Distribution and abundance of cephalopods in UK waters: long-term trends and environmental relationships

As part of a project which aimed to evaluate the feasibility of developing indicators of marine ecosystem status based on cephalopods, we analysed spatiotemporal variation in abundance,, and environmental relationships, using trawl survey catch data for cephalopods in UK waters (1980-2013) from Cefas and Marine Scotland Science databases. These data presented some challenges, notably the use of several different trawl gears, variable tow durations, and varying levels of taxonomic resolution. Accounting for gear type and tow duration, data were analysed separately for each cephalopod family and season to account for different phases of the life cycles being present at different times of year. The families investigated were Loliginidae, Octopodidae, Ommastrephidade, Sepiidae and Sepiolidae. A GAM framework was used to summarise spatiotemporal variation in abundance at family level and the relationships of spatial and long-term temporal variation with environmental variables, including depth, substrate (available for inshore waters) and several oceanographic variables (e.g., SST, chl signals), also considering fishing pressure. Long-term trends for each family varied between areas and seasons, although this may reflect the presence of several species within families. In Scotland, where Loligo vulgaris is rare and L. forbesii is normally distinguished from Alloteuthis spp., survey data suggested a peak in abundance of this species around 1990 and a generally increasing trend since the mid-1990s. Spatial patterns in distribution in all families were related to both physiographic and oceanographic features. As expected substrate type had most effect on those families in which eggs are attached to objects on the seabed

Automated workflow-based exploitation of pathway databases provides new insights into genetic associations of metabolite profiles

Background: Genome-wide association studies (GWAS) have identified many common single nucleotide polymorphisms (SNPs) that associate with clinical phenotypes, but these SNPs usually explain just a small part of the heritability and have relatively modest effect sizes. In contrast, SNPs that associate with metabolite levels generally explain a higher percentage of the genetic variation and demonstrate larger effect sizes. Still, the discovery of SNPs associated with metabolite levels is challenging since testing all metabolites measured in typical metabolomics studies with all SNPs comes with a severe multiple testing penalty. We have developed an automated workflow approach that utilizes prior knowledge of biochemical pathways present in databases like KEGG and BioCyc to generate a smaller SNP set relevant to the metabolite. This paper explores the opportunities and challenges in the analysis of GWAS of metabolomic phenotypes and provides novel insights into the genetic basis of metabolic variation through the re-analysis of published GWAS datasets. Results: Re-analysis of the published GWAS dataset from Illig et al. (Nature Genetics, 2010) using a pathway-based workflow (http://www.myexperiment.org/packs/319.html), confirmed previously identified hits and identified a new locus of human metabolic individuality, associating Aldehyde dehydrogenase family1 L1 (ALDH1L1) with serine/glycine ratios in blood. Replication in an independent GWAS dataset of phospholipids (Demirkan et al., PLoS Genetics, 2012) identified two novel loci supported by additional literature evidence: GPAM (Glycerol-3 phosphate acyltransferase) and CBS (Cystathionine beta-synthase). In addition, the workflow approach provided novel insight into the affected pathways and relevance of some of these gene-metabolite pairs in disease development and progression. Conclusions: We demonstrate the utility of automated exploitation of background knowledge present in pathway databases for the analysis of GWAS datasets of metabolomic phenotypes. We report novel loci and potential biochemical mechanisms that contribute to our understanding of the genetic basis of metabolic variation and its relationship to disease development and progression

Novel Loci for Adiponectin Levels and Their Influence on Type 2 Diabetes and Metabolic Traits : A Multi-Ethnic Meta-Analysis of 45,891 Individuals

J. Kaprio, S. Ripatti ja M.-L. Lokki työryhmien jäseniä.Peer reviewe

The Influence of Age and Sex on Genetic Associations with Adult Body Size and Shape : A Large-Scale Genome-Wide Interaction Study

Genome-wide association studies (GWAS) have identified more than 100 genetic variants contributing to BMI, a measure of body size, or waist-to-hip ratio (adjusted for BMI, WHRadjBMI), a measure of body shape. Body size and shape change as people grow older and these changes differ substantially between men and women. To systematically screen for age-and/or sex-specific effects of genetic variants on BMI and WHRadjBMI, we performed meta-analyses of 114 studies (up to 320,485 individuals of European descent) with genome-wide chip and/or Metabochip data by the Genetic Investigation of Anthropometric Traits (GIANT) Consortium. Each study tested the association of up to similar to 2.8M SNPs with BMI and WHRadjBMI in four strata (men 50y, women 50y) and summary statistics were combined in stratum-specific meta-analyses. We then screened for variants that showed age-specific effects (G x AGE), sex-specific effects (G x SEX) or age-specific effects that differed between men and women (G x AGE x SEX). For BMI, we identified 15 loci (11 previously established for main effects, four novel) that showed significant (FDR= 50y). No sex-dependent effects were identified for BMI. For WHRadjBMI, we identified 44 loci (27 previously established for main effects, 17 novel) with sex-specific effects, of which 28 showed larger effects in women than in men, five showed larger effects in men than in women, and 11 showed opposite effects between sexes. No age-dependent effects were identified for WHRadjBMI. This is the first genome-wide interaction meta-analysis to report convincing evidence of age-dependent genetic effects on BMI. In addition, we confirm the sex-specificity of genetic effects on WHRadjBMI. These results may providefurther insights into the biology that underlies weight change with age or the sexually dimorphism of body shape.Peer reviewe

Measurement of the Photodissociation Coefficient of NO2 in the Atmosphere: II. Stratospheric Measurements

The photodissociation coefficient of NO2, J NO 2, has been measured from a balloon platform in the stratosphere. Results from two balloon flights are reported. High Sun values of J NO 2 measured were 10.5±0.3 and 10.3±0.3×10-3 s-1 at 24 and 32 km respectively. The decrease in J NO 2 at sunset was monitored in both flights. The measurements are found to be in good agreement with calculations of J NO 2 using a simplified isotropic multiple scattering computer routine

The distribution of nitrogen oxides off the East Coast of North America

Measurements of NO and NOx' (as measured by a chemiluminescent analyzer equipped with a FeSO4 converter) were made from an aircraft off the east coast of North America in January and February 1986. These measurements show the mixing ratios of the nitrogen oxides to be higher than encountered in remote continental or marine environments. Both the free troposphere and boundary layer mixing ratio distributions are skewed to ward high mixing ratios and are best described by a gamma probability distribution. The mean mixing ratios observed were 2.9 parts per billion by volume (ppbv) in the boundary layer and 0.55 ppbv in the free troposphere for NOx', and 0.56 ppbv in the boundary layer and 0.18 in the free troposphere for NO

Measurement of the Photodissociation Coefficient of NO2 in the Atmosphere: I. Method and Surface Measurements

The photodissociation coefficient of NO2, J NO 2, has been measured from a balloon platform in the stratosphere. Results from two balloon flights are reported. High Sun values of J NO 2 measured were 10.5±0.3 and 10.3±0.3×10-3 s-1 at 24 and 32 km respectively. The decrease in J NO 2 at sunset was monitored in both flights. The measurements are found to be in good agreement with calculations of J NO 2 using a simplified isotropic multiple scattering computer routine

Calculations of the Temperature Dependence of the NO2 Photodissociation Coefficient in the Atmosphere

The photodissociation coefficient, J NO2 of NO2 in the atmosphere was calculated at 235 and 298 K using the measured temperature dependences of the absorption cross-sections and quantum yields. These calculations gave a ratio J NO2(298 K)/J NO2(235 K)=1.155±0.010 which is only weakly dependent on altitude, surface albedo and solar zenith angle