Table of Contents Introduction- Autophagosome and Phagosome Vojo Deretic, Ph.D. 1. Fine Structure of the Autophagosome Eeva-Liisa Eskelinen, Ph.D. 2. Methods for Assessing Autophagy and Autophagic Cell Death Ezgi Tasdemir, Lorenzo Galluzzi, M. Chiara Maiuri, Alfredo Criollo, Ilio Vitale, Emilie Hangen, Nazanine Modjtahedi and Guido Kroemer, Ph.D. 3. LC3 and Autophagy Isei Tanida, Ph.D., Takashi Ueno, Ph.D., and Eiki Kominami, Ph.D. 4. Amino Acid Regulation of Autophagosome Formation Alfred J. Meijer, Ph.D. 5. Autophagic Proteolysis of Long-lived Proteins in Non-liver Cells Esteban A. Roberts, Ph.D. and Vojo Deretic, Ph.D. 6. Autophagosomes in Transgenic Mice Noboru Mizushima, M.D., Ph.D. and Akiko Kuma, Ph.D. 7. Experimental Control and Characterization of Autophagy in Drosophila Gabor Juhasz, Ph.D. and Thomas P. Neufeld, Ph.D. 8. Analysis of Autophagosome Membrane Cycling by Fluorescence Microscopy Julie E. Legakis, Ph.D. and Daniel J. Klionsky, Ph.D. 9. Protein Trafficking into Autophagosomes Andrew Young, Ph.D. and Sharon Tooze, Ph.D. 10. Sphingolipids in Macroautophagy Gregory Lavieu, Francesca Scarlatti, Giusy Sala, Stephane Carpentier, Thierry Levade, Riccardo Ghidoni, Joelle Botti and Patrice Codogno, Ph.D. 11. Clearance of Mutant Aggregate-prone Proteins by Autophagy Brinda Ravikumar, Ph.D., Sovan Sarkar, Ph.D. and David C. Rubinsztein, Ph.D. 12. Localization and MHC Class II Presentation of Antigens Targeted for Macroautophagy Dorothee Schmid, Ph.D. and Christian Munz, Ph.D. 13. Chaperone-mediated Autophagy S. Kaushik, Ph.D. and Anna Maria Cuervo, M.D., Ph.D. 14. Microautophagy in the Yeast Saccharomyces cerevisiae Andreas Uttenweiler, Ph.D. and Andreas Mayer, Ph.D. 15. EM Analysis of Phagosomes Chantal de Chastellier, PhD. 16. Analysis of Phosphoinositide Dynamics During Phagocytosis Using Genetically Encoded Fluorescent Biosensors Gabriela Cosio, Ph.D. and Sergio Grinstein, Ph.D. 17. In vitro Phagosome-Endosome Fusion Isabelle Vergne, Ph.D. 18. Real-time Spectrofluorometric Assays for the Lumenal Environment of the Maturing Phagosome. Robin M. Yates, Ph.D. and David G. Russell, Ph.D. 19. Monitoring Time Dependent Maturation Changes in Purified Phagosomes from Dictyostelium discoideum Regis Dieckmann, Ph.D., Navin Gopaldass, Ph.D., Caroline Escalera, Ph.D. and Thierry Soldati, Ph.D. 20. Large Scale Purification of Latex Bead Phagosomes from Mouse Macrophage Cell Lines and Subsequent Preparation For High Throughput Quantitative Proteomics Adam Rupper, Ph.D. and James Cardelli, Ph.D. 21. Class II MHC Antigen Processing in Phagosomes Running title: Phagosome antigen processing Lakshmi Ramachandra, M.S., Ph.D., W. Henry Boom, M.D. and Clifford V. Harding, M.D., Ph.D. 22. Analyzing Association of the Endoplasmic Reticulum with the Legionella pneumophila -- containing Vacuole By Fluorescence Microscopy Running head: Recruitment of ER markers to the L. pneumophila -- containing vacuole Alyssa Ingmundson, Ph.D. and Craig R. Roy, Ph.D. 23. Fractionation of the Coxiella burnetii Parasitophorous Vacuole Dale Howe, Ph.D. and Robert A. Heinzen, Ph.D. 24. Bacterial Phagosome Acidification Within IFN-y-activated Macrophages: Role of Host p47 Immunity-related GTPases (IRGs) Sangeeta Tiwari, Ph.D. and John D. MacMicking, Ph.D. 25. SopE-mediated Recruitment of Host Rab5 on Phagosomes inhibits Salmonella transport to lysosomes Richa Madan, Ph.D., Ganga Krishnamurthy, Ph.D. and Amitabha Mukhopadhyay, Ph.D. 26. The Mycobacterium tuberculosis Phagosome Esteban A. Roberts, Ph.D.