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1. Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

Author

Klionsky, Daniel J, Abdelmohsen, Kotb, Abe, Akihisa, Abedin, Md Joynal, Abeliovich, Hagai, Acevedo Arozena, Abraham, Adachi, Hiroaki, Adams, Christopher M, Adams, Peter D, Adeli, Khosrow, Adhihetty, Peter J, Adler, Sharon G, Agam, Galila, Agarwal, Rajesh, Aghi, Manish K, Agnello, Maria, Agostinis, Patrizia, Aguilar, Patricia V, Aguirre-Ghiso, Julio, Airoldi, Edoardo M, Ait-Si-Ali, Slimane, Akematsu, Takahiko, Akporiaye, Emmanuel T, Al-Rubeai, Mohamed, Albaiceta, Guillermo M, Albanese, Chris, Albani, Diego, Albert, Matthew L, Aldudo, Jesus, Algül, Hana, Alirezaei, Mehrdad, Alloza, Iraide, Almasan, Alexandru, Almonte-Beceril, Maylin, Alnemri, Emad S, Alonso, Covadonga, Altan-Bonnet, Nihal, Altieri, Dario C, Alvarez, Silvia, Alvarez-Erviti, Lydia, Alves, Sandro, Amadoro, Giuseppina, Amano, Atsuo, Amantini, Consuelo, Ambrosio, Santiago, Amelio, Ivano, Amer, Amal O, Amessou, Mohamed, Amon, Angelika, An, Zhenyi, Anania, Frank A, Andersen, Stig U, Andley, Usha P, Andreadi, Catherine K, Andrieu-Abadie, Nathalie, Anel, Alberto, Ann, David K, Anoopkumar-Dukie, Shailendra, Antonioli, Manuela, Aoki, Hiroshi, Apostolova, Nadezda, Aquila, Saveria, Aquilano, Katia, Araki, Koichi, Arama, Eli, Aranda, Agustin, Araya, Jun, Arcaro, Alexandre, Arias, Esperanza, Arimoto, Hirokazu, Ariosa, Aileen R, Armstrong, Jane L, Arnould, Thierry, Arsov, Ivica, Asanuma, Katsuhiko, Askanas, Valerie, Asselin, Eric, Atarashi, Ryuichiro, Atherton, Sally S, Atkin, Julie D, Attardi, Laura D, Auberger, Patrick, Auburger, Georg, Aurelian, Laure, Autelli, Riccardo, Avagliano, Laura, Avantaggiati, Maria Laura, Avrahami, Limor, Awale, Suresh, Azad, Neelam, Bachetti, Tiziana, Backer, Jonathan M, Bae, Dong-Hun, Bae, Jae-Sung, Bae, Ok-Nam, Bae, Soo Han, Baehrecke, Eric H, Baek, Seung-Hoon, Baghdiguian, Stephen, and Bagniewska-Zadworna, Agnieszka

Subjects
Biochemistry and Cell Biology, Biological Sciences, Animals, Autophagy, Biological Assay, Computer Simulation, Humans, autolysosome, autophagosome, chaperone-mediated autophagy, flux, LC3, lysosome, macroautophagy, phagophore, stress, vacuole, Biochemistry & Molecular Biology, Biochemistry and cell biology
Published
2016

2. Guidelines for the use and interpretation of assays for monitoring autophagy.

Author

Klionsky, Daniel J, Abdalla, Fabio C, Abeliovich, Hagai, Abraham, Robert T, Acevedo-Arozena, Abraham, Adeli, Khosrow, Agholme, Lotta, Agnello, Maria, Agostinis, Patrizia, Aguirre-Ghiso, Julio A, Ahn, Hyung Jun, Ait-Mohamed, Ouardia, Ait-Si-Ali, Slimane, Akematsu, Takahiko, Akira, Shizuo, Al-Younes, Hesham M, Al-Zeer, Munir A, Albert, Matthew L, Albin, Roger L, Alegre-Abarrategui, Javier, Aleo, Maria Francesca, Alirezaei, Mehrdad, Almasan, Alexandru, Almonte-Becerril, Maylin, Amano, Atsuo, Amaravadi, Ravi, Amarnath, Shoba, Amer, Amal O, Andrieu-Abadie, Nathalie, Anantharam, Vellareddy, Ann, David K, Anoopkumar-Dukie, Shailendra, Aoki, Hiroshi, Apostolova, Nadezda, Arancia, Giuseppe, Aris, John P, Asanuma, Katsuhiko, Asare, Nana YO, Ashida, Hisashi, Askanas, Valerie, Askew, David S, Auberger, Patrick, Baba, Misuzu, Backues, Steven K, Baehrecke, Eric H, Bahr, Ben A, Bai, Xue-Yuan, Bailly, Yannick, Baiocchi, Robert, Baldini, Giulia, Balduini, Walter, Ballabio, Andrea, Bamber, Bruce A, Bampton, Edward TW, Bánhegyi, Gábor, Bartholomew, Clinton R, Bassham, Diane C, Bast, Robert C, Batoko, Henri, Bay, Boon-Huat, Beau, Isabelle, Béchet, Daniel M, Begley, Thomas J, Behl, Christian, Behrends, Christian, Bekri, Soumeya, Bellaire, Bryan, Bendall, Linda J, Benetti, Luca, Berliocchi, Laura, Bernardi, Henri, Bernassola, Francesca, Besteiro, Sébastien, Bhatia-Kissova, Ingrid, Bi, Xiaoning, Biard-Piechaczyk, Martine, Blum, Janice S, Boise, Lawrence H, Bonaldo, Paolo, Boone, David L, Bornhauser, Beat C, Bortoluci, Karina R, Bossis, Ioannis, Bost, Frédéric, Bourquin, Jean-Pierre, Boya, Patricia, Boyer-Guittaut, Michaël, Bozhkov, Peter V, Brady, Nathan R, Brancolini, Claudio, Brech, Andreas, Brenman, Jay E, Brennand, Ana, Bresnick, Emery H, Brest, Patrick, Bridges, Dave, Bristol, Molly L, Brookes, Paul S, Brown, Eric J, and Brumell, John H

Subjects
Animals, Humans, Biological Assay, Models, Biological, Autophagy, Generic health relevance, autolysosome, autophagosome, flux, LC3, lysosome, phagophore, stress, vacuole, Biochemistry and Cell Biology, Biochemistry & Molecular Biology
Abstract

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.

Published
2012

31. Abnormalities of aneural and innervated cultured muscle fibers from patients with myotonic atrophy (dystrophy)

Author

Kobayashi, Takayoshi, Askanas, Valerie, Saito, Koji, Engel, W. King, and Ishikawa, Koichi

Subjects
Atrophy, Muscular -- Research, Tissue culture -- Usage, Myotonic dystrophy -- Physiological aspects, Muscle diseases -- Physiological aspects, Genetic disorders -- Research, Neuromuscular junction -- Research, Health
Abstract

Tissue cultures have been a tremendous boon to biomedical research, since careful controls can be established in culture dishes which would be impossible to obtain in human and animal studies. However, since the environment in the tissue culture dish is so different from that within the body, the cells cannot be assumed to behave the same as in their normal milieu. This has been a problem in the use of tissue culture techniques to study the muscle cells of patients with myotonic atrophy. Myotonic atrophy (MA) is a rare and slowly progressive muscle disease which is inherited as an autosomal dominant trait. The condition is also known as myotonic dystrophy and Steinert's disease. Researchers have now shown that the inclusion of the spinal cord, complete with dorsal root ganglia, from laboratory rats into the cultures of human muscle cells, along with the addition of specific nutrient factors, promotes the development of muscle cells in culture which more strongly resemble adult human muscle cells. When this technique was used to study cells from patients with myotonic atrophy, abnormalities were seen at the neuromuscular junctions formed between the nerves and the muscle cells. Only 4 percent of the cells from the MA patients were capable of forming mature connections in the culture dishes, in contrast with 37 percent of the cells from normal control subjects. The intrinsic deficits of these muscle cells grown in culture may be further studied in hopes of gaining a deeper understanding of myotonic atrophy. (Consumer Summary produced by Reliance Medical Information, Inc.)

Published
1990

40. Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

Author

Klionsky, Daniel J., Abdelmohsen, Kotb, Abe, Akihisa, Abedin, Md Joynal, Abeliovich, Hagai, Acevedo Arozena, Abraham, Adachi, Hiroaki, Adams, Christopher M., Adams, Peter D., Adeli, Khosrow, Adhihetty, Peter J., Adler, Sharon G., Agam, Galila, Agarwal, Rajesh, Aghi, Manish K., Agnello, Maria, Agostinis, Patrizia, Aguilar, Patricia V., Aguirre-Ghiso, Julio, Airoldi, Edoardo M., Ait-Si-Ali, Slimane, Akematsu, Takahiko, Akporiaye, Emmanuel T., Al-Rubeai, Mohamed, Albaiceta, Guillermo M., Albanese, Chris, Albani, Diego, Albert, Matthew L., Aldudo, Jesus, Algül, Hana, Alirezaei, Mehrdad, Alloza, Iraide, Almasan, Alexandru, Almonte-Beceril, Maylin, Alnemri, Emad S., Alonso, Covadonga, Altan-Bonnet, Nihal, Altieri, Dario C., Alvarez, Silvia, Alvarez-Erviti, Lydia, Alves, Sandro, Amadoro, Giuseppina, Amano, Atsuo, Amantini, Consuelo, Ambrosio, Santiago, Amelio, Ivano, Amer, Amal O., Amessou, Mohamed, Amon, Angelika, An, Zhenyi, Anania, Frank A., Andersen, Stig U., Andley, Usha P., Andreadi, Catherine K., Andrieu-Abadie, Nathalie, Anel, Alberto, Ann, David K., Anoopkumar-Dukie, Shailendra, Antonioli, Manuela, Aoki, Hiroshi, Apostolova, Nadezda, Aquila, Saveria, Aquilano, Katia, Araki, Koichi, Arama, Eli, Aranda, Agustin, Araya, Jun, Arcaro, Alexandre, Arias, Esperanza, Arimoto, Hirokazu, Ariosa, Aileen R., Armstrong, Jane L., Arnould, Thierry, Arsov, Ivica, Asanuma, Katsuhiko, Askanas, Valerie, Asselin, Eric, Atarashi, Ryuichiro, Atherton, Sally S., Atkin, Julie D., Attardi, Laura D., Auberger, Patrick, Auburger, Georg, Aurelian, Laure, Autelli, Riccardo, Avagliano, Laura, Avantaggiati, Maria Laura, Avrahami, Limor, Awale, Suresh, Azad, Neelam, Bachetti, Tiziana, Backer, Jonathan M., Bae, Dong-Hun, Bruhat, Alain, Candau, Robin, Favier, François B., Michaeli, Simon, Ramonatxo, Christelle, Seiliez, Iban, University of Michigan [Ann Arbor], University of Michigan System, Biomedical Research Center, Tokyo Medical University, University of Minnesota [Twin Cities], University of Minnesota System, The Hebrew University of Jerusalem (HUJ), Mammalian Genetics Unit, Medical Research Council Harwell, University of Occupational and Environmental Health School of Medicine, Partenaires INRAE, University of Iowa [Iowa City], Cancer Research UK, University of Toronto, University of Florida [Gainesville], Los Angeles Biomedical Research Institute (LA BioMed), Ben-Gurion University of the Negev (BGU), University of Colorado [Boulder], University of California [San Francisco] (UCSF), University of California, Università degli Studi di Palermo, Université Catholique de Louvain (UCL), University of Texas, Icahn School of Medicine at Mount Sinai, Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Centre épigénétique et destin cellulaire (EDC (UMR_7216)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), University of Vienna [Vienna], Sidra Medical and Research Center, University College Dublin (UCD), Universidad de Oviedo [Oviedo], Georgetown University, Candiolo Cancer Institute (IRCCS), Institut Pasteur [Paris], Center for Biomedical Research in Neurodegenerative Diseases Network (CIBERNED), Technical University of Munich (TUM), Department of Immunology and Microbial Science, Scripps Research Institute, Ikerbasque - Basque Foundation for Science, Cleveland Clinic, Institute for Biomedical Research, Department of Biochemistry and Molecular Biology, Thomas Jefferson University-Jefferson Medical College, National Heart, Lung, and Blood Institute [Bethesda] (NHLBI), The Wistar Institute, Universidad de Buenos Aires (UBA), Department of Clinical Neurosciences, University College of London [London] (UCL)-Institute of Neurology, Thérapie génique, Génomique et Epigénomique (U 1169), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, Consiglio Nazionale delle Ricerche (CNR), Osaka University, School of Biosciences and Veterinary Medicine, University of Camerino, University of Barcelona, Toxicology Unit, Medical Research Council, Ohio State University, Wayne State University, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology (MIT), Department of Neurology, University of California-University of California, Unité de Nutrition Humaine (UNH), Institut National de la Recherche Agronomique (INRA)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Clermont Université, Dynamique Musculaire et Métabolisme (DMEM), Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM), Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Nutrition, Métabolisme, Aquaculture (NuMéA), and Institut National de la Recherche Agronomique (INRA)-Université de Pau et des Pays de l'Adour (UPPA)

Subjects
flux, phagophore, stress, autophagy, macroautophagy, vacuole, lysosome, autophagosome, LC3, chaperonemediated, [SDV.BDD]Life Sciences [q-bio]/Development Biology, autolysosome
Abstract

Seuls les 100 premiers auteurs dont les auteurs INRA ont été entrés dans la notice. La liste complète des auteurs et de leurs affiliations est accessible sur la publication.

Published
2016

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