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1. Correction: Perinatal foodborne titanium dioxide exposure-mediated dysbiosis predisposes mice to develop colitis through life

Author

Caroline Carlé, Delphine Boucher, Luisa Morelli, Camille Larue, Ekaterina Ovtchinnikova, Louise Battut, Kawthar Boumessid, Melvin Airaud, Muriel Quaranta-Nicaise, Jean-Luc Ravanat, Gilles Dietrich, Sandrine Menard, Gérard Eberl, Nicolas Barnich, Emmanuel Mas, Marie Carriere, Ziad Al Nabhani, and Frédérick Barreau

Subjects
Toxicology. Poisons, RA1190-1270, Industrial hygiene. Industrial welfare, HD7260-7780.8
Published
2024
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2. Perinatal foodborne titanium dioxide exposure-mediated dysbiosis predisposes mice to develop colitis through life

Author

Caroline Carlé, Delphine Boucher, Luisa Morelli, Camille Larue, Ekaterina Ovtchinnikova, Louise Battut, Kawthar Boumessid, Melvin Airaud, Muriel Quaranta-Nicaise, Jean-Luc Ravanat, Gilles Dietrich, Sandrine Menard, Gérard Eberl, Nicolas Barnich, Emmanuel Mas, Marie Carriere, Ziad Al Nabhani, and Frédérick Barreau

Subjects
Perinatal period, Foodborne TiO2, Intestinal barrier function, Intestinal stem cells, Microbiota, Colitis, Toxicology. Poisons, RA1190-1270, Industrial hygiene. Industrial welfare, HD7260-7780.8
Abstract

Abstract Background Perinatal exposure to titanium dioxide (TiO2), as a foodborne particle, may influence the intestinal barrier function and the susceptibility to develop inflammatory bowel diseases (IBD) later in life. Here, we investigate the impact of perinatal foodborne TiO2 exposure on the intestinal mucosal function and the susceptibility to develop IBD-associated colitis. Pregnant and lactating mother mice were exposed to TiO2 until pups weaning and the gut microbiota and intestinal barrier function of their offspring was assessed at day 30 post-birth (weaning) and at adult age (50 days). Epigenetic marks was studied by DNA methylation profile measuring the level of 5-methyl-2′-deoxycytosine (5-Me-dC) in DNA from colic epithelial cells. The susceptibility to develop IBD has been monitored using dextran-sulfate sodium (DSS)-induced colitis model. Germ-free mice were used to define whether microbial transfer influence the mucosal homeostasis and subsequent exacerbation of DSS-induced colitis. Results In pregnant and lactating mice, foodborne TiO2 was able to translocate across the host barriers including gut, placenta and mammary gland to reach embryos and pups, respectively. This passage modified the chemical element composition of foetus, and spleen and liver of mothers and their offspring. We showed that perinatal exposure to TiO2 early in life alters the gut microbiota composition, increases the intestinal epithelial permeability and enhances the colonic cytokines and myosin light chain kinase expression. Moreover, perinatal exposure to TiO2 also modifies the abilities of intestinal stem cells to survive, grow and generate a functional epithelium. Maternal TiO2 exposure increases the susceptibility of offspring mice to develop severe DSS-induced colitis later in life. Finally, transfer of TiO2-induced microbiota dysbiosis to pregnant germ-free mice affects the homeostasis of the intestinal mucosal barrier early in life and confers an increased susceptibility to develop colitis in adult offspring. Conclusions Our findings indicate that foodborne TiO2 consumption during the perinatal period has negative long-lasting consequences on the development of the intestinal mucosal barrier toward higher colitis susceptibility. This demonstrates to which extent environmental factors influence the microbial-host interplay and impact the long-term mucosal homeostasis.

Published
2023
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3. Inflammatory and oxidative status in European captive black rhinoceroses: A link with Iron Overload Disorder?

Author

Hanae Pouillevet, Nicolas Soetart, Delphine Boucher, Rudy Wedlarski, and Laetitia Jaillardon

Subjects
Medicine, Science
Abstract

Iron Overload Disorder (IOD) is a syndrome developed by captive browsing rhinoceroses like black rhinoceroses (Diceros bicornis), in which hemosiderosis develops in vital organs while free iron accumulates in the body, potentially predisposing to various secondary diseases. Captive grazing species like white rhinoceroses (Ceratotherium simum) do not seem to be affected. The authors hypothesized that inflammation and oxidative stress may be implicated in the pathogenesis of IOD in captive black rhinoceroses, making this syndrome a potential common denominator to various diseases described in captivity in this species. In this prospective study, 15 black (BR) and 29 white rhinoceroses (WR) originating from 22 European zoos were blood-sampled and compared for their iron status (serum iron), liver/muscle biochemical parameters (AST, GGT, cholesterol), inflammatory status (total proteins, protein electrophoresis) and oxidative stress markers (SOD, GPX, dROMs). Results showed higher serum iron and liver enzyme levels in black rhinoceroses (P < 0.01), as well as higher dROMs (P < 0.01) and a trend for higher GPX (P = 0.06) levels. The albumin/globulin ratio was lower in black rhinoceroses (P < 0.05) due to higher α2-globulin levels (P < 0.001). The present study suggests a higher inflammatory and oxidative profile in captive BR than in WR, possibly in relation to iron status. This could be either a consequence or a cause of iron accumulation. Further investigations are needed to assess the prognostic value of the inflammatory and oxidative markers in captive black rhinoceroses, particularly for evaluating the impact of reduced-iron and antioxidant-supplemented diets.

Published
2020
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4. Distribution of Dehalococcoidia in the Anaerobic Deep Water of a Remote Meromictic Crater Lake and Detection of Dehalococcoidia-Derived Reductive Dehalogenase Homologous Genes.

Author

Corinne Biderre-Petit, Eric Dugat-Bony, Mickaël Mege, Nicolas Parisot, Lorenz Adrian, Anne Moné, Jérémie Denonfoux, Eric Peyretaillade, Didier Debroas, Delphine Boucher, and Pierre Peyret

Subjects
Medicine, Science
Abstract

Here we describe the natural occurrence of bacteria of the class Dehalococcoidia (DEH) and their diversity at different depths in anoxic waters of a remote meromictic lake (Lake Pavin) using 16S rRNA gene amplicon sequencing and quantitative PCR. Detected DEH are phylogenetically diverse and the majority of 16S rRNA sequences have less than 91% similarity to previously isolated DEH 16S rRNA sequences. To predict the metabolic potential of detected DEH subgroups and to assess if they encode genes to transform halogenated compounds, we enriched DEH-affiliated genomic DNA by using a specific-gene capture method and probes against DEH-derived 16S rRNA genes, reductive dehalogenase genes and known insertion sequences. Two reductive dehalogenase homologous sequences were identified from DEH-enriched genomic DNA, and marker genes in the direct vicinity confirm that gene fragments were derived from DEH. The low sequence similarity with known reductive dehalogenase genes suggests yet-unknown catabolic potential in the anoxic zone of Lake Pavin.

Published
2016
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13. Phage Therapy Against Adherent-invasive E. coli: Towards a Promising Treatment of Crohn’s Disease Patients?

Author

Delphine Boucher, Nicolas Barnich, Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), MESRI [Ministere de l'Enseignement Superieur, de la Recherche et de l'Innovation], INSERM, INRAE, University of Clermont Auvergne (I-SITE project [CAP 2025]), and ANR-16-IDEX-0001,CAP 20-25,CAP 20-25(2016)

Subjects
Mice, Disease Models, Animal, Crohn Disease, Escherichia coli, Gastroenterology, Animals, [SDV.MHEP.HEG]Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology, Bacteriophages, Phage Therapy, General Medicine, Intestinal Mucosa, Colitis
Abstract

International audience

Published
2022

14. Reply to López-Cortés et al

Author

Anne-Gaëlle Leroy, Delphine Boucher, Olivia Peuchant, Pierre Danneels, Fabrice Camou, Stéphane Corvec, Marie Kempf, Raphaël Lecomte, Vincent Dubée, Nahema Issa, and David Boutoille

Subjects
Microbiology (medical), Infectious Diseases, Endocarditis, business.industry, Recurrence, Chronic Disease, Medicine, Humans, business, Humanities
Published
2021

15. An Overview on Skew Constacyclic Codes and their Subclass of LCD Codes

Author

Delphine Boucher, Ranya Djihad Boulanouar, Aicha Batoul, University of Sciences and Technology Houari Boumediene [Alger] (USTHB), Institut de Recherche Mathématique de Rennes (IRMAR), 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)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), ANR-11-LABX-0020,LEBESGUE,Centre de Mathématiques Henri Lebesgue : fondements, interactions, applications et Formation(2011), Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Rennes (ENS Rennes)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Université des Sciences et de la Technologie Houari Boumediene = University of Sciences and Technology Houari Boumediene [Alger] (USTHB), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-INSTITUT AGRO Agrocampus Ouest, 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
Computer Networks and Communications, 0102 computer and information sciences, 02 engineering and technology, Hardware_PERFORMANCEANDRELIABILITY, Characterization (mathematics), 01 natural sciences, Microbiology, Equivalence, Subclass, law.invention, law, 0202 electrical engineering, electronic engineering, information engineering, Hardware_INTEGRATEDCIRCUITS, LCD codes, skew constacyclic codes, Discrete Mathematics and Combinatorics, Equivalence (measure theory), Mathematics, Discrete mathematics, Algebra and Number Theory, Liquid-crystal display, Applied Mathematics, Skew, [MATH.MATH-IT]Mathematics [math]/Information Theory [math.IT], 020206 networking & telecommunications, Skew polynomial rings, Finite field, 010201 computation theory & mathematics, MDS codes
Abstract

International audience; This text is about the derivation of some necessary and sufficient conditions for the equiv-alency between skew constacyclic codes, skew cyclic codes and skew negacyclic codes defined over finite fields. A first characterization of LCD skew constacyclic codes is also given and some constructions of LCD MDS skew cyclic and skew negacyclic codes are derived over F p 2 .

Published
2021

16. Sarilumab in patients admitted to hospital with severe or critical COVID-19: a randomised, double-blind, placebo-controlled, phase 3 trial

Author

François-Xavier Lescure, Hitoshi Honda, Robert A Fowler, Jennifer Sloane Lazar, Genming Shi, Peter Wung, Naimish Patel, Owen Hagino, Ignacio J. Bazzalo, Marcelo M. Casas, Sebastián A. Nuñez, Yael Pere, Carlos M. Ibarrola, Marco A. Solis Aramayo, Maria C. Cuesta, Andrea E. Duarte, Pablo M. Gutierrez Fernandez, Maria A. Iannantuono, Erica A. Miyazaki, Javier P. Silvio, Dario G. Scublinsky, Alessandra Bales, Daniela Catarino, Elie Fiss, Sara Mohrbacher, Victor Sato, Antonio Baylao, Adilson Cavalcante, Francini Correa, Celso A. de Andrade, Juvencio Furtado, Nelson Ribeiro Filho, Valéria Telles, Leopoldo T. Trevelin, Ricardo Vipich, Rodrigo Boldo, Paula Borges, Suzana Lobo, Graziela Luckemeyer, Luana Machado, Maysa B. Alves, Ana C. Iglessias, Marianna M. Lago, Daniel W. Santos, Hugo Chapdelaine, Emilia L. Falcone, Rahima Jamal, Me-Linh Luong, Madeleine Durand, Stephane Doucet, François-Martin Carrier, Bryan A. Coburn, Lorenzo Del Sorbo, Sharon L. Walmsley, Sara Belga, Luke Y. Chen, Allison D. Mah, Theodore Steiner, Alissa J. Wright, J. Hajek, Neill Adhikari, Robert A. Fowler, Nick Daneman, Kosar A. Khwaja, Jason Shahin, Carolina Gonzalez, Rafael Silva, Marcelo Lindh, Gabriel Maluenda, Patricia Fernandez, Maite Oyonarte, Martin Lasso, Alexandre Boyer, Didier Bronnimann, Hoang-Nam Bui, Charles Cazanave, Helene Chaussade, Arnaud Desclaux, Mailys Ducours, Alexandre Duvignaud, Denis Malvy, Lisa Martin, Didier Neau, Duc Nguyen, Thierry Pistone, Gaetane Soubrane-Wirth, Julie Leitao, Clotilde Allavena, Charlotte Biron, Sabelline Bouchez, Benjamin Gaborit, Antoine Gregoire, Paul Le Turnier, Anne-Sophie Lecompte, Raphael Lecomte, Maeva Lefebvre, Francois Raffi, David Boutoille, Pascale H. Morineau, Romain Guéry, Emmanuel Chatelus, Nathalie Dumoussaud, Renaud Felten, Florina Luca, Bernard Goichot, Francis Schneider, Marie-Caroline Taquet, Matthieu Groh, Mathilde Roumier, Mathilde Neuville, Antoine Bachelard, Valentina Isernia, F-Xavier Lescure, Bao-Chau Phung, Anne Rachline, Aurelie Sautereau, Dorothee Vallois, Yves Bleher, Delphine Boucher, Clémentine Coudon, Jean Esnault, Thomas Guimard, Sophie Leautez-Nainville, Dominique Merrien, Marine Morrier, Pauline Motte-Vincent, Romain Gabeff, Hélène Leclerc, Céline Cozic, Romain Decours, Ronan Février, Gwenhael Colin, Sophie Abgrall, Dorothee Vignes, Raluca Sterpu, Mira Kuellmar, Melanie Meersch-Dini, Raphael Weiss, Alexander Zarbock, Christiane Antony, Marc Berger, Thorsten Brenner, Christian Taube, Frank Herbstreit, Sebastian Dolff, Margarethe Konik, Karsten Schmidt, Markus Zettler, Oliver Witzke, Boris Boell, Jorge Garcia Borrega, Philipp Koehler, Thomas Zander, Fabian Dusse, Othman Al-Sawaf, Philipp Köhler, Dennis Eichenauer, Matthias Kochanek, Alexander Shimabukuro-Vornhagen, Sibylle Mellinghoff, Annika Claßen, Jan-Michel Heger, Charlotte Meyer-Schwickerath, Paul Liedgens, Katrin Heindel, Ana Belkin, Asaf Biber, Mayan Gilboa, Itzchak Levy, Vladislav Litachevsky, Galia Rahav, Anat Finesod Wiedner, Tal Zilberman-Daniels, Yonatan Oster, Jacob Strahilevitz, Sigal Sviri, Elena M. Baldissera, Corrado Campochiaro, Giulio Cavalli, Lorenzo Dagna, Giacomo De Luca, Emanuel Della Torre, Alessandro Tomelleri, Davide Bernasconi De Luca, Amedeo F. Capetti, Massimo Coen, Maria V. Cossu, Massimo Galli, Andrea Giacomelli, Guido A. Gubertini, Stefano Rusconi, Giulia J. Burastero, Margherita Digaetano, Giovanni Guaraldi, Marianna Meschiari, Cristina Mussini, Cinzia Puzzolante, Sara Volpi, Marina Aiello, Alarico Ariani, Alfredo A. Chetta, Annalisa Frizzelli, Andrea Ticinesi, Domenico Tuttolomondo, Stefano Aliberti, Francesco B. Blasi, Marta F. Di Pasquale, Sofia Misuraca, Tommaso Pilocane, Edoardo Simonetta, Alessio M. Aghelmo, Claudio Angelini, Enrico Brunetta, Giorgio W. Canonica, Michele Ciccarelli, Sara Dal Farra, Maria De Santis, Sebastian Ferri, Marco Folci, Giacomo M. Guidelli, Enrico M. Heffler, Ferdinando Loiacono, Giacomo Malipiero, Giovanni Paoletti, Rosa Pedale, Francesca A. Puggioni, Francesca Racca, Aurora Zumbo, Morihiko Satou, Tatyana Lisun, Denis Protsenko, Nikolay Rubtsov, Irina Beloglazova, Daria Fomina, Mariana Lysenko, Sofia Serdotetskova, Vitali Firstov, Ivan Gordeev, Ilia Kokorin, Ksenia Komissarova, Nina Lapochkina, Elena Luchinkina, Valentin Malimon, Sevinch Mamedguseyinova, Ksenia Polubatonova, Natalia Suvorova, Jose Arribas, Alberto M. Borobia Perez, Fernando de la Calle Prieto, Juan Carlos Figueira, Rocio Motejano Sanchez, Marta Mora-Rillo, Concepcion Prados Sanchez, Javier Queiruga Parada, Francisco Fernandez Arnalich, Maria Guerro Barrientos, Alejandro Bendala Estrada, Aranzazu Caballero Marcos, Maria E. Garcia Leoni, Rita García-Martínez, Ana María Collado, Patricia Munoz Garcia, Ana Torres do Rego, María V. Villalba García, Almudena Burrillo, Maricela Valerio Minero, Paloma Gijon Vidaurreta, Sonsoles Infante Herrero, Elena Velilla, Marina Machado, Maria Olmedo, Blanca Pinilla, Benito Almirante Gragera, Maria de la Esperanza Cañas Ruano, Sofia Contreras Medina, Alejandro Cortés Herrera, Vicenç Falcó Ferrer, Ricard Ferrer Roca, Xavier Nuvials Casals, Esteve Ribera Pascuet, Paula Suanzes Diez, Pedro Rebollo Castro, Felipe Garcia Alcaide, Alejandro Soriano, Aina Oliver Caldes, Ana González Cordón, Celia Cardozo, Lorena De la Mora Cañizo, Romina Pena López, Sandra Chamorro, Clara Crespillo-Andujar, Rosa Escudero Sanchez, Jesús Fortún-Abete, Begoña Monge-Maillo, Ana Moreno Zamora, Francesca Norman, Matilde Sanchez Conde, Sergio Serrano Villar, Pilar Vizcarra, Lescure, F. -X., Honda, H., Fowler, R. A., Lazar, J. S., Shi, G., Wung, P., Patel, N., Hagino, O., Bazzalo, I. J., Casas, M. M., Nunez, S. A., Pere, Y., Ibarrola, C. M., Solis Aramayo, M. A., Cuesta, M. C., Duarte, A. E., Gutierrez Fernandez, P. M., Iannantuono, M. A., Miyazaki, E. A., Silvio, J. P., Scublinsky, D. G., Bales, A., Catarino, D., Fiss, E., Mohrbacher, S., Sato, V., Baylao, A., Cavalcante, A., Correa, F., de Andrade, C. A., Furtado, J., Ribeiro Filho, N., Telles, V., Trevelin, L. T., Vipich, R., Boldo, R., Borges, P., Lobo, S., Luckemeyer, G., Machado, L., Alves, M. B., Iglessias, A. C., Lago, M. M., Santos, D. W., Chapdelaine, H., Falcone, E. L., Jamal, R., Luong, M. -L., Durand, M., Doucet, S., Carrier, F. -M., Coburn, B. A., Del Sorbo, L., Walmsley, S. L., Belga, S., Chen, L. Y., Mah, A. D., Steiner, T., Wright, A. J., Hajek, J., Adhikari, N., Daneman, N., Khwaja, K. A., Shahin, J., Gonzalez, C., Silva, R., Lindh, M., Maluenda, G., Fernandez, P., Oyonarte, M., Lasso, M., Boyer, A., Bronnimann, D., Bui, H. -N., Cazanave, C., Chaussade, H., Desclaux, A., Ducours, M., Duvignaud, A., Malvy, D., Martin, L., Neau, D., Nguyen, D., Pistone, T., Soubrane-Wirth, G., Leitao, J., Allavena, C., Biron, C., Bouchez, S., Gaborit, B., Gregoire, A., Le Turnier, P., Lecompte, A. -S., Lecomte, R., Lefebvre, M., Raffi, F., Boutoille, D., Morineau, P. H., Guery, R., Chatelus, E., Dumoussaud, N., Felten, R., Luca, F., Goichot, B., Schneider, F., Taquet, M. -C., Groh, M., Roumier, M., Neuville, M., Bachelard, A., Isernia, V., Phung, B. -C., Rachline, A., Sautereau, A., Vallois, D., Bleher, Y., Boucher, D., Coudon, C., Esnault, J., Guimard, T., Leautez-Nainville, S., Merrien, D., Morrier, M., Motte-Vincent, P., Gabeff, R., Leclerc, H., Cozic, C., Decours, R., Fevrier, R., Colin, G., Abgrall, S., Vignes, D., Sterpu, R., Kuellmar, M., Meersch-Dini, M., Weiss, R., Zarbock, A., Antony, C., Berger, M., Brenner, T., Taube, C., Herbstreit, F., Dolff, S., Konik, M., Schmidt, K., Zettler, M., Witzke, O., Boell, B., Garcia Borrega, J., Koehler, P., Zander, T., Dusse, F., Al-Sawaf, O., Kohler, P., Eichenauer, D., Kochanek, M., Shimabukuro-Vornhagen, A., Mellinghoff, S., Classen, A., Heger, J. -M., Meyer-Schwickerath, C., Liedgens, P., Heindel, K., Belkin, A., Biber, A., Gilboa, M., Levy, I., Litachevsky, V., Rahav, G., Finesod Wiedner, A., Zilberman-Daniels, T., Oster, Y., Strahilevitz, J., Sviri, S., Baldissera, E. M., Campochiaro, C., Cavalli, G., Dagna, L., De Luca, Giacomo., Della Torre, E., Tomelleri, A., Bernasconi De Luca, D., Capetti, A. F., Coen, M., Cossu, M. V., Galli, M., Giacomelli, A., Gubertini, G. A., Rusconi, S., Burastero, G. J., Digaetano, M., Guaraldi, G., Meschiari, M., Mussini, C., Puzzolante, C., Volpi, S., Aiello, M., Ariani, A., Chetta, A. A., Frizzelli, A., Ticinesi, A., Tuttolomondo, D., Aliberti, S., Blasi, F. B., Di Pasquale, M. F., Misuraca, S., Pilocane, T., Simonetta, E., Aghelmo, A. M., Angelini, C., Brunetta, E., Canonica, G. W., Ciccarelli, M., Dal Farra, S., De Santis, M., Ferri, S., Folci, M., Guidelli, G. M., Heffler, E. M., Loiacono, F., Malipiero, G., Paoletti, G., Pedale, R., Puggioni, F. A., Racca, F., Zumbo, A., Satou, M., Lisun, T., Protsenko, D., Rubtsov, N., Beloglazova, I., Fomina, D., Lysenko, M., Serdotetskova, S., Firstov, V., Gordeev, I., Kokorin, I., Komissarova, K., Lapochkina, N., Luchinkina, E., Malimon, V., Mamedguseyinova, S., Polubatonova, K., Suvorova, N., Arribas, J., Borobia Perez, A. M., de la Calle Prieto, F., Figueira, J. C., Motejano Sanchez, R., Mora-Rillo, M., Prados Sanchez, C., Queiruga Parada, J., Fernandez Arnalich, F., Guerro Barrientos, M., Bendala Estrada, A., Caballero Marcos, A., Garcia Leoni, M. E., Garcia-Martinez, R., Collado, A. M., Munoz Garcia, P., Torres do Rego, A., Villalba Garcia, M. V., Burrillo, A., Valerio Minero, M., Gijon Vidaurreta, P., Infante Herrero, S., Velilla, E., Machado, M., Olmedo, M., Pinilla, B., Almirante Gragera, B., Canas Ruano, M. D. L. E., Contreras Medina, S., Cortes Herrera, A., Falco Ferrer, V., Ferrer Roca, R., Nuvials Casals, X., Ribera Pascuet, E., Suanzes Diez, P., Rebollo Castro, P., Garcia Alcaide, F., Soriano, A., Oliver Caldes, A., Gonzalez Cordon, A., Cardozo, C., De la Mora Canizo, L., Pena Lopez, R., Chamorro, S., Crespillo-Andujar, C., Escudero Sanchez, R., Fortun-Abete, J., Monge-Maillo, B., Moreno Zamora, A., Norman, F., Sanchez Conde, M., Serrano Villar, S., and Vizcarra, P.

Subjects
Male, Pulmonary and Respiratory Medicine, medicine.medical_specialty, Critical Care, International Cooperation, Population, Antibodies, Monoclonal, Humanized, Placebo, Severity of Illness Index, law.invention, 03 medical and health sciences, 0302 clinical medicine, Randomized controlled trial, law, Internal medicine, Intensive care, Severity of illness, medicine, Clinical endpoint, Humans, Immunologic Factors, 030212 general & internal medicine, Mortality, education, Respiratory Distress Syndrome, education.field_of_study, Dose-Response Relationship, Drug, SARS-CoV-2, business.industry, Hazard ratio, COVID-19, Articles, Middle Aged, Receptors, Interleukin-6, Sarilumab, Treatment Outcome, 030228 respiratory system, Female, Drug Monitoring, Cytokine Release Syndrome, business
Abstract

Summary Background Elevated proinflammatory cytokines are associated with greater COVID-19 severity. We aimed to assess safety and efficacy of sarilumab, an interleukin-6 receptor inhibitor, in patients with severe (requiring supplemental oxygen by nasal cannula or face mask) or critical (requiring greater supplemental oxygen, mechanical ventilation, or extracorporeal support) COVID-19. Methods We did a 60-day, randomised, double-blind, placebo-controlled, multinational phase 3 trial at 45 hospitals in Argentina, Brazil, Canada, Chile, France, Germany, Israel, Italy, Japan, Russia, and Spain. We included adults (≥18 years) admitted to hospital with laboratory-confirmed SARS-CoV-2 infection and pneumonia, who required oxygen supplementation or intensive care. Patients were randomly assigned (2:2:1 with permuted blocks of five) to receive intravenous sarilumab 400 mg, sarilumab 200 mg, or placebo. Patients, care providers, outcome assessors, and investigators remained masked to assigned intervention throughout the course of the study. The primary endpoint was time to clinical improvement of two or more points (seven point scale ranging from 1 [death] to 7 [discharged from hospital]) in the modified intention-to-treat population. The key secondary endpoint was proportion of patients alive at day 29. Safety outcomes included adverse events and laboratory assessments. This study is registered with ClinicalTrials.gov, NCT04327388; EudraCT, 2020-001162-12; and WHO, U1111-1249-6021. Findings Between March 28 and July 3, 2020, of 431 patients who were screened, 420 patients were randomly assigned and 416 received placebo (n=84 [20%]), sarilumab 200 mg (n=159 [38%]), or sarilumab 400 mg (n=173 [42%]). At day 29, no significant differences were seen in median time to an improvement of two or more points between placebo (12·0 days [95% CI 9·0 to 15·0]) and sarilumab 200 mg (10·0 days [9·0 to 12·0]; hazard ratio [HR] 1·03 [95% CI 0·75 to 1·40]; log-rank p=0·96) or sarilumab 400 mg (10·0 days [9·0 to 13·0]; HR 1·14 [95% CI 0·84 to 1·54]; log-rank p=0·34), or in proportions of patients alive (77 [92%] of 84 patients in the placebo group; 143 [90%] of 159 patients in the sarilumab 200 mg group; difference −1·7 [−9·3 to 5·8]; p=0·63 vs placebo; and 159 [92%] of 173 patients in the sarilumab 400 mg group; difference 0·2 [−6·9 to 7·4]; p=0·85 vs placebo). At day 29, there were numerical, non-significant survival differences between sarilumab 400 mg (88%) and placebo (79%; difference +8·9% [95% CI −7·7 to 25·5]; p=0·25) for patients who had critical disease. No unexpected safety signals were seen. The rates of treatment-emergent adverse events were 65% (55 of 84) in the placebo group, 65% (103 of 159) in the sarilumab 200 mg group, and 70% (121 of 173) in the sarilumab 400 mg group, and of those leading to death 11% (nine of 84) were in the placebo group, 11% (17 of 159) were in the sarilumab 200 mg group, and 10% (18 of 173) were in the sarilumab 400 mg group. Interpretation This trial did not show efficacy of sarilumab in patients admitted to hospital with COVID-19 and receiving supplemental oxygen. Adequately powered trials of targeted immunomodulatory therapies assessing survival as a primary endpoint are suggested in patients with critical COVID-19. Funding Sanofi and Regeneron Pharmaceuticals.

Published
2021

17. An algorithm for decoding skew Reed-Solomon codes with respect to the skew metric

Author

Delphine Boucher, Institut de Recherche Mathématique de Rennes (IRMAR), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-INSTITUT AGRO 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), ANR-11-LABX-0020,LEBESGUE,Centre de Mathématiques Henri Lebesgue : fondements, interactions, applications et Formation(2011), 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)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), Institut de Recherche Mathématique de Rennes ( IRMAR ), Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -AGROCAMPUS OUEST-École normale supérieure - Rennes ( ENS Rennes ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National des Sciences Appliquées ( INSA ) -Université de Rennes 2 ( UR2 ), and Université de Rennes ( UNIV-RENNES ) -Centre National de la Recherche Scientifique ( CNRS )

Subjects
Decoding, List decoding, Cryptography, 0102 computer and information sciences, 02 engineering and technology, [ MATH.MATH-IT ] Mathematics [math]/Information Theory [math.IT], Data_CODINGANDINFORMATIONTHEORY, 01 natural sciences, Interpretation (model theory), Reed–Solomon error correction, 0202 electrical engineering, electronic engineering, information engineering, Hardware_ARITHMETICANDLOGICSTRUCTURES, Mathematics, Computer Science::Information Theory, 12Y05, 16Z05, 68W30, 94B05, 94B35, business.industry, Applied Mathematics, Skew, [MATH.MATH-IT]Mathematics [math]/Information Theory [math.IT], 020206 networking & telecommunications, Hamming distance, Computer Science Applications, Skew polynomial rings, 010201 computation theory & mathematics, Metric (mathematics), business, Algorithm, Error-correcting codes, Decoding methods
Abstract

After giving a new interpretation of the skew metric defined in [8], we show that the decoding algorithm of [4] for skew Reed–Solomon codes in the Hamming metric remains valid with respect to the skew metric. This enables us to make a first step towards a list decoding algorithm in the skew metric.

Published
2020

18. Inflammatory and oxidative status in European captive black rhinoceroses: A link with Iron Overload Disorder?

Author

Delphine Boucher, Laetitia Jaillardon, Nicolas Soetart, Rudy Wedlarski, and Hanae Pouillevet

Subjects
Male, Serum Proteins, Antioxidant, medicine.medical_treatment, Physiology, Hemosiderosis, medicine.disease_cause, Biochemistry, 0403 veterinary science, Geographical Locations, chemistry.chemical_compound, Medical Conditions, Medicine and Health Sciences, Prospective Studies, Immune Response, 0303 health sciences, Multidisciplinary, medicine.diagnostic_test, biology, Liver Diseases, 04 agricultural and veterinary sciences, Blood proteins, Oxygen Metabolism, Enzymes, Europe, Dismutases, Liver, Serum iron, Medicine, Female, Hemochromatosis, Disease Susceptibility, Research Article, medicine.medical_specialty, Iron Overload, Globulin, 040301 veterinary sciences, Science, Inflammatory Diseases, Iron, Immunology, Gastroenterology and Hepatology, Superoxide dismutase, 03 medical and health sciences, Signs and Symptoms, Internal medicine, medicine, Animals, Perissodactyla, 030304 developmental biology, Inflammation, Cholesterol, Superoxide Dismutase, Albumin, Biology and Life Sciences, Proteins, Cell Biology, medicine.disease, Oxidative Stress, Endocrinology, Metabolism, chemistry, Ageing, People and Places, biology.protein, Enzymology, Animals, Zoo, Clinical Medicine, Oxidative stress
Abstract

Iron Overload Disorder (IOD) is a syndrome developed by captive browsing rhinoceroses like black rhinoceroses (Diceros bicornis) in which hemosiderosis settles in vital organs while free iron accumulates in the body, potentially predisposing to various secondary diseases. Captive grazing species like white rhinoceroses (Ceratotherium simum) do not seem to be affected. The pro-oxidant and pro-inflammatory properties of iron, associated with the poor antioxidant capacities of black rhinoceroses, could enhance high levels of inflammation and oxidative stress leading to rapid ageing and promoting diseases. In this prospective study, 15 black (BR) and 29 white rhinoceroses (WR) originating from 22 European zoos were blood-sampled and compared for their iron status (serum iron), liver/muscle biochemical parameters (AST, GGT, cholesterol), inflammatory status (total proteins, protein electrophoresis) and oxidative stress markers (SOD, GPX, dROMs). Results showed higher serum iron and liver enzyme levels in black rhinoceroses (P2-globulin levels (P

Published
2020

19. Microbial markers in colorectal cancer detection and/or prognosis

Author

Delphine Boucher, Elisabeth Billard, Johan Gagnière, Nicolas Barnich, Mathilde Bonnet, Julie Veziant, Romain Villeger, Amélie Lopès, Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte - Clermont Auvergne (M2iSH), Institut National de la Recherche Agronomique (INRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne (UCA)-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne), Centre Hospitalier Universitaire Clermont Ferrand, CHU Clermont-Ferrand, Service Chirurgie Disgestive, Centre Hospitalier Universitaire Estaing, Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH), Institut National de la Recherche Agronomique (INRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne), CHU Estaing [Clermont-Ferrand], CHU Clermont-Ferrand-CHU Clermont-Ferrand, Inserm, Universite Clermont Auvergne UMR 1071, INRA (USC), Conseil regional Auvergne-Rhones-Alpes, and FDER/CPER

Subjects
0301 basic medicine, Oncology, Colorectal cancer, Microbiota, F. nucleatum, Colibactin-producing E. coli, Prognostic markers, Diagnostic markers, Dysbiosis, Carcinogenesis, diagnostic, Review, Gut flora, marqueur, medicine.disease_cause, Feces, 0302 clinical medicine, Early Detection of Cancer, biology, Gastroenterology, General Medicine, Prognosis, 3. Good health, cancer colorectal, 030220 oncology & carcinogenesis, Metabolome, escherichia coli, Colorectal Neoplasms, Treatment response, medicine.medical_specialty, Adenoma, [SDV.CAN]Life Sciences [q-bio]/Cancer, Sensitivity and Specificity, 03 medical and health sciences, microbiote, Internal medicine, medicine, Humans, business.industry, Cancer, [SDV.MHEP.HEG]Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology, medicine.disease, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, digestive system diseases, Gastrointestinal Microbiome, Hépatologie et Gastroentérologie, 030104 developmental biology, colibactine, Hépatology and Gastroenterology, business, Biomarkers
Abstract

International audience; Colorectal cancer (CRC) is the second leading cause of cancer worldwide. CRC is still associated with a poor prognosis among patients with advanced disease. On the contrary, due to its slow progression from detectable precancerous lesions, the prognosis for patients with early stages of CRC is encouraging. While most robust methods are invasive and costly, actual patient-friendly screening methods for CRC suffer of lack of sensitivity and specificity. Therefore, the development of sensitive, non-invasive and cost-effective methods for CRC detection and prognosis are necessary for increasing the chances of a cure. Beyond its beneficial functions for the host, increasing evidence suggests that the intestinal microbiota is a key factor associated with carcinogenesis. Many clinical studies have reported a disruption in the gut microbiota balance and an alteration in the faecal metabolome of CRC patients, suggesting the potential use of a microbial-based test as a non-invasive diagnostic and/or prognostic tool for CRC screening. This review aims to discuss the microbial signatures associated with CRC known to date, including dysbiosis and faecal metabolome alterations, and the potential use of microbial variation markers for non-invasive early diagnosis and/or prognostic assessment of CRC and advanced adenomas. We will finally discuss the possible use of these markers as predicators for treatment response and their limitations.

Published
2018

20. Construction and number of self-dual skew codes over $\mathbb{F}_{p^2}$

Author

Delphine Boucher

Subjects
Discrete mathematics, Algebra and Number Theory, Computer Networks and Communications, Applied Mathematics, Skew, 020206 networking & telecommunications, 0102 computer and information sciences, 02 engineering and technology, Construct (python library), Automorphism, 01 natural sciences, Dual (category theory), Finite field, 010201 computation theory & mathematics, 0202 electrical engineering, electronic engineering, information engineering, Discrete Mathematics and Combinatorics, Mathematics
Abstract

The aim of this text is to construct and to count self-dual θ-cyclic and θ-negacyclic codes over IF p 2 where θ is the Frobenius automorphism.

Published
2016

21. IMPACTS OF ADDITIVE FOOD E171 (TITANIUM DIOXIDE) ON THE GUT MICROBIOTA AND COLORECTAL CARCINOGENESIS IN APCMIN/+ MURINE MODEL

Author

Sandrine Brugiroux, Thomas Sauvaitre, Gwenaelle Roche, Célia Ledieu, Caroline Chevarin, Catherine Godfraind, Christophe Massard, Komla Oscar Awitor, Nicolas Barnich, Mathilde Bonnet, Delphine Boucher, Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH), Institut National de la Recherche Agronomique (INRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne), Institut Universitaire de Technologie - Clermont-Ferrand (IUT Clermont-Ferrand), Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), OUERTANI, jeannette, Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte - Clermont Auvergne (M2iSH), Institut National de la Recherche Agronomique (INRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne (UCA)-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne), IUT de Clermont-Ferrand (IUT de Clermont-Ferrand), Université Clermont Auvergne (UCA), and Massard, Christophe

Subjects
[SDV.CAN] Life Sciences [q-bio]/Cancer, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, [SDV.CAN]Life Sciences [q-bio]/Cancer, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV.BBM.BM] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, [SDV.BC] Life Sciences [q-bio]/Cellular Biology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience; Background and aim: Contaminant molecules could play a key role in the initiation and/or promotion of colorectal cancer (CRC) which is the second leading cause of cancer worldwide. Among the different pollutants, titanium dioxide (TiO2) is a white natural metal oxide which is particularly monitored. It is one of the most widely used engineered nanomaterials in daily consumer products, including food. Long-term inhalation studies with TiO2 nanoparticles (NPs) in rats reported development of lung tumors leading to classify this compound as a possible carcinogen for humans by International Agency for Research on Cancer. The food additive TiO2, referred to as E171 in the European Union, is commonly used as a whitening and brightening agent in sugar confectionary, sauces, ice creams and pastries. The gastro-intestinal tract may be an important absorption route for TiO2 NPs and additive E171 could be involved in the CRC etiology. Thus, this project aimed to assess the impact of chronic exposure of food additive E171 in CRC development using APCmin/+ mouse model which spontaneously develop intestinal tumors. Because intestinal microbiota play a role in colorectal carcinogenesis, carcinogenic properties of TiO2 will be evaluated in association with microbiota dysbiosis.Methods: Additive E171 composition was characterized by X-ray diffraction (XRD) and thermogravimetric analysis (TGA). APCmin/+ mice were chronically exposed (twice per week) to E171 (1 and 10 mg/kg of body weight (BW)) or vehicle (water) for 28 days via intragastric gavage. Micro-inflammation was assessed by the quantification of fecal lipocalin-2 (LCN-2) marker. At the end of the experimental protocol, macroscopic and histologic examinations of colon were performed and colonic mucosa-associated microbiota was analyzed by quantitative PCR.Results: As shown by the TGA analysis, the E171 compound is purely mineral and the size of NPs administrated to mice in this study did not exceed 28 nm (XRD analysis). No significant body weight loss was observed between mice groups suggesting no toxicity in our experimental conditions. However macroscopic and histological observations showed a more advanced tumor development in mice receiving the additive E171 (at a dose of 10 mg/kg of BW) compared to control animals. At the end of the experiment, high level of fecal LCN-2 concentration correlated with increase of tumoral volume. Mice with adenocarcinoma within this group also exhibit an increase of Bacteroides and Akkermansia as well as a higher prevalence of Escherichia coli and a decrease of Bifidobacterium.Conclusion: Additive E171 promotes colonic tumorigenesis and induces change in gut microbiota composition. Underlying carcinogenic mechanisms focusing on microbiota dysbiosis implication are in progress. This study supports the carcinogenic properties of TiO2 in the context of colorectal cancer.

Published
2019

22. Capturing prokaryotic dark matter genomes

Author

Pierre Peyret, Nicolas Parisot, Eric Peyretaillade, Réjane Beugnot, Clémence Defois, Delphine Boucher, Corinne Petit-Biderre, Céline Ribière, Cyrielle Gasc, Conception, Ingénierie et Développement de l'Aliment et du Médicament (CIDAM), Université d'Auvergne - Clermont-Ferrand I (UdA), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Auvergne Regional Council, European Regional Development Fund, program Investissements d'Avenir AMI VALTEX, French 'Ministere de l'Enseignement Superieur et de la Recherche', French 'Direction Generale de l'Armement' (DGA), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA)

Subjects
Single-cell genomics, [SDV]Life Sciences [q-bio], Dark matter, Biology, Microbiology, Genome, Cellular life, 03 medical and health sciences, Genome, Archaeal, Ecosystem, Molecular Biology, ComputingMilieux_MISCELLANEOUS, Complete genome reconstruction, 030304 developmental biology, 0303 health sciences, Bacteria, 030306 microbiology, Ecology, High-Throughput Nucleotide Sequencing, General Medicine, 15. Life on land, Archaea, Prokaryotic Cells, Metagenomics, Evolutionary biology, Single-Cell Analysis, Genome, Bacterial, Function (biology)
Abstract

Prokaryotes are the most diverse and abundant cellular life forms on Earth. Most of them, identified by indirect molecular approaches, belong to microbial dark matter. The advent of metagenomic and single-cell genomic approaches has highlighted the metabolic capabilities of numerous members of this dark matter through genome reconstruction. Thus, linking functions back to the species has revolutionized our understanding of how ecosystem function is sustained by the microbial world. This review will present discoveries acquired through the illumination of prokaryotic dark matter genomes by these innovative approaches.

Published
2015

23. A first step towards the skew duadic codes

Author

Delphine Boucher, Institut de Recherche Mathématique de Rennes (IRMAR), 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)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), Institut de Recherche Mathématique de Rennes ( IRMAR ), Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -AGROCAMPUS OUEST-École normale supérieure - Rennes ( ENS Rennes ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National des Sciences Appliquées ( INSA ) -Université de Rennes 2 ( UR2 ), Université de Rennes ( UNIV-RENNES ) -Centre National de la Recherche Scientifique ( CNRS ), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-INSTITUT AGRO Agrocampus Ouest, 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
Computer Networks and Communications, 0102 computer and information sciences, 02 engineering and technology, [ MATH.MATH-IT ] Mathematics [math]/Information Theory [math.IT], 01 natural sciences, Microbiology, Square (algebra), Combinatorics, 0202 electrical engineering, electronic engineering, information engineering, Enumeration, Discrete Mathematics and Combinatorics, Link (knot theory), Mathematics, Discrete mathematics, [INFO.INFO-SC]Computer Science [cs]/Symbolic Computation [cs.SC], Algebra and Number Theory, Applied Mathematics, Prime number, Skew, [MATH.MATH-IT]Mathematics [math]/Information Theory [math.IT], 020206 networking & telecommunications, Automorphism, [ INFO.INFO-SC ] Computer Science [cs]/Symbolic Computation [cs.SC], Finite field, 010201 computation theory & mathematics, Binary code
Abstract

International audience; This text gives a first definition of the $\theta$-duadic codes where $\theta$ is an automorphism of $F q$. A link with the weakly self-dual $\theta$-cyclic codes is established. A construction and an enumeration are provided when $q$ is the square of a prime number $p$. In addition, new self-dual binary codes $ [72, 36, 12] $ are obtained from extended $\theta$-duadic codes defined on $F 4$.

Published
2018

24. Su1976 – Impacts of Additive Food E171 (Titanium Dioxide) on the Gut Microbiota and Colorectal Carcinogenesis in ApcMIN/+ Murine Model

Author

Oscar Komla Awitor, Caroline Chevarin, Célia Ledieu, Delphine Boucher, Gwenaëlle Roche, Thomas Sauvaitre, Nicolas Barnich, Mathilde Bonnet, Sandrine Brugiroux, Christophe Massard, and Catherine Godfraind

Subjects
Hepatology, biology, Chemistry, Gastroenterology, Cancer, Context (language use), Akkermansia, Pharmacology, Gut flora, biology.organism_classification, medicine.disease, medicine, media_common.cataloged_instance, European union, Dysbiosis, Carcinogen, media_common, Bifidobacterium
Abstract

Background and aim: Contaminant molecules could play a key role in the initiation and/or promotion of colorectal cancer (CRC) which is the second leading cause of cancer worldwide. Among the different pollutants, titanium dioxide (TiO2) is a white natural metal oxide which is particularly monitored. It is one of the most widely used engineered nanomaterials in daily consumer products, including food. Long-term inhalation studies with TiO2 nanoparticles (NPs) in rats reported development of lung tumors leading to classify this compound as a possible carcinogen for humans by International Agency for Research on Cancer. The food additive TiO2, referred to as E171 in the European Union, is commonly used as a whitening and brightening agent in sugar confectionary, sauces, ice creams and pastries. The gastro-intestinal tract may be an important absorption route for TiO2 NPs and additive E171 could be involved in the CRC etiology. Thus, this project aimed to assess the impact of chronic exposure of food additive E171 in CRC development using APCmin/+ mouse model which spontaneously develop intestinal tumors. Because intestinal microbiota play a role in colorectal carcinogenesis, carcinogenic properties of TiO2 will be evaluated in association with microbiota dysbiosis. Methods: Additive E171 composition was characterized by X-ray diffraction (XRD) and thermogravimetric analysis (TGA). APCmin/+ mice were chronically exposed (twice per week) to E171 (1 and 10 mg/kg of body weight (BW)) or vehicle (water) for 28 days via intragastric gavage. Micro-inflammation was assessed by the quantification of fecal lipocalin-2 (LCN-2) marker. At the end of the experimental protocol, macroscopic and histologic examinations of colon were performed and colonic mucosa-associated microbiota was analyzed by quantitative PCR. Results: As shown by the TGA analysis, the E171 compound is purely mineral and the size of NPs administrated to mice in this study did not exceed 28 nm (XRD analysis). No significant body weight loss was observed between mice groups suggesting no toxicity in our experimental conditions. However macroscopic and histological observations showed a more advanced tumor development in mice receiving the additive E171 (at a dose of 10 mg/kg of BW) compared to control animals. At the end of the experiment, high level of fecal LCN-2 concentration correlated with increase of tumoral volume. Mice with adenocarcinoma within this group also exhibit an increase of Bacteroides and Akkermansia as well as a higher prevalence of Escherichia coli and a decrease of Bifidobacterium. Conclusion: Additive E171 promotes colonic tumorigenesis and induces change in gut microbiota composition. Underlying carcinogenic mechanisms focusing on microbiota dysbiosis implication are in progress. This study supports the carcinogenic properties of TiO2 in the context of colorectal cancer.

Published
2019

25. Targeted Gene Capture by Hybridization to Illuminate Ecosystem Functioning

Author

Céline, Ribière, Réjane, Beugnot, Nicolas, Parisot, Cyrielle, Gasc, Clémence, Defois, Jérémie, Denonfoux, Delphine, Boucher, Eric, Peyretaillade, and Pierre, Peyret

Subjects
DNA, Bacterial, Computational Biology, High-Throughput Nucleotide Sequencing, Metagenome, Nucleic Acid Hybridization, Metagenomics, RNA Probes, Sequence Analysis, DNA, Biomarkers, Ecosystem
Abstract

Microbial communities are extremely abundant and diverse on earth surface and play key role in the ecosystem functioning. Thus, although next-generation sequencing (NGS) technologies have greatly improved knowledge on microbial diversity, it is necessary to reduce the biological complexity to better understand the microorganism functions. To achieve this goal, we describe a promising approach, based on the solution hybrid selection (SHS) method for the selective enrichment in a target-specific biomarker from metagenomic and metatranscriptomic samples. The success of this method strongly depends on the determination of sensitive, specific, and explorative probes to assess the complete targeted gene repertoire. Indeed, in this method, RNA probes were used to capture large DNA or RNA fragments harboring biomarkers of interest that potentially allow to link structure and function of communities of interest.

Published
2016

26. Targeted Gene Capture by Hybridization to Illuminate Ecosystem Functioning

Author

Cyrielle Gasc, Réjane Beugnot, Jérémie Denonfoux, Delphine Boucher, Clémence Defois, Céline Ribière, Eric Peyretaillade, Nicolas Parisot, Pierre Peyret, Conception, Ingénierie et Développement de l'Aliment et du Médicament (CIDAM), and Université d'Auvergne - Clermont-Ferrand I (UdA)

Subjects
0301 basic medicine, Genetics, Microbial diversity, 030106 microbiology, RNA, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Computational biology, Biology, DNA sequencing, Earth surface, 03 medical and health sciences, 030104 developmental biology, RNA Probes, Metagenomics, Ecosystem, Gene
Abstract

Microbial communities are extremely abundant and diverse on earth surface and play key role in the ecosystem functioning. Thus, although next-generation sequencing (NGS) technologies have greatly improved knowledge on microbial diversity, it is necessary to reduce the biological complexity to better understand the microorganism functions. To achieve this goal, we describe a promising approach, based on the solution hybrid selection (SHS) method for the selective enrichment in a target-specific biomarker from metagenomic and metatranscriptomic samples. The success of this method strongly depends on the determination of sensitive, specific, and explorative probes to assess the complete targeted gene repertoire. Indeed, in this method, RNA probes were used to capture large DNA or RNA fragments harboring biomarkers of interest that potentially allow to link structure and function of communities of interest.

Published
2016

27. Oral exposure to environmental pollutant benzo[a]pyrene impacts the intestinal epithelium and induces gut microbial shifts in murine model

Author

Claude Darcha, Pierre Déchelotte, Delphine Boucher, Nicolas Barnich, Nicolas Parisot, Pierre Peyret, Céline Ribière, Eric Peyretaillade, EA4678 CIDAM, Université d'Auvergne - Clermont-Ferrand I (UdA), CHU Clermont-Ferrand, Retinoids, Development and Developmental Diseases (R2D2), Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH), Institut National de la Recherche Agronomique (INRA)-Université d'Auvergne - Clermont-Ferrand I (UdA), and Ministère de l'Enseignement Supérieur et de la Recherche (France)

Subjects
Male, 0301 basic medicine, [SDV]Life Sciences [q-bio], Administration, Oral, 010501 environmental sciences, Gut flora, souris, 01 natural sciences, Article, Microbiology, maladie intestinale, Feces, Mice, 03 medical and health sciences, chemistry.chemical_compound, Intestinal mucosa, Benzo(a)pyrene, medicine, Genetic predisposition, Animals, Humans, Intestinal Mucosa, 0105 earth and related environmental sciences, Multidisciplinary, biology, Environmental Exposure, Environmental exposure, Inflammatory Bowel Diseases, biology.organism_classification, medicine.disease, Intestinal epithelium, Gastrointestinal Microbiome, 3. Good health, Mice, Inbred C57BL, Disease Models, Animal, 030104 developmental biology, benzo à pyrene, chemistry, 13. Climate action, inflammation, Toxicity, Dysbiosis, Environmental Pollutants, séquençage de gènes
Abstract

Gut microbiota dysbiosis are associated with a wide range of human diseases, including inflammatory bowel diseases. The physiopathology of these diseases has multifactorial aetiology in which environmental factors, particularly pollution could play a crucial role. Among the different pollutants listed, Polycyclic Aromatic Hydrocarbons (PAHs) are subject to increased monitoring due to their wide distribution and high toxicity on Humans. Here, we used 16S rRNA gene sequencing to investigate the impact of benzo[a]pyrene (BaP, most toxic PAH) oral exposure on the faecal and intestinal mucosa-associated bacteria in C57BL/6 mice. Intestinal inflammation was also evaluated by histological observations. BaP oral exposure significantly altered the composition and the abundance of the gut microbiota and led to moderate inflammation in ileal and colonic mucosa. More severe lesions were observed in ileal segment. Shifts in gut microbiota associated with moderate inflammatory signs in intestinal mucosa would suggest the establishment of a pro-inflammatory intestinal environment following BaP oral exposure. Therefore, under conditions of genetic susceptibility and in association with other environmental factors, exposure to this pollutant could trigger and/or accelerate the development of inflammatory pathologies.

Published
2016

28. Distribution of dehalococcoidia in the anaerobic deep water of a remote meromictic crater lake and detection of dehalococcoidia-derived reductive dehalogenase homologous genes

Author

Eric Peyretaillade, Delphine Boucher, Corinne Biderre-Petit, Pierre Peyret, Mickaël Mege, Jérémie Denonfoux, Lorenz Adrian, Didier Debroas, Eric Dugat-Bony, Nicolas Parisot, Anne Moné, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Microorganismes : Génome et Environnement - Clermont Auvergne (LMGE), Université Clermont Auvergne (UCA)-Centre National de la Recherche Scientifique (CNRS), Génie et Microbiologie des Procédés Alimentaires (GMPA), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Helmholtz Centre for Environmental Research (UFZ), Conception, Ingénierie et Développement de l'Aliment et du Médicament (CIDAM), Université d'Auvergne - Clermont-Ferrand I (UdA), Deutsche Forschungsgemeinschaft FOR1530 Direction Generale de l'Armement (DGA) CNRS Agence De l'Environnement et de la Maitrise de l'Energie (ADEME) French National Programme INSU-EC2CO (EChlore Project) ANR Programme PRECODD (EVASOL Project) Universite Blaise Pascal Ministere de la Recherche et de la Technologie Region Auvergne l'Agence De l'Environnement et de la Maitrise de l'Energie (ADEME), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), and Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ)

Subjects
0301 basic medicine, genome sequence, [SDV]Life Sciences [q-bio], 030106 microbiology, vertical-distribution, lcsh:Medicine, microbial communities, Biology, Real-Time Polymerase Chain Reaction, 03 medical and health sciences, Bacterial Proteins, RNA, Ribosomal, 16S, Insertion sequence, lcsh:Science, Gene, Phylogeny, Dehalogenase, Genetics, Whole genome sequencing, Multidisciplinary, tetrachloroethene, sediments, france, lac pavin, single-cell, strain cbdb1, polychlorinated-biphenyls, lcsh:R, Temperature, Chloroflexi, Sequence Analysis, DNA, Ribosomal RNA, 16S ribosomal RNA, Oxygen, Lakes, genomic DNA, 030104 developmental biology, Metagenomics, lcsh:Q, Oxidoreductases, Genome, Bacterial, Research Article
Abstract

Here we describe the natural occurrence of bacteria of the class Dehalococcoidia (DEH) and their diversity at different depths in anoxic waters of a remote meromictic lake (Lake Pavin) using 16S rRNA gene amplicon sequencing and quantitative PCR. Detected DEH are phylogenetically diverse and the majority of 16S rRNA sequences have less than 91% similarity to previously isolated DEH 16S rRNA sequences. To predict the metabolic potential of detected DEH subgroups and to assess if they encode genes to transform halogenated compounds, we enriched DEH-affiliated genomic DNA by using a specific-gene capture method and probes against DEH-derived 16S rRNA genes, reductive dehalogenase genes and known insertion sequences. Two reductive dehalogenase homologous sequences were identified from DEH-enriched genomic DNA, and marker genes in the direct vicinity confirm that gene fragments were derived from DEH. The low sequence similarity with known reductive dehalogenase genes suggests yet-unknown catabolic potential in the anoxic zone of Lake Pavin.

Published
2016

29. Linear codes using skew polynomials with automorphisms and derivations

Author

Delphine Boucher, Felix Ulmer, Institut de Recherche Mathématique de Rennes (IRMAR), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-INSTITUT AGRO 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), Institut de Recherche Mathématique de Rennes ( IRMAR ), Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -AGROCAMPUS OUEST-École normale supérieure - Rennes ( ENS Rennes ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National des Sciences Appliquées ( INSA ) -Université de Rennes 2 ( UR2 ), Université de Rennes ( UNIV-RENNES ) -Centre National de la Recherche Scientifique ( CNRS ), 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)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), and Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)

Subjects
Block code, Decoding, Polynomial ring, [ MATH.MATH-IT ] Mathematics [math]/Information Theory [math.IT], Data_CODINGANDINFORMATIONTHEORY, 0102 computer and information sciences, 01 natural sciences, Combinatorics, [ INFO.INFO-IT ] Computer Science [cs]/Information Theory [cs.IT], Reed–Solomon error correction, ComputingMethodologies_SYMBOLICANDALGEBRAICMANIPULATION, 94Bxx, 94B05, 16S36, 0101 mathematics, Computer Science::Information Theory, Mathematics, Discrete mathematics, Applied Mathematics, Concatenated error correction code, 010102 general mathematics, Skew, [MATH.MATH-IT]Mathematics [math]/Information Theory [math.IT], Linear code, Computer Science Applications, Skew polynomial rings, Finite field, [INFO.INFO-IT]Computer Science [cs]/Information Theory [cs.IT], 010201 computation theory & mathematics, Finite fields, Error-correcting codes, BCH code
Abstract

In this work the definition of codes as modules over skew polynomial rings of automorphism type is generalized to skew polynomial rings, whose multiplication is defined using an automorphism and a derivation. This produces a more general class of codes which, in some cases, produce better distance bounds than module skew codes constructed only with an automorphism. Extending the approach of Gabidulin codes, we introduce new notions of evaluation of skew polynomials with derivations and the corresponding evaluation codes. We propose several approaches to generalize Reed-Solomon and BCH codes to module skew codes and for two classes we show that the dual of such a Reed-Solomon type skew code is an evaluation skew code. We generalize a decoding algorithm due to Gabidulin for the rank metric and derive families of Maximum Distance Separable and Maximum Rank Distance codes.

Published
2012

30. In situ TCE degradation mediated by complex dehalorespiring communities during biostimulation processes

Author

Faouzi Jaziri, Timothy M. Vogel, Maude M. David, Corinne Biderre-Petit, Jean-Yves Richard, Delina Lyon, Eric Peyretaillade, Pierre Peyret, Cyrille Curvers, Eric Dugat-Bony, Jérémie Denonfoux, and Delphine Boucher

Subjects
Dehalococcoides, 0303 health sciences, Trichloroethylene, biology, Bioengineering, Dehalobacter, 010501 environmental sciences, biology.organism_classification, 01 natural sciences, Applied Microbiology and Biotechnology, Biochemistry, 6. Clean water, Microbiology, Biostimulation, 03 medical and health sciences, chemistry.chemical_compound, Bioremediation, chemistry, Metagenomics, Environmental chemistry, Desulfitobacterium, 030304 developmental biology, 0105 earth and related environmental sciences, Biotechnology, Geobacter
Abstract

The bioremediation of chloroethene contaminants in groundwater polluted systems is still a serious environmental challenge. Many previous studies have shown that cooperation of several dechlorinators is crucial for complete dechlorination of trichloroethene to ethene. In the present study, we used an explorative functional DNA microarray (DechloArray) to examine the composition of specific functional genes in groundwater samples in which chloroethene bioremediation was enhanced by delivery of hydrogen-releasing compounds. Our results demonstrate for the first time that complete biodegradation occurs through spatial and temporal variations of a wide diversity of dehalorespiring populations involving both Sulfurospirillum, Dehalobacter, Desulfitobacterium, Geobacter and Dehalococcoides genera. Sulfurospirillum appears to be the most active in the highly contaminated source zone, while Geobacter was only detected in the slightly contaminated downstream zone. The concomitant detection of both bvcA and vcrA genes suggests that at least two different Dehalococcoides species are probably responsible for the dechlorination of dichloroethenes and vinyl chloride to ethene. These species were not detected on sites where cis-dichloroethene accumulation was observed. These results support the notion that monitoring dechlorinators by the presence of specific functional biomarkers using a powerful tool such as DechloArray will be useful for surveying the efficiency of bioremediation strategies.

Published
2012

31. Bacterial community changes during bioremediation of aliphatic hydrocarbon-contaminated soil

Author

Cédric Vachelard, Vincent Barra, Delphine Boucher, Eric Peyretaillade, Geoffrey Perchet, Cécile Militon, Pierre Peyret, and Julien Troquet

Subjects
Phylotype, 0303 health sciences, food.ingredient, Ecology, biology, 030306 microbiology, Acidimicrobium, 15. Life on land, 010501 environmental sciences, biology.organism_classification, 01 natural sciences, Applied Microbiology and Biotechnology, Microbiology, Actinobacteria, Biostimulation, 03 medical and health sciences, food, Bioremediation, Microbial population biology, 13. Climate action, Gammaproteobacteria, Botany, Soil microbiology, 0105 earth and related environmental sciences
Abstract

The microbial community response during the oxygen biostimulation process of aged oil-polluted soils is poorly documented and there is no reference for the long-term monitoring of the unsaturated zone. To assess the potential effect of air supply on hydrocarbon fate and microbial community structure, two treatments (0 and 0.056 mol h⁻¹ molar flow rate of oxygen) were performed in fixed bed reactors containing oil-polluted soil. Microbial activity was monitored continuously over 2 years throughout the oxygen biostimulation process. Microbial community structure before and after treatment for 12 and 24 months was determined using a dual rRNA/rRNA gene approach, allowing us to characterize bacteria that were presumably metabolically active and therefore responsible for the functionality of the community in this polluted soil. Clone library analysis revealed that the microbial community contained many rare phylotypes. These have never been observed in other studied ecosystems. The bacterial community shifted from Gammaproteobacteria to Actinobacteria during the treatment. Without aeration, the samples were dominated by a phylotype linked to the Streptomyces. Members belonging to eight dominant phylotypes were well adapted to the aeration process. Aeration stimulated an Actinobacteria phylotype that might be involved in restoring the ecosystem studied. Phylogenetic analyses suggested that this phylotype is a novel, deep-branching member of the Actinobacteria related to the well-studied genus Acidimicrobium.

Published
2010

33. Impact of environmental factors on couplings between bacterial community composition and ectoenzymatic activities in a lacustrine ecosystem

Author

Didier Debroas and Delphine Boucher

Subjects
0106 biological sciences, 0303 health sciences, Ecology, 010604 marine biology & hydrobiology, Biodiversity, Community structure, Biology, 01 natural sciences, Applied Microbiology and Biotechnology, Microbiology, 03 medical and health sciences, Terminal restriction fragment length polymorphism, Nutrient, Microbial population biology, 13. Climate action, Ecosystem, Leucine, Leucyl aminopeptidase, 030304 developmental biology
Abstract

This study examined the effects of temporal changes in bacterial community composition (BCC) and environmental factors on potential ectoenzymatic activities (alpha-glucosidase, beta-glucosidase, alkaline phosphatase and leucine aminopeptidase) in a lacustrine ecosystem (Sep reservoir, France). BCC was assessed by terminal restriction fragment length polymorphism. Physical parameters, and inorganic and organic nutrient concentrations (dissolved carbohydrates and proteins) were measured in lakes and tributaries. According to the multivariate statistics (redundancy analysis), physical and chemical factors explained the largest part of leucine aminopeptidase activity, whereas the temporal changes of other ectoenzymatic activities were partly dependent on the variations in the BCC. In particular, the occurrence of occasional bacterial populations seemed to explain a lot of the variation in rates and patterns of polymer hydrolysis. The relation observed in this study between the bacterial structure and activity is discussed within the framework of biodiversity-ecosystem functioning.

Published
2009

34. Skew constacyclic codes over Galois rings

Author

Felix Ulmer, Patrick Solé, Delphine Boucher, Institut de Recherche Mathématique de Rennes ( IRMAR ), Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -AGROCAMPUS OUEST-École normale supérieure - Rennes ( ENS Rennes ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National des Sciences Appliquées ( INSA ) -Université de Rennes 2 ( UR2 ), Université de Rennes ( UNIV-RENNES ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire d'Informatique, Signaux, et Systèmes de Sophia-Antipolis (I3S) / Equipe MC3, Modèles Discrets pour les Systèmes Complexes ( MDSC ), Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis ( I3S ), Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ) -Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis ( I3S ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ), Institut de Recherche Mathématique de Rennes (IRMAR), 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)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), Modèles Discrets pour les Systèmes Complexes (Laboratoire I3S - MDSC), Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis (I3S), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis (I3S), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-INSTITUT AGRO 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), Université Nice Sophia Antipolis (1965 - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS)

Subjects
94B60, 16S36, cyclic codes, Computer Networks and Communications, Polynomial ring, 0102 computer and information sciences, 02 engineering and technology, Commutative ring, Z 4 −codes, 01 natural sciences, Microbiology, Expander code, Combinatorics, Cyclic code, self-dual codes, 0202 electrical engineering, electronic engineering, information engineering, Discrete Mathematics and Combinatorics, Mathematics, Algebra and Number Theory, Mathematics::Commutative Algebra, Applied Mathematics, [MATH.MATH-RA]Mathematics [math]/Rings and Algebras [math.RA], Skew, Z(4)-codes, 020206 networking & telecommunications, modular lattices, Linear code, [ MATH.MATH-RA ] Mathematics [math]/Rings and Algebras [math.RA], Finite field, 010201 computation theory & mathematics, Group code, skew polynomial rings
Abstract

International audience; We generalize the construction of linear codes via skew polynomial rings by using Galois rings instead of finite fields as coefficients. The resulting non commutative rings are no longer left and right Euclidean. Codes that are principal ideals in quotient rings of skew polynomial rings by a two sided ideals are studied. As an application, skew constacyclic self-dual codes over GR(4, 2) are constructed. Euclidean self-dual codes give self-dual Z(4)-codes. Hermitian self-dual codes yield 3-modular lattices and quasi-cyclic self-dual Z(4)-codes.

Published
2008

35. Incorporation of 3H-Thymidine by Different Prokaryotic Groups in Relation to Temperature and Nutrients in a Lacustrine Ecosystem

Author

Aurélie Thénot, Didier Debroas, M. Richardot, Delphine Boucher, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Cytophagaceae, Uptake, Cytophaga, In situ, Molecular hybridization, Nutrient, MESH: Biomass, MESH: Ecosystem, Biomass, MESH: In Situ Hybridization, Fluorescence, Food science, MESH: Phosphorus, MESH: Nitrogen, Incubation, In Situ Hybridization, Fluorescence, Soil Microbiology, Phylogeny, 2. Zero hunger, 0303 health sciences, Ecology, biology, Temperature, Bacteriosis, Phosphorus, Adaptation, Physiological, Nitrogen, MESH: Temperature, 6. Clean water, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Infection, Soil Science, chemistry.chemical_element, MESH: Carbon, Tritium, Microbiology, 03 medical and health sciences, Microbial ecology, Proteobacteria, Cytophagales, Microbial community, Ecosystem, Archaeobacteria, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Bacteria, MESH: Cytophaga, 030306 microbiology, MESH: Proteobacteria, biology.organism_classification, MESH: Adaptation, Physiological, Carbon, Treatment, Eubacteria, MESH: Bacteria, MESH: Soil Microbiology, MESH: Tritium, chemistry, Microbial population biology, Thymidine, MESH: Thymidine, Archaea
Abstract

International audience; The incorporation of [3H-methyl] thymidine (3H-TdR) by Eubacteria, bacterial groups (alpha- and beta-Proteobacteria, Cytophaga-Flavobacter), and Archaea was measured according to temperature (7 and 17 degrees C) and nutrient levels (nitrogen, phosphorus, and carbon) in a lacustrine system (Sep, France). Short-term incubation was performed using a combination of microautoradiography and fluorescent in situ hybridization. Irrespective of the temperatures and nutrients studied, all the major phylogenetic bacterial groups assimilated 3H-TdR, and in most of the treatments studied, the proportion of beta-Proteobacteria taking up 3H-TdR was higher than those in the other bacterial groups. The proportion of Bacteria and different bacterial groups studied incorporating 3H-TdR were significantly increased, approximately 1.5-fold, by temperature except for alpha-Proteobacteria (7.6-fold). The nutrient effect was not the same for the different bacterial groups according to the temperatures studied. The proportions of alpha-Proteobacteria (at both temperatures) and Cytophaga-Flavobacter (at 7 degrees C) taking up 3H-TdR were significantly decreased and increased by adding N and P, respectively. Also, adding N, P, and C increased and decreased the percentage of beta-Proteobacteria incorporating 3H-TdR at 7 and 17 degrees C, respectively. The archaeal community showed a similar proportion of active cells (i.e., 3H-TdR) to the bacterial community, and uptake of 3H-TdR by Archaea was significantly increased (P < 0.05) by both temperature and nutrients. Thus, the assimilation of 3H-TdR by bacterial groups and Archaea in lacustrine system is significantly controlled by both temperature and nutrients.

Published
2006

36. Succession of bacterial community composition over two consecutive years in two aquatic systems: a natural lake and a lake-reservoir

Author

Didier Debroas, Delphine Boucher, and Ludwig Jardillier

Subjects
Terminal restriction fragment length polymorphism, Ecology, Microbial population biology, Epilimnion, Aquatic ecosystem, Community structure, Ecosystem, Ecological succession, Hypolimnion, Biology, Applied Microbiology and Biotechnology, Microbiology
Abstract

The succession in bacterial community composition was studied over two years in the epilimnion and hypolimnion of two freshwater systems: a natural lake (Pavin Lake) and a lake-reservoir (Sep Reservoir). The bacterial community composition was determined by cloning-sequencing of 16S rRNA and by terminal restriction fragment length polymorphism. Despite large hydrogeological differences, in the Sep Reservoir and Pavin Lake the dominant bacteria were from the same taxonomic divisions, particularly Actinobacteria and Betaproteobacteria. In both ecosystems, these major bacterial divisions showed temporal fluctuations that were much less marked than those occurring at a finer phylogenetic scale. Nutrient availability and mortality factors, the nature of which differed from one lake to another, covaried with the temporal variations in the bacterial community composition at all sampling depths, whereas factors related to seasonal forces (temperature and outflow for Sep Reservoir) seemed to account only for the variation of the hypolimnion bacterial community composition. No seasonal reproducibility in temporal evolution of bacterial community from one year to the next was observed.

Published
2006

37. Relative importance of nutrients and mortality factors on prokaryotic community composition in two lakes of different trophic status: Microcosm experiments

Author

Stéphan Jacquet, Aurélie Thénot, Delphine Boucher, Christian Amblard, Denis Sargos, Sébastien Personnic, Didier Debroas, Ludwig Jardillier, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Institut National de la Recherche Agronomique (INRA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), and Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS)

Subjects
DNA, Bacterial, Food Chain, Nitrogen, Fresh Water, Biology, Applied Microbiology and Biotechnology, Microbiology, Freshwater ecosystem, 03 medical and health sciences, Food chain, Nutrient, TERMINAL RESTRICTION FRAGMENT LENGTH POLYMORPHISM, Animals, Ecosystem, 14. Life underwater, PROKARYOTIC COMMUNITY COMPOSITION, ComputingMilieux_MISCELLANEOUS, In Situ Hybridization, Fluorescence, 030304 developmental biology, Trophic level, 2. Zero hunger, 0303 health sciences, Bacteria, Ecology, 030306 microbiology, Phosphorus, Biodiversity, Archaea, Invertebrates, 6. Clean water, TOP DOWN, Terminal restriction fragment length polymorphism, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, DNA, Archaeal, BOTTOM UP, Prokaryotic Cells, Predatory Behavior, Viruses, France, VARIATION PARTITIONING ANALYSIS, Microcosm, Eutrophication, HYBRIDIZATION, Polymorphism, Restriction Fragment Length
Abstract

The effect of nutrient resources (N and P enrichment) and of different grazing communities on the prokaryotic community composition (PCC) was investigated in two freshwater ecosystems: Sep reservoir (oligomesotrophic) and lake Aydat (eutrophic). An experimental approach using microcosms was chosen, that allowed control of both predation levels, by size fractionation of predators, and resources, by nutrient amendments. Changes in PCC were monitored by fluorescent in situ hybridization (FISH) and terminal-restriction fragment length polymorphism (T-RFLP). The main mortality agents were (i) heterotrophic nanoflagellates and virus-like particles in Aydat and (ii) cladocerans in Sep. All the nutritional elements assayed (N-NO3, P-PO4 and N-NH4) together with prokaryotic production (PP) always accounted for a significant part of the variations in PCC. Overall, prokaryotic diversity was mainly explained by resources in Sep, by a comparable contribution of resources and mortality factors in lake Aydat and, to a lesser extent, by the combined action of both.

Published
2005

38. Exploiting the architecture and the features of the microsporidian genomes to investigate diversity and impact of these parasites on ecosystems

Author

Eric Peyretaillade, Emmanuelle Lerat, Robert R. Butler, Nicolas Parisot, Cyrielle Gasc, Pierre Peyret, Jean-François Pombert, Delphine Boucher, Conception, Ingénierie et Développement de l'Aliment et du Médicament (CIDAM), Université d'Auvergne - Clermont-Ferrand I (UdA), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Eléments transposables, évolution, populations, Département génétique, interactions et évolution des génomes [LBBE] (GINSENG), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Insecta, [SDV]Life Sciences [q-bio], Population, Biodiversity, Genomics, Review, Biology, Genome, Genetics, Animals, education, Ecosystem, Genetics (clinical), Trophic level, education.field_of_study, Obligate, Ecology, fungi, 15. Life on land, biology.organism_classification, Evolutionary biology, Microsporidia, DNA Transposable Elements, Identification (biology), Genome, Fungal
Abstract

International audience; Fungal species play extremely important roles in ecosystems. Clustered at the base of the fungal kingdom are Microsporidia, a group of obligate intracellular eukaryotes infecting multiple animal lineages. Because of their large host spectrum and their implications in host population regulation, they influence food webs, and accordingly, ecosystem structure and function. Unfortunately, their ecological role is not well understood. Present also as highly resistant spores in the environment, their characterisation requires special attention. Different techniques based on direct isolation and/or molecular approaches can be considered to elucidate their role in the ecosystems, but integrating environmental and genomic data (for example, genome architecture, core genome, transcriptional and translational signals) is crucial to better understand the diversity and adaptive capacities of Microsporidia. Here, we review the current status of Microsporidia in trophic networks; the various genomics tools that could be used to ensure identification and evaluate diversity and abundance of these organisms; and how these tools could be used to explore the microsporidian life cycle in different environments. Our understanding of the evolution of these widespread parasites is currently impaired by limited sampling, and we have no doubt witnessed but a small subset of their diversity.

Published
2014

39. Self-dual skew codes and factorization of skew polynomials

Author

Felix Ulmer, Delphine Boucher, Institut de Recherche Mathématique de Rennes (IRMAR), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-INSTITUT AGRO 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), 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)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), Institut de Recherche Mathématique de Rennes ( IRMAR ), Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -AGROCAMPUS OUEST-École normale supérieure - Rennes ( ENS Rennes ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National des Sciences Appliquées ( INSA ) -Université de Rennes 2 ( UR2 ), and Université de Rennes ( UNIV-RENNES ) -Centre National de la Recherche Scientifique ( CNRS )

Subjects
Block code, Discrete mathematics, Polynomial, Algebra and Number Theory, Polynomial code, [MATH.MATH-RA]Mathematics [math]/Rings and Algebras [math.RA], corps finis, 020206 networking & telecommunications, 0102 computer and information sciences, 02 engineering and technology, polynômes non commutatifs, 01 natural sciences, [ MATH.MATH-RA ] Mathematics [math]/Rings and Algebras [math.RA], Square-free polynomial, Combinatorics, Computational Mathematics, Reciprocal polynomial, Finite field, Factorization, codes correcteurs d'erreurs, 010201 computation theory & mathematics, Factorization of polynomials, 0202 electrical engineering, electronic engineering, information engineering, 12Y05, 16Z05, 94B05, Mathematics
Abstract

International audience; The construction of cyclic codes can be generalized to so called module $\theta$-cyclic codes using noncommutative polynomials. The product of the generator polynomial $g$ of a self-dual module $\theta$-cyclic code and its "skew reciprocal polynomial" is known to be a noncommutative polynomial of the form $X^n-a$, reducing the problem of the computation of all such codes to a Gröbner basis problem where the unknowns are the coefficients of $g$. In previous work, with the exception of the length $2^s$, over $\FF_4$ a large number of self-dual codes were found. In this paper we show that $a$ must be $\pm 1$ and that for $n=2^s$ the decomposition of $X^n\pm 1$ into a product of $g$ and its "skew reciprocal polynomial" has some rigidity properties which explains the small number of codes found for those particular lengths over $\FF_4$. In order to overcome the complexity limitation resulting from the Gröbner basis computation we present, in the case $\theta$ of order two, an iterative construction of self-dual codes based on least common multiples and factorization of noncommutative polynomials. We use this approach to construct a $[78,39,19]_4$ self-dual code and a $[52,26,17]_9$ self-dual code which improve the best previously known minimal distances for these lengths.

Published
2014

40. Sur la non-intégrabilité du problème plan des trois corps de masses égales

Author

Delphine Boucher

Subjects
Differential equation, Variational equation, Galois group, General Medicine, Abelian group, Linear equation, Mathematics, Mathematical physics, Hamiltonian system
Abstract

Resume Nous considerons le probleme plan des trois corps le long de la solution de Lagrange indexee par un parametre c . Nous supposons que les corps ont tous une masse egale a un. A l'aide du theoreme de non-integrabilite de Morales–Ramis, nous montrons que ce probleme n'est pas integrable quand c est non nul. Nous menons pour cela une etude a la fois locale et globale d'une equation normale variationnelle scalaire calculee le long de cette solution particuliere.

Published
2000

41. Geographic distance and ecosystem size determine the distribution of smallest protists in lacustrine ecosystems

Author

Najwa Taib, Didier Debroas, Jean-François Mangot, Isabelle Domaizon, Delphine Boucher, Gisèle Bronner, Cécile Lepère, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Institut National de la Recherche Agronomique (INRA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Conception, Ingénierie et Développement de l'Aliment et du Médicament (CIDAM), Université d'Auvergne - Clermont-Ferrand I (UdA), INSU EC2CO, Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), and Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de la Recherche Agronomique (INRA)

Subjects
0106 biological sciences, Rare biosphere, beta-diversity, Insular biogeography, Beta diversity, AREA RELATIONSHIPS, Biology, Spatial distribution, 010603 evolutionary biology, 01 natural sciences, Applied Microbiology and Biotechnology, Microbiology, 03 medical and health sciences, SMALL EUKARYOTES, parasitic diseases, lakes, RNA, Ribosomal, 18S, 14. Life underwater, DEEP-SEA, Ecosystem, biogeography, 030304 developmental biology, protists, 0303 health sciences, Ecology, SPECIES RICHNESS, Community structure, Eukaryota, 15. Life on land, RARE BIOSPHERE, AQUATIC PROTISTS, UniFrac, 13. Climate action, Alpha diversity, Species richness, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, COMMUNITIES, alpha-diversity, MICROBIAL DIVERSITY, PRIMARY PRODUCTIVITY
Abstract

International audience; Understanding the spatial distribution of aquatic microbial diversity and the underlying mechanisms causing differences in community composition is a challenging and central goal for ecologists. Recent insights into protistan diversity and ecology are increasing the debate over their spatial distribution. In this study, we investigate the importance of spatial and environmental factors in shaping the small protists community structure in lakes. We analyzed small protists community composition (beta-diversity) and richness (alpha-diversity) at regional scale by different molecular methods targeting the gene coding for 18S rRNA gene (T-RFLP and 454 pyrosequencing). Our results show a distance-decay pattern for rare and dominant taxa and the spatial distribution of the latter followed the prediction of the island biogeography theory. Furthermore, geographic distances between lakes seem to be the main force shaping the protists community composition in the lakes studied here. Finally, the spatial distribution of protists was discussed at the global scale (11 worldwide distributed lakes) by comparing these results with those present in the public database. UniFrac analysis showed 18S rRNA gene OTUs compositions significantly different among most of lakes, and this difference does not seem to be related to the trophic status.

Published
2013

42. Gene Capture Coupled to High-Throughput Sequencing as a Strategy for Targeted Metagenome Exploration

Author

Eric Peyretaillade, Pierre Peyret, Eric Dugat-Bony, Corinne Biderre-Petit, Denis Le Paslier, Jérémie Denonfoux, Nicolas Parisot, Delphine Boucher, Diego P. Morgavi, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Conception, Ingénierie et Développement de l'Aliment et du Médicament (CIDAM), Université d'Auvergne - Clermont-Ferrand I (UdA), Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), 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 la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Unité Mixte de Recherches sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique (INRA), 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)-Université Paris-Saclay, Laboratoire Microorganismes : Génome et Environnement ( LMGE ), Université Blaise Pascal - Clermont-Ferrand 2 ( UBP ) -Université d'Auvergne - Clermont-Ferrand I ( UdA ) -Centre National de la Recherche Scientifique ( CNRS ), Conception, Ingénierie et Développement de l'Aliment et du Médicament ( CIDAM ), Université d'Auvergne - Clermont-Ferrand I ( UdA ), Unité Mixte de Recherches sur les Herbivores ( UMR 1213 Herbivores ), VetAgro Sup ( VAS ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique ( INRA ), Genoscope - Centre national de séquençage [Evry] ( GENOSCOPE ), and Commissariat à l'énergie atomique et aux énergies alternatives ( CEA )

Subjects
DNA, Bacterial, Rare biosphere, Biology, DNA sequencing, a-subunit of the methyl-coenzyme M reductase, 03 medical and health sciences, chemistry.chemical_compound, diversité microbienne, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Operon, Genetics, Molecular Biology, Gene, 030304 developmental biology, métagénomique, 0303 health sciences, metagenomics, a -subunit of the methyl-coenzyme M reductase, sequence capture, 454 pyrosequencing, microbial diversity, Base Sequence, 030306 microbiology, α-subunit of the methyl-coenzyme M reductase, High-Throughput Nucleotide Sequencing, General Medicine, Methanosarcina, Full Papers, Amplicon, biology.organism_classification, pyroséquençage, chemistry, [ SDV.BBM.GTP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Metagenomics, Metagenome, Pyrosequencing, Oxidoreductases, Genome, Bacterial, DNA
Abstract

International audience; Next-generation sequencing (NGS) allows faster acquisition of metagenomic data, but complete exploration of complex ecosystems is hindered by the extraordinary diversity of microorganisms. To reduce the environmental complexity, we created an innovative solution hybrid selection (SHS) method that is combined with NGS to characterize large DNA fragments harbouring biomarkers of interest. The quality of enrichment was evaluated after fragments containing the methyl coenzyme M reductase subunit A gene (mcrA), the biomarker of methanogenesis, were captured from a Methanosarcina strain and a metagenomic sample from a meromictic lake. The methanogen diversity was compared with direct metagenome and mcrA-based amplicon pyrosequencing strategies. The SHS approach resulted in the capture of DNA fragments up to 2.5 kb with an enrichment efficiency between 41 and 100%, depending on the sample complexity. Compared with direct metagenome and amplicons sequencing, SHS detected broader mcrA diversity, and it allowed efficient sampling of the rare biosphere and unknown sequences. In contrast to amplicon-based strategies, SHS is less biased and GC independent, and it recovered complete biomarker sequences in addition to conserved regions. Because this method can also isolate the regions flanking the target sequences, it could facilitate operon reconstructions.

Published
2013

43. A note on the dual codes of module skew codes

Author

Felix Ulmer, Delphine Boucher, Institut de Recherche Mathématique de Rennes ( IRMAR ), Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -AGROCAMPUS OUEST-École normale supérieure - Rennes ( ENS Rennes ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National des Sciences Appliquées ( INSA ) -Université de Rennes 2 ( UR2 ), Université de Rennes ( UNIV-RENNES ) -Centre National de la Recherche Scientifique ( CNRS ), Liqun Chen, Institut de Recherche Mathématique de Rennes (IRMAR), 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)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-INSTITUT AGRO Agrocampus Ouest, 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
Discrete mathematics, Finite ring, Ring (mathematics), 94Bxx, 16S36, error-correcting codes, Polynomial ring, 010102 general mathematics, Code word, [MATH.MATH-IT]Mathematics [math]/Information Theory [math.IT], Order (ring theory), 0102 computer and information sciences, [ MATH.MATH-IT ] Mathematics [math]/Information Theory [math.IT], 01 natural sciences, Linear code, Combinatorics, Finite field, [ INFO.INFO-IT ] Computer Science [cs]/Information Theory [cs.IT], [INFO.INFO-IT]Computer Science [cs]/Information Theory [cs.IT], 010201 computation theory & mathematics, Cyclic code, skew polynomial rings, 0101 mathematics, finite fields, Mathematics
Abstract

In [4], starting from an automorphism θ of a finite field ${\mathbb F}_q$ and a skew polynomial ring $R={\mathbb F}_q[X;\theta]$ , module θ -codes are defined as left R -submodules of R /Rf where f ∈R . In [4] it is conjectured that an Euclidean self-dual module θ -code is a θ -constacyclic code and a proof is given in the special case when the order of θ divides the length of the code. In this paper we prove that this conjecture holds in general by showing that the dual of a module θ -code is a module θ -code if and only if it is a θ -constacyclic code. Furthermore, we establish that a module θ -code which is not θ -constacyclic is a shortened θ -constacyclic code and that its dual is a punctured θ -constacyclic code. This enables us to give the general form of a parity-check matrix for module θ -codes and for module (θ ,δ )-codes over ${\mathbb F}_q[X;\theta,\delta]$ where δ is a derivation over ${\mathbb F}_q$ . We also prove the conjecture for module θ -codes who are defined over a ring A [X ;θ ] where A is a finite ring. Lastly we construct self-dual θ -cyclic codes of length 2s over ${\mathbb F}_4$ for s ≥3 which are asymptotically bad and conjecture that there exists no other self-dual module θ -code of this length over ${\mathbb F}_4$ .

Published
2011

44. Bacterial community composition of biological degreasing systems and health risk assessment for workers

Author

Philippe Duquenne, Delphine Boucher, Eric Peyretaillade, Christine David, Pierre Peyret, Jean Baptiste Laffaire, Faouzi Jaziri, Corinne Biderre-Petit, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Informatique, de Modélisation et d'optimisation des Systèmes (LIMOS), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-SIGMA Clermont (SIGMA Clermont)-Ecole Nationale Supérieure des Mines de St Etienne (ENSM ST-ETIENNE)-Centre National de la Recherche Scientifique (CNRS), Institut national de recherche et de sécurité (Vandoeuvre lès Nancy) (INRS ( Vandoeuvre lès Nancy)), Laboratoire de Métrologie des Aérosols, Département Métrologie des Polluants (MP), Institut national de recherche et de sécurité (Vandoeuvre lès Nancy) (INRS ( Vandoeuvre lès Nancy))-Institut national de recherche et de sécurité (Vandoeuvre lès Nancy) (INRS ( Vandoeuvre lès Nancy)), and SIGMA Clermont (SIGMA Clermont)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Ecole Nationale Supérieure des Mines de St Etienne-Centre National de la Recherche Scientifique (CNRS)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)

Subjects
Microorganism, Colony Count, Microbial, Soil Science, 010501 environmental sciences, MESH: Industrial Microbiology, MESH: Risk Assessment, 01 natural sciences, Risk Assessment, Waste Disposal, Fluid, MESH: Occupational Exposure, 03 medical and health sciences, Industrial Microbiology, Degreasing, Microbial ecology, Occupational Exposure, RNA, Ribosomal, 16S, MESH: Phylogeny, MESH: Colony Count, Microbial, Ecology, Evolution, Behavior and Systematics, Phylogeny, 030304 developmental biology, 0105 earth and related environmental sciences, 0303 health sciences, Ecology, biology, Health risk assessment, Bacteria, business.industry, Klebsiella oxytoca, Industrial microbiology, biology.organism_classification, [SDE.ES]Environmental Sciences/Environmental and Society, Pantoea agglomerans, Biotechnology, MESH: RNA, Ribosomal, 16S, MESH: Bacteria, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, MESH: Waste Disposal, Fluid, business, Waste disposal
Abstract

International audience; Biological degreasing system is a new technology based on the degradation capabilities of microorganisms to remove oil, grease, or lubricants from metal parts. No data is available about the potential biological health hazards in such system. Thus, a health risk assessment linked to the bacterial populations present in this new degreasing technology is, therefore, necessary for workers. We performed both cultural and molecular approaches in several biological degreasing systems for various industrial contexts to investigate the composition and dynamics of bacterial populations. These biological degreasing systems did not work with the original bacterial populations. Indeed, they were colonized by a defined and restricted group of bacteria. This group replaced the indigenous bacterial populations known for degrading complex substrates. Klebsiella pneumoniae, Klebsiella oxytoca, Pseudomonas aeruginosa, and Pantoea agglomerans were important members of the microflora found in most of the biological degreasing systems. These bacteria might represent a potential health hazard for workers.

Published
2010

45. Bacterial community changes during bioremediation of aliphatic hydrocarbon-contaminated soil

Author

Cécile, Militon, Delphine, Boucher, Cédric, Vachelard, Geoffrey, Perchet, Vincent, Barra, Julien, Troquet, Eric, Peyretaillade, and Pierre, Peyret

Subjects
Actinobacteria, DNA, Bacterial, Oxygen, Soil, Biodegradation, Environmental, Bioreactors, RNA, Ribosomal, 16S, Soil Pollutants, Pilot Projects, Gammaproteobacteria, Hydrocarbons, Phylogeny, Soil Microbiology
Abstract

The microbial community response during the oxygen biostimulation process of aged oil-polluted soils is poorly documented and there is no reference for the long-term monitoring of the unsaturated zone. To assess the potential effect of air supply on hydrocarbon fate and microbial community structure, two treatments (0 and 0.056 mol h⁻¹ molar flow rate of oxygen) were performed in fixed bed reactors containing oil-polluted soil. Microbial activity was monitored continuously over 2 years throughout the oxygen biostimulation process. Microbial community structure before and after treatment for 12 and 24 months was determined using a dual rRNA/rRNA gene approach, allowing us to characterize bacteria that were presumably metabolically active and therefore responsible for the functionality of the community in this polluted soil. Clone library analysis revealed that the microbial community contained many rare phylotypes. These have never been observed in other studied ecosystems. The bacterial community shifted from Gammaproteobacteria to Actinobacteria during the treatment. Without aeration, the samples were dominated by a phylotype linked to the Streptomyces. Members belonging to eight dominant phylotypes were well adapted to the aeration process. Aeration stimulated an Actinobacteria phylotype that might be involved in restoring the ecosystem studied. Phylogenetic analyses suggested that this phylotype is a novel, deep-branching member of the Actinobacteria related to the well-studied genus Acidimicrobium.

Published
2010

46. Identification of sulfur-cycle prokaryotes in a low-sulfate lake (Lake Pavin) using aprA and 16S rRNA gene markers

Author

Guillaume Borrel, Didier Jézéquel, Delphine Boucher, Brigitte Chebance, Gérard Fonty, Corinne Biderre-Petit, Patrick Albéric, Jan Kuever, Pierre Peyret, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Bremen Institute for Materials Testing, Institut des Sciences de la Terre d'Orléans - UMR7327 (ISTO), Bureau de Recherches Géologiques et Minières (BRGM) (BRGM)-Observatoire des Sciences de l'Univers en région Centre (OSUC), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université d'Orléans (UO)-Observatoire de Paris, PSL Research University (PSL)-PSL Research University (PSL)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université d'Orléans (UO)-Observatoire de Paris, PSL Research University (PSL)-PSL Research University (PSL)-Institut national des sciences de l'Univers (INSU - CNRS)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS), Interactions et dynamique des environnements de surface (IDES), Université Paris-Sud - Paris 11 (UP11)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de géochimie des Eaux (LGE), Université Paris Diderot - Paris 7 (UPD7)-Institut de Physique du Globe de Paris, Institut de Physique du Globe de Paris (IPGP), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-IPG PARIS-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Centre National de la Recherche Scientifique (CNRS), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Institute of Materials Engineering [Bremen] (IWT ), University of Bremen, Centre National de la Recherche Scientifique (CNRS)-Université d'Orléans (UO)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers en région Centre (OSUC), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Bureau de Recherches Géologiques et Minières (BRGM) (BRGM), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS), Université Paris Diderot - Paris 7 (UPD7)-Institut de Physique du Globe de Paris (IPG Paris), and Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Institut de Physique du Globe de Paris (IPG Paris)-Centre National de la Recherche Scientifique (CNRS)

Subjects
DNA, Bacterial, Biogeochemical cycle, Geologic Sediments, Methanogenesis, Molecular Sequence Data, Soil Science, Fresh Water, 03 medical and health sciences, chemistry.chemical_compound, Microbial ecology, Dissimilatory sulfate reduction, RNA, Ribosomal, 16S, Amino Acid Sequence, Sulfate, Ecology, Evolution, Behavior and Systematics, Phylogeny, 030304 developmental biology, DNA Primers, 0303 health sciences, Epsilonproteobacteria, Ecology, biology, Sulfur-Reducing Bacteria, 030306 microbiology, Sulfates, Sulfur cycle, Sequence Analysis, DNA, biology.organism_classification, chemistry, France, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Water Microbiology, Bacteria
Abstract

International audience; Geochemical researches at Lake Pavin, a low-sulfate-containing freshwater lake, suggest that the dominant biogeochemical processes are iron and sulfate reduction, and methanogenesis. Although the sulfur cycle is one of the main active element cycles in this lake, little is known about the sulfate-reducer and sulfur-oxidizing bacteria. The aim of this study was to assess the vertical distribution of these microbes and their diversities and to test the hypothesis suggesting that only few SRP populations are involved in dissimilatory sulfate reduction and that Epsilonproteobacteria are the likely key players in the oxidative phase of sulfur cycle by using a PCR aprA gene-based approach in comparison with a 16S rRNA gene-based analysis. The results support this hypothesis. Finally, this preliminary work points strongly the likelihood of novel metabolic processes upon the availability of sulfate and other electron acceptors.

Published
2010

47. Detecting variants with Metabolic Design, a new software tool to design probes for explorative functional DNA microarray development

Author

Anne Moné, Eric Peyretaillade, Sébastien Terrat, Corinne Biderre-Petit, Julien Troquet, Fabrice N. Gravelat, Olivier Gonçalves, Eric Dugat-Bony, Pierre Peyret, Delphine Boucher, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Bioprocédés Appliqués aux Microalgues (GEPEA-BAM), Laboratoire de génie des procédés - environnement - agroalimentaire (GEPEA), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-Ecole Polytechnique de l'Université de Nantes (EPUN), Université de Nantes (UN)-Université de Nantes (UN)-Institut Universitaire de Technologie - Nantes (IUT Nantes), Université de Nantes (UN)-Institut Universitaire de Technologie Saint-Nazaire (IUT Saint-Nazaire), Université de Nantes (UN)-Institut Universitaire de Technologie - La Roche-sur-Yon (IUT La Roche-sur-Yon), Université de Nantes (UN)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Université Bretagne Loire (UBL)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Université Bretagne Loire (UBL), Biopôle Clermont-Limagne, Biobasic Environnement, Ministere de l'Enseignement Superieur et de la Recherche Scientifique, FLAveur, VIsion et Comportement du consommateur (FLAVIC), Institut National de la Recherche Agronomique (INRA)-Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Université de Bourgogne (UB), EA4678 CIDAM, Université d'Auvergne - Clermont-Ferrand I (UdA), Institut Universitaire de Technologie - Nantes (IUT Nantes), Université de Nantes (UN)-Université de Nantes (UN)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Institut Universitaire de Technologie Saint-Nazaire (IUT Saint-Nazaire), Université de Nantes (UN)-Ecole Polytechnique de l'Université de Nantes (EPUN), Université de Nantes (UN)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Centre National de la Recherche Scientifique (CNRS)-Université Bretagne Loire (UBL)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut Universitaire de Technologie - La Roche-sur-Yon (IUT La Roche-sur-Yon), Université de Nantes (UN)-Institut Universitaire de Technologie - Nantes (IUT Nantes), Université de Nantes (UN), McGill University = Université McGill [Montréal, Canada], Development and Cell Biology (Department of Genetics), Iowa State University (ISU), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Unité de Microbiologie (MIC), Institut National de la Recherche Agronomique (INRA), Université de Nantes (UN)-École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Centre National de la Recherche Scientifique (CNRS)-Université Bretagne Loire (UBL)-IMT Atlantique (IMT Atlantique), Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Université d'Auvergne (Clermont Ferrand 1) (UdA), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes (UN)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Centre National de la Recherche Scientifique (CNRS)-Université Bretagne Loire (UBL)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), McGill University, Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Laboratoire Microorganismes : Génome et Environnement - Clermont Auvergne (LMGE), Université Clermont Auvergne (UCA)-Centre National de la Recherche Scientifique (CNRS), Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), and Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix

Subjects
phenanthrene, Microarray, degradation, genes, database, sequence, identification, microbial communities, oligonucleotide microarrays, sp strain p2, polycyclic aromatic-hydrocarbons, Biochemistry, [SPI]Engineering Sciences [physics], Structural Biology, Gene expression, Soil Pollutants, Polycyclic Aromatic Hydrocarbons, lcsh:QH301-705.5, Soil Microbiology, ComputingMilieux_MISCELLANEOUS, Oligonucleotide Array Sequence Analysis, Genetics, 0303 health sciences, Applied Mathematics, Hybridization probe, Computer Science Applications, Biodegradation, Environmental, Software design, lcsh:R858-859.7, DNA microarray, DNA Probes, Algorithms, Research Article, Biology, lcsh:Computer applications to medicine. Medical informatics, Sphingomonas, 03 medical and health sciences, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Gene, Molecular Biology, 030304 developmental biology, DNA Primers, 030306 microbiology, Microarray analysis techniques, Genetic Variation, Microarray Analysis, Metabolic pathway, lcsh:Biology (General), 13. Climate action, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Software
Abstract

Background Microorganisms display vast diversity, and each one has its own set of genes, cell components and metabolic reactions. To assess their huge unexploited metabolic potential in different ecosystems, we need high throughput tools, such as functional microarrays, that allow the simultaneous analysis of thousands of genes. However, most classical functional microarrays use specific probes that monitor only known sequences, and so fail to cover the full microbial gene diversity present in complex environments. We have thus developed an algorithm, implemented in the user-friendly program Metabolic Design, to design efficient explorative probes. Results First we have validated our approach by studying eight enzymes involved in the degradation of polycyclic aromatic hydrocarbons from the model strain Sphingomonas paucimobilis sp. EPA505 using a designed microarray of 8,048 probes. As expected, microarray assays identified the targeted set of genes induced during biodegradation kinetics experiments with various pollutants. We have then confirmed the identity of these new genes by sequencing, and corroborated the quantitative discrimination of our microarray by quantitative real-time PCR. Finally, we have assessed metabolic capacities of microbial communities in soil contaminated with aromatic hydrocarbons. Results show that our probe design (sensitivity and explorative quality) can be used to study a complex environment efficiently. Conclusions We successfully use our microarray to detect gene expression encoding enzymes involved in polycyclic aromatic hydrocarbon degradation for the model strain. In addition, DNA microarray experiments performed on soil polluted by organic pollutants without prior sequence assumptions demonstrate high specificity and sensitivity for gene detection. Metabolic Design is thus a powerful, efficient tool that can be used to design explorative probes and monitor metabolic pathways in complex environments, and it may also be used to study any group of genes. The Metabolic Design software is freely available from the authors and can be downloaded and modified under general public license.

Published
2010

48. Codes as modules over skew polynomial rings

Author

Felix Ulmer, Delphine Boucher, Institut de Recherche Mathématique de Rennes (IRMAR), 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)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), Hervé, Dominique, Institut de Recherche Mathématique de Rennes ( IRMAR ), Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -AGROCAMPUS OUEST-École normale supérieure - Rennes ( ENS Rennes ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National des Sciences Appliquées ( INSA ) -Université de Rennes 2 ( UR2 ), Université de Rennes ( UNIV-RENNES ) -Centre National de la Recherche Scientifique ( CNRS ), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-INSTITUT AGRO Agrocampus Ouest, 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
Block code, Polynomial ring, 0102 computer and information sciences, 02 engineering and technology, [ MATH.MATH-IT ] Mathematics [math]/Information Theory [math.IT], 01 natural sciences, linear codes, Combinatorics, [MATH.MATH-IT] Mathematics [math]/Information Theory [math.IT], [ INFO.INFO-IT ] Computer Science [cs]/Information Theory [cs.IT], 0202 electrical engineering, electronic engineering, information engineering, Quotient, Mathematics, 94Bxx, 94B05, 94B15, 16P10, 16S36, 16Dxx, Discrete mathematics, finite rings, modules, Skew, [MATH.MATH-AG] Mathematics [math]/Algebraic Geometry [math.AG], [MATH.MATH-IT]Mathematics [math]/Information Theory [math.IT], 020206 networking & telecommunications, 16. Peace & justice, Automorphism, Linear code, Hermitian matrix, [ MATH.MATH-AG ] Mathematics [math]/Algebraic Geometry [math.AG], 010201 computation theory & mathematics, [INFO.INFO-IT]Computer Science [cs]/Information Theory [cs.IT], skew polynomial rings, [INFO.INFO-IT] Computer Science [cs]/Information Theory [cs.IT], [MATH.MATH-AG]Mathematics [math]/Algebraic Geometry [math.AG], BCH code
Abstract

In previous works we considered codes defined as ideals of quotients of skew polynomial rings, so called Ore rings of automorphism type. In this paper we consider codes defined as modules over skew polynomial rings, removing therefore some of the constraints on the length of the skew codes defined as ideals. The notion of BCH codes can be extended to this new approach and the skew codes whose duals are also defined as modules can be characterized. We conjecture that self-dual skew codes defined as modules must be constacyclic and prove this conjecture for the Hermitian scalar product and under some assumptions for the Euclidean scalar product. We found new [56, 28, 15], [60,30,16], [62,31,17], [66,33,17] Euclidean self-dual skew codes and new [50,25,14], [58,29,16] Hermitian self-dual skew codes over F 4 , improving the best known distances for self-dual codes of these lengths over F 4 .

Published
2009

49. About the non-integrability in the Friedmann-Robertson-Walker cosmological model

Author

Delphine Boucher, Jacques-Arthur Weil, Institut de Recherche Mathématique de Rennes ( IRMAR ), Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -AGROCAMPUS OUEST-École normale supérieure - Rennes ( ENS Rennes ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National des Sciences Appliquées ( INSA ) -Université de Rennes 2 ( UR2 ), Université de Rennes ( UNIV-RENNES ) -Centre National de la Recherche Scientifique ( CNRS ), DMI, XLIM ( XLIM ), Université de Limoges ( UNILIM ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Limoges ( UNILIM ) -Centre National de la Recherche Scientifique ( CNRS ), Institut de Recherche Mathématique de Rennes (IRMAR), 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)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), XLIM (XLIM), Université de Limoges (UNILIM)-Centre National de la Recherche Scientifique (CNRS)-Université de Limoges (UNILIM)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-INSTITUT AGRO 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), and Hervé, Dominique

Subjects
Work (thermodynamics), Integrable system, [MATH.MATH-DS]Mathematics [math]/Dynamical Systems [math.DS], [ MATH.MATH-DS ] Mathematics [math]/Dynamical Systems [math.DS], [MATH.MATH-DS] Mathematics [math]/Dynamical Systems [math.DS], General Physics and Astronomy, 68W30, Integrability, Lambda, integrability, 01 natural sciences, 010305 fluids & plasmas, Hamiltonian system, Continuation, 0103 physical sciences, Morales-Ramis-Simo theorem, Hamiltonian systems, computer algebra, Mathematical physics, Physics, Conjecture, 010308 nuclear & particles physics, Cosmological model, Surface (topology), Computer algebra, Morales-Ramis-Simo Theorem
Abstract

We study the non integrability of the Friedmann-Robertson-Walker cosmological model, in continuation of the work [5] of Coehlo, Skea and Stuchi. Using Morales-Ramis theorem ([10]) and applying a practical non-integrability criterion deduced from it, we find that the system is not completely integrable for almost all values of the parameters lambda and lambda, which was already proved by the authors of [5] applying Kovacic's algorithm. Working on a level surface H = h with h ¹ 0 and h ¹ -1/4\lambda and using the Morales-Ramis-Simo ''higher variational'' theory ([11]), we prove that the hamiltonian system cannot be integrable for particular values of lambda among the exceptional values and that it is completely integrable in two special cases (lambda = lambda = -m² and lambda = lambda = m^2/3). We conjecture that there is no other case of complete integrability and give detailed arguments towards this.

Published
2007

50. Skew-cyclic codes

Author

Delphine Boucher, Willi Geiselmann, Felix Ulmer, Institut de Recherche Mathématique de Rennes (IRMAR), 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)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), Universität Karlsruhe (TH), Institut de Recherche Mathématique de Rennes ( IRMAR ), Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -AGROCAMPUS OUEST-École normale supérieure - Rennes ( ENS Rennes ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National des Sciences Appliquées ( INSA ) -Université de Rennes 2 ( UR2 ), Université de Rennes ( UNIV-RENNES ) -Centre National de la Recherche Scientifique ( CNRS ), Universität Karlsruhe ( IAKS ), Universität Karlsruhe, Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-INSTITUT AGRO Agrocampus Ouest, 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
Block code, 94B05, 0102 computer and information sciences, 02 engineering and technology, Luby transform code, 01 natural sciences, BCH codes, Expander code, linear codes, Combinatorics, Reed–Solomon error correction, Cyclic code, FOS: Mathematics, 0202 electrical engineering, electronic engineering, information engineering, error connecting codes, Mathematics, Discrete mathematics, Algebra and Number Theory, Applied Mathematics, [MATH.MATH-RA]Mathematics [math]/Rings and Algebras [math.RA], Reed–Muller code, 020206 networking & telecommunications, Mathematics - Rings and Algebras, Linear code, [ MATH.MATH-RA ] Mathematics [math]/Rings and Algebras [math.RA], Rings and Algebras (math.RA), 010201 computation theory & mathematics, Hamming code
Abstract

International audience; We generalize the notion of cyclic codes by using generator polynomials in (non commutative) skew polynomial rings. Since skew polynomial rings are left and right euclidean, the obtained codes share most properties of cyclic codes. Since there are much more skew-cyclic codes, this new class of codes allows to systematically search for codes with good properties. We give many examples of codes which improve the previously best known linear codes.

Published
2007

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