Identification de marques épigénétiques marqueurs de prédisposition aux maladies métaboliques

Identification de marques épigénétiques marqueurs de prédisposition aux maladies métaboliques. 22. Journée de l’Ecole Doctorale Sciences de la vie, Santé, Agronomie & Environnement JED 201

Protéines de la matrice extracellulaire bovine et rôle potentiel dans la qualité de la viande : Premier recueil in silico Bos taurus

International audienceThe extracellular matrix (ECM) is a three-dimensional set of proteins that binds tissues and defines their biomechanical properties. Among the ECM components known to be involved in beef sensory qualities, authors have often studied fibrillar collagens but also, although less often, proteoglycans and some glycoproteins. The ECM contains many other proteins. Our hypothesis is that to deepen the role of ECM proteins in beef qualities and to identify new ones among the vast amount of data generated by high throughput methods, it is necessary to have a list of proteins of this matrix to refer to for the bovine species. We have therefore defined the Bos taurus matrisome known as the set of genes encoding ECM (core matrisome proteins and matrisome-associated proteins). We have used orthology, as a reference method, and a bioinformatic approach based on a computational pipeline previously published for Homo sapiens, Mus musculus and Danio rerio for the definition of their respective matrisome. We have reported here that the Bos taurus matrisome is composed of 1022 genes that we have classified according to the different matrisome categories. This list is the only matrisome of a livestock species to be defined to date. SIGNIFICANCE: In this study, we provide the first definition of matrisome of a livestock species, the Bos taurus. We believe that the Bos taurus matrisome will be of great interest for several reasons. It comes as a complement to the matrisomes of several other species such as Homo sapiens, Mus musculus, Danio rerio, Drosophila melanogaster and Caenorabditis elegans previously defined by other authors. It could be used to identify matrisome molecules among the vast amount of data generated by the high throughput methods. It thus can be used in addition to the other matrisomes as a model by the scientific community to study cell behavior and mechanotransduction and could lead to the identification of novel biomarkers for several diseases and cancers in which ECM is involved. Moreover, in the domain of studies on livestock, the dataset that we have provided here can be used in the context of product quality studies, especially meat quality, but also, for example, for lactation studies

"Do my qPCR calculation", a web tool

eCollection 2019In order to automatically process qPCR raw data, we present the tool "Do my qPCR calculation". We offer a website to automatically calculate the data normalization and represent the different samples graphically in an Excel file. This tool is also available on Github for installation and local use with or without web interface

Protein function easily investigated by genomics data mining using the proteINSIDE online tool

Nowadays, genomic and proteomic studies produce vast amounts of data. To get the biological meaning of these data and to generate testable new hypothesis, scientists must use several tools often not designed for ruminant studies. Here we present ProteINSIDE: an online tool to analyse lists of protein or gene identifiers from well-annotated species (human, rat, and mouse) and ruminants (cow, sheep, and goat). The aims of ProteINSIDE modules are to gather biological information stores in well-updated public databases, to proceed to annotations according to the Gene Ontology consortium, to predict potentially secreted proteins, and to search for proteins interactions. ProteINSIDE provides results from several software and databases in a single query. From a list of identifiers, ProteINSIDE uses orthologs or homologs to extend analyses and biological information retrieval. As a tutorial, we presented how to launch, to recover, to view, and to interpret the results provided by the two types of analysis available with ProteINSIDE (basic and custom analyses). ProteINSIDE is freely available using a simple internet browser at www.proteinside.org. The results of this article are provided on the home page of ProteINSIDE website as the example of an analysis results

Talkmine, a workflow for the prediction of the interactions between secretome and surfaceome in the dialogue between cellular types

International audienc

Metavir 2: new tools for viral metagenome comparison and assembled virome analysis.

International audienceBACKGROUND: Metagenomics, based on culture-independent sequencing, is a well-fitted approach to provide insights into the composition, structure and dynamics of environmental viral communities. Following recent advances in sequencing technologies, new challenges arise for existing bioinformatic tools dedicated to viral metagenome (i.e. virome) analysis as (i) the number of viromes is rapidly growing and (ii) large genomic fragments can now be obtained by assembling the huge amount of sequence data generated for each metagenome. RESULTS: To face these challenges, a new version of Metavir was developed. First, all Metavir tools have been adapted to support comparative analysis of viromes in order to improve the analysis of multiple datasets. In addition to the sequence comparison previously provided, viromes can now be compared through their k-mer frequencies, their taxonomic compositions, recruitment plots and phylogenetic trees containing sequences from different datasets. Second, a new section has been specifically designed to handle assembled viromes made of thousands of large genomic fragments (i.e. contigs). This section includes an annotation pipeline for uploaded viral contigs (gene prediction, similarity search against reference viral genomes and protein domains) and an extensive comparison between contigs and reference genomes. Contigs and their annotations can be explored on the website through specifically developed dynamic genomic maps and interactive networks. CONCLUSIONS: The new features of Metavir 2 allow users to explore and analyze viromes composed of raw reads or assembled fragments through a set of adapted tools and a user-friendly interface

Talkmine, a workflow for the prediction of the interactions between secretome and surfaceome in the dialogue between cellular types

International audienc

Intégration de données "omics" provenant du tissu adipeux ou musculaire

National audienc

Investigating the effect of divergent residual feed intake phenotypes on the bovine rumen microbiota across contrasting diet in fattening bulls

International audienceImproving the feed efficiency of cattle contributes to the environmental and economic challenges facing ruminant production. Within this context, a study with 99 fattening Charolais bulls was conducted over two consecutive years (n=49 the first year and n=50 the second). Each year, bulls were allocated to two groups fed ad libitum, corn silage, or a grass silage diet. Bulls were tested for residual feed intake (RFI) during 84 days, and extreme RFI animals were identified thereafter (n = 32; balanced for RFI group, diet and year). Total rumen contents from the eight most extreme RFI+ and RFI- bulls on each diet were sampled at the abattoir (4 bulls/diet/year, n=32). All 49 animals from the first year were also sampled for rumen fluid by stomach-tubing. Total genomic DNA was extracted and subjected to PCR amplification using universal primers targeting the 16S rRNA gene prior to Ilumina sequencing. Raw reads were analyzed using the QIIME2 pipeline with default parameters, and genus-level tables for rumen fluid and total contents were separated and used to assess alpha- and beta-diversity in R using vegan package. Effects of diet, RFI group and the interaction diet×RFI were analyzed using the Kruskal-Walis test. For rumen fluid, Simpson and Shannon diversity indexes were higher in corn-fed bulls, but this effect was not observed for total contents sampled at the abattoir. For both groups of samples, permanova analysis highlighted the effect of diet and diet×RFI on rumen microbial community structure, while the effect of RFI was non-significant. Permanova analysis within each dietary group did not show major changes in microbial community structure. Research from this study indicates that there are no shifts in the overall prokaryotic community structure related to RFI. Further analysis will explore the impact of individual microbial taxa on animal’s feed efficiency

Potentially secreted proteins with a signal peptide in bovine foetal AT, muscle or both tissues.

<p>¹ confirmed by GO terms</p><p>² confirmed by TargetP</p><p>³ confirmed by Subcellular location provided by UniProt resource</p><p>Potentially secreted proteins with a signal peptide in bovine foetal AT, muscle or both tissues.</p