Main 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.

Contents:

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 Gonzalez, 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

Andras Gorzsas and Bjoern 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 Boutte 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 Stroeher, 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 Schlukling, Julian I. Schroeder, and Joerg 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 Koester and Dorothee Staiger

36. High Throughput Analysis of Protein-DNA Binding Affinity

Jose M. Franco-Zorrilla and Roberto Solano