Autophagy: Methods and Protocols

Description

This volume details a comprehensive and extensive set of protocols for the study of autophagy in vitro and in vivo. Chapters focus on mammals, various model organisms, and provide protocols for the study of autophagy-related processes outside of the canonical autophagy pathways. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Autophagy: Methods and Protocols aims to ensure successful results in the further study of this vital field. Front Matter ....Pages i-xvii Front Matter ....Pages 1-1 Recombinant Expression, Purification, and Assembly of p62 Filaments (Abul K. Tarafder, Audrey Guesdon, Tanja Kuhm, Carsten Sachse)....Pages 3-15 Structural Studies of Autophagy-Related Proteins (Melanie Schwarten, Oliver H. Weiergräber, Dušan Petrović, Birgit Strodel, Dieter Willbold)....Pages 17-56 Structural Studies of Mammalian Autophagy Lipidation Complex (Kazuto Ohashi, Chinatsu Otomo, Zoltan Metlagel, Takanori Otomo)....Pages 57-75 Structural Studies of Selective Autophagy in Yeast (Akinori Yamasaki, Yasunori Watanabe, Nobuo N. Noda)....Pages 77-90 Biophysical Studies of LC3 Family Proteins (Javier H. Hervás, Zuriñe Antón, Alicia Alonso)....Pages 91-117 Reconstituting Autophagy Initiation from Purified Components (Peter Mayrhofer, Thomas Wollert)....Pages 119-133 Cell-Free Reconstitution of Autophagic Membrane Formation (Min Zhang, Liang Ge)....Pages 135-148 Use of Peptide Arrays for Identification and Characterization of LIR Motifs (Mads Skytte Rasmussen, Åsa Birna Birgisdottir, Terje Johansen)....Pages 149-161 Studying Autophagic Lysosome Reformation in Cells and by an In Vitro Reconstitution System (Yang Chen, Qian Peter Su, Li Yu)....Pages 163-172 Formation of Autophagosomes Coincides with Relaxation of Membrane Curvature (Jaime Agudo-Canalejo, Roland L. Knorr)....Pages 173-188 Studies of Receptor-Atg8 Interactions During Selective Autophagy (Christine Abert, Sascha Martens)....Pages 189-196 Front Matter ....Pages 197-197 Correlative Light and Electron Microscopy of Autophagosomes (Sigurdur Gudmundsson, Jenny Kahlhofer, Nastassia Baylac, Katri Kallio, Eeva-Liisa Eskelinen)....Pages 199-209 Improved Electron Microscopy Fixation Methods for Tracking Autophagy-Associated Membranes in Cultured Mammalian Cells (Ritsuko Arai, Satoshi Waguri)....Pages 211-221 Three-Color Simultaneous Live Imaging of Autophagy-Related Structures (Hiroyuki Ueda, Ouin Kunitaki, Maho Hamasaki)....Pages 223-230 Correlative Live-Cell Imaging and Super-Resolution Microscopy of Autophagy (Eleftherios Karanasios)....Pages 231-242 Methods for Imaging Autophagosome Dynamics in Primary Neurons (Audrey Dong, Vineet Vinay Kulkarni, Sandra Maday)....Pages 243-256 Imaging Autophagy in hiPSC-Derived Midbrain Dopaminergic Neuronal Cultures for Parkinson’s Disease Research (Petros Stathakos, Natalia Jimenez-Moreno, Lucy Crompton, Paul Nistor, Maeve A. Caldwell, Jon D. Lane)....Pages 257-280 Correlative Light and Electron Microscopy to Analyze LC3 Proteins in Caenorhabditis elegans Embryo (Céline Largeau, Renaud Legouis)....Pages 281-293 Imaging Noncanonical Autophagy and LC3-Associated Phagocytosis in Cultured Cells (Elise Jacquin, Katherine Fletcher, Oliver Florey)....Pages 295-303 Front Matter ....Pages 305-305 Measurement of Bulk Autophagy by a Cargo Sequestration Assay (Nikolai Engedal, Morten Luhr, Paula Szalai, Per O. Seglen)....Pages 307-313 Methods to Detect Loss of Lysosomal Membrane Integrity (Sonja Aits)....Pages 315-329 Monitoring of Autophagy and Cell Volume Regulation in Kidney Epithelial Cells in Response to Fluid Shear Stress (Maria M. Lazari, Idil Orhon, Patrice Codogno, Nicolas Dupont)....Pages 331-340 Identification and Regulation of Multimeric Protein Complexes in Autophagy via SILAC-Based Mass Spectrometry Approaches (Stéphanie Kaeser-Pebernard, Britta Diedrich, Jörn Dengjel)....Pages 341-357 Identification and Validation of Novel Autophagy Regulators Using an Endogenous Readout siGENOME Screen (Maria New, Tim Van Acker, Ming Jiang, Rebecca Saunders, Jaclyn S. Long, Jun-Ichi Sakamaki et al.)....Pages 359-374 Autophagy Pathway Mapping to Elucidate the Function of Novel Autophagy Regulators Identified by High-Throughput Screening (Martina Wirth, Sharon A. Tooze)....Pages 375-387 In Vitro Screening Platforms for Identifying Autophagy Modulators in Mammalian Cells (Elena Seranova, Carl Ward, Miruna Chipara, Tatiana R. Rosenstock, Sovan Sarkar)....Pages 389-428 Automated Detection of Autophagy Response Using Single Cell-Based Microscopy Assays (Amelie J. Mueller, Tassula Proikas-Cezanne)....Pages 429-445 Methods for the Study of Entotic Cell Death (Jens C. Hamann, Sung Eun Kim, Michael Overholtzer)....Pages 447-454 MHC Class I Internalization via Autophagy Proteins (Monica Loi, Laure-Anne Ligeon, Christian Münz)....Pages 455-477 Front Matter ....Pages 479-479 Analysis of Autophagy for Liver Pathogenesis (Nazmul Huda, Hui Zou, Shengmin Yan, Bilon Khambu, Xiao-Ming Yin)....Pages 481-489 Autophagy in 3D In Vitro and Ex Vivo Cancer Models (Carlo Follo, Dario Barbone, William G. Richards, Raphael Bueno, V. Courtney Broaddus)....Pages 491-510 Autophagy in Platelets (Meenakshi Banerjee, Yunjie Huang, Madhu M. Ouseph, Smita Joshi, Irina Pokrovskaya, Brian Storrie et al.)....Pages 511-528 Methods to Image Macroautophagy in the Brain In Vivo (Xigui Chen, Kanoh Kondo, Hitoshi Okazawa)....Pages 529-534 Measuring Nonselective and Selective Autophagy in the Liver (Takashi Ueno, Masaaki Komatsu)....Pages 535-540 Measuring Autophagy in Pancreatitis (Alejandro Ropolo, Daniel Grasso, Maria I. Vaccaro)....Pages 541-554 Characterization of the “Autophagic Flux” in Prostate Cancer Tissue Biopsies by LC3A/LAMP2a Immunofluorescence and Confocal Microscopy (D. Kalamida, A. Giatromanolaki, M. I. Koukourakis)....Pages 555-560 Methods to Determine the Role of Autophagy Proteins in C. elegans Aging (Sivan Henis-Korenblit, Alicia Meléndez)....Pages 561-586 Front Matter ....Pages 587-587 Investigating Non-selective Autophagy in Drosophila (Szabolcs Takáts, Sarolta Tóth, Győző Szenci, Gábor Juhász)....Pages 589-600 Imaging the Dynamics of Mitophagy in Live Cells (Andrew S. Moore, Erika L. F. Holzbaur)....Pages 601-610 Triggering Mitophagy with Photosensitizers (Cheng-Wei Hsieh, Wei Yuan Yang)....Pages 611-619 Investigating Mitophagy and Mitochondrial Morphology In Vivo Using mito-QC: A Comprehensive Guide (Thomas G. McWilliams, Ian G. Ganley)....Pages 621-642 Assays to Monitor Mitophagy in Drosophila (Panagiotis Tsapras, Anne-Claire Jacomin, Ioannis P. Nezis)....Pages 643-653 Mitophagy Dynamics in Caenorhabditis elegans (Konstantinos Palikaras, Eirini Lionaki, Nektarios Tavernarakis)....Pages 655-668 Methods for Studying Mitophagy in Yeast (Panagiota Kolitsida, Hagai Abeliovich)....Pages 669-678 Measuring Antibacterial Autophagy (Keith B. Boyle, Felix Randow)....Pages 679-690 Quantitative Phosphoproteomics of Selective Autophagy Receptors (Thomas Juretschke, Petra Beli, Ivan Dikic)....Pages 691-701 Analysis of Chaperone-Mediated Autophagy (Y. R. Juste, A. M. Cuervo)....Pages 703-727 Interactive Autophagy: Monitoring a Novel Form of Selective Autophagy by Macroscopic Observations (Jana Petri, Roland L. Knorr)....Pages 729-738 Back Matter ....Pages 739-741