Draft Genome Sequence of the Yeast Rhodotorula sp. Strain CCFEE 5036, Isolated from McMurdo Dry Valleys, Antarctica.

A draft genome sequence was assembled and annotated of the basidiomycetous yeast Rhodotorula sp. strain CCFEE 5036, isolated from Antarctic soil communities. The genome assembly is 19.07 megabases and encodes 6,434 protein-coding genes. The sequence will contribute to understanding the diversity of fungi inhabiting polar regions

Rider energy expenditure during high intensity horse activity and the potential for health benefits

Obesity and disease associated with sedentary lifestyles have become major concerns in the United States. Exercise has been described as a crucial part of disease prevention and overall health, with activities such as biking or running cited as examples. Horseback riding is a popular activity; however, little information on the exercise value of horseback riding exists. The objective of this experiment was to define the energy expenditure of participants in several common riding events. All procedures were approved by the Texas A&M Institutional Review Board and Institutional Animal Care and Use Committee; subjects gave written consent prior to participation. Twenty subjects completed each of three riding tests: a 45min walk-trot-canter ride (WTC), a reining pattern, and a cutting pattern while wearing a telemetric gas analyzer. Anthropometric data were obtained for each subject through DEXA scans. Total energy expenditure (tEE), as well as mean and peak energy expenditure per minute (EE/min), metabolic equivalents of task (MET), heart rate (HR), respiratory frequency (RF), pulmonary ventilation (VE), oxygen consumption (VO2), relative oxygen consumption (relVO2) and carbon dioxide production (­VCO2)were measured. Mean energy expenditure per minute, and HR responses were greater (P \u3c 0.05) for reining (6.96±0.23Kcal/min, 163.28±4.2bpm) and cutting (4.98±0.23Kcal/min, 146.9±4.2bpm) than for WTC (4.27±0.23Kcal/min, 131.5±4.2bpm). When WTC test was evaluated by gait component, mean EE/min and MET increased as gait speed increased. Mean EE/min and MET were higher (P \u3c 0.05) for riders at long trot (6.9±0.21Kcal/min, 6.19±0.21MET) and canter (6.93±0.21Kcal/min, 5.95±0.21MET) gaits than during the walk (2.34±0.21Kcal.min, 2.01±0.21MET) or trot (3.5±0.21Kcal/min, 3.2±0.21MET) gaits. Similar patterns were observed for RF, VE, VO2, VCO2 and RelVO2 across disciplines and by gait component. The tEE (194.7±3.84kcal/min) and mean MET (4.27±0.23MET) observed during the 45-min WTC ride were within current national recommendations of intensity (3-6MET), time (\u3e30min) and calories burned (~1000Kcal/wk). The results of this study provide novel information about exercise intensity values for horseback activities and differences among riding disciplines measured in real time using a portable system. Riders engaged in cutting and reining experienced more intense exercise in short durations, while WTC provided a greater total energy expenditure. These data suggest that it is possible, if riding at the more intense gaits such as long trot and canter, for health benefits to be achieved through accumulated weekly horseback riding exercise

Performance of a non-invasive test for detecting mycobacterium bovis shedding in European badger (meles meles) populations

The incidence of Mycobacterium bovis, the causative agent of bovine tuberculosis, in cattle herds in the United Kingdom is increasing, resulting in substantial economic losses. The European badger (Meles meles) is implicated as a wildlife reservoir and is the subject of control measures aimed at reducing incidence in cattle populations. Understanding the epidemiology of M. bovis in badger populations is essential to direct control interventions and understand disease spread; however, accurate diagnosis in live animals is challenging and currently uses invasive methods. Here we present a non-invasive diagnostic procedure and sampling regime using field sampling of latrines and detection of M. bovis with qPCR, the results of which strongly correlate with the results of immunoassay testing in the field at the social group level. This method allows M. bovis infection in badger populations to be monitored without trapping and provides additional information on the quantity of bacterial DNA shed. Our approach may therefore provide valuable insights into the epidemiology of bovine tuberculosis in badger populations and inform disease control interventions

The variability and seasonality of the environmental reservoir of Mycobacterium bovis shed by wild European badgers

The incidence of Mycobacterium bovis, the causative agent of bovine tuberculosis, has been increasing in UK cattle herds resulting in substantial economic losses. The European badger (Meles meles) is implicated as a wildlife reservoir of infection. One likely route of transmission to cattle is through exposure to infected badger urine and faeces. The relative importance of the environment in transmission remains unknown, in part due to the lack of information on the distribution and magnitude of environmental reservoirs. Here we identify potential infection hotspots in the badger population and quantify the heterogeneity in bacterial load; with infected badgers shedding between 1 × 103 − 4 × 105 M. bovis cells g−1 of faeces, creating a substantial and seasonally variable environmental reservoir. Our findings highlight the potential importance of monitoring environmental reservoirs of M. bovis which may constitute a component of disease spread that is currently overlooked and yet may be responsible for a proportion of transmission amongst badgers and onwards to cattle

Evidence that breast cancer risk at the 2q35 locus is mediated through IGFBP5 regulation.

GWAS have identified a breast cancer susceptibility locus on 2q35. Here we report the fine mapping of this locus using data from 101,943 subjects from 50 case-control studies. We genotype 276 SNPs using the 'iCOGS' genotyping array and impute genotypes for a further 1,284 using 1000 Genomes Project data. All but two, strongly correlated SNPs (rs4442975 G/T and rs6721996 G/A) are excluded as candidate causal variants at odds against >100:1. The best functional candidate, rs4442975, is associated with oestrogen receptor positive (ER+) disease with an odds ratio (OR) in Europeans of 0.85 (95% confidence interval=0.84-0.87; P=1.7 × 10(-43)) per t-allele. This SNP flanks a transcriptional enhancer that physically interacts with the promoter of IGFBP5 (encoding insulin-like growth factor-binding protein 5) and displays allele-specific gene expression, FOXA1 binding and chromatin looping. Evidence suggests that the g-allele confers increased breast cancer susceptibility through relative downregulation of IGFBP5, a gene with known roles in breast cell biology

Breast cancer risk variants at 6q25 display different phenotype associations and regulate ESR1, RMND1 and CCDC170.

We analyzed 3,872 common genetic variants across the ESR1 locus (encoding estrogen receptor α) in 118,816 subjects from three international consortia. We found evidence for at least five independent causal variants, each associated with different phenotype sets, including estrogen receptor (ER(+) or ER(-)) and human ERBB2 (HER2(+) or HER2(-)) tumor subtypes, mammographic density and tumor grade. The best candidate causal variants for ER(-) tumors lie in four separate enhancer elements, and their risk alleles reduce expression of ESR1, RMND1 and CCDC170, whereas the risk alleles of the strongest candidates for the remaining independent causal variant disrupt a silencer element and putatively increase ESR1 and RMND1 expression.This is the author accepted manuscript. The final version is available from Nature Publishing Group via http://dx.doi.org/10.1038/ng.352

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

United States Midwest Soil and Weather Conditions Influence Anaerobic Potentially Mineralizable Nitrogen

Nitrogen provided to crops through mineralization is an important factor in N management guidelines. Understanding of the interactive effects of soil and weather conditions on N mineralization needs to be improved. Relationships between anaerobic potentially mineralizable N (PMNan) and soil and weather conditions were evaluated under the contrasting climates of eight US Midwestern states. Soil was sampled (0–30 cm) for PMNan analysis before pre-plant N application (PP0N) and at the V5 development stage from the pre-plant 0 (V50N) and 180 kg N ha−1 (V5180N) rates and incubated for 7, 14, and 28 d. Even distribution of precipitation and warmer temperatures before soil sampling and greater soil organic matter (SOM) increased PMNan. Soil properties, including total C, SOM, and total N, had the strongest relationships with PMNan (R2 ≤ 0.40), followed by temperature (R2 ≤ 0.20) and precipitation (R2 ≤ 0.18) variables. The strength of the relationships between soil properties and PMNan from PP0N, V50N, and V5180N varied by ≤10%. Including soil and weather in the model greatly increased PMNan predictability (R2 ≤ 0.69), demonstrating the interactive effect of soil and weather on N mineralization at different times during the growing season regardless of N fertilization. Delayed soil sampling (V50N) and sampling after fertilization (V5180N) reduced PMNan predictability. However, longer PMNan incubations improved PMNan predictability from both V5 soil samplings closer to the PMNan predictability from PP0N, indicating the potential of PMNan from longer incubations to provide improved estimates of N mineralization when N fertilizer is applied

Soil sample timing, nitrogen fertilization, and incubation length influence anaerobic potentially mineralizable nitrogen

Understanding the variables that affect the anaerobic potentially mineralizable N (PMNan) test should lead to a standard procedure of sample collection and incubation length, improving PMNan as a tool in corn (Zea mays L.) N management. We evaluated the effect of soil sample timing (preplant and V5 corn development stage [V5]), N fertilization (0 and 180 kg ha−1) and incubation length (7, 14, and 28 d) on PMNan (0–30 cm) across a range of soil properties and weather conditions. Soil sample timing, N fertilization, and incubation length affected PMNan differently based on soil and weather conditions. Preplant vs. V5 PMNan tended to be greater at sites that received \u3c 183 mm of precipitation or \u3c 359 growing degree-days (GDD) between preplant and V5, or had soil C/N ratios \u3e 9.7:1; otherwise, V5 PMNan tended to be greater than preplant PMNan. The PMNan tended to be greater in unfertilized vs. fertilized soil in sites with clay content \u3e 9.5%, total C \u3c 24.2 g kg−1, soil organic matter (SOM) \u3c 3.9 g kg−1, or C to N ratios \u3c 11.0:1; otherwise, PMNan tended to be greater in fertilized vs. unfertilized soil. Longer incubation lengths increased PMNan at all sites regardless of sampling methods. Since PMNan is sensitive to many factors (sample timing, N fertilization, incubation length, soil properties, and weather conditions), it is important to follow a consistent protocol to compare PMNan among sites and potentially use PMNan to improve corn N management