Search

Your search keyword '"Piégu, Benoît"' showing total 172 results
Start Over Author "Piégu, Benoît"
172 results on '"Piégu, Benoît"'

1. Effect of the social environment on olfaction and social skills in WT and mouse model of autism

Author

Gora, Caroline, Dudas, Ana, Court, Lucas, Annamneedi, Anil, Lefort, Gaëlle, Picoreti-Nakahara, Thiago-Seike, Azzopardi, Nicolas, Acquistapace, Adrien, Lainé, Anne-Lyse, Trouillet, Anne-Charlotte, Drobecq, Lucile, Pecnard, Emmanuel, Piegu, Benoit, Crépieux, Pascale, Chamero, Pablo, and Pellissier, Lucie P.

Subjects
Quantitative Biology - Neurons and Cognition, Physics - Physics and Society
Abstract

Autism spectrum disorders are complex, polygenic and heterogenous neurodevelopmental conditions, imposing a substantial economic burden. Genetics are influenced by the environment, specifically the social experience during the critical neurodevelopmental period. Despite efficacy of early behavior interventions targeted specific behaviors in some autistic children, there is no sustainable treatment for the two core symptoms: deficits in social interaction and communication, and stereotyped or restrained behaviors or interests. In this study, we investigated the impact of the social environment on both wild-type (WT) and Shank3 knockout (KO) mice, a mouse model that reproduces core autism-like symptoms. Our findings revealed that WT mice raised in an enriched social environment maintained social interest towards new conspecifics across multiple trials. Additionally, we observed that 2 hours or chronic social isolation induced social deficits or enhanced social interaction and olfactory neuron responses in WT animals, respectively. Notably, chronic social isolation restored both social novelty and olfactory deficits, and normalized self-grooming behavior in Shank3 KO mice. These results novel insights for the implementation of behavioral intervention and inclusive classrooms programs for children with ASD.

Published
2023

2. CoNIC Challenge: Pushing the Frontiers of Nuclear Detection, Segmentation, Classification and Counting

Author

Graham, Simon, Vu, Quoc Dang, Jahanifar, Mostafa, Weigert, Martin, Schmidt, Uwe, Zhang, Wenhua, Zhang, Jun, Yang, Sen, Xiang, Jinxi, Wang, Xiyue, Rumberger, Josef Lorenz, Baumann, Elias, Hirsch, Peter, Liu, Lihao, Hong, Chenyang, Aviles-Rivero, Angelica I., Jain, Ayushi, Ahn, Heeyoung, Hong, Yiyu, Azzuni, Hussam, Xu, Min, Yaqub, Mohammad, Blache, Marie-Claire, Piégu, Benoît, Vernay, Bertrand, Scherr, Tim, Böhland, Moritz, Löffler, Katharina, Li, Jiachen, Ying, Weiqin, Wang, Chixin, Kainmueller, Dagmar, Schönlieb, Carola-Bibiane, Liu, Shuolin, Talsania, Dhairya, Meda, Yughender, Mishra, Prakash, Ridzuan, Muhammad, Neumann, Oliver, Schilling, Marcel P., Reischl, Markus, Mikut, Ralf, Huang, Banban, Chien, Hsiang-Chin, Wang, Ching-Ping, Lee, Chia-Yen, Lin, Hong-Kun, Liu, Zaiyi, Pan, Xipeng, Han, Chu, Cheng, Jijun, Dawood, Muhammad, Deshpande, Srijay, Bashir, Raja Muhammad Saad, Shephard, Adam, Costa, Pedro, Nunes, João D., Campilho, Aurélio, Cardoso, Jaime S., S, Hrishikesh P, Puthussery, Densen, G, Devika R, C V, Jiji, Zhang, Ye, Fang, Zijie, Lin, Zhifan, Zhang, Yongbing, Lin, Chunhui, Zhang, Liukun, Mao, Lijian, Wu, Min, Vo, Vi Thi-Tuong, Kim, Soo-Hyung, Lee, Taebum, Kondo, Satoshi, Kasai, Satoshi, Dumbhare, Pranay, Phuse, Vedant, Dubey, Yash, Jamthikar, Ankush, Vuong, Trinh Thi Le, Kwak, Jin Tae, Ziaei, Dorsa, Jung, Hyun, Miao, Tianyi, Snead, David, Raza, Shan E Ahmed, Minhas, Fayyaz, and Rajpoot, Nasir M.

Subjects
Computer Science - Computer Vision and Pattern Recognition, Computer Science - Machine Learning
Abstract

Nuclear detection, segmentation and morphometric profiling are essential in helping us further understand the relationship between histology and patient outcome. To drive innovation in this area, we setup a community-wide challenge using the largest available dataset of its kind to assess nuclear segmentation and cellular composition. Our challenge, named CoNIC, stimulated the development of reproducible algorithms for cellular recognition with real-time result inspection on public leaderboards. We conducted an extensive post-challenge analysis based on the top-performing models using 1,658 whole-slide images of colon tissue. With around 700 million detected nuclei per model, associated features were used for dysplasia grading and survival analysis, where we demonstrated that the challenge's improvement over the previous state-of-the-art led to significant boosts in downstream performance. Our findings also suggest that eosinophils and neutrophils play an important role in the tumour microevironment. We release challenge models and WSI-level results to foster the development of further methods for biomarker discovery.

Published
2023

3. Chronic dietary exposure to a glyphosate-based herbicide alters ovarian functions in young female broilers

Author

Freville Mathias, Estienne Anthony, Ramé Christelle, Lefort Gaëlle, Piégu Benoît, Chahnamian Marine, Froment Pascal, and Dupont Joëlle

Subjects
glyphosate, young broiler, food intake, ovary, transcriptomic approach, Animal culture, SF1-1100
Abstract

ABSTRACT: Glyphosate (GLY)-based herbicide (GBH) formulations are widely used pesticides in agriculture. The European Union recently decided to extend the use of GLY in Europe until 2034. Previously, we showed that chronic dietary GBH exposure in adult hens resulted in a reversible increase in early mortality in chicken embryos. In this present study, we investigated the GBH effects on metabolism and ovarian functions by using a transcriptomic approach in vivo in young female broilers and in vitro in ovarian explant cultures. We exposed 11-day-old female broilers to 13 mg GLY equivalent/kg body weight/d (GBH13, n = 20), 34 mg GLY equivalent/kg body weight/d (GBH34, n = 20), or a standard diet (control [CT], n = 20) for 25 d. These 2 GBH concentrations correspond to approximatively one-eighth and one-third of the no observed adverse effect level (NOAEL) as defined by European Food Safety Authority in birds. During this period, we evaluated body weight, fattening, food intake, and the weight of organs (including the ovaries). Chronic dietary GBH exposure dose dependently reduced food intake, body weight, and fattening, but increased oxidative stress and relative ovary weight. We analyzed the ovarian gene expression profile in CT, GBH13, and GBH34 broilers with RNA sequencing and showed that differentially expressed genes are mainly enriched in pathways related to cholesterol metabolism, steroidogenesis, and RNA processing. With quantitative polymerase chain reaction and western blotting, we confirmed that GBH decreased ovarian STAR and CYP19A1 messenger RNA and protein expression, respectively. Furthermore, we confirmed that GBH altered steroid production in ovarian explants. We have identified potential regulatory networks associated with GBH. These data provide valuable support for understanding the ovarian transcriptional regulatory mechanism of GBH in growing broilers.

Published
2024
Full Text
View/download PDF

5. CoNIC Challenge: Pushing the frontiers of nuclear detection, segmentation, classification and counting

Author

Graham, Simon, Vu, Quoc Dang, Jahanifar, Mostafa, Weigert, Martin, Schmidt, Uwe, Zhang, Wenhua, Zhang, Jun, Yang, Sen, Xiang, Jinxi, Wang, Xiyue, Rumberger, Josef Lorenz, Baumann, Elias, Hirsch, Peter, Liu, Lihao, Hong, Chenyang, Aviles-Rivero, Angelica I., Jain, Ayushi, Ahn, Heeyoung, Hong, Yiyu, Azzuni, Hussam, Xu, Min, Yaqub, Mohammad, Blache, Marie-Claire, Piégu, Benoît, Vernay, Bertrand, Scherr, Tim, Böhland, Moritz, Löffler, Katharina, Li, Jiachen, Ying, Weiqin, Wang, Chixin, Snead, David, Raza, Shan E. Ahmed, Minhas, Fayyaz, and Rajpoot, Nasir M.

Published
2024
Full Text
View/download PDF

11. Facial blushing and feather fluffing are indicators of emotions in domestic fowl (Gallus gallus domesticus).

Author

Arnould, Cécile, Love, Scott A., Piégu, Benoît, Lefort, Gaëlle, Blache, Marie-Claire, Parias, Céline, Soulet, Delphine, Lévy, Frédéric, Nowak, Raymond, Lansade, Léa, and Bertin, Aline

Subjects
EMOTIONS, FEATHERS, FACIAL expression, FOWLING, HENS
Abstract

The study of facial expressions in mammals provided great advances in the identification of their emotions and then in the comprehension of their sentience. So far, this area of research has excluded birds. With a naturalist approach, we analysed facial blushing and feather displays in domestic fowl. Hens were filmed in situations contrasting in emotional valence and arousal level: situations known to indicate calm states (positive valence / low arousal), have rewarding effects (positive valence / high arousal) or induce fear-related behaviour (negative valence / high arousal). Head feather position as well as skin redness of comb, wattles, ear lobes and cheeks varied across these situations. Skin of all four areas was less red in situations with low arousal compared to situations with higher arousal. Furthermore, skin redness of the cheeks and ear lobes also varied depending on the valence of the situation: redness was higher in situations with negative valence compared to situations with positive valence. Feather position also varied with the situations. Feather fluffing was mostly observed in positively valenced situations, except when hens were eating. We conclude that hens have facial displays that reveal their emotions and that blushing is not exclusive to humans. This opens a promising way to explore the emotional lives of birds, which is a critical step when trying to improve poultry welfare. [ABSTRACT FROM AUTHOR]

Published
2024
Full Text
View/download PDF

12. Effect of the social environment on olfaction and social skills in WT and a mouse model of autism

Author

Pellissier, Lucie, primary, Gora, Caroline, additional, Dudas, Ana, additional, Court, Lucas, additional, Annamneedi, Anil, additional, Lefort, Gaëlle, additional, Nakahara, Thiago, additional, Azzopardi, Nicolas, additional, Acquistapace, Adrien, additional, Laine, Anne-Lyse, additional, Trouillet, Anne-Charlotte, additional, Drobecq, Lucile, additional, Pecnard, Emmanuel, additional, Piégu, Benoît, additional, Crepieux, Pascale, additional, and Chamero, Pablo, additional

Published
2024
Full Text
View/download PDF

13. Combined Multiplexed Phage Display, High-Throughput Sequencing, and Functional Assays as a Platform for Identifying Modulatory VHHs Targeting the FSHR

Author

Zehnaker, Anielka, primary, Vallet, Amandine, additional, Gourdon, Juliette, additional, Sarti, Caterina, additional, Jugnarain, Vinesh, additional, Haj Hassan, Maya, additional, Mathias, Laetitia, additional, Gauthier, Camille, additional, Raynaud, Pauline, additional, Boulo, Thomas, additional, Beauclair, Linda, additional, Bigot, Yves, additional, Casarini, Livio, additional, Crépieux, Pascale, additional, Poupon, Anne, additional, Piégu, Benoît, additional, Jean-Alphonse, Frédéric, additional, Bruneau, Gilles, additional, and Reiter, Éric, additional

Published
2023
Full Text
View/download PDF

18. Genetics of the Maize Proteome

Author

de Vienne, Dominique, Damerval, Catherine, Leonardi, Agnès, Bost, Bruno, Piégu, Benoît, Dillmann, Christine, Zivy, Michel, and Gustafson, J. Perry, editor

Published
2000
Full Text
View/download PDF

20. Green Evolution and Dynamic Adaptations Revealed by Genomes of the Marine Picoeukaryotes Micromonas

Author

Worden, Alexandra Z., Lee, Jae-Hyeok, Mock, Thomas, Rouzé, Pierre, Simmons, Melinda P., Aerts, Andrea L., Allen, Andrew E., Cuvelier, Marie L., Derelle, Evelyne, Everett, Meredith V., Foulon, Elodie, Grimwood, Jane, Gundlach, Heidrun, Henrissat, Bernard, Napoli, Carolyn, McDonald, Sarah M., Parker, Micaela S., Rombauts, Stephane, Salamov, Aasf, Von Dassow, Peter, Badger, Jonathan H., Coutinho, Pedro M., Demir, Elif, Dubchak, Inna, Gentemann, Chelle, Eikrem, Wenche, Gready, Jill E., John, Uwe, Lanier, William, Lindquist, Erika A., Lucas, Susan, Mayer, Klaus F. X., Moreau, Herve, Not, Fabrice, Otillar, Robert, Panaud, Olivier, Pangilinan, Jasmyn, Paulsen, Ian, Piegu, Benoit, Poliakov, Aaron, Robbens, Steven, Schmutz, Jeremy, Toulza, Eve, Wyss, Tania, Zelensky, Alexander, Zhou, Kemin, Armbrust, E. Virginia, Bhattacharya, Debashish, Goodenough, Ursula W., Van de Peer, Yves, and Grigoriev, Igor V.

Published
2009
Full Text
View/download PDF

22. Genome Analysis of the Smallest Free-Living Eukaryote Ostreococcus tauri Unveils Many Unique Features

Author

Derelle, Evelyne, Ferraz, Conchita, Rombauts, Stephane, Rouzé, Pierre, Worden, Alexandra Z., Robbens, Steven, Partensky, Frédéric, Degroeve, Sven, Echeynié, Sophie, Cooke, Richard, Saeys, Yvan, Wuyts, Jan, Jabbari, Kamel, Bowler, Chris, Panaud, Olivier, Piégu, Benoît, Ball, Steven G., Ral, Jean-Philippe, Bouget, François-Yves, Piganeau, Gwenael, De Baets, Bernard, Picard, André, Delseny, Michel, Demaille, Jacques, Van de Peer, Yves, and Moreau, Hervé

Published
2006
Full Text
View/download PDF

30. Variations in genome size between wild and domesticated lineages of fowls belonging to the Gallus gallus species

Author

Piégu, Benoît, primary, Arensburger, Peter, additional, Beauclair, Linda, additional, Chabault, Marie, additional, Raynaud, Emilie, additional, Coustham, Vincent, additional, Brard, Sophie, additional, Guizard, Sébastien, additional, Burlot, Thierry, additional, Le Bihan-Duval, Elisabeth, additional, and Bigot, Yves, additional

Published
2020
Full Text
View/download PDF

31. Thermal Manipulation During Embryogenesis Impacts H3K4me3 and H3K27me3 Histone Marks in Chicken Hypothalamus

Author

David, Sarah-Anne, primary, Vitorino Carvalho, Anaïs, additional, Gimonnet, Coralie, additional, Brionne, Aurélien, additional, Hennequet-Antier, Christelle, additional, Piégu, Benoît, additional, Crochet, Sabine, additional, Couroussé, Nathalie, additional, Bordeau, Thierry, additional, Bigot, Yves, additional, Collin, Anne, additional, and Coustham, Vincent, additional

Published
2019
Full Text
View/download PDF

32. Transgenerational analysis of embryonic heat exposure in Japanese quail

Author

Vitorino Carvalho, Anaïs, Gimonnet, Coralie, Hennequet-Antier, Christelle, Piégu, Benoît, Brionne, Aurélien, Crochet, Sabine, Couroussé, Nathalie, Bordeau, Thierry, Lemarchand, Julie, Constantin, Paul, Rouger, R., Calandreau, Ludovic, Pitel, Frederique, Collin, Anne, COUSTHAM, Vincent, Biologie des Oiseaux et Aviculture (BOA), Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, ANR-15-CE02-0009-01, Institut National de la Recherche Agronomique (INRA)-Université de Tours, and Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS)

Subjects
effet transgénérationnel, [SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, adaptation à la chaleur, [SDV]Life Sciences [q-bio], caille japonaise, [INFO]Computer Science [cs], épigénome, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2019

35. Analyse bioinformatique des modifications post-traductionnelles des histones chez le poulet thermomanipulé durant l'embryogenèse

Author

Gimonnet, Coralie, David, Sarah-Anne, Vitorino Carvalho, Anais, Piégu, Benoît, Hennequet-Antier, Christelle, Brionne, Aurélien, Bigot, Yves, Collin, Anne, COUSTHAM, Vincent, Biologie des Oiseaux et Aviculture (BOA), Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), INRA PHASE, Financement INRA sur crédit incitatif « Stressepimark » (2015), Institut National de la Recherche Agronomique (INRA)-Université de Tours, and Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS)

Subjects
stress thermique, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, poulet, embryogénèse, histone, Sciences agricoles, ComputingMilieux_MISCELLANEOUS, Agricultural sciences, embryon de poulet
Abstract

National audience

Published
2018

37. Identification of precursor transcripts for 6 novel miRNAs expands the diversity on the genomic organisation and expression of miRNA genes in rice

Author

Panaud Olivier, Brice Claire, Cao Xiaofeng, Hirsch Judith, Brugidou Christophe, Guiderdoni Emmanuel, Breitler Jean-Christophe, Bangratz Martine, Piégu Benoît, Duval David, Santi Carole, Nagasaki Hiroshi, Lacombe Séverine, Karlowski Wojciech M, Sato Yutaka, and Echeverria Manuel

Subjects
Botany, QK1-989
Abstract

Abstract Background The plant miRNAs represent an important class of endogenous small RNAs that guide cleavage of an mRNA target or repress its translation to control development and adaptation to stresses. MiRNAs are nuclear-encoded genes transcribed by RNA polymerase II, producing a primary precursor that is subsequently processed by DCL1 an RNase III Dicer-like protein. In rice hundreds of miRNAs have been described or predicted, but little is known on their genes and precursors which are important criteria to distinguish them from siRNAs. Here we develop a combination of experimental approaches to detect novel miRNAs in rice, identify their precursor transcripts and genes and predict or validate their mRNA targets. Results We produced four cDNA libraries from small RNA fractions extracted from distinct rice tissues. By in silico analysis we selected 6 potential novel miRNAs, and confirmed that their expression requires OsDCL1. We predicted their targets and used 5'RACE to validate cleavage for three of them, targeting a PPR, an SPX domain protein and a GT-like transcription factor respectively. In addition, we identified precursor transcripts for the 6 miRNAs expressed in rice, showing that these precursors can be efficiently processed using a transient expression assay in transfected Nicotiana benthamiana leaves. Most interestingly, we describe two precursors producing tandem miRNAs, but in distinct arrays. We focus on one of them encoding osa-miR159a.2, a novel miRNA produced from the same stem-loop structure encoding the conserved osa-miR159a.1. We show that this dual osa-miR159a.2-osa-miR159a.1 structure is conserved in distant rice species and maize. Finally we show that the predicted mRNA target of osa-miR159a.2 encoding a GT-like transcription factor is cleaved in vivo at the expected site. Conclusion The combination of approaches developed here identified six novel miRNAs expressed in rice which can be clearly distinguished from siRNAs. Importantly, we show that two miRNAs can be produced from a single precursor, either from tandem stem-loops or tandemly arrayed in a single stem-loop. This suggests that processing of these precursors could be an important regulatory step to produce one or more functional miRNAs in plants and perhaps coordinate cleavage of distinct targets in the same plant tissue.

Published
2008
Full Text
View/download PDF

38. Impact of embryonic thermal manipulation on quail transcriptome and methylome

Author

Vitorino Carvalho, Anais, Couroussé, Nathalie, Crochet, Sabine, David, Sarah-Anne, Bordeau, Thierry, Godet, Estelle, Piégu, Benoît, Hennequet-Antier, Christelle, Brionne, Aurélien, Noirot, Celine, Bigot, Yves, Pitel, Frederique, Collin, Anne, Coustham, Vincent, Recherches Avicoles (SRA), Institut National de la Recherche Agronomique (INRA), Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Centre National de la Recherche Scientifique (CNRS)-Université de Tours-Institut Français du Cheval et de l'Equitation [Saumur]-Institut National de la Recherche Agronomique (INRA), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Unité de Recherches Avicoles (URA), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), and Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS)

Subjects
thermal manipulation, DNA methylation, epigenetics, méthylation de l'adn, chicken, [SDV]Life Sciences [q-bio], quail, transcriptome, poulet, incubation des oeufs, coturnix japonica, embryogenèse, effet thermique, caille, thermal stimulation, phénotype, épigénétique, stimulation thermique, température, thermal effect
Abstract

Impact of embryonic thermal manipulation on quail transcriptome and methylome. Incubation and Fertility Research Group (IFRG). Fundamental Physiology and Perinatal Development Group (WPSA)

Published
2017

39. Epigenetics for heat tolerance

Author

Collin-Chenot, Anne, David, Sarah-Anne, Pitel, Frederique, Piégu, Benoît, Hennequet-Antier, Christelle, Carvalho, Anais, Loyau, Thomas, Nyuiadzi, Dzidzo, Noirot, Celine, Bigot, Yves, Tona, Jacob Kokou, Coustham, Vincent, Recherches Avicoles (SRA), Institut National de la Recherche Agronomique (INRA), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Centre National de la Recherche Scientifique (CNRS)-Université de Tours-Institut Français du Cheval et de l'Equitation [Saumur]-Institut National de la Recherche Agronomique (INRA), Unité de Recherches Zootechniques (URZ), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), CERSA, Université de Lomé [Togo], Agence Nationale de la Recherche Projets ‘Jeunes Chercheuses et Jeunes Chercheurs’ ANR-09-JCJC-0015-01 THERMOCHICK et ANR-15-CE02-0009 QuailHeatE, INRA Departements PHASE et GA, projets Epitherm et StressEpiMark, métaprogramme INRA Gestion Intégrée de la Santé des Animaux Projet GISA-ROBUSTCHICK (www.gisa.inra.fr/en). PPAAO Togo, Région Centre Val de Loire, MESR, Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Unité de Recherches Avicoles (URA), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), and Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS)

Subjects
épigénétique, [SDV]Life Sciences [q-bio], education, oiseau, food and beverages, élevage, reproductive and urinary physiology, health care economics and organizations, humanities, résistance à la température
Abstract

Epigenetics for heat tolerance. Symposium CERSA Poultry Production under ho and humid climate conditions

Published
2017

40. Etude de l’impact de l’acclimatation embryonnaire à la chaleur du poulet de chair sur des modifications épigénétiques

Author

David, Sarah-Anne, Piégu, Benoît, Hennequet-Antier, Christelle, Bigot, Yves, Bordeau, Thierry, Crochet, Sabine, Couroussé, Nathalie, Beauclair, Linda, Collin-Chenot, Anne, Coustham, Vincent, Recherches Avicoles (SRA), Institut National de la Recherche Agronomique (INRA), Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Centre National de la Recherche Scientifique (CNRS)-Université de Tours-Institut Français du Cheval et de l'Equitation [Saumur]-Institut National de la Recherche Agronomique (INRA), Département INRA PHASE, Région Centre Val-de-Loire, Financement INRA sur crédit incitatif « Stressepimark » (2015), Unité de Recherches Avicoles (URA), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), and ProdInra, Archive Ouverte

Subjects
modification épigénique, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], broilers, [SDV.OT] Life Sciences [q-bio]/Other [q-bio.OT], embryon, séquençage à haut débit, embryo, acclimatation au chaud, bioinformatique, poulet de chair
Abstract

Broilers genetically selected for their performance suffer from heat exposure at slaughter age (D35). In a contextof global warming, it is possible to enhance heat tolerance by heat acclimation during embryogenesis. Thetreatment consists in increasing cyclically the incubation temperature of the eggs during the embryonic days E7to E16. This heat acclimation modifies physiology, metabolism and gene expression in the long term. Thealteration of the early environment can impact gene expression by epigenetic modifications. Therefore the geneexpression variations observed at D35 could be linked to a modification of the epigenome induced by theembryonic treatment, which persists throughout development. Two post-translational modifications could beimplicated, the tri-methylation of lysine 27 on the histone H3 (H3K27me3) involved in epigenetic memory underan environmental stimulus and the tri-methylation of lysine 4 on the histone H3 (H3K4me3) linked to genetranscriptional activation. To study these marks we have adjusted the chromatin immunoprecipitation (ChIP)technique to the hypothalamus, which is the center of thermoregulation. ChIP was followed by high throughputsequencing to study without bias the differentially enriched regions between the controls and the heat acclimatedchicken. Preliminary sequencing results for the hypothalamus will be presented., Les poulets sélectionnés pour leurs performances de croissance sont sensibles aux variations de température. Le traitement d’acclimatation embryonnaire à la chaleur permet de rendre les animaux plus tolérants à la chaleur à l’âge d’abattage (J35). Ce traitement consiste à augmenter de façon cyclique la température d’incubation desoeufs entre les jours E7 et E16 de l’embryogenèse. Il modifie la physiologie, le métabolisme et l’expression desgènes à long terme. L’altération de l’environnement précoce peut avoir un impact à long terme sur l’expressiondes gènes notamment par le biais de modifications épigénétiques. Les modifications d’expression de gènesobservées chez les poulets à J35 pourraient être dues à une altération de l’épigénome induite par le traitementlors de l’embryogenèse et persistant au cours du développement. Nous étudions deux modifications posttraductionnelles des histones, la triméthylation de la lysine 27 sur l’histone H3 (H3K27me3) décrite commeayant un rôle dans la mémoire épigénétique sous l’influence de l’environnement et la triméthylation de la lysine4 sur l’histone H3 (H3K4me3) associée à des gènes transcriptionnellement actifs. Afin de caractériser cesmarques nous avons mis au point la technique d’immuno-précipitation de la chromatine (ChIP) pourl’hypothalamus, centre de la thermorégulation. Le ChIP a été suivi d’un séquençage haut débit afin dedéterminer sans a priori les régions différentiellement enrichies en ces deux marques entre les individus témoinset acclimatés. Les premiers résultats issus du séquençage sur l’hypothalamus seront présentés.

Published
2017

41. Additional file 1: Fig. S1. of An Assessment of Fixed and Native Chromatin Preparation Methods to Study Histone Post-Translational Modifications at a Whole Genome Scale in Skeletal Muscle Tissue

Author

Sarah-Anne David, Piégu, Benoît, Hennequet-Antier, Christelle, Pannetier, Maëlle, Aguirre-Lavin, Tiphaine, Crochet, Sabine, Bordeau, Thierry, Couroussé, Nathalie, Brionne, Aurélien, Bigot, Yves, Collin, Anne, and Coustham, Vincent

Abstract

Setup of chromatin preparation conditions. Table S1. ChIP-qPCR primers. Table S2. Quantity of chromatin and DNA used throughout the protocol. Fig. S2. Quality assessment of the sequencing reads. Fig. S3. Boxplot representing the distribution of the 40 M peaks lengths. Fig. S4. X-ChIP-seq and N-ChIP-seq peaks analysis. Table S3. Broad peak detection analysis by MACS2 for both H3K27me3 X-ChIP-seq and N-ChIP-seq experiments. Fig. S5. Comparison of H3K27me3-enriched peak regions detected by MACS2 and between MACS2 and epic. Supplemental methods X-ChIP-seq protocol for hypothalamus tissue samples. Table S4. Sequencing results of hypothalamus X-ChIP-seq analyzed using epic. Fig. S6. Fragmentation assessment of chromatin before immunoprecipitation for hypothalamus samples and X-ChIP results at three control loci. (PDF 1487 kb)

Published
2017
Full Text
View/download PDF

42. Epigenetics for heat tolerance

Author

David, Sarah-Anne, Pitel, Frederique, Piégu, Benoît, Hennequet-Antier, Christelle, Vitorino Carvalho, Anais, Loyau, Thomas, Nyuiadzi, Dzidzo, Noirot, Celine, Bigot, Yves, Tona, Jacob Kokou, Coustham, Vincent, and Collin, Anne

Subjects
épigénétique, oiseau, élevage, résistance à la température
Published
2017

43. Impact of embryonic heat acclimation on histone post-translational modifications in chicken

Author

David, Sarah-Anne, Piégu, Benoît, Hennequet-Antier, Christelle, Bordeau, Thierry, Crochet, Sabine, Couroussé, Nathalie, Jacques, Aurore, Beauclair, Linda, Bigot, Yves, Collin, Anne, Coustham, Vincent, Unité de Recherches Avicoles (URA), Institut National de la Recherche Agronomique (INRA), Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS), Recherches Avicoles (SRA), Centre National de la Recherche Scientifique (CNRS)-Université de Tours-Institut Français du Cheval et de l'Equitation [Saumur]-Institut National de la Recherche Agronomique (INRA), World's Poultry Science Association (WPSA). INT., Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), and ProdInra, Archive Ouverte

Subjects
[SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], [SDV.GEN]Life Sciences [q-bio]/Genetics, sélection génétique, [SDV.OT] Life Sciences [q-bio]/Other [q-bio.OT], chicken, [SDV]Life Sciences [q-bio], poulet, embryo, embryogénèse, effet thermique, histone, poussin, stress, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, thermotolérance, embryon, altération epigénétique, [INFO]Computer Science [cs], acclimatation au chaud, faune aviaire, ComputingMilieux_MISCELLANEOUS
Abstract

Impact of embryonic heat acclimation on histone post-translational modifications in chicken. 2016 Meeting WPSA "Incubation and Fertility Research Group"

Published
2016

45. Additional file 16: of Deep landscape update of dispersed and tandem repeats in the genome model of the red jungle fowl, Gallus gallus, using a series of de novo investigating tools

Author

Guizard, Sébastien, Piégu, Benoît, Arensburger, Peter, Guillou, Florian, and Bigot, Yves

Abstract

Histograms showing the densities of TEs and TE hot spots in galGal4 chromosomes for the 8 sub-families of CR1 elements. Histograms of TE model density and TE hot spot density were calculated for all galGal4 chromosomes, except chromosome 32 (too small; 1028 bp). (PDF 532 kb)

Published
2016
Full Text
View/download PDF

46. An Assessment of Fixed and Native Chromatin Preparation Methods to Study Histone Post-Translational Modifications at a Whole Genome Scale in Skeletal Muscle Tissue

Author

David, Sarah-Anne, primary, Piégu, Benoît, additional, Hennequet-Antier, Christelle, additional, Pannetier, Maëlle, additional, Aguirre-Lavin, Tiphaine, additional, Crochet, Sabine, additional, Bordeau, Thierry, additional, Couroussé, Nathalie, additional, Brionne, Aurélien, additional, Bigot, Yves, additional, Collin, Anne, additional, and Coustham, Vincent, additional

Published
2017
Full Text
View/download PDF

47. First landscape of binding to chromosomes for a domesticated mariner transposase in the human genome: diversity of genomic targets of SETMAR isoforms in two colorectal cell lines

Author

Antoine-Lorquin, Aymeric, primary, Arnaoty, Ahmed, additional, Asgari, Sassan, additional, Batailler, Martine, additional, Beauclair, Linda, additional, Belleannée, Catherine, additional, Bire, Solenne, additional, Buisine, Nicolas, additional, Coustham, Vincent, additional, Girault, Alban, additional, Guyetant, Serge, additional, Lecomte, Thierry, additional, Piégu, Benoît, additional, Pitard, Bruno, additional, Stévant, Isabelle, additional, and Bigot, Yves, additional

Published
2017
Full Text
View/download PDF

49. An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies

Author

Blanc Mathieu, Romain, Verhelst, Bram, Derelle, Evelyne, Rombauts, Stephane, Bouget, Francois-Yves, Carré, Isabelle, Château, Annie, Eyre Walker, Adam, Grimsley, Nigel, Moreau, Hervé, Piégu, Benoît, Rivals, Eric, Schackwitz, Wendy, Van de Peer, Yves, and Piganeau, Gwenaël

Subjects
Molecular Sequence Data, GREEN LINEAGE, Biotechnologies, organisme modèle, Illumina re-sequencing, Evolution, Molecular, QH301, Chlorophyta, Genetics, TRANSCRIPTION, Picoeukaryote, SH, QH426, EUKARYOTE, micro-algue, Correctness of short reads assembly, genome evolution, domestication of microalgae, plant glutamate receptor, illumina re sequencing, correctness of short reads assembly, picoeukaryote, ostreococcus tauri, algue marine, génome, ALGORITHMS, eucaryote, Biology and Life Sciences, Computational Biology, Genetic Variation, High-Throughput Nucleotide Sequencing, Molecular Sequence Annotation, Genomics, PRASINOPHYCEAE, EVOLUTION, Genome evolution, QR, séquence du génome, BIAS, PICOEUKARYOTE OSTREOCOCCUS, Ostreococcus tauri, Plant glutamate receptor, CHLOROPHYTA, Ostreococcus touri, Domestication of microalgae, Genome, Plant, Autre (Sciences du Vivant), Biotechnology, SACCHAROMYCES, Research Article
Abstract

Background Cost effective next generation sequencing technologies now enable the production of genomic datasets for many novel planktonic eukaryotes, representing an understudied reservoir of genetic diversity. O. tauri is the smallest free-living photosynthetic eukaryote known to date, a coccoid green alga that was first isolated in 1995 in a lagoon by the Mediterranean sea. Its simple features, ease of culture and the sequencing of its 13 Mb haploid nuclear genome have promoted this microalga as a new model organism for cell biology. Here, we investigated the quality of genome assemblies of Illumina GAIIx 75 bp paired-end reads from Ostreococcus tauri, thereby also improving the existing assembly and showing the genome to be stably maintained in culture. Results The 3 assemblers used, ABySS, CLCBio and Velvet, produced 95% complete genomes in 1402 to 2080 scaffolds with a very low rate of misassembly. Reciprocally, these assemblies improved the original genome assembly by filling in 930 gaps. Combined with additional analysis of raw reads and PCR sequencing effort, 1194 gaps have been solved in total adding up to 460 kb of sequence. Mapping of RNAseq Illumina data on this updated genome led to a twofold reduction in the proportion of multi-exon protein coding genes, representing 19% of the total 7699 protein coding genes. The comparison of the DNA extracted in 2001 and 2009 revealed the fixation of 8 single nucleotide substitutions and 2 deletions during the approximately 6000 generations in the lab. The deletions either knocked out or truncated two predicted transmembrane proteins, including a glutamate-receptor like gene. Conclusion High coverage (>80 fold) paired-end Illumina sequencing enables a high quality 95% complete genome assembly of a compact ~13 Mb haploid eukaryote. This genome sequence has remained stable for 6000 generations of lab culture. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1103) contains supplementary material, which is available to authorized users.

Published
2014

Catalog

Books, media, physical & digital resources
See catalog results