Protein domains as units of genetic transfer

Genomes evolve as modules. In prokaryotes (and some eukaryotes), genetic material can be transferred between species and integrated into the genome via homologous or illegitimate recombination. There is little reason to imagine that the units of transfer correspond to entire genes; however, such units have not been rigorously characterized. We examined fragmentary genetic transfers in single-copy gene families from 144 prokaryotic genomes and found that breakpoints are located significantly closer to the boundaries of genomic regions that encode annotated structural domains of proteins than expected by chance, particularly when recombining sequences are more divergent. This correlation results from recombination events themselves and not from differential nucleotide substitution. We report the first systematic study relating genetic recombination to structural features at the protein level

Observed Reductions in Schistosoma mansoni Transmission from Large-Scale Administration of Praziquantel in Uganda: A Mathematical Modelling Study

To date schistosomiasis control programmes based on chemotherapy have largely aimed at controlling morbidity in treated individuals rather than at suppressing transmission. In this study, a mathematical modelling approach was used to estimate reductions in the rate of Schistosoma mansoni reinfection following annual mass drug administration (MDA) with praziquantel in Uganda over four years (2003-2006). In doing this we aim to elucidate the benefits of MDA in reducing community transmission.Age-structured models were fitted to a longitudinal cohort followed up across successive rounds of annual treatment for four years (Baseline: 2003, TREATMENT: 2004-2006; n = 1,764). Instead of modelling contamination, infection and immunity processes separately, these functions were combined in order to estimate a composite force of infection (FOI), i.e., the rate of parasite acquisition by hosts.MDA achieved substantial and statistically significant reductions in the FOI following one round of treatment in areas of low baseline infection intensity, and following two rounds in areas with high and medium intensities. In all areas, the FOI remained suppressed following a third round of treatment.This study represents one of the first attempts to monitor reductions in the FOI within a large-scale MDA schistosomiasis morbidity control programme in sub-Saharan Africa. The results indicate that the Schistosomiasis Control Initiative, as a model for other MDA programmes, is likely exerting a significant ancillary impact on reducing transmission within the community, and may provide health benefits to those who do not receive treatment. The results obtained will have implications for evaluating the cost-effectiveness of schistosomiasis control programmes and the design of monitoring and evaluation approaches in general

Uncertainty assessment in river flow projections for Ethiopia’s Upper Awash Basin using multiple GCMs and hydrological models

Uncertainty in climate change impacts on river discharge in the Upper Awash Basin, Ethiopia, is assessed using five MIKE SHE hydrological models, six CMIP5 general circulation models (GCMs) and two representative concentration pathways (RCP) scenarios for the period 2071–2100. Hydrological models vary in their spatial distribution and process representations of unsaturated and saturated zones. Very good performance is achieved for 1975–1999 (NSE: 0.65–0.8; r: 0.79–0.93). GCM-related uncertainty dominates variability in projections of high and mean discharges (mean: –34% to +55% for RCP4.5,–2% to +195% for RCP8.5). Although GCMs dominate uncertainty in projected low flows, inter-hydrological model uncertainty is considerable (RCP4.5: –60% to +228%, RCP8.5: –86% to +337%). Analysis of variance uncertainty attribution reveals that GCM-related uncertainty occupies, on average, 68% of total uncertainty for median and high flows and hydrological models no more than 1%. For low flows, hydrological model uncertainty occupies, on average, 18% of total uncertainty; GCM-related uncertainty remains substantial (average: 28%)

Risk-Averse Matchings over Uncertain Graph Databases

A large number of applications such as querying sensor networks, and analyzing protein-protein interaction (PPI) networks, rely on mining uncertain graph and hypergraph databases. In this work we study the following problem: given an uncertain, weighted (hyper)graph, how can we efficiently find a (hyper)matching with high expected reward, and low risk? This problem naturally arises in the context of several important applications, such as online dating, kidney exchanges, and team formation. We introduce a novel formulation for finding matchings with maximum expected reward and bounded risk under a general model of uncertain weighted (hyper)graphs that we introduce in this work. Our model generalizes probabilistic models used in prior work, and captures both continuous and discrete probability distributions, thus allowing to handle privacy related applications that inject appropriately distributed noise to (hyper)edge weights. Given that our optimization problem is NP-hard, we turn our attention to designing efficient approximation algorithms. For the case of uncertain weighted graphs, we provide a $\frac{1}{3}$-approximation algorithm, and a $\frac{1}{5}$-approximation algorithm with near optimal run time. For the case of uncertain weighted hypergraphs, we provide a $\Omega(\frac{1}{k})$-approximation algorithm, where $k$ is the rank of the hypergraph (i.e., any hyperedge includes at most $k$ nodes), that runs in almost (modulo log factors) linear time. We complement our theoretical results by testing our approximation algorithms on a wide variety of synthetic experiments, where we observe in a controlled setting interesting findings on the trade-off between reward, and risk. We also provide an application of our formulation for providing recommendations of teams that are likely to collaborate, and have high impact.Comment: 25 page

A girl with sternal malformation/vascular dysplasia association

Sternal malformation/vascular dysplasia association is a rare congenital dysmorphology, which has not yet been reported in Korea. Its typical clinical features include a sternal cleft covered with atrophic skin, a median abdominal raphe extending from the sternal defect to the umbilicus, and cutaneous craniofacial hemangiomata. We report a case of a full-term newborn who presented with no anomalies at birth, except for a skin defect over the sternum and a supraumbilical raphe. Multiple hemangiomas appeared subsequently on her chin and upper chest wall, and respiratory distress due to subglottic hemangioma developed during the first 2 months of life. Her symptoms were controlled with oral prednisolone administration. No respiratory distress have recurred during the 3-year follow-up period

Inhaled or Ingested, Which Is Worse, E-Vaping or High-Fat Diet?

Long term e-cigarette vaping induces inflammation, which is largely nicotine independent. High-fat diet (HFD) consumption is anoter cause of systemic low-grade inflammation. The likelihood of using e-cigarettes as a weight control strategy is concomitant with the increase in obesity. In Australia, only nicotine-free e-fluid is legal for sale. Therefore, this study aimed to investigate how nicotine-free e-cigarette vapour exposure affects inflammatory responses in mice with long term HFD consumption. Mice were fed a HFD for 16 weeks, while in the last 6 weeks, half of the chow and HFD groups were exposed to nicotine-free e-vapour, while the other half to ambient air. Serum, lung, liver and epididymal fat were collected to measure inflammatory markers. While both e-vapour exposure and HFD consumption independently increased serum IFN-γ, CX3CL1, IL-10, CCL20, CCL12, and CCL5 levels, the levels of IFN-γ, CX3CL1, and IL-10 were higher in mice exposed to e-vapour than HFD. The mRNA expression pattern in the epididymal fat mirrors that in the serum, suggesting the circulating inflammatory response to e-vapour is from the fat tissue. Of the upregulated cytokines in serum, none were found to change in the lungs. The anti-inflammatory cytokine IL-10 was increased by combining e-vapour and HFD in the liver. We conclude that short-term nicotine-free e-vapour is more potent than long term HFD consumption in causing systemic inflammation. Future studies will be needed to examine the long-term health impact of nicotine-free e-cigarettes.</jats:p

The scale of genetic differentiation in the Dunes Sagebrush-Lizard (Sceloporus arenicolus), an endemic habitat specialist

Abstract The Dunes Sagebrush-Lizard (Sceloporus arenicolus) is a North American species endemic to sandshinnery oak habitats of the Mescalero and Monahans sand dunes in eastern New Mexico and western Texas. This lizard is listed as Endangered in New Mexico and exhibits habitat specificity at several geographic scales. Dunes Sagebrush-Lizards are only found in topographically complex shinnery oak (Quercus havardii) dominated landscapes within their small geographic distribution and are not found in surrounding human-altered landscapes. Within suitable sand-shinnery oak habitat, individuals predominantly occupy non-vegetated sand dune blowouts and utilize blowouts with particular physical characteristics due to thermoregulatory, reproduction, and foraging requirements. Here, we examined historical and contemporary patterns of genetic differentiation with respect to the current distribution of suitable habitat at multiple spatial scales using mitochondrial DNA sequences and microsatellite data from individuals throughout the entire range. We found three genetic clusters of individuals generally concordant with geographic regions and low sequence divergence at mitochondrial loci suggesting a recent origin of these populations. We also found high levels of genetic structure at microsatellite loci among populations within each of these groups indicating restricted gene flow at intermediate scales. Despite high habitat specificity, we did not detect genetic structure among sand blowouts at finer spatial scales. Within each population, matrices comprised of both sand blowouts and vegetated shinnery oak patches are necessary for genetic connectivity, but the fine scale spatial arrangement of blowouts may not be as critical. We discuss our results with respect to the scale of landscape heterogeneity and habitat connectivity and consider the conservation implications for this threatened taxon