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- 2019
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Tidskriftsartikel (refereegranskat)
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| 2. |
- 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. |
- 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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| 4. |
- 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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| 5. |
- Jones, Benedict C, et al.
(författare)
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To which world regions does the valence-dominance model of social perception apply?
- 2021
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Ingår i: Nature Human Behaviour. - : Springer Science and Business Media LLC. - 2397-3374. ; 5:1, s. 159-169
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Tidskriftsartikel (refereegranskat)abstract
- Over the past 10 years, Oosterhof and Todorov's valence-dominance model has emerged as the most prominent account of how people evaluate faces on social dimensions. In this model, two dimensions (valence and dominance) underpin social judgements of faces. Because this model has primarily been developed and tested in Western regions, it is unclear whether these findings apply to other regions. We addressed this question by replicating Oosterhof and Todorov's methodology across 11 world regions, 41 countries and 11,570 participants. When we used Oosterhof and Todorov's original analysis strategy, the valence-dominance model generalized across regions. When we used an alternative methodology to allow for correlated dimensions, we observed much less generalization. Collectively, these results suggest that, while the valence-dominance model generalizes very well across regions when dimensions are forced to be orthogonal, regional differences are revealed when we use different extraction methods and correlate and rotate the dimension reduction solution. PROTOCOL REGISTRATION: The stage 1 protocol for this Registered Report was accepted in principle on 5 November 2018. The protocol, as accepted by the journal, can be found at https://doi.org/10.6084/m9.figshare.7611443.v1 .
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| 6. |
- Denler, Melissa C., et al.
(författare)
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Mn IV -Oxo complex of a bis(benzimidazolyl)-containing N5 ligand reveals different reactivity trends for Mn IV -oxo than Fe IV -oxo species
- 2019
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Ingår i: Dalton Transactions. - : Royal Society of Chemistry (RSC). - 1477-9226 .- 1477-9234. ; 48:15, s. 5007-5021
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Tidskriftsartikel (refereegranskat)abstract
- Using the pentadentate ligand (N-bis(1-methyl-2-benzimidazolyl)methyl-N-(bis-2-pyridylmethyl)amine, 2pyN2B), presenting two pyridyl and two (N-methyl)benzimidazolyl donor moieties in addition to a central tertiary amine, new Mn II and Mn IV -oxo complexes were generated and characterized. The [Mn IV (O)(2pyN2B)] 2+ complex showed spectroscopic signatures (i.e., electronic absorption band maxima and intensities, EPR signals, and Mn K-edge X-ray absorption edge and near-edge data) similar to those observed for other Mn IV -oxo complexes with neutral, pentadentate N 5 supporting ligands. The near-IR electronic absorption band maximum of [Mn IV (O)(2pyN2B)] 2+ , as well as DFT-computed metric parameters, are consistent with the equatorial (N-methyl)benzimidazolyl ligands being stronger donors to the Mn IV center than the pyridyl and quinolinyl ligands found in analogous Mn IV -oxo complexes. The hydrogen- and oxygen-atom transfer reactivities of [Mn IV (O)(2pyN2B)] 2+ were assessed through reactions with hydrocarbons and thioanisole, respectively. When compared with related Mn IV -oxo adducts, [Mn IV (O)(2pyN2B)] 2+ showed muted reactivity in hydrogen-atom transfer reactions with hydrocarbons. This result stands in contrast to observations for the analogous Fe IV -oxo complexes, where [Fe IV (O)(2pyN2B)] 2+ was found to be one of the more reactive members of its class.
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| 7. |
- Massie, Allyssa A., et al.
(författare)
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Equatorial Ligand Perturbations Influence the Reactivity of Manganese(IV)-Oxo Complexes
- 2017
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Ingår i: Angewandte Chemie (International edition). - : Wiley. - 1433-7851. ; 56:15, s. 4178-4182
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Tidskriftsartikel (refereegranskat)abstract
- Manganese(IV)-oxo complexes are often invoked as intermediates in Mn-catalyzed C-H bond activation reactions. While many synthetic MnIV-oxo species are mild oxidants, other members of this class can attack strong C-H bonds. The basis for these reactivity differences is not well understood. Here we describe a series of MnIV-oxo complexes with N5 pentadentate ligands that modulate the equatorial ligand field of the MnIV center, as assessed by electronic absorption, electron paramagnetic resonance, and Mn K-edge X-ray absorption methods. Kinetic experiments show dramatic rate variations in hydrogen-atom and oxygen-atom transfer reactions, with faster rates corresponding to weaker equatorial ligand fields. For these MnIV-oxo complexes, the rate enhancements are correlated with both 1)the energy of a low-lying 4E excited state, which has been postulated to be involved in a two-state reactivity model, and 2)the MnIII/IV reduction potentials.
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| 8. |
- Singh, Priya, et al.
(författare)
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Enhanced Understanding of Structure-Function Relationships for Oxomanganese(IV) Complexes
- 2023
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Ingår i: Inorganic Chemistry. - 0020-1669. ; 62:45, s. 18357-18374
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Tidskriftsartikel (refereegranskat)abstract
- A series of manganese(II) and oxomanganese(IV) complexes supported by neutral, pentadentate ligands with varied equatorial ligand-field strength (N3pyQ, N2py2I, and N4pyMe2) were synthesized and then characterized using structural and spectroscopic methods. On the basis of electronic absorption spectroscopy, the [MnIV(O)(N4pyMe2)]2+ complex has the weakest equatorial ligand field among a set of similar MnIV-oxo species. In contrast, [MnIV(O)(N2py2I)]2+ shows the strongest equatorial ligand-field strength for this same series. We examined the influence of these changes in electronic structure on the reactivity of the oxomanganese(IV) complexes using hydrocarbons and thioanisole as substrates. The [MnIV(O)(N3pyQ)]2+ complex, which contains one quinoline and three pyridine donors in the equatorial plane, ranks among the fastest MnIV-oxo complexes in C-H bond and thioanisole oxidation. While a weak equatorial ligand field has been associated with high reactivity, the [MnIV(O)(N4pyMe2)]2+ complex is only a modest oxidant. Buried volume plots suggest that steric factors dampen the reactivity of this complex. Trends in reactivity were examined using density functional theory (DFT)-computed bond dissociation free energies (BDFEs) of the MnIIIO-H and MnIV ≡ O bonds. We observe an excellent correlation between MnIV≡O BDFEs and rates of thioanisole oxidation, but more scatter is observed between hydrocarbon oxidation rates and the MnIIIO-H BDFEs.
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