Agrocampus Ouest

About: Agrocampus Ouest is a education organization based out in Rennes, France. It is known for research contribution in the topics: Population & Soil water. The organization has 2160 authors who have published 3219 publications receiving 75606 citations. The organization is also known as: Institut supérieur des sciences agronomiques, agroalimentaires, horticoles et du paysage & Higher Institute for agricultural sciences, food industry, horticulture and landscape management.

Heterosis and inbreeding depression in bottlenecked populations: a test in the hermaphroditic freshwater snail Lymnaea stagnalis.

Abstract: Small population size is expected to induce heterosis, due to the random fixation and accumulation of mildly deleterious mutations, whereas within-population inbreeding depression should decrease due to increased homozygosity. Population bottlenecks, although less effective, may have similar consequences. We tested this hypothesis in the self-fertile freshwater snail Lymnaea stagnalis, by subjecting experimental populations to a single bottleneck of varied magnitude. Although patterns were not strong, heterosis was significant in the most severely bottlenecked populations, under stressful conditions. This was mainly due to hatching rate, suggesting that early acting and highly deleterious alleles were involved. Although L. stagnalis is a preferential outcrosser, inbreeding depression was very low and showed no clear relationship with bottleneck size. In the less reduced populations, inbreeding depression for hatching success increased under high inbreeding. This may be consistent with the occurence of synergistic epistasis between fitness loci, which may contribute to favour outcrossing in L. stagnalis.

A new unsupervised gene clustering algorithm based on the integration of biological knowledge into expression data

Abstract: Gene clustering algorithms are massively used by biologists when analysing omics data. Classical gene clustering strategies are based on the use of expression data only, directly as in Heatmaps, or indirectly as in clustering based on coexpression networks for instance. However, the classical strategies may not be sufficient to bring out all potential relationships amongst genes. We propose a new unsupervised gene clustering algorithm based on the integration of external biological knowledge, such as Gene Ontology annotations, into expression data. We introduce a new distance between genes which consists in integrating biological knowledge into the analysis of expression data. Therefore, two genes are close if they have both similar expression profiles and similar functional profiles at once. Then a classical algorithm (e.g. K-means) is used to obtain gene clusters. In addition, we propose an automatic evaluation procedure of gene clusters. This procedure is based on two indicators which measure the global coexpression and biological homogeneity of gene clusters. They are associated with hypothesis testing which allows to complement each indicator with a p-value. Our clustering algorithm is compared to the Heatmap clustering and the clustering based on gene coexpression network, both on simulated and real data. In both cases, it outperforms the other methodologies as it provides the highest proportion of significantly coexpressed and biologically homogeneous gene clusters, which are good candidates for interpretation. Our new clustering algorithm provides a higher proportion of good candidates for interpretation. Therefore, we expect the interpretation of these clusters to help biologists to formulate new hypothesis on the relationships amongst genes.

Assessing interacting impacts of artisanal and recreational fisheries in a small Marine Protected Area (Portofino, NW Mediterranean Sea)

Abstract: Marine Protected Areas (MPAs) have spread across the Mediterranean to protect its rich biodiversity and manage human activities for a more sustainable coastal development. Within MPAs, traditional artisanal fishing is competing for space and resources with increasing recreational fishing, likely leading to interacting ecological effects. Such effects are difficult to unravel, given the multispecies character of both fisheries and the complexity of the food webs upon which they both impact. To address these issues, we developed an Ecopath and EcoTroph trophic model for the Portofino MPA case study (NW Mediterranean), in particular to (1) identify keystone species and assess fishing impact on them; (2) analyze the interacting impact of artisanal and recreational fishing on ecosystem biomass and trophic structure; and (3) assess the impact of recreational fishing on artisanal fishing catches. Two high trophic level predator (HTLP) groups coupled important keystone roles with high sensitivity to fishing pressure and should thus be regarded as “sentinels” to be prioritized for the definition of management actions. Recreational fishing had the widest impact on the food web, strongly impacting HTLP. Simulation of different mortality scenarios for each fishery highlighted that the ecosystem is far from its carrying capacity for HTLP. Forbidding recreational fishing allowed a 24% increase in HTLP biomass and benefited artisanal fishing by increased availability of HTLP catches. Artisanal fishing alone could instead be maintained with a moderate impact on the food web. Overall, Ecopath and EcoTroph modeling is a valuable tool to advise MPA management, but it is essential to increase data availability and quality by developing long-term monitoring programs on key species and on artisanal and recreational fishing.

Biocatalyzed modifications of milk lipids: applications and potentialities

Abstract: Biocatalyzed modifications of bovine milk triacylglycerols and polar lipids over the last 25 years, using exogenous commercial enzymes, are reviewed. Due to its mildness, biocatalysis is more adapted than chemical catalysis in order to tailor lipids with improved physical and nutritional properties or with new functionalities. Biocatalyzed modification of milk fat is becoming all the more attractive, as the number of efficient and specific commercial lipolytic enzymes is increasing. In addition to lipase-catalyzed hydrolysis of milk fat, several other applications, such as interesterification or phospholipase-catalyzed modifications are technically mature and very promising to diversify milk fat functionalities and uses.