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- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)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.
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- Kim, Dae-Kyum, et al.
(author)
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EVpedia: A Community Web Portal for Extracellular Vesicles Research
- 2015
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In: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 31:6, s. 933-939
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Journal article (peer-reviewed)abstract
- Motivation: Extracellular vesicles (EVs) are spherical bilayered proteolipids, harboring various bioactive molecules. Due to the complexity of the vesicular nomenclatures and components, online searches for EV-related publications and vesicular components are currently challenging. Results: We present an improved version of EVpedia, a public database for EVs research. This community web portal contains a database of publications and vesicular components, identification of orthologous vesicular components, bioinformatic tools and a personalized function. EVpedia includes 6879 publications, 172 080 vesicular components from 263 high-throughput datasets, and has been accessed more than 65 000 times from more than 750 cities. In addition, about 350 members from 73 international research groups have participated in developing EVpedia. This free web-based database might serve as a useful resource to stimulate the emerging field of EV research.
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- Kim, Jihee, et al.
(author)
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Mass Budget of Methylmercury in the East Siberian Sea: The Importance of Sediment Sources
- 2020
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In: Environmental Science and Technology. - : American Chemical Society (ACS). - 1086-931X .- 1520-6912 .- 0013-936X .- 1520-5851.
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Journal article (peer-reviewed)abstract
- Biological concentrations of methylmercury(MeHg) are elevated throughout the Arctic Ocean; however, to date, the major sources and the spatial variability of MeHg are not well quantified. To identify the major inputs and outputs of MeHg to the Arctic shelf water column, we measured MeHg concentrations in the seawater and sediment samples from the East Siberian Sea collected from August to September 2018. We found that the MeHg concentrations in seawater and pore water were higher on the slope than on the shelf, while the MeHg concentrations in the sediment were higher on the shelf than on the slope. We created a mass budget for MeHg and found that the benthic diffusion and resuspension largely exceed other sources, such as atmospheric deposition and river water input. The major sinks of MeHg in the water column were dark demethylation and evasion. When we extrapolated our findings on benthic diffusion to the entire Arctic shelf system, the annual MeHg diffusion from the shelf sediments was estimated to be 23,065 ± 939 mol yr−1, about 2 times higher than previously proposed river discharges. Our study suggests that the MeHg input from shelf sediments in the Arctic Ocean is significant and has been previously underestimated.
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