Wageningen University and Research Centre

About: Wageningen University and Research Centre is a education organization based out in Wageningen, Netherlands. It is known for research contribution in the topics: Population & Sustainability. The organization has 23474 authors who have published 54833 publications receiving 2608897 citations.

Accuracy of predicting the genetic risk of disease using a genome-wide approach.

Abstract: Background: The prediction of the genetic disease risk of an individual is a powerful public health tool. While predicting risk has been successful in diseases which follow simple Mendelian inheritance, it has proven challenging in complex diseases for which a large number of loci contribute to the genetic variance. The large numbers of single nucleotide polymorphisms now available provide new opportunities for predicting genetic risk of complex diseases with high accuracy. Methodology/Principal Findings: We have derived simple deterministic formulae to predict the accuracy of predicted genetic risk from population or case control studies using a genome-wide approach and assuming a dichotomous disease phenotype with an underlying continuous liability. We show that the prediction equations are special cases of the more general problem of predicting the accuracy of estimates of genetic values of a continuous phenotype. Our predictive equations are responsive to all parameters that affect accuracy and they are independent of allele frequency and effect distributions. Deterministic prediction errors when tested by simulation were generally small. The common link among the expressions for accuracy is that they are best summarized as the product of the ratio of number of phenotypic records per number of risk loci and the observed heritability. Conclusions/Significance: This study advances the understanding of the relative power of case control and population studies of disease. The predictions represent an upper bound of accuracy which may be achievable with improved effect estimation methods. The formulae derived will help researchers determine an appropriate sample size to attain a certain accuracy when predicting genetic risk.

Conserved Fungal LysM Effector Ecp6 Prevents Chitin-Triggered Immunity in Plants

Abstract: Multicellular organisms activate immunity upon recognition of pathogen-associated molecular patterns (PAMPs). Chitin is the major component of fungal cell walls, and chitin oligosaccharides act as PAMPs in plant and mammalian cells. Microbial pathogens deliver effector proteins to suppress PAMP-triggered host immunity and to establish infection. Here, we show that the LysM domain-containing effector protein Ecp6 of the fungal plant pathogen Cladosporium fulvum mediates virulence through perturbation of chitin-triggered host immunity. During infection, Ecp6 sequesters chitin oligosaccharides that are released from the cell walls of invading hyphae to prevent elicitation of host immunity. This may represent a common strategy of host immune suppression by fungal pathogens, because LysM effectors are widely conserved in the fungal kingdom.

Climate change effects on agriculture: Economic responses to biophysical shocks

Abstract: Agricultural production is sensitive to weather and thus directly affected by climate change. Plausible estimates of these climate change impacts require combined use of climate, crop, and economic models. Results from previous studies vary substantially due to differences in models, scenarios, and data. This paper is part of a collective effort to systematically integrate these three types of models. We focus on the economic component of the assessment, investigating how nine global economic models of agriculture represent endogenous responses to seven standardized climate change scenarios produced by two climate and five crop models. These responses include adjustments in yields, area, consumption, and international trade. We apply biophysical shocks derived from the Intergovernmental Panel on Climate Change’s representative concentration pathway with end-of-century radiative forcing of 8.5 W/m2. The mean biophysical yield effect with no incremental CO2 fertilization is a 17% reduction globally by 2050 relative to a scenario with unchanging climate. Endogenous economic responses reduce yield loss to 11%, increase area of major crops by 11%, and reduce consumption by 3%. Agricultural production, cropland area, trade, and prices show the greatest degree of variability in response to climate change, and consumption the lowest. The sources of these differences include model structure and specification; in particular, model assumptions about ease of land use conversion, intensification, and trade. This study identifies where models disagree on the relative responses to climate shocks and highlights research activities needed to improve the representation of agricultural adaptation responses to climate change.

Special topics--Mitigation of methane and nitrous oxide emissions from animal operations: I. A review of enteric methane mitigation options.

Abstract: The goal of this review was to analyze published data related to mitigation of enteric methane (CH 4 ) emissions from ruminant animals to document the most effective and sustainable strategies. Increas- ing forage digestibility and digestible forage intake was one of the major recommended CH 4 mitigation practices. Although responses vary, CH 4 emissions can be reduced when corn silage replaces grass silage in the diet. Feeding legume silages could also lower CH 4 emissions compared to grass silage due to their lower fiber concentration. Dietary lipids can be effec- tive in reducing CH 4 emissions, but their applicabil- ity will depend on effects on feed intake, fiber digest- ibility, production, and milk composition. Inclusion of concentrate feeds in the diet of ruminants will likely decrease CH 4 emission intensity (Ei; CH 4 per unit animal product), particularly when inclusion is above 40% of dietary dry matter and rumen function is not impaired. Supplementation of diets containing medium to poor quality forages with small amounts of concen- trate feed will typically decrease CH 4 Ei. Nitrates show promise as CH 4 mitigation agents, but more studies are needed to fully understand their impact on whole-farm greenhouse gas emissions, animal productivity, and animal health. Through their effect on feed efficiency and rumen stoichiometry, ionophores are likely to have a moderate CH 4 mitigating effect in ruminants fed high-grain or mixed grain-forage diets. Tannins may also reduce CH 4 emissions although in some situations intake and milk production may be compromised. Some direct-fed microbials, such as yeast-based products, might have a moderate CH 4 -mitigating effect through increasing animal productivity and feed efficiency, but the effect is likely to be inconsistent. Vaccines against rumen archaea may offer mitigation opportunities in the future although the extent of CH 4 reduction is like- ly to be small and adaptation by ruminal microbes and persistence of the effect is unknown. Overall, improv- ing forage quality and the overall efficiency of dietary nutrient use is an effective way of decreasing CH 4 Ei. Several feed supplements have a potential to reduce CH 4 emission from ruminants although their long-term effect has not been well established and some are toxic or may not be economically feasible.

A climatic stratification of the environment of Europe

Abstract: Aim To produce a statistical stratification of the European environment, suitable for stratified random sampling of ecological resources, the selection of sites for representative studies across the continent, and to provide strata for modelling exercises and reporting. Location A ‘Greater European Window’ with the following boundaries: 11 ° W, 32 ° E, 34 ° N, 72 ° N. Methods Tw enty of the most relevant available environmental variables were selected, based on experience from previous studies. Principal components analysis (PCA) was used to explain 88% of the variation into three dimensions, which were subsequently clustered using an ISODATA clustering routine. The mean first principal component values of the classification variables were used to aggregate the strata into Environmental Zones and to provide a basis for consistent nomenclature. Results The Environmental Stratification of Europe (EnS) consists of 84 strata, which have been aggregated into 13 Environmental Zones. The stratification has a 1 km 2 resolution. Aggregations of the strata have been compared to other European classifications using the Kappa statistic, and show ‘good’ comparisons. The individual strata have been described using data from available environmental databases. The EnS is available for noncommercial use by applying to the corresponding author. Main conclusions The Environmental Stratification of Europe has been constructed using tried and tested statistical procedures. It forms an appropriate stratification for stratified random sampling of ecological resources, the selection of sites for representative studies across the continent and for the provision of strata for modelling exercises and reporting at the European scale.