Linkage mapping bovine EST-based SNP

BACKGROUND: Existing linkage maps of the bovine genome primarily contain anonymous microsatellite markers. These maps have proved valuable for mapping quantitative trait loci (QTL) to broad regions of the genome, but more closely spaced markers are needed to fine-map QTL, and markers associated with genes and annotated sequence are needed to identify genes and sequence variation that may explain QTL. RESULTS: Bovine expressed sequence tag (EST) and bacterial artificial chromosome (BAC)sequence data were used to develop 918 single nucleotide polymorphism (SNP) markers to map genes on the bovine linkage map. DNA of sires from the MARC reference population was used to detect SNPs, and progeny and mates of heterozygous sires were genotyped. Chromosome assignments for 861 SNPs were determined by twopoint analysis, and positions for 735 SNPs were established by multipoint analyses. Linkage maps of bovine autosomes with these SNPs represent 4585 markers in 2475 positions spanning 3058 cM . Markers include 3612 microsatellites, 913 SNPs and 60 other markers. Mean separation between marker positions is 1.2 cM. New SNP markers appear in 511 positions, with mean separation of 4.7 cM. Multi-allelic markers, mostly microsatellites, had a mean (maximum) of 216 (366) informative meioses, and a mean 3-lod confidence interval of 3.6 cM Bi-allelic markers, including SNP and other marker types, had a mean (maximum) of 55 (191) informative meioses, and were placed within a mean 8.5 cM 3-lod confidence interval. Homologous human sequences were identified for 1159 markers, including 582 newly developed and mapped SNP. CONCLUSION: Addition of these EST- and BAC-based SNPs to the bovine linkage map not only increases marker density, but provides connections to gene-rich physical maps, including annotated human sequence. The map provides a resource for fine-mapping quantitative trait loci and identification of positional candidate genes, and can be integrated with other data to guide and refine assembly of bovine genome sequence. Even after the bovine genome is completely sequenced, the map will continue to be a useful tool to link observable phenotypes and animal genotypes to underlying genes and molecular mechanisms influencing economically important beef and dairy traits

Ensembl 2014

Ensembl (http://www.ensembl.org) creates tools and data resources to facilitate genomic analysis in chordate species with an emphasis on human, major vertebrate model organisms and farm animals. Over the past year we have increased the number of species that we support to 77 and expanded our genome browser with a new scrollable overview and improved variation and phenotype views. We also report updates to our core datasets and improvements to our gene homology relationships from the addition of new species. Our REST service has been extended with additional support for comparative genomics and ontology information. Finally, we provide updated information about our methods for data access and resources for user training

Aetiology and risk factors of musculoskeletal disorders in physically active conscripts: a follow-up study in the Finnish Defence Forces

<p>Abstract</p> <p>Background</p> <p>Musculoskeletal disorders (MSDs) are the main reason for morbidity during military training. MSDs commonly result in functional impairment leading to premature discharge from military service and disabilities requiring long-term rehabilitation. The purpose of the study was to examine associations between various risk factors and MSDs with special attention to the physical fitness of the conscripts.</p> <p>Methods</p> <p>Two successive cohorts of 18 to 28-year-old male conscripts (<it>N </it>= 944, median age 19) were followed for six months. MSDs, including overuse and acute injuries, treated at the garrison clinic were identified and analysed. Associations between MSDs and risk factors were examined by multivariate Cox's proportional hazard models.</p> <p>Results</p> <p>During the six-month follow-up of two successive cohorts there were 1629 MSDs and 2879 health clinic visits due to MSDs in 944 persons. The event-based incidence rate for MSD was 10.5 (95% confidence interval (CI): 10.0-11.1) per 1000 person-days. Most MSDs were in the lower extremities (65%) followed by the back (18%). The strongest baseline factors associated with MSDs were poor result in the combined outcome of a 12-minute running test and back lift test (hazard ratio (HR) 2.9; 95% CI: 1.9-4.6), high waist circumference (HR 1.7; 95% CI: 1.3-2.2), high body mass index (HR 1.8; 95% CI: 1.3-2.4), poor result in a 12-minute running test (HR 1.6; 95% CI: 1.2-2.2), earlier musculoskeletal symptoms (HR 1.7; 95% CI: 1.3-2.1) and poor school success (educational level and grades combined; HR 2.0; 95% CI: 1.3-3.0). In addition, risk factors of long-term MSDs (≥10 service days lost due to one or several MSDs) were analysed: poor result in a 12-minute running test, earlier musculoskeletal symptoms, high waist circumference, high body mass index, not belonging to a sports club and poor result in the combined outcome of the 12-minute running test and standing long jump test were strongly associated with long-term MSDs.</p> <p>Conclusions</p> <p>The majority of the observed risk factors are modifiable and favourable for future interventions. An appropriate intervention based on the present study would improve both aerobic and muscular fitness prior to conscript training. Attention to appropriate waist circumference and body mass index would strengthen the intervention. Effective results from well-planned randomised controlled studies are needed before initiating large-scale prevention programmes in a military environment.</p

Synergistic Interactions between the NS3hel and E Proteins Contribute to the Virulence of Dengue Virus Type 1

Dengue virus constitutes a significant public health problem in tropical regions of the world. Despite the high morbidity and mortality of this infection, no effective antiviral drugs or vaccines are available for the treatment or prevention of dengue infections. The profile of clinical signs associated with dengue infection has changed in recent years with an increase in the number of episodes displaying unusual signs. We use reverse genetics technology to engineer DENV-1 viruses with subsets of mutations previously identified in highly neurovirulent strains to provide insights into the molecular mechanisms underlying dengue neuropathogenesis. We found that single mutations affecting the E and NS3hel proteins, introduced in a different genetic context, had a synergistic effect increasing DENV replication capacity in human and mosquito derived cells in vitro. We also demonstrated correlations between the presence of these mutations and viral replication efficiency, viral loads, the induction of innate immune response genes and pathogenesis in a mouse model. These results should improve our understanding of the DENV-host cell interaction and contribute to the development of effective antiviral strategies

Quality of life after high-dose-rate brachytherapy monotherapy for prostate cancer

Purpose There is little information in the literature on health-related quality of life (HRQOL) changes due to high-dose-rate (HDR) brachytherapy monotherapy for prostate cancer. Materials and Methods We conducted a prospective study of HRQOL changes due to HDR brachytherapy monotherapy for low risk or favorable intermediate risk prostate cancer. Sixty-four of 84 (76%) patients who were treated between February 2011 and April 2013 completed 50 questions comprising the Expanded Prostate Cancer Index Composite (EPIC) before treatment and 6 and/or 12 months after treatment. Results Six months after treatment, there was a significant decrease (p<0.05) in EPIC urinary, bowel, and sexual scores, including urinary overall, urinary function, urinary bother, urinary irritative, bowel overall, bowel bother, sexual overall, and sexual bother scores. By one year after treatment, EPIC urinary, bowel, and sexual scores had increased and only the bowel overall and bowel bother scores remained significantly below baseline values. Conclusions HDR brachytherapy monotherapy is well-tolerated in patients with low and favorable intermediate risk prostate cancer. EPIC urinary and sexual domain scores returned to close to baseline 12 months after HDR brachytherapy

Prevalence, withdrawal symptoms and associated factors of khat chewing among students at Jimma University in Ethiopia

Background: Recently, khat chewing has become a common practice among high school, college, and university students. Regular khat chewing is thought to be a predisposing factor for different physical and mental health problems. It can lead to absenteeism from work and classes. In Ethiopia, to our knowledge no published study has investigated khat withdrawal symptoms. Therefore, this study was conducted to determine the prevalence, withdrawal symptoms, and associated factors of khat chewing among regular undergraduate students on the main campus of Jimma University in Ethiopia. Methods: The institution-based, cross-sectional study was conducted in January 2016. Data were collected from 651 main campus regular undergraduate students with a structured, self-administered questionnaire, entered into Epidata 3.1 and exported to SPSS version 20 for Windows. Bivariate and multivariate logistic regressions were used to explore associations and identify variables independently associated with khat chewing. Results: The study found that the lifetime and current prevalence of khat chewing among students were 26.3% (95% CI: 24.3, 28.3) and 23.9% (95% CI: 21.94, 25.86), respectively. About 25.7% of students started chewing after joining university, and 60.5% of these students started during their first year. The main reason given for starting khat chewing was for study purposes (54.6%), followed by socialization purposes (42.3%). Among current khat chewers, 72.9% reported that they had chewed khat for 1 year or more and 68.2% reported that they had experienced various withdrawal symptoms. The most frequently reported withdrawal symptoms were feeling depressed, craving, and feeling fatigued. Being male, attending a place of worship daily/2-3 times per week, cannabis use, smoking cigarettes, and having family members currently chewing khat were independently associated with khat chewing. Conclusions: This study found that large numbers of university students were currently chewing khat. In this study withdrawal symptoms and factors that significantly affect khat chewing were identified. Besides it gave new ideas regarding khat withdrawal symptoms in Ethiopia. It serves as a critical role of providing information to form rational foundation for public health policy, prevention and planning to bring change in contributing factors for Khat chewing. The finding will be serving as base line information for further study