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Improving accuracy of predicting breeding values in Brazilian Holstein population by adding data from Nordic and French Holstein populations
No full textInternational audienceThe present study investigated the improvement of prediction reliabilities for 3 production traits in Brazilian Holsteins that had no genotype information by adding information from Nordic and French Holstein bulls that had genotypes. The estimated across-country genetic correlations (ranging from 0.604 to 0.726) indicated that an important genotype by environment interaction exists between Brazilian and Nordic (or Nordic and French) populations. Prediction reliabilities for Brazilian genotyped bulls were greatly increased by including data of Nordic and French bulls, and a 2-trait single-step genomic BLUP performed much better than the corresponding pedigree-based BLUP. However, only a minor improvement in prediction reliabilities was observed in nongenotyped Brazilian cows. The results indicate that although there is a large genotype by environment interaction, inclusion of a foreign reference population can improve accuracy of genetic evaluation for the Brazilian Holstein population. However, a Brazilian reference population is necessary to obtain a more accurate genomic evaluation
MAGGnet: An international network to foster mitigation of agricultural greenhouse gases
No full textla publication contient 47 auteurs "Short Communication"International audienceResearch networks provide a framework for review, synthesis and systematic testing of theories by multiple scientists across international borders critical for addressing global-scale issues. In 2012, a GHG research network referred to as MAGGnet (Managing Agricultural Greenhouse Gases Network) was established within the Croplands Research Group of the Global Research Alliance on Agricultural Greenhouse Gases (GRA). With involvement from 46 alliance member countries, MAGGnet seeks to provide a platform for the inventory and analysis of agricultural GHG mitigation research throughout the world. To date, metadata from 315 experimental studies in 20 countries have been compiled using a standardized spreadsheet. Most studies were completed (74%) and conducted within a 1–3-year duration (68%). Soil carbon and nitrous oxide emissions were measured in over 80% of the studies. Among plant variables, grain yield was assessed across studies most frequently (56%), followed by stover (35%) and root (9%) biomass. MAGGnet has contributed to modeling efforts and has spurred other research groups in the GRA to collect experimental site metadata using an adapted spreadsheet. With continued growth and investment, MAGGnet will leverage limited-resource investments by any one country to produce an inclusive, globally shared meta-database focused on the science of GHG mitigation
Respective roles of hematopoietic and nonhematopoietic nod2 on the gut microbiota and mucosal homeostasis
No full textInternational audienceBackground: NOD2 mutations are associated with Crohn's disease (CD). Both CD (in human) and Nod2 deficiency (in mice) are characterized by increased mucosal CD4(+) T-cells, an altered permeability and a microbial dysbiosis. However, the respective roles of the gut epithelial and immune compartments on the phenotype are not known. Methods: Microbial composition, epithelial peptide secretion, intestinal permeability, and immune cell composition of Peyer patches were studied in Nod2 knock-out mice transplanted with wild-type bone marrow cells and vice versa. Results: The nonhematopoietic cells control the microbiota composition and epithelial secretion of mucins and antimicrobial peptides. These parameters are correlated with recurrent associations between bacterial species and luminal products. In contrast, Nod2 in the hematopoietic compartment regulates the epithelial permeability and the gut-associated lymphoid tissue independently of the bacterial composition. Conclusions: The immune system and the gut permeability in one hand and the microbial and epithelial peptide compositions in the other hand are separate couples of interdependent parameters, both controlled by Nod2 in either the hematopoietic or nonhematopoietic lineages
<em>Staphylococcus aureus</em> Transcriptome Architecture: From Laboratory to Infection-Mimicking Conditions
No full textInternational audienceStaphylococcus aureus is a major pathogen that colonizes about 20% of the human population. Intriguingly, this Gram-positive bacterium can survive and thrive under a wide range of different conditions, both inside and outside the human body. Here, we investigated the transcriptional adaptation of S. aureus HG001, a derivative of strain NCTC 8325, across experimental conditions ranging from optimal growth in vitro to intracellular growth in host cells. These data establish an extensive repertoire of transcription units and non-coding RNAs, a classification of 1412 promoters according to their dependence on the RNA polymerase sigma factors SigA or SigB, and allow identification of new potential targets for several known transcription factors. In particular, this study revealed a relatively low abundance of antisense RNAs in S. aureus, where they overlap only 6% of the coding genes, and only 19 antisense RNAs not co-transcribed with other genes were found. Promoter analysis and comparison with Bacillus subtilis links the small number of antisense RNAs to a less profound impact of alternative sigma factors in S. aureus. Furthermore, we revealed that Rho-dependent transcription termination suppresses pervasive antisense transcription, presumably originating from abundant spurious transcription initiation in this A+T-rich genome, which would otherwise affect expression of the overlapped genes. In summary, our study provides genome-wide information on transcriptional regulation and non-coding RNAs in S. aureus as well as new insights into the biological function of Rho and the implications of spurious transcription in bacteria
<em>Akkermansia muciniphila</em> and improved metabolic health during a dietary intervention in obesity: relationship with gut microbiome richness and ecology
No full textInternational audienceObjectives :Individuals with obesity and type 2 diabetes differ from lean and healthy individuals in their abundance of certain gut microbial species and microbial gene richness. Abundance of Akkermansia muciniphila, a mucin-degrading bacterium, has been inversely associated with body fat mass and glucose intolerance in mice, but more evidence is needed in humans. The impact of diet and weight loss on this bacterial species is unknown. Our objective was to evaluate the association between faecal A. muciniphila abundance, faecal microbiome gene richness, diet, host characteristics, and their changes after calorie restriction (CR). Design : The intervention consisted of a 6-week CR period followed by a 6-week weight stabilisation diet in overweight and obese adults (N=49, including 41 women). Faecal A. muciniphila abundance, faecal microbial gene richness, diet and bioclinical parameters were measured at baseline and after CR and weight stabilisation. Results : At baseline A. muciniphila was inversely related to fasting glucose, waist-to-hip ratio and subcutaneous adipocyte diameter. Subjects with higher gene richness and A. muciniphila abundance exhibited the healthiest metabolic status, particularly in fasting plasma glucose, plasma triglycerides and body fat distribution. Individuals with higher baseline A. muciniphila displayed greater improvement in insulin sensitivity markers and other clinical parameters after CR. These participants also experienced a reduction in A. muciniphila abundance, but it remained significantly higher than in individuals with lower baseline abundance. A. muciniphila was associated with microbial species known to be related to health. Conclusions : A. muciniphila is associated with a healthier metabolic status and better clinical outcomes after CR in overweight/obese adults. The interaction between gut microbiota ecology and A. muciniphila warrants further investigation
Drivers of household food availability in sub-Saharan Africa based on big data from small farms
No full textInternational audienceWe calculated a simple indicator of food availability using data from 93 sites in 17 countries across contrasted agroecologies in sub-Saharan Africa (>13,000 farm households) and analyzed the drivers of variations in food availability. Crop production was the major source of energy, contributing 60% of food availability. The off-farm income contribution to food availability ranged from 12% for households without enough food available (18% of the total sample) to 27% for the 58% of households with sufficient food available. Using only three explanatory variables (household size, number of livestock, and land area), we were able to predict correctly the agricultural determined status of food availability for 72% of the households, but the relationships were strongly influenced by the degree of market access. Our analyses suggest that targeting poverty through improving market access and off-farm opportunities is a better strategy to increase food security than focusing on agricultural production and closing yield gaps. This calls for multisectoral policy harmonization, incentives, and diversification of employment sources rather than a singular focus on agricultural development. Recognizing and understanding diversity among smallholder farm households in sub-Saharan Africa is key for the design of policies that aim to improve food security
Endosperm and nucellus develop antagonistically in arabidopsis seeds
No full textInternational audienceIn angiosperms, seed architecture is shaped by the coordinated development of three genetically different components: embryo, endosperm, and maternal tissues. The relative contribution of these tissues to seed mass and nutrient storage varies considerably among species. The development of embryo, endosperm, or nucellus maternal tissue as primary storage compartments defines three main typologies of seed architecture. It is still debated whether the ancestral angiosperm seed accumulated nutrients in the endosperm or the nucellus. During evolution, plants shifted repeatedly between these two storage strategies through molecular mechanisms that are largely unknown. Here, we characterize the regulatory pathway underlying nucellus and endosperm tissue partitioning in Arabidopsis thaliana. We show that Polycomb-group proteins repress nucellus degeneration before fertilization. A signal initiated in the endosperm by the AGAMOUS-LIKE62 MADS box transcription factor relieves this Polycomb-mediated repression and therefore allows nucellus degeneration. Further downstream in the pathway, the TRANSPARENT TESTA16 (TT16) and GORDITA MADS box transcription factors promote nucellus degeneration. Moreover, we demonstrate that TT16 mediates the crosstalk between nucellus and seed coat maternal tissues. Finally, we characterize the nucellus cell death program and its feedback role in timing endosperm development. Altogether, our data reveal the antagonistic development of nucellus and endosperm, in coordination with seed coat differentiation
Modelling anaerobic digestion and compost of organic residues: towards organic matter fate prediction in soils during land spreading
No full textNational audienc
Durable strategies for fungicides use: lessons from the past and leads for improving the future Preliminary results from the FONDU project
No full textInternational audienceThe durability of strategies aiming to delay fungicide resistance evolution in populations of plant fungi relies on the skillful deployment in time and space of the various molecules registered for a specific usage. Therefore, the optimization of these strategies constitutes a major challenge of integrated pest management, all the more in the context of new regulations aiming to decrease pesticide use (e.g. in France, the “Ecophyto II” and “Agroécologie” plans). The respective interests and drawbacks of anti-resistance strategies (namely mixture, alternation, mosaic and dose modulation) are a matter of debate in the scientific community and should be more efficiently deployed in agricultural landscapes. In this context, this paper reports the preliminary results of the FONDU project, aiming at (1) identifying and characterizing sustainable anti-resistance strategies and (2) disentangling the social and economic imits to their wide use on large territories. This project has a generic outcome but was first focused on Zymoseptoria tritici, the causal agent of septoria leaf blotch. Empirical data (e.g. the pluriannual dataset “Performance”, managed by the technical institute Arvalis-Institut du Végétal), as well as a specific model were mined to answer the first objective. Interviews with key French resistance managers, as well as economic models were carried to answer the second aim
Understand the structuring of wheat-legume cakes to promote product innovation and to design new formulation tools for the industry
No full textUnderstand the structuring of wheat-legume cakes to promote product innovation and to design new formulation tools for the industry. Second International Legume Society Conferenc