A maize bacterial artificial chromosome (BAC) library from the European flint inbred line F2

We report here the construction and characterisation of a BAC library from the maize flint inbred line F2, widely used in European maize breeding programs. The library contains 86,858 clones with an average insert size of approximately 90 kb, giving approximately 3.2-times genome coverage. High-efficiency BAC cloning was achieved through the use of a single size selection for the high-molecular-weight genomic DNA, and co-transformation of the ligation with yeast tRNA to optimise transformation efficiency. Characterisation of the library showed that less than 0.5% of the clones contained no inserts, while 5.52% of clones consisted of chloroplast DNA. The library was gridded onto 29 nylon filters in a double-spotted 8 × 8 array, and screened by hybridisation with a number of single-copy and gene-family probes. A 3-dimensional DNA pooling scheme was used to allow rapid PCR screening of the library based on primer pairs from simple sequence repeat (SSR) and expressed sequence tag (EST) markers. Positive clones were obtained in all hybridisation and PCR screens carried out so far. Six BAC clones, which hybridised to a portion of the cloned Rp1-D rust resistance gene, were further characterised and found to form contigs covering most of this complex resistance locus.

Evaluation of regional climate simulations for air quality modelling purposes

In order to evaluate the future potential benefits of emission regulation on regional air quality, while taking into account the effects of climate change, off-line air quality projection simulations are driven using weather forcing taken from regional climate models. These regional models are themselves driven by simulations carried out using global climate models (GCM) and economical scenarios. Uncertainties and biases in climate models introduce an additional “climate modeling” source of uncertainty that is to be added to all other types of uncertainties in air quality modeling for policy evaluation. In this article we evaluate the changes in air quality-related weather variables induced by replacing reanalyses-forced by GCM-forced regional climate simulations. As an example we use GCM simulations carried out in the framework of the ERA-interim programme and of the CMIP5 project using the Institut Pierre-Simon Laplace climate model (IPSLcm), driving regional simulations performed in the framework of the EURO-CORDEX programme. In summer, we found compensating deficiencies acting on photochemistry: an overestimation by GCM-driven weather due to a positive bias in short-wave radiation, a negative bias in wind speed, too many stagnant episodes, and a negative temperature bias. In winter, air quality is mostly driven by dispersion, and we could not identify significant differences in either wind or planetary boundary layer height statistics between GCM-driven and reanalyses-driven regional simulations. However, precipitation appears largely overestimated in GCM-driven simulations, which could significantly affect the simulation of aerosol concentrations. The identification of these biases will help interpreting results of future air quality simulations using these data. Despite these, we conclude that the identified differences should not lead to major difficulties in using GCM-driven regional climate simulations for air quality projections.

Changes in tropical Atlantic interannual variability from a substantial weakening of the meridional overturning circulation

In response to a substantial weakening of the Atlantic Meridional Overturning Circulation (AMOC)— from a coupled ocean–atmosphere general circulation model experiment—significant changes in the interannual variability are found over the tropical Atlantic, characterized by an increase of variance (by ~150 %) in boreal late spring-early summer and a decrease of variance (by ~60 %) in boreal autumn. This study focuses on understanding physical mechanisms responsible for these changes in interannual variability in the tropical Atlantic. It demonstrates that the increase of variability in spring is a consequence of an increase in the variance of the El Niño-Southern Oscillation, which has a large impact on the tropical Atlantic via anomalous surface heat fluxes. Winter El Niño (La Niña) affects the eastern equatorial Atlantic by decreasing (increasing) cloud cover and surface wind speed which is associated with anomalous downward (upward) short wave radiation and reduced (enhanced) upward latent heat fluxes, creating anomalous positive (negative) sea surface temperature (SST) anomalies over the region from winter to spring. On the other hand, the decrease of SST variance in autumn is due to a deeper mean thermocline which weakens the impact of the thermocline movement on SST variation. The comparison between the model results and observations is not straightforward owing to the influence of model biases and the lack of a major MOC weakening event in the instrumental record. However, it is argued that the basic physical mechanisms found in the model simulations are likely to be robust and therefore have relevance to understanding tropical Atlantic variability in the real world, perhaps with modified seasonality.

Identifying uncertainties in Arctic climate change projections

Wide ranging climate changes are expected in the Arctic by the end of the 21st century, but projections of the size of these changes vary widely across current global climate models. This variation represents a large source of uncertainty in our understanding of the evolution of Arctic climate. Here we systematically quantify and assess the model uncertainty in Arctic climate changes in two CO2 doubling experiments: a multimodel ensemble (CMIP3) and an ensemble constructed using a single model (HadCM3) with multiple parameter perturbations (THC-QUMP). These two ensembles allow us to assess the contribution that both structural and parameter variations across models make to the total uncertainty and to begin to attribute sources of uncertainty in projected changes. We find that parameter uncertainty is an major source of uncertainty in certain aspects of Arctic climate. But also that uncertainties in the mean climate state in the 20th century, most notably in the northward Atlantic ocean heat transport and Arctic sea ice volume, are a significant source of uncertainty for projections of future Arctic change. We suggest that better observational constraints on these quantities will lead to significant improvements in the precision of projections of future Arctic climate change.

Statistical modelling of grapevine yield in the Port Wine region under present and future climate conditions

The impact of projected climate change on wine production was analysed for the Demarcated Region of Douro, Portugal. A statistical grapevine yield model (GYM) was developed using climate parameters as predictors. Statistically significant correlations were identified between annual yield and monthly mean temperatures and monthly precipitation totals during the growing cycle. These atmospheric factors control grapevine yield in the region, with the GYM explaining 50.4% of the total variance in the yield time series in recent decades. Anomalously high March rainfall (during budburst, shoot and inflorescence development) favours yield, as well as anomalously high temperatures and low precipitation amounts in May and June (May: flowering and June: berry development). The GYM was applied to a regional climate model output, which was shown to realistically reproduce the GYM predictors. Finally, using ensemble simulations under the A1B emission scenario, projections for GYM-derived yield in the Douro Region, and for the whole of the twenty-first century, were analysed. A slight upward trend in yield is projected to occur until about 2050, followed by a steep and continuous increase until the end of the twenty-first century, when yield is projected to be about 800 kg/ha above current values. While this estimate is based on meteorological parameters alone, changes due to elevated CO2 may further enhance this effect. In spite of the associated uncertainties, it can be stated that projected climate change may significantly benefit wine yield in the Douro Valley.

Response of the Atlantic meridional overturning circulation to a reversal of greenhouse gas increases

The reversibility of the Atlantic meridional overturning circulation (AMOC) is investigated in multi-model experiments using global climate models (GCMs) where CO2 concentrations are increased by 1 or 2 % per annum to 2× or 4× preindustrial conditions. After a period of stabilisation the CO2 is decreased back to preindustrial conditions. In most experiments when the CO2 decreases, the AMOC recovers before becoming anomalously strong. This "overshoot" is up to an extra 18.2Sv or 104 % of its preindustrial strength, and the period with an anomalously strong AMOC can last for several hundred years. The magnitude of this overshoot is shown to be related to the build up of salinity in the subtropical Atlantic during the previous period of high CO2 levels. The magnitude of this build up is partly related to anthropogenic changes in the hydrological cycle. The mechanisms linking the subtropical salinity increase to the subsequent overshoot are analysed, supporting the relationship found. This understanding is used to explain differences seen in some models and scenarios. In one experiment there is no overshoot because there is little salinity build up, partly as a result of model differences in the hydrological cycle response to increased CO2 levels and partly because of a less aggressive scenario. Another experiment has a delayed overshoot, possibly as a result of a very weak AMOC in that GCM when CO2 is high. This study identifies aspects of overshoot behaviour that are robust across a multi-model and multi-scenario ensemble, and those that differ between experiments. These results could inform an assessment of the real-world AMOC response to decreasing CO2.

Maximum principles for vectorial approximate minimisers on non-convex functionals

We establish Maximum Principles which apply to vectorial approximate minimizers of the general integral functional of Calculus of Variations. Our main result is a version of the Convex Hull Property. The primary advance compared to results already existing in the literature is that we have dropped the quasiconvexity assumption of the integrand in the gradient term. The lack of weak Lower semicontinuity is compensated by introducing a nonlinear convergence technique, based on the approximation of the projection onto a convex set by reflections and on the invariance of the integrand in the gradient term under the Orthogonal Group. Maximum Principles are implied for the relaxed solution in the case of non-existence of minimizers and for minimizing solutions of the Euler–Lagrange system of PDE.

The role of horizontal resolution in simulating drivers of the global hydrological cycle

The role of atmospheric general circulation model (AGCM) horizontal resolution in representing the global energy budget and hydrological cycle is assessed, with the aim of improving the understanding of model uncertainties in simulating the hydrological cycle. We use two AGCMs from the UK Met Office Hadley Centre: HadGEM1-A at resolutions ranging from 270 to 60 km, and HadGEM3-A ranging from 135 to 25 km. The models exhibit a stable hydrological cycle, although too intense compared to reanalyses and observations. This over-intensity is explained by excess surface shortwave radiation, a common error in general circulation models (GCMs). This result is insensitive to resolution. However, as resolution is increased, precipitation decreases over the ocean and increases over the land. This is associated with an increase in atmospheric moisture transport from ocean to land, which changes the partitioning of moisture fluxes that contribute to precipitation over land from less local to more non-local moisture sources. The results start to converge at 60-km resolution, which underlines the excessive reliance of the mean hydrological cycle on physical parametrization (local unresolved processes) versus model dynamics (large-scale resolved processes) in coarser HadGEM1 and HadGEM3 GCMs. This finding may be valid for other GCMs, showing the necessity to analyze other chains of GCMs that may become available in the future with such a range of horizontal resolutions. Our finding supports the hypothesis that heterogeneity in model parametrization is one of the underlying causes of model disagreement in the Coupled Model Intercomparison Project (CMIP) exercises.

Response of tropical cyclones to idealized climate change experiments in a global high resolution coupled general circulation model

We present an assessment of how tropical cyclone activity might change due to the influence of increased atmospheric carbon dioxide concentrations, using the UK’s High Resolution Global Environment Model (HiGEM) with N144 resolution (~90 km in the atmosphere and ~40 km in the ocean). Tropical cyclones are identified using a feature tracking algorithm applied to model output. Tropical cyclones from idealized 30-year 2×CO2 (2CO2) and 4×CO2 (4CO2) simulations are compared to those identified in a 150-year present-day simulation, which is separated into a 5-member ensemble of 30-year integrations. Tropical cyclones are shown to decrease in frequency globally by 9% in the 2CO2 and 26% in the 4CO2. Tropical cyclones only become more intese in the 4CO2, however uncoupled time slice experiments reveal an increase in intensity in the 2CO2. An investigation into the large-scale environmental conditions, known to influence tropical cyclone activity in the main development regions, is used to determine the response of tropical cyclone activity to increased atmospheric CO2. A weaker Walker circulation and a reduction in zonally averaged regions of updrafts lead to a shift in the location of tropical cyclones in the northern hemisphere. A decrease in mean ascent at 500 hPa contributes to the reduction of tropical cyclones in the 2CO2 in most basins. The larger reduction of tropical cyclones in the 4CO2 arises from further reduction of mean ascent at 500 hPa and a large enhancement of vertical wind shear, especially in the southern hemisphere, North Atlantic and North East Pacific.

Expression of epitope-tagged LMW glutenin subunits in the starchy endosperm of transgenic wheat and their incorporation into glutenin polymers

The low-molecular-weight (LMW) glutenin subunits are components of the highly cross-linked glutenin polymers that confer viscoelastic properties to gluten and dough. They have both quantitative and qualitative effects on dough quality that may relate to differences in their ability to form the inter-chain disulphide bonds that stabilise the polymers. In order to determine the relationship between dough quality and the amounts and properties of the LMW subunits, we have transformed the pasta wheat cultivars Svevo and Ofanto with three genes encoding proteins, which differ in their numbers or positions of cysteine residues. The transgenes were delivered under control of the high-molecular-weight (HMW) subunit 1Dx5 gene promoter and terminator regions, and the encoded proteins were C-terminally tagged by the introduction of the c-myc epitope. Stable transformants were obtained with both cultivars, and the use of a specific antibody to the c-myc epitope tag allowed the transgene products to be readily detected in the complex mixture of LMW subunits. A range of transgene expression levels was observed. The addition of the epitope tag did not compromise the correct folding of the trangenic subunits and their incorporation into the glutenin polymers. Our results demonstrate that the ability to specifically epitope-tag LMW glutenin transgenes can greatly assist in the elucidation of their individual contributions to the functionality of the complex gluten system.

Analysis of precipitation climatology simulated by high resolution coupled global models over the South America

The results of coupled high resolution global models (CGCMs) over South America are discussed. HiGEM1.2 and HadGEM1.2 simulations, with horizontal resolution of ~90 and 135 km, respectively, are compared. Precipitation estimations from CMAP (Climate Prediction Center—Merged Analysis of Precipitation), CPC (Climate Prediction Center) and GPCP (Global Precipitation Climatology Project) are used for validation. HiGEM1.2 and HadGEM1.2 simulated seasonal mean precipitation spatial patterns similar to the CMAP. The positioning and migration of the Intertropical Convergence Zone and of the Pacific and Atlantic subtropical highs are correctly simulated by the models. In HiGEM1.2 and HadGEM1.2, the intensity and locations of the South Atlantic Convergence Zone are in agreement with the observed dataset. The simulated annual cycles are in phase with estimations of rainfall for most of the six regions considered. An important result is that HiGEM1.2 and HadGEM1.2 eliminate a common problem of coarse resolution CGCMs, which is the simulation of a semiannual cycle of precipitation due to the semiannual solar forcing. Comparatively, the use of high resolution in HiGEM1.2 reduces the dry biases in the central part of Brazil during austral winter and spring and in most part of the year over an oceanic box in eastern Uruguay.

Atmospheric blocking in a high resolution climate model: influences of mean state, orography and eddy forcing

An underestimate of atmospheric blocking occurrence is a well-known limitation of many climate models. This article presents an analysis of Northern Hemisphere winter blocking in an atmospheric model with increased horizontal resolution. European blocking frequency increases with model resolution, and this results from an improvement in the atmospheric patterns of variability as well as a simple improvement in the mean state. There is some evidence that the transient eddy momentum forcing of European blocks is increased at high resolution, which could account for this. However, it is also shown that the increase in resolution of the orography is needed to realise the improvement in blocking, consistent with the increase in height of the Rocky Mountains acting to increase the tilt of the Atlantic jet stream and giving higher mean geopotential heights over northern Europe. Blocking frequencies in the Pacific sector are also increased with atmospheric resolution, but in this case the improvement in orography actually leads to a decrease in blocking

Improved evaporative flux partitioning and carbon flux in the land surface model JULES: impact on the simulation of land surface processes in temperate Europe

The primary role of land surface models embedded in climate models is to partition surface available energy into upwards, radiative, sensible and latent heat fluxes. Partitioning of evapotranspiration, ET, is of fundamental importance: as a major component of the total surface latent heat flux, ET affects the simulated surface water balance, and related energy balance, and consequently the feedbacks with the atmosphere. In this context it is also crucial to credibly represent the CO2 exchange between ecosystems and their environment. In this study, JULES, the land surface model used in UK weather and climate models, has been evaluated for temperate Europe. Compared to eddy covariance flux measurements, the CO2 uptake by the ecosystem is underestimated and the ET overestimated. In addition, the contribution to ET from soil and intercepted water evaporation far outweighs the contribution of plant transpiration. To alleviate these biases, adaptations have been implemented in JULES, based on key literature references. These adaptations have improved the simulation of the spatio-temporal variability of the fluxes and the accuracy of the simulated GPP and ET, including its partitioning. This resulted in a shift of the seasonal soil moisture cycle. These adaptations are expected to increase the fidelity of climate simulations over Europe. Finally, the extreme summer of 2003 was used as evaluation benchmark for the use of the model in climate change studies. The improved model captures the impact of the 2003 drought on the carbon assimilation and the water use efficiency of the plants. It, however, underestimates the 2003 GPP anomalies. The simulations showed that a reduction of evaporation from the interception and soil reservoirs, albeit not of transpiration, largely explained the good correlation between the carbon and the water fluxes anomalies that was observed during 2003. This demonstrates the importance of being able to discriminate the response of individual component of the ET flux to environmental forcing.

Causal relationship between obesity and vitamin D status: bi-directional mendelian randomization analysis of multiple cohorts

BACKGROUND: Obesity is associated with vitamin D deficiency, and both are areas of active public health concern. We explored the causality and direction of the relationship between body mass index (BMI) and 25-hydroxyvitamin D [25(OH)D] using genetic markers as instrumental variables (IVs) in bi-directional Mendelian randomization (MR) analysis. METHODS AND FINDINGS: We used information from 21 adult cohorts (up to 42,024 participants) with 12 BMI-related SNPs (combined in an allelic score) to produce an instrument for BMI and four SNPs associated with 25(OH)D (combined in two allelic scores, separately for genes encoding its synthesis or metabolism) as an instrument for vitamin D. Regression estimates for the IVs (allele scores) were generated within-study and pooled by meta-analysis to generate summary effects. Associations between vitamin D scores and BMI were confirmed in the Genetic Investigation of Anthropometric Traits (GIANT) consortium (n = 123,864). Each 1 kg/m(2) higher BMI was associated with 1.15% lower 25(OH)D (p = 6.52×10⁻²⁷). The BMI allele score was associated both with BMI (p = 6.30×10⁻⁶²) and 25(OH)D (-0.06% [95% CI -0.10 to -0.02], p = 0.004) in the cohorts that underwent meta-analysis. The two vitamin D allele scores were strongly associated with 25(OH)D (p≤8.07×10⁻⁵⁷ for both scores) but not with BMI (synthesis score, p = 0.88; metabolism score, p = 0.08) in the meta-analysis. A 10% higher genetically instrumented BMI was associated with 4.2% lower 25(OH)D concentrations (IV ratio: -4.2 [95% CI -7.1 to -1.3], p = 0.005). No association was seen for genetically instrumented 25(OH)D with BMI, a finding that was confirmed using data from the GIANT consortium (p≥0.57 for both vitamin D scores). CONCLUSIONS: On the basis of a bi-directional genetic approach that limits confounding, our study suggests that a higher BMI leads to lower 25(OH)D, while any effects of lower 25(OH)D increasing BMI are likely to be small. Population level interventions to reduce BMI are expected to decrease the prevalence of vitamin D deficiency.

Six new loci associated with body mass index highlight a neuronal influence on body weight regulation

Common variants at only two loci, FTO and MC4R, have been reproducibly associated with body mass index (BMI) in humans. To identify additional loci, we conducted meta-analysis of 15 genome-wide association studies for BMI (n > 32,000) and followed up top signals in 14 additional cohorts (n > 59,000). We strongly confirm FTO and MC4R and identify six additional loci (P < 5 x 10(-8)): TMEM18, KCTD15, GNPDA2, SH2B1, MTCH2 and NEGR1 (where a 45-kb deletion polymorphism is a candidate causal variant). Several of the likely causal genes are highly expressed or known to act in the central nervous system (CNS), emphasizing, as in rare monogenic forms of obesity, the role of the CNS in predisposition to obesity.