Chloroplast research in arabidopsis : methods and protocols

Part I: Multiprotein Complexes and Protein-Protein Interactions 1. One- and Two-Dimensional Blue Native (BN) PAGE and Immunodetection of Low-Abundance Chloroplast Membrane Protein Complexes Shingo Kikuchi, Jocelyn Bedard, and Masato Nakai 2. Analysis of Thylakoid Protein Complexes by Two Dimensional Electrophoretic Systems Sari Sirpio, Marjaana Suorsa, and Eva-Mari Aro 3. Preparation of Multiprotein Complexes from Arabidopsis Chloroplasts Using Tandem Affinity Purification Charles Andres, Birgit Agne, and Felix Kessler 4. Studying Interactions between Chloroplast Proteins in Intact Plant Cells Using Bimolecular Fluorescence Complementation (BiFC) and Forster Resonance Energy Transfer (FRET) Jodi Maple and Simon G. Moller 5. Studying Chloroplast Protein Interactions In Vitro: An Overview of the Available Methods Joanna Tripp and Enrico Schleiff Part II: Omics and Large-Scale Analyses 6. Proteome Databases and Other Online Resources for Chloroplast Research in Arabidopsis Diogo Ribeiro Demartini, Celia Regina Carlini, and Jay J. Thelen 7. Use of Transcriptomics to Analyse Chloroplast Processes in Arabidopsis Tatjana Kleine and Dario Leister 8. Use of Non-Aqueous Fractionation and Metabolomics to Study Chloroplast Function in Arabidopsis Peter Geigenberger, Axel Tiessen, and Jorg Meurer 9. Chloroplast Phenomics: Systematic Phenotypic Screening of Chloroplast Protein Mutants in Arabidopsis Yan Lu, Linda J. Savage, and Robert L. Last Part III: Proteomics and Suborganellar Fractionation 10. Preparation of Envelope Membrane Fractions from Arabidopsis Chloroplasts for Proteomic Analysis and Other Studies Daniel Salvi, Lucas Moyet, Daphne Seigneurin-Berny, Myriam Ferro, Jacques Joyard, and Norbert Rolland 11. Preparation of Stroma, Thylakoid Membrane, and Lumen Fractions from Arabidopsis thaliana Chloroplasts for Proteomic Analysis Michael Hall, Yogesh Mishra, and Wolfgang P. Schroder 12. Preparation of Plastoglobules from Arabidopsis Plastids for Proteomic Analysis and Other Studies Celine Besagni, Lucia Eugeni Piller, and Claire Brehelin 13. Preparation and Proteomic Analysis of Chloroplast Ribosomes Kenichi Yamaguchi 14. The Workflow for Quantitative Proteome Analysis of Chloroplast Development and Differentiation, Chloroplast Mutants, and Protein Interactions by Spectral Counting Giulia Friso, Paul Dominic B. Olinares, and Klaas J. van Wijk 15. Use of Phosphoproteomics to Study Post-Translational Protein Modifications in Arabidopsis Chloroplasts Anne Endler and Sacha Baginsky Part IV: Photosynthesis and Biochemical Analysis 16. Use of a Pulse-Amplitude Modulated (PAM) Chlorophyll Fluorometer to Study the Efficiency of Photosynthesis in Arabidopsis Plants Matthew D. Brooks and Krishna K. Niyogi 17. Gas Exchange Measurements for the Determination of Photosynthetic Efficiency in Arabidopsis Leaves Giles Johnson and Erik Murchie 18. Measurement of the DELTApH and Electric Field Developed Across Arabidopsis Thylakoids in the Light Steven M. Theg and Curtis Tom 19. Measurement of Chloroplast ATP Synthesis Activity in Arabidopsis Aleel K. Grennan and Donald R. Ort 20. Methods for Analysis of Photosynthetic Pigments and Steady-State Levels of Intermediates of Tetrapyrrole Biosynthesis Olaf Czarnecki, Enrico Peter, and Bernhard Grimm 21. Analysis of Starch Metabolism in Chloroplasts Carmen Hostettler, Katharina Kolling, Diana Santelia, Sebastian Streb, Oliver Kotting, and Samuel C. Zeeman 22. The Analysis of Lipid Content and Quality in Arabidopsis Plastids Anna Maria Zbierzak, Peter Dormann, and Georg Holzl