Autophagy: Methods and Protocols

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