Autophagy: Methods and Protocols

ISBN-13: 9781493988723 / Angielski / Twarda / 2019 / 741 str.

Nicholas Ktistakis; Oliver Florey

Spis treści

Part I: Autophagry In Vitro

1. Recombinant Expression, Purification and Assembly of p62 Filaments

Abul K. Tarafder, Audrey Guesdon, Tanja Kuhm, and Carsten Sachse

 

2. Structural Studies of Autophagy-related Proteins

Melanie Schwarten, Oliver H. Weiergräber, Dušan Petrović, Birgit Strodel, and Dieter Willbold

 

3. Structural Studies of Mammalian Autophagy Lipidation Complex

Kazuto Ohashi, Chinatsu Otomo, Zoltan Metlagel, and Takanori Otomo

 

4. Structural Studies of Selective Autophagy in Yeast

Akinori Yamasaki, Yasunori Watanabe and Nobuo N. Noda

 

5. Biophysical Studies of LC3 Family Proteins                                                               

Javier H. Hervás, Zuriñe Antón, and Alicia Alonso

  6. Reconstituting Autophagy Initiation from Purified Components

Peter Mayrhofer and Thomas Wollert

 

7. Cell-free Reconstitution of Autophagic Membrane Formation

Min Zhang and Liang Ge

 

8. Use of Peptide Arrays for Identification and Characterization of LIR Motifs

Mads Skytte Rasmussen, Åsa Birna Birgisdottir and Terje Johansen

 

9. Studying Autophagic Lysosome Reformation in Cells and by an in vitro Reconstitution System

Yang Chen, Qian Peter Su, and Li Yu

 

10. Formation of Autophagosomes Coincides With Relaxation of Membrane Curvature

Jaime Agudo-Canalejo and Roland L. Knorr

  11. Studies of Receptor-Atg8 Interactions during Selective Autophagy Christine Abert and Sascha Martens

 

Part II: Imaging Autophagy in Tissue Culture

12. Correlative Light and Electron Miscopy of Autophagosomes

Sigurdur Gudmundsson, Jenny Kahlhofer, Nastassia Baylac, Katri Kallio, and Eeva-Liisa Eskelinen

 

13. Improved Electron Microscopy (EM) Fixation Methods for Tracking Autophagy-associated Membranes in Cultured Mammalian Cells

Ritsuko Arai and Satoshi Waguri

 

14. 3-color Simultaneous Live Imaging of Autophagy-related Structures

Maho Hamasaki, Hiroyuki Ueda, Ouin Kunitaki,  and Tamotsu Yoshimori

 

15. Correlative Live-cell Imaging and Super-resolution Microscopy of Autophagy

Eleftherios Karanasios

 

16. Methods for Imaging Autophagosome Dynamics in Primary Neurons

Audrey Dong, Vineet Vinay Kulkarni, and Sandra Maday

 

17. Imaging Autophagy in hiPSC-derived Midbrain Dopaminergic Neuronal Cultures for Parkinson’s Disease Research

Stathakos, P., Jimenez-Moreno, N., Crompton, L., Nistor, P, Caldwell, M.A., and Lane, J.D

 

18. Correlative Light Electron Microscopy to analyze LC3 Proteins in Caenorhabditis elegans embryo

Céline Largeau and Renaud Legouis

 

19. Imaging Non-canonical Autophagy and LC3-associated Phagocytosis in Cultured Cells

Elise Jacquin, Katherine Fletcher, and Oliver Florey

 

Part III: Assays to Measure (and Screen For) Autophagy and Related Processes

20. Measurement of Bulk Autophagy by a Cargo Sequestration Assay

Nikolai Engedal, Morten Luhr, Paula Szalai, and Per O. Seglen

 

21. Methods to Detect Loss of Lysosomal Membrane Integrity

Sonja Aits

 

22. ­­Monitoring of Autophagy and Cell Volume Regulation in Kidney Epithelial Cells in Response to Fluid Shear Stress

Maria M. Lazari, Idil Orhon, Patrice Codogno, and Nicolas Dupont

 

23. Identification and Regulation of Multimeric Protein Complexes in Autophagy via SILAC- based Mass Spectrometry Approaches

Stéphanie Kaeser-Pebernard, Britta Diedrich, and Jörn Dengjel

 

24. 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, Kevin M. Ryan, Michael Howell, and Sharon A. Tooze

 

25. Autophagy Pathway Mapping to Elucidate the Function of Novel Autophagy Regulators Identified by High-throughput Screening

Martina Wirth1 and Sharon A. Tooze

 

26. In vitro Screening Platforms for Identifying Autophagy Modulators in Mammalian Cells

Elena Seranova, Carl Ward, Miruna Chipara, Ratul Banerjee, Tatiana R. Rosenstock, and Sovan Sarkar

 

27. In vitro Screening Platforms for Identifying Autophagy Modulators in Mammalian Cells

Elena Seranova, Carl Ward, Miruna Chipara, Ratul Banerjee, Tatiana R. Rosenstock, and Sovan Sarkar

 

28. Methods for the Study of Entotic Cell Death

Jens C. Hamann, Sung Eun Kim, and Michael Overholtzer

 

29. MHC Class I Internalization via Autophagy Proteins

Monica Loi, Laure-Anne Ligeon and Christian Münz

 

Part IV: Measuring and Imaging Autophagy In Vitro

30. Analysis of Autophagy for Liver Pathogenesis

Nazmul Huda, Hui Zou, Shengmin Yan, Bilon Khambu, and Xiao-Ming Yin

 

31. Autophagy in 3D In Vitro and Ex Vivo Cancer Models

Carlo Follo, Dario Barbone, William G. Richard2, Raphael Bueno, and V. Courtney Broaddus

 

32. Autophagy in Platelets

Meenakshi Banerjee , Yunjie Huang, Madhu M. Ouseph , Smita Joshi , Irina Pokrovskaya , Brian Storrie , Jinchao Zhang , Sidney W. Whiteheart , and Qing Jun Wang

 

33. Methods to Image Macroautophagy in the Brain In Vivo

Xigui Chen, Kanoh Kondo, and Hitoshi Okazawa

 

34. Measuring Nonselective and Selective Autophagy in the Liver

Takashi Ueno and Masaaki Komatsu

 

35. Measuring Autophagy in Pancreatitis

Alejandro Ropolo, Daniel Grasso, and Maria I. Vaccaro

 

36. Characterization of the “autophagic flux” in Prostate Cancer Tissue Biopsies by LC3A/LAMP2a Immunofluorescence and Confocal Microscopy

Kalamida D., Giatromanolaki A., and Koukourakis M.I

 

37. Methods to Determine the Role of Autophagy Proteins in C. elegans Ageing

Sivan Henis-Korenblita and Alicia Meléndez

 

 

Part V: Mitophagy and Other Selective Autophagy Pathways

38. Investigating Non-selective Autophagy in Drosophila

Szabolcs Takáts, Sarolta Tóth, Győző Szenci, and Gábor Juhász

 

39. Imaging the Dynamics of Mitophagy in Live Cells

Andrew S. Moore and Erika L.F. Holzbaur

 

40. Triggering Mitophagy with Photosensitizers

Cheng-Wei Hsieh and Wei Yuan Yang

 

41. Investigating Mitophagy and Mitochondrial Morphology in vivo using mito-QC

Thomas G. McWilliams and Ian G. Ganley

 

42. Assays to Monitor Mitophagy in Drosophila

Panagiotis Tsapras, Anne-Claire Jacomin, and Ioannis P.  Nezis

 

43. Mitophagy Dynamics in Caenorhabditis elegans

Konstantinos Palikaras, Eirini Lionaki, and Nektarios Tavernarakis

 

44. Methods for Studying Mitophagy in Yeast

Panagiota Kolitsida and Hagai Abeliovich

 

45. Measuring Anti-bacterial Autophagy

Keith B Boyle and  Felix Randow

 

46. Quantitative Phosphoproteomics of Selective Autophagy Receptors

Thomas Juretschke, Petra Beli, and Ivan Dikic

 

47. Analysis of Chaperone-mediated Autophagy

Y.R. Juste and A.M. Cuervo

 

48. Interactive Autophagy: Monitoring a Novel Form of Selective Autophagy by Macroscopic Observations

Jana Petri and Roland L. Knorr

Blurb

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.