Protocols
Using LC3 to monitor autophagy flux in the retinal pigment epithelium
Ai Ling Wang, Michael E. Boulton, William A. Dunn, Jr., Harripriya Vittal Rao, Jun Cai, Thomas J. Lukas and Arthur H. Neufeld
Pages 1190 – 1193
Methods to monitor autophagy in H. pylori vacuolating cytotoxin A (VacA)-treated cells
Deepa Raju and Nicola L. Jones
Pages 138 – 143
Investigating autophagy: Quantitative morphometric analysis using electron microscopy
Jamie M. Swanlund, Kevin C. Kregel and Terry D. Oberley
Pages 270 – 277
Reticulocyte mitophagy: Monitoring mitochondrial clearance in a mammalian model
Ji Zhang and Paul Ney
Pages 405 – 408
Purification of autophagosomes from rat hepatocytes
Per O. Seglen and Monica Fengsrud Brinchmann
Pages 542 – 547
A proteolytic cleavage assay to monitor autophagy in Dictyostelium discoideum
Javier Calvo-Garrido, Sergio Carilla-Latorre, Ana Mesquita and Ricardo Escalante
Pages 1063 – 1068
Measuring piecemeal microautophagy of the nucleus in Saccharomyces cerevisiae
Jonathan I. Millen, Roswitha Krick, Tanja Prick, Michael Thumm and David S. Goldfarb
Pages 75 – 81
Monitoring mitophagy in yeast: The Om45-GFP processing assay
Tomotake Kanki, Dongchon Kang and Daniel J. Klionsky
Pages 1186 – 1189
Determining Atg protein stoichiometry at the phagophore assembly site by fluorescence microscopy
Jiefei Geng and Daniel J. Klionsky
Pages 144 – 147
Quantification of nonselective bulk autophagy in S. cerevisiae using Pgk1-GFP
Evelyn Welter, Michael Thumm and Roswitha Krick
Pages 794 – 797
Analyzing autophagy in Magnaporthe oryzae
Fei Xu, Xiao-Hong Liu, Fei-Long Zhuang, Jun Zhu and Fu-Cheng Lin
Pages 525 – 530
GFP-Atg8 protease protection as a tool to monitor autophagosome biogenesis
Usha Nair, Michael Thumm, Daniel J. Klionsky and Roswitha Krick
Pages 1546 – 1550
Analyzing autophagy in zebrafish
Congcong He and Daniel J. Klionsky
Pages 642 – 644
Toolboxes
Indirect estimation of the area density of Atg8 on the phagophore
Zhiping Xie, Usha Nair, Jiefei Geng, Maciej B. Szefler, Edward D. Rothman and Daniel J. Klionsky
Pages 217 – 220
Quantitation of autophagy by luciferase release assay
Robin Ketteler and Brian Seed
Pages 801 – 806
Quantitation of selective autophagic protein aggregate degradation in vitro and in vivo using luciferase reporters
Jeong-Sun Ju, Sara E. Miller, Erin Jackson, Ken Cadwell, David Piwnica-Worms and Conrad C. Weihl
Pages 511 – 519
Identification of novel autophagy regulators by a luciferase-based assay for the kinetics of autophagic flux
Thomas Farkas, Maria Høyer-Hansen and Marja Jäättelä
Pages 1018 – 1025
A novel quantitative flow cytometry-based assay for autophagy
Kai Er Eng, Marc D. Panas, Gunilla B. Karlsson Hedestam and Gerald M. McInerney
Pages 634 – 641
A reporter cell system to monitor autophagy based on p62/SQSTM1
Kenneth Bowitz Larsen, Trond Lamark, Aud Øvervatn, Ingvill Harneshaug, Terje Johansen and Geir Bjørkøy
Pages 784 – 793
Quantitation of "autophagic flux" in mature skeletal muscle
Jeong-Sun Ju, Arun S. Varadhachary, Sara E. Miller and Conrad C. Weihl
Pages 929 – 935
Synthetic substrates for measuring activity of autophagy proteases-autophagins (Atg4)
Chih-Wen Shu, Marcin Drag, Miklos Bekes, Dayong Zhai, Guy S. Salvesen and John C. Reed
Pages 936 – 947
A quantitative assay for the monitoring of autophagosome accumulation in different phases of the cell cycle
Vitaliy Kaminskyy, Azadeh Abdi and Boris Zhivotovsky
Pages 83 – 90
Characterization of macroautophagic flux in vivo using a leupeptin-based assay
Jeffrey Haspel, Rahamthulla S. Shaik, Emeka Ifedigbo, Kiichi Nakahira, Tamas Dolinay, Joshua A. Englert and Augustine M.K. Choi
Pages 629 – 642
The acquisition of resistance to TNFα in breast cancer cells is associated with constitutive activation of autophagy as revealed by a transcriptome analysis using a custom microarray
Etienne Moussay, Tony Kaoma, Joanna Baginska, Arnaud Muller, Kris Van Moer, Nathalie Nicot, Petr V. Nazarov, Laurent Vallar, Salem Chouaib, Guy Berchem and Bassam Janji
Pages 760 – 770
A fluorescence-microscopic and cytofluorometric system for monitoring the turnover of the autophagic substrate p62/SQSTM1
Amena BenYounès, Nicolas Tajeddine, Maximilien Tailler, Shoaib Ahmad Malik, Shensi Shen, Didier Métivier, Oliver Kepp, Ilio Vitale, Maria Chiara Maiuri and Guido Kroemer
Pages 883 – 891
A monitoring method for Atg4 activation in living cells using peptide-conjugated polymeric nanoparticles
Kyung-Mi Choi, Hae Yun Nam, Jin Hee Na, Seong Who Kim, Sang Yoon Kim, Kwangmeyung Kim, Ick Chan Kwon and Hyung Jun Ahn
Pages 1052 – 1062
Simultaneous assessment of autophagy and apoptosis using multispectral imaging cytometry
Claire de la Calle, Pierre-Emmanuel Joubert, Helen K.W. Law, Milena Hasan and Matthew Albert
Pages 1045 – 1051
Spatiotemporally controlled initiation of Parkin-mediated mitophagy within single cells
Jin-Yi Yang and Wei Yuan Yang
Pages 1230 – 1238
"Autophagic flux" in normal mouse tissues: Focus on endogenous LC3A processing
Christos E. Zois, Alexandra Giatromanolaki, Efthimios Sivridis, Marina Papaiakovou, Heikki Kainulainen and Michael I. Koukourakis
Pages 1371 – 1378
A high-throughput FRET-based assay for determination of Atg4 activity
Min Li, Xi Chen, Qi-Zhuang Ye, Andreas Vogt and Xiao-Ming Yin
Localization of autophagy-related proteins in yeast using a versatile plasmid-based resource of fluorescent protein fusions
Jun Ma, Nikë Bharucha, Craig J. Dobry, Ryan L. Frisch, Sarah K. Lawson and Anuj Kumar
Pages 792 – 800
A multiple ATG gene knockout strain for yeast two-hybrid analysis
Yang Cao, Usha Nair, Kyoko Yasumura-Yorimitsu and Daniel J. Klionsky
Pages 699 – 705
Assaying autophagic activity in transgenic GFP-Lc3 and GFP-Gabarap zebrafish embryos
Congcong He, Clinton R. Bartholomew, Weibin Zhou and Daniel J. Klionsky
Pages 520 – 526
