| 3. |
- 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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| 4. |
- Liu, Yuhuai, et al.
(författare)
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Effects of root exudate stoichiometry on CO2 emission from paddy soil
- 2020
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Ingår i: European Journal of Soil Biology. - : Elsevier BV. - 1164-5563 .- 1778-3615. ; 101
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Tidskriftsartikel (refereegranskat)abstract
- Root exudates are a labile source of carbon (C) for microorganisms that can lead to increased CO2 emission. Root exudates can vary in C:N stoichiometric ratio and their impact on microbially driven soil organic matter (SOM) turnover in paddy soils still remains unclear. The objective was to explore the underlying mechanisms involved in SOM decomposition due to root exudate (artificial) addition with three different C:N ratios (10, 20, and 40) during 45 days incubation. Different root exudates C:N ratios were obtained by adding mineral N and exudate components (glucose, oxalic acid, and glutamate) to paddy soil. N-only addition decreased dissolved organic C to limit CO2 emissions, which is an indicative of C sequestration. Conversely, simulated C:N stoichiometric ratios of root exudates significantly increased both microbial activity and metabolism without altering the microbial biomass C:N ratio. However, soil available dissolved organic C to NH4+ ratio decreased by exudates addition. The stoichiometric ratio of key C and N compound degrading enzymes activities increased only with C:N = 10 and remained unchanged with exudates C:N = 20 and 40. The qCO2 values increased with decreasing N-containing compounds in root exudates (i.e. highest CO2 emission was observed under C:N = 40 exudates addition). The results suggest that increasing exudates C:N ratio intensify CO2 emission due to high microbial N demand. Overall result show that root exudates C:N ratio and soil available N co-regulate on CO2 emission, which was controlled by microbial and potential extracellular enzyme activities.
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