AutoSNPdb: an annotated single nucleotide polymorphism database for crop plants

Single nucleotide polymorphisms (SNPs) may be considered the ultimate genetic marker as they represent the finest resolution of a DNA sequence (a single nucleotide), are generally abundant in populations and have a low mutation rate. Analysis of assembled EST sequence data provides a cost-effective means to identify large numbers of SNPs associated with functional genes. We have developed an integrated SNP discovery pipeline, which identifies SNPs from assembled EST sequences. The results are maintained in a custom relational database along with EST source and annotation information. The current database hosts data for the important crops rice, barley and Brassica. Users may rapidly identify polymorphic sequences of interest through BLAST sequence comparison, keyword searches of annotations derived from UniRef90 and GenBank comparisons, GO annotations or in genes corresponding to syntenic regions of reference genomes. In addition, SNPs between specific varieties may be identified for targeted mapping and association studies. SNPs are viewed using a user-friendly graphical interface. The database is freely accessible at http://autosnpdb.qfab.org.au/

Caribou herd dynamics : impacts of climate change on traditional and sport harvesting

Caribou (Rangifer tarandus) are a key species in Arctic ecosystems including northern Québec and Labrador. They play a central role in the ecology of predators and the structure of Arctic plant communities. In addition, caribou provide socioeconomic and cultural benefits from subsistence and sport hunting activities. Changes in the distribution and abundance of caribou due to global climate change would have serious biological, societal, and economic implications. Direct and indirect consequences of climate change on migratory caribou herds may include alteration in habitat use, migration patterns, foraging behaviour and demography. For example, caribou may experience a further northerly shift in distribution due to several factors including longer ice-free periods, increases in snowfall and extreme weather events, alterations in the fire regime, and changes in the distribution of insects and predators. Future research by Caribou Ungava, a research group interested in the ecology of migratory caribou in the context of climate change, will address the factors outlining variations in the population dynamics of caribou, implications for survival and reproduction, as well as the response of caribou habitat to different climate change scenarios. Management efforts focusing on mitigating greenhouse gases to reduce the potential effects of climate change, preserving high quality habitat, limiting anthropogenic landscape disturbances, and managing hunting in a sustainable manner, could alleviate stressors on migratory caribou of the QuébecLabrador peninsula

Community professionals' management of client care : a mixed-methods systematic review

This is the final draft, after peer-review, of a manuscript published in Journal of Health Services Research & Policy. The definitive version, detailed above, is available online at www.rsmjournals.com.Peer reviewedPostprin

Soil Resources Area Affects Herbivore Health

Soil productivity effects nutritive quality of food plants, growth of humans and animals, and reproductive health of domestic animals. Game-range surveys sometimes poorly explained variations in wildlife populations, but classification of survey data by major soil types improved effectiveness. Our study evaluates possible health effects of lower condition and reproductive rates for wild populations of Odocoileus virginianus Zimmerman (white-tailed deer) in some physiographic regions of Mississippi. We analyzed condition and reproductive data for 2400 female deer from the Mississippi Department of Wildlife, Fisheries, and Parks herd health evaluations from 1991–1998. We evaluated age, body mass (Mass), kidney mass, kidney fat mass, number of corpora lutea (CL) and fetuses, as well as fetal ages. Region affected kidney fat index (KFI), which is a body condition index, and numbers of fetuses of adults (P ≤ 0.001). Region affected numbers of CL of adults (P ≤ 0.002). Mass and conception date (CD) were affected (P ≤ 0.001) by region which interacted significantly with age for Mass (P ≤ 0.001) and CD (P < 0.04). Soil region appears to be a major factor influencing physical characteristics of female deer

Identification of recruitment and retention strategies for rehabilitation professionals in Ontario, Canada: results from expert panels

<p>Abstract</p> <p>Background</p> <p>Demand for rehabilitation services is expected to increase due to factors such as an aging population, workforce pressures, rise in chronic and complex multi-system disorders, advances in technology, and changes in interprofessional health service delivery models. However, health human resource (HHR) strategies for Canadian rehabilitation professionals are lagging behind other professional groups such as physicians and nurses. The objectives of this study were: 1) to identify recruitment and retention strategies of rehabilitation professionals including occupational therapists, physical therapists and speech language pathologists from the literature; and 2) to investigate both the importance and feasibility of the identified strategies using expert panels amongst HHR and education experts.</p> <p>Methods</p> <p>A review of the literature was conducted to identify recruitment and retention strategies for rehabilitation professionals. Two expert panels, one on <it>Recruitment and Retention </it>and the other on <it>Education </it>were convened to determine the importance and feasibility of the identified strategies. A modified-delphi process was used to gain consensus and to rate the identified strategies along these two dimensions.</p> <p>Results</p> <p>A total of 34 strategies were identified by the <it>Recruitment and Retention </it>and <it>Education </it>expert panels as being important and feasible for the development of a HHR plan for recruitment and retention of rehabilitation professionals. Seven were categorized under the <it>Quality of Worklife and Work Environment </it>theme, another seven in <it>Financial Incentives and Marketing</it>, two in <it>Workload and Skill Mix</it>, thirteen in <it>Professional Development </it>and five in <it>Education and Training</it>.</p> <p>Conclusion</p> <p>Based on the results from the expert panels, the three major areas of focus for HHR planning in the rehabilitation sector should include strategies addressing <it>Quality of Worklife and Work Environment</it>, <it>Financial Incentives and Marketing </it>and <it>Professional Development</it>.</p

The precarious supply of physical therapists across Canada: exploring national trends in health human resources (1991 to 2005)

<p>Abstract</p> <p>Background</p> <p>Health Human Resource (HHR) ratios are one measure of workforce supply, and are often expressed as a ratio in the number of health professionals to a sub-set of the population. In this study, we explore national trends in HHR among physical therapists (PTs) across Canada.</p> <p>Methods</p> <p>National population data were combined with provincial databases of registered physical therapists in order to estimate the HHR ratio in 2005, and to establish trends between 1991 and 2005.</p> <p>Results</p> <p>The national HHR ratio was 4.3 PTs per 10,000 population in 1991, which increased to 5.0 by 2000. In 2005, the HHR ratios varied widely across jurisdictions; however, we estimate that the national average dropped to 4.8 PTs per 10,000. Although the trend in HHR between 1991 and 2005 suggests positive growth of 11.6%, we have found negative growth of 4.0% in the latter 5-years of this study period.</p> <p>Conclusion</p> <p>Demand for rehabilitation services is projected to escalate in the next decade. Identifying benchmarks or targets regarding the optimal number of PTs, along with other health professionals working within inter professional teams, is necessary to establish a stable supply of health providers to meet the emerging rehabilitation and mobility needs of an aging and increasingly complex Canadian population.</p

The Evolutionary Analysis of Emerging Low Frequency HIV-1 CXCR4 Using Variants through Time—An Ultra-Deep Approach

Large-scale parallel pyrosequencing produces unprecedented quantities of sequence data. However, when generated from viral populations current mapping software is inadequate for dealing with the high levels of variation present, resulting in the potential for biased data loss. In order to apply the 454 Life Sciences' pyrosequencing system to the study of viral populations, we have developed software for the processing of highly variable sequence data. Here we demonstrate our software by analyzing two temporally sampled HIV-1 intra-patient datasets from a clinical study of maraviroc. This drug binds the CCR5 coreceptor, thus preventing HIV-1 infection of the cell. The objective is to determine viral tropism (CCR5 versus CXCR4 usage) and track the evolution of minority CXCR4-using variants that may limit the response to a maraviroc-containing treatment regimen. Five time points (two prior to treatment) were available from each patient. We first quantify the effects of divergence on initial read k-mer mapping and demonstrate the importance of utilizing population-specific template sequences in relation to the analysis of next-generation sequence data. Then, in conjunction with coreceptor prediction algorithms that infer HIV tropism, our software was used to quantify the viral population structure pre- and post-treatment. In both cases, low frequency CXCR4-using variants (2.5–15%) were detected prior to treatment. Following phylogenetic inference, these variants were observed to exist as distinct lineages that were maintained through time. Our analysis, thus confirms the role of pre-existing CXCR4-using virus in the emergence of maraviroc-insensitive HIV. The software will have utility for the study of intra-host viral diversity and evolution of other fast evolving viruses, and is available from http://www.bioinf.manchester.ac.uk/segminator/

An integrated approach to the interpretation of Single Amino Acid Polymorphisms within the framework of CATH and Gene3D

Background The phenotypic effects of sequence variations in protein-coding regions come about primarily via their effects on the resulting structures, for example by disrupting active sites or affecting structural stability. In order better to understand the mechanisms behind known mutant phenotypes, and predict the effects of novel variations, biologists need tools to gauge the impacts of DNA mutations in terms of their structural manifestation. Although many mutations occur within domains whose structure has been solved, many more occur within genes whose protein products have not been structurally characterized.&lt;p&gt;&lt;/p&gt; Results Here we present 3DSim (3D Structural Implication of Mutations), a database and web application facilitating the localization and visualization of single amino acid polymorphisms (SAAPs) mapped to protein structures even where the structure of the protein of interest is unknown. The server displays information on 6514 point mutations, 4865 of them known to be associated with disease. These polymorphisms are drawn from SAAPdb, which aggregates data from various sources including dbSNP and several pathogenic mutation databases. While the SAAPdb interface displays mutations on known structures, 3DSim projects mutations onto known sequence domains in Gene3D. This resource contains sequences annotated with domains predicted to belong to structural families in the CATH database. Mappings between domain sequences in Gene3D and known structures in CATH are obtained using a MUSCLE alignment. 1210 three-dimensional structures corresponding to CATH structural domains are currently included in 3DSim; these domains are distributed across 396 CATH superfamilies, and provide a comprehensive overview of the distribution of mutations in structural space.&lt;p&gt;&lt;/p&gt; Conclusion The server is publicly available at http://3DSim.bioinfo.cnio.es/ webcite. In addition, the database containing the mapping between SAAPdb, Gene3D and CATH is available on request and most of the functionality is available through programmatic web service access.&lt;p&gt;&lt;/p&gt