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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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| 3. |
- Thompson, Paul M., et al.
(författare)
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The ENIGMA Consortium : large-scale collaborative analyses of neuroimaging and genetic data
- 2014
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Ingår i: BRAIN IMAGING BEHAV. - : Springer Science and Business Media LLC. - 1931-7557 .- 1931-7565. ; 8:2, s. 153-182
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Tidskriftsartikel (refereegranskat)abstract
- The Enhancing NeuroImaging Genetics through Meta-Analysis (ENIGMA) Consortium is a collaborative network of researchers working together on a range of large-scale studies that integrate data from 70 institutions worldwide. Organized into Working Groups that tackle questions in neuroscience, genetics, and medicine, ENIGMA studies have analyzed neuroimaging data from over 12,826 subjects. In addition, data from 12,171 individuals were provided by the CHARGE consortium for replication of findings, in a total of 24,997 subjects. By meta-analyzing results from many sites, ENIGMA has detected factors that affect the brain that no individual site could detect on its own, and that require larger numbers of subjects than any individual neuroimaging study has currently collected. ENIGMA's first project was a genome-wide association study identifying common variants in the genome associated with hippocampal volume or intracranial volume. Continuing work is exploring genetic associations with subcortical volumes (ENIGMA2) and white matter microstructure (ENIGMA-DTI). Working groups also focus on understanding how schizophrenia, bipolar illness, major depression and attention deficit/hyperactivity disorder (ADHD) affect the brain. We review the current progress of the ENIGMA Consortium, along with challenges and unexpected discoveries made on the way.
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| 4. |
- Reitzel, Kasper, et al.
(författare)
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Diagenesis of settling seston : identity and transformations of organic phosphorus
- 2012
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Ingår i: Journal of Environmental Monitoring. - : Royal Society of Chemistry (RSC). - 1464-0325 .- 1464-0333. ; 14:3, s. 1098-1106
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Tidskriftsartikel (refereegranskat)abstract
- Solution (31)phosphorus NMR spectroscopy and sequential fractionation were used to follow diagenetic changes in phosphorus forms during decomposition of settling seston in Lake Nordborg, a shallow eutrophic lake in Denmark. In a decomposition experiment, seston released >60% of their total phosphorus during similar to 50 days incubation, although seston collected during summer contained more phosphorus and released it over a longer period compared to seston collected during spring. Seston decomposition increased concentrations of potentially bioavailable polyphosphate and phosphodiesters, but also promoted the formation of refractory phosphorus forms that might be buried permanently in the sediment. Combining these results with in situ measurements of phosphorus concentrations in lake water and sediment traps revealed that the release from settling seston plays only a minor role in the accumulation of phosphorus in the hypolimnion of Lake Nordborg.
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| 5. |
- Vestergren, Johan, 1968-
(författare)
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Analysis and speciation of organic phosphorus in environmental matrices : Development of methods to improve 31P NMR analysis
- 2014
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Phosphorus (P) is an essential element for life on our planet. It is central in numerous biochemical processes in terrestrial and aqueous ecosystems including food production; and it is the primary growth-limiting nutrient in some of the world’s biomes. The main source of P for use as agricultural fertilizer is mining of non-renewable mineral phosphate. In terrestrial ecosystems the main source is soil P, where the largest fraction is organic P, composed of many species with widely differing properties. This fraction controls the utilization of P by plants and microorganisms and influences ecosystem development and productivity. However, there is only scarce knowledge about the molecular composition of the organic P pool, about the processes controlling its bioavailability, and about its changes as soils develop. Therefore, the aim of this thesis was to develop robust solution- and solid-state 31P nuclear magnetic resonance spectroscopy (NMR) methods to provide molecular information about speciation of the organic P pool, and to study its dynamics in boreal and tropical soils. By studying humus soils of a groundwater recharge/discharge productivity gradient in a Fennoscandian boreal forest by solution- and solid-state NMR, it was found that P speciation changed with productivity. In particular, the level of orthophosphate diesters decreased with increasing productivity while mono-esters such as inositol phosphates increased. Because the use of solution NMR on conventional NaOH/EDTA extracts of soils was limited due to severe line broadening caused by the presence of paramagnetic metal ions, a new extraction method was developed and validated. Based on the removal of these paramagnetic impurities by sulfide precipitation, a dramatic decrease in NMR linewidths was obtained, allowing for the first time to apply modern multi-dimensional solution NMR techniques to soil extracts. Identification of individual soil P-species, and tracking changes in the organic P pools during soil development provided information for connecting P-speciation to bioavailability and ecosystem properties. Using this NMR approach we studied the transformation of organic P in humus soils along a chronosequence (7800 years) in Northern Sweden. While total P varied little, the composition of the soil P pool changed particularly among young sites, where also the largest shift in the composition of the plant community and of soil microorganisms was observed. Very old soils, such as found Africa, are thought to strongly adsorb P, limiting plant productivity. I used NMR to study the effect of scattered agroforestry trees on P speciation in two semi-arid tropical woodlands with different soil mineralogy (Burkina Faso). While the total P concentration was low, under the tree canopies higher amounts of P and higher diversity of P-species were found, presumably reflecting higher microbial activity.
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