Comparative genomics of Salmonella enterica serovars Derby and Mbandaka, two prevalent serovars associated with different livestock species in the UK

Background Despite the frequent isolation of Salmonella enterica sub. enterica serovars Derby and Mbandaka from livestock in the UK and USA little is known about the biological processes maintaining their prevalence. Statistics for Salmonella isolations from livestock production in the UK show that S. Derby is most commonly associated with pigs and turkeys and S. Mbandaka with cattle and chickens. Here we compare the first sequenced genomes of S. Derby and S. Mbandaka as a basis for further analysis of the potential host adaptations that contribute to their distinct host species distributions. Results Comparative functional genomics using the RAST annotation system showed that predominantly mechanisms that relate to metabolite utilisation, in vivo and ex vivo persistence and pathogenesis distinguish S. Derby from S. Mbandaka. Alignment of the genome nucleotide sequences of S. Derby D1 and D2 and S. Mbandaka M1 and M2 with Salmonella pathogenicity islands (SPI) identified unique complements of genes associated with host adaptation. We also describe a new genomic island with a putative role in pathogenesis, SPI-23. SPI-23 is present in several S. enterica serovars, including S. Agona, S. Dublin and S. Gallinarum, it is absent in its entirety from S. Mbandaka. Conclusions We discovered a new 37 Kb genomic island, SPI-23, in the chromosome sequence of S. Derby, encoding 42 ORFS, ten of which are putative TTSS effector proteins. We infer from full-genome synonymous SNP analysis that these two serovars diverged, between 182kya and 625kya coinciding with the divergence of domestic pigs. The differences between the genomes of these serovars suggest they have been exposed to different stresses including, phage, transposons and prolonged externalisation. The two serovars possess distinct complements of metabolic genes; many of which cluster into pathways for catabolism of carbon sources

The Sex and Race Specific Relationship between Anthropometry and Body Fat Composition Determined from Computed Tomography: Evidence from the Multi-Ethnic Study of Atherosclerosis.

BackgroundFew studies have investigated the relationship of anthropometric measurements with computed tomography (CT) body fat composition, and even fewer determined if these relationships differ by sex and race.MethodsCT scans from 1,851 participants in the population based Multi-Ethnic Study of Atherosclerosis were assessed for visceral and subcutaneous fat areas by semi-automated segmentation of body compartments. Regression models were used to investigate relationships for anthropometry with visceral and subcutaneous fat separately by sex and race/ethnicity.ResultsParticipants were 50% female, 41% Caucasian, 13% Asian, 21% African American, and 25% Hispanic. For visceral fat, the positive relationship with weight (p = 0.028), waist circumference (p<0.001), waist to hip ratio (p<0.001), and waist to height ratio (p = 0.05) differed by sex, with a steeper slope for men. That is, across the range of these anthropometric measures the rise in visceral fat is faster for men than for women. Additionally, there were differences by race/ethnicity in the relationship with height (p<0.001), weight (p<0.001), waist circumference (p<0.001), hip circumference (p = 0.006), and waist to hip ratio (p = 0.001) with the Hispanic group having shallower slopes. For subcutaneous fat, interaction by sex was found for all anthropometric indices at p<0.05, but not for race/ethnicity.ConclusionThe relationship between anthropometry and underlying adiposity differs by sex and race/ethnicity. When anthropometry is used as a proxy for visceral fat in research, sex-specific models should be used

Escherichia coli isolates from extraintestinal organs of livestock animals harbour diverse virulence genes and belong to multiple genetic lineages

Escherichia coli, the most common cause of bacteraemia in humans in the UK, can also cause serious diseases in animals. However the population structure, virulence and antimicrobial resistance genes of those from extraintestinal organs of livestock animals are poorly characterised. The aims of this study were to investigate the diversity of these isolates from livestock animals and to understand if there was any correlation between the virulence and antimicrobial resistance genes and the genetic backbone of the bacteria and if these isolates were similar to those isolated from humans. Here 39 E. coli isolates from liver (n=31), spleen (n=5) and blood (n=3) of cattle (n=34), sheep (n=3), chicken (n=1) and pig (n=1) were assigned to 19 serogroups with O8 being the most common (n=7), followed by O101, O20 (both n=3) and O153 (n=2). They belong to 29 multi-locus sequence types, 20 clonal complexes with ST23 (n=7), ST10 (n=6), ST117 and ST155 (both n=3) being most common and were distributed among phylogenetic group A (n=16), B1 (n=12), B2 (n=2) and D (n=9). The pattern of a subset of putative virulence genes was different in almost all isolates. No correlation between serogroups, animal hosts, MLST types, virulence and antimicrobial resistance genes was identified. The distributions of clonal complexes and virulence genes were similar to other extraintestinal or commensal E. coli from humans and other animals, suggesting a zoonotic potential. The diverse and various combinations of virulence genes implied that the infections were caused by different mechanisms and infection control will be challenging

Sedimentological characterization of Antarctic moraines using UAVs and Structure-from-Motion photogrammetry

In glacial environments particle-size analysis of moraines provides insights into clast origin, transport history, depositional mechanism and processes of reworking. Traditional methods for grain-size classification are labour-intensive, physically intrusive and are limited to patch-scale (1m2) observation. We develop emerging, high-resolution ground- and unmanned aerial vehicle-based ‘Structure-from-Motion’ (UAV-SfM) photogrammetry to recover grain-size information across an moraine surface in the Heritage Range, Antarctica. SfM data products were benchmarked against equivalent datasets acquired using terrestrial laser scanning, and were found to be accurate to within 1.7 and 50mm for patch- and site-scale modelling, respectively. Grain-size distributions were obtained through digital grain classification, or ‘photo-sieving’, of patch-scale SfM orthoimagery. Photo-sieved distributions were accurate to <2mm compared to control distributions derived from dry sieving. A relationship between patch-scale median grain size and the standard deviation of local surface elevations was applied to a site-scale UAV-SfM model to facilitate upscaling and the production of a spatially continuous map of the median grain size across a 0.3 km2 area of moraine. This highly automated workflow for site scale sedimentological characterization eliminates much of the subjectivity associated with traditional methods and forms a sound basis for subsequent glaciological process interpretation and analysis

Blue-ice moraines formation in the Heritage Range, West Antarctica: implications for ice sheet history and climate reconstruction

Blue ice is found in areas of Antarctica where katabatic winds, focussed by steep surface slopes or by topography around nunataks, cause enhanced surface ablation. This process draws up deeper, older ice to the ice sheet surface, often bringing with it englacial sediment. Prevailing theories for dynamically stable moraine surfaces in East Antarctica suggest that: (i) it is this material, once concentrated, that forms blue-ice moraines (BIM), (ii) that the moraine formation can be dated using cosmogenic isotope approaches, and that, (iii) since we expect an increase in exposure age moving away from the ice margin towards bedrock, dating across the moraine can be used to constrain ice-sheet history. To test this lateral accretion model for BIM formation we visited Patriot, Marble and Independence Hills in the southern Heritage Range, West Antarctica. Detailed field surveys of surface form, sediment and moraine dynamics were combined with geophysical surveys of the englacial structure of the moraines and cosmogenic nuclide analysis of surface clasts. Results suggest sediment is supplied mainly by basal entrainment, supplemented by debris-covered valley glaciers transferring material onto the ice sheet surface, direct deposition from rock-fall and slope processes from nunataks. We find that once sediment coalesces in BIM, significant reworking occurs through differential ablation, slope and periglacial processes. We bring these processes together in a conceptual model, concluding that many BIM in West Antarctica are dynamic and, whilst they persist through glacial cycles, they do not always neatly record ice sheet retreat patterns since linear distance from the ice margin does not always relate to increased clast exposure age. Understanding the dynamic processes involved in moraine formation is critical to the effective interpretation of the typically large scatter of cosmogenic nuclide exposure ages, opening a deep window into the million-year history of the West Antarctic Ice Sheet

Images of survival, stories of destruction: Nuclear war on British screens from 1945 to the early 1960s

This article discusses a range of depictions and discussions of nuclear war, which appeared on British screens in the first half of the Cold War, in order to understand the changing way nuclear weapons were viewed within British culture. Using such screened images to understand how nuclear war was constructed and represented within British culture, the article argues that the hydrogen bomb, not the atomic bomb, was the true harbinger of the nuclear revolution that transformed cultural understandings of warfare and destruction. Although the atomic bomb created a great deal of anxiety within British popular culture, representations of atomic attack elided atomic destruction with that experienced in 1939-45, emphasising the 'survivability' of atomic war. In the thermonuclear era, the Second World War could not undertake the same symbolic work. The image of the city-destroying bomb was an imaginative as well as technological step-change. Screened representations stressed that a thermonuclear war would literally end the world. As such, they preceded, and indeed provided the cultural climate for, the rise of the Campaign for Nuclear Disarmament (CND). The Campaign exploited and further popularised this idea of the apocalyptic nuclear war as a key aspect of its political and moral standpoint. The article concludes, however, that the cultural hegemony of this vision of nuclear war equally helped underpin notions of nuclear deterrence. The basic assumptions about the nature of nuclear war constructed and circulated on British screens therefore formed part of CND's 'cultural' victory but the article also explains why this did not translate into the political realm. © Edinburgh University Press

Comparing the interobserver reproducibility of different regions of interest on multi-parametric renal magnetic resonance imaging in healthy volunteers, patients with heart failure and renal transplant recipients

Objective: To assess interobserver reproducibility of different regions of interest (ROIs) on multi-parametric renal MRI using commercially available software. Materials and methods: Healthy volunteers (HV), patients with heart failure (HF) and renal transplant recipients (Tx) were recruited. Localiser scans, T1 mapping and pseudo-continuous arterial spin labelling (pCASL) were performed. HV and Tx also underwent diffusion-weighted imaging to allow calculation of apparent diffusion coefficient (ADC). For T1, pCASL and ADC, ROIs were drawn for whole kidney (WK), cortex (Cx), user-defined representative cortex (rep-Cx) and medulla. Intraclass correlation coefficient (ICC) and coefficient of variation (CoV) were assessed. Results: Forty participants were included (10 HV, 10 HF and 20 Tx). The ICC for renal volume was 0.97 and CoV 6.5%. For T1 and ADC, WK, Cx, and rep-Cx were highly reproducible with ICC ≥ 0.76 and CoV &lt; 5%. However, cortical pCASL results were more variable (ICC &gt; 0.86, but CoV up to 14.2%). While reproducible, WK values were derived from a wide spread of data (ROI standard deviation 17% to 55% of the mean value for ADC and pCASL, respectively). Renal volume differed between groups (p &lt; 0.001), while mean cortical T1 values were greater in Tx compared to HV (p = 0.009) and HF (p = 0.02). Medullary T1 values were also higher in Tx than HV (p = 0.03), while medullary pCASL values were significantly lower in Tx compared to HV and HF (p = 0.03 for both). Discussion: Kidney volume calculated by manually contouring a localiser scan was highly reproducible between observers and detected significant differences across patient groups. For T1, pCASL and ADC, Cx and rep-Cx ROIs are generally reproducible with advantages over WK values

Corrigendum to “The million-year evolution of the glacial trimline in the southernmost Ellsworth Mountains, Antarctica” [Earth and Planetary Science Letters 469 (2017) 42–52]

No abstract available