| 1. |
- Wishart, David S., et al.
(författare)
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HMDB 5.0 : the Human Metabolome Database for 2022
- 2022
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 50:D1, s. D622-D631
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Tidskriftsartikel (refereegranskat)abstract
- The Human Metabolome Database or HMDB (https://hmdb.ca) has been providing comprehensive reference information about human metabolites and their associated biological, physiological and chemical properties since 2007. Over the past 15 years, the HMDB has grown and evolved significantly to meet the needs of the metabolomics community and respond to continuing changes in internet and computing technology. This year's update, HMDB 5.0, brings a number of important improvements and upgrades to the database. These should make the HMDB more useful and more appealing to a larger cross-section of users. In particular, these improvements include: (i) a significant increase in the number of metabolite entries (from 114 100 to 217 920 compounds); (ii) enhancements to the quality and depth of metabolite descriptions; (iii) the addition of new structure, spectral and pathway visualization tools; (iv) the inclusion of many new and much more accurately predicted spectral data sets, including predicted NMR spectra, more accurately predicted MS spectra, predicted retention indices and predicted collision cross section data and (v) enhancements to the HMDB's search functions to facilitate better compound identification. Many other minor improvements and updates to the content, the interface, and general performance of the HMDB website have also been made. Overall, we believe these upgrades and updates should greatly enhance the HMDB's ease of use and its potential applications not only in human metabolomics but also in exposomics, lipidomics, nutritional science, biochemistry and clinical chemistry.
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| 2. |
- Behle, Anna, et al.
(författare)
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Manipulation of topoisomerase expression inhibits cell division but not growth and reveals a distinctive promoter structure in Synechocystis
- 2022
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 50:22, s. 12790-12808
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Tidskriftsartikel (refereegranskat)abstract
- In cyanobacteria DNA supercoiling varies over the diurnal cycle and is integrated with temporal programs of transcription and replication. We manipulated DNA supercoiling in Synechocystis sp. PCC 6803 by CRISPRi-based knockdown of gyrase subunits and overexpression of topoisomerase I (TopoI). Cell division was blocked but cell growth continued in all strains. The small endogenous plasmids were only transiently relaxed, then became strongly supercoiled in the TopoI overexpression strain. Transcript abundances showed a pronounced 5'/3' gradient along transcription units, incl. the rRNA genes, in the gyrase knockdown strains. These observations are consistent with the basic tenets of the homeostasis and twin-domain models of supercoiling in bacteria. TopoI induction initially led to downregulation of G+C-rich and upregulation of A+T-rich genes. The transcriptional response quickly bifurcated into six groups which overlap with diurnally co-expressed gene groups. Each group shows distinct deviations from a common core promoter structure, where helically phased A-tracts are in phase with the transcription start site. Together, our data show that major co-expression groups (regulons) in Synechocystis all respond differentially to DNA supercoiling, and suggest to re-evaluate the long-standing question of the role of A-tracts in bacterial promoters.
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| 3. |
- Blöschl, Günter, et al.
(författare)
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Current European flood-rich period exceptional compared with past 500 years
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 583:7817, s. 560-566
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Tidskriftsartikel (refereegranskat)abstract
- There are concerns that recent climate change is altering the frequency and magnitude of river floods in an unprecedented way(1). Historical studies have identified flood-rich periods in the past half millennium in various regions of Europe(2). However, because of the low temporal resolution of existing datasets and the relatively low number of series, it has remained unclear whether Europe is currently in a flood-rich period from a long-term perspective. Here we analyse how recent decades compare with the flood history of Europe, using a new database composed of more than 100 high-resolution (sub-annual) historical flood series based on documentary evidence covering all major regions of Europe. We show that the past three decades were among the most flood-rich periods in Europe in the past 500 years, and that this period differs from other flood-rich periods in terms of its extent, air temperatures and flood seasonality. We identified nine flood-rich periods and associated regions. Among the periods richest in floods are 1560-1580 (western and central Europe), 1760-1800 (most of Europe), 1840-1870 (western and southern Europe) and 1990-2016 (western and central Europe). In most parts of Europe, previous flood-rich periods occurred during cooler-than-usual phases, but the current flood-rich period has been much warmer. Flood seasonality is also more pronounced in the recent period. For example, during previous flood and interflood periods, 41 per cent and 42 per cent of central European floods occurred in summer, respectively, compared with 55 per cent of floods in the recent period. The exceptional nature of the present-day flood-rich period calls for process-based tools for flood-risk assessment that capture the physical mechanisms involved, and management strategies that can incorporate the recent changes in risk. Analysis of thousands of historical documents recording floods in Europe shows that flooding characteristics in recent decades are unlike those of previous centuries.
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| 4. |
- Breinl, Korbinian, et al.
(författare)
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Extreme dry and wet spells face changes in their duration and timing
- 2020
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Ingår i: Environmental Research Letters. - : IOP Publishing. - 1748-9326. ; 15:7
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Tidskriftsartikel (refereegranskat)abstract
- Dry spells are sequences of days without precipitation. They can have negative implications for societies, including water security and agriculture. For example, changes in their duration and within-year timing can pose a threat to food production and wildfire risk. Conversely, wet spells are sequences of days with precipitation above a certain threshold, and changes in their duration and within-year timing can impact agriculture, flooding or the prevalence of water-related vector-borne diseases. Here we assess changes in the duration and within-year timing of extreme dry and wet spells over 60 years (1958-2017) using a consistent global land surface precipitation dataset of 5093 rain gauge locations. The dataset allowed for detailed spatial analyses of the United States, Europe and Australia. While many locations exhibit statistically significant changes in the duration of extreme dry and wet spells, the changes in the within-year timing are less often significant. Our results show consistencies with observations and projections from state-of-the-art climate and water resources research. In addition, we provide new insights regarding trends in the timing of extreme dry and wet spells, an aspect being equally important for possible future implications of extremes in a changing climate, which has not yet received the same level of attention and is characterized by larger uncertainty.
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| 5. |
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| 6. |
- Van Lun, Michiel, et al.
(författare)
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CO2 and O-2 Distribution in Rubisco Suggests the Small Subunit Functions as a CO2 Reservoir
- 2014
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 136:8, s. 3165-3171
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Tidskriftsartikel (refereegranskat)abstract
- Protein gas interactions are important in biology. The enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyzes two competing reactions involving CO2 and O-2 as substrates. Carboxylation of the common substrate ribulose-1,5-bisphosphate leads to photosynthetic carbon assimilation, while the oxygenation reaction competes with carboxylation and reduces photosynthetic productivity. The migration of the two gases in and around Rubisco was investigated using molecular dynamics simulations. The results indicate that at equal concentrations of the gases, Rubisco binds CO2 stronger than it does O-2. Amino acids with small hydrophobic side chains are the most proficient in attracting CO2, indicating a significant contribution of the hydrophobic effect in the interaction. On average, residues in the small subunit bind approximately twice as much CO2 as do residues in the large subunit. We did not detect any cavities that would provide a route to the active site for the gases. Instead, CO2 appears to be guided toward the active site through a CO2 binding region around the active site opening that extends to the closest neighboring small subunits. Taken together, these results suggest the small subunit may function as a "reservoir" for CO2 storage.
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| 7. |
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| 8. |
- Van Lun, Michiel, et al.
(författare)
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Subunit Interface Dynamics in Hexadecameric Rubisco
- 2011
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Ingår i: Journal of Molecular Biology. - : Elsevier BV. - 0022-2836 .- 1089-8638. ; 411:5, s. 1083-1098
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Tidskriftsartikel (refereegranskat)abstract
- Ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase (Rubisco) plays an important role in the global carbon cycle as a hub for biomass. Rubisco catalyzes not only the carboxylation of RuBP with carbon dioxide but also a competing oxygenation reaction of RuBP with a negative impact on photosynthetic yield. The functional active site is built from two large (L) subunits that form a dimer. The octameric core of four L(2) dimers is held at each end by a cluster of four small (S) subunits, forming a hexadecamer. Each large subunit contacts more than one S subunit. These interactions exploit the dynamic flexibility of Rubisco, which we address in this study. Here, we describe seven different types of interfaces of hexadecameric Rubisco. We have analyzed these interfaces with respect to the size of the interface area and the number of polar interactions, including salt bridges and hydrogen bonds in a variety of Rubisco enzymes from different organisms and different kingdoms of life, including the Rubisco-like proteins. We have also performed molecular dynamics simulations of Rubisco from Chlamydomonas reinhardtii and mutants thereof. From our computational analyses, we propose structural checkpoints of the S subunit to ensure the functionality and/or assembly of the Rubisco holoenzyme. These checkpoints appear to fine-tune the dynamics of the enzyme in a way that could influence enzyme performance.
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| 9. |
- Yim, Chi Ming, et al.
(författare)
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CO and O overlayers on Pd nanocrystals supported on TiO2(110)
- 2013
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Ingår i: Faraday Discussions. - : Royal Society of Chemistry (RSC). - 1364-5498 .- 1359-6640. ; 162, s. 191-200
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Tidskriftsartikel (refereegranskat)abstract
- We have prepared a model catalytic system by depositing Pd onto a TiO2(110) surface held at similar to 720 K. Scanning tunneling microscopy (STM) reveals well-defined Pd nanocrystals consisting of (111) top facets with {111} and {100} side facets. The Pd nanocrystals go down to about 10 nm in width and 1.3 nm in height. Top facets can be imaged with atomic resolution, indicating the absence of TiOx encapsulation. The model catalyst was probed by exposure to CO and O-2. By varying the CO exposure, different CO overlayers were formed on the (111) top facets, with coverages ranging from 0.33 to 0.75 of a monolayer. Near edge X-ray absorption fine structure (NEXAFS) measurements at 300 K reveal that at around 0.5 ML coverage, CO is oriented with the molecular axis more or less normal to TiO2(110). Dosing small amounts of O-2 separately on a Pd/TiO2(110) surface led to an overlayer of p(2 x 2)-O formed on the (111) top facet of the Pd nanocrystals at 190 K.
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