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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

6. 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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8. 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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10. Leaf metabolomic data of eight sunflower lines and their sixteen hybrids under water deficit☆

Author

Berton Thierry, Bernillon Stéphane, Fernandez Olivier, Duruflé Harold, Flandin Amélie, Cassan Cédric, Jacob Daniel, Langlade Nicolas B., Gibon Yves, and Moing Annick

Subjects
helianthus, abiotic stress, drought stress, lc-ms, metabolomic profiling, Oils, fats, and waxes, TP670-699
Abstract

This article describes how metabolomic data were produced on sunflower plants subjected to water deficit. Twenty-four sunflower (Helianthus annuus L.) genotypes were selected to represent genetic diversity within cultivated sunflower and included both inbred lines and their hybrids. Drought stress was applied at the vegetative stage to plants cultivated in pots using the high-throughput phenotyping facility Heliaphen. Here, we provide untargeted and targeted metabolomic data of sunflower leaves. These compositional data differentiate both plant water status and different genotype groups. They constitute a valuable resource for the community to study the adaptation of crops to drought and the metabolic bases of heterosis.

Published
2021
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16. 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

19. 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

20. 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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24. Biomass composition explains fruit relative growth rate and discriminates climacteric from non-climacteric species

Author

Roch, Léa, Prigent, Sylvain, Klose, Holger, Cakpo, Coffi-Belmys, Beauvoit, Bertrand, Deborde, Catherine, Fouillen, Laetitia, van Delft, Pierre, Jacob, Daniel, Usadel, Björn, Dai, Zhanwu, Génard, Michel, Vercambre, Gilles, Colombié, Sophie, Moing, Annick, Gibon, Yves, Biologie du fruit et pathologie (BFP), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), RWTH Aachen University, Unité de recherche Plantes et Systèmes de Culture Horticoles (PSH), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Platetorme Métabolome Bordeaux, Institut National de la Recherche Agronomique (INRA), Laboratoire de biogenèse membranaire (LBM), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), Ecophysiologie et Génomique Fonctionnelle de la Vigne (UMR EGFV), Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-11-INBS-0012,PHENOME,Centre français de phénomique végétale(2011), ANR-11-INBS-0010,METABOHUB,Développement d'une infrastructure française distribuée pour la métabolomique dédiée à l'innovation(2011), and ANR-15-CE20-0009,FRIMOUSS,Modélisation intégrative du fruit pour un système de sélection unifié(2015)

Subjects
AcademicSubjects/SCI01210, [SDV]Life Sciences [q-bio], Actinidia, Biomass composition, food and beverages, fruit, Ethylenes, Research Papers, climacteric, modelling, Plant Breeding, ddc:580, relative growth rate, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Growth and Development, Biomass, metaphenomics, metabolism
Abstract

A comparison of eight fruit species (herbaceous, vines, and trees) throughout their development shows that biomass composition and fruit relative growth rate are closely linked., Fleshy fruits are very varied, whether in terms of their composition, physiology, or rate and duration of growth. To understand the mechanisms that link metabolism to phenotypes, which would help the targeting of breeding strategies, we compared eight fleshy fruit species during development and ripening. Three herbaceous (eggplant, pepper, and cucumber), three tree (apple, peach, and clementine) and two vine (kiwifruit and grape) species were selected for their diversity. Fruit fresh weight and biomass composition, including the major soluble and insoluble components, were determined throughout fruit development and ripening. Best-fitting models of fruit weight were used to estimate relative growth rate (RGR), which was significantly correlated with several biomass components, especially protein content (R=84), stearate (R=0.72), palmitate (R=0.72), and lignocerate (R=0.68). The strong link between biomass composition and RGR was further evidenced by generalized linear models that predicted RGR with R-values exceeding 0.9. Comparison of the fruit also showed that climacteric fruit (apple, peach, kiwifruit) contained more non-cellulosic cell-wall glucose and fucose, and more starch, than non-climacteric fruit. The rate of starch net accumulation was also higher in climacteric fruit. These results suggest that the way biomass is constructed has a major influence on performance, especially growth rate.

Published
2020

25. Comparative Metabolomics and Molecular Phylogenetics of Melon (Cucumis melo, Cucurbitaceae) Biodiversity

Author

Moing, Annick, Allwood, J. William, Aharoni, Asaph, Baker, John, Beale, Michael H., Ben-Dor, Shifra, Biais, Benoit, Brigante, Federico, Burger, Yosef, Deborde, Catherine, Erban, Alexander, Faigenboim, Adi, Gur, Amit, Goodacre, Royston, Hansen, Thomas H., Jacob, Daniel, Katzir, Nurit, Kopka, Joachim, Lewinsohn, Efraim, Maucourt, Mickael, Meir, Sagit, Miller, Sonia, Mumm, Roland, Oren, Elad, Paris, Harry S., Rogachev, Ilana, Rolin, Dominique, Saar, Uzi, Schjoerring, Jan K., Tadmor, Yaakov, Tzuri, Galil, de Vos, Ric C. H., Ward, Jane L., Yeselson, Elena, Hall, Robert D., Schaffer, Arthur A., Moing, Annick, Allwood, J. William, Aharoni, Asaph, Baker, John, Beale, Michael H., Ben-Dor, Shifra, Biais, Benoit, Brigante, Federico, Burger, Yosef, Deborde, Catherine, Erban, Alexander, Faigenboim, Adi, Gur, Amit, Goodacre, Royston, Hansen, Thomas H., Jacob, Daniel, Katzir, Nurit, Kopka, Joachim, Lewinsohn, Efraim, Maucourt, Mickael, Meir, Sagit, Miller, Sonia, Mumm, Roland, Oren, Elad, Paris, Harry S., Rogachev, Ilana, Rolin, Dominique, Saar, Uzi, Schjoerring, Jan K., Tadmor, Yaakov, Tzuri, Galil, de Vos, Ric C. H., Ward, Jane L., Yeselson, Elena, Hall, Robert D., and Schaffer, Arthur A.

Abstract

The broad variability of Cucumis melo (melon, Cucurbitaceae) presents a challenge to conventional classification and organization within the species. To shed further light on the infraspecific relationships within C. melo, we compared genotypic and metabolomic similarities among 44 accessions representative of most of the cultivar-groups. Genotyping-by-sequencing (GBS) provided over 20,000 single-nucleotide polymorphisms (SNPs). Metabolomics data of the mature fruit flesh and rind provided over 80,000 metabolomic and elemental features via an orchestra of six complementary metabolomic platforms. These technologies probed polar, semi-polar, and non-polar metabolite fractions as well as a set of mineral elements and included both flavor- and taste-relevant volatile and non-volatile metabolites. Together these results enabled an estimate of "metabolomic/elemental distance" and its correlation with the genetic GBS distance of melon accessions. This study indicates that extensive and non-targeted metabolomics/elemental characterization produced classifications that strongly, but not completely, reflect the current and extensive genetic classification. Certain melon Groups, such as Inodorous, clustered in parallel with the genetic classifications while other genome to metabolome/element associations proved less clear. We suggest that the combined genomic, metabolic, and element data reflect the extensive sexual compatibility among melon accessions and the breeding history that has, for example, targeted metabolic quality traits, such as taste and flavor.

Published
2020

26. Special Issue on “fruit metabolism and metabolomics”

Author

Ministerio de Ciencia, Innovación y Universidades (España), Junta de Andalucía, Agence Nationale de la Recherche (France), Agencia Estatal de Investigación (España), Osorio, Sonia [nº ORCID:0000-0002-0159-6091], Moing, Annick, Pétriacq, Pierre, Osorio, Sonia, Ministerio de Ciencia, Innovación y Universidades (España), Junta de Andalucía, Agence Nationale de la Recherche (France), Agencia Estatal de Investigación (España), Osorio, Sonia [nº ORCID:0000-0002-0159-6091], Moing, Annick, Pétriacq, Pierre, and Osorio, Sonia

Abstract

Over the past 10 years, knowledge about several aspects of fruit metabolism has been greatly improved. Notably, high-throughput metabolomic technologies have allowed quantifying metabolite levels across various biological processes, and identifying the genes that underly fruit development and ripening. This Special Issue is designed to exemplify the current use of metabolomics studies of temperate and tropical fruit for basic research as well as practical applications. It includes articles about different aspects of fruit biochemical phenotyping, fruit metabolism before and after harvest, including primary and specialized metabolisms, and bioactive compounds involved in growth and environmental responses. The effect of genotype, stages of development or fruit tissue on metabolomic profiles and corresponding metabolism regulations are addressed, as well as the combination of other omics with metabolomics for fruit metabolism studies. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.

Published
2020

27. Food crop metabolomics - the quest for quality

Author

MOING, Annick, Biologie du fruit et pathologie (BFP), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Experimental Plant Sciences graduate school

Subjects
Métabolisme, qualité, Culture vivrière, [SDV]Life Sciences [q-bio], plante, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, ComputingMilieux_MISCELLANEOUS, Métabolomique
Abstract

International audience

Published
2019

29. Metabolite Fruit Profile Is Altered in Response to Source–Sink Imbalance and Can Be Used as an Early Predictor of Fruit Quality in Nectarine

Author

Covarrubias, María Paz, primary, Lillo-Carmona, Victoria, additional, Melet, Lorena, additional, Benedetto, Gianfranco, additional, Andrade, Diego, additional, Maucourt, Mickael, additional, Deborde, Catherine, additional, Fuentealba, Claudia, additional, Moing, Annick, additional, Valenzuela, María Luisa, additional, Pedreschi, Romina, additional, and Almeida, Andréa Miyasaka, additional

Published
2021
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31. Proton-NMR Metabolomics of Rainbow Trout Fed a Plant-Based Diet Supplemented with Graded Levels of a Protein-Rich Yeast Fraction Reveal Several Metabolic Processes Involved in Growth

Author

Roques, Simon, primary, Deborde, Catherine, additional, Richard, Nadège, additional, Marchand, Yann, additional, Larroquet, Laurence, additional, Prigent, Sylvain, additional, Skiba-Cassy, Sandrine, additional, Moing, Annick, additional, and Fauconneau, Benoit, additional

Published
2020
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32. The Tomato Guanylate-Binding Protein SlGBP1 Enables Fruit Tissue Differentiation by Maintaining Endopolyploid Cells in a Non-Proliferative State

Author

Musseau, Constance, primary, Jorly, Joana, additional, Gadin, Stéphanie, additional, Sørensen, Iben, additional, Deborde, Catherine, additional, Bernillon, Stéphane, additional, Mauxion, Jean-Philippe, additional, Atienza, Isabelle, additional, Moing, Annick, additional, Lemaire-Chamley, Martine, additional, Rose, Jocelyn K.C., additional, Chevalier, Christian, additional, Rothan, Christophe, additional, Fernandez-Lochu, Lucie, additional, and Gévaudant, Frédéric, additional

Published
2020
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34. Model-assisted comparison of sugar accumulation patterns in ten fleshy fruits highlights differences between herbaceous and woody species

Author

Cakpo, Coffi Belmys, primary, Vercambre, Gilles, additional, Baldazzi, Valentina, additional, Roch, Léa, additional, Dai, Zhanwu, additional, Valsesia, Pierre, additional, Memah, Mohamed-Mahmoud, additional, Colombié, Sophie, additional, Moing, Annick, additional, Gibon, Yves, additional, and Génard, Michel, additional

Published
2020
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35. Omics Data Reveal Putative Regulators of Einkorn Grain Protein Composition under Sulfur Deficiency

Author

Bonnot, Titouan, primary, Martre, Pierre, additional, Hatte, Victor, additional, Dardevet, Mireille, additional, Leroy, Philippe, additional, Bénard, Camille, additional, Falagán, Natalia, additional, Martin-Magniette, Marie-Laure, additional, Deborde, Catherine, additional, Moing, Annick, additional, Gibon, Yves, additional, Pailloux, Marie, additional, Bancel, Emmanuelle, additional, and Ravel, Catherine, additional

Published
2020
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36. Comparative Metabolomics and Molecular Phylogenetics of Melon (Cucumis melo, Cucurbitaceae) Biodiversity

Author

Moing, Annick, primary, Allwood, J. William, additional, Aharoni, Asaph, additional, Baker, John, additional, Beale, Michael H., additional, Ben-Dor, Shifra, additional, Biais, Benoît, additional, Brigante, Federico, additional, Burger, Yosef, additional, Deborde, Catherine, additional, Erban, Alexander, additional, Faigenboim, Adi, additional, Gur, Amit, additional, Goodacre, Royston, additional, Hansen, Thomas H., additional, Jacob, Daniel, additional, Katzir, Nurit, additional, Kopka, Joachim, additional, Lewinsohn, Efraim, additional, Maucourt, Mickael, additional, Meir, Sagit, additional, Miller, Sonia, additional, Mumm, Roland, additional, Oren, Elad, additional, Paris, Harry S., additional, Rogachev, Ilana, additional, Rolin, Dominique, additional, Saar, Uzi, additional, Schjoerring, Jan K., additional, Tadmor, Yaakov, additional, Tzuri, Galil, additional, de Vos, Ric C.H., additional, Ward, Jane L., additional, Yeselson, Elena, additional, Hall, Robert D., additional, and Schaffer, Arthur A., additional

Published
2020
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38. Présentation of Bordeaux Metabolome Facility

Author

Moing, Annick, Biologie du fruit et pathologie (BFP), and Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
Métabolisme, [SDV]Life Sciences [q-bio], plante, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Plateforme Métabolome Bordeaux, ComputingMilieux_MISCELLANEOUS, Métabolomique
Abstract

International audience

Published
2019

39. Using metabolomic data to predict Maize yield

Author

Prigent, Sylvain, Fernandez, Olivier, Bernillon, Stéphane, Pétriacq, Pierre, Moing, Annick, Berton, Thierry, Cabrera-Bosquet, Llorenç, Millet, Émilie, Welcker, Claude, Tardieu, François, Gibon, Yves, Biologie du fruit et pathologie (BFP), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Plateforme Metabolome MetaboHUB INRA Nouvelle Aquitaine, 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 Gauthier, Muriel

Subjects
[SDV] Life Sciences [q-bio], Métabolome, Plante céréalière, Métabolisme, [SDV]Life Sciences [q-bio], Métabolite, Maïs, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, rendement, ComputingMilieux_MISCELLANEOUS, Métabolomique
Abstract

International audience

Published
2019

40. Exploring the adaptation of rainbow trout metabolome to novel aquafeeds by H-NMR metabolomics

Author

Roques, Simon, Deborde, Catherine, Richard, Nadege, Skiba-Cassy, Sandrine, Moing, Annick, Fauconneau, Benoit, Nutrition, Métabolisme, Aquaculture (NuMéA), Institut National de la Recherche Agronomique (INRA)-Université de Pau et des Pays de l'Adour (UPPA), Phileo Lesaffre Animal Care, Biologie du fruit et pathologie (BFP), Université Sciences et Technologies - Bordeaux 1-Institut National de la Recherche Agronomique (INRA)-Université Bordeaux Segalen - Bordeaux 2, FUI 2014 (NINAQUA with le Gouessant, COPALIS, Algae Natural food, Phileo-Lesaffre Animal Care), ANRT (CIFRE 2016/0775) and MetaboHUB (ANR-11-INBS-0010), ProdInra, Archive Ouverte, Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), and Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1

Subjects
trout, métabolome, [SDV.BA] Life Sciences [q-bio]/Animal biology, rainbow, animal nutrition, [SDV.BA]Life Sciences [q-bio]/Animal biology, novelty foods, nutrition animale, métabolomique, truite arc en ciel, aliment nouveau
Abstract

Résumé; Exploring the adaptation of rainbow trout metabolome to novel aquafeeds by H-NMR metabolomics. Metabolomics 2019. 15. Annual Conference of the Metabolomics Society

Published
2019

41. An overview of NMR applications in metabolite profiling of small molecules for plant metabolism studies

Author

Deborde, Catherine, Jacob, Daniel, Fontaine, Jean-Xavier, Molinie, R., Roch, Léa, Clave, Anaïs, Gibon, Yves, Batsale, M., Mesnard, François, Moing, Annick, Biologie du fruit et pathologie (BFP), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1 (UB), MetaboHUB, Biologie des Plantes et Innovation - UR UPJV 3900 (BIOPI), Université de Picardie Jules Verne (UPJV)-Transfrontalière BioEcoAgro - UMR 1158 (BioEcoAgro), Université d'Artois (UA)-Université de Liège-Université de Picardie Jules Verne (UPJV)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-JUNIA (JUNIA), Université catholique de Lille (UCL)-Université catholique de Lille (UCL)-Université d'Artois (UA)-Université de Liège-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-JUNIA (JUNIA), Université catholique de Lille (UCL)-Université catholique de Lille (UCL), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, Université de Picardie Jules Verne (UPJV), and ProdInra, Migration

Subjects
[SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, ComputingMilieux_MISCELLANEOUS
Abstract

UMR BFP - Equipe Métabolisme; International audience

Published
2019

42. Front. plant sci

Author

ROCH, Léa, Dai, Zhanwu, GOMES, Eric, Bernillon, Stéphane, Wang, Jiaojiao, Gibon, Yves, Moing, Annick, Biologie du fruit et pathologie (BFP), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ecophysiologie et Génomique Fonctionnelle de la Vigne (UMR EGFV), and Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
Organic Acids, Cross-Species, food and beverages, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Inter-Species, Metabolism Regulation, Qualité du fruit, Amino Acids, Primary Metabolism, Plante Fruitière, Sugars, Fleshy Fruit, Développement du fruit
Abstract

UMR BFP - Equipe Métabolisme; Although fleshy fruit species are economically important worldwide and crucial for human nutrition, the regulation of their fruit metabolism remains to be described finely. Fruit species differ in the origin of the tissue constituting the flesh, duration

Published
2019

43. NMR-based metabolomics at Bordeaux Metabolome Facility: 4 short stories

Author

Deborde, Catherine, Jacob, Daniel, Roques, Simon, Roch, Léa, CLAVE, Anaïs, Batsale, Marguerite, Moing, Annick, ProdInra, Migration, Biologie du fruit et pathologie (BFP), Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), MetaboHUB, Nutrition, Métabolisme, Aquaculture (NuMéA), and Institut National de la Recherche Agronomique (INRA)-Université de Pau et des Pays de l'Adour (UPPA)

Subjects
[SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2019

44. NMR-based metabolomics workflow for quality and effect assessment of alternative plant-based diets in rainbow trout

Author

DEBORDE, Catherine, MADJI HOUNOUM, Blandine, JACOB, Daniel, MAUCOURT, Mickael, ROQUES, Simon, TERRIER, Frédéric, CORRAZE, Geneviève, MÉDALE, Françoise, SKIBA-CASSY, Sandrine, MOING, Annick, FAUCONNEAU, Benoit, Biologie du fruit et pathologie (BFP), Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), Platetorme Métabolome Bordeaux, Institut National de la Recherche Agronomique (INRA), Nutrition, Métabolisme, Aquaculture (NuMéA), and Institut National de la Recherche Agronomique (INRA)-Université de Pau et des Pays de l'Adour (UPPA)

Subjects
[CHIM.ANAL]Chemical Sciences/Analytical chemistry, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, ComputingMilieux_MISCELLANEOUS, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM]
Abstract

International audience

Published
2018

45. A systems biology study in tomato fruit reveals correlations between the ascorbate pool and genes involved in ribosome biogenesis, translation, and the heat-shock response

Author

Stevens, Rebecca, Baldet, Pierre, Bouchet, Jean-Paul, Causse, Mathilde, Deborde, Catherine, DESCHODT, Claire, Faurobert, Mireille, Garchery, Cecile, Garcia, Virginie, Gautier, Hélène, Gouble, Barbara, Maucourt, Mickael, Moing, Annick, Page, David, Petit, Johann, Poëssel, Jean-Luc, Truffault, Vincent, Rothan, Christophe, Unité de recherche Génétique et amélioration des fruits et légumes (GALF), Institut National de la Recherche Agronomique (INRA), Biologie du fruit et pathologie (BFP), Université Sciences et Technologies - Bordeaux 1-Institut National de la Recherche Agronomique (INRA)-Université Bordeaux Segalen - Bordeaux 2, Unité de recherche Plantes et Systèmes de Culture Horticoles (PSH), Sécurité et Qualité des Produits d'Origine Végétale (SQPOV), Avignon Université (AU)-Institut National de la Recherche Agronomique (INRA), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, Génétique et Amélioration des Fruits et Légumes (GAFL), Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), and Avignon Université (AU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
enzymic activity, [SDV]Life Sciences [q-bio], choc thermique, activité enzymatique, heat shock protein, ribosome biogenesis, translation, Plant Science, tomato, heat-shock response, ascorbate, analyse métabolomique, tomate, redox, cellular signaling, tomato (Solanum lycopersicum), transcriptome, métabolisme phénolique, Original Research, expression des gènes
Abstract

Changing the balance between ascorbate, monodehydroascorbate, and dehydroascorbate in plant cells by manipulating the activity of enzymes involved in ascorbate synthesis or recycling of oxidized and reduced forms leads to multiple phenotypes. A systems biology approach including network analysis of the transcriptome, proteome and metabolites of RNAi lines for ascorbate oxidase, monodehydroascorbate reductase and galactonolactone dehydrogenase has been carried out in orange fruit pericarp of tomato (Solanum lycopersicum). The transcriptome of the RNAi ascorbate oxidase lines is inversed compared to the monodehydroascorbate reductase and galactonolactone dehydrogenase lines. Differentially expressed genes are involved in ribosome biogenesis and translation. This transcriptome inversion is also seen in response to different stresses in Arabidopsis. The transcriptome response is not well correlated with the proteome which, with the metabolites, are correlated to the activity of the ascorbate redox enzymes—ascorbate oxidase and monodehydroascorbate reductase. Differentially accumulated proteins include metacaspase, protein disulphide isomerase, chaperone DnaK and carbonic anhydrase and the metabolites chlorogenic acid, dehydroascorbate and alanine. The hub genes identified from the network analysis are involved in signaling, the heat-shock response and ribosome biogenesis. The results from this study therefore reveal one or several putative signals from the ascorbate pool which modify the transcriptional response and elements downstream.

Published
2018

46. 1H-NMR metabolomic investigation of the effect of alternative diets on rainbow trout plasma profiles

Author

Roques, Simon, Deborde, Catherine, Richard, Nadège, Skiba-Cassy, Sandrine, Moing, Annick, Fauconneau, Benoit, Nutrition, Métabolisme, Aquaculture (NuMéA), Institut National de la Recherche Agronomique (INRA)-Université de Pau et des Pays de l'Adour (UPPA), Biologie du fruit et pathologie (BFP), Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), Phileo Lesaffre Animal Care, This research was funded by FUI 2014 (NINAQUA with Le Gouessant, COPALIS, Algae Natural Food and Phileo Lesaffre Animal Care), ANRT (CIFRE 2016/0775) and MetaboHUB (ANR-11-INBS-0010), European Aquaculture Society (EAS)., Université Sciences et Technologies - Bordeaux 1-Institut National de la Recherche Agronomique (INRA)-Université Bordeaux Segalen - Bordeaux 2, and Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1

Subjects
Animal biology, oncorhynchus mykiss, alimentation animale, [SDV.BA]Life Sciences [q-bio]/Animal biology, Biologie animale, animal feeding, rainbow trout, micromass, plasma, métabolomique, alimentation alternative, analyse métabolomique
Abstract

Résumé; Fish farming needs high quality feeds to support the growing global demand for fish. Over the last two decades, the development of sustainable feeds based on plant feedstuffs has strongly reduced the use of marine resources. However, full plant-based feeds still reduce growth performances in carnivorous species such as salmonids. Thus, active research programmes are conducted on alternative feedstuffs in order to provide sustainable feeds for aquaculture especially trout farming. Our project aims at establishing a link between feed composition and plasma metabolome of rainbow trout (Oncorhynchus mykiss) through i) the characterization of plant-based diets devoid of marine resources complemented with insect, microalgae or yeast products, and ii) the analysis of trout plasma metabolome fed these alternative diets. Fish were fed ad libitum for three months with nine, iso-proteic and iso-energetic experimental diets: a control plant-based diet (PB) and eight diets containing 5%, 10% and 15% of either insects (INS), micro-algae (SPI) or yeast (YST). Ethanolic extracts of diets were prepared and analysed. Fish blood was collected 48 h after feeding and centrifuged to obtain plasma. The 1D 1 H-NMR profiles of both diet extracts and plasmas were acquired on a 500 MHz NMR spectrometer. Spectra were processed to select and integrate spectral regions with NMRProcFlow (nmrprocflow.org) and statistical analyses were realised with BioStatFlow webtool (biostatflow.org). Diet extract 1 H-NMR spectra showed specific compounds for INS and SPI diets compared to PB. These signals were related to triglyceride residues and organic acids and account for the origin of feedstuff and the effect of process. Multivariate analysis of plasma spectral data showed a classification of individuals based on diets according to highly discriminant signals variables. Several specific signals showed an increasing trend with graduate incorporation of alternative feedstuffs. Integrative metabolomics combining diet and trout plasma characterization highlights the significance of the soluble fraction of alternative diets and their extended impact on plasma metabolome.

Published
2018

47. A systems biology study in tomato fruit reveals correlations between the ascorbate pool and genes involved in ribosome biogenesis, translation, and the heat-shock response

Author

Baldet, Pierre, Bouchet, Jean-Paul, Causse, Mathilde, Deborde, Catherine, DESCHODT, Claire, Faurobert, Mireille, Garchery, Cecile, Garcia, Virginie, Gautier, Helene, Gouble, Barbara, Maucourt, Mickael, Moing, Annick, Page, David, Petit, Johann, Poëssel, Jean-Luc, Truffault, Vincent, Rothan, Christophe, and Stevens, Rebecca

Subjects
tomate, ascorbate, cellular signaling, heat-shock response, redox, ribosome biogenesis, translation, tomato (Solanum lycopersicum), choc thermique, activité enzymatique, heat shock protein, transcriptome, métabolisme phénolique, expression des gènes, analyse métabolomique
Abstract

Changing the balance between ascorbate, monodehydroascorbate, and dehydroascorbate in plant cells by manipulating the activity of enzymes involved in ascorbate synthesis or recycling of oxidized and reduced forms leads to multiple phenotypes. A systems biology approach including network analysis of the transcriptome, proteome and metabolites of RNAi lines for ascorbate oxidase, monodehydroascorbate reductase and galactonolactone dehydrogenase has been carried out in orange fruit pericarp of tomato (Solanum lycopersicum). The transcriptome of the RNAi ascorbate oxidase lines is inversed compared to the monodehydroascorbate reductase and galactonolactone dehydrogenase lines. Differentially expressed genes are involved in ribosome biogenesis and translation. This transcriptome inversion is also seen in response to different stresses in Arabidopsis. The transcriptome response is not well correlated with the proteome which, with the metabolites, are correlated to the activity of the ascorbate redox enzymes—ascorbate oxidase and monodehydroascorbate reductase. Differentially accumulated proteins include metacaspase, protein disulphide isomerase, chaperone DnaK and carbonic anhydrase and the metabolites chlorogenic acid, dehydroascorbate and alanine. The hub genes identified from the network analysis are involved in signaling, the heat-shock response and ribosome biogenesis. The results from this study therefore reveal one or several putative signals from the ascorbate pool which modify the transcriptional response and elements downstream.

Published
2018

48. Mycotoxin biosynthesis and central metabolism are two interlinked pathways in Fusarium graminearum, as demonstrated by the extensive metabolic changes induced by caffeic acid exposure

Author

Chéreau, Sylvain, Atanasova-Penichon, Vessela, Legoahec, Laurie, Bernillon, Stéphane, Deborde, Catherine, Maucourt, Mickael, Verdal-Bonnin, Marie-Noëlle, Pinson-Gadais, Laetitia, Moing, Annick, Ponts, Nadia, Richard-Forget, Florence, Unité de recherche Mycologie et Sécurité des Aliments (MycSA), Institut National de la Recherche Agronomique (INRA), Unité de recherche sur les Biopolymères, Interactions Assemblages (BIA), Biologie du fruit et pathologie (BFP), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, and Universität für Bodenkultur Wien [Vienne, Autriche] (BOKU). AUT.

Subjects
[SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, [SDV.IDA]Life Sciences [q-bio]/Food engineering, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2018

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