Molecular Characterization of Autophagic Responses Part B
Methods in Enzymology Series

Molecular Characterization of Autophagic Responses, Part B presents a collection of methods for the qualitative and quantitative evaluation of virtually all the morphological, biochemical, and functional manifestations of autophagy, in vitro, ex vivo and in vivo, in organisms as distant as yeast and man.

Autophagy is an evolutionarily conserved mechanism for the lysosomal degradation of superfluous or dangerous cytoplasmic entities, and plays a critical role in the preservation of cellular and organismal homeostasis. Monitoring the biochemical processes that accompany autophagy is fundamental for understanding whether autophagic responses are efficient or dysfunctional.

1. Renilla Luciferase-LC3 Based Reporter Assay for Measuring Autophagic Flux 2. Measurement of Autolysosomal pH by Dual-Wavelength Ratio Imaging 3. Long-Lived Protein Degradation During Autophagy 4. Proteomic Profiling of De Novo Protein Synthesis in Starvation-Induced Autophagy Using Bioorthogonal Noncanonical Amino Acid Tagging 5. Methods to Monitor and Manipulate TFEB Activity During Autophagy 6. Application of CRISPR/Cas9 to Autophagy Research 7. A Molecular Reporter for Monitoring Autophagic Flux in Nervous System In Vivo 8. Magnetic Resonance Spectroscopy to Study Glycolytic Metabolism During Autophagy 9. Assessment of Glycolytic Flux and Mitochondrial Respiration in the Course of Autophagic Responses 10. Methods to Assess Mitochondrial Morphology in Mammalian Cells Mounting Autophagic or Mitophagic Responses 11. Monitoring Mitophagy in Mammalian Cells 12. Cytofluorometric Assessment of Mitophagic Flux in Mammalian Cells and Tissues 13. Automated Analysis of Fluorescence Colocalization: Application to Mitophagy 14. Assays to Monitor Lysophagy 15. Kinetics of Protein Aggregates Disposal by Aggrephagy 16. Methods to Study Chaperone-Mediated Autophagy 17. Quantitative Assay of Macroautophagy Using Pho8?60 Assay and GFP-Cleavage Assay in Yeast 18. Monitoring the Formation of Autophagosomal Precursor Structures in Yeast Saccharomyces cerevisiae 19. Methods to Assess Autophagy and Chronological Aging in Yeast 20. Methods to Measure Lipophagy in Yeast 21. Assays to Monitor Pexophagy in Yeast 22. Monitoring Autophagic Responses in Caenorhabditis elegans 23. Characterization of Autophagic Responses in Drosophila melanogaster 24. Methods to Study Autophagy in Zebrafish 25. Biochemical Methods to Monitor Autophagic Responses in Plants 26. Using Photoconvertible and Extractable Fluorescent Proteins to Study Autophagy in Plants

• Offers a detailed overview of the protocols used to study autophagy and various aspects of autophagic responses
• Written in an accessible style by renowned experts in the field