Coanalysis of GWAS with eQTLs reveals disease-tissue associations.

Expression quantitative trait loci (eQTL), or genetic variants associated with changes in gene expression, have the potential to assist in interpreting results of genome-wide association studies (GWAS). eQTLs also have varying degrees of tissue specificity. By correlating the statistical significance of eQTLs mapped in various tissue types to their odds ratios reported in a large GWAS by the Wellcome Trust Case Control Consortium (WTCCC), we discovered that there is a significant association between diseases studied genetically and their relevant tissues. This suggests that eQTL data sets can be used to determine tissues that play a role in the pathogenesis of a disease, thereby highlighting these tissue types for further post-GWAS functional studies

Continuous Measurements of Greenhouse Gases and Atmospheric Oxygen in the Namib Desert

A new, near-coastal background site was established for observations of greenhouse gases (GHGs) and atmospheric oxygen in the central Namib Desert near Gobabeb, Namibia. The location of the site was chosen to provide observations in a data-poor region in the global sampling network for GHGs. Semi-automated, continuous measurements of carbon dioxide, methane, nitrous oxide, carbon monoxide, atmospheric oxygen, and basic meteorology are made at a height of 21 m a.g.l., 50 km from the coast at the northern border of the Namib Sand Sea. Atmospheric oxygen is measured with a differential fuel cell analyzer. Carbon dioxide and methane are measured with an early-model cavity ring-down spectrometer; nitrous oxide and carbon monoxide are measured with an off-axis integrated cavity output spectrometer. Instrument-specific water corrections are employed for both instruments in lieu of drying. The representativity of the site was assessed within the context of atmospheric transport. During austral summer, strong equatorward winds are present as a result of the Hadley circulation. This brings marine boundary layer air inland to Gobabeb. In austral winter, the descending branch of the southern Hadley cell is at the same latitude as NDAO, which encourages the establishment of anticyclonic conditions over southern Africa. The variability of air mass history during this time of year is quite high, alternating between marine and terrestrial air masses, as well as air that was recently in contact with the surface and air that had descended from heights greater than 2 km. NOAA ask samples taken at Gobabeb from 1996 to the present appeared to respond to these seasonal patterns in atmospheric dynamics, when compared to other marine background sites at the same latitude as NDAO. Two years of data are presented from the observatory. Diurnal variability was noted at times for all species, particularly for atmospheric oxygen. Through stoichiometry and phasing, this was attributed primarily to the local wind system, which features a prominent sea breeze, and daily boundary layer oscillations. Large anomalies in carbon monoxide and methane were observed in the time series on a synoptic time scale, during the ascending portion of the seasonal cycle. These were attributed to an alternation between polluted air masses from the continental interior and marine boundary layer air. The continental air masses were progressively in uenced by biomass burning as the fire season developed. The concentration of re activity close to the station increased throughout the year, peaking in September, a fact re ected in the enhancement ratio of CH4 to CO. During such synoptic events the molar exchange ratio of O2 to CO2 also supported this interpretation. Finally, the NDAO time series was used to make top-down estimates of air-sea fl uxes of the main measurands from the Lüderitz and Walvis Bay upwelling cells in the Benguela Current region, during upwelling events. Flux densities were evaluated using shipboard measurements within the study area, showing good agreement with the top-down estimates. Average flux densities for CO2 were 0.450.4 µmol m-2 sec-1, -3.92.6 µmol m-2 sec-1 for O2, 6.05.0 nmol m-2 sec-1 for CH4, 0.50.4 nmol m-2 sec-1 for N2O, and 2.71.7 nmol m-2 sec-1 for CO. N2O uxes were fairly low, in accord with previous work, suggesting that the evasion of this gas from the Benguela is smaller than in other upwelling systems. Conversely, methane release was very high for the marine environment, which adds to mounting evidence of a large sedimentary source of methane in the Walvis Bay area. Carbon dioxide and oxygen uxes were substantial and probably not accounted for in current budgets

Biotic interactions in soil and dung shape parasite transmission in temperate ruminant systems : An integrative framework

ACKNOWLEDGMENTS We are thankful to QUADRAT doctoral training partnership for providing the opportunity to complete this work. This work was supported by a QUADRAT doctoral training program PhD studentship from UK Research and Innovation, via the Natural Environment Research Council. Natural Environment Research Council (NERC). Grant Number: NE/S007377/1 UKRIPeer reviewe

OpWise: Operons aid the identification of differentially expressed genes in bacterial microarray experiments

BACKGROUND: Differentially expressed genes are typically identified by analyzing the variation between replicate measurements. These procedures implicitly assume that there are no systematic errors in the data even though several sources of systematic error are known. RESULTS: OpWise estimates the amount of systematic error in bacterial microarray data by assuming that genes in the same operon have matching expression patterns. OpWise then performs a Bayesian analysis of a linear model to estimate significance. In simulations, OpWise corrects for systematic error and is robust to deviations from its assumptions. In several bacterial data sets, significant amounts of systematic error are present, and replicate-based approaches overstate the confidence of the changers dramatically, while OpWise does not. Finally, OpWise can identify additional changers by assigning genes higher confidence if they are consistent with other genes in the same operon. CONCLUSION: Although microarray data can contain large amounts of systematic error, operons provide an external standard and allow for reasonable estimates of significance. OpWise is available at

Using Net Groundwater Extractions for Farm Level Groundwater Sustainability Monitoring

The Cal Poly Irrigation Training and Research Center (ITRC) has developed a method for computing net groundwater extraction and recharge at the farm level for district management and regulation of sustainable/safe yields. This method is called Net To/From Groundwater (NTFGW). Net groundwater extraction is preferred for assessing sustainable yield in unconfined aquifer systems over direct metering of gross groundwater pumping. A recent pilot project with the Lower Tule River and Pixley Irrigation Districts’ Groundwater Sustainability Agencies (GSAs) compared actual metered groundwater pumping, surface deliveries, and evapotranspiration to the NTFGW outputs on 19 farms within the GSAs over a 3-year period (2014-2016). In nearly all cases gross metered pumping was greater than net groundwater use, as it should be. In the few instances where this was not the case, intensive investigations identified the issues, which will be presented. The average difference between gross and net groundwater extractions was approximately 14”. The variation of this difference was substantial between farms, indicating the difficulty in using gross pumping from flow/volume metering of actual pumping for sustainability. The NTFGW can incorporate seepage and recharge basin operation on a GSA level. It is also capable of tracking banked groundwater supplies on a farm level

Microspectrophotometric Analysis of Yellow Polyester Fiber Dye Loadings with Chemometric Techniques

Microspectrophotometry is a quick, accurate, and reproducible method to compare colored fibers for forensic purposes. Applying chemometric techniques to spectroscopic data can provide valuable information, especially when looking at a complex dataset. In this study, background subtracted and normalized visible spectra from ten yellow polyester exemplars dyed with different concentrations of the same dye ranging from 0.1% to 3.5% (w/w), were analyzed by agglomerative hierarchical clustering (AHC), principal component analysis (PCA), and discriminant analysis (DA). Systematic changes in the wavelength of maximum absorption, peak shape and signal-to-background ratio were noted as dye loading increased. In general, classifying the samples into ten groups (one for each exemplar) had poor accuracy (i.e., 51%). However, classification was much more accurate (i.e., 96%) using three classes of fibers that were identified by AHC as having low (0.10–0.20 wt%), medium (0.40–0.75 wt%), and high (1.5–3.5 wt%) dye loadings. An external validation with additional fibers and data generated by independent analysts confirmed these findings. Lastly, it was also possible to discriminating pairs of exemplars with small differences in dye loadings as a simulation of questioned (Q) versus known (K) comparisons

A novel method for accurate operon predictions in all sequenced prokaryotes

We combine comparative genomic measures and the distance separating adjacent genes to predict operons in 124 completely sequenced prokaryotic genomes. Our method automatically tailors itself to each genome using sequence information alone, and thus can be applied to any prokaryote. For Escherichia coli K12 and Bacillus subtilis, our method is 85 and 83% accurate, respectively, which is similar to the accuracy of methods that use the same features but are trained on experimentally characterized transcripts. In Halobacterium NRC-1 and in Helicobacter pylori, our method correctly infers that genes in operons are separated by shorter distances than they are in E.coli, and its predictions using distance alone are more accurate than distance-only predictions trained on a database of E.coli transcripts. We use microarray data from six phylogenetically diverse prokaryotes to show that combining intergenic distance with comparative genomic measures further improves accuracy and that our method is broadly effective. Finally, we survey operon structure across 124 genomes, and find several surprises: H.pylori has many operons, contrary to previous reports; Bacillus anthracis has an unusual number of pseudogenes within conserved operons; and Synechocystis PCC 6803 has many operons even though it has unusually wide spacings between conserved adjacent genes

Perceived sports competence mediates the relationship between childhood motor skill proficiency and adolescent physical activity and fitness: a longitudinal assessment

Background: The purpose of this paper was to investigate whether perceived sports competence mediates the relationship between childhood motor skill proficiency and subsequent adolescent physical activity and fitness.Methods: In 2000, children\u27s motor skill proficiency was assessed as part of a school-based physical activity intervention. In 2006/07, participants were followed up as part of the Physical Activity and Skills Study and completed assessments for perceived sports competence (Physical Self-Perception Profile), physical activity (Adolescent Physical Activity Recall Questionnaire) and cardiorespiratory fitness (Multistage Fitness Test). Structural equation modelling techniques were used to determine whether perceived sports competence mediated between childhood object control skill proficiency (composite score of kick, catch and overhand throw), and subsequent adolescent self-reported time in moderate-to-vigorous physical activity and cardiorespiratory fitness.Results: Of 928 original intervention participants, 481 were located in 28 schools and 276 (57%) were assessed with at least one follow-up measure. Slightly more than half were female (52.4%) with a mean age of 16.4 years (range 14.2 to 18.3 yrs). Relevant assessments were completed by 250 (90.6%) students for the Physical Activity Model and 227 (82.3%) for the Fitness Model. Both hypothesised mediation models had a good fit to the observed data, with the Physical Activity Model accounting for 18% (R2 = 0.18) of physical activity variance and the Fitness Model accounting for 30% (R2 = 0.30) of fitness variance. Sex did not act as a moderator in either model.Conclusion: Developing a high perceived sports competence through object control skill development in childhood is important for both boys and girls in determining adolescent physical activity participation and fitness. Our findings highlight the need for interventions to target and improve the perceived sports competence of youth.<br /