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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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| 4. |
- Vedovato, Laura B., et al.
(författare)
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Ancient fires enhance Amazon forest drought resistance
- 2023
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Ingår i: Frontiers in Forests and Global Change. - : Frontiers Media SA. - 2624-893X. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Drought and fire reduce productivity and increase tree mortality in tropical forests. Fires also produce pyrogenic carbon (PyC), which persists in situ for centuries to millennia, and represents a legacy of past fires, potentially improving soil fertility and water holding capacity and selecting for the survival and recruitment of certain tree life-history (or successional) strategies. We investigated whether PyC is correlated with physicochemical soil properties, wood density, aboveground carbon (AGC) dynamics and forest resistance to severe drought. To achieve our aim, we used an Amazon-wide, long-term plot network, in forests without known recent fires, integrating site-specific measures of forest dynamics, soil properties and a unique soil PyC concentration database. We found that forests with higher concentrations of soil PyC had both higher soil fertility and lower wood density. Soil PyC was not associated with AGC dynamics in non-drought years. However, during extreme drought events (10% driest years), forests with higher concentrations of soil PyC experienced lower reductions in AGC gains (woody growth and recruitment), with this drought-immunizing effect increasing with drought severity. Forests with a legacy of ancient fires are therefore more likely to continue to grow and recruit under increased drought severity. Forests with high soil PyC concentrations (third quartile) had 3.8% greater AGC gains under mean drought, but 33.7% greater under the most extreme drought than forests with low soil PyC concentrations (first quartile), offsetting losses of up to 0.68 Mg C ha–1yr–1 of AGC under extreme drought events. This suggests that ancient fires have legacy effects on current forest dynamics, by altering soil fertility and favoring tree species capable of continued growth and recruitment during droughts. Therefore, mature forest that experienced fires centuries or millennia ago may have greater resistance to current short-term droughts.
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| 5. |
- Bartholomew, David C., et al.
(författare)
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Overcoming the challenges of incorporating rare and threatened flora into ecosystem restoration
- 2023
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Ingår i: Restoration Ecology. - : John Wiley & Sons. - 1061-2971 .- 1526-100X. ; 31:4
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Tidskriftsartikel (refereegranskat)abstract
- Developing strategies that enhance the incorporation of rare and threatened flora into ecosystem restoration is urgently needed to capitalize on the United Nations Decade on Ecosystem Restoration. We outline six major challenges that impede the widespread use of rare and threatened flora in restoration: (1) a lack of information about threatened species; (2) a lack of propagation material; (3) low survival rates and regeneration potential; (4) a lack of coordination and collaboration; (5) a lack of financial incentives; and (6) a lack of policy incentives. We also outline several potential solutions to overcome each of them, including changes to funding, legislation, and markets, advancing use of modern technologies and knowledge, and development of new collaborations. All stakeholders have a role to play, including practitioners, academics, funders, and policymakers.
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| 6. |
- Kaput, J, et al.
(författare)
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The case for strategic international alliances to harness nutritional genomics for public and personal health
- 2005
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Ingår i: The British journal of nutrition. - : Cambridge University Press (CUP). - 0007-1145 .- 1475-2662. ; 94:5, s. 623-632
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Tidskriftsartikel (refereegranskat)abstract
- Nutrigenomics is the study of how constituents of the diet interact with genes, and their products, to alter phenotype and, conversely, how genes and their products metabolise these constituents into nutrients, antinutrients, and bioactive compounds. Results from molecular and genetic epidemiological studies indicate that dietary unbalance can alter gene–nutrient interactions in ways that increase the risk of developing chronic disease. The interplay of human genetic variation and environmental factors will make identifying causative genes and nutrients a formidable, but not intractable, challenge. We provide specific recommendations for how to best meet this challenge and discuss the need for new methodologies and the use of comprehensive analyses of nutrient–genotype interactions involving large and diverse populations. The objective of the present paper is to stimulate discourse and collaboration among nutrigenomic researchers and stakeholders, a process that will lead to an increase in global health and wellness by reducing health disparities in developed and developing countries.
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| 7. |
- Abbadessa, G, et al.
(författare)
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Unsung hero Robert C. Gallo
- 2009
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Ingår i: Science (New York, N.Y.). - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 323:5911, s. 206-207
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 8. |
- Clason, Caroline C., et al.
(författare)
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Modelling the transfer of supraglacial meltwater to the bed of Leverett Glacier, Southwest Greenland
- 2015
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Ingår i: The Cryosphere. - : Copernicus GmbH. - 1994-0416 .- 1994-0424. ; 9:1, s. 123-138
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Tidskriftsartikel (refereegranskat)abstract
- Meltwater delivered to the bed of the Greenland Ice Sheet is a driver of variable ice-motion through changes in effective pressure and enhanced basal lubrication. Ice surface velocities have been shown to respond rapidly both to meltwater production at the surface and to drainage of supraglacial lakes, suggesting efficient transfer of meltwater from the supraglacial to subglacial hydrological systems. Although considerable effort is currently being directed towards improved modelling of the controlling surface and basal processes, modelling the temporal and spatial evolution of the transfer of melt to the bed has received less attention. Here we present the results of spatially distributed modelling for prediction of moulins and lake drainages on the Leverett Glacier in Southwest Greenland. The model is run for the 2009 and 2010 ablation seasons, and for future increased melt scenarios. The temporal pattern of modelled lake drainages are qualitatively comparable with those documented from analyses of repeat satellite imagery. The modelled timings and locations of delivery of meltwater to the bed also match well with observed temporal and spatial patterns of ice surface speed-ups. This is particularly true for the lower catchment (< 1000 m a.s.l.) where both the model and observations indicate that the development of moulins is the main mechanism for the transfer of surface meltwater to the bed. At higher elevations (e.g. 1250-1500 m a.s.l.) the development and drainage of supraglacial lakes becomes increasingly important. At these higher elevations, the delay between modelled melt generation and subsequent delivery of melt to the bed matches the observed delay between the peak air temperatures and subsequent velocity speed-ups, while the instantaneous transfer of melt to the bed in a control simulation does not. Although both moulins and lake drainages are predicted to increase in number for future warmer climate scenarios, the lake drainages play an increasingly important role in both expanding the area over which melt accesses the bed and in enabling a greater proportion of surface melt to reach the bed.
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