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Protein Function Easily Investigated by Genomics Data Mining Using the ProteINSIDE Online Tool

Nicolas Kaspric, Matthieu Reichstadt, Brigitte Picard, Jérémy Tournayre, Muriel Bonnet
2015 Genomics and Computational Biology  
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
more » ... ted 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.
doi:10.18547/gcb.2015.vol1.iss1.e16 fatcat:7dbkgig4hffshfgxlffjmld2bq

"Do my qPCR calculation", a web tool

Jérémy Tournayre, Université Clermont Auvergne, INRA, UNH, Unité de Nutrition Humaine, CRNH Auvergne, F-63000 Clermont-Ferrand, France, Matthieu Reichstadt, Laurent Parry, Pierre Fafournoux, Céline Jousse
2019 Bioinformation  
In 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.
doi:10.6026/97320630015369 pmid:31249441 pmcid:PMC6589476 fatcat:urivycssvrdkbjtlnszfrlh4du

Molecular signatures of muscle growth and composition deciphered by the meta-analysis of age-related public transcriptomics data

Jeanne Bazile, Florence Jaffrezic, Patrice Dehais, Matthieu Reichstadt, Christophe Klopp, Denis Laloe, Muriel Bonnet
2020 Physiological Genomics  
The lean-to-fat ratio is a major issue in beef meat industry both for carcass and meat production perspectives. This industrial perspective has motivated meat physiologists to use transcriptomics technologies to decipher mechanisms behind fat deposition within muscle during the time course of muscle growth. However, synthetic biological information from this volume of data remains to be produced to identify mechanisms found in various breeds and rearing practices. We conducted a meta-analysis
more » ... 10 transcriptomic datasets stored in public databases, from the Longissimus thoracis of five different bovine breeds divergent by the age. We updated gene identifiers on the last version of the bovine genome (UCD1.2) and the 715 genes common to the 10 studies were subjected to the meta-analysis. Of the 238 genes differentially expressed (DEG), we identified a transcriptional signature of the dynamic regulation of glycolytic and oxidative metabolisms that agrees with a known shift between those two pathways from the animal puberty. We proposed some master genes of the myogenesis, namely MYOG and MAPK14, as probable regulators of the glycolytic and oxidative metabolisms. We also identified overexpressed genes related to lipid metabolism (APOE, LDLR, MXRA8 and HSP90AA1) that may contribute to the expected enhanced marbling as the age increases. Lastly, we proposed a transcriptional signature related to the induction (YBX1) or repression (MAPK14, YWAH, ERBB2) of the commitment of myogenic progenitors into the adipogenic lineage. The relationships between the abundance of the identified mRNA and marbling values remain to be analyzed in a marbling biomarkers discovery perspectives.
doi:10.1152/physiolgenomics.00020.2020 pmid:32657225 fatcat:xtxxmbce4nep7cvx36jwkft67i

ATOL: The Multi-species Livestock Trait Ontology [chapter]

Wiktoria Golik, Olivier Dameron, Jérôme Bugeon, Alice Fatet, Isabelle Hue, Catherine Hurtaud, Matthieu Reichstadt, Marie-Christine Salaün, Jean Vernet, Léa Joret, Frédéric Papazian, Claire Nédellec (+1 others)
2012 Communications in Computer and Information Science  
This paper presents the multi-species Animal Trait Ontology for Livestock (ATOL) and the methodology used for its design. ATOL has been designed as a reference source for indexing phenotype databases and scientific papers. It covers five major topics related to animal productions: growth and meat quality, animal nutrition, milk production, reproduction and welfare. It is composed of species-independent concepts subsuming species-specific ones so that cross-species and species-specific reasoning
more » ... can be performed consistently. In order to ensure a large consensus, three complementary approaches have successively been applied to its design: reuse of existing ontologies, integration of production-specific livestock traits by a large team of domain experts and curators and terminology analysis of scientific papers. It resulted in a detailed taxonomy of 1,654 traits that is available at
doi:10.1007/978-3-642-35233-1_28 fatcat:vloi43ivjff47aslnd2udwtwz4

ProteINSIDE to Easily Investigate Proteomics Data from Ruminants: Application to Mine Proteome of Adipose and Muscle Tissues in Bovine Foetuses

Nicolas Kaspric, Brigitte Picard, Matthieu Reichstadt, Jérémy Tournayre, Muriel Bonnet, Frederique Lisacek
2015 PLoS ONE  
Genomics experiments are widely acknowledged to produce a huge amount of data to be analysed. The challenge is to extract meaningful biological context for proteins or genes which is currently difficult because of the lack of an integrative workflow that hinders the efficiency and the robustness of data mining performed by biologists working on ruminants. Thus, we designed ProteINSIDE, a free web service (www.proteinside.org) that (I) provides an overview of the biological information stored in
more » ... public databases or provided by annotations according to the Gene Ontology, (II) predicts proteins that are secreted to search for proteins that mediate signalisation between cells or tissues, and (III) analyses protein-protein interactions to identify proteins contributing to a process or to visualize functional pathways. Using lists of proteins or genes as a unique input, ProteINSIDE is an original all-inone tool that merges data from these searches to present a fast overview and integrative analysis of genomic and proteomic data from Bovine, Ovine, Caprine, Human, Rat, and Murine species. ProteINSIDE was bench tested with 1000 proteins identifiers from each species by comparison with DAVID, BioMyn, AgBase, PrediSi, and Phobius. Compared to DAVID or BioMyn, identifications and annotations provided by ProteINSIDE were similar from monogastric proteins but more numerous and relevant for ruminants proteins. ProteIN-SIDE, thanks to SignalP, listed less proteins potentially secreted with a signal peptide than PrediSi and Phobius, in agreement with the low false positive rate of SignalP. In addition ProteINSIDE is the only resource that predicts proteins secreted by cellular processes that do not involve a signal peptide. Lastly, we reported the usefulness of ProteINSIDE to bring new biological hypotheses of research from proteomics data: the biological meaning of the uptake of adiponectin by the foetal muscle and a role for autophagy during ontogenesis of adipose and muscle tissues.
doi:10.1371/journal.pone.0128086 pmid:26000831 pmcid:PMC4441380 fatcat:vybzki3owjhchioy22flfzctoq

Draft Genome Sequence of Tubulinosema ratisbonensis, a Microsporidian Species Infecting the Model Organism Drosophila melanogaster

Valérie Polonais, Sebastian Niehus, Ivan Wawrzyniak, Adrien Franchet, Christine Gaspin, Abdel Belkorchia, Matthieu Reichstadt, Caroline Belser, Karine Labadie, Arnaud Couloux, Frédéric Delbac, Eric Peyretaillade (+2 others)
2019 Microbiology Resource Announcements  
Reichstadt, S. Rimour, I. Wawrzyniak, and F. Delbac, unpublished data) combining homology search, transcriptional regulatory motif detection, and GLIMMER gene prediction (15, 16) .  ... 
doi:10.1128/mra.00077-19 pmid:31371528 pmcid:PMC6675976 fatcat:ebjgpm5rubao7ki7rplkyhfcpy

Virtual screening on large scale grids

Nicolas Jacq, Vincent Breton, Hsin-Yen Chen, Li-Yung Ho, Martin Hofmann, Vinod Kasam, Hurng-Chun Lee, Yannick Legré, Simon C. Lin, Astrid Maaß, Emmanuel Medernach, Ivan Merelli (+7 others)
2007 Parallel Computing  
Large scale grids for in silico drug discovery open opportunities of particular interest to neglected and emerging diseases. In 2005 and 2006, we have been able to deploy large scale virtual docking within the framework of the WISDOM initiative against malaria and avian influenza requiring about 100 years of CPU on the EGEE, Auvergrid and TWGrid infrastructures. These achievements demonstrated the relevance of large scale grids for the virtual screening by molecular docking. This also allowed
more » ... aluating the performances of the grid infrastructures and to identify specific issues raised by large scale deployment.
doi:10.1016/j.parco.2007.02.010 fatcat:4zghjxovejesfdwl25gdirpoie

PDB_REDO: automated re-refinement of X-ray structure models in the PDB

Robbie P. Joosten, Jean Salzemann, Vincent Bloch, Heinz Stockinger, Ann-Charlott Berglund, Christophe Blanchet, Erik Bongcam-Rudloff, Christophe Combet, Ana L. Da Costa, Gilbert Deleage, Matteo Diarena, Roberto Fabbretti (+12 others)
2009 Journal of Applied Crystallography  
Structural biology, homology modelling and rational drug design require accurate three-dimensional macromolecular coordinates. However, the coordinates in the Protein Data Bank (PDB) have not all been obtained using the latest experimental and computational methods. In this study a method is presented for automated re-refinement of existing structure models in the PDB. A large-scale benchmark with 16 807 PDB entries showed that they can be improved in terms of fit to the deposited experimental
more » ... -ray data as well as in terms of geometric quality. The re-refinement protocol uses TLS models to describe concerted atom movement. The resulting structure models are made available through the PDB_REDO databank (http://www.cmbi.ru.nl/pdb_redo/). Grid computing techniques were used to overcome the computational requirements of this endeavour.
doi:10.1107/s0021889809008784 pmid:22477769 pmcid:PMC3246819 fatcat:6l4ybg6wkfckbm65zi2dq3v7cq

ATOL and EOL ontologies, steps towards embryonic phenotypes shared worldwide?

I. Hue, J. Bugeon, O. Dameron, A. Fatet, C. Hurtaud, L. Joret, M.C. Meunier-Salaün, C. Nédellec, M. Reichstadt, J. Vernet, P.Y. Le Bail
2014 Animal Reproduction Science  
Reichstadt, Jean Vernet, et al.  ...  Reichstadt 7 , J. Vernet 7 , P.Y. Le Bail 2 ATOL and EOL ontologies, steps towards embryonic phenotypes shared worldwide?  ... 
doi:10.1016/j.anireprosci.2014.06.013 fatcat:oranxqefjfempai657y7ojh6cy

Un mariage fascinant d'histoire et de fiction : Charlotte de Saxe-Cobourg-Gotha et Maximilien de Habsbourg

Isabelle Moreels, Universidad de Extremadura (España)
2021 Çédille: Revista de Estudios Franceses  
Or 150 ans séparent les dessins de Matthieu Bonhomme, illustrant le scénario de Fabien Nury, des versions successives du célèbre tableau d'Édouard Manet sur le thème de L'Exécution de l'empereur Maximilien  ...  de Maximilien, frère puîné de l'empereur d'Autriche François-Joseph, protagoniste pouvant, selon plusieurs sources, s'avérer issu d'une relation extraconjugale de l'archiduchesse Sophie et du duc de Reichstadt  ... 
doi:10.25145/j.cedille.2021.19.32 fatcat:bg2vg5s5jzf43eguwv5jvfsdoe

Impact of animal and management factors on collagen characteristics in beef: a meta-analysis approach

M. Blanco, C. Jurie, D. Micol, J. Agabriel, B. Picard, F. Garcia-Launay
2013 Animal  
Acknowledgements The authors thank Matthieu Reichstadt, the staff of the Experimental Unit, the staff of the Theix Experimental Slaughterhouse and the technicians of the 'Croissance et Métabolisme du Muscle  ... 
doi:10.1017/s1751731113000177 pmid:23438472 fatcat:6mgevbrx2fatpd3tjj2cwdyx5e

Historiografía Publicación semestral-pvp: 23 euros Revista de Les enjeux religieux du discours historique à l'époque moderne : Histoire-Pouvoir-Religion Historiografía Número 21 Revista de

Susanne Rau, Gérard Laudin, Revhisto Director, Jaime Ezquerra, Secretaria Mirella, Romero Recio
unpublished
había articulado el proyecto de investigación "Pouvoir et Histoire", financiado por el Centre de Recherches du Château de Versailles, bajo la dirección académica de Chantal Grell y la coordinación de Matthieu  ...  Dabei fragt er imil a deja sauvé trois fois de la mort et chez qui on m'at assuré d'ailleurs qu'il peut beaucoup»[es geht um die Empfehlung des Christian Thomasius, sich die Bibliothek von Schloss Reichstädt  ... 
fatcat:puufkmexkbc5hntvm2j4txz62m