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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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| 2. |
- Makoto, Kobayashi, et al.
(author)
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Contribution of charcoal to short-term nutrient dynamics after surface fire in the humus layer of a dwarf bamboo-dominated forest
- 2012
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In: Biology and Fertility of Soils. - : Springer Science and Business Media LLC. - 0178-2762 .- 1432-0789. ; 48:5, s. 569-577
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Journal article (peer-reviewed)abstract
- Ecological function of charcoal has been mainly investigated by adding charcoal to soil, which is not fully adequate to understand in situ the role in fire-prone forest ecosystem. To determine in situ effects of charcoal on ecosystem functions, such as nutrient availability, we conducted an experimental burning in a Japanese white birch forest with dense coverage of dwarf bamboo in the understory with or without removal of charcoal. Ammonium-N in the remaining humus layer increased immediately after the burning, but decreased to the level of unburnt plots within 1 month of the burning. Removal of charcoal had no significant effect on the NH4 (+)-N dynamics. Although burning did not affect NO3 (-)-N dynamics during the sampling period, charcoal removal led to a slight increase in NO3 (-)-N. The available P increased immediately after the burning, but then fell at 1 month after burning. Charcoal inhibited the available P depletion and prolonged the high availability of P. Greater availability of P might be due to the adsorption of phosphate in charcoal pores. Exchangeable Ca and Mg increased gradually; charcoal appeared to extend the period of higher concentration of exchangeable Ca and Mg. Charcoal deriving from fire is a key factor in influencing available nutrient in the humus layer of post-fire forests.
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| 3. |
- Makoto, Kobayashi, et al.
(author)
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Effects of fire-derived charcoal on soil properties and seedling regeneration in a recently burned Larix gmelinii/Pinus sylvestris forest
- 2011
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In: Journal of Soils and Sediments. - Heidelberg : Springer Berlin/Heidelberg. - 1439-0108 .- 1614-7480. ; 11:8, s. 1317-1322
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Journal article (peer-reviewed)abstract
- Purpose: Fire is a primary form of disturbance in boreal ecosystems. Charcoal is an important by-product of forest fire and has been reported to have the potential to influence the plant community establishing after fire. To date, however, no study has effectively tested the relationship between charcoal and plant regeneration in the actual post-fire forests. To determine the contribution of charcoal to soil properties and plant regeneration after forest fires, we conducted in situ investigations concerning the relationship between charcoal and the plant-soil system. Materials and methods: We conducted a field investigation in a recently burnt Gmelin larch (Larix gmelinii)/Scots pine (Pinus sylvestris) forest in the Russian Far East to investigate charcoal contents, pH, water contents, and nutrient availability in soil together with the regeneration of larch and pine seedlings. Results and discussion: Positive correlations were found between charcoal contents and soil pH, water contents, and available P contents. Additionally, charcoal contents and the number of pine seedlings were positively correlated. There was, however, no significant relationship between charcoal content and extractable NH(4) (+) content or the number of larch seedlings. These results suggest that while charcoal influences are somewhat obscure in the field, charcoal significantly contributes to the amelioration of water and nutrient availability together with the success of regeneration of pine seedling. Conclusions: Charcoal produced during fire events in Gmelin larch and Scots pine forests of eastern Russia has a modest influence on soil properties, but has the potential to improve regeneration in these fire-prone ecosystems.
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