DraGnET: Software for storing, managing and analyzing annotated draft genome sequence data

BackgroundNew next generation DNA sequencing technologies offer individual researchers the ability to rapidly generate large amounts of genome sequence data at dramatically reduced costs. As a result, a need has arisen for new software tools for storage, management and analysis of genome sequence data. Although bioinformatic tools are available for the analysis and management of genome sequences, limitations still remain. For example, restrictions on the submission of data and use of these tools may be imposed, thereby making them unsuitable for sequencing projects that need to remain in-house or proprietary during their initial stages. Furthermore, the availability and use of next generation sequencing in industrial, governmental and academic environments requires biologist to have access to computational support for the curation and analysis of the data generated; however, this type of support is not always immediately available. ResultsTo address these limitations, we have developed DraGnET (Draft Genome Evaluation Tool). DraGnET is an open source web application which allows researchers, with no experience in programming and database management, to setup their own in-house projects for storing, retrieving, organizing and managing annotated draft and complete genome sequence data. The software provides a web interface for the use of BLAST, allowing users to perform preliminary comparative analysis among multiple genomes. We demonstrate the utility of DraGnET for performing comparative genomics on closely related bacterial strains. Furthermore, DraGnET can be further developed to incorporate additional tools for more sophisticated analyses. Conclusions DraGnET is designed for use either by individual researchers or as a collaborative tool available through Internet (or Intranet) deployment. For genome projects that require genome sequencing data to initially remain proprietary, DraGnET provides the means for researchers to keep their data in-house for analysis using local programs or until it is made publicly available, at which point it may be uploaded to additional analysis software applications. The DraGnET home page is available at http://www.dragnet.cvm.iastate.edu and includes example files for examining the functionalities, a link for downloading the DraGnET setup package and a link to the DraGnET source code hosted with full documentation on SourceForge

The Effectiveness of “Emolabeling” to Promote Healthy Food Choices in Children Preschool Through 5th Grade

Obesity has become a growing global concern. Evidence indicates that ecological factors are most predictive of obesity among children, and that a new strategy, referred to as emolabeling, may effectively address ecological factors, although the extent to which it can influence food choice is not yet known, but tested here. Specifically, we tested the hypothesis that children aged 3 to 11 years will use emolabels, or emotional correlates of health (i.e. healthy-happy, unhealthy-sad), to make healthy food choices. A cross-sectional design was used with two phases. In Phase 1, children were taught how to use emolabels with a “faces of health” lesson. In Phase 2, children made choices between containers that were laid out on a large table in pairs and varied by taste (tastes good, no information), social norms (popular, not popular), branding (image of a minion, no image), or preference (told what food was in each container). A control pair was labeled with only emoticons. The order and presentation of the containers were counterbalanced for each variation. Results showed that a significant proportion of children in the pre-literacy and the early literacy grades used emoticons to specifically make healthy food choices in each variation (p < .05 for all tests), except when children were told what foods were in the containers. In all, emolabeling effectively influenced food choices for healthy foods among children aged 3 to 11 years, more so than labeling for taste, social norms, and branding, but not preference

Gradient Particle Magnetohydrodynamics

We introduce Gradient Particle Magnetohydrodynamics (GPM), a new Lagrangian method for magnetohydrodynamics based on gradients corrected for the locally disordered particle distribution. The development of a numerical code for MHD simulation using the GPM algorithm is outlined. Validation tests simulating linear and nonlinear sound waves, linear MHD waves, advection of magnetic fields in a magnetized vortex, hydrodynamical shocks, and three-dimensional collapse are presented, demonstrating the viability of an MHD code using GPM. The characteristics of a GPM code are discussed and possible avenues for further development and refinement are mentioned. We conclude with a view of how GPM may complement other methods currently in development for the next generation of computational astrophysics.Comment: 26 pages, 11 figure

Differential Effects of Bacitracin Methylene Disalicylate (BMD) on the Distal Colon and Cecal Microbiota of Young Broiler Chickens

Antibiotics have been used extensively for growth promotion in poultry, along with other food production animals, as well as therapeutically to treat infectious diseases. However, with concerns over selection for drug antibiotic resistant bacteria the practice of using subtherapeutic doses of antibiotics is under increased scrutiny. Consequently, we assessed the impact of the commonly used antibiotic bacitracin methylene disalicylate (BMD) on the gastrointestinal microbiota of chickens. For this we administered therapeutic doses of BMD as a feed additive and 16s rRNA gene amplicon sequencing to measure changes in taxonomic abundance on the distal colon and cecal microbiota of young broiler chickens. While BMD treatment was found to impact the abundance of selected taxa and overall beta diversity, significant changes were, in general, limited to the colon of the treated birds. Selected taxa at the phylum, class, and genus levels that were most impacted were identified. The composition of the cecum remained relatively stable in BMD-treated animals. As poultry production practices seek alternatives to growth promoting antibiotic feed additives, manipulation of the gastrointestinal microbiota holds promise. These results suggest that targeting the cecum may offer a means to promote changes to the microbiota that maximize the benefits for the hosts

Evaluations of Livestock Protection Dogs for Deterring Deer and Cattle Interactions

Bovine Tuberculosis (bovine TB) in northern Michigan has proven a dilemma necessitating aggressive measures including depopulation of livestock operations, culling of wildlife, banning the feeding of wildlife, and fencing livestock feed with high fences. Bovine TB is believed to be transmitted from white-tailed deer (Odocoileus virginianus) to domestic cattle through feces, urine, saliva, and nasal secretions on contaminated feed (indirect transmission) and from animal to animal (direct transmission). Effective methods for excluding deer from cattle enclosures would minimize the potential for indirect and direct transmission of bovine TB between infected deer and cattle. We combined an idea used historically in Europe to control predation on sheep with the concept of modem frightening devices that often fall short when the motivation of offending species is high. The use of livestock protection dogs (LPDs) seemed like an ideal solution in controlling the transmission of bovine TB from white-tailed deer to cattle. We felt LPDs raised and bonded with cattle would reduce use of cattle pastures and cattle feed by deer and minimize contact between deer and cattle, thereby reducing the potential for the transmission of bovine TB. We evaluated 4 LPDs over a 5-month period utilizing 2 primary data collection methods (direct observations and motion-activated video) on farmed deer facilities in Michigan. Following the initial evaluation of the LPDs, we relocated the dogs to working livestock operations in Michigan for further evaluation to gain an understanding of their practicality and long-term efficacy. Pastures protected by dogs had fewer intrusions by deer, fewer contacts (within 5m) between deer and cattle, and lower use of cattle feed by deer. Overall, we successfully decreased the potential for disease transmission with 66% fewer intrusions by deer into protected pastures, 96% fewer contacts (within 5m) between deer and cattle, and 100% lower use of cattle feed by deer (based of observation data). Livestock protection dogs were more effective in protecting animals and their immediate surroundings than excluding animals from entire study pastures. We found a strong treatment effect within the High Density Site; while within the Very High Density Site, we had high variability within intrusion rates at protected pastures and relatively low use of unprotected pastures resulting in no significant treatment effect. In conclusion, when properly trained and confined with the protected animals, LPDs minimize the potential for livestock to contract bovine TB from infected deer

The RNA Binding Protein Quaking Regulates Formation of circRNAs

SummaryCircular RNAs (circRNAs), formed by non-sequential back-splicing of pre-mRNA transcripts, are a widespread form of non-coding RNA in animal cells. However, it is unclear whether the majority of circRNAs represent splicing by-products without function or are produced in a regulated manner to carry out specific cellular functions. We show that hundreds of circRNAs are regulated during human epithelial-mesenchymal transition (EMT) and find that the production of over one-third of abundant circRNAs is dynamically regulated by the alternative splicing factor, Quaking (QKI), which itself is regulated during EMT. Furthermore, by modulating QKI levels, we show the effect on circRNA abundance is dependent on intronic QKI binding motifs. Critically, the addition of QKI motifs is sufficient to induce de novo circRNA formation from transcripts that are normally linearly spliced. These findings demonstrate circRNAs are both purposefully synthesized and regulated by cell-type specific mechanisms, suggesting they play specific biological roles in EMT

Physical Activity and Immunity in HIV-Infected Individuals

The purpose of this study was to determine what relationship exists among physical activity levels and viral load and CD4+ cell count in HIV-infected individuals. Increased viral load is associated with disease progression and symptom severity. A convenience sample of 66 male and female subjects between the ages of 18 and 64 years of age (mean 399/8) was recruited from a hospital-based HIV/AIDS clinic. Components of PA were assessed for three continuous days using a mini-motion logger wrist actigraph. These components included mean PA level, and PA index and acceleration index. Pearson’s correlational analysis was used to test the strength of association between PA components and viral load or CD4+ cell count. A significant inverse relationship was found between mean PA level and viral load (p=0.047). An inverse relationship was also observed between PA index and viral load (p=0.0061). Neither mean PA nor PA index scores correlated with CD4+ cell counts. Acceleration index, a measure of PA intensity, showed no correlation to viral load or CD4+ cell counts. These findings suggest that increasing levels of physical activity might have beneficial effects on viral load in HIV-infected individuals

Individual winter movement strategies in two species of Murre (Uria spp.) in the Northwest Atlantic

Individual wintering strategies and patterns of winter site fidelity in successive years are highly variable among seabird species. Yet, an understanding of consistency in timing of movements and the degree of site fidelity is essential for assessing how seabird populations might be influenced by, and respond to, changing conditions on wintering grounds. To explore annual variation in migratory movements and wintering areas, we applied bird-borne geolocators on Thick-billed Murres (Uria lomvia, n = 19) and Common Murres (U. aalge, n = 20) from 5 colonies in the Northwest Atlantic for 2–4 consecutive years. Thick-billed Murres ranged widely and among-individual wintering strategies were highly variable, whereas most Common Murres wintered relatively near their colonies, with among-individual variation represented more by the relative use of inshore vs. offshore habitat. Within individuals, some aspects of the wintering strategy were more repeatable than others: colony arrival and departure dates were more consistent by individual Common than Thick-billed Murres, while the sizes of home ranges (95% utilization distributions) and distances travelled to wintering area were more repeatable for both species. In consecutive years, individual home ranges overlapped from 0–64% (Thick-billed Murres) and 0–95% (Common Murres); and the winter centroids were just 239 km and 169 km apart (respectively). Over the 3–4 year timescale of our study, individuals employed either fixed or flexible wintering strategies; although most birds showed high winter site fidelity, some shifted core ranges after 2 or 3 years. The capacity among seabird species for a combination of fidelity and flexibility, in which individuals may choose from a range of alternative strategies, deserves further, longer term attention