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Life Sciences - Plant Sciences | Chloroplast Research in Arabidopsis - Methods and Protocols, Volume II

Chloroplast Research in Arabidopsis

Methods and Protocols, Volume II

Series: Methods in Molecular Biology, Vol. 775

Jarvis, R Paul (Ed.)

2011, XI, 432p. 61 illus., 5 illus. in color.

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  • Brings together the most important and current techniques in chloroplast research through the unifying lens of the Arabidopsis model system
  • Features subjects like protein aspects, omics studies, and photosynthesis and biochemical analysis
  • Includes expert tips and implementation advice to guarantee ideal experimental results

Chloroplasts are essential for the survival and flourishing of life on Earth. Over the years, chloroplast biology has been studied in a variety of different organisms, leading to the significant disadvantage that findings which were made by using different experimental systems or species were not always directly cross-comparable.  The relatively recent adoption of Arabidopsis thaliana as the model organism of choice for plant science research, across the globe, has led to its emergence as a pre-eminent system for research on chloroplasts and other types of plastid.  In Chloroplast Research in Arabidopsis: Methods and Protocols, expert researchers bring together some of the most important, modern techniques and approaches for chloroplast research, with the unifying theme of Arabidopsis as the model system. Volume II explores topics such as multiprotein complexes, protein-protein interactions, omics and large-scale analyses, proteomics and suborganellar fractionation, as well as photosynthesis and biochemical analysis.  Written in the highly 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 laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.


Authoritative and convenient, Chloroplast Research in Arabidopsis: Methods and Protocols serves as an ideal reference for all researchers with a general interest in chloroplasts, plastids, or related processes.

Content Level » Professional/practitioner

Keywords » Arabidopsis thaliana - Biochemical analysis - Large-scale analyses - Model organism - Multiprotein complexes - Omics - Photosynthesis - Plastids - Protein-protein interactions - Proteomics - Suborganellar fractionation

Related subjects » Biochemistry & Biophysics - Plant Sciences

Table of contents 

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 Bédard, and Masato Nakai


2. Analysis of Thylakoid Protein Complexes by Two Dimensional Electrophoretic Systems

            Sari Sirpiö, Marjaana Suorsa, and Eva-Mari Aro


3. Preparation of Multiprotein Complexes from Arabidopsis Chloroplasts Using Tandem Affinity Purification

            Charles Andrès, Birgit Agne, and Felix Kessler


4. Studying Interactions between Chloroplast Proteins in Intact Plant Cells Using Bimolecular Fluorescence Complementation (BiFC) and Förster Resonance Energy Transfer (FRET)

            Jodi Maple and Simon G. Møller


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, Célia 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 Jörg 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, Daphné 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. Schröder


12. Preparation of Plastoglobules from Arabidopsis Plastids for Proteomic Analysis and Other Studies

            Celine Besagni, Lucia Eugeni Piller, and Claire Bréhélin


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 ΔpH 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 Kölling, Diana Santelia, Sebastian Streb, Oliver Kötting, and Samuel C. Zeeman


22. The Analysis of Lipid Content and Quality in Arabidopsis Plastids

            Anna Maria Zbierzak, Peter Dörmann, and Georg Hölzl

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