Refine
Year of publication
Language
- English (62)
Has Fulltext
- yes (62)
Is part of the Bibliography
- no (62)
Keywords
- CheF (1)
- CheY (1)
- Data sharing (1)
- Di-hadron correlations (1)
- Interference fragmentation function (1)
- Neolithic (1)
- Transversity (1)
- alleles (1)
- archaellum (1)
- autism spectrum disorder (1)
- autistic disorder (1)
- axions (1)
- chemotaxis (1)
- copy number polymorphism (1)
- dark matter experiments (1)
- distributive justice (1)
- domestication (1)
- evolution (1)
- gene flow (1)
- genes (1)
- genetics (1)
- genome (1)
- genotype (1)
- genotype determination (1)
- global change (1)
- habitat destruction (1)
- improvement (1)
- land use (1)
- natural resources (1)
- phenotype (1)
- protein evolution (1)
- response regulator (1)
- signal transduction (1)
- single nucleotide polymorphism (1)
- solar physics (1)
- territorial rights (1)
- value (1)
- wellbeing (1)
- white and brown dwarfs (1)
Archaea are motile by the rotation of the archaellum. The archaellum switches between clockwise and counterclockwise rotation, and movement along a chemical gradient is possible by modulation of the switching frequency. This modulation involves the response regulator CheY and the archaellum adaptor protein CheF. In this study, two new crystal forms and protein structures of CheY are reported. In both crystal forms, CheY is arranged in a domain-swapped conformation. CheF, the protein bridging the chemotaxis signal transduction system and the motility apparatus, was recombinantly expressed, purified and subjected to X-ray data collection.
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 – www.predicts.org.uk). We make site-level summary data available alongside this article. The full database will be publicly available in 2015.
Emissions of halogenated very short-lived substances (VSLS) are poorly constrained. However, their inclusion in global models is required to simulate a realistic inorganic bromine (Bry) loading in both the troposphere, where bromine chemistry perturbs global oxidizing capacity, and in the stratosphere, where it is a major sink for ozone (O3). We have performed simulations using a 3-D chemical transport model (CTM) including three top-down and a single bottom-up derived emission inventory of the major brominated VSLS bromoform (CHBr3) and dibromomethane (CH2Br2). We perform the first concerted evaluation of these inventories, comparing both the magnitude and spatial distribution of emissions. For a quantitative evaluation of each inventory, model output is compared with independent long-term observations at National Oceanic and Atmospheric Administration (NOAA) ground-based stations and with aircraft observations made during the NSF HIAPER Pole-to-Pole Observations (HIPPO) project. For CHBr3, the mean absolute deviation between model and surface observation ranges from 0.22 (38%) to 0.78 (115%) parts per trillion (ppt) in the tropics, depending on emission inventory. For CH2Br2, the range is 0.17 (24%) to 1.25 (167%) ppt. We also use aircraft observations made during the 2011 "Stratospheric Ozone: Halogen Impacts in a Varying Atmosphere" (SHIVA) campaign, in the tropical West Pacific. Here, the performance of the various inventories also varies significantly, but overall the CTM is able to reproduce observed CHBr3 well in the free troposphere using an inventory based on observed sea-to-air fluxes. Finally, we identify the range of uncertainty associated with these VSLS emission inventories on stratospheric bromine loading due to VSLS (BryVSLS). Our simulations show BryVSLS ranges from ~ 4.0 to 8.0 ppt depending on the inventory. We report an optimised estimate at the lower end of this range (~ 4 ppt) based on combining the CHBr3 and CH2Br2 inventories which give best agreement with the compilation of observations in the tropics.
Emissions of halogenated very short-lived substances (VSLS) are poorly constrained. However, their inclusion in global models is required to simulate a realistic inorganic bromine (Bry) loading in both the troposphere, where bromine chemistry perturbs global oxidising capacity, and in the stratosphere, where it is a major sink for ozone (O3). We have performed simulations using a 3-D chemical transport model (CTM) including three top-down and a single bottom-up derived emission inventory of the major brominated VSLS bromoform (CHBr3) and dibromomethane (CH2Br2). We perform the first concerted evaluation of these inventories, comparing both the magnitude and spatial distribution of emissions. For a quantitative evaluation of each inventory, model output is compared with independent long-term observations at National Oceanic and Atmospheric Administration (NOAA) ground-based stations and with aircraft observations made during the NSF (National Science Foundation) HIAPER Pole-to-Pole Observations (HIPPO) project. For CHBr3, the mean absolute deviation between model and surface observation ranges from 0.22 (38%) to 0.78 (115%) parts per trillion (ppt) in the tropics, depending on emission inventory. For CH2Br2, the range is 0.17 (24%) to 1.25 (167%) ppt. We also use aircraft observations made during the 2011 Stratospheric Ozone: Halogen Impacts in a Varying Atmosphere (SHIVA) campaign, in the tropical western Pacific. Here, the performance of the various inventories also varies significantly, but overall the CTM is able to reproduce observed CHBr3 well in the free troposphere using an inventory based on observed sea-to-air fluxes. Finally, we identify the range of uncertainty associated with these VSLS emission inventories on stratospheric bromine loading due to VSLS (BryVSLS). Our simulations show BryVSLS ranges from ~4.0 to 8.0 ppt depending on the inventory. We report an optimised estimate at the lower end of this range (~4 ppt) based on combining the CHBr3 and CH2Br2 inventories which give best agreement with the compilation of observations in the tropics.
The first concerted multi-model intercomparison of halogenated very short-lived substances (VSLS) has been performed, within the framework of the ongoing Atmospheric Tracer Transport Model Intercomparison Project (TransCom). Eleven global models or model variants participated (nine chemical transport models and two chemistry–climate models) by simulating the major natural bromine VSLS, bromoform (CHBr3) and dibromomethane (CH2Br2), over a 20-year period (1993–2012). Except for three model simulations, all others were driven offline by (or nudged to) reanalysed meteorology. The overarching goal of TransCom-VSLS was to provide a reconciled model estimate of the stratospheric source gas injection (SGI) of bromine from these gases, to constrain the current measurement-derived range, and to investigate inter-model differences due to emissions and transport processes. Models ran with standardised idealised chemistry, to isolate differences due to transport, and we investigated the sensitivity of results to a range of VSLS emission inventories. Models were tested in their ability to reproduce the observed seasonal and spatial distribution of VSLS at the surface, using measurements from NOAA's long-term global monitoring network, and in the tropical troposphere, using recent aircraft measurements – including high-altitude observations from the NASA Global Hawk platform.
The models generally capture the observed seasonal cycle of surface CHBr3 and CH2Br2 well, with a strong model–measurement correlation (r ≥ 0.7) at most sites. In a given model, the absolute model–measurement agreement at the surface is highly sensitive to the choice of emissions. Large inter-model differences are apparent when using the same emission inventory, highlighting the challenges faced in evaluating such inventories at the global scale. Across the ensemble, most consistency is found within the tropics where most of the models (8 out of 11) achieve best agreement to surface CHBr3 observations using the lowest of the three CHBr3 emission inventories tested (similarly, 8 out of 11 models for CH2Br2). In general, the models reproduce observations of CHBr3 and CH2Br2 obtained in the tropical tropopause layer (TTL) at various locations throughout the Pacific well. Zonal variability in VSLS loading in the TTL is generally consistent among models, with CHBr3 (and to a lesser extent CH2Br2) most elevated over the tropical western Pacific during boreal winter. The models also indicate the Asian monsoon during boreal summer to be an important pathway for VSLS reaching the stratosphere, though the strength of this signal varies considerably among models.
We derive an ensemble climatological mean estimate of the stratospheric bromine SGI from CHBr3 and CH2Br2 of 2.0 (1.2–2.5) ppt, ∼ 57 % larger than the best estimate from the most recent World Meteorological Organization (WMO) Ozone Assessment Report. We find no evidence for a long-term, transport-driven trend in the stratospheric SGI of bromine over the simulation period. The transport-driven interannual variability in the annual mean bromine SGI is of the order of ±5 %, with SGI exhibiting a strong positive correlation with the El Niño–Southern Oscillation (ENSO) in the eastern Pacific. Overall, our results do not show systematic differences between models specific to the choice of reanalysis meteorology, rather clear differences are seen related to differences in the implementation of transport processes in the models.
The first concerted multi-model intercomparison of halogenated very short-lived substances (VSLS) has been performed, within the framework of the ongoing Atmospheric Tracer Transport Model Intercomparison Project (TransCom). Eleven global models or model variants participated, simulating the major natural bromine VSLS, bromoform (CHBr3) and dibromomethane (CH2Br2), over a 20-year period (1993-2012). The overarching goal of TransCom-VSLS was to provide a reconciled model estimate of the stratospheric source gas injection (SGI) of bromine from these gases, to constrain the current measurement-derived range, and to investigate inter-model differences
due to emissions and transport processes. Models ran with standardised idealised chemistry, to isolate differences due to transport, and we investigated the sensitivity of results to a range of VSLS emission inventories. Models were tested in their ability to reproduce the observed seasonal and spatial distribution of VSLS at the surface, using measurements from NOAA’s long-term global monitoring network, and in the tropical troposphere, using recent aircraft measurements - including high altitude observations from the NASA Global Hawk platform.
The models generally capture the seasonal cycle of surface CHBr3 and CH2Br2 well, with a strong model measurement correlation (r ≥0.7) and a low sensitivity to the choice of emission inventory, at most sites. In a given model, the absolute model-measurement agreement is highly sensitive to the choice of emissions and inter-model differences are also apparent, even when using the same inventory, highlighting the challenges faced in evaluating such inventories at the global scale. Across the ensemble, most consistency is found within the tropics where most of the models (8 out of 11) achieve optimal agreement to surface CHBr3 observations using the lowest of the three CHBr3 emission inventories tested (similarly, 8 out of 11 models for CH2Br2). In general, the models are able to reproduce well observations of CHBr3 and CH2Br2 obtained in the tropical tropopause layer (TTL) at various locations throughout the Pacific. Zonal variability in VSLS loading in the TTL is generally consistent among models, with CHBr3 (and to a lesser extent CH2Br2) most elevated over the tropical West Pacific during boreal winter. The models also indicate the Asian Monsoon during boreal summer to be an important pathway for VSLS reaching the stratosphere, though the strength of this signal varies considerably among models.
We derive an ensemble climatological mean estimate of the stratospheric bromine SGI from CHBr3 and CH2Br2 of 2.0 (1.2-2.5) ppt, ∼57% larger than the best estimate from the most re- cent World Meteorological Organization (WMO) Ozone Assessment Report. We find no evidence for a long-term, transport-driven trend in the stratospheric SGI of bromine over the simulation period. However, transport-driven inter-annual variability in the annual mean bromine SGI is of the order of a ±5%, with SGI exhibiting a strong positive correlation with ENSO in the East Pacific
Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local European wild boars, although it is also possible that European wild boars were domesticated independently without any genetic contribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process.
The E4 allele of the ApoE gene has consistently been shown to be related to an increased risk of Alzheimer's disease (AD). The E4 allele is also associated with functional and structural grey matter (GM) changes in healthy young, middle-aged and older subjects. Here, we assess volumes of deep grey matter structures of 22 healthy younger ApoE4 carriers and 22 non-carriers (20–38 years). Volumes of the nucleus accumbens, amygdala, caudate nucleus, hippocampus, pallidum, putamen, thalamus and brain stem were calculated by FMRIB's Integrated Registration and Segmentation Tool (FIRST) algorithm. A significant drop in volume was found in the right hippocampus of ApoE4 carriers (ApoE4+) relative to non-carriers (ApoE4−), while there was a borderline significant decrease in the volume of the left hippocampus of ApoE4 carriers. The volumes of no other structures were found to be significantly affected by genotype. Atrophy has been found to be a sensitive marker of neurodegenerative changes, and our results show that within a healthy young population, the presence of the ApoE4+ carrier gene leads to volume reduction in a structure that is vitally important for memory formation. Our results suggest that the hippocampus may be particularly vulnerable to further degeneration in ApoE4 carriers as they enter middle and old age. Although volume reductions were noted bilaterally in the hippocampus, atrophy was more pronounced in the right hippocampus. This finding relates to previous work which has noted a compensatory increase in right hemisphere activity in ApoE4 carriers in response to preclinical declines in memory function. Possession of the ApoE4 allele may lead to greater predilection for right hemisphere atrophy even in healthy young subjects in their twenties.
The apolipoprotein E4 (ApoE4) is an established risk factor for Alzheimer's disease (AD). Previous work has shown that this allele is associated with functional (fMRI) changes as well structural grey matter (GM) changes in healthy young, middle-aged and older subjects. Here, we assess the diffusion characteristics and the white matter (WM) tracts of healthy young (20-38 years) ApoE4 carriers and non-carriers. No significant differences in diffusion indices were found between young carriers (ApoE4+) and non-carriers (ApoE4-). There were also no significant differences between the groups in terms of normalised GM or WM volume. A feature selection algorithm (ReliefF) was used to select the most salient voxels from the diffusion data for subsequent classification with support vector machines (SVMs). SVMs were capable of classifying ApoE4 carrier and non-carrier groups with an extremely high level of accuracy. The top 500 voxels selected by ReliefF were then used as seeds for tractography which identified a WM network that included regions of the parietal lobe, the cingulum bundle and the dorsolateral frontal lobe. There was a non-significant decrease in volume of this WM network in the ApoE4 carrier group. Our results indicate that there are subtle WM differences between healthy young ApoE4 carriers and non-carriers and that the WM network identified may be particularly vulnerable to further degeneration in ApoE4 carriers as they enter middle and old age.
Autism spectrum disorder (ASD) is a highly heritable disorder of complex and heterogeneous aetiology. It is primarily characterized by altered cognitive ability including impaired language and communication skills and fundamental deficits in social reciprocity. Despite some notable successes in neuropsychiatric genetics, overall, the high heritability of ASD (~90%) remains poorly explained by common genetic risk variants. However, recent studies suggest that rare genomic variation, in particular copy number variation, may account for a significant proportion of the genetic basis of ASD. We present a large scale analysis to identify candidate genes which may contain low-frequency recessive variation contributing to ASD while taking into account the potential contribution of population differences to the genetic heterogeneity of ASD. Our strategy, homozygous haplotype (HH) mapping, aims to detect homozygous segments of identical haplotype structure that are shared at a higher frequency amongst ASD patients compared to parental controls. The analysis was performed on 1,402 Autism Genome Project trios genotyped for 1 million single nucleotide polymorphisms (SNPs). We identified 25 known and 1,218 novel ASD candidate genes in the discovery analysis including CADM2, ABHD14A, CHRFAM7A, GRIK2, GRM3, EPHA3, FGF10, KCND2, PDZK1, IMMP2L and FOXP2. Furthermore, 10 of the previously reported ASD genes and 300 of the novel candidates identified in the discovery analysis were replicated in an independent sample of 1,182 trios. Our results demonstrate that regions of HH are significantly enriched for previously reported ASD candidate genes and the observed association is independent of gene size (odds ratio 2.10). Our findings highlight the applicability of HH mapping in complex disorders such as ASD and offer an alternative approach to the analysis of genome-wide association data.