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Evolutionary history of DNA methylation related genes in chordates: new insights from multiple whole genome duplications
No full textDNA methylation is an important epigenetic mechanism involved in many biological processes, i.e.gametogenesis and embryonic development. However, increased copy numbers of DNA methylation related genes (dnmt, tet and tdg) have been found during chordate evolution due to successive whole genome duplication (WGD) events. Their evolutionary history and phylogenetic relationships remain unclear. The present study is the first to clarify the evolutionary history of DNA methylation genes in chordates. In particular, our results highlight the fixation of several dnmt3-related genes following successive WGD throughout evolution. The rainbow trout genome offered a unique opportunity to study the early evolutionary fates of duplicated genes due to a recent round of WGD at the radiation of
salmonids. Differences highlighted in transcriptional patterns of these genes during gametogenesis and ontogenesis in trout indicated that they might be subjected to sub- or neo-functionalisation after WDG. The fixation of multiple dnmt3 genes in genomes after WGD could contribute to the diversification and plastic adaptation of the teleost
Beneficial Propionibacteria within a Probiotic Emmental Cheese: Impact on Dextran Sodium Sulphate-Induced Colitis in Mice
No full textBackgrounds and Aims. Inflammatory Bowel Diseases (IBD), including Ulcerative Colitis (UC), coincide with alterations in the gut microbiota. Consumption of immunomodulatory strains of probiotic bacteria may induce or prolong remission in UC patients. Fermented foods, including cheeses, constitute major vectors for bacteria consumption. New evidences revealed anti-inflammatory effects in selected strains of Propionibacterium freudenreichii. We thus hypothesized that consumption of a functional cheese, fermented by such a strain, may exert a positive effect on IBD. Methods. We investigated the impact of cheese fermented by P. freudenreichii on gut inflammation. We developed an experimental single-strain cheese solely fermented by a selected immunomodulatory strain of P. freudenreichii, CIRM-BIA 129. We moreover produced, in industrial conditions, an Emmental cheese using the same strain, in combination with Lactobacillus delbrueckii CNRZ327 and Streptococcus thermophilus LMD-9, as starters. Consumption of both cheeses was investigated with respect to prevention of Dextran Sodium Sulphate (DSS)-induced colitis in mice. Results. Consumption of the single-strain experimental cheese, or of the industrial Emmental, both fermented by P. freudenreichii CIRM-BIA 129, reduced severity of subsequent DSS-induced colitis, weight loss, disease activity index and histological score. Both treatments, in a preventive way, reduced small bowel Immunoglobulin A (IgA) secretion, restored occludin gene expression and prevented induction of Tumor Necrosis Factor (TNF ), Interferon (IFN ) and Interleukin-17 (IL-17). Conclusions. A combination of immunomodulatory strains of starter bacteria can be used tomanufacture an anti-inflammatory cheese, as revealed in an animalmodel of colitis. This opens new perspectives for personalised nutrition in the context of IBD
Return of the moth: rethinking the effect of climate on insect outbreaks
No full textThe sudden interruption of recurring larch budmoth (LBM; Zeiraphera diniana or griseana Gn.) outbreaks across the European Alps after 1982 was surprising, because populations had regularly oscillated every 8-9 years for the past 1200 years or more. Although ecophysiological evidence was limited and underlying processes remained uncertain, climate change has been indicated as a possible driver of this disruption. An unexpected, recent return of LBM population peaks in 2017 and 2018 provides insight into this insect's climate sensitivity. Here, we combine meteorological and dendrochronological data to explore the influence of temperature variation and atmospheric circulation on cyclic LBM outbreaks since the early 1950s. Anomalous cold European winters, associated with a persistent negative phase of the North Atlantic Oscillation, coincide with four consecutive epidemics between 1953 and 1982, and any of three warming-induced mechanisms could explain the system's failure thereafter: (1) high egg mortality, (2) asynchrony between egg hatch and foliage growth, and (3) upward shifts of outbreak epicentres. In demonstrating that LBM populations continued to oscillate every 8-9 years at sub-outbreak levels, this study emphasizes the relevance of winter temperatures on trophic interactions between insects and their host trees, as well as the importance of separating natural from anthropogenic climate forcing on population behaviour
Dissecting the control of shoot development in grapevine: genetics and genomics identify potential regulators
No full textCarbon and phosphorus allocation in annual plants: an optimal functioning approach
No full textPhosphorus (P) is the second most important nutrient after nitrogen (N) and can greatly diminish plant productivity if P supply is not adequate. Plants respond to soil P availability by adjusting root biomass to maintain uptake and productivity due to P use. In spite of our vast knowledge on P effects on plant growth, how to functionally model enhanced root biomass allocation in low P environments is not fully explored. We develop a dynamic plant model based on the principle of optimal carbon (C) and P allocation to investigate growth and functional response to contrasting levels of soil P availability. By describing plant growth as a balance of growth and respiration processes, we optimize C and P allocation in order to maximize leaf productivity and drive plant response. We compare our model to a field trial and a set of hydroponic experiments which describe plant response at varying P availabilities. The model is able to reproduce long-term plant functional response to different P levels like change in root-shoot ratio (RSR), total biomass and organ P concentration. But it is not capable of fully describing the time evolution of organ P uptake and cycling within the plant. Most notable is the underestimation of organ P uptake during the vegetative growth stage which is due to the model's leaf productivity formalism. In spite of the model's parsimonious nature, which optimizes for and predicts whole plant response through leaf productivity alone, the optimal growth hypothesis can provide a reasonable framework for modelling plant response to environmental change that can be used in more physically driven vegetation models
Decentralisation of agri-environmental policy design
No full textWe theoretically examine the gains of the decentralisation of agri-environmental policy design. We consider a model with homogeneous regions and joint production of local and global public goods from agriculture. Assuming that governments are characterised by different agency costs and knowledge of the PG values, we evaluate whether decentralisation is a suitable strategy to improve the efficiency of agri-environmental payments.We find that partial decentralisation always improves the welfare.We apply our theoretical model to the case of abandoned wetlands in Brittany. We find that national governments are the most suitable to design agri-environmental policies. Our results contribute to reflections on future Common Agricultural Policy.Nous examinons théoriquement les gains liés à la décentralisation de la conception des politiques agroenvironnementales dans le cas où (i) les régions sont homogènes, (ii) l’agriculture produit conjointement des biens publics locaux et globaux et (iii) les différents gouvernements hiérarchiques se caractérisent par des coûts d'agence différents et une connaissance hétérogène de la valeur des biens publiques locaux et globaux. Dans cette situation, nous constatons qu’une décentralisation partielle, comme celle en réflexion pour la future Politique Agricole Commune, améliore toujours le bien-être
Effects of cholesterol content on activity of P-glycoproteins and membrane physical state, and consequences for anthelmintic resistance in the nematode Haemonchus contortus
No full textEukaryote plasma membranes protect cells from chemical attack. Xenobiotics, taken up through passive diffusion, accumulate in the membranes, where they are captured by transporters, among which P-glycoproteins (Pgps). In nematodes such as Haemonchus contortus, eggshells and cuticles provide additional protective barriers against xenobiotics. Little is known about the role of these structures in the transport of chemical molecules. Pgps, members of the ABC transporter family, are present in eggshells and cuticles. Changes in the activity of these proteins have also been correlated with alterations in lipids, such as cholesterol content, in eggshells. However, the cellular mechanisms underlying these effects remain unclear. We show here that an experimental decrease in the cholesterol content of eggshells of Haemonchus contortus, with Methyl-beta-CycloDextrin (MβCD), results in an increase in membrane fluidity, favouring Pgp activity and leading to an increase in resistance to anthelmintics. This effect is modulated by the initial degree of anthelminthic resistance of the eggs. These results suggest that eggshell fluidity plays a major role in the modulation of Pgp activity. They confirm that Pgp activity is highly influenced by the local microenvironment, in particular sterols, as observed in some vertebrate models. Thus, eggshell barriers could play an active role in the transport of xenobiotics
All practices are shared, but some more than others: Sharedness of social practices and time-use in food consumption
No full textEven though we spend less and less time cooking and eating, food consumption remains a corner stone of the temporal organisation of everyday life. This paper is interested in how and to which extent food practices can be described as shared. We situate our investigationat the confluence ofpractice theories and the empirical analysis of time-use surveys.While qualitative research highlights the interrelations between many activities and agents necessary to consume food, quantitative data,such as time-use surveys,underscore the shared temporality of eating. Weaskwhetherpractices are shared beyond being socially recognized and mutually understandable forms of actions. Accordingly, we are interested inhowsome practices might be described as more shared than others, or shared in different ways?Weidentify three characteristics of sharedness: participation, commitment and temporal concentration. The latter isa key indicator of dispersed collective activity, inasmuch as participantsengage in the practicein similar ways even without coordinating explicitly around it. We measure and compare the characteristics of sharedness by analysingthe Dutch time-use survey 2011 (N=2,005). Such an analysisoffersempirical evidence for our characterisation of sharednessby mapping fivefood-relatedpractices (eating a meal, snacking, cooking, shopping, cleaning)onto five dimensions of temporality (duration, sequence, periodicity, synchronisation, tempo).The characteristics of sharedness afforda systematic framework to analyseculture in dispersed collective activity.Our analysis also providesnovel vistasto reflect upon power in shared practicesby investigatingtheirtemporal concentration
Aggregation of omic data and secretome prediction enable the discovery of candidate plasma biomarkers for beef tenderness
No full textBeef quality is a complex phenotype that can be evaluated only after animal slaughtering.
Previous research has investigated the potential of genetic markers or muscle-derived proteins to
assess beef tenderness. Thus, the use of low-invasive biomarkers in living animals is an issue for the
beef sector. We hypothesized that publicly available data may help us discovering candidate plasma
biomarkers. Thanks to a review of the literature, we built a corpus of articles on beef tenderness.
Following data collection, aggregation, and computational reconstruction of the muscle secretome,
the putative plasma proteins were searched by comparison with a bovine plasma proteome atlas
and submitted to mining of biological information. Of the 44 publications included in the study,
469 unique gene names were extracted for aggregation. Seventy-one proteins putatively released
in the plasma were revealed. Among them 13 proteins were predicted to be secreted in plasma, 44
proteins as hypothetically secreted in plasma, and 14 additional candidate proteins were detected
thanks to network analysis. Among these 71 proteins, 24 were included in tenderness quantitative
trait loci. The in-silico workflow enabled the discovery of candidate plasma biomarkers for beef
tenderness from reconstruction of the secretome, to be examined in the cattle plasma proteome