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2. A digital twin of bacterial metabolism during cheese production

Author

Maxime Lecomte, Wenfan Cao, Julie Aubert, David James Sherman, Hélène Falentin, Clémence Frioux, Simon Labarthe, Science et Technologie du Lait et de l'Oeuf (STLO), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, 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), from patterns to models in computational biodiversity and biotechnology (PLEIADE), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS)-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Mathématiques et Informatique Appliquées (MIA Paris-Saclay), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Inria Exploratory Action SLIMMEST., CNIEL, and ANR-22-PEAE-0011,MISTIC,France 2030 PEPR Agroé- cologie et Numérique MISTIC ANR-22-PEAE-0011

Subjects
Cheese, Fermentation, Microbial community, Flux Balance Analysis, Systems biology, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Digital twin, Metabolic modeling, Dynamics
Abstract

Cheese organoleptic properties result from complex metabolic processes occurring in microbial communities. A deeper understanding of such mechanisms makes it possible to improve both industrial production processes and end-product quality through the design of microbial consortia. In this work, we caracterise the metabolism of a three-species community consisting ofLactococcus lactis,Lactobacillus plantarumandPropionibacterium freudenreichiiduring a seven-week cheese production process. Using genome-scale metabolic models and omics data integration, we modeled and calibrated individual dynamics using monoculture experiments, and coupled these models to capture the metabolism of the community. This digital twin accurately predicted the dynamics of the community, enlightening the contribution of each microbial species to organoleptic compound production. Further metabolic exploration raised additional possible interactions between the bacterial species. This work provides a methodological framework for the prediction of community-wide metabolism and highlights the added-value of dynamic metabolic modeling for the comprehension of fermented food processes.

Published
2023

3. Subclinical endometritis in dairy cattle is associated with distinct mRNA expression patterns in blood and endometrium.

Author

Mariam Raliou, Doulaye Dembélé, Anna Düvel, Philippe Bolifraud, Julie Aubert, Tristan Mary-Huard, Dominique Rocha, François Piumi, Sophie Mockly, Maike Heppelmann, Isabelle Dieuzy-Labaye, Peter Zieger, David G E Smith, Hans-Joachim Schuberth, Iain Martin Sheldon, and Olivier Sandra

Subjects
Medicine, Science
Abstract

Cattle with subclinical endometritis (SCE) are sub-fertile and diagnosing subclinical uterine disease remains a challenge. The hypothesis for this study was that endometrial inflammation is reflected in mRNA expression patterns of peripheral blood leucocytes. Transcriptome profiles were evaluated in healthy cows and in cows with SCE using circulating white blood cells (WBC) and endometrial biopsy samples collected from the same animals at 45-55 days postpartum. Bioinformatic analyses of microarray-based transcriptional data identified gene profiles associated with distinct biological functions in circulating WBC and endometrium. In circulating WBC, SCE promotes a pro-inflammatory environment, whereas functions related to tissue remodeling are also affected in the endometrium. Nineteen differentially expressed genes associated with SCE were common to both circulating WBC and the endometrium. Among these genes, transcript abundance of immune factors C3, C2, LTF, PF4 and TRAPPC13 were up-regulated in SCE cows at 45-55 days postpartum. Moreover, mRNA expression of C3, CXCL8, LTF, TLR2 and TRAPPC13 was temporally regulated during the postpartum period in circulating WBC of healthy cows compared with SCE cows. This observation might indicate an advantageous modulation of the immune system in healthy animals. The transcript abundance of these genes represents a potential source of indicators for postpartum uterine health.

Published
2019
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4. Modèles à blocs latents pour la détection de structures dans les réseaux écologiques

Author

Julie AUBERT, Pierre BARBILLON, Sophie DONNET, and Vincent MIELE

Abstract

Nous nous intéressons aux interactions entre espèces. Les données d'interactions sont représentées par un réseau dont la structure est étudiée pour comprendre l'organisation de l'écosystème. Pour ce faire, nous présentons les modèles à blocs stochastiques qui sont des modèles de mélange adaptés aux réseaux et qui permettent d'obtenir une classification des espèces sur la base de leurs patrons d'interactions.

Published
2022
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5. Model‐based biclustering for overdispersed count data with application in microbial ecology

Author

Julie Aubert, Stéphane Robin, Sophie Schbath, Mathématiques et Informatique Appliquées (MIA-Paris), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-AgroParisTech-Université Paris-Saclay, Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and ANR-17-CE32-0011,NGB,Biosurveillance Next-Gen des changements dans la structure et le fonctionnement des écosystèmes(2017)

Subjects
Gamma distribution, 0303 health sciences, variational EM algorithm, Ecological Modeling, based biclustering, Computational biology, Biology, microbial interactions, count data, 01 natural sciences, Biclustering, 010104 statistics & probability, 03 medical and health sciences, Microbial ecology, latent block model, metabarcoding, Poisson&#8211, [MATH]Mathematics [math], 0101 mathematics, model&#8208, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Count data
Abstract

International audience; Different studies have shown that microbial communities living in animals (humans included), in or around plants have a significant impact on health and disease of their host and on various services, such as adaptation under stressing environment. The basic input data to study microbiomes is a matrix representing abundance data of micro-organisms across different sampling units. Such a matrix typically corresponds to taxonomic profiles derived from the high-throughput sequencing of environmental samples. Biclustering is one way to study the interactions between the structure of micro-organism communities and the environmental samples they come from.We propose a latent block model (LBM) and an associated inference procedure for the biclustering of rows and columns of abundance matrices. The LBM assumes that micro-organisms (rows) and environmental samples (columns) can both be clustered into groups characterizing preferential interaction or avoidance. We use the Poisson-Gamma distribution to model the overdispersion observed in microbial abundance data and introduce row and column effects to account for the sequencing effort in each sample and the mean abundance of each micro-organism. Because the latent variables are not independent conditionally on the observed ones, classical maximum likelihood inference is intractable. We then derive a variational-based inference algorithm and propose a strategy to select the number of biclusters.We illustrate the flexibility and performance of our approach both on a simulation study and on three ecological datasets. The model-based framework allows us to adapt to peculiarities of microbial ecological abundance data and allows us to explore relationships between entities of two different natures.We implemented our method in the cobiclust R package available on the CRAN and built a website with example of usage ().

Published
2021
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8. Overview of a surface-ripened cheese community functioning by meta-omics analyses.

Author

Eric Dugat-Bony, Cécile Straub, Aurélie Teissandier, Djamila Onésime, Valentin Loux, Christophe Monnet, Françoise Irlinger, Sophie Landaud, Marie-Noëlle Leclercq-Perlat, Pascal Bento, Sébastien Fraud, Jean-François Gibrat, Julie Aubert, Frédéric Fer, Eric Guédon, Nicolas Pons, Sean Kennedy, Jean-Marie Beckerich, Dominique Swennen, and Pascal Bonnarme

Subjects
Medicine, Science
Abstract

Cheese ripening is a complex biochemical process driven by microbial communities composed of both eukaryotes and prokaryotes. Surface-ripened cheeses are widely consumed all over the world and are appreciated for their characteristic flavor. Microbial community composition has been studied for a long time on surface-ripened cheeses, but only limited knowledge has been acquired about its in situ metabolic activities. We applied metagenomic, metatranscriptomic and biochemical analyses to an experimental surface-ripened cheese composed of nine microbial species during four weeks of ripening. By combining all of the data, we were able to obtain an overview of the cheese maturation process and to better understand the metabolic activities of the different community members and their possible interactions. Furthermore, differential expression analysis was used to select a set of biomarker genes, providing a valuable tool that can be used to monitor the cheese-making process.

Published
2015
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9. Fine-Tuning of Process Parameters Modulates Specific Metabolic Bacterial Activities and Aroma Compound Production in Semi-Hard Cheese

Author

Wenfan, Cao, Julie, Aubert, Marie-Bernadette, Maillard, Françoise, Boissel, Arlette, Leduc, Jean-Luc, Thomas, Stéphanie-Marie, Deutsch, Bénédicte, Camier, Ali, Kerjouh, Sandrine, Parayre, Marielle, Harel-Oger, Gilles, Garric, Anne, Thierry, and Hélène, Falentin

Subjects
Lactococcus lactis, Cheese, Odorants, Food Microbiology
Abstract

The formation of cheese flavor mainly results from the production of volatile compounds by microorganisms. We investigated how fine-tuning cheese-making process parameters changed the cheese volatilome in a semi-hard cheese inoculated with

Published
2021

11. A temporal-omic study of Propionibacterium freudenreichii CIRM-BIA1 adaptation strategies in conditions mimicking cheese ripening in the cold.

Author

Marion Dalmasso, Julie Aubert, Valérie Briard-Bion, Victoria Chuat, Stéphanie-Marie Deutsch, Sergine Even, Hélène Falentin, Gwénaël Jan, Julien Jardin, Marie-Bernadette Maillard, Sandrine Parayre, Michel Piot, Jarna Tanskanen, and Anne Thierry

Subjects
Medicine, Science
Abstract

Propionibacterium freudenreichii is used as a ripening culture in Swiss cheese manufacture. It grows when cheeses are ripened in a warm room (about 24°C). Cheeses with an acceptable eye formation level are transferred to a cold room (about 4°C), inducing a marked slowdown of propionic fermentation, but P. freudenreichii remains active in the cold. To investigate the P. freudenreichii strategies of adaptation and survival in the cold, we performed the first global gene expression profile for this species. The time-course transcriptomic response of P. freudenreichii CIRM-BIA1(T) strain was analyzed at five times of incubation, during growth at 30°C then for 9 days at 4°C, under conditions preventing nutrient starvation. Gene expression was also confirmed by RT-qPCR for 28 genes. In addition, proteomic experiments were carried out and the main metabolites were quantified. Microarray analysis revealed that 565 genes (25% of the protein-coding sequences of P. freudenreichii genome) were differentially expressed during transition from 30°C to 4°C (P1). At 4°C, a general slowing down was observed for genes implicated in the cell machinery. On the contrary, P. freudenreichii CIRM-BIA1(T) strain over-expressed genes involved in lactate, alanine and serine conversion to pyruvate, in gluconeogenesis, and in glycogen synthesis. Interestingly, the expression of different genes involved in the formation of important cheese flavor compounds, remained unchanged at 4°C. This could explain the contribution of P. freudenreichii to cheese ripening even in the cold. In conclusion, P. freudenreichii remains metabolically active at 4°C and induces pathways to maintain its long-term survival.

Published
2012
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15. Invading basement membrane matrix is sufficient for MDA-MB-231 breast cancer cells to develop a stable in vivo metastatic phenotype.

Author

Mohamed Abdelkarim, Nadejda Vintonenko, Anna Starzec, Aniela Robles, Julie Aubert, Marie-Laure Martin, Samia Mourah, Marie-Pierre Podgorniak, Sylvie Rodrigues-Ferreira, Clara Nahmias, Pierre-Olivier Couraud, Christelle Doliger, Odile Sainte-Catherine, Nicole Peyri, Lei Chen, Jérémie Mariau, Monique Etienne, Gerard-Yves Perret, Michel Crepin, Jean-Luc Poyet, Abdel-Majid Khatib, and Mélanie Di Benedetto

Subjects
Medicine, Science
Abstract

INTRODUCTION: The poor efficacy of various anti-cancer treatments against metastatic cells has focused attention on the role of tumor microenvironment in cancer progression. To understand the contribution of the extracellular matrix (ECM) environment to this phenomenon, we isolated ECM surrogate invading cell populations from MDA-MB-231 breast cancer cells and studied their genotype and malignant phenotype. METHODS: We isolated invasive subpopulations (INV) from non invasive populations (REF) using a 2D-Matrigel assay, a surrogate of basal membrane passage. INV and REF populations were investigated by microarray assay and for their capacities to adhere, invade and transmigrate in vitro, and to form metastases in nude mice. RESULTS: REF and INV subpopulations were stable in culture and present different transcriptome profiles. INV cells were characterized by reduced expression of cell adhesion and cell-cell junction genes (44% of down regulated genes) and by a gain in expression of anti-apoptotic and pro-angiogenic gene sets. In line with this observation, in vitro INV cells showed reduced adhesion and increased motility through endothelial monolayers and fibronectin. When injected into the circulation, INV cells induced metastases formation, and reduced injected mice survival by up to 80% as compared to REF cells. In nude mice, INV xenografts grew rapidly inducing vessel formation and displaying resistance to apoptosis. CONCLUSION: Our findings reveal that the in vitro ECM microenvironment per se was sufficient to select for tumor cells with a stable metastatic phenotype in vivo characterized by loss of adhesion molecules expression and induction of pro-angiogenic and survival factors.

Published
2011
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16. Can soil microbial diversity influence plant metabolites and life history traits of a rhizophagous insect? A demonstration in oilseed rape

Author

Valérie Chaminade, Anne-Marie Cortesero, Chrystelle Paty, Christophe Mougel, Juliette Linglin, Anne-Yvonne Guillerm-Erckelboudt, Julie Aubert, Tom Lachaise, Morgane Ourry, Nathalie Marnet, Lionel Lebreton, and Denis Poinsot

Subjects
0106 biological sciences, 0301 basic medicine, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, Life history theory, 03 medical and health sciences, Botany, Plant defense against herbivory, Ecology, Evolution, Behavior and Systematics, 2. Zero hunger, Rhizosphere, Herbivore, Larva, Biotic component, biology, Ecology, fungi, food and beverages, 15. Life on land, biology.organism_classification, 030104 developmental biology, Insect Science, Adaptation, Agronomy and Crop Science, Delia radicum, 010606 plant biology & botany
Abstract

Interactions between plants and phytophagous insects play an important part in shaping the biochemical composition of plants. Reciprocally plant metabolites can influence major life history traits in these insects and largely contribute to their fitness. Plant rhizospheric microorganisms are an important biotic factor modulating plant metabolites and adaptation to stress. While plant-insects or plant-microorganisms interactions and their consequences on the plant metabolite signature are well-documented, the impact of soil microbial communities on plant defenses against phytophagous insects remains poorly known. In this study, we used oilseed rape (Brassica napus) and the cabbage root fly (Delia radicum) as biological models to tackle this question. Even though D. radicum is a belowground herbivore as a larva, its adult life history traits depend on aboveground signals. We therefore tested whether soil microbial diversity influenced emergence rate and fitness but also fly oviposition behavior, and tried to link possible effects to modifications in leaf and root metabolites. Through a removal-recolonization experiment, 3 soil microbial modalities ("high," "medium," "low") were established and assessed through amplicon sequencing of 16S and 18S ribosomal RNA genes. The "medium" modality in the rhizosphere significantly improved insect development traits. Plant-microorganism interactions were marginally associated to modulations of root metabolites profiles, which could partly explain these results. We highlighted the potential role of plant-microbial interaction in plant defenses against Delia radicum. Rhizospheric microbial communities must be taken into account when analyzing plant defenses against herbivores, being either below or aboveground.

Published
2017
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17. Subclinical endometritis in dairy cattle is associated with distinct mRNA expression patterns in blood and endometrium

Author

Doulaye Dembélé, Iain Martin Sheldon, Mariam Raliou, M. Heppelmann, Sophie Mockly, Hans-Joachim Schuberth, Peter Zieger, Julie Aubert, Isabelle Dieuzy-Labaye, Tristan Mary-Huard, Dominique Rocha, Francois Piumi, Anna Düvel, David Smith, Philippe Bolifraud, Olivier Sandra, Biologie du développement et reproduction (BDR), École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Université Paris Saclay (COMUE), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), University of Veterinary Medicine Hanover, Mathématiques et Informatique Appliquées (MIA-Paris), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Zoetis [Zaventem], Zoetis [Berlin], Institute of Infection, Immunology and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Swansea University, ERA-NET EMIDA (Coordination of European Research on Emerging and Major Infectious Diseases of Livestock), 2010, Biologie du Développement et Reproduction (BDR), École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), ProdInra, Archive Ouverte, and École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)

Subjects
0301 basic medicine, Microarray, Physiology, Biopsy, subclinical endometritis, cow, Gene Expression, Endometrium, Transcriptome, White Blood Cells, Animal Cells, Leukocytes, Medicine and Health Sciences, dairy cows, postpartum, Subclinical infection, 2. Zero hunger, Mammals, Multidisciplinary, medicine.diagnostic_test, microarray, circulating white blood cells, endometrium, Eukaryota, 04 agricultural and veterinary sciences, Ruminants, Body Fluids, Dairying, medicine.anatomical_structure, Blood, Veterinary Diseases, expression de l'arn m, vache, Vertebrates, endomètre, Medicine, Veterinary medicine and animal Health, Female, Endometritis, Anatomy, Cellular Types, Research Article, Science, Immune Cells, Immunology, Cattle Diseases, Surgical and Invasive Medical Procedures, Estrous Cycle, Biology, Andrology, 03 medical and health sciences, Bovines, medicine, Genetics, Animals, RNA, Messenger, Estrous cycle, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, Blood Cells, Uterus, [SDV.BA.MVSA] Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, 0402 animal and dairy science, Reproductive System, Organisms, Biology and Life Sciences, Cell Biology, medicine.disease, 040201 dairy & animal science, 030104 developmental biology, Médecine vétérinaire et santé animal, Amniotes, Cattle, Veterinary Science, Physiological Processes, Postpartum period, Endometrial biopsy
Abstract

Cattle with subclinical endometritis (SCE) are sub-fertile and diagnosing subclinical uterine disease remains a challenge. The hypothesis for this study was that endometrial inflammation is reflected in mRNA expression patterns of peripheral blood leucocytes. Transcriptome profiles were evaluated in healthy cows and in cows with SCE using circulating white blood cells (WBC) and endometrial biopsy samples collected from the same animals at 45-55 days postpartum. Bioinformatic analyses of microarray-based transcriptional data identified gene profiles associated with distinct biological functions in circulating WBC and endometrium. In circulating WBC, SCE promotes a pro-inflammatory environment, whereas functions related to tissue remodeling are also affected in the endometrium. Nineteen differentially expressed genes associated with SCE were common to both circulating WBC and the endometrium. Among these genes, transcript abundance of immune factors C3, C2, LTF, PF4 and TRAPPC13 were up-regulated in SCE cows at 45-55 days postpartum. Moreover, mRNA expression of C3, CXCL8, LTF, TLR2 and TRAPPC13 was temporally regulated during the postpartum period in circulating WBC of healthy cows compared with SCE cows. This observation might indicate an advantageous modulation of the immune system in healthy animals. The transcript abundance of these genes represents a potential source of indicators for postpartum uterine health.

Published
2019
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18. Variational Inference for Coupled Hidden Markov Models Applied to the Joint Detection of Copy Number Variations

Author

Emilie Lebarbier, Stéphane Robin, Julie Aubert, Xiaoqiang Wang, School of Mathematics and Statistics [Sydney] (UNSW), University of New South Wales [Sydney] (UNSW), Université Paris Saclay (COmUE), Mathématiques et Informatique Appliquées (MIA-Paris), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Modélisation aléatoire de Paris X (MODAL'X), Université Paris Nanterre (UPN), CNV-Maize program - french National Research Agency [ANR-10-GENM-104], France Agrimer [11000415], CNV-Maize project, National Natural Science Foundation of ChinaNational Natural Science Foundation of China [11601286], and Institut National de la Recherche Agronomique (INRA)-AgroParisTech

Subjects
FOS: Computer and information sciences, Statistics and Probability, DNA Copy Number Variations, Inference, Context (language use), 01 natural sciences, Methodology (stat.ME), 010104 statistics & probability, 03 medical and health sciences, Expectation–maximization algorithm, Humans, [INFO]Computer Science [cs], Copy-number variation, [MATH]Mathematics [math], 0101 mathematics, Hidden Markov model, Statistics - Methodology, Selection (genetic algorithm), Probability, 030304 developmental biology, 0303 health sciences, Models, Statistical, business.industry, copy number variation, Probability and statistics, Pattern recognition, General Medicine, Markov Chains, coupled Hidden Markov models, Approximate inference, Research Design, variational approximation, Artificial intelligence, Statistics, Probability and Uncertainty, business, Algorithms
Abstract

Hidden Markov models provide a natural statistical framework for the detection of the copy number variations (CNV) in genomics. In this context, we define a hidden Markov process that underlies all individuals jointly in order to detect and to classify genomics regions in different states (typically, deletion, normal or amplification). Structural variations from different individuals may be dependent. It is the case in agronomy where varietal selection program exists and species share a common phylogenetic past. We propose to take into account these dependencies inthe HMM model. When dealing with a large number of series, maximum likelihood inference (performed classically using the EM algorithm) becomes intractable. We thus propose an approximate inference algorithm based on a variational approach (VEM), implemented in the CHMM R package. A simulation study is performed to assess the performance of the proposed method and an application to the detection of structural variations in plant genomes is presented.

Published
2019
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22. Transcriptomic response of Debaryomyces hansenii during mixed culture in a liquid model cheese medium with Yarrowia lipolytica

Author

Valentin Loux, Julie Aubert, Françoise Irlinger, Jean-Marie Beckerich, Pascal Bonnarme, Djamila Onesime, Reine Malek, Pascale Frey-Klett, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Génie et Microbiologie des Procédés Alimentaires (GMPA), Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Mathématiques et Informatique Appliquées (MIA-Paris), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), and Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
0301 basic medicine, Debaryomyces, [SDV]Life Sciences [q-bio], 030106 microbiology, Yarrowia, Cheese ripening, Lactose, Microbiology, 03 medical and health sciences, chemistry.chemical_compound, Ammonia, Cheese, Debaryomyces hansenii, Lactic Acid, Amino Acids, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, biology, Debaryomyces hansenii 1L25, Catabolism, Respiration, Gene Expression Profiling, General Medicine, biology.organism_classification, Yeast, Coculture Techniques, Flavoring Agents, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, 030104 developmental biology, Mitochondrial respiratory chain, Biochemistry, chemistry, Growth inhibition, Fermentation, Food Microbiology, Microbial Interactions, Transcriptome, Yarrowia lipolytica 1E07, Food Science
Abstract

on line novembre 2017paper : janvier 2018; Yeasts play a crucial role in cheese ripening. They contribute to the curd deacidification, the establishment of acid-sensitive bacterial communities, and flavour compounds production via proteolysis and catabolism of amino acids (AA). Negative yeast-yeast interaction was observed between the yeast Yarrowia lipolytica 1E07 (YL1E07) and the yeast Debaryomyces hansenii 1L25 (DH1L25) in a model cheese but need elucidation. YL1E07 and DH1L25 were cultivated in mono and co-cultures in a liquid synthetic medium (SM) mimicking the cheese environment and the growth inhibition of DH1L25 in the presence of YL1E07 was reproduced. We carried out microbiological, biochemical (lactose, lactate, AA consumption and ammonia production) and transcriptomic analyses by microarray technology to highlight the interaction mechanisms. We showed that the DH1L25 growth inhibition in the presence of YL1E07 was neither due to the ammonia production nor to the nutritional competition for the medium carbon sources between the two yeasts. The transcriptomic study was the key toward the comprehension of yeast-yeast interaction, and revealed that the inhibition of DH1L25 in co-culture is due to a decrease of the mitochondrial respiratory chain functioning.

Published
2017
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23. Elucidating the response of Kluyveromyces lactis to arsenite and peroxide stress and the role of the transcription factor KlYap8

Author

Julie Aubert, Markus J. Tamás, Magdalena Migocka, Ewa Maciaszczyk-Dziubinska, Ewa Sloma, Nallani Vijay Kumar, Robert W. Wysocki, Jenny Veide Vilg, Djamila Onesime, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Chemistry and Molecular Biology [Gothenburg], University of Gothenburg (GU), Institute of Experimental Biology, University of Wrocław [Poland], MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Mathématiques et Informatique Appliquées (MIA-Paris), AgroParisTech-Institut National de la Recherche Agronomique (INRA), foundations Carl Tryggers Stiftelse CTS11:467 CTS12:488, Magnus Bergvalls Stiftelse MBS2013-01-15, Wilhelm and Martina Lundgrens Vetenskapsfond vet1-518/2012, Stiftelsen 01 le Englcvist Byggmastare SOEB/65, National Science Centre, Poland 2012/07/B/NZ1/02804, and University of Wrocław [Poland] (UWr)

Subjects
Metalloid, Arsenites, [SDV]Life Sciences [q-bio], Mutant, Biophysics, Biochemistry, Arsenic, Fungal Proteins, resistance, BZIP proteins, Kluyveromyces, chemistry.chemical_compound, Stress, Physiological, Structural Biology, Gene Expression Regulation, Fungal, Gene expression, Genetics, oxidative stress, KNQ1, factor yap8p, Molecular Biology, Gene, Transcription factor, AP-1 protein, ComputingMilieux_MISCELLANEOUS, Arsenite, Kluyveromyces lactis, biology, Wild type, Hydrogen Peroxide, DNA, Membrane transport, Microarray Analysis, biology.organism_classification, YAP1P, gene-expression, Yeast, Basic-Leucine Zipper Transcription Factors, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, chemistry, saccharomyces-cerevisiae, Transcriptome
Abstract

All organisms need to sense and respond to a range of stress conditions. In this study, we used transcriptional profiling to identify genes and cellular processes that are responsive during arsenite and tert-butyl hydroperoxide exposure in Kluyveromyces lactis. Many arsenite-responsive genes encode proteins involved in redox processes, protein folding and stabilization, and transmembrane transport. The majority of peroxide-responsive genes encode functions related to transcription, translation, redox processes, metabolism and transport. A substantial number of these stress-regulated genes contain binding motifs for the AP-1 like transcription factors KlYap1 and KlYap8. We demonstrate that KlYap8 binds to and regulates gene expression through a 13 base-pair promoter motif, and that KlYap8 provides protection against arsenite, antimonite, cadmium and peroxide toxicity. Direct transport assays show that Klyap8 Delta cells accumulate more arsenic and cadmium than wild type cells and that the Klyap8 Delta mutant is defective in arsenic and cadmium export. KlYap8 regulates gene expression in response to both arsenite and peroxide, and might cooperate with KlYap1 in regulation of specific gene targets. Comparison of KlYap8 with its Saccharomyces cerevisiae orthologue ScYap8 indicates that KlYap8 senses and responds to multiple stress signals whereas ScYap8 is only involved in the response to arsenite and antimonite. Thus, our data suggest that functional specialization of ScYap8 has occurred after the whole genome duplication event. This is the first genome-wide stress response analysis in K. lactis and the first demonstration of KlYap8 function.

Published
2014
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24. Specific and extensive endometrial deregulation is present before conception in IVF/ICSI repeated implantation failures (IF) or recurrent miscarriages

Author

Jean-Michel Foidart, Carine Munaut, Mona Rahmati, Valérie Serazin, Julie Aubert, Olivier Sandra, Gérard Chaouat, and Nathalie Lédée

Subjects
0303 health sciences, 030219 obstetrics & reproductive medicine, Microarray, medicine.diagnostic_test, Biology, Luteal phase, Endometrium, medicine.disease, Cell morphology, 3. Good health, Pathology and Forensic Medicine, Gene expression profiling, Andrology, 03 medical and health sciences, Pregnancy rate, 0302 clinical medicine, medicine.anatomical_structure, Recurrent miscarriage, medicine, 030304 developmental biology, Endometrial biopsy
Abstract

The objective was to examine if IVF/ICSI repeated implantation failures (IF) or recurrent miscarriages (RM) could be related to preconceptional endometrial deregulations. IF was defined as the absence of pregnancy despite the transfer of at least ten IVF/ICSI good quality embryos, and RM as having at least three unexplained miscarriages. Fertile controls (FC) were women who had given birth at least once. Endometrial biopsy was performed in the mild luteal phase of a non-conceptual cycle (five women were selected in each group). Affymetrix chips (GeneChip Human Genome U133 Plus2.0 Array) were used for hybridization. Data were normalized by the gcRMA method, and raw p values adjusted by the Bonferroni procedure (1%). Differential expression of selected genes was analysed using real-time PCR. Gene networks and biological functions were explored using the Ingenuity Pathways Analysis software. Endometrial gene expression profiles at the time of uterine receptivity differ dramatically in the endometrium among FC, RM, and IF patients. Compared to FC, 2126 and 2477 genes are differentially expressed in IF and RM groups, respectively, and 2363 between IF and RM. In both conditions, differential gene expression referred mainly to DNA transcription and expression. Other main cellular functions deregulated in IF conditions correspond to cell morphology, cellular development, cell cycle, and cellular assembly, while in RM conditions, deregulated cellular functions relate to cell signalling (degradation of cyclic AMP and calcium metabolism) and cellular maintenance. In both conditions, there is an over-representation of deregulations related to the haematological system. In the IF condition, cell-mediated immune response and nervous system development and function are highly deregulated, while in RM patients, main deregulations are in organ and tissue development, humoral immune response, and muscular system development and function. Extensive endometrial deregulations are present before conception in patients who experienced IF or RM with both distinct and common deregulation.

Published
2011
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25. An insight into normal and pathological pregnancies using large-scale microarrays: lessons from microarrays

Author

Mona Rahmati, Olivier Sandra, Nathalie Coqué, Gérard Chaouat, Valérie Serazin, Jean-Michel Foidart, Sandrine Zourbas, Julie Aubert, Francesco Tedesco, Nathalie Rodde, Carine Munaut, Sylvie Dubanchet, Jacques Martal, Roberta Bulla, Jens C. Jensenius, Marie Petitbarat, Thiel Steffen, Isabelle Bataillon, Nathalie Lédée, Benoit Hennuy, Chaouat, G., Rodde, N., Petitbarat, M., Bulla, Roberta, Rahmati, M., Dubanchet, S., Zourbas, S., Bataillon, I., Coqué, N., Hennuy, B., Martal, J., Munaut, C., Aubert, J., Sérazin, V., Steffen, T., Jensenius, J. C., Foidart, J. M., Sandra, O., Tedesco, Francesco, Lédée, N., U782, Institut National de la Santé et de la Recherche Médicale (INSERM), UMR 0782, Hôpital Antoine Béclère, Université Paris-Sud - Paris 11 (UP11), Biologie du Développement et Reproduction (BDR), Institut National de la Recherche Agronomique (INRA), Department of Life Sciences, Università degli studi di Trieste, UMR INRA-ENVA 1198 (BDR), École nationale vétérinaire d'Alfort (ENVA), Mathématiques et Informatique Appliquées (MIA-Paris), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Laboratoire de Biologie des Tumeurs et Dévelopement, Université de Liège, Gamètes, implantation, gestation (GIG), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Aarhus University [Aarhus], Tumour & Development Laboratory, INSERM, Université Paris-Sud, AP-HP - Hôpital Antoine Béclère [Clamart], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Biologie du développement et reproduction (BDR), Centre National de la Recherche Scientifique (CNRS)-École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), and European Society for Reproductive Immunology (ESRI). POL.

Subjects
Male, Microarray, Immunology, preeclampsia, recurrent pregnancy loss, Immune tolerance, Preeclampsia, Mice, 03 medical and health sciences, 0302 clinical medicine, Immune system, Pre-Eclampsia, Pregnancy, Immune Tolerance, medicine, Animals, Humans, Immunology and Allergy, Pathological, Oligonucleotide Array Sequence Analysis, 030304 developmental biology, cba mice, Mice, Inbred BALB C, 0303 health sciences, business.industry, Gene Expression Profiling, First pregnancy, Obstetrics and Gynecology, [SDV.BDLR]Life Sciences [q-bio]/Reproductive Biology, medicine.disease, Disease Models, Animal, Gene Expression Regulation, Reproductive Medicine, Mice, Inbred DBA, Mice, Inbred CBA, [SDV.IMM]Life Sciences [q-bio]/Immunology, Female, DNA microarray, business, microarray, 030215 immunology
Abstract

In the introduction, we briefly recall old but classic evidence that there is no tolerance to paternal alloantigens in a first pregnancy. Therefore, we performed small- and large-scale microarrays in CBA × DBA/2 and CBA × BALB/c combinations, recently described as a murine model for preeclampsia. Our results are in line with other data suggesting a very early deregulation of local immune vascular events rather than a break of immune tolerance. Other data presented at the Tioman 2010 Preeclampsia Workshop supporting this hypothesis are briefly summarised, as well as indications and caveats from a recent human microarray on implantation failure and recurrent pregnancy loss.

Published
2011
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26. Qualité des données NGS : de la séquence aux bases de données

Author

Pierre Peyret, Julie Aubert, Vincent Breton, François Enault, Line Le Gall, Denis Le Paslier, Tiphaine Martin, Guy Perriere, Eric Peyretaillade, Unité de Microbiologie (MIC), Institut National de la Recherche Agronomique (INRA), Mathématiques et Informatique Appliquées (MIA-Paris), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Inconnu, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Muséum national d'Histoire naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne (UCA), Microbiologie Environnement Digestif Santé (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), and Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix

Subjects
base de données, [SDV]Life Sciences [q-bio], séquence, données NGS
Abstract

Qualité des données NGS : de la séquence aux bases de données

Published
2016

27. New insights into sulfur metabolism in yeasts as revealed by studies of yarrowia lipolytica

Author

Agnès Hébert, Marie-Pierre Forquin-Gomez, Jean-François Heilier, Julie Aubert, Jean-Marie Beckerich, Pascal Bonnarme, Christophe Junot, Aurelie Roux, Sophie Landaud, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Génie et Microbiologie des Procédés Alimentaires (GMPA), Laboratoire d'Etudes et de Recherches en Immunoanalyses (LERI), Service de Pharmacologie et Immunoanalyse (SPI), Médicaments et Technologies pour la Santé (MTS), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Médicaments et Technologies pour la Santé (MTS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Mathématiques et Informatique Appliquées (MIA-Paris), Louvain Ctr Toxicol & Appl Pharmacol LTAP, Université Catholique de Louvain = Catholic University of Louvain (UCL), EcoMet program [ANR-06-PNRA-014], French National Research Agency (ANR), ANR, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Médicaments et Technologies pour la Santé (MTS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), AgroParisTech-Institut National de la Recherche Agronomique (INRA), and Université Catholique de Louvain (UCL)

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Sulfur metabolism, Cystine, chemistry.chemical_element, Yarrowia, Applied Microbiology and Biotechnology, SACCHAROMYCES-CEREVISIAE, 03 medical and health sciences, chemistry.chemical_compound, Methionine, Stress, Physiological, HYDROGEN-SULFIDE PRODUCTION, Gene Expression Regulation, Fungal, TOLERANCE, Sulfate assimilation, 030304 developmental biology, GENE-EXPRESSION, 2. Zero hunger, 0303 health sciences, Ecology, biology, IDENTIFICATION, 030306 microbiology, Sulfates, TRANSCRIPTIONAL REGULATION, biology.organism_classification, Sulfur, Yeast, L-METHIONINE, CATABOLISM, CHEESE-RIPENING MICROORGANISMS, chemistry, Biochemistry, Metabolome, Food Microbiology, CYSTEINE, Transcriptome, Metabolic Networks and Pathways, Food Science, Biotechnology, Cysteine
Abstract

Yarrowia lipolytica , located at the frontier of hemiascomycetous yeasts and fungi, is an excellent candidate for studies of metabolism evolution. This yeast, widely recognized for its technological applications, in particular produces volatile sulfur compounds (VSCs) that fully contribute to the flavor of smear cheese. We report here a relevant global vision of sulfur metabolism in Y. lipolytica based on a comparison between high- and low-sulfur source supplies (sulfate, methionine, or cystine) by combined approaches (transcriptomics, metabolite profiling, and VSC analysis). The strongest repression of the sulfate assimilation pathway was observed in the case of high methionine supply, together with a large accumulation of sulfur intermediates. A high sulfate supply seems to provoke considerable cellular stress via sulfite production, resulting in a decrease of the availability of the glutathione pathway's sulfur intermediates. The most limited effect was observed for the cystine supply, suggesting that the intracellular cysteine level is more controlled than that of methionine and sulfate. Using a combination of metabolomic profiling and genetic experiments, we revealed taurine and hypotaurine metabolism in yeast for the first time. On the basis of a phylogenetic study, we then demonstrated that this pathway was lost by some of the hemiascomycetous yeasts during evolution.

Published
2013
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28. Comprehensive evaluation of normalization methods for High-throughput rnaSequencing Data analysis

Author

Julie Aubert, Marie-Agnes Dillies, Andrea Rau, Christelle Hennequet-Antier, Marine Jeanmougin, Nicolas Servant, Céline Keime, Stéphane Le Crom, Mickaël Guedj, Florence Jaffrezic, Mathématiques et Informatique Appliquées (MIA-Paris), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Recherches Avicoles (SRA), Institut National de la Recherche Agronomique (INRA), Université d'Evry Val d'Essonne, Institut Pasteur de Madagascar, Réseau International des Instituts Pasteur (RIIP), Institut Curie, Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie (Paris 6), Laboratoire Statistique et Génome (SG), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Transcriptome et Epigénome (PF2), Institut Pasteur [Paris] (IP), Unité de Recherches Avicoles (URA), Université d'Évry-Val-d'Essonne (UEVE), Université Pierre et Marie Curie - Paris 6 (UPMC), and Institut Pasteur [Paris]

Subjects
[SDV]Life Sciences [q-bio], High-throughput rnaSequencing Data analysis, evaluation of normalization methods
Abstract

Comprehensive evaluation of normalization methods for High-throughput rnaSequencing Data analysis. 4 Workshop of StatSeq COST Action TD0801

Published
2012

29. Correction: A Temporal -omic Study of Propionibacterium freudenreichii CIRM-BIA1 T Adaptation Strategies in Conditions Mimicking Cheese Ripening in the Cold

Author

Gwénaël Jan, Julie Aubert, Jarna Tanskanen, Anne Thierry, Sergine Even, Marie-Bernadette Maillard, Stéphanie-Marie Deutsch, Marion Dalmasso, Sandrine Parayre, Briard-Bion, Hélène Falentin, Chuat, Piot M, Julien Jardin, Science et Technologie du Lait et de l'Oeuf (STLO), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Mathématiques et Informatique Appliquées (MIA-Paris), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Ltd , PO Box 30, VALIO, and 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)

Subjects
0303 health sciences, Multidisciplinary, 030306 microbiology, Science, Correction, Cheese ripening, Computational biology, Biology, Adaptation strategies, 03 medical and health sciences, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Medicine, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology
Abstract

International audience

Published
2012
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30. A Temporal -omic study of propionibacterium freudenreichii CIRM-BIA1T adaptation strategies in conditions mimicking cheese ripening in the cold

Author

Gwénaël Jan, Anne Thierry, Sandrine Parayre, Sergine Even, Marion Dalmasso, Julie Aubert, Stéphanie-Marie Deutsch, Jarna Tanskanen, Julien Jardin, Marie-Bernadette Maillard, Victoria Chuat, Valérie Briard-Bion, Hélène Falentin, Michel Piot, Thierry, Anne, Science et Technologie du Lait et de l'Oeuf (STLO), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, 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), Mathématiques et Informatique Appliquées (MIA-Paris), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Valio, Tekes, INRA (French National Institute for Agricultural Research), Valio Ltd, and Institut National de la Recherche Agronomique (INRA)-AgroParisTech

Subjects
Proteomics, Time Factors, flaveru, Proteome, Cheese Flavor, [SDV]Life Sciences [q-bio], Propionibacterium freudenreichii, fromage, affinage, chambre froide, composé volatil, lcsh:Medicine, Cheese ripening, Biochemistry, Cheese, Gene expression, Electrophoresis, Gel, Two-Dimensional, Food science, lcsh:Science, 2. Zero hunger, bactérie, 0303 health sciences, Multidisciplinary, biology, Ecology, food and beverages, Ripening, Genomics, Adaptation, Physiological, Cold Temperature, Swiss cheese, Research Article, Biotechnology, Propionibacterium, bactérie lactique, Microbiology, 03 medical and health sciences, Bacterial Proteins, Stress, Physiological, Genome Analysis Tools, Biology, 030304 developmental biology, Microbial Viability, 030306 microbiology, Gene Expression Profiling, lcsh:R, Proteins, Computational Biology, Gene Expression Regulation, Bacterial, biology.organism_classification, Carbon, Genes, Bacterial, lcsh:Q, Fermentation, Transcriptome, Developmental Biology
Abstract

Propionibacterium freudenreichii is used as a ripening culture in Swiss cheese manufacture. It grows when cheeses are ripened in a warm room (about 24°C). Cheeses with an acceptable eye formation level are transferred to a cold room (about 4°C), inducing a marked slowdown of propionic fermentation, but P. freudenreichii remains active in the cold. To investigate the P. freudenreichii strategies of adaptation and survival in the cold, we performed the first global gene expression profile for this species. The time-course transcriptomic response of P. freudenreichii CIRM-BIA1(T) strain was analyzed at five times of incubation, during growth at 30°C then for 9 days at 4°C, under conditions preventing nutrient starvation. Gene expression was also confirmed by RT-qPCR for 28 genes. In addition, proteomic experiments were carried out and the main metabolites were quantified. Microarray analysis revealed that 565 genes (25% of the protein-coding sequences of P. freudenreichii genome) were differentially expressed during transition from 30°C to 4°C (P1). At 4°C, a general slowing down was observed for genes implicated in the cell machinery. On the contrary, P. freudenreichii CIRM-BIA1(T) strain over-expressed genes involved in lactate, alanine and serine conversion to pyruvate, in gluconeogenesis, and in glycogen synthesis. Interestingly, the expression of different genes involved in the formation of important cheese flavor compounds, remained unchanged at 4°C. This could explain the contribution of P. freudenreichii to cheese ripening even in the cold. In conclusion, P. freudenreichii remains metabolically active at 4°C and induces pathways to maintain its long-term survival.

Published
2012
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31. Accumulation of intracellular glycogen and trehalose by [i]Propionibacterium Freudenreichii[/i] under conditions mimicking cheese ripening in the cold

Author

Anne Thierry, Jarna Tanskanen, Marion Dalmasso, Marie-Bernadette Maillard, Sandrine Parayre, Hélène Falentin, Julie Aubert, Valentin Loux, Sergine Even, Science et Technologie du Lait et de l'Oeuf (STLO), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Mathématiques et Informatique Appliquées (MIA-Paris), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Unité Mathématique, Informatique et Génome (MIG), Institut National de la Recherche Agronomique (INRA), Valio Ltd, 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), Plateforme Bio-Informatique - Génotoul, Ltd , PO Box 30, and VALIO

Subjects
Propionibacterium, [SDV]Life Sciences [q-bio], Cell, Cheese ripening, fromage, Applied Microbiology and Biotechnology, 03 medical and health sciences, chemistry.chemical_compound, Cheese, Stress, Physiological, glygogene, medicine, tréhalose, Glycogen synthase, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Ecology, biology, Glycogen, 030306 microbiology, Propionibacterium freudenreichii, Trehalose, food and beverages, biology.organism_classification, probiotique, Carbon, Cold Temperature, medicine.anatomical_structure, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Biochemistry, chemistry, propionibacterium freudenreichii, biology.protein, Food Microbiology, Intracellular, Food Science, Biotechnology
Abstract

Seven Propionibacterium freudenreichii strains exhibited similar responses when placed at 4°C. They slowed down cell machinery, displayed cold stress responses, and rerouted their carbon metabolism toward trehalose and glycogen synthesis, both accumulated in cells. These results highlight the molecular basis of long-term survival of P. freudenreichii in the cold.

Published
2012
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32. A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis

Author

Luc Jouneau, Mickaël Guedj, Denis Laloë, Jordi Estellé, Stéphane Le Crom, Céline Keime, Julie Aubert, Gregory Guernec, Marine Jeanmougin, Christelle Hennequet-Antier, Brigitte Schaeffer, Nicolas Servant, Florence Jaffrézic, David Castel, Caroline Le Gall, Andrea Rau, Bernd Jagla, Marie-Agnès Dillies, Guillemette Marot, Puces à ADN (Plate-Forme 2) (PF2), Institut Pasteur [Paris], Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Mathématiques et Informatique Appliquées (MIA-Paris), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Centre Médical de l'Institut Pasteur (CMIP), Laboratoire Statistique et Génome (SG), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Cancer et génome: Bioinformatique, biostatistiques et épidémiologie d'un système complexe, MINES ParisTech - École nationale supérieure des mines de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Institute of Genetics [Illkirch], Molecular and Cellular Biology, MOdel for Data Analysis and Learning (MODAL), Laboratoire Paul Painlevé - UMR 8524 (LPP), Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Université de Lille, Sciences et Technologies-Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Evaluation des technologies de santé et des pratiques médicales - ULR 2694 (METRICS), Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-École polytechnique universitaire de Lille (Polytech Lille), Evaluation des technologies de santé et des pratiques médicales - ULR 2694 (METRICS), Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Laboratoire d'Exploration Fonctionnelle des Génomes (LEFG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7), Centro Nacional de Análisi Genómico (CNAG), Centro Nacional de Análisis Genómico, Epidémiologie des maladies infectieuses et modélisation (ESIM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), INRA, UR 0341 Mathématiques et Informatique Appliquées, Methodomics, Plateforme Génomique de l'IBENS, Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), This work was supported by the Groupe de Rercherche Bioinformatique Moléculaire (GdR BiM, http://www.gdr-bim.u-psud.fr)., Centre Médical de l'Institut Pasteur, Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Paul Painlevé - UMR 8524 (LPP), Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Evaluation des technologies de santé et des pratiques médicales - ULR 2694 (METRICS), Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-École polytechnique universitaire de Lille (Polytech Lille)-Université de Lille, Sciences et Technologies, Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Cancer et génôme: Bioinformatique, biostatistiques et épidémiologie d'un système complexe, MINES ParisTech - École nationale supérieure des mines de Paris-Institut Curie-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Santé publique : épidémiologie et qualité des soins-EA 2694 (CERIM), Santé publique : épidémiologie et qualité des soins-EA 2694 (CERIM), École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP), Mines Paris - PSL (École nationale supérieure des mines de Paris), Laboratoire Paul Painlevé (LPP), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Sciences et Technologies-Inria Lille - Nord Europe, INRA - Mathématiques et Informatique Appliquées (Unité MIAJ), Institut National de la Recherche Agronomique (INRA), GenomiqueENS (Genomique ENS), École normale supérieure - Paris (ENS-PSL), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL)

Subjects
Normalization (statistics), Computer science, differential analysis, [SDV]Life Sciences [q-bio], Sequencing data, computer.software_genre, DNA sequencing, Differential analysis, 03 medical and health sciences, 0302 clinical medicine, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Molecular Biology, 030304 developmental biology, 0303 health sciences, [STAT.AP]Statistics [stat]/Applications [stat.AP], High-Throughput RNA Sequencing, Sequence Analysis, RNA, Design of experiments, High-Throughput Nucleotide Sequencing, high-throughput sequencing, normalization, Comparison study, Data mining, RNA-seq, computer, [STAT.ME]Statistics [stat]/Methodology [stat.ME], 030217 neurology & neurosurgery, Information Systems
Abstract

The French StatOmique Consortium gathers more than 40 statisticians and bioinformaticians involved in high-throughput transcriptome data analysis in France. The objective of this group, created in 2008, is to share among researchers and practitioners knowledge of the statistical analysis of high-throughput data. Chantier qualité GA; International audience; During the last 3 years, a number of approaches for the normalization of RNA sequencing data have emerged in the literature, differing both in the type of bias adjustment and in the statistical strategy adopted. However, as data continue to accumulate, there has been no clear consensus on the appropriate normalization method to be used or the impact of a chosen method on the downstream analysis. In this work, we focus on a comprehensive comparison of seven recently proposed normalization methods for the differential analysis of RNA-seq data, with an emphasis on the use of varied real and simulated datasets involving different species and experimental designs to represent data characteristics commonly observed in practice. Based on this comparison study, we propose practical recommendations on the appropriate normalization method to be used and its impact on the differential analysis of RNA-seq data.

Published
2012
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33. Specific and extensive endometrial deregulation is present before conception in IVF/ICSI repeated implantation failures (IF) or recurrent miscarriages

Author

Nathalie, Lédée, Carine, Munaut, Julie, Aubert, Valérie, Sérazin, Mona, Rahmati, Gérard, Chaouat, Olivier, Sandra, and Jean Michel, Foidart

Subjects
Abortion, Habitual, Endometrium, Pregnancy Rate, Pregnancy, Gene Expression Profiling, Pregnancy Outcome, Gene Expression Regulation, Developmental, Humans, Female, Embryo Implantation, RNA, Messenger, Sperm Injections, Intracytoplasmic, Infertility, Female
Abstract

The objective was to examine if IVF/ICSI repeated implantation failures (IF) or recurrent miscarriages (RM) could be related to preconceptional endometrial deregulations. IF was defined as the absence of pregnancy despite the transfer of at least ten IVF/ICSI good quality embryos, and RM as having at least three unexplained miscarriages. Fertile controls (FC) were women who had given birth at least once. Endometrial biopsy was performed in the mild luteal phase of a non-conceptual cycle (five women were selected in each group). Affymetrix chips (GeneChip Human Genome U133 Plus2.0 Array) were used for hybridization. Data were normalized by the gcRMA method, and raw p values adjusted by the Bonferroni procedure (1%). Differential expression of selected genes was analysed using real-time PCR. Gene networks and biological functions were explored using the Ingenuity Pathways Analysis software. Endometrial gene expression profiles at the time of uterine receptivity differ dramatically in the endometrium among FC, RM, and IF patients. Compared to FC, 2126 and 2477 genes are differentially expressed in IF and RM groups, respectively, and 2363 between IF and RM. In both conditions, differential gene expression referred mainly to DNA transcription and expression. Other main cellular functions deregulated in IF conditions correspond to cell morphology, cellular development, cell cycle, and cellular assembly, while in RM conditions, deregulated cellular functions relate to cell signalling (degradation of cyclic AMP and calcium metabolism) and cellular maintenance. In both conditions, there is an over-representation of deregulations related to the haematological system. In the IF condition, cell-mediated immune response and nervous system development and function are highly deregulated, while in RM patients, main deregulations are in organ and tissue development, humoral immune response, and muscular system development and function. Extensive endometrial deregulations are present before conception in patients who experienced IF or RM with both distinct and common deregulation.

Published
2011

34. Global regulation of the response to sulfur availability in the cheese-related bacterium Brevibacterium aurantiacum

Author

Caroline Proux, Julie Aubert, Marie-Pierre Forquin, Pascal Bonnarme, Christophe Junot, Agnès Hébert, Jean-François Heilier, Isabelle Martin-Verstraete, Sophie Landaud, Aurelie Roux, Génie et Microbiologie des Procédés Alimentaires (GMPA), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Pathogénèse des Bactéries Anaérobies / Pathogenesis of Bacterial Anaerobes (PBA (U-Pasteur_6)), Institut Pasteur [Paris] (IP)-Université Paris Diderot - Paris 7 (UPD7), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Laboratoire d'Etudes et de Recherches en Immunoanalyses (LERI), Service de Pharmacologie et Immunoanalyse (SPI), Médicaments et Technologies pour la Santé (MTS), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Médicaments et Technologies pour la Santé (MTS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Mathématiques et Informatique Appliquées (MIA-Paris), Puces à ADN (Plate-Forme 2) (PF2), Institut Pasteur [Paris] (IP), Louvain Centre for Toxicology and Applied Pharmacology, Université Catholique de Louvain = Catholic University of Louvain (UCL), French National Research Agency (ANR) ANR-06-PNRA-014, Institut Pasteur [Paris]-Université Paris Diderot - Paris 7 (UPD7), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Médicaments et Technologies pour la Santé (MTS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Institut Pasteur [Paris], and Université Catholique de Louvain (UCL)

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Homocysteine, Carbon-Oxygen Lyases, Cystine, Sulfur metabolism, chemistry.chemical_element, Genetics and Molecular Biology, Transsulfuration pathway, Biology, Applied Microbiology and Biotechnology, cheese, 03 medical and health sciences, chemistry.chemical_compound, Methionine, Brevibacterium, Cysteine, Sulfate assimilation, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Ecology, Reverse Transcriptase Polymerase Chain Reaction, 030306 microbiology, Gene Expression Profiling, Gene Expression Regulation, Bacterial, bacterium, Sulfur, Carbon-Sulfur Lyases, chemistry, Biochemistry, sulfur, Metabolome, Food Science, Biotechnology
Abstract

In this study, we combined metabolic reconstruction, growth assays, and metabolome and transcriptome analyses to obtain a global view of the sulfur metabolic network and of the response to sulfur availability in Brevibacterium aurantiacum . In agreement with the growth of B. aurantiacum in the presence of sulfate and cystine, the metabolic reconstruction showed the presence of a sulfate assimilation pathway, thiolation pathways that produce cysteine ( cysE and cysK ) or homocysteine ( metX and metY ) from sulfide, at least one gene of the transsulfuration pathway ( aecD ), and genes encoding three MetE-type methionine synthases. We also compared the expression profiles of B. aurantiacum ATCC 9175 during sulfur starvation or in the presence of sulfate. Under sulfur starvation, 690 genes, including 21 genes involved in sulfur metabolism and 29 genes encoding amino acids and peptide transporters, were differentially expressed. We also investigated changes in pools of sulfur-containing metabolites and in expression profiles after growth in the presence of sulfate, cystine, or methionine plus cystine. The expression of genes involved in sulfate assimilation and cysteine synthesis was repressed in the presence of cystine, whereas the expression of metX , metY , metE1 , metE2 , and BL613 , encoding a probable cystathionine-γ-synthase, decreased in the presence of methionine. We identified three ABC transporters: two operons encoding transporters were transcribed more strongly during cysteine limitation, and one was transcribed more strongly during methionine depletion. Finally, the expression of genes encoding a methionine γ-lyase ( BL929 ) and a methionine transporter ( metPS ) was induced in the presence of methionine in conjunction with a significant increase in volatile sulfur compound production.

Published
2011
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35. Exploration of sulfur metabolism in the yeast Kluyveromyces lactis

Author

Valentin Loux, Agnès Hébert, Jean-François Heilier, Pascal Bonnarme, Christophe Junot, Marie-Pierre Forquin-Gomez, Julie Aubert, Jean Marie Beckerich, Sophie Landaud, Aurelie Roux, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Génie et Microbiologie des Procédés Alimentaires (GMPA), Laboratoire d'Etudes et de Recherches en Immunoanalyses (LERI), Service de Pharmacologie et Immunoanalyse (SPI), Médicaments et Technologies pour la Santé (MTS), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Médicaments et Technologies pour la Santé (MTS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Mathématiques et Informatique Appliquées (MIA-Paris), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Unité Mathématique, Informatique et Génome (MIG), Institut National de la Recherche Agronomique (INRA), Louvain Center for Toxicology and Applied Pharmacology, Université Catholique de Louvain = Catholic University of Louvain (UCL), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Médicaments et Technologies pour la Santé (MTS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université Catholique de Louvain (UCL), and Unité Mathématique Informatique et Génome (MIG)

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Sulfur metabolism, chemistry.chemical_element, Applied Microbiology and Biotechnology, Fungal Proteins, 03 medical and health sciences, chemistry.chemical_compound, Kluyveromyces, Methionine, Sulfur assimilation, Gene Expression Regulation, Fungal, Sulfate assimilation, volatile sulfur compounds, 030304 developmental biology, 2. Zero hunger, Kluyveromyces lactis, 0303 health sciences, biology, Sulfur Compounds, 030306 microbiology, General Medicine, biology.organism_classification, Sulfur, Yeast, chemistry, Biochemistry, sulfur metabolism, metabolome, transcriptome, kluyveromyces lactis, Biotechnology, Cysteine
Abstract

Hemiascomycetes are separated by considerable evolutionary distances and, as a consequence, the mechanisms involved in sulfur metabolism in the extensively studied yeast, Saccharomyces cerevisiae, could be different from those of other species of the phylum. This is the first time that a global view of sulfur metabolism is reported in the biotechnological yeast Kluyveromyces lactis. We used combined approaches based on transcriptome analysis, metabolome profiling, and analysis of volatile sulfur compounds (VSCs). A comparison between high and low sulfur source supplies, i.e., sulfate, methionine, or cystine, was carried out in order to identify key steps in the biosynthetic and catabolic pathways of the sulfur metabolism. We found that sulfur metabolism of K. lactis is mainly modulated by methionine. Furthermore, since sulfur assimilation is highly regulated, genes coding for numerous transporters, key enzymes involved in sulfate assimilation and the interconversion of cysteine to methionine pathways are repressed under conditions of high sulfur supply. Consequently, as highlighted by metabolomic results, intracellular pools of homocysteine and cysteine are maintained at very low concentrations, while the cystathionine pool is highly expandable. Moreover, our results suggest a new catabolic pathway for methionine to VSCs in this yeast: methionine is transaminated by the ARO8 gene product into 4-methylthio-oxobutyric acid (KMBA), which could be exported outside of the cell by the transporter encoded by PDR12 and demethiolated by a spontaneous reaction into methanethiol and its derivatives.

Published
2011
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36. Invading basement membrane matrix is sufficient for MDA-MB-231 breast cancer cells to develop a atable in vivo metastatic phenotype

Author

Clara Nahmias, Marie-Pierre Podgorniak, Sylvie Rodrigues-Ferreira, Abdel-Majid Khatib, Nicole Peyri, Julie Aubert, Nadejda Vintonenko, Michel Crépin, Lei Chen, Anna Starzec, Mélanie Di Benedetto, Pierre-Olivier Couraud, Christelle Doliger, Odile Sainte-Catherine, Gérard-Yves Perret, Jean-Luc Poyet, Aniela Robles, Jérémie Mariau, Monique Etienne, Marie-Laure Martin, Mohamed Abdelkarim, Samia Mourah, Chimie, Structures et Propriétés de Biomatériaux et d'Agents Thérapeutiques (CSPBAT), Université Paris 13 (UP13)-Institut Galilée-Université Sorbonne Paris Cité (USPC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), and Di Benedetto, Mélanie

Subjects
Mouse, Angiogenesis, [SDV]Life Sciences [q-bio], Cell, lcsh:Medicine, Basement Membrane, ANGIOGENESIS, Extracellular matrix, Mice, 0302 clinical medicine, Molecular Cell Biology, Breast Tumors, Angiogenic Proteins, Neoplasm Metastasis, [MATH]Mathematics [math], lcsh:Science, Oligonucleotide Array Sequence Analysis, 0303 health sciences, Multidisciplinary, Cell adhesion molecule, Reverse Transcriptase Polymerase Chain Reaction, DEATH, EPITHELIAL-CELLS, TGF-BETA, Animal Models, Immunohistochemistry, 3. Good health, Tumor Burden, APOPTOSIS, Gene Expression Regulation, Neoplastic, Drug Combinations, medicine.anatomical_structure, Phenotype, Oncology, 030220 oncology & carcinogenesis, Medicine, Female, Proteoglycans, Collagen, Research Article, EXPRESSION, Histology, CARCINOMA, PROTEINS, Transplantation, Heterologous, Mice, Nude, Breast Neoplasms, Biology, 03 medical and health sciences, Model Organisms, Cell Line, Tumor, medicine, Cell Adhesion, Genetics, Cancer Genetics, EXTRACELLULAR-MATRIX, Animals, Humans, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Neoplasm Invasiveness, [INFO]Computer Science [cs], Cell adhesion, 030304 developmental biology, Tumor microenvironment, Gene Expression Profiling, lcsh:R, Transendothelial and Transepithelial Migration, Mammary Neoplasms, Experimental, Cancers and Neoplasms, biochemical phenomena, metabolism, and nutrition, Molecular biology, Fibronectin, Cell culture, ENDOTHELIAL GROWTH-FACTOR, biology.protein, Cancer research, lcsh:Q, Laminin, Apoptosis Regulatory Proteins, Transcriptome, vivo metastatic phenotype, tumor microenvironment, extracellular matrix
Abstract

1 - Article; Introduction: The poor efficacy of various anti-cancer treatments against metastatic cells has focused attention on the role of tumor microenvironment in cancer progression. To understand the contribution of the extracellular matrix (ECM) environment to this phenomenon, we isolated ECM surrogate invading cell populations from MDA-MB-231 breast cancer cells and studied their genotype and malignant phenotype. Methods: We isolated invasive subpopulations (INV) from non invasive populations (REF) using a 2D-Matrigel assay, a surrogate of basal membrane passage. INV and REF populations were investigated by microarray assay and for their capacities to adhere, invade and transmigrate in vitro, and to form metastases in nude mice. Results: REF and INV subpopulations were stable in culture and present different transcriptome profiles. INV cells were characterized by reduced expression of cell adhesion and cell-cell junction genes (44% of down regulated genes) and by a gain in expression of anti-apoptotic and pro-angiogenic gene sets. In line with this observation, in vitro INV cells showed reduced adhesion and increased motility through endothelial monolayers and fibronectin. When injected into the circulation, INV cells induced metastases formation, and reduced injected mice survival by up to 80% as compared to REF cells. In nude mice, INV xenografts grew rapidly inducing vessel formation and displaying resistance to apoptosis. Conclusion: Our findings reveal that the in vitro ECM microenvironment per se was sufficient to select for tumor cells with a stable metastatic phenotype in vivo characterized by loss of adhesion molecules expression and induction of proangiogenic and survival factors.

Published
2011
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37. The preconceptional endometrial environment affects both implantation and gestation in human

Author

N. Lédée, Julie Aubert, B. Hennuy, Carine Munaut, Gérard Chaouat, Sylvie Dubanchet, Marie Petitbarat, Olivier Sandra, Valérie Serazin, Institut National de la Santé et de la Recherche Médicale (INSERM), EMBIC, Mathématiques et Informatique Appliquées (MIA-Paris), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Centre Hospitalier Universitaire de Liège (CHU-Liège), EA 2493, UFR des sciences de la santé, Biologie du développement et reproduction (BDR), and Centre National de la Recherche Scientifique (CNRS)-École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)

Subjects
0303 health sciences, medicine.medical_specialty, GENE EXPRESSION, 030219 obstetrics & reproductive medicine, Obstetrics, business.industry, [SDV]Life Sciences [q-bio], Immunology, ENDOMETRIUM, Obstetrics and Gynecology, 3. Good health, 03 medical and health sciences, 0302 clinical medicine, Reproductive Medicine, medicine, Immunology and Allergy, Gestation, [INFO]Computer Science [cs], IMPLANTATION, GESTATION, business, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology
Abstract

International audience

Published
2009

38. Endometrium as an early sensor of in vitro embryo manipulation technologies

Author

Corinne Giraud-Delville, Yvan Heyman, Harris A. Lewin, Isabelle Hue, X. Cindy Tian, Laurent Galio, Julie Aubert, Xiangzhong Yang, Séverine A. Degrelle, Nadéra Mansouri-Attia, Jean-Paul Renard, Robin E. Everts, Olivier Sandra, Biologie du Développement et Reproduction (BDR), Institut National de la Recherche Agronomique (INRA), Mathématiques et Informatique Appliquées (MIA-Paris), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Department of Animal Sciences, University of Illinois System, Génomique et Physiologie de la Lactation (GPL), Center for Regenerative Biology, Institut National de la Recherche Agronomique (INRA)-Institut National Agronomique Paris-Grignon (INA P-G), Ecole Nationale du Génie Rural, des Eaux et des Forêts (ENGREF)-Institut National de la Recherche Agronomique (INRA)-Institut National Agronomique Paris-Grignon (INA P-G), Department of Animal Sciences [Urbana, IL, USA], University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System, Unité de recherche génomique et physiologie de la lactation, Department of Animal Science and Center for Regenerative Biology [Storrs, CT, USA], University of Connecticut (UCONN), This work was supported by an Ministry of Education, Research and Technology grant (to N.M-A.) and partially supported by the European Network of Excellence on Embryo Implantation Control funded by European Union Grant LSHN-CT-2004-512040., Biologie du développement et reproduction (BDR), Centre National de la Recherche Scientifique (CNRS)-École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), Unité de recherche génomique et physiologie de la lactation (GPL), École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), and DEGRELLE, Séverine

Subjects
Nuclear Transfer Techniques, bovin, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, croissance fœtale, Microarray, [SDV]Life Sciences [q-bio], BOVINE, IMPLANTATION, MICROARRAY, NUCLEAR TRANSFER, reproduction animale, Uterus, Endometrium, 0302 clinical medicine, Pregnancy, 0303 health sciences, [SDV.BDLR.RS] Life Sciences [q-bio]/Reproductive Biology/Sexual reproduction, 030219 obstetrics & reproductive medicine, Multidisciplinary, Pregnancy Outcome, Gene Expression Regulation, Developmental, Embryo, Anatomy, Biological Sciences, medicine.anatomical_structure, embryonic structures, endomètre, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Gestation, Somatic cell nuclear transfer, Female, transfert d'embryon, Embryonic Development, Fertilization in Vitro, Biology, [SDV.BDLR.RS]Life Sciences [q-bio]/Reproductive Biology/Sexual reproduction, Andrology, 03 medical and health sciences, gestation, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], medicine, Animals, Embryo Implantation, 030304 developmental biology, Embryogenesis, medicine.disease, Embryo, Mammalian, [SDV.BIO] Life Sciences [q-bio]/Biotechnology, développement embryonnaire, embryon, Fertilization, Cattle
Abstract

International audience; Implantation is crucial for placental development that will subsequently impact fetal growth and pregnancy success with consequences on postnatal health. We postulated that the pattern of genes expressed by the endometrium when the embryo becomes attached to the mother uterus could account for the final outcome of a pregnancy. As a model, we used the bovine species where the embryo becomes progressively and permanently attached to the endometrium from day 20 of gestation onwards. At that stage, we compared the endometrial genes profiles in the presence of an in vivo fertilized embryo (AI) with the endometrial patterns obtained in the presence of nuclear transfer (SCNT) or in vitro fertilized embryos (IVF), both displaying lower and different potentials for term development. Our data provide evidence that the endome-trium can be considered as a biological sensor able to fine-tune its physiology in response to the presence of embryos whose development will become altered much later after the implantation process. Compared with AI, numerous biological functions and several canonical pathways with a major impact on metabolism and immune function were found to be significantly altered in the endometrium of SCNT pregnancies at implantation, whereas the differences were less pronounced with IVF embryos. Determining the limits of the endometrial plasticity at the onset of implantation should bring new insights on the contribution of the maternal environment to the development of an embryo and the success of pregnancy. bovine ͉ implantation ͉ microarray ͉ nuclear transfer

Published
2009
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39. Gene expression profiles of bovine caruncular and intercaruncular endometrium at implantation

Author

Harris A. Lewin, Nadéra Mansouri-Attia, Laurent Galio, Julie Aubert, Olivier Sandra, Corinne Giraud-Delville, Géraldine Taghouti, Pierrette Reinaud, Séverine A. Degrelle, Christophe Richard, Isabelle Hue, X. Cindy Tian, Jean-Paul Renard, Robin E. Everts, Xiangzhong Yang, Biologie du Développement et Reproduction (BDR), Institut National de la Recherche Agronomique (INRA), Mathématiques et Informatique Appliquées (MIA-Paris), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Génomique et Physiologie de la Lactation (GPL), Department of Animal Sciences, University of Illinois at Urbana-Champaign [Urbana], University of Illinois System-University of Illinois System, UE 1298 Unité Commune d'Expérimentation Animale, Institut National de la Recherche Agronomique (INRA)-Physiologie Animale et Systèmes d'Elevage (PHASE), Institut National de la Recherche Agronomique (INRA)-Unité Commune d'Expérimentation Animale (UCEA), Center for Regenerative Biology, Biologie du développement et reproduction (BDR), Centre National de la Recherche Scientifique (CNRS)-École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), AgroParisTech-Institut National de la Recherche Agronomique (INRA), and Unité de recherche génomique et physiologie de la lactation (GPL)

Subjects
medicine.medical_specialty, bovin, expression génique, Physiology, CATTLE, [SDV]Life Sciences [q-bio], reproduction animale, Estrous Cycle, Pregnancy Proteins, Biology, Endometrium, Transcriptome, 03 medical and health sciences, 0302 clinical medicine, gestation, Internal medicine, Gene expression, Genetics, medicine, Animals, Conceptus, Embryo Implantation, RNA, Messenger, TRANSCRIPTOME, INTERFERON-TAU, In Situ Hybridization, Oligonucleotide Array Sequence Analysis, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, 030219 obstetrics & reproductive medicine, Reverse Transcriptase Polymerase Chain Reaction, Gene Expression Profiling, Trophoblast, PREGNANCY, IMPLANTATION, Cell biology, Interferon tau, Endocrinology, medicine.anatomical_structure, Gene Expression Regulation, embryon, Interferon Type I, Cattle, Female, Subcellular Fractions
Abstract

At implantation the endometrium undergoes modifications necessary for its physical interactions with the trophoblast as well as the development of the conceptus. We aim to identify endometrial factors and pathways essential for a successful implantation in the caruncular (C) and the intercaruncular (IC) areas in cattle. Using a 13,257-element bovine oligonucleotide array, we established expression profiles at day 20 of the estrous cycle or pregnancy (implantation), revealing 446 and 1,295 differentially expressed genes (DEG) in C and IC areas, respectively (false discovery rate = 0.08). The impact of the conceptus was higher on the immune response function in C but more prominent on the regulation of metabolism function in IC. The C vs. IC direct comparison revealed 1,177 and 453 DEG in cyclic and pregnant animals respectively (false discovery rate = 0.05), with a major impact of the conceptus on metabolism and cell adhesion. We selected 15 genes including C11ORF34, CXCL12, CXCR4, PLAC8, SCARA5, and NPY and confirmed their differential expression by quantitative RT-PCR. The cellular localization was analyzed by in situ hybridization and, upon pregnancy, showed gene-specific patterns of cell distribution, including a high level of expression in the luminal epithelium for C11ORF34 and MX1. Using primary cultures of bovine endometrial cells, we identified PTN, PLAC8, and CXCL12 as interferon-τ (IFNT) target genes and MSX1 and CXCR7 as IFNT-regulated genes, whereas C11ORF34 was not an IFNT-regulated gene. Our transcriptomic data provide novel molecular insights accounting for the biological functions related to the C or IC endometrial areas and may contribute to the identification of potential biomarkers for normal and perturbed early pregnancy.

Published
2009
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40. Normalization for triple-target microarray experiments

Author

Frédéric Magniette, Julie Aubert, Jean-Jacques Daudin, Marie Laure Martin-Magniette, Avner Bar-Hen, Samira Elftieh, Jean-Pierre Renou, Mathématiques et Informatique Appliquées (MIA-Paris), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Unité de recherche en génomique végétale (URGV), Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), Laboratoire Leprince-Ringuet (LLR), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Unité MOY300, Délégation CNRS, Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Unité de recherche en génomique végétale ( URGV ), Institut National de la Recherche Agronomique ( INRA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -Centre National de la Recherche Scientifique ( CNRS ), Mathématiques et Informatique Appliquées ( MIA-Paris ), Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech, Mathématiques Appliquées à Paris 5 ( MAP5 - UMR 8145 ), Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National des Sciences Mathématiques et de leurs Interactions-Centre National de la Recherche Scientifique ( CNRS ), Unité de Recherche en Genomique Végétale, Institut National de la Recherche Agronomique ( INRA ), Structure tissulaire et intramoléculaire ( STIM ), Unité de Recherche en Génomique Végétale - INRA ( URGV ), Model selection in statistical learning ( SELECT ), Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Laboratoire de Mathématiques d'Orsay ( LMO ), Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Centre National de la Recherche Scientifique ( CNRS ), Martin-Magniette, Marie-Laure, Mathématiques Appliquées Paris 5 (MAP5 - UMR 8145), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Mathématiques et de leurs Interactions (INSMI)-Université Paris Descartes - Paris 5 (UPD5), Structure tissulaire et intramoléculaire (STIM), Institut National de la Recherche Agronomique (INRA), Model selection in statistical learning (SELECT), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire de Mathématiques d'Orsay (LMO), Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Université Paris Descartes - Paris 5 (UPD5)-Institut National des Sciences Mathématiques et de leurs Interactions (INSMI)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Mathématiques d'Orsay (LMO), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS)-Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), and Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Inria Saclay - Ile de France

Subjects
arabidopsis, genetics, calibration, carbocyanines, analysis, fluorescent dyes analysis, gene expression profiling methods, microarray, plant, information storage and retrieval, organic chemicals analysis, reference standards, reproducibility of results, sensitivity and specificity, sequence analysis, dna, génétique, analyse, Biochemistry, normalisation, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], Structural Biology, False positive paradox, échantillon, Organic Chemicals, [ SDV.BIBS ] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], lcsh:QH301-705.5, Oligonucleotide Array Sequence Analysis, 0303 health sciences, Applied Mathematics, Design of experiments, 030305 genetics & heredity, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [ STAT.TH ] Statistics [stat]/Statistics Theory [stat.TH], expérience, Computer Science Applications, méthode, puce à adn, lcsh:R858-859.7, Bio-informatique, DNA microarray, Artifacts, Research Article, Normalization (statistics), Scanner, Channel (digital image), Bioinformatics, Biology, lcsh:Computer applications to medicine. Medical informatics, Genes, Plant, Statistical power, 03 medical and health sciences, [ INFO.INFO-BI ] Computer Science [cs]/Bioinformatics [q-bio.QM], Calibration, Statistiques (Mathématiques), [ MATH.MATH-ST ] Mathematics [math]/Statistics [math.ST], Molecular Biology, Fluorescent Dyes, 030304 developmental biology, business.industry, Gene Expression Profiling, gène, Pattern recognition, Sequence Analysis, DNA, [STAT.TH]Statistics [stat]/Statistics Theory [stat.TH], Molecular biology, lcsh:Biology (General), analyse par biopuce, Artificial intelligence, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], business, hybridation
Abstract

Background Most microarray studies are made using labelling with one or two dyes which allows the hybridization of one or two samples on the same slide. In such experiments, the most frequently used dyes are Cy3 and Cy5. Recent improvements in the technology (dye-labelling, scanner and, image analysis) allow hybridization up to four samples simultaneously. The two additional dyes are Alexa488 and Alexa494. The triple-target or four-target technology is very promising, since it allows more flexibility in the design of experiments, an increase in the statistical power when comparing gene expressions induced by different conditions and a scaled down number of slides. However, there have been few methods proposed for statistical analysis of such data. Moreover the lowess correction of the global dye effect is available for only two-color experiments, and even if its application can be derived, it does not allow simultaneous correction of the raw data. Results We propose a two-step normalization procedure for triple-target experiments. First the dye bleeding is evaluated and corrected if necessary. Then the signal in each channel is normalized using a generalized lowess procedure to correct a global dye bias. The normalization procedure is validated using triple-self experiments and by comparing the results of triple-target and two-color experiments. Although the focus is on triple-target microarrays, the proposed method can be used to normalize p differently labelled targets co-hybridized on a same array, for any value of p greater than 2. Conclusion The proposed normalization procedure is effective: the technical biases are reduced, the number of false positives is under control in the analysis of differentially expressed genes, and the triple-target experiments are more powerful than the corresponding two-color experiments. There is room for improving the microarray experiments by simultaneously hybridizing more than two samples.

Published
2008
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41. Impact du conceptus sur le transcriptome de l’endomètre bovin à l’implantation

Author

Olivier Sandra, Nadera Mansouri, Julie Aubert, Pierrette Reinaud, Corinne Giraud-Delville, Laurent GALIO, Severine Degrelle, Isabelle Hue, Yvan Heyman, Everts, R., Christophe Richard, Daniel Krauss, Yang, J., Lewin, H. A., Jean Paul Renard, Biologie du développement et reproduction (BDR), Centre National de la Recherche Scientifique (CNRS)-École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), Mathématiques et Informatique Appliquées (MIA-Paris), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Unité de recherche génomique et physiologie de la lactation (GPL), Institut National de la Recherche Agronomique (INRA), Department of Animal Sciences, University of Illinois System, Unité Commune d'Expérimentation Animale de Bressonvilliers (UCEA), Domaine expérimental Bourges-La Sapinière (BOURGES), Department of Animal Science, Center for Regenerative Biology, University of Connecticut (UCONN), Biologie du Développement et Reproduction (BDR), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Génomique et Physiologie de la Lactation (GPL), and Unité commune d'expérimentation animale de Bressonvilliers

Subjects
bovin, gestation, Implantation embryonnaire, [SDV]Life Sciences [q-bio], Marqueur, endomètre, transcriptome, métabolisme
Abstract

Chez les bovins, la période péri-implantatoire est une étape critique, associée à l’essentiel des échecs de gestation. L’objectif principal de ce projet vise à identifier des facteurs endométriaux cruciaux lors de l’implantation. A partir d’endomètres bovins (vingt jours de cycle ou de gestation) et de puces bovines de 13300 oligonucléotides, les profils d’expression génique montrent que la gestation affecte le transcriptome endométrial avec un impact majeur sur la croissance et la différenciation cellulaire, la réponse immunitaire ou le métabolisme. Les niveaux d’expression d’une sélection de gènes ont été confirmés par qRT-PCR, leurs localisations cellulaires analysées par hybridation in situ. La régulation directe par l’IFNtau des gènes sélectionnés a été établie à l’aide de cultures primaires endométriales. Nos données peuvent contribuer à identifier de nouveaux facteurs présentant un intérêt potentiel comme marqueurs de la gestation précoce., In cattle, peri-implantation is a critical step associated to the highest rate of pregnancy failures. Our project aims at identifying endometrial factors that play crucial functions at implantation. Using a bovine microarray (13330 oligonucleotides) dedicated to the study of pregnancy, expression profiles of the endometrium were established at day 20 of the oestrous cycle or pregnancy. Pregnancy deeply affects various biological functions in the endometrium including “cell growth and differentiation”, “immune response” or “metabolism”. Twenty genes were selected and their differential expressions were confirmed by quantitative RT-PCR, their cellular localisations were analysed by in situ hybridisation, and the direct regulation by IFNtau was established using primary cultures of bovine endometrial cells. Our data may contribute to identify new genes as potential biological markers for early pregnancy.

Published
2008

42. Analysis of gene expression profiles in the ruminant endometrium using a 13K microarray

Author

Nadera Mansouri, Olivier Sandra, Julie Aubert, Everts, R., Laurent GALIO, Yvan Heyman, Daniel Krauss, Severine Degrelle, Isabelle Hue, Yang, X., Lewin, H. A., Jean Paul Renard, Biologie du Développement et Reproduction (BDR), Institut National de la Recherche Agronomique (INRA), European Network of Excellence 'EMBryo Implantation Control' (EMBIC), Mathématiques et Informatique Appliquées (MIA-Paris), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, University of Illinois System, Génomique et Physiologie de la Lactation (GPL), Domaine expérimental Bourges-La Sapinière (BOURGES), University of Connecticut (UCONN), Biologie du développement et reproduction (BDR), Centre National de la Recherche Scientifique (CNRS)-École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), AgroParisTech-Institut National de la Recherche Agronomique (INRA), and Unité de recherche génomique et physiologie de la lactation (GPL)

Subjects
animal structures, [SDV]Life Sciences [q-bio], embryonic structures, education, GENETIQUE, human activities, health care economics and organizations
Abstract

Poster Session 5: Embryo-maternal crosstalk; absent

Published
2007

43. Gene expression profiles in endometrium of cyclic and pregnant cows during the peri-implantation period

Author

Nadera Mansouri, Laurent GALIO, Isabelle Hue, Severine Degrelle, Xavier Vignon, Christophe Richard, Jean Paul Renard, Olivier Sandra, Carine Bigorne, Julie Aubert, Everts, Robin E., Harris Lewin, Yang, J., Biologie du Développement et Reproduction (BDR), Institut National de la Recherche Agronomique (INRA), Génomique et Physiologie de la Lactation (GPL), Unité Commune d'Expérimentation Animale de Bressonvilliers (UCEA), Mathématiques et Informatique Appliquées (MIA-Paris), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, University of Illinois System, University of Connecticut (UCONN), Biologie du développement et reproduction (BDR), Centre National de la Recherche Scientifique (CNRS)-École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), Unité de recherche génomique et physiologie de la lactation (GPL), and AgroParisTech-Institut National de la Recherche Agronomique (INRA)

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

absent

Published
2007

44. Classification of human chromosome 21 gene-expression variations in down syndrome: Impact on disease phenotypes

Author

Henri Bléhaut, L. Personnaz, Jean M. Delabar, G. Golfier, E. Aït Yahya-Graison, Luce Dauphinot, Jean Rossier, Marguerite Prieur, Isabelle Rivals, M.-C. Potier, Nicole Créau, Julie Aubert, Stéphane Robin, UMR7637, Centre National de la Recherche Scientifique (CNRS), Ecole Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI ParisTech), Université Paris Diderot - Paris 7 (UPD7), Mathématiques et Informatique Appliquées (MIA-Paris), AgroParisTech-Institut National de la Recherche Agronomique (INRA), CHU Necker - Enfants Malades [AP-HP], Institut Jérôme Lejeune, Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL), and Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)

Subjects
Male, Down syndrome, Transcription, Genetic, Chromosomes, Human, Pair 21, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Aneuploidy, Gene Expression, Biology, PHENOTYPE, Article, 03 medical and health sciences, Chromosome 15, 0302 clinical medicine, HUMAN CHROMOSOME 21, DOWN SYNDROME, medicine, Genetics, Humans, Genetics(clinical), Gene, Genetics (clinical), 030304 developmental biology, Oligonucleotide Array Sequence Analysis, GENE-EXPRESSION, 0303 health sciences, Base Sequence, Microarray analysis techniques, Genetic Variation, medicine.disease, Phenotype, Molecular biology, GENE, 3. Good health, Female, Trisomy, Chromosome 21, 030217 neurology & neurosurgery
Abstract

Down syndrome caused by chromosome 21 trisomy is the most common genetic cause of mental retardation in humans. Disruption of the phenotype is thought to be the result of gene-dosage imbalance. Variations in chromosome 21 gene expression in Down syndrome were analyzed in lymphoblastoid cells derived from patients and control individuals. Of the 359 genes and predictions displayed on a specifically designed high-content chromosome 21 microarray, one-third were expressed in lymphoblastoid cells. We performed a mixed-model analysis of variance to find genes that are differentially expressed in Down syndrome independent of sex and interindividual variations. In addition, we identified genes with variations between Down syndrome and control samples that were significantly different from the gene-dosage effect (1.5). Microarray data were validated by quantitative polymerase chain reaction. We found that 29% of the expressed chromosome 21 transcripts are overexpressed in Down syndrome and correspond to either genes or open reading frames. Among these, 22% are increased proportional to the gene-dosage effect, and 7% are amplified. The other 71% of expressed sequences are either compensated (56%, with a large proportion of predicted genes and antisense transcripts) or highly variable among individuals (15%). Thus, most of the chromosome 21 transcripts are compensated for the gene-dosage effect. Overexpressed genes are likely to be involved in the Down syndrome phenotype, in contrast to the compensated genes. Highly variable genes could account for phenotypic variations observed in patients. Finally, we show that alternative transcripts belonging to the same gene are similarly regulated in Down syndrome but sense and antisense transcripts are not.

Published
2007
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45. Profiling at mRNA, protein and metabolite level reveals alterations in renal amino acid handling and glutathione metabolism in kidney tissue of Pept2-I- mice

Author

Daniela Sailer, Isabelle M. Frey, Isabel Rubio-Aliaga, Anne Siewert, Oliver Fiehn, Julie Aubert, Aleksey Drobyshev, Avner Bar Hen, Hans M. Eichinger, Hannelore Daniel, Johannes Beckers, Martin Hrabé de Angelis, Molecular Nutrition Unit, Technical University of Munich (TUM), Institute of Experimental Genetics, GSF-National Research Center for Environment and Health, Mathématiques et Informatique Appliquées (MIA-Paris), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, University of California [Davis] (UC Davis), University of California, Laboratory of Bioanalysis, Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), and AgroParisTech-Institut National de la Recherche Agronomique (INRA)

Subjects
Proteomics, Physiology, Metabolite, analyse, Biology, Kidney, Models, Biological, 03 medical and health sciences, chemistry.chemical_compound, Mice, 0302 clinical medicine, Genetics, medicine, Animals, Electrophoresis, Gel, Two-Dimensional, RNA, Messenger, Amino Acids, Integral membrane protein, métabolisme, 030304 developmental biology, Oligonucleotide Array Sequence Analysis, chemistry.chemical_classification, Mice, Knockout, 0303 health sciences, Messenger RNA, [SDV.GEN]Life Sciences [q-bio]/Genetics, Symporters, Gene Expression Profiling, Transporter, peptide transport, Dipeptides, glutathione metabolism, Apical membrane, Molecular biology, Glutathione, Amino acid, pathway analysis, Mice, Inbred C57BL, medicine.anatomical_structure, chemistry, Biochemistry, Peptide transport, protéine, 030220 oncology & carcinogenesis, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, pept2
Abstract

PEPT2 is an integral membrane protein in the apical membrane of renal epithelial cells that operates as a rheogenic transporter for di- and tripeptides and structurally related drugs. Its prime role is thought to be the reabsorption of filtered di- and tripeptides contributing to amino acid homeostasis. To elucidate the role of PEPT2 in renal amino acid metabolism we submitted kidney tissues of wild-type and a Pept2−/−mouse line to a comprehensive transcriptome, proteome and metabolome profiling and analyzed urinary amino acids and dipeptides. cDNA microarray analysis identified 147 differentially expressed transcripts in transporter-deficient animals, and proteome analysis by 2D-PAGE and MALDI-TOF-MS identified 37 differentially expressed proteins. Metabolite profiling by GC-MS revealed predominantly altered concentrations of amino acids and derivatives. Urinary excretion of amino acids demonstrated increased glycine and cysteine/cystine concentrations and dipeptides in urine were assessed by amino acid analysis of urine samples before and after in vitro dipeptidase digestion. Dipeptides constituted a noticeable fraction of urinary amino acids in Pept2−/−animals, only, and dipeptide-bound glycine and cystine were selectively increased in Pept2−/−urine samples. These findings were confirmed by a drastically increased excretion of cysteinyl-glycine (cys-gly). Urinary loss of cys-gly together with lower concentrations of cysteine, glycine, and oxoproline in kidney tissue and altered expression of mRNA and proteins involved in glutathione (GSH) metabolism suggests that PEPT2 is predominantly a system for reabsorption of cys-gly originating from GSH break-down, thus contributing to resynthesis of GSH.

Published
2007
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46. Correction: Determination of the differentially expressed genes in microarray experiments using local FDR

Author

Jean-Jacques Daudin, Avner Bar-Hen, Julie Aubert, and Stéphane Robin

Subjects
Microarray, business.industry, Computer science, Applied Mathematics, Correction, lcsh:Computer applications to medicine. Medical informatics, Mixture model, computer.software_genre, Biochemistry, Computer Science Applications, Differentially expressed genes, Text mining, lcsh:Biology (General), Structural Biology, lcsh:R858-859.7, Data mining, DNA microarray, business, lcsh:QH301-705.5, Molecular Biology, computer
Abstract

Following publication of this work [1], the authors became aware that Local FDR has been originally defined by Efron & al. (2001) in a mixture model framework [2].

Published
2005

47. How LAB can cooperate to improve soy juice fermentation?

Author

Stéphanie-Marie Deutsch, Olivier Harlé, Jérôme Niay, Florence Valence-Bertel, Sandrine Parayre, Julie Aubert, Marie-Bernadette Maillard, Gwenaele Henry, Anne Thierry, Eric Guedon, Hélène Falentin, Science et Technologie du Lait et de l'Oeuf (STLO), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-AGROCAMPUS OUEST, 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), Laiteries H. Triballat, Partenaires INRAE, Triballat Noyal, AgroParisTech, Fred van de Velde (NIZO, and chair) René Floris (NIZO) John Giezen (NIZO) Marie-Claire Morley (Elsevier)

Subjects
[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, positive interactions, dual transcriptomics, food and beverages, lactic fermentation, cooperation, soy juice, metabolomics, redox potential
Abstract

International audience; Lactic acid bacteria (LAB) are largely used in coculture in food fermentations. The use of different LAB species or strains as starter can bring complementary functionalities participating to the overall quality of fermented food. Fermentation can benefit from LAB’s interactions, resulting in a more efficient fermentation. Few is known about positive LAB’s interactions that are beneficial to fermentation processes. Lactobacillus delbrueckii CIRM-BIA865 (Ld865) and Lactiplantibacillus plantarum CIRM-BIA777 (Lp777) are two strains able to ferment soy juice (SJ). In SJ monocultures, Ld865 was obligately homolactic and released 17 amino acids while Lp777 was facultatively heterofermentative and consumed 10 of the 17 amino acids released by Lp777. When these strains were cocultivated in SJ, the fermentation time was reduced of 30% compared to monocultures. Furthermore, Ld865 cells were four times shorter in coculture than in monoculture and Ld865 population increased tenfold. In this work, we aimed to reveal how Lp777 and Ld865 interact with each other to improve SJ fermentation. Thanks to transcriptomic and metabolic analyses carried out along the kinetic of fermentation, we compared the adaptations of their metabolisms in coculture versus in monoculture. Transcriptomics data showed, among others, that Lp777 induced the expression of genes involved in the regulation of oxidation-reduction potential at a higher level in coculture than in monoculture. The oxidation-reduction potential measured in cocultured SJ was intermediate between those measured in monocultures. The better regulation of the oxidation-reduction potential in coculture seems to involve methionine released by Ld865. Lp777 and Ld865 could also cooperate to metabolize carbon. In conclusion, LABs with distinct and complementary metabolic profiles can be useful to take over SJ fermentation. This work opens new avenues for strains selection intended to cooperate in plant-based fermentation. Several examples of positive LAB’s interactions that are beneficial in SJ fermentation will be provided during this communication.

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