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      Developing a set of guidelines for your research field: a practical approach

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      Molecular Biology of the Cell
      The American Society for Cell Biology

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          Abstract

          Since 2008, the autophagy community has periodically published a set of guidelines, currently titled “Guidelines for the Use and Interpretation of Assays for Monitoring Autophagy.” The newest version of the guidelines was published in 2016. There are many reasons for establishing a set of guidelines in a given research field. This Perspective explores some of these reasons, including standardizing nomenclature for better communication, improving reproducibility, and making it easier for newcomers to enter the field. It also includes the approach I have used to generate and update the guidelines that are now widely used in the autophagy field. The suggestions are not meant to be formulaic, and the method is certainly not perfect. Instead, this should be viewed as a starting set of, well, guidelines.

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          Most cited references9

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

          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.
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            A unified nomenclature for yeast autophagy-related genes.

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              A comprehensive glossary of autophagy-related molecules and processes (2nd edition).

              The study of autophagy is rapidly expanding, and our knowledge of the molecular mechanism and its connections to a wide range of physiological processes has increased substantially in the past decade. The vocabulary associated with autophagy has grown concomitantly. In fact, it is difficult for readers--even those who work in the field--to keep up with the ever-expanding terminology associated with the various autophagy-related processes. Accordingly, we have developed a comprehensive glossary of autophagy-related terms that is meant to provide a quick reference for researchers who need a brief reminder of the regulatory effects of transcription factors and chemical agents that induce or inhibit autophagy, the function of the autophagy-related proteins, and the roles of accessory components and structures that are associated with autophagy.
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                Author and article information

                Contributors
                Role: Monitoring Editor
                Journal
                Mol Biol Cell
                Mol. Biol. Cell
                molbiolcell
                mbc
                Mol. Bio. Cell
                Molecular Biology of the Cell
                The American Society for Cell Biology
                1059-1524
                1939-4586
                01 March 2016
                : 27
                : 5
                : 733-738
                Affiliations
                [1]Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2216
                University of California, Berkeley
                Author notes
                *Address correspondence to: Daniel J. Klionsky ( klionsky@ 123456umich.edu ).
                Article
                E15-09-0618
                10.1091/mbc.E15-09-0618
                4803299
                26915690
                f621cab0-ccf7-4db5-8ef8-2e4b77270513
                © 2016 Klionsky. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License ( http://creativecommons.org/licenses/by-nc-sa/3.0).

                “ASCB®,” “The American Society for Cell Biology®,” and “Molecular Biology of the Cell®” are registered trademarks of The American Society for Cell Biology.

                History
                : 26 October 2015
                : 06 January 2016
                : 06 January 2016
                Categories
                Perspective

                Molecular biology
                Molecular biology

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