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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. |
- Poeplau, Christopher, et al.
(författare)
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Qualitative and quantitative response of soil organic carbon to 40 years of crop residue incorporation under contrasting nitrogen fertilisation regimes
- 2017
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Ingår i: Soil Research. - 1838-675X .- 1838-6768. ; 55, s. 1-9
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Tidskriftsartikel (refereegranskat)abstract
- Crop residue incorporation (RI) is recommended to increase soil organic carbon (SOC) stocks. However, the positive effect on SOC is often reported to be relatively low and alternative use of crop residues, e.g. as a bioenergy source, may be more climate smart. In this context, it is important to understand: (i) the response of SOC stocks to long-term crop residue incorporation; and (ii) the qualitative SOC change, in order to judge the sustainability of this measure. We investigated the effect of 40 years of RI combined with five different nitrogen (N) fertilisation levels on SOC stocks and five SOC fractions differing in turnover times on a clay loam soil in Padua, Italy. The average increase in SOC stock in the 0-30 cm soil layer was 3.1Mg ha(-1) or 6.8%, with no difference between N fertilisation rates. Retention coefficients of residues did not exceed 4% and decreased significantly with increasing N rate (R-2 = 0.49). The effect of RI was higher after 20 years (4.6 Mg ha(-1)) than after 40 years, indicating that a new equilibrium has been reached and no further gains in SOC can be expected. Most (92%) of the total SOC was stored in the silt and clay fraction and 93% of the accumulated carbon was also found in this fraction, showing the importance of fine mineral particles for SOC storage, stabilisation and sequestration in arable soils. No change was detected in more labile fractions, indicating complete turnover of the annual residue-derived C in these fractions under a warm humid climate and in a highly base-saturated soil. The applied fractionation was thus useful to elucidate drivers and mechanisms of SOC formation and stabilisation. We conclude that residue incorporation is not a significant management practice affecting soil C storage in warm temperate climatic regions.
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