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4. BioStatFlow -Statistical Analysis Workflow for 'Omics' Data

Author

Jacob, Daniel, Deborde, Catherine, and Moing, Annick

Subjects
Quantitative Biology - Quantitative Methods
Abstract

BioStatFlow is a free web application, useful to facilitate the performance of statistical analyses of "omics", including metabolomics, data using R packages. It is a fast and easy on-line tool for biologists who are not experts in univariate and multivariate statistics, do not have time to learn R language, and only have basic notions in biostatistics. It guides the biologist through the different steps of a statistical workflow, from data normalization and imputation of missing data to univariate and multivariate analyses. It also includes tools to reconstruct and visualize networks based on correlations. All outputs are easily saved in a session or downloaded. New analytical modules can be easily included upon request. BioStatFlow is available online: http://biostatflow.org

Published
2020

7. PeakForest: a multi-platform digital infrastructure for interoperable metabolite spectral data and metadata management

Author

Paulhe, Nils, Canlet, Cécile, Damont, Annelaure, Peyriga, Lindsay, Durand, Stéphanie, Deborde, Catherine, Alves, Sandra, Bernillon, Stephane, Berton, Thierry, Bir, Raphael, Bouville, Alyssa, Cahoreau, Edern, Centeno, Delphine, Costantino, Robin, Debrauwer, Laurent, Delabrière, Alexis, Duperier, Christophe, Emery, Sylvain, Flandin, Amelie, Hohenester, Ulli, Jacob, Daniel, Joly, Charlotte, Jousse, Cyril, Lagree, Marie, Lamari, Nadia, Lefebvre, Marie, Lopez-Piffet, Claire, Lyan, Bernard, Maucourt, Mickael, Migne, Carole, Olivier, Marie-Francoise, Rathahao-Paris, Estelle, Petriacq, Pierre, Pinelli, Julie, Roch, Léa, Roger, Pierrick, Roques, Simon, Tabet, Jean-Claude, Tremblay-Franco, Marie, Traïkia, Mounir, Warnet, Anna, Zhendre, Vanessa, Rolin, Dominique, Jourdan, Fabien, Thévenot, Etienne, Moing, Annick, Jamin, Emilien, Fenaille, François, Junot, Christophe, Pujos-Guillot, Estelle, and Giacomoni, Franck

Published
2022
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9. New alternative ingredients and genetic selection are the next game changers in rainbow trout nutrition: a metabolomics appraisal

Author

Roques, Simon, primary, Deborde, Catherine, additional, Skiba-Cassy, Sandrine, additional, Médale, Françoise, additional, Dupont-Nivet, Mathilde, additional, Lefevre, Florence, additional, Bugeon, Jérome, additional, Labbé, Laurent, additional, Marchand, Yann, additional, Moing, Annick, additional, and Fauconneau, Benoit, additional

Published
2023
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11. Comparative constraint‐based modelling of fruit development across species highlights nitrogen metabolism in the growth‐defence trade‐off

Author

Colombié, Sophie, primary, Prigent, Sylvain, additional, Cassan, Cédric, additional, Hilbert‐Masson, Ghislaine, additional, Renaud, Christel, additional, Dell'Aversana, Emilia, additional, Carillo, Petronia, additional, Moing, Annick, additional, Beaumont, Chloé, additional, Beauvoit, Bertrand, additional, McCubbin, Tim, additional, Nielsen, Lars Keld, additional, and Gibon, Yves, additional

Published
2023
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15. Identification of metabolic and protein markers representative of the impact of mild nitrogen deficit on agronomic performance of maize hybrids

Author

Urrutia, Maria, primary, Blein-Nicolas, Mélisande, additional, Fernandez, Ollivier, additional, Bernillon, Stéphane, additional, Maucourt, Mickaël, additional, Deborde, Catherine, additional, Balliau, Thierry, additional, Rabier, Dominique, additional, Bénard, Camille, additional, Prigent, Sylvain, additional, Quillere, Isabelle, additional, Jacob, Daniel, additional, Gibon, Yves, additional, Zivy, Michel, additional, Giauffret, Catherine, additional, Hirel, Bertrand, additional, and Moing, Annick, additional

Published
2023
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22. Preliminary results of a MetaboHUB 2.0 inter-laboratory test on 1D 1H NMR metabolite quantification of a synthetic urine

Author

Deborde, Catherine, Giraudeau, Patrick, Cahoreau, Edern, da Costa, Gregory, Gautier, Roselyne, Jacob, Daniel, Jousse, Cyril, Lacaze, Melia, Le Mao, Inès, Martineau, Estelle, Moing, Annick, Peyriga, Lindsay, Richard, Tristan, Silvestre, Virginie, Traïkia, Mounir, Canlet, Cécile, Plateforme Bordeaux Metabolome, Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-MetaboHUB-Bordeaux, MetaboHUB-MetaboHUB, Biologie du fruit et pathologie (BFP), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Chimie Et Interdisciplinarité : Synthèse, Analyse, Modélisation (CEISAM), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Nantes université - UFR des Sciences et des Techniques (Nantes univ - UFR ST), Nantes Université - pôle Sciences et technologie, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes Université - pôle Sciences et technologie, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ), Toulouse Biotechnology Institute (TBI), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), MetaToul FluxoMet (TBI-MetaToul), MetaboHUB-MetaToul, MetaboHUB-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-MetaboHUB-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Toulouse Biotechnology Institute (TBI), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Recherche Œnologie [Villenave d'Ornon] (OENO), Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ToxAlim (ToxAlim), Université de Toulouse (UT)-Ecole d'Ingénieurs de Purpan (INP - PURPAN), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Metatoul AXIOM (E20 ), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-ToxAlim (ToxAlim), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Ecole d'Ingénieurs de Purpan (INP - PURPAN), Institut de Chimie de Clermont-Ferrand (ICCF), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA)-Institut national polytechnique Clermont Auvergne (INP Clermont Auvergne), Université Clermont Auvergne (UCA)-Université Clermont Auvergne (UCA), Plateforme Exploration du Métabolisme (PFEM), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-MetaboHUB-Clermont, CAPACITÉS SAS, and Nantes Université (Nantes Univ)

Subjects
[CHIM.ANAL]Chemical Sciences/Analytical chemistry, [SDV]Life Sciences [q-bio]
Abstract

International audience

Published
2022

29. COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access

Author

Salek, Reza M., Neumann, Steffen, Schober, Daniel, Hummel, Jan, Billiau, Kenny, Kopka, Joachim, Correa, Elon, Reijmers, Theo, Rosato, Antonio, Tenori, Leonardo, Turano, Paola, Marin, Silvia, Deborde, Catherine, Jacob, Daniel, Rolin, Dominique, Dartigues, Benjamin, Conesa, Pablo, Haug, Kenneth, Rocca-Serra, Philippe, O’Hagan, Steve, Hao, Jie, van Vliet, Michael, Sysi-Aho, Marko, Ludwig, Christian, Bouwman, Jildau, Cascante, Marta, Ebbels, Timothy, Griffin, Julian L., Moing, Annick, Nikolski, Macha, Oresic, Matej, Sansone, Susanna-Assunta, Viant, Mark R., Goodacre, Royston, Günther, Ulrich L., Hankemeier, Thomas, Luchinat, Claudio, Walther, Dirk, and Steinbeck, Christoph

Published
2015
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33. Combining phenotypic, metabolome and proteome data to study maize response to a mild nitrogen deficit

Author

Urrutia, Maria, Blein-Nicolas, Melisande, Fernandez, Olivier, Bernillon, Stéphane, Maucourt, Mickael, Deborde, Catherine, Balliau, Thierry, Bénard, Camille, Prigent, Sylvain, Quilleré, Isabelle, Jacob, Daniel, Gibon, Yves, Zivy, Michel, Giauffret, Catherine, Hirel, Bertrand, Moing, Annick, and Blein-Nicolas, Mélisande

Subjects
[SDV] Life Sciences [q-bio], [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BV.AP] Life Sciences [q-bio]/Vegetal Biology/Plant breeding
Abstract

To decipher the biochemical bases of nitrogen (N) utilization and metabolism of silage maize inrelation to growth and productivity, an untargeted metabolomic (proton NMR- and LC-QTOF-MSbased) and proteomic approach was conducted on leaves of 29 hybrids cultivated in the field underoptimal and reduced N fertilization. The corresponding biochemical data were analyzed eitherindividually (PCA, ANOVA), or integrated with that of eco-physiological, developmental and yield-related traits (multi-block sparse PLS-DA). Such integrated analysis was conducted to interpret theunderlying physiology concerning the plant response to a mild N deficit often occurring underagronomic conditions. The genetic diversity of the core panel of 29 European dent hybrids crossed toa flint tester was exploited to highlight common N-responsive metabolites and proteins in order toidentify putative biological markers that could be used to pilot and rationalize N fertilization. Theresponses of metabolites, proteins, and yield-related traits to the reduced N treatment were alsoexploited to identify biochemical markers representative of a maize ideotype exhibiting betteragronomic performances when N fertilization is limited. These markers could be used to select high-yielding commercial maize hybrids used for silage production requiring less N fertilizer inputs.

Published
2022

34. Presence/absence variations and SNPs equally contribute to the variations of protein and metabolite abundance

Author

Djabali, Yacine, Blein-Nicolas, Melisande, Moing, Annick, Duarte, Jorge, Bernillon, Stéphane, Prigent, Sylvain, Mabire, Clément, Madur, Delphine, Cabrera-Bosquet, Llorenç, Welcker, Claude, Tardieu, Francois, Gibon, Yves, Zivy, Michel, Charcosset, Alain, Nicolas, Stephane, and Blein-Nicolas, Mélisande

Subjects
[SDV] Life Sciences [q-bio], [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV.BBM.MN] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular Networks [q-bio.MN], [SDV.GEN.GPL] Life Sciences [q-bio]/Genetics/Plants genetics, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BV.AP] Life Sciences [q-bio]/Vegetal Biology/Plant breeding
Abstract

Understanding the mechanisms of adaptation to the environment in cultivated plants is a promising way to meet the challenge of maintaining food security in the context of global warming. In the case of maize, high-throughput sequencing has revealed that structural variations represent a large part of the genome and could have huge phenotypic effects. Among these, Presence Absence Variants (PAVs, which include insertion/deletion of large DNA sequences) may be involved in adaptation of maize to its environment, but their contribution to the genetic determinism of traits and genotype by environment interactions remains largely unknown. To address this issue, we performed a genome-wide association study between two types of polymorphisms, SNPs and InDels, and molecular traits obtained from proteomics and metabolomics analyses to detect quantitative trait loci (QTLs). The genetic panel used for this study was composed of 254 dent inbred lines genotyped with 978,134 SNPs and 72,041 InDels. The latter encompassed from 37 to 129,700 pb, including thousands of PAVs that are not present in the B73 reference genome. Proteins and metabolites were quantified by mass spectrometry in leaf samples from F1 hybrids obtained by crossing the inbred lines with one flint tester line. Hybrid plants were grown under two watering conditions (well-watered and water deficit) in greenhouse. In total, we detected 61,225 QTLs associated with proteome or metabolome variations. Among these, 4,766 QTLs were exclusively detected by InDels. To take into account the difference of marker density between InDels and SNPs, we used a re-sampling approach which showed that there was no difference between InDels and SNPs regarding the number and effect of the QTLs detected . Additionally, the QTLs detected by the two types of polymorphism were equally distributed in the two watering conditions. These preliminary results show that InDels are worse considering to detect new genetic regions of interest. They also suggest that InDels and SNPs equally contribute to molecular trait variation and response to drought stress.

Published
2022

36. Extensive metabolic cross-talk in melon fruit revealed by spatial and developmental combinatorial metabolomics

Author

Moing, Annick, Aharoni, Asaph, Biais, Benoit, Rogachev, Ilana, Meir, Sagit, Brodsky, Leonid, Allwood, J. William, Erban, Alexander, Dunn, Warwick B., Kay, Lorraine, de Koning, Sjaak, de Vos, Ric C. H., Jonker, Harry, Mumm, Roland, Deborde, Catherine, Maucourt, Michael, Bernillon, Stéphane, Gibon, Yves, Hansen, Thomas H., Husted, Søren, Goodacre, Royston, Kopka, Joachim, Schjoerring, Jan K., Rolin, Dominique, and Hall, Robert D.

Published
2011

40. Spatial localization of metabolites in fruits by NMR: tissue dissection and metabolic profiling or non-invasive whole fruit imaging?

Author

Lemaire-Chamley, Martine, Pagès, Guilhem, Deborde, Catherine, Mounet, Fabien, Maucourt, Mickaël, Bonny, J.-M., Moing, Annick, Biologie du fruit et pathologie (BFP), and Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Bordeaux (UB)

Subjects
[SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2021

41. To dissect or not to dissect for fruit spatial metabolomics: tissue profiling or MRI?

Author

Lemaire-Chamley, Martine, Pagès, Guilhem, Deborde, Catherine, Mounet, Fabien, Maucourt, Mickaël, Bonny, J.-M., Moing, Annick, Biologie du fruit et pathologie (BFP), and Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Bordeaux (UB)

Subjects
[SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2021

42. RMN métabolomique, aliments & nutrition : quelques exemples de la plateforme Métabolome-MetaboHUB -Bordeaux

Author

Deborde, Catherine, Hounoum, Blandine, Roques, Simon, Jacob, Daniel, Maucourt, Mickaël, Moing, Annick, Fauconneau, Benoît, Plateforme Bordeaux Metabolome, Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-MetaboHUB-Bordeaux, MetaboHUB-MetaboHUB, Biologie du fruit et pathologie (BFP), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Nutrition, Métabolisme, Aquaculture (NuMéA), Université de Pau et des Pays de l'Adour (UPPA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Phileo Lesaffre Animal Care, FUI NINAquaANRT Convention Cifre (S Roques), UR370 QuaPA et PF AgroResonance, INRAE, ANR-11-INBS-0010,METABOHUB,Développement d'une infrastructure française distribuée pour la métabolomique dédiée à l'innovation(2011), and European Project: 288925,EC:FP7:KBBE,FP7-KBBE-2011-5,ARRAINA(2012)

Subjects
[SDV]Life Sciences [q-bio], [SDV.SA.SPA]Life Sciences [q-bio]/Agricultural sciences/Animal production studies, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition
Abstract

International audience

Published
2021

43. The GMO90+ Project: Absence of Evidence for Biologically Meaningful Effects of Genetically Modified Maize-based Diets on Wistar Rats After 6-Months Feeding Comparative Trial

Author

Coumoul, Xavier, Servien, Rémi, Juricek, Ludmila, Kaddouch-Amar, Yael, Lippi, Yannick, Berthelot, Laureline, Naylies, Claire, Morvan, Marie-Line, Antignac, Jean-Philippe, Desdoits-Lethimonier, Christèle, Jégou, Bernard, Tremblay-Franco, Marie, Canlet, Cécile, Debrauwer, Laurent, Le Gall, Caroline, Laurent, Julie, Gouraud, Pierre-Antoine, Cravedi, Jean Pierre, Jeunesse, Élisabeth, Savy, Nicolas, Dandere-Abdoulkarim, Kadidiatou, Arnich, Nathalie, Fourès, Franck, Cotton, Jérôme, Broudin, Simon, Corman, Bruno, Moing, Annick, Laporte, Bérengère, RICHARD-FORGET, Florence, Barouki, Robert, Rogowsky, Peter, Salles, Bernard, Toxicité environnementale, cibles thérapeutiques, signalisation cellulaire (T3S - UMR_S 1124), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), ToxAlim (ToxAlim), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Centre de Recherche en Transplantation et Immunologie (U1064 Inserm - CRTI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN), Laboratoire de Génétique Cellulaire (LGC), Ecole Nationale Vétérinaire de Toulouse (ENVT), Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), Institut de recherche en santé, environnement et travail (Irset), Université d'Angers (UA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Groupe d'Etude de la Reproduction Chez l'Homme et les Mammiferes (GERHM), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-IFR140-Institut National de la Santé et de la Recherche Médicale (INSERM), Xénobiotiques, MethodOmics [Toulouse] (Recherche-Développement en Biotechnologie), Methodomics, Laboratoire de sécurité des aliments de Maisons-Alfort, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Profilomic, Biologie du fruit et pathologie (BFP), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, MycSA, Institut National de la Recherche Agronomique (INRA), CHU Necker - Enfants Malades [AP-HP], Reproduction et développement des plantes (RDP), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Institut de pharmacologie et de biologie structurale (IPBS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Coumoul, Xavier, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Transcriptomic impact of Xenobiotics (E23 TRiX), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), Université d'Angers (UA)-Université de Rennes (UR)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM), Analyse de Xénobiotiques, Identification, Métabolisme (E20 Metatoul-AXIOM), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-MetaboHUB-MetaToul, Direction de l'Evaluation des Risques (DER), Profilomic [Boulogne-Billancourt], Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1 (UB), Unité de recherche Mycologie et Sécurité des Aliments (MycSA), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Ecole d'Ingénieurs de Purpan (INP - PURPAN), Université de Toulouse (UT)-Université de Toulouse (UT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Plateforme Génome & Transcriptome (GET), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), MetaToul AXIOM (E20), Université de Toulouse (UT)-Université de Toulouse (UT)-MetaboHUB-MetaToul, MetaboHUB-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-MetaboHUB-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université Paris Descartes - Paris 5 (UPD5), Université Sorbonne Paris Cité (USPC), Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse III - Paul Sabatier (UPS), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Centre de recherche sur l'Inflammation (CRI), Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), École des Hautes Études en Santé Publique [EHESP] (EHESP), Institut de recherche, santé, environnement et travail (Irset), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de la Santé et de la Recherche Médicale (INSERM)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université d'Angers (UA), Institut de Mathématiques de Toulouse UMR5219 (IMT), Université Toulouse 1 Capitole (UT1)-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UPS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-PRES Université de Toulouse-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), ANSES - Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Université Paris Descartes - Paris 5 (UPD5)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-MetaToul-MetaboHUB, Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA)-MetaToul-MetaboHUB, Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), and Université de Nantes (UN)-Université de Nantes (UN)-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
[SDE] Environmental Sciences, genetically modified maize, OECD TG408, Male, [SDV]Life Sciences [q-bio], Food, Genetically Modified, [SDV.CAN]Life Sciences [q-bio]/Cancer, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], [SDV.TOX.TCA]Life Sciences [q-bio]/Toxicology/Toxicology and food chain, [SDV.BBM.BM] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Zea mays, MON810, transcriptomics, [SDV.CAN] Life Sciences [q-bio]/Cancer, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Toxicity Tests, [SDV.BC.BC] Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], [SDV.EE.SANT] Life Sciences [q-bio]/Ecology, environment/Health, Animals, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Rats, Wistar, [SDV.BBM.BC] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], ComputingMilieux_MISCELLANEOUS, 6-month rat feeding trial, [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Plants, Genetically Modified, [SDE.ES]Environmental Sciences/Environmental and Society, metabolomics, Animal Feed, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], NK603, Rats, [SDV.TOX] Life Sciences [q-bio]/Toxicology, [SDV.TOX.TCA] Life Sciences [q-bio]/Toxicology/Toxicology and food chain, Consumer Product Safety, [SDV.TOX]Life Sciences [q-bio]/Toxicology, [SDE]Environmental Sciences, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Safety Study of Gmo Maize, Female, [SDE.ES] Environmental Sciences/Environmental and Society, Edible Grain
Abstract

International audience; The GMO90+ project was designed to identify biomarkers of exposure or health effects in Wistar Han RCC rats exposed in their diet to 2 genetically modified plants (GMP) and assess additional information with the use of metabolomic and transcriptomic techniques. Rats were fed for 6-months with 8 maize-based diets at 33% that comprised either MON810 (11% and 33%) or NK603 grains (11% and 33% with or without glyphosate treatment) or their corresponding near-isogenic controls. Extensive chemical and targeted analyses undertaken to assess each diet demonstrated that they could be used for the feeding trial. Rats were necropsied after 3 and 6 months. Based on the Organization for Economic Cooperation and Development test guideline 408, the parameters tested showed a limited number of significant differences in pairwise comparisons, very few concerning GMP versus non-GMP. In such cases, no biological relevance could be established owing to the absence of difference in biologically linked variables, dose-response effects, or clinical disorders. No alteration of the reproduction function and kidney physiology was found. Metabolomics analyses on fluids (blood, urine) were performed after 3, 4.5, and 6 months. Transcriptomics analyses on organs (liver, kidney) were performed after 3 and 6 months. Again, among the significant differences in pairwise comparisons, no GMP effect was observed in contrast to that of maize variety and culture site. Indeed, based on transcriptomic and metabolomic data, we could differentiate MON- to NK-based diets. In conclusion, using this experimental design, no biomarkers of adverse health effect could be attributed to the consumption of GMP diets in comparison with the consumption of their near-isogenic non-GMP controls.

Published
2018

44. Presence/absence variations and SNPs equally contribute to the variations of protein and metabolite abundance

Author

Djabali, Yacine, Blein, Mélisande, Moing, Annick, Duarte, Jorge, Berton, Thierry, Bernillon, Stéphane, Prigent, Sylvain, Fernandez, Olivier, Pétriacq, Pierre, Mabire, Clément, Madur, Delphine, Cabrera-Bosquet, Llorenç, Welcker, Claude, Tardieu, Francois, Gibon, Yves, Zivy, Michel, Charcosset, Alain, Nicolas, Stephane, Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Plateforme Metabolome Bordeaux, INRAE, 2018, MetaboHUB, Centre INRAE Nouvelle Aquitaine Bordeaux, doi: 10.15454/1.5572412770331912E12 (PMB), Institut National de la Recherche Agronomique (INRA), Groupe Limagrain, Biologie du fruit et pathologie (BFP), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Paris-Sud - Paris 11 (UP11)-Institut National de la Recherche Agronomique (INRA), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and ANR-10-BTBR-0001,AMAIZING,Développer de nouvelles variétés de maïs pour une agriculture durable: une approche intégrée de la génomique à la sélection(2010)

Subjects
[SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], food and beverages
Abstract

International audience; Understanding the mechanisms of adaptation to the environment in cultivated plants is a promising way to meet the challenge of maintaining food security in the context of global warming. In the case of maize, high-throughput sequencing has revealed that structural variations represent a large part of the genome and could have huge phenotypic effects. Among these, Presence Absence Variants (PAVs) may be involved in adaptation of maize to its environment, but their contribution to the genetic determinism of traits and genotype by environment interactions remains largely unknown. To address this issue, we performed a genome-wide association study between two types of polymorphisms, SNPs and Insetions/Deletions (InDels), and molecular traits obtained from proteomics and metabolomics analyses. The genetic panel used for this study was composed of 254 dent inbred lines genotyped with 978,134 SNPs and 72,041 InDels. The latter encompassed from 37 to 129,700 pb, including thousands of PAVs that are not present in the B73 reference genome. Proteins and metabolites were quantified by mass spectrometry in leaf samples from F1 hybrids obtained by crossing the inbred lines with one flint tester line. Hybrid plants were grown under two watering conditions (well-watered and water deficit) in greenhouse. In total, we detected 61,225 QTLs associated with proteome or metabolome variations. Among these, 4,766 QTLs were exclusively detected by InDels. To take into account the difference of marker density between InDels and SNPs, we used a re-sampling approach which showed that there is no difference for effect size distribution of QTLs between InDels and SNPs and for the number of QTLs detected by InDels or SNPs. Additionally, the QTLs detected by the two types of polymorphism were equally distributed in the two watering conditions. Our results suggest that InDels and SNPs equally contributed to molecular trait variation and response to drought stress.

Published
2021

45. Development, Validation, and Use of 1 H-NMR Spectroscopy for Evaluating the Quality of Acerola-Based Food Supplements and Quantifying Ascorbic Acid.

Author

Bourafai-Aziez, Asma, Jacob, Daniel, Charpentier, Gwladys, Cassin, Emmanuel, Rousselot, Guillaume, Moing, Annick, and Deborde, Catherine

Subjects
FOOD quality, NUCLEAR magnetic resonance spectroscopy, FRUIT processing, SPECTROMETRY, PHENOLS, DIETARY supplements, VITAMIN C
Abstract

Acerola (Malpighia emarginata D.C.) is an exotic fruit with high agro-industrial potential due to its high content of ascorbic acid (AA), phenolic compounds, and carotenoid pigments. Acerola fruit is processed into concentrated juice or powder to be incorporated into food supplements. The ascorbic acid content of concentrated juice or powders must be controlled and well assessed. Therefore, the development of optimal methods and procedures for the rapid and accurate determination of the ascorbic acid content in juice concentrate and juice powder remains of considerable commercial interest. NMR spectroscopy is currently a powerful spectroscopic tool for the qualitative and quantitative analysis of molecules of all types and sizes. Firstly, this article presents the NMR-based metabolomic profiling of acerola juice and concentrate powder to describe and compare their composition. Thirty-six metabolites were identified. The AA over choline ratio and the NMR metabolomic profiles could be used for authentication in the future. Secondly, a rapid (8 min), reliable, and non-destructive method for the quantification of ascorbic acid by 1D 1H-NMR spectroscopy was developed and validated. The LOD and LOQ were 0.05 and 0.15 mg/mL, respectively. These two approaches could be combined to better characterize ingredients derived from acerola and incorporated into food supplements. [ABSTRACT FROM AUTHOR]

Published
2022
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