Darrell Desveaux, and David S. Guttman 18. Chemical Fingerprinting of Arabidopsis Using Fourier-transform Infrared (FT-IR) Spectroscopic Approaches Andrs Gorzss and Bjrn Sundberg 19. A Pipeline for 15N Metabolic Labeling and Phosphoproteome Analysis in Arabidopsis thaliana Benjamin B. Minkoff, Heather L. Burch, and Michael R. Sussman 20. Gene Expression Profiling Using DNA Microarrays Kionoshin Maruyama, Kazuko Yamaguchi-Shinozaki, and Kazuo Shinozaki 21. Forward Chemical Genetic Screening Hyunmo Choi, Jun-Young Kim, Young Tae Chang, and Hong Gil Nam 22. Highly-Reproducible ChIP-On-Chip Analysis to Identify Genome-Wide Protein Binding and Chromatin Status in Arabidopsis thaliana Jong-Myong Kim, Taiko Kim To, Maho Tanaka, Takaho A. Endo, Akihiro Matsui, Junko Ishida, Fiona C. Robertson, Tetsuro Toyoda, and Motoaki Seki Part V. Cell biological techniques 23. Fluorescence Microscopy Sebastien Peter, Klaus Harter, and Frank Schleifenbaum 24. Immunocytochemical Fluorescent In Situ Visualization of Proteins in Arabidopsis Yohann Boutt and Markus Grebe 25. High Pressure Freezing and Freeze Substitution of Arabidopsis For Electron Microscopy Jotham R. Austin, II. 26. Applications of Fluorescent Marker Proteins in Plant Cell Biology Michael R. Blatt and Christopher Grefen 27. Flow Cytometry and Sorting in Arabidopsis David W. Galbraith 28. Live Imaging of Arabidopsis Development Daniel von Wangenheim, Gabor Daum, Jan U. Lohmann , Ernst K. Stelzer, and Alexis Maizel 29. Arabidopsis Organelle Isolation and Characterisation Nicolas L. Taylor, Elke Strher, and A. Harvey Millar Part VI. Biochemical and physiological techniques 30. Analysis of Subcellular Metabolite Distributions within Arabidopsis thaliana Leaf Tissue: A Primer for Subcellular Metabolomics Stephan Krueger, Dirk Steinhauser, Jan Lisec, and Patrick Giavalisco 31. Hormone Profiling Gaetan Glauser, Armelle Vallat, and Dirk Balmer 32. Purification of Protein Complexes and Characterization of Protein-Protein Interactions Kirby N. Swatek, Chris B. Lee, and Jay J. Thelen 33. Protein Fragment Bimolecular Fluorescence Complementation Analysis for the In vivo Study of Protein-Protein Interactions and Cellular Protein Complex Localizations Rainer Waadt, Kathrin Schlkling, Julian I. Schroeder, and Jrg Kudla 34. The Split Ubiquitin System for the Analysis of Three-Component Interactions Christopher Grefen 35. RNA-Binding Protein Immunoprecipitation from Whole Cell Extracts Tino Kster and Dorothee Staiger 36. High Throughput Analysis of Protein-DNA Binding Affinity Jos M. Franco-Zorrilla and Roberto Solano
