| 1. |
- 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. |
- Kyrpides, Nikos C, et al.
(författare)
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Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains.
- 2014
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Ingår i: PLoS biology. - : Public Library of Science (PLoS). - 1545-7885. ; 12:8
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Tidskriftsartikel (refereegranskat)abstract
- Microbes hold the key to life. They hold the secrets to our past (as the descendants of the earliest forms of life) and the prospects for our future (as we mine their genes for solutions to some of the planet's most pressing problems, from global warming to antibiotic resistance). However, the piecemeal approach that has defined efforts to study microbial genetic diversity for over 20 years and in over 30,000 genome projects risks squandering that promise. These efforts have covered less than 20% of the diversity of the cultured archaeal and bacterial species, which represent just 15% of the overall known prokaryotic diversity. Here we call for the funding of a systematic effort to produce a comprehensive genomic catalog of all cultured Bacteria and Archaea by sequencing, where available, the type strain of each species with a validly published name (currently∼11,000). This effort will provide an unprecedented level of coverage of our planet's genetic diversity, allow for the large-scale discovery of novel genes and functions, and lead to an improved understanding of microbial evolution and function in the environment.
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| 3. |
- Meyer-Jacob, Carsten, 1984-, et al.
(författare)
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Re-browning of Sudbury (Ontario, Canada) lakes now approaches pre-acid deposition lake-water dissolved organic carbon levels
- 2020
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Ingår i: Science of the Total Environment. - : Elsevier. - 0048-9697 .- 1879-1026. ; 725
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Tidskriftsartikel (refereegranskat)abstract
- Since the implementation of large-scale lake monitoring in the similar to 1980s, water color and dissolved organic carbon (DOC) concentrations have increased in many northern lakes (i.e., lake browning), impacting the functioning of aquatic ecosystems. In regions that formerly experienced high levels of acid deposition, this browning trend has been largely attributed to the recovery from the impacts of past acid deposition. However, the extent to which DOC levels have now returned to naturally higher, pre-industrial conditions is still poorly understood. In this study, we assessed whether DOC levels are still influenced by acid deposition in lakes near Sudbury, Ontario, a region that has been heavily affected by sulfur dioxide emissions from local metal smelting during the 20th century. We analyzed water chemistry monitoring data (1981-2018), together with comparisons between modern and pre-industrial DOC levels inferred from sediment spectroscopy, for 51 acid-sensitive and 24 buffered reference lakes across the Sudbury landscape. Since 1981, DOC concentrations doubled in acid-sensitive lakes, with a mean increase of +1.6 mg/L, whereas in more buffered reference lakes, mean DOC levels increased by only 0.8 mg/L. Similarly, sediment-inferred DOC trends indicate that current DOC levels are, on average, similar to 22% below pre-industrial levels in acid sensitive systems compared to only similar to 10% in buffered lakes. Weakening correlations between DOC and acidification-related water chemistry variables (e.g., pH, alkalinity, metals) further indicate a diminishing influence of acid deposition on DOC in Sudbury lakes. These results highlight the strong impact that acid deposition has historically had on lake-water DOC dynamics in this region, but also suggest that DOC levels are approaching natural baseline levels in less acid-sensitive lakes, and that other drivers, such as changes in climate or vegetation cover, are now becoming the dominant controls on changes in DOC concentrations.
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| 4. |
- Anderson, Cynthia M., et al.
(författare)
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Permanent Genetic Resources added to Molecular Ecology Resources Database 1 December 2009-31 January 2010
- 2010
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Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 10:3, s. 576-579
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Tidskriftsartikel (refereegranskat)abstract
- This article documents the addition of 220 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Allanblackia floribunda, Amblyraja radiata, Bactrocera cucurbitae, Brachycaudus helichrysi, Calopogonium mucunoides, Dissodactylus primitivus, Elodea canadensis, Ephydatia fluviatilis, Galapaganus howdenae howdenae, Hoplostethus atlanticus, Ischnura elegans, Larimichthys polyactis, Opheodrys vernalis, Pelteobagrus fulvidraco, Phragmidium violaceum, Pistacia vera, and Thunnus thynnus. These loci were cross-tested on the following species: Allanblackia gabonensis, Allanblackia stanerana, Neoceratitis cyanescens, Dacus ciliatus, Dacus demmerezi, Bactrocera zonata, Ceratitis capitata, Ceratitis rosa, Ceratits catoirii, Dacus punctatifrons, Ephydatia mulleri, Spongilla lacustris, Geodia cydonium, Axinella sp., Ischnura graellsii, Ischnura ramburii, Ischnura pumilio, Pistacia integerrima and Pistacia terebinthus.
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| 5. |
- Bowers, Robert M., et al.
(författare)
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Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
- 2017
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Ingår i: Nature Biotechnology. - : NATURE PUBLISHING GROUP. - 1087-0156 .- 1546-1696. ; 35:8, s. 725-731
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Tidskriftsartikel (refereegranskat)abstract
- We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled Genome (MIMAG), including, but not limited to, assembly quality, and estimates of genome completeness and contamination. These standards can be used in combination with other GSC checklists, including the Minimum Information about a Genome Sequence (MIGS), Minimum Information about a Metagenomic Sequence (MIMS), and Minimum Information about a Marker Gene Sequence (MIMARKS). Community-wide adoption of MISAG and MIMAG will facilitate more robust comparative genomic analyses of bacterial and archaeal diversity.
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| 6. |
- Przewoski, Barbara, et al.
(författare)
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Spin Exchange in Polarized Deuterium
- 2003
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Ingår i: Physical Review A: covering atomic, molecular, and optical physics and quantum information. - : American Physical Society. - 2469-9926 .- 2469-9934. ; 68:042705, s. 4-
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Tidskriftsartikel (refereegranskat)abstract
- We have measured the vector and tensor polarization of an atomic deuterium targte as a function of the target density. Th epolarized deuterium was produced in an atomic beam source and injected into a storage cell. For this experiment, the atomic beam sou
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| 7. |
- Meyer-Jacob, Carsten, 1984-, et al.
(författare)
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The browning and re-browning of lakes : Divergent lake-water organic carbon trends linked to acid deposition and climate change
- 2019
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Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Dissolved organic carbon (DOC) concentrations and water colour are increasing in many inland waters across northern Europe and northeastern North America. This inland-water "browning" has profound physical, chemical and biological repercussions for aquatic ecosystems affecting water quality, biological community structures and aquatic productivity. Potential drivers of this "browning" trend are complex and include reductions in atmospheric acid deposition, changes in land use/cover, increased nitrogen deposition and climate change. However, because of the overlapping impacts of these stressors, their relative contributions to DOC dynamics remain unclear, and without appropriate long-term monitoring data, it has not been possible to determine whether the ongoing "browning" is unprecedented or simply a "re-browning" to pre-industrial DOC levels. Here, we demonstrate the long-term impacts of acid deposition and climate change on lake-water DOC concentrations in low and high acid-deposition areas using infrared spectroscopic techniques on similar to 200-year-long lake-sediment records from central Canada. We show that acid deposition suppressed naturally higher DOC concentrations during the 20th century, but that a "re-browning" of lakes is now occurring with emissions reductions in formerly high deposition areas. In contrast, in low deposition areas, climate change is forcing lakes towards new ecological states, as lake-water DOC concentrations now often exceed pre-industrial levels.
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| 8. |
- Shumilova, Oleksandra, et al.
(författare)
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Simulating rewetting events in intermittent rivers and ephemeral streams : A global analysis of leached nutrients and organic matter
- 2019
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Ingår i: Global Change Biology. - : WILEY. - 1354-1013 .- 1365-2486. ; 25:5, s. 1591-1611
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Tidskriftsartikel (refereegranskat)abstract
- Climate change and human pressures are changing the global distribution and the extent of intermittent rivers and ephemeral streams (IRES), which comprise half of the global river network area. IRES are characterized by periods of flow cessation, during which channel substrates accumulate and undergo physico-chemical changes (preconditioning), and periods of flow resumption, when these substrates are rewetted and release pulses of dissolved nutrients and organic matter (OM). However, there are no estimates of the amounts and quality of leached substances, nor is there information on the underlying environmental constraints operating at the global scale. We experimentally simulated, under standard laboratory conditions, rewetting of leaves, riverbed sediments, and epilithic biofilms collected during the dry phase across 205 IRES from five major climate zones. We determined the amounts and qualitative characteristics of the leached nutrients and OM, and estimated their areal fluxes from riverbeds. In addition, we evaluated the variance in leachate characteristics in relation to selected environmental variables and substrate characteristics. We found that sediments, due to their large quantities within riverbeds, contribute most to the overall flux of dissolved substances during rewetting events (56%-98%), and that flux rates distinctly differ among climate zones. Dissolved organic carbon, phenolics, and nitrate contributed most to the areal fluxes. The largest amounts of leached substances were found in the continental climate zone, coinciding with the lowest potential bioavailability of the leached OM. The opposite pattern was found in the arid zone. Environmental variables expected to be modified under climate change (i.e. potential evapotranspiration, aridity, dry period duration, land use) were correlated with the amount of leached substances, with the strongest relationship found for sediments. These results show that the role of IRES should be accounted for in global biogeochemical cycles, especially because prevalence of IRES will increase due to increasing severity of drying events.
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| 9. |
- Wernet, Philippe, et al.
(författare)
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Mapping chemical bonding of reaction intermediates with femtosecond X-ray laser spectroscopy
- 2013
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Ingår i: XVIIIth International Conference on Ultrafast Phenomena. - : EDP Sciences. - 9782759809561 ; , s. 05025-
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- We determine the pathways in the photo-dissociation reactions of Fe(CO)5 both in the gas phase and in solution by mapping the valence electronic structure of the reaction intermediates with femtosecond X-ray laser spectroscopy.
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