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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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- Hudson, Lawrence N, et al.
(författare)
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The database of the PREDICTS (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems) project
- 2017
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Ingår i: Ecology and Evolution. - : John Wiley & Sons. - 2045-7758. ; 7:1, s. 145-188
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Tidskriftsartikel (refereegranskat)abstract
- The PREDICTS project-Projecting Responses of Ecological Diversity In Changing Terrestrial Systems (www.predicts.org.uk)-has collated from published studies a large, reasonably representative database of comparable samples of biodiversity from multiple sites that differ in the nature or intensity of human impacts relating to land use. We have used this evidence base to develop global and regional statistical models of how local biodiversity responds to these measures. We describe and make freely available this 2016 release of the database, containing more than 3.2 million records sampled at over 26,000 locations and representing over 47,000 species. We outline how the database can help in answering a range of questions in ecology and conservation biology. To our knowledge, this is the largest and most geographically and taxonomically representative database of spatial comparisons of biodiversity that has been collated to date; it will be useful to researchers and international efforts wishing to model and understand the global status of biodiversity.
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- Hudson, Lawrence N., et al.
(författare)
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The PREDICTS database : a global database of how local terrestrial biodiversity responds to human impacts
- 2014
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Ingår i: Ecology and Evolution. - : Wiley. - 2045-7758. ; 4:24, s. 4701-4735
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Tidskriftsartikel (refereegranskat)abstract
- Biodiversity continues to decline in the face of increasing anthropogenic pressures such as habitat destruction, exploitation, pollution and introduction of alien species. Existing global databases of species' threat status or population time series are dominated by charismatic species. The collation of datasets with broad taxonomic and biogeographic extents, and that support computation of a range of biodiversity indicators, is necessary to enable better understanding of historical declines and to project - and avert - future declines. We describe and assess a new database of more than 1.6 million samples from 78 countries representing over 28,000 species, collated from existing spatial comparisons of local-scale biodiversity exposed to different intensities and types of anthropogenic pressures, from terrestrial sites around the world. The database contains measurements taken in 208 (of 814) ecoregions, 13 (of 14) biomes, 25 (of 35) biodiversity hotspots and 16 (of 17) megadiverse countries. The database contains more than 1% of the total number of all species described, and more than 1% of the described species within many taxonomic groups - including flowering plants, gymnosperms, birds, mammals, reptiles, amphibians, beetles, lepidopterans and hymenopterans. The dataset, which is still being added to, is therefore already considerably larger and more representative than those used by previous quantitative models of biodiversity trends and responses. The database is being assembled as part of the PREDICTS project (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems - ). We make site-level summary data available alongside this article. The full database will be publicly available in 2015.
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- Bansal, Sheel, et al.
(författare)
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Practical Guide to Measuring Wetland Carbon Pools and Fluxes
- 2023
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Ingår i: Wetlands (Wilmington, N.C.). - : SPRINGER. - 0277-5212 .- 1943-6246. ; 43:8
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Forskningsöversikt (refereegranskat)abstract
- Wetlands cover a small portion of the world, but have disproportionate influence on global carbon (C) sequestration, carbon dioxide and methane emissions, and aquatic C fluxes. However, the underlying biogeochemical processes that affect wetland C pools and fluxes are complex and dynamic, making measurements of wetland C challenging. Over decades of research, many observational, experimental, and analytical approaches have been developed to understand and quantify pools and fluxes of wetland C. Sampling approaches range in their representation of wetland C from short to long timeframes and local to landscape spatial scales. This review summarizes common and cutting-edge methodological approaches for quantifying wetland C pools and fluxes. We first define each of the major C pools and fluxes and provide rationale for their importance to wetland C dynamics. For each approach, we clarify what component of wetland C is measured and its spatial and temporal representativeness and constraints. We describe practical considerations for each approach, such as where and when an approach is typically used, who can conduct the measurements (expertise, training requirements), and how approaches are conducted, including considerations on equipment complexity and costs. Finally, we review key covariates and ancillary measurements that enhance the interpretation of findings and facilitate model development. The protocols that we describe to measure soil, water, vegetation, and gases are also relevant for related disciplines such as ecology. Improved quality and consistency of data collection and reporting across studies will help reduce global uncertainties and develop management strategies to use wetlands as nature-based climate solutions.
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- Bergvall, Ulrika A., et al.
(författare)
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Anti-browsing effects of birch bark extract on fallow deer
- 2013
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Ingår i: European Journal of Forest Research. - : Springer Science and Business Media LLC. - 1612-4669 .- 1612-4677. ; 132:5-6, s. 717-725
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Tidskriftsartikel (refereegranskat)abstract
- A major problem within forest industry is unwanted browsing on seedlings from mammalian herbivores. The aim of this study was to evaluate the effects of birch bark extracts as repellents towards fallow deer. Birch bark was extracted in a conventional way with ethanol as solvent at ambient temperature and with a new method, liquid CO2 extraction. An analysis of the ethanol-extracted birch bark showed that it contained large amounts of terpenoids, of which the most abundant was betulin. In seven different treatment trials, we used 15 individually handled fallow deer. To investigate the binary taste preferences, birch bark extract was added to food and presented in two bowls in typical two-choice tests. We found that the amount of a food type consumed during a trial and the number of shifts between food bowls were dependent on the amount of the birch extract the food contained. Concentrations of above 1 % by dry weight of birch extract acted as a repellent. In addition, such concentrations produced shorter feeding bouts by a greater willingness to change bowls. Therefore, our conclusion is that birch bark extract acts as a repellent towards fallow deer and is therefore likely to act as a repellent against other deer species. In addition, we show that birch bark extract produced by the new and more environmentally sustainable method employing liquid CO2 mixed with ethanol has the same repellent effect as the traditional ethanol extraction.
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- Yu, Changxun, 1983-, et al.
(författare)
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Manganese cycling and transport in boreal estuaries impacted by acidic Mn-rich drainage
- 2024
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Ingår i: GEOCHIMICA ET COSMOCHIMICA ACTA. - : Elsevier. - 0016-7037 .- 1872-9533 .- 0046-564X. ; 365, s. 136-157
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Tidskriftsartikel (refereegranskat)abstract
- As critical transition zones between the land and the sea, estuaries are not only hotspots of hydrogeochemical and microbial processes/reactions, but also play a vital role in processing and transferring terrestrial fluxes of metals and nutrients to the sea. This study focused on three estuaries in the Gulf of Bothnia. All of them expe-rience frequent inputs of acidic and Mn/metal-rich creek waters due to flushing of acid sulfate soils that are widespread in the creeks catchments. Analyzing existing long-term water chemistry data revealed a strong sea-sonal variation of Mn loads, with the highest values in spring (after snow melt) and autumn (after heavy rains). We sampled surface waters, suspended particulate matter (SPM), and sediments from the estuarine mixing zones and determined the loads and solid-phase speciation of Mn as well as the composition and metabolic potentials of microbial communities. The results showed that the removal, cycling, and lateral transport of Mn were governed by similar phases and processes in the three estuaries. Manganese X-ray absorption spectroscopy data of the SPM suggested that the removal of Mn was regulated by silicates (e.g., biotite), organically complexed Mn(II), and MnOx (dominated by groutite and phyllomanganates). While the fractional amounts of silicate-bound Mn(II) were overall low and constant throughout the estuaries, MnOx was strongly correlated with the Mn loadings of the SPM and thus the main vector for the removal of Mn in the central and outer parts of the estuaries, along with organically complexed Mn(II). Down estuary, both the fractional amounts and average Mn oxidation state of the MnOx phases increased with (i) the total Mn loads on the SPM samples and (ii) the relative abundances of several potential Mn-oxidizing bacteria (Flavobacterium, Caulobacter, Mycobacterium, and Pedobacter) in the surface waters. These features collectively suggested that the oxidation of Mn, probably mediated by the potential Mn-oxidizing microorganisms, became more extensive and complete towards the central and outer parts of the es-tuaries. At two sites in the central parts of one estuary, abundant phyllomanganates occurred in the surface sediments, but were converted to surface-sorbed Mn(II) phases at deeper layers (>3-4 cm). The occurrence of phyllomanganates may have suppressed the reduction of sulfate in the surface sediments, pushing down the methane sulfate transition zone that is typically shallow in estuarine sediments. At the outermost site in the estuary, deposited MnOx were reduced immediately at the water-sediment interface and converted most likely to Mn carbonate. The mobile Mn species produced by the Mn reduction processes (e.g., aqueous Mn(II) and ligand complexed Mn(III)) could partly diffuse into the overlying waters and, together with the estuarine Mn loads carried by the surface waters, transfer large amounts of reactive Mn into open coastal areas and subsequently contribute to Mn shuttling and inter-linked biogeochemical processes over the seafloor. Given the widespread occurrence of acid sulfate soils and other sulfidic geological materials on many coastal plains worldwide, the identified Mn attenuation and transport mechanisms are relevant for many estuaries globally.
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