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- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)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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| 2. |
- Peura, Sari, et al.
(författare)
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Enhanced greenhouse gas emissions and changes in plankton communities following an experimental increase in organic carbon loading to a humic lake
- 2014
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Ingår i: Biogeochemistry. - : Springer Science and Business Media LLC. - 0168-2563 .- 1573-515X. ; 118:1-3, s. 177-194
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Tidskriftsartikel (refereegranskat)abstract
- Organic carbon concentrations in the surface waters of the boreal region have increased during the past two decades. We investigated the impact of elevated dissolved organic carbon (DOC) loading to a humic lake by a whole-lake experiment in which DOC in the form of cane sugar was added monthly during the ice-free period over two consecutive years. The sugar addition represented an increased concentration of 2 mg l(-1) of DOC in the epilimnion and led to an increase in CO2 emission and also an apparent increase in CH4 emission to the atmosphere from the lake surface. The composition of the bacterial, phytoplankton and zooplankton communities altered during the study period and the bacterial abundance in the metalimnion and hypolimnion of the lake decreased. No changes were detected in epilimnetic primary production or respiration, but there was an increase in bacterial production in the epilimnion. The nutrient and particulate organic carbon concentrations also suggested possible changes in the activity of heterotrophic bacteria in the metalimnion. Carbon stable isotope analyses indicated transfer of some added sugar carbon through the food web to zooplankton consumers. Overall the results suggest that future increases in organic carbon loading to boreal lakes will increase greenhouse gas emissions, although the magnitude of any change is likely to depend on the availability of nutrients like phosphorus and nitrogen which influence organic matter processing and the development of plankton communities.
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