PPARGC1A sequence variation and cardiovascular risk-factor levels: a study of the main genetic effects and gene x environment interactions in children from the European Youth Heart Study.

AIMS/HYPOTHESIS: The PPARGC1A gene coactivates multiple nuclear transcription factors involved in cellular energy metabolism and vascular stasis. In the present study, we genotyped 35 tagging polymorphisms to capture all common PPARGC1A nucleotide sequence variations and tested for association with metabolic and cardiovascular traits in 2,101 Danish and Estonian boys and girls from the European Youth Heart Study, a multicentre school-based cross-sectional cohort study. METHODS: Fasting plasma glucose concentrations, anthropometric variables and blood pressure were measured. Habitual physical activity and aerobic fitness were objectively assessed using uniaxial accelerometry and a maximal aerobic exercise stress test on a bicycle ergometer, respectively. RESULTS: In adjusted models, nominally significant associations were observed for BMI (rs10018239, p = 0.039), waist circumference (rs7656250, p = 0.012; rs8192678 [Gly482Ser], p = 0.015; rs3755863, p = 0.02; rs10018239, beta = -0.01 cm per minor allele copy, p = 0.043), systolic blood pressure (rs2970869, p = 0.018) and fasting glucose concentrations (rs11724368, p = 0.045). Stronger associations were observed for aerobic fitness (rs7656250, p = 0.005; rs13117172, p = 0.008) and fasting glucose concentrations (rs7657071, p = 0.002). None remained significant after correcting for the number of statistical comparisons. We proceeded by testing for gene x physical activity interactions for the polymorphisms that showed nominal evidence of association in the main effect models. None of these tests was statistically significant. CONCLUSIONS/INTERPRETATION: Variants at PPARGC1A may influence several metabolic traits in this European paediatric cohort. However, variation at PPARGC1A is unlikely to have a major impact on cardiovascular or metabolic health in these children.

Genetic variation in GABRB3 is associated with Asperger syndrome and multiple endophenotypes relevant to autism.

BACKGROUND: Autism spectrum conditions (ASC) are associated with deficits in social interaction and communication, alongside repetitive, restricted, and stereotyped behavior. ASC is highly heritable. The gamma-aminobutyric acid (GABA)-ergic system has been associated consistently with atypicalities in autism, in both genetic association and expression studies. A key component of the GABA-ergic system is encoded by the GABRB3 gene, which has been previously implicated both in ASC and in individual differences in empathy. METHODS: In this study, 45 genotyped single nucleotide polymorphisms (SNPs) within GABRB3 were tested for association with Asperger syndrome (AS), and related quantitative traits measured through the following tests: the Empathy Quotient (EQ), the Autism Spectrum Quotient (AQ), the Systemizing Quotient-Revised (SQ-R), the Embedded Figures Test (EFT), the Reading the Mind in the Eyes Test (RMET), and the Mental Rotation Test (MRT). Two-loci, three-loci, four-loci haplotype analyses, and one seven-loci haplotype analysis were also performed in the AS case--control sample. RESULTS: Three SNPs (rs7180158, rs7165604, rs12593579) were significantly associated with AS, and two SNPs (rs9806546, rs11636966) were significantly associated with EQ. Two SNP-SNP pairs, rs12438141-rs1035751 and rs12438141-rs7179514, showed significant association with variation in the EFT scores. One SNP-SNP pair, rs7174437-rs1863455, was significantly associated with variation in the MRT scores. Additionally, a few haplotypes, including a 19 kb genomic region that formed a linkage disequilibrium (LD) block in our sample and contained several nominally significant SNPs, were found to be significantly associated with AS. CONCLUSION: The current study confirms the role of GABRB3 as an important candidate gene in both ASC and normative variation in related endophenotypes.

Optimal planning of cocoa clonal selection programmes

Data from three cocoa (Theobroma cacao) clonal selection trials are used to investigate the genetic and environmental components of variation in yield and the percentage of total pods affected by black pod disease (Phytophtora pod rot). Simulations based on these estimated components of variation are then used to discuss the best choice in future of numbers of clones, replicates and years of harvest to maximise selection advances in the traits measured. The three main conclusions are the need to increase the number of clones at the expense of the number of replicates of each clone, the diminishing returns from additional years of harvesting and the importance of widening the genetic base of the clones chosen to be tested.

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.

C. colchicum - variation measured by DNA sequence

Cyclamen colchicum has a mixed history in the hands of botanists. This paper examines the genetic identity of a group of wild Cyclamen populations from the Caucasus to discover whther they are Cyclamen colchicum, C. purpurascens or a mixture of the two. The collections supplemented by material collected at the type locality for C. colchicum, proved to be a single but variable genetic group of C. colchicum that was distinct from C. purpurascens.

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.

Association between Mediterranean and Nordic diet scores and changes in weight and waist circumference: influence of FTO and TCF7L2 loci

BACKGROUND: Several studies have shown that adherence to the Mediterranean Diet measured by using the Mediterranean diet score (MDS) is associated with lower obesity risk. The newly proposed Nordic Diet could hold similar beneficial effects. Because of the increasing focus on the interaction between diet and genetic predisposition to adiposity, studies should consider both diet and genetics. OBJECTIVE: We investigated whether FTO rs9939609 and TCF7L2 rs7903146 modified the association between the MDS and Nordic diet score (NDS) and changes in weight (Δweight), waist circumference (ΔWC), and waist circumference adjusted for body mass index (BMI) (ΔWCBMI). DESIGN: We conducted a case-cohort study with a median follow-up of 6.8 y that included 11,048 participants from 5 European countries; 5552 of these subjects were cases defined as individuals with the greatest degree of unexplained weight gain during follow-up. A randomly selected subcohort included 6548 participants, including 5496 noncases. Cases and noncases were compared in analyses by using logistic regression. Continuous traits (ie, Δweight, ΔWC, and ΔWCBMI) were analyzed by using linear regression models in the random subcohort. Interactions were tested by including interaction terms in models. RESULTS: A higher MDS was significantly inversely associated with case status (OR: 0.98; 95% CI: 0.96, 1.00), ΔWC (β = -0.010 cm/y; 95% CI: -0.020, -0.001 cm/y), and ΔWCBMI (β = -0.008; 95% CI:-0.015, -0.001) per 1-point increment but not Δweight (P = 0.53). The NDS was not significantly associated with any outcome. There was a borderline significant interaction between the MDS and TCF7L2 rs7903146 on weight gain (P = 0.05), which suggested a beneficial effect of the MDS only in subjects who carried 1 or 2 risk alleles. FTO did not modify observed associations. CONCLUSIONS: A high MDS is associated with a lower ΔWC and ΔWCBMI, regardless of FTO and TCF7L2 risk alleles. For Δweight, findings were less clear, but the effect may depend on the TCF7L2 rs7903146 variant. The NDS was not associated with anthropometric changes during follow-up.

Optical properties of Saharan dust aerosol and contribution from the coarse mode as measured during the Fennec 2011 aircraft campaign

New in-situ aircraft measurements of Saharan dust originating from Mali, Mauritania and Algeria taken during the Fennec 2011 aircraft campaign over a remote part of the Sahara Desert are presented. Size distributions extending to 300 μm are shown, representing measurements extending further into the coarse mode than previously published for airborne Saharan dust. A significant coarse mode was present in the size distribution measurements with effective diameter (deff) from 2.3 to 19.4 μm and coarse mode volume median diameter (dvc) from 5.8 to 45.3 μm. The mean size distribution had a larger relative proportion of coarse mode particles than previous aircraft measurements. The largest particles (with deff >12 μm, or dvc >25 μm) were only encountered within 1 km of the ground. Number concentration, mass loading and extinction coefficient showed inverse relationships to dust age since uplift. Dust particle size showed a weak exponential relationship to dust age. Two cases of freshly uplifted dust showed quite different characteristics of size distribution and number concentration. Single Scattering Albed (SSA) values at 550 nm calculated from the measured size distributions revealed high absorption ranging from 0.70 to 0.97 depending on the refractive index. SSA was found to be strongly related to deff. New instrumentation revealed that direct measurements, behind Rosemount inlets, overestimate SSA by up to 0.11 when deff is greater than 2 μm. This is caused by aircraft inlet inefficiencies and sampling losses. Previous measurements of SSA from aircraft measurements may also have been overestimates for this reason. Radiative transfer calculations indicate that the range of SSAs during Fennec 2011 can lead to underestimates in shortwave atmospheric heating rates by 2.0 to 3.0 times if the coarse mode is neglected. This will have an impact on Saharan atmospheric dynamics and circulation,which should be taken into account by numerical weather prediction and climate models.

Long term changes in EUV and X-ray emissions from the solar corona and chromosphere as measured by the response of the Earth’s ionosphere during total solar eclipses from 1932 to 1999

Measurements of the ionospheric E region during total solar eclipses in the period 1932-1999 have been used to investigate the fraction of Extreme Ultra Violet and soft X-ray radiation, phi, that is emitted from the limb corona and chromosphere. The relative apparent sizes of the Moon and the Sun are different for each eclipse, and techniques are presented which correct the measurements and, therefore, allow direct comparisons between different eclipses. The results show that the fraction of ionising radiation emitted by the limb corona has a clear solar cycle variation and that the underlying trend shows this fraction has been increasing since 1932. Data from the SOHO spacecraft are used to study the effects of short-term variability and it is shown that the observed long-term rise in phi has a negligible probability of being a chance occurrence.

Is it me? Self-recognition bias across sensory modalities and its relationship to autistic traits

Background Atypical self-processing is an emerging theme in autism research, suggested by lower self-reference effect in memory, and atypical neural responses to visual self-representations. Most research on physical self-processing in autism uses visual stimuli. However, the self is a multimodal construct, and therefore, it is essential to test self-recognition in other sensory modalities as well. Self-recognition in the auditory modality remains relatively unexplored and has not been tested in relation to autism and related traits. This study investigates self-recognition in auditory and visual domain in the general population and tests if it is associated with autistic traits. Methods Thirty-nine neurotypical adults participated in a two-part study. In the first session, individual participant’s voice was recorded and face was photographed and morphed respectively with voices and faces from unfamiliar identities. In the second session, participants performed a ‘self-identification’ task, classifying each morph as ‘self’ voice (or face) or an ‘other’ voice (or face). All participants also completed the Autism Spectrum Quotient (AQ). For each sensory modality, slope of the self-recognition curve was used as individual self-recognition metric. These two self-recognition metrics were tested for association between each other, and with autistic traits. Results Fifty percent ‘self’ response was reached for a higher percentage of self in the auditory domain compared to the visual domain (t = 3.142; P < 0.01). No significant correlation was noted between self-recognition bias across sensory modalities (τ = −0.165, P = 0.204). Higher recognition bias for self-voice was observed in individuals higher in autistic traits (τ AQ = 0.301, P = 0.008). No such correlation was observed between recognition bias for self-face and autistic traits (τ AQ = −0.020, P = 0.438). Conclusions Our data shows that recognition bias for physical self-representation is not related across sensory modalities. Further, individuals with higher autistic traits were better able to discriminate self from other voices, but this relation was not observed with self-face. A narrow self-other overlap in the auditory domain seen in individuals with high autistic traits could arise due to enhanced perceptual processing of auditory stimuli often observed in individuals with autism.

Field phenotyping of potato to assess root and shoot characteristics associated with drought tolerance

Aims Potatoes are a globally important source of food whose production requires large inputs of fertiliser and water. Recent research has highlighted the importance of the root system in acquiring resources. Here measurements, previously generated by field phenotyping, tested the effect of root size on maintenance of yield under drought (drought tolerance). Methods Twelve potato genotypes, including genotypes with extremes of root size, were grown to maturity in the field under a rain shelter and either irrigated or subjected to drought. Soil moisture, canopy growth, carbon isotope discrimination and final yields were measured. Destructively harvested field phenotype data were used as explanatory variables in a general linear model (GLM) to investigate yield under conditions of drought or irrigation. Results Drought severely affected the small rooted genotype Pentland Dell but not the large rooted genotype Cara. More plantlets, longer and more numerous stolons and stolon roots were associated with drought tolerance. Previously measured carbon isotope discrimination did not correlate with the effect of drought. Conclusions These data suggest that in-field phenotyping can be used to identify useful characteristics when known genotypes are subjected to an environmental stress. Stolon root traits were associated with drought tolerance in potato and could be used to select genotypes with resilience to drought.

Simple measures of climate, soil properties and plant traits predict national scale grassland soil carbon stocks

1. Soil carbon (C) storage is a key ecosystem service. Soil C stocks play a vital role in soil fertility and climate regulation, but the factors that control these stocks at regional and national scales are unknown, particularly when their composition and stability are considered. As a result, their mapping relies on either unreliable proxy measures or laborious direct measurements. 2. Using data from an extensive national survey of English grasslands we show that surface soil (0-7cm) C stocks in size fractions of varying stability can be predicted at both regional and national scales from plant traits and simple measures of soil and climatic conditions. 3. Soil C stocks in the largest pool, of intermediate particle size (50-250 µm), were best explained by mean annual temperature (MAT), soil pH and soil moisture content. The second largest C pool, highly stable physically and biochemically protected particles (0.45-50 µm), was explained by soil pH and the community abundance weighted mean (CWM) leaf nitrogen (N) content, with the highest soil C stocks under N rich vegetation. The C stock in the small active fraction (250-4000 µm) was explained by a wide range of variables: MAT, mean annual precipitation, mean growing season length, soil pH and CWM specific leaf area; stocks were higher under vegetation with thick and/or dense leaves. 4. Testing the models describing these fractions against data from an independent English region indicated moderately strong correlation between predicted and actual values and no systematic bias, with the exception of the active fraction, for which predictions were inaccurate. 5. Synthesis and Applications: Validation indicates that readily available climate, soils and plant survey data can be effective in making local- to landscape-scale (1-100,000 km2) soil C stock predictions. Such predictions are a crucial component of effective management strategies to protect C stocks and enhance soil C sequestration.