Genetic association analysis of vitamin D pathway with obesity traits

Objective:Observational studies have examined the link between vitamin D deficiency and obesity traits. Some studies have reported associations between vitamin D pathway genes such as VDR, GC and CYP27B1 with body mass index (BMI) and waist circumference (WC); however, the findings have been inconsistent. Therefore, we investigated the involvement of vitamin D metabolic pathway genes in obesity-related traits in a large population-based study.Methods:We undertook a comprehensive analysis between 100 tagging single nucleotide polymorphisms (tagSNPs) in genes encoding for DHCR7, CYP2R1, VDBP, CYP27B1, CYP27A1, CYP24A1, VDR and RXRG, and obesity traits in 5224 participants (aged 45 years) in the 1958 British birth cohort (1958BC). We further extended our analyses to investigate the associations between SNPs and obesity traits using the summary statistics from the GIANT (Genetic Investigation of Anthropometric Traits) consortium (n=123 865).Results:In the 1958BC (n=5224), after Bonferroni correction, none of the tagSNPs were associated with obesity traits except for one tagSNP from CYP24A1 that was associated with waist-hip ratio (WHR) (rs2296239, P=0.001). However, the CYP24A1 SNP was not associated with BMI-adjusted WHR (WHRadj) in the 1958BC (rs2296239, P=1.00) and GIANT results (n=123 865, P=0.18). There was also no evidence for an interaction between the tagSNPs and obesity on BMI, WC, WHR and WHRadj in the 1958BC. In the GIANT consortium, none of the tagSNPs were associated with obesity traits.Conclusions:Despite a very large study, our findings suggest that the vitamin D pathway genes are unlikely to have a major role in obesity-related traits in the general population.

Dietary factors impact on the association between CTSS variants and obesity related traits

BACKGROUND/AIMS: Cathepsin S, a protein coded by the CTSS gene, is implicated in adipose tissue biology--this protein enhances adipose tissue development. Our hypothesis is that common variants in CTSS play a role in body weight regulation and in the development of obesity and that these effects are influenced by dietary factors--increased by high protein, glycemic index and energy diets. METHODS: Four tag SNPs (rs7511673, rs11576175, rs10888390 and rs1136774) were selected to capture all common variation in the CTSS region. Association between these four SNPs and several adiposity measurements (BMI, waist circumference, waist for given BMI and being a weight gainer-experiencing the greatest degree of unexplained annual weight gain during follow-up or not) given, where applicable, both as baseline values and gain during the study period (6-8 years) were tested in 11,091 European individuals (linear or logistic regression models). We also examined the interaction between the CTSS variants and dietary factors--energy density, protein content (in grams or in % of total energy intake) and glycemic index--on these four adiposity phenotypes. RESULTS: We found several associations between CTSS polymorphisms and anthropometric traits including baseline BMI (rs11576175 (SNP N°2), p = 0.02, β = -0.2446), and waist change over time (rs7511673 (SNP N°1), p = 0.01, β = -0.0433 and rs10888390 (SNP N°3), p = 0.04, β = -0.0342). In interaction with the percentage of proteins contained in the diet, rs11576175 (SNP N°2) was also associated with the risk of being a weight gainer (p(interaction) = 0.01, OR = 1.0526)--the risk of being a weight gainer increased with the percentage of proteins contained in the diet. CONCLUSION: CTSS variants seem to be nominally associated to obesity related traits and this association may be modified by dietary protein intake.

Up-gradient eddy fluxes of potential vorticity near the subtropical jet

The role of eddy fluxes in the general circulation is often approached by treating eddies as (macro)turbulence. In this approach, the eddies act to diffuse certain quasiconservative quantities, such as potential vorticity (PV), along isentropic surfaces in the free atmosphere. The eddy fluxes are determined primarily by the eddy diffusivities and are necessarily down-gradient of the basic state PV field. Support for the (macro)turbulence approach stems from the fact that the eddy fluxes of PV in the free atmosphere are generally down-gradient in the long-term mean. Here we call attention to a pronounced and significant region of upgradient eddy PV fluxes on the poleward flank of the jet core in both hemispheres. The region of up-gradient (i.e., notionally “antidiffusive”) eddy PV fluxes is most pronounced during the winter and spring seasons and partially contradicts the turbulence approach described above. Analyses of the PV variance (potential enstrophy) budget suggest that the up-gradient PV fluxes represent local wave decay and are maintained by poleward fluxes of PV variance. Finite-amplitude effects thus represent leading order contributions to the PV variance budget, whereas dissipation is only of secondary importance locally. The appearance of up-gradient PV fluxes in the long-term mean is associated with the poleward shift of the jet—and thus the region of wave decay relative to wave growth—following wave-breaking events.

Changes of the equilibrium line altitude since the Little Ice Age in the Nepalese Himalayas

Changes of the equilibrium-line altitude (ELA) since the end of the Little Ice Age (LIA) in eastern Nepal have been studied using glacier inventory data. The toe-to-headwall altitude ratios (THARs) for individual glaciers were calculated for 1992, and used to estimate the ELA in 1959 and at the end of the LIA. THAR for debris-free glaciers is found to be smaller than for debris-covered glaciers. The ELAs for debris-covered glaciers are higher than those for debris-free glaciers in eastern Nepal. There is considerable variation in the reconstructed change in ELA (ΔELA) between glaciers within specific regions and between regions. This is not related to climate gradients, but results from differences in glacier aspect: southeast- and south-facing glaciers show larger ΔELAs in eastern Nepal than north- or west-facing glaciers. The data suggest that the rate of ELA rise may have accelerated in the last few decades. The limited number of climate records from Nepal, and analyses using a simple ELA–climate model, suggest that the higher rate of the ΔELA between 1959 and 1992 is a result of increased warming that occurred after the 1970s at higher altitudes in Nepal.

Relationships between plant traits and climate in the Mediterranean region: an analysis based on pollen data

Question: What are the correlations between the degree of drought stress and temperature, and the adoption of specific adaptive strategies by plants in the Mediterranean region? Location: 602 sites across the Mediterranean region. Method: We considered 12 plant morphological and phenological traits, and measured their abundance at the sites as trait scores obtained from pollen percentages. We conducted stepwise regression analyses of trait scores as a function of plant available moisture (α) and winter temperature (MTCO). Results: Patterns in the abundance for the plant traits we considered are clearly determined by α, MTCO or a combination of both. In addition, trends in leaf size, texture, thickness, pubescence and aromatic leaves and other plant level traits such as thorniness and aphylly, vary according to the life form (tree, shrub, forb), the leaf type (broad, needle) and phenology (evergreen, summer-green). Conclusions: Despite conducting this study based on pollen data we have identified ecologically plausible trends in the abundance of traits along climatic gradients. Plant traits other than the usual life form, leaf type and leaf phenology carry strong climatic signals. Generally, combinations of plant traits are more climatically diagnostic than individual traits. The qualitative and quantitative relationships between plant traits and climate parameters established here will help to provide an improved basis for modelling the impact of climate changes on vegetation and form a starting point for a global analysis of pollen-climate relationships

Autistic traits modulate frontostriatal connectivity during processing of rewarding faces

Deficits in facial mimicry have been widely reported in autism. Some studies have suggested that these deficits are restricted to spontaneous mimicry and do not extend to volitional mimicry. We bridge these apparently inconsistent observations, by testing the impact of reward value on neural indices of mimicry, and how autistic traits modulate this impact. Neutral faces were conditioned with high and low reward. Subsequently, functional connectivity between the ventral striatum (VS) and inferior frontal gyrus (IFG) was measured whilst neurotypical adults (n = 30) watched happy expressions made by these conditioned faces. We found greater VS-IFG connectivity in response to high-reward vs. low-reward happy faces. This difference was negatively proportional to autistic traits, suggesting that reduced spontaneous mimicry of social stimuli seen in autism, maybe related to a failure in the modulation of the mirror system by the reward system rather than a circumscribed deficit in the mirror system.

Interaction between allelic variations in vitamin D receptor and retinoid X receptor genes on metabolic traits

BACKGROUND: Low vitamin D status has been shown to be a risk factor for several metabolic traits such as obesity, diabetes and cardiovascular disease. The biological actions of 1, 25-dihydroxyvitamin D, are mediated through the vitamin D receptor (VDR), which heterodimerizes with retinoid X receptor, gamma (RXRG). Hence, we examined the potential interactions between the tagging polymorphisms in the VDR (22 tag SNPs) and RXRG (23 tag SNPs) genes on metabolic outcomes such as body mass index, waist circumference, waist-hip ratio (WHR), high- and low-density lipoprotein (LDL) cholesterols, serum triglycerides, systolic and diastolic blood pressures and glycated haemoglobin in the 1958 British Birth Cohort (1958BC, up to n = 5,231). We used Multifactor- dimensionality reduction (MDR) program as a non-parametric test to examine for potential interactions between the VDR and RXRG gene polymorphisms in the 1958BC. We used the data from Northern Finland Birth Cohort 1966 (NFBC66, up to n = 5,316) and Twins UK (up to n = 3,943) to replicate our initial findings from 1958BC. RESULTS: After Bonferroni correction, the joint-likelihood ratio test suggested interactions on serum triglycerides (4 SNP - SNP pairs), LDL cholesterol (2 SNP - SNP pairs) and WHR (1 SNP - SNP pair) in the 1958BC. MDR permutation model testing analysis showed one two-way and one three-way interaction to be statistically significant on serum triglycerides in the 1958BC. In meta-analysis of results from two replication cohorts (NFBC66 and Twins UK, total n = 8,183), none of the interactions remained after correction for multiple testing (Pinteraction >0.17). CONCLUSIONS: Our results did not provide strong evidence for interactions between allelic variations in VDR and RXRG genes on metabolic outcomes; however, further replication studies on large samples are needed to confirm our findings.

Effects of planting density and nitrogen application on seed yield and other morphological traits of the leafy vegetable kale (Brassica oleracea).

The relationship between food security and sustainable land use is considered to be of the uttermost importance to increase yields without having to increase the agricultural land area over which crops are grown. In the present study nitrogen concentration (25 and 85 kg ha-1) and planting density (6.7, 10 and 25 plants m-2) were investigated for their effect on whole plant physiology and pod seed yield in kale (Brassica oleracea), to determine if the fruit (pod) yield could be manipulated agronomically. Nitrogen concentration did not significantly affect seed yield and it is therefore recommended that the lower concentration be used commercially. Conversely planting density did have a significant effect with increases in seed yield observed at the highest planting density of 25 plants m-2, therefore this high planting density would be recommended commercially to maximise area efficiency, highlighting that simple agronomic changes are capable of increasing crop yields over a set area.

Use of synteny to identify candidate genes underlying QTL controlling stomatal traits in faba bean (Vicia faba L.)

Key message We have identified QTLs for stomatal characteristics on chromosome II of faba bean by applying SNPs derived from M. truncatula , and have identified candidate genes within these QTLs using synteny between the two species. Abstract Faba bean (Vicia faba L.) is a valuable food and feed crop worldwide, but drought often limits its production, and its genome is large and poorly mapped. No information is available on the effects of genomic regions and genes on drought adaptation characters such as stomatal characteristics in this species, but the synteny between the sequenced model legume, Medicago truncatula, and faba bean can be used to identify candidate genes. A mapping population of 211 F5 recombinant inbred lines (Mélodie/2 × ILB 938/2) were phenotyped to identify quantitative trait loci (QTL) affecting stomatal morphology and function, along with seed weight, under well-watered conditions in a climate-controlled glasshouse in 2013 and 2014. Canopy temperature (CT) was evaluated in 2013 under water-deficit (CTd). In total, 188 polymorphic single nucleotide polymorphisms (SNPs), developed from M. truncatula genome data, were assigned to nine linkage groups that covered ~928 cM of the faba bean genome with an average inter-marker distance of 5.8 cM. 15 putative QTLs were detected, of which eight (affecting stomatal density, length and conductance and CT) co-located on chromosome II, in the vicinity of a possible candidate gene—a receptor-like protein kinase found in the syntenic interval of M. truncatula chromosome IV. A ribose-phosphate pyrophosphokinase from M. truncatula chromosome V, postulated as a possible candidate gene for the QTL for CTd, was found some distance away in the same chromosome. These results demonstrate that genomic information from M. truncatula can successfully be translated to the faba bean genome.

Probabilistic parameterisation of the surface mass balance--elevation feedback in regional climate model simulations of the Greenland ice sheet

We present a new parameterisation that relates surface mass balance (SMB: the sum of surface accumulation and surface ablation) to changes in surface elevation of the Greenland ice sheet (GrIS) for the MAR (Modèle Atmosphérique Régional: Fettweis, 2007) regional climate model. The motivation is to dynamically adjust SMB as the GrIS evolves, allowing us to force ice sheet models with SMB simulated by MAR while incorporating the SMB–elevation feedback, without the substantial technical challenges of coupling ice sheet and climate models. This also allows us to assess the effect of elevation feedback uncertainty on the GrIS contribution to sea level, using multiple global climate and ice sheet models, without the need for additional, expensive MAR simulations. We estimate this relationship separately below and above the equilibrium line altitude (ELA, separating negative and positive SMB) and for regions north and south of 77� N, from a set of MAR simulations in which we alter the ice sheet surface elevation. These give four “SMB lapse rates”, gradients that relate SMB changes to elevation changes. We assess uncertainties within a Bayesian framework, estimating probability distributions for each gradient from which we present best estimates and credibility intervals (CI) that bound 95% of the probability. Below the ELA our gradient estimates are mostly positive, because SMB usually increases with elevation: 0.56 (95% CI: −0.22 to 1.33) kgm−3 a−1 for the north, and 1.91 (1.03 to 2.61) kgm−3 a−1 for the south. Above the ELA, the gradients are much smaller in magnitude: 0.09 (−0.03 to 0.23) kgm−3 a−1 in the north, and 0.07 (−0.07 to 0.59) kgm−3 a−1 in the south, because SMB can either increase or decrease in response to increased elevation. Our statistically founded approach allows us to make probabilistic assessments for the effect of elevation feedback uncertainty on sea level projections (Edwards et al., 2014).

Sources, sinks, and transatlantic transport of North African dust aerosol: a multimodel analysis and comparison with remote sensing data

This study evaluates model-simulated dust aerosols over North Africa and the North Atlantic from five global models that participated in the Aerosol Comparison between Observations and Models phase II model experiments. The model results are compared with satellite aerosol optical depth (AOD) data from Moderate Resolution Imaging Spectroradiometer (MODIS), Multiangle Imaging Spectroradiometer (MISR), and Sea-viewing Wide Field-of-view Sensor, dust optical depth (DOD) derived from MODIS and MISR, AOD and coarse-mode AOD (as a proxy of DOD) from ground-based Aerosol Robotic Network Sun photometer measurements, and dust vertical distributions/centroid height from Cloud Aerosol Lidar with Orthogonal Polarization and Atmospheric Infrared Sounder satellite AOD retrievals. We examine the following quantities of AOD and DOD: (1) the magnitudes over land and over ocean in our study domain, (2) the longitudinal gradient from the dust source region over North Africa to the western North Atlantic, (3) seasonal variations at different locations, and (4) the dust vertical profile shape and the AOD centroid height (altitude above or below which half of the AOD is located). The different satellite data show consistent features in most of these aspects; however, the models display large diversity in all of them, with significant differences among the models and between models and observations. By examining dust emission, removal, and mass extinction efficiency in the five models, we also find remarkable differences among the models that all contribute to the discrepancies of model-simulated dust amount and distribution. This study highlights the challenges in simulating the dust physical and optical processes, even in the best known dust environment, and stresses the need for observable quantities to constrain the model processes.

Coordinated ground-based, low altitude satellite and Cluster observations on global and local scales during a transient post-noon sector excursion of the magnetospheric cusp

On 14 January 2001, the four Cluster spacecraft passed through the northern magnetospheric mantle in close conjunction to the EISCAT Svalbard Radar (ESR) and approached the post-noon dayside magnetopause over Greenland between 13:00 and 14:00 UT During that interval, a sudden reorganisation of the high-latitude dayside convection pattern accurred after 13:20 UT most likely caused by a direction change of the Solar wind magnetic field. The result was an eastward and poleward directed flow-channel, as monitored by the SuperDARN radar network and also by arrays of ground-based magnetometers in Canada, Greenland and Scandinavia. After an initial eastward and later poleward expansion of the flow-channel between 13:20 and 13:40 UT, the four Cluster spacecraft, and the field line footprints covered by the eastward looking scan cycle of the Sondre Stromfjord incoherent scatter radar were engulfed by cusp-like precipitation with transient magnetic and electric field signatures. In addition, the EISCAT Svalbard Radar detected strong transient effects of the convection reorganisation, a poleward moving precipitation, and a fast ion flow-channel in association with the auroral structures that suddenly formed to the west and north of the radar. From a detailed analysis of the coordinated Cluster and ground-based data, it was found that this extraordinary transient convection pattern, indeed, had moved the cusp precipitation from its former pre-noon position into the late post-noon sector, allowing for the first and quite unexpected encounter of the cusp by the Cluster spacecraft. Our findings illustrate the large amplitude of cusp dynamics even in response to moderate solar wind forcing. The global ground-based data proves to be an invaluable tool to monitor the dynamics and width of the affected magnetospheric regions.

Coordinated Cluster, ground-based instrumentation and low-altitude satellite observations of transient poleward-moving events in the ionosphere and in the tail lobe

During the interval between 8:00-9:30 on 14 January 2001, the four Cluster spacecraft were moving from the central magnetospheric lobe, through the dusk sector mantle, on their way towards intersecting the magnetopause near 15:00 MLT and 15:00 UT. Throughout this interval, the EIS-CAT Svalbard Radar (ESR) at Longyearbyen observed a series of poleward-moving transient events of enhanced F-region plasma concentration ("polar cap patches"), with a repetition period of the order of 10 min. Allowing for the estimated solar wind propagation delay of 75 ( 5) min, the interplanetary magnetic field (IMF) had a southward component during most of the interval. The magnetic footprint of the Cluster spacecraft, mapped to the ionosphere using the Tsyganenko T96 model (with input conditions prevailing during this event), was to the east of the ESR beams. Around 09:05 UT, the DMSP-F12 satellite flew over the ESR and showed a sawtooth cusp ion dispersion signature that also extended into the electrons on the equatorward edge of the cusp, revealing a pulsed magnetopause reconnection. The consequent enhanced ionospheric flow events were imaged by the SuperDARN HF backscatter radars. The average convection patterns (derived using the AMIE technique on data from the magnetometers, the EISCAT and SuperDARN radars, and the DMSP satellites) show that the associated poleward-moving events also convected over the predicted footprint of the Cluster spacecraft. Cluster observed enhancements in the fluxes of both electrons and ions. These events were found to be essentially identical at all four spacecraft, indicating that they had a much larger spatial scale than the satellite separation of the order of 600 km. Some of the events show a correspondence between the lowest energy magnetosheath electrons detected by the PEACE instrument on Cluster (10-20 eV) and the topside ionospheric enhancements seen by the ESR (at 400-700 km). We suggest that a potential barrier at the magnetopause, which prevents the lowest energy electrons from entering the magnetosphere, is reduced when and where the boundary-normal magnetic field is enhanced and that the observed polar cap patches are produced by the consequent enhanced precipitation of the lowest energy electrons, making them and the low energy electron precipitation fossil remnants of the magnetopause reconnection rate pulses.

Location and characteristics of the reconnection X line deduced from low-altitude satellite and ground-based observations: 2. Defense Meteorological Satellite Program and European Incoherent Scatter data

We present an analysis of a cusp ion step, observed by the Defense Meteorological Satellite Program (DMSP) F10 spacecraft, between two poleward moving events of enhanced ionospheric electron temperature, observed by the European Incoherent Scatter (EISCAT) radar. From the ions detected by the satellite, the variation of the reconnection rate is computed for assumed distances along the open-closed field line separatrix from the satellite to the X line, do. Comparison with the onset times of the associated ionospheric events allows this distance to be estimated, but with an uncertainty due to the determination of the low-energy cutoff of the ion velocity distribution function, ƒ(ν). Nevertheless, the reconnection site is shown to be on the dayside magnetopause, consistent with the reconnection model of the cusp during southward interplanetary magnetic field (IMF). Analysis of the time series of distribution function at constant energies, ƒ(ts), shows that the best estimate of the distance do is 14.5±2 RE. This is consistent with various magnetopause observations of the signatures of reconnection for southward IMF. The ion precipitation is used to reconstruct the field-parallel part of the Cowley D ion distribution function injected into the open low-latitude boundary layer in the vicinity of the X line. From this reconstruction, the field-aligned component of the magnetosheath flow is found to be only −55±65 km s−1 near the X line, which means either that the reconnection X line is near the stagnation region at the nose of the magnetosphere, or that it is closely aligned with the magnetosheath flow streamline which is orthogonal to the magnetosheath field, or both. In addition, the sheath Alfvén speed at the X line is found to be 220±45 km s−1, and the speed with which newly opened field lines are ejected from the X line is 165±30 km s−1. We show that the inferred magnetic field, plasma density, and temperature of the sheath near the X line are consistent with a near-subsolar reconnection site and confirm that the magnetosheath field makes a large angle (>58°) with the X line.