Molecular Characterization of Autophagic Responses Part A

<p>1. Correlative Live Cell and Super Resolution Imaging of Autophagosome Formation<br>2. Quantifying Autophagic Structures in Mammalian Cells Using Confocal Microscopy<br>3. The Use of DQ-BSA to Monitor the Turnover of Autophagy-Associated Cargo<br>4. Turnover of Lipidated LC3 and Autophagic Cargoes in Mammalian Cells<br>5. High-Throughput Quantification of GFP-LC3<SUP>+</SUP> Dots by Automated Fluorescence Microscopy<br>6. Use of pHlurorin-mKate2-human LC3 to Monitor Autophagic Responses<br>7. Production of Human ATG Proteins for Lipidation Assays<br>8. Investigating Structure and Dynamics of Atg8 Family Proteins<br>9. Methods for Studying Interactions Between Atg8/LC3/GABARAP and LIR-Containing Proteins<br>10. Assessment of Posttranslational Modifications of ATG proteins<br>11. Tagged ATG8-Coding Constructs for the In Vitro and In Vivo Assessment of ATG4 Activity<br>12. Measurement of the Activity of the Atg4 Cysteine Proteases<br>13. Crystallographic Characterization of ATG Proteins and Their Interacting Partners<br>14. Dynamics of Atg5–Atg12–Atg16L1 Aggregation and Deaggregation<br>15. Fluorescent FYVE Chimeras to Quantify PtdIns3P Synthesis During Autophagy<br>16. Quantification of Phosphatidylinositol Phosphate Species in Purified Membranes<br>17. Mass Assays to Quantify Bioactive PtdIns3P and PtdIns5P During Autophagic Responses<br>18. Fluorescence-Based Assays to Analyse Phosphatidylinositol 5-Phosphate in Autophagy<br>19. Ultrastructural Characterization of Phagophores Using Electron Tomography on Cryoimmobilized and Freeze Substituted Samples<br>20. A Simple Cargo Sequestration Assay for Quantitative Measurement of Nonselective Autophagy in Cultured Cells<br>21. In Vitro Reconstitution of Autophagosome–Lysosome Fusion<br>22. In Vitro Reconstitution of Atg8 Conjugation and Deconjugation<br>23. Study of ULK1 Catalytic Activity and Its Regulation<br>24. Evaluating the mTOR Pathway in Physiological and Pharmacological Settings<br>25. Methods to Study the BECN1 Interactome in the Course of Autophagic Responses<br>26. In Vitro Characterization of VPS34 Lipid Kinase Inhibition by Small Molecules<br>27. Methods to Study Lysosomal AMPK Activation<br>28. Allosteric Modulation of AMPK Enzymatic Activity: In Vitro Characterization<br>29. Assessing the Catalytic Activity of Transglutaminases in the Context of Autophagic Responses</p>