Molecular characterization of autophagic responses
Author(s)
Bibliographic Information
Molecular characterization of autophagic responses
（Methods in enzymology / editors in chief, Sidney P. Colowick, Nathan O. Kaplan, v. 587-588）
Academic Press, 2017
1st ed
- pt. A
- pt. B
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Note
Includes bibliographical references and indexes
Description and Table of Contents
- Volume
-
pt. B ISBN 9780128096741
Description
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.
Table of Contents
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
- Volume
-
pt. A ISBN 9780128096758
Description
Molecular Characterization of Autophagic Responses, Part A, 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.
Table of Contents
1. Correlative Live Cell and Super Resolution Imaging of Autophagosome Formation 2. Quantifying Autophagic Structures in Mammalian Cells Using Confocal Microscopy 3. The Use of DQ-BSA to Monitor the Turnover of Autophagy-Associated Cargo 4. Turnover of Lipidated LC3 and Autophagic Cargoes in Mammalian Cells 5. High-Throughput Quantification of GFP-LC3+ Dots by Automated Fluorescence Microscopy 6. Use of pHlurorin-mKate2-human LC3 to Monitor Autophagic Responses 7. Production of Human ATG Proteins for Lipidation Assays 8. Investigating Structure and Dynamics of Atg8 Family Proteins 9. Methods for Studying Interactions Between Atg8/LC3/GABARAP and LIR-Containing Proteins 10. Assessment of Posttranslational Modifications of ATG proteins 11. Tagged ATG8-Coding Constructs for the In Vitro and In Vivo Assessment of ATG4 Activity 12. Measurement of the Activity of the Atg4 Cysteine Proteases 13. Crystallographic Characterization of ATG Proteins and Their Interacting Partners 14. Dynamics of Atg5-Atg12-Atg16L1 Aggregation and Deaggregation 15. Fluorescent FYVE Chimeras to Quantify PtdIns3P Synthesis During Autophagy 16. Quantification of Phosphatidylinositol Phosphate Species in Purified Membranes 17. Mass Assays to Quantify Bioactive PtdIns3P and PtdIns5P During Autophagic Responses 18. Fluorescence-Based Assays to Analyse Phosphatidylinositol 5-Phosphate in Autophagy 19. Ultrastructural Characterization of Phagophores Using Electron Tomography on Cryoimmobilized and Freeze Substituted Samples 20. A Simple Cargo Sequestration Assay for Quantitative Measurement of Nonselective Autophagy in Cultured Cells 21. In Vitro Reconstitution of Autophagosome-Lysosome Fusion 22. In Vitro Reconstitution of Atg8 Conjugation and Deconjugation 23. Study of ULK1 Catalytic Activity and Its Regulation 24. Evaluating the mTOR Pathway in Physiological and Pharmacological Settings 25. Methods to Study the BECN1 Interactome in the Course of Autophagic Responses 26. In Vitro Characterization of VPS34 Lipid Kinase Inhibition by Small Molecules 27. Methods to Study Lysosomal AMPK Activation 28. Allosteric Modulation of AMPK Enzymatic Activity: In Vitro Characterization 29. Assessing the Catalytic Activity of Transglutaminases in the Context of Autophagic Responses
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