Genetic structure of community acquired methicillin-resistant Staphylococcus aureus USA300.

BackgroundCommunity-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is a significant bacterial pathogen that poses considerable clinical and public health challenges. The majority of the CA-MRSA disease burden consists of skin and soft tissue infections (SSTI) not associated with significant morbidity; however, CA-MRSA also causes severe, invasive infections resulting in significant morbidity and mortality. The broad range of disease severity may be influenced by bacterial genetic variation.ResultsWe sequenced the complete genomes of 36 CA-MRSA clinical isolates from the predominant North American community acquired clonal type USA300 (18 SSTI and 18 severe infection-associated isolates). While all 36 isolates shared remarkable genetic similarity, we found greater overall time-dependent sequence diversity among SSTI isolates. In addition, pathway analysis of non-synonymous variations revealed increased sequence diversity in the putative virulence genes of SSTI isolates.ConclusionsHere we report the first whole genome survey of diverse clinical isolates of the USA300 lineage and describe the evolution of the pathogen over time within a defined geographic area. The results demonstrate the close relatedness of clinically independent CA-MRSA isolates, which carry implications for understanding CA-MRSA epidemiology and combating its spread

Development and testing of a checklist to assess compliance with the faculty of pain medicine’s core standards for pain management services: experience in a new national tertiary pain service

Introduction: The Faculty of Pain Medicine recently published the first UK-focused Core Standards for Pain Management Services (CSPMS). We present an audit checklist tool developed to map compliance to the CSPMS, which offers a practical method of auditing any pain management service against the standards. Methods: The checklist tool was developed and its utility was field-tested in the Scottish National Residential Pain Management Programme (SNRPMP), a newly established service offering residential service to people in Scotland. Results: The checklist tool developed provides an easy and practical approach to evaluating any pain service against the national standards. Its application to evaluate the SNRPMP indicates that the service meets the majority of CSPMS standards and highlights aspects of the service requiring improvement. Conclusion: The layout of the developed checklist tool offers an alternative format for the structuring of the national standards in possible future revisions. The audit checklist tool enables evaluation of services with a numerical score, enabling monitoring of their compliance with national standards as well as comparisons between pain services

Field-to-farm gate greenhouse gas emissions from corn stover production in the Midwestern U.S.

Measured field data were used to compare two allocation methods on life cycle greenhouse gas emissions from corn (Zea mays L.) stover production in the Midwest U.S. We used publicly-available crop yield, nitrogen fertilizer, and direct soil nitrous oxide emissions data from the USDA-ARS Resilient Economic Agricultural Practices research program. Field data were aggregated from 9 locations across 26 site-years for 3 stover harvest rates (no removal; moderate removal e 3.1Mg ha-1; high removal e 7.2Mg ha-1) and 2 tillage practices (conventional; reduced/no-till). Net carbon uptake by crops was computed from measured plant carbon content. Monte Carlo simulations sampled input distributions to assess variability in farm-to-gate GHG emissions. The base analysis assumed no change in soil organic carbon stocks. In all cases, net CO2 uptake during crop growth and soil-respired CO2 dominated system emissions. Emissions were most sensitive to co-product accounting method, with system expansion emissions ~15% lower than mass allocation. Regardless of accounting method, lowest emissions occurred for a moderate removal rate under reduced/no-till management. The absence of correlations between N fertilization rate and stover removal rate or soil N2O emissions in this study challenges the use of such assumptions typically employed in life cycle assessments Storage of all carbon retained on the field as SOC could reduce emissions by an additional 15%. Our results highlight how variability in GHG emissions due to location and weather can overshadow the impact of farm management practices on field-to-farm gate emissions

A Classifier-based approach to identify genetic similarities between diseases

Motivation: Genome-wide association studies are commonly used to identify possible associations between genetic variations and diseases. These studies mainly focus on identifying individual single nucleotide polymorphisms (SNPs) potentially linked with one disease of interest. In this work, we introduce a novel methodology that identifies similarities between diseases using information from a large number of SNPs. We separate the diseases for which we have individual genotype data into one reference disease and several query diseases. We train a classifier that distinguishes between individuals that have the reference disease and a set of control individuals. This classifier is then used to classify the individuals that have the query diseases. We can then rank query diseases according to the average classification of the individuals in each disease set, and identify which of the query diseases are more similar to the reference disease. We repeat these classification and comparison steps so that each disease is used once as reference disease

ProKinO: An Ontology for Integrative Analysis of Protein Kinases in Cancer

Protein kinases are a large and diverse family of enzymes that are genomically altered in many human cancers. Targeted cancer genome sequencing efforts have unveiled the mutational profiles of protein kinase genes from many different cancer types. While mutational data on protein kinases is currently catalogued in various databases, integration of mutation data with other forms of data on protein kinases such as sequence, structure, function and pathway is necessary to identify and characterize key cancer causing mutations. Integrative analysis of protein kinase data, however, is a challenge because of the disparate nature of protein kinase data sources and data formats., where the mutations are spread over 82 distinct kinases. We also provide examples of how ontology-based data analysis can be used to generate testable hypotheses regarding cancer mutations.

MoKCa database - mutations of kinases in cancer

Members of the protein kinase family are amongst the most commonly mutated genes in human cancer, and both mutated and activated protein kinases have proved to be tractable targets for the development of new anticancer therapies The MoKCa database (Mutations of Kinases in Cancer, http://strubiol.icr.ac.uk/extra/mokca) has been developed to structurally and functionally annotate, and where possible predict, the phenotypic consequences of mutations in protein kinases implicated in cancer. Somatic mutation data from tumours and tumour cell lines have been mapped onto the crystal structures of the affected protein domains. Positions of the mutated amino-acids are highlighted on a sequence-based domain pictogram, as well as a 3D-image of the protein structure, and in a molecular graphics package, integrated for interactive viewing. The data associated with each mutation is presented in the Web interface, along with expert annotation of the detailed molecular functional implications of the mutation. Proteins are linked to functional annotation resources and are annotated with structural and functional features such as domains and phosphorylation sites. MoKCa aims to provide assessments available from multiple sources and algorithms for each potential cancer-associated mutation, and present these together in a consistent and coherent fashion to facilitate authoritative annotation by cancer biologists and structural biologists, directly involved in the generation and analysis of new mutational data

Gene set of nuclear-encoded mitochondrial regulators is enriched for common inherited variation in obesity

There are hints of an altered mitochondrial function in obesity. Nuclear-encoded genes are relevant for mitochondrial function (3 gene sets of known relevant pathways: (1) 16 nuclear regulators of mitochondrial genes, (2) 91 genes for oxidative phosphorylation and (3) 966 nuclear-encoded mitochondrial genes). Gene set enrichment analysis (GSEA) showed no association with type 2 diabetes mellitus in these gene sets. Here we performed a GSEA for the same gene sets for obesity. Genome wide association study (GWAS) data from a case-control approach on 453 extremely obese children and adolescents and 435 lean adult controls were used for GSEA. For independent confirmation, we analyzed 705 obesity GWAS trios (extremely obese child and both biological parents) and a population-based GWAS sample (KORA F4, n = 1,743). A meta-analysis was performed on all three samples. In each sample, the distribution of significance levels between the respective gene set and those of all genes was compared using the leading-edge-fraction-comparison test (cut-offs between the 50(th) and 95(th) percentile of the set of all gene-wise corrected p-values) as implemented in the MAGENTA software. In the case-control sample, significant enrichment of associations with obesity was observed above the 50(th) percentile for the set of the 16 nuclear regulators of mitochondrial genes (p(GSEA,50) = 0.0103). This finding was not confirmed in the trios (p(GSEA,50) = 0.5991), but in KORA (p(GSEA,50) = 0.0398). The meta-analysis again indicated a trend for enrichment (p(MAGENTA,50) = 0.1052, p(MAGENTA,75) = 0.0251). The GSEA revealed that weak association signals for obesity might be enriched in the gene set of 16 nuclear regulators of mitochondrial genes

Non-homologous end-joining pathway associated with occurrence of myocardial infarction: gene set analysis of genome-wide association study data

<p>Purpose: DNA repair deficiencies have been postulated to play a role in the development and progression of cardiovascular disease (CVD). The hypothesis is that DNA damage accumulating with age may induce cell death, which promotes formation of unstable plaques. Defects in DNA repair mechanisms may therefore increase the risk of CVD events. We examined whether the joints effect of common genetic variants in 5 DNA repair pathways may influence the risk of CVD events.</p> <p>Methods: The PLINK set-based test was used to examine the association to myocardial infarction (MI) of the DNA repair pathway in GWAS data of 866 subjects of the GENetic DEterminants of Restenosis (GENDER) study and 5,244 subjects of the PROspective Study of Pravastatin in the Elderly at Risk (PROSPER) study. We included the main DNA repair pathways (base excision repair, nucleotide excision repair, mismatch repair, homologous recombination and non-homologous end-joining (NHEJ)) in the analysis.</p> <p>Results: The NHEJ pathway was associated with the occurrence of MI in both GENDER (P = 0.0083) and PROSPER (P = 0.014). This association was mainly driven by genetic variation in the MRE11A gene (PGENDER = 0.0001 and PPROSPER = 0.002). The homologous recombination pathway was associated with MI in GENDER only (P = 0.011), for the other pathways no associations were observed.</p> <p>Conclusion: This is the first study analyzing the joint effect of common genetic variation in DNA repair pathways and the risk of CVD events, demonstrating an association between the NHEJ pathway and MI in 2 different cohorts.</p&gt

Evidence for the role of EPHX2 gene variants in anorexia nervosa.

Anorexia nervosa (AN) and related eating disorders are complex, multifactorial neuropsychiatric conditions with likely rare and common genetic and environmental determinants. To identify genetic variants associated with AN, we pursued a series of sequencing and genotyping studies focusing on the coding regions and upstream sequence of 152 candidate genes in a total of 1205 AN cases and 1948 controls. We identified individual variant associations in the Estrogen Receptor-ß (ESR2) gene, as well as a set of rare and common variants in the Epoxide Hydrolase 2 (EPHX2) gene, in an initial sequencing study of 261 early-onset severe AN cases and 73 controls (P=0.0004). The association of EPHX2 variants was further delineated in: (1) a pooling-based replication study involving an additional 500 AN patients and 500 controls (replication set P=0.00000016); (2) single-locus studies in a cohort of 386 previously genotyped broadly defined AN cases and 295 female population controls from the Bogalusa Heart Study (BHS) and a cohort of 58 individuals with self-reported eating disturbances and 851 controls (combined smallest single locus P<0.01). As EPHX2 is known to influence cholesterol metabolism, and AN is often associated with elevated cholesterol levels, we also investigated the association of EPHX2 variants and longitudinal body mass index (BMI) and cholesterol in BHS female and male subjects (N=229) and found evidence for a modifying effect of a subset of variants on the relationship between cholesterol and BMI (P<0.01). These findings suggest a novel association of gene variants within EPHX2 to susceptibility to AN and provide a foundation for future study of this important yet poorly understood condition

Comparing Effect of Safranal and Diazepam in Reducing Preoperative Anxiety and Improving Vital Symptoms

Aim: Preoperative anxiety is an unpleasant manner created by fear of surgery. The aim of the present study was to compare the effects of diazepam pill with Safranal in reducing preoperative anxiety and improving vital symptoms. Material and Methods: In this double blind randomized clinical trial, 54 patients who were candidates of urology surgery (varicocele) in 15th Khordad Hospital, Gonabad, Iran, were selected by purposive sampling method, using a randomized numbers table; they were divided into intervention (n=29) and control group (n=25). The patients in intervention group received 15mg Safranal and the patients in control group received 5mg oral diazepam 3 hours before surgery. The State-Trait Anxiety Inventory (STAI) questionnaire was completed by the patients prior to the intervention and just at the entrance to the surgery room, and the vital symptoms of the patient were evaluated. The data were analyzed by SPSS 11.5 software, using of Chi-square and independent sample t-test. Findings: After intervention, the trait anxiety in the Safranal group was significantly lower than diazepam group (p=0.007) and before the intervention (p=0.002). Also, diastolic blood pressure decreased significantly in the Safranal group compared with the diazepam group (p=0.049). Conclusion: Saffranal consumption before surgery is more effective than diazepam consumption in reducing the trait anxiety, but it does not affect state anxiety. Also, compared to diazepam, Saffranal consumption leads to a more reduction in diastolic blood pressure, while it does not affect systolic blood pressure and heart rate