Part I: Genetics, Cytology, and In Vivo Analysis

1. Screening or Selection for Chloroplast Biogenesis Mutants of Arabidopsis, Following Chemical or Insertional Mutagenesis

Enrique López-Juez and Alison Hills

2. Analysis of Plastid Number, Size, and Distribution in Arabidopsis Plants by Light and Fluorescence Microscopy

Kevin Pyke

3. Immunofluorescence Microscopy for Localization of Arabidopsis Chloroplast Proteins

Stanislav Vitha and Katherine W. Osteryoung

4. Transient Expression and Analysis of Chloroplast Proteins in Arabidopsis Protoplasts

Dong Wook Lee and Inhwan Hwang

5. Visualisation of Stromules on Arabidopsis Plastids

John C. Gray, James A. Sullivan, and Christine A. Newell

6. Analysis of Chloroplast Movement and Relocation in Arabidopsis

Masamitsu Wada and Sam-Geun Kong

7. Studying Starch Content and Sedimentation of Amyloplast Statoliths In Arabidopsis Roots

John Stanga, Allison Strohm, and Patrick H. Masson

8. Studying Arabidopsis Chloroplast Structural Organization Using Transmission Electron Microscopy

Stefan Hyman and R. Paul Jarvis

9. Transplastomics in Arabidopsis: Progress Towards Developing an Efficient Method

Kerry Ann Lutz, Arun Azhagiri, and Pal Maliga

Part II: Gene Expression and Protein Accumulation

10. Isolation, Quantification, and Analysis of Chloroplast DNA

Beth A. Rowan and Arnold J. Bendich

11. Measurement of Transcription Rates in Arabidopsis Chloroplasts

Yan O. Zubo, Thomas Börner, and Karsten Liere

12. Studying the Structure and Processing of Chloroplast Transcripts

Alice Barkan

13. In Vitro RNA Binding Assay for Studying Trans-Factors for RNA Editing in Chloroplasts

Toshiharu Shikanai and Kenji Okuda

14. Studying Translation in Arabidopsis Chloroplasts

Paolo Pesaresi

15. Studying Proteases and Protein Turnover in Arabidopsis Chloroplasts

Lars L.E. Sjögren and Adrian K. Clarke

Part III: Protein Transport, Localization, and Topology

16. In Silico Methods for the Identification of Organellar and Suborganellar Targeting Peptides in Arabidopsis Chloroplast Proteins and for Predicting the Topology of Membrane Proteins

Sandra Tanz and Ian Small

17. Rapid Isolation of Arabidopsis Chloroplasts and Their Use for In Vitro Protein Import Assays

Henrik Aronsson and R. Paul Jarvis

18. Energetic Manipulation of Chloroplast Protein Import and the Use of Chemical Cross-Linkers to Map Protein-Protein Interactions

Hitoshi Inoue, Fei Wang, Takehito Inaba, and Danny J. Schnell

19. Isolation of Arabidopsis Thylakoid Membranes and Their Use for In Vitro Protein Insertion or Transport Assays

Thomas Bals and Danja Schünemann

20. Determining the Location of an Arabidopsis Chloroplast Protein Using In Vitro Import Followed by Fractionation and Alkaline Extraction

Chiung-Chih Chu and Hsou-min Li

21. Studying Arabidopsis Envelope Protein Localization and Topology Using Thermolysin and Trypsin Proteases

John Froehlich