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Poivet E, Gallot A, Montagné N, Senin P, Monsempès C, Legeai F, Jacquin-Joly E. Transcriptome Profiling of Starvation in the Peripheral Chemosensory Organs of the Crop Pest Spodoptera littoralis Caterpillars. Insects 2021; 12:insects12070573. [PMID: 34201462 PMCID: PMC8303696 DOI: 10.3390/insects12070573] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/05/2021] [Accepted: 06/18/2021] [Indexed: 11/25/2022]
Abstract
Simple Summary Starvation increases olfactory sensitivity in a manner that enhances the search for food in animals, including insects. However, the molecular mechanisms via which starvation modulates olfactory receptor neuron function are poorly understood. In this study, we sequenced and compared the whole transcriptomes of the main olfactory organs (antennae and palps) of fed and starved caterpillars from the species Spodoptera littoralis. We revealed that transcripts involved in several biological processes are regulated upon starvation. These processes include glucose metabolism, immune defense, foraging activity, and olfaction. In this last process, we evidenced regulation of chemosensory proteins and odorant-degrading enzymes, known to play a role in the dynamics and the sensitivity of the olfactory receptor neuron response. Our results identify new elements in the cascade of olfactory neuron modulation, in addition to insulin, GABA, and short neuropeptide F signaling. Abstract Starvation is frequently encountered by animals under fluctuating food conditions in nature, and response to it is vital for life span. Many studies have investigated the behavioral and physiological responses to starvation. In particular, starvation is known to induce changes in olfactory behaviors and olfactory sensitivity to food odorants, but the underlying mechanisms are not well understood. Here, we investigated the transcriptional changes induced by starvation in the chemosensory tissues of the caterpillar Spodoptera littoralis, using Illumina RNA sequencing. Gene expression profiling revealed 81 regulated transcripts associated with several biological processes, such as glucose metabolism, immune defense, response to stress, foraging activity, and olfaction. Focusing on the olfactory process, we observed changes in transcripts encoding proteins putatively involved in the peri-receptor events, namely, chemosensory proteins and odorant-degrading enzymes. Such modulation of their expression may drive fluctuations in the dynamics and the sensitivity of the olfactory receptor neuron response. In combination with the enhanced presynaptic activity mediated via the short neuropeptide F expressed during fasting periods, this could explain an enhanced olfactory detection process. Our observations suggest that a coordinated transcriptional response of peripheral chemosensory organs participates in the regulation of olfactory signal reception and olfactory-driven behaviors upon starvation.
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Affiliation(s)
- Erwan Poivet
- Institute of Ecology and Environmental Sciences of Paris, INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, 78000 Versailles, France; (E.P.); (A.G.); (N.M.); (C.M.)
| | - Aurore Gallot
- Institute of Ecology and Environmental Sciences of Paris, INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, 78000 Versailles, France; (E.P.); (A.G.); (N.M.); (C.M.)
| | - Nicolas Montagné
- Institute of Ecology and Environmental Sciences of Paris, INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, 78000 Versailles, France; (E.P.); (A.G.); (N.M.); (C.M.)
| | - Pavel Senin
- IRISA, INRIA, CNRS, Université de Rennes, 35000 Rennes, France; (P.S.); (F.L.)
| | - Christelle Monsempès
- Institute of Ecology and Environmental Sciences of Paris, INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, 78000 Versailles, France; (E.P.); (A.G.); (N.M.); (C.M.)
| | - Fabrice Legeai
- IRISA, INRIA, CNRS, Université de Rennes, 35000 Rennes, France; (P.S.); (F.L.)
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35000 Rennes, France
| | - Emmanuelle Jacquin-Joly
- Institute of Ecology and Environmental Sciences of Paris, INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, 78000 Versailles, France; (E.P.); (A.G.); (N.M.); (C.M.)
- Correspondence:
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Aubé J, Senin P, Bonin P, Pringault O, Jeziorski C, Bouchez O, Klopp C, Guyoneaud R, Goñi-Urriza M. Meta-omics Provides Insights into the Impact of Hydrocarbon Contamination on Microbial Mat Functioning. Microb Ecol 2020; 80:286-295. [PMID: 32076743 DOI: 10.1007/s00248-020-01493-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 02/04/2020] [Indexed: 06/10/2023]
Abstract
Photosynthetic microbial mats are stable, self-supported communities. Due to their coastal localization, these mats are frequently exposed to hydrocarbon contamination and are able to grow on it. To decipher how this contamination disturbs the functioning of microbial mats, we compared two mats: a contaminated mat exposed to chronic petroleum contamination and a reference mat. The taxonomic and metabolic structures of the mats in spring and fall were determined using metagenomic and metatranscriptomic approaches. Extremely high contamination disturbed the seasonal variations of the mat. ABC transporters, two-component systems, and type IV secretion system-related genes were overabundant in the contaminated mats. Xenobiotic degradation metabolism was minor in the metagenomes of both mats, and only the expression of genes involved in polycyclic aromatic hydrocarbon degradation was higher in the contaminated mat. Interestingly, the expression rates of genes involved in hydrocarbon activation decreased during the 1-year study period, concomitant with the decrease in easily degradable hydrocarbons, suggesting a transient effect of hydrocarbon contamination. Alteromonadales and Oceanospirillales hydrocarbonoclastic bacteria appeared to be key in hydrocarbon remediation in the contaminated mat. Overall, the contaminated microbial mat was able to cope with hydrocarbon contamination and displayed an adaptive functioning that modified seasonal behaviour.
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Affiliation(s)
- Johanne Aubé
- Environmental Microbiology, Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
- Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, IFREMER, CNRS, Université de Bretagne Occidentale, Plouzané, France
| | - Pavel Senin
- Environmental Microbiology, Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
- Plateforme Bioinformatique Genotoul, UR875 Biométrie et Intelligence Artificielle, INRA, Castanet-Tolosan, France
| | - Patricia Bonin
- Mediterranean Institute of Oceanography (MIO), Aix Marseille University, Université de Toulon, CNRS/INSU/IRD, UM 110, Marseille, France
| | - Olivier Pringault
- UMR 9190 MARBEC IRD-Ifremer-CNRS, Université de Montpellier, Place Eugène Bataillon, Montpellier, France
| | | | - Olivier Bouchez
- GeT-PlaGe, Genotoul, INRA Auzeville, Castanet-Tolosan, France
| | - Christophe Klopp
- Plateforme Bioinformatique Genotoul, UR875 Biométrie et Intelligence Artificielle, INRA, Castanet-Tolosan, France
| | - Rémy Guyoneaud
- Environmental Microbiology, Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Marisol Goñi-Urriza
- Environmental Microbiology, Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France.
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Forestier G, Petitjean F, Senin P, Despinoy F, Huaulmé A, Fawaz HI, Weber J, Idoumghar L, Muller PA, Jannin P. Surgical motion analysis using discriminative interpretable patterns. Artif Intell Med 2018; 91:3-11. [PMID: 30172445 DOI: 10.1016/j.artmed.2018.08.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 07/06/2018] [Accepted: 08/13/2018] [Indexed: 11/29/2022]
Abstract
OBJECTIVE The analysis of surgical motion has received a growing interest with the development of devices allowing their automatic capture. In this context, the use of advanced surgical training systems makes an automated assessment of surgical trainee possible. Automatic and quantitative evaluation of surgical skills is a very important step in improving surgical patient care. MATERIAL AND METHOD In this paper, we present an approach for the discovery and ranking of discriminative and interpretable patterns of surgical practice from recordings of surgical motions. A pattern is defined as a series of actions or events in the kinematic data that together are distinctive of a specific gesture or skill level. Our approach is based on the decomposition of continuous kinematic data into a set of overlapping gestures represented by strings (bag of words) for which we compute comparative numerical statistic (tf-idf) enabling the discriminative gesture discovery via its relative occurrence frequency. RESULTS We carried out experiments on three surgical motion datasets. The results show that the patterns identified by the proposed method can be used to accurately classify individual gestures, skill levels and surgical interfaces. We also present how the patterns provide a detailed feedback on the trainee skill assessment. CONCLUSIONS The proposed approach is an interesting addition to existing learning tools for surgery as it provides a way to obtain a feedback on which parts of an exercise have been used to classify the attempt as correct or incorrect.
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Affiliation(s)
- Germain Forestier
- IRIMAS, Université de Haute-Alsace, Mulhouse, France; Faculty of Information Technology, Monash University, Melbourne, Australia.
| | - François Petitjean
- Faculty of Information Technology, Monash University, Melbourne, Australia.
| | - Pavel Senin
- Los Alamos National Laboratory, University Of Hawai'i at Mānoa, United States.
| | - Fabien Despinoy
- Univ Rennes, Inserm, LTSI - UMR_S 1099, F35000 Rennes, France.
| | - Arnaud Huaulmé
- Univ Rennes, Inserm, LTSI - UMR_S 1099, F35000 Rennes, France.
| | | | | | | | | | - Pierre Jannin
- Univ Rennes, Inserm, LTSI - UMR_S 1099, F35000 Rennes, France.
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Forestier G, Petitjean F, Senin P, Riffaud L, Henaux PL, Jannin P. Finding discriminative and interpretable patterns in sequences of surgical activities. Artif Intell Med 2017; 82:11-19. [PMID: 28943333 DOI: 10.1016/j.artmed.2017.09.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 08/28/2017] [Accepted: 09/01/2017] [Indexed: 10/18/2022]
Abstract
OBJECTIVE Surgery is one of the riskiest and most important medical acts that is performed today. Understanding the ways in which surgeries are similar or different from each other is of major interest to understand and analyze surgical behaviors. This article addresses the issue of identifying discriminative patterns of surgical practice from recordings of surgeries. These recordings are sequences of low-level surgical activities representing the actions performed by surgeons during surgeries. MATERIALS AND METHOD To discover patterns that are specific to a group of surgeries, we use the vector space model (VSM) which is originally an algebraic model for representing text documents. We split long sequences of surgical activities into subsequences of consecutive activities. We then compute the relative frequencies of these subsequences using the tf*idf framework and we use the Cosine similarity to classify the sequences. This process makes it possible to discover which patterns discriminate one set of surgeries recordings from another set. RESULTS Experiments were performed on 40 neurosurgeries of anterior cervical discectomy (ACD). The results demonstrate that our method accurately identifies patterns that can discriminate between (1) locations where the surgery took place, (2) levels of expertise of surgeons (i.e., expert vs. intermediate) and even (3) individual surgeons who performed the intervention. We also show how the tf*idf weight vector can be used to both visualize the most interesting patterns and to highlight the parts of a given surgery that are the most interesting. CONCLUSIONS Identifying patterns that discriminate groups of surgeon is a very important step in improving the understanding of surgical processes. The proposed method finds discriminative and interpretable patterns in sequences of surgical activities. Our approach provides intuitive results, as it identifies automatically the set of patterns explaining the differences between the groups.
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Affiliation(s)
- Germain Forestier
- MIPS EA 2332, University of Haute-Alsace, Mulhouse, France; Faculty of Information Technology, Monash University, Melbourne, Australia.
| | - François Petitjean
- Faculty of Information Technology, Monash University, Melbourne, Australia.
| | - Pavel Senin
- Los Alamos National Laboratory, Los Alamos, NM 87544, United States.
| | - Laurent Riffaud
- INSERM MediCIS, Unit U1099 LTSI, University of Rennes 1, Rennes, France; Department of Neurosurgery, Pontchaillou University Hospital, Rennes, France.
| | - Pierre-Louis Henaux
- INSERM MediCIS, Unit U1099 LTSI, University of Rennes 1, Rennes, France; Department of Neurosurgery, Pontchaillou University Hospital, Rennes, France.
| | - Pierre Jannin
- INSERM MediCIS, Unit U1099 LTSI, University of Rennes 1, Rennes, France.
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Aubé J, Senin P, Pringault O, Bonin P, Deflandre B, Bouchez O, Bru N, Biritxinaga-Etchart E, Klopp C, Guyoneaud R, Goñi-Urriza M. The impact of long-term hydrocarbon exposure on the structure, activity, and biogeochemical functioning of microbial mats. Mar Pollut Bull 2016; 111:115-125. [PMID: 27449831 DOI: 10.1016/j.marpolbul.2016.07.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 07/11/2016] [Accepted: 07/16/2016] [Indexed: 06/06/2023]
Abstract
Photosynthetic microbial mats are metabolically structured systems driven by solar light. They are ubiquitous and can grow in hydrocarbon-polluted sites. Our aim is to determine the impact of chronic hydrocarbon contamination on the structure, activity, and functioning of a microbial mat. We compared it to an uncontaminated mat harboring similar geochemical characteristics. The mats were sampled in spring and fall for 2years. Seasonal variations were observed for the reference mat: sulfur cycle-related bacteria dominated spring samples, while Cyanobacteria dominated in autumn. The contaminated mat showed minor seasonal variation; a progressive increase of Cyanobacteria was noticed, indicating a perturbation of the classical seasonal behavior. Hydrocarbon content was the main factor explaining the differences in the microbial community structure; however, hydrocarbonoclastic bacteria were among rare or transient Operational Taxonomic Units (OTUs) in the contaminated mat. We suggest that in long-term contaminated systems, hydrocarbonoclastic bacteria cannot be considered a sentinel of contamination.
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Affiliation(s)
- Johanne Aubé
- Equipe Environnement et Microbiologie, IPREM UMR CNRS 5254, Université de Pau et des Pays de l'Adour, IBEAS, BP 1155, 64013 Pau Cedex, France.
| | - Pavel Senin
- Equipe Environnement et Microbiologie, IPREM UMR CNRS 5254, Université de Pau et des Pays de l'Adour, IBEAS, BP 1155, 64013 Pau Cedex, France; Plateforme Bioinformatique Genotoul, UR875, Biométrie et Intelligence Artificielle, INRA, 31326 Castanet-Tolosan, France.
| | - Olivier Pringault
- UMR 9190 MARBEC IRD-Ifremer-CNRS, Université de Montpellier, Place Eugène Bataillon, Case 093, 34095 Montpellier Cedex 5, France.
| | - Patricia Bonin
- MIO, Institut Méditerranéen d'Océanologie, UMR 7294, F13288 Marseille, France.
| | - Bruno Deflandre
- EPOC, UMR 5805, Université de Bordeaux, F33615 Pessac, France.
| | - Olivier Bouchez
- GeT-PlaGe, Genotoul, INRA Auzeville, F31326 Castanet-Tolosan, France.
| | - Noëlle Bru
- Université de Pau et des Pays de l'Adour, Laboratoire de Mathématiques et de leurs Applications de Pau, UMR CNRS 5142, FED 4155 MIRA, Campus Montaury, 64600 Anglet, France.
| | - Edurne Biritxinaga-Etchart
- Université de Pau et des Pays de l'Adour, Laboratoire de Mathématiques et de leurs Applications de Pau, UMR CNRS 5142, FED 4155 MIRA, Campus Montaury, 64600 Anglet, France.
| | - Christophe Klopp
- Plateforme Bioinformatique Genotoul, UR875, Biométrie et Intelligence Artificielle, INRA, 31326 Castanet-Tolosan, France.
| | - Rémy Guyoneaud
- Equipe Environnement et Microbiologie, IPREM UMR CNRS 5254, Université de Pau et des Pays de l'Adour, IBEAS, BP 1155, 64013 Pau Cedex, France.
| | - Marisol Goñi-Urriza
- Equipe Environnement et Microbiologie, IPREM UMR CNRS 5254, Université de Pau et des Pays de l'Adour, IBEAS, BP 1155, 64013 Pau Cedex, France.
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Rupp R, Senin P, Sarry J, Allain C, Tasca C, Ligat L, Portes D, Woloszyn F, Bouchez O, Tabouret G, Lebastard M, Caubet C, Foucras G, Tosser-Klopp G. A Point Mutation in Suppressor of Cytokine Signalling 2 (Socs2) Increases the Susceptibility to Inflammation of the Mammary Gland while Associated with Higher Body Weight and Size and Higher Milk Production in a Sheep Model. PLoS Genet 2015; 11:e1005629. [PMID: 26658352 PMCID: PMC4676722 DOI: 10.1371/journal.pgen.1005629] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 10/06/2015] [Indexed: 11/18/2022] Open
Abstract
Mastitis is an infectious disease mainly caused by bacteria invading the mammary gland. Genetic control of susceptibility to mastitis has been widely evidenced in dairy ruminants, but the genetic basis and underlying mechanisms are still largely unknown. We describe the discovery, fine mapping and functional characterization of a genetic variant associated with elevated milk leukocytes count, or SCC, as a proxy for mastitis. After implementing genome-wide association studies, we identified a major QTL associated with SCC on ovine chromosome 3. Fine mapping of the region, using full sequencing with 12X coverage in three animals, provided one strong candidate SNP that mapped to the coding sequence of a highly conserved gene, suppressor of cytokine signalling 2 (Socs2). The frequency of the SNP associated with increased SCC was 21.7% and the Socs2 genotype explained 12% of the variance of the trait. The point mutation induces the p.R96C substitution in the SH2 functional domain of SOCS2 i.e. the binding site of the protein to various ligands, as well-established for the growth hormone receptor GHR. Using surface plasmon resonance we showed that the p.R96C point mutation completely abrogates SOCS2 binding affinity for the phosphopeptide of GHR. Additionally, the size, weight and milk production in p.R96C homozygote sheep, were significantly increased by 24%, 18%, and 4.4%, respectively, when compared to wild type sheep, supporting the view that the point mutation causes a loss of SOCS2 functional activity. Altogether these results provide strong evidence for a causal mutation controlling SCC in sheep and highlight the major role of SOCS2 as a tradeoff between the host’s inflammatory response to mammary infections, and body growth and milk production, which are all mediated by the JAK/STAT signaling pathway. Mastitis is an inflammation of the mammary gland mainly caused by invading bacteria. Ruminants show natural variability in their predisposition to mastitis, and therefore provide unique models for study of the genetics and physiology of host response to bacterial infection. A genome-wide association study was conducted in a dairy sheep population for milk somatic cell counts as a proxy for mastitis. Fine mapping, using whole genome sequencing, led to the identification of a mutation in the Suppressor of Cytokine Signaling 2 gene (socs2). This mutation was shown to cause a loss of functional activity of the SOCS2 protein, which suggested impairment of feedback control of the JAK/STAT signaling pathways in susceptible animals. Additionally, size, weight and milk production were increased in animals carrying the susceptible variant suggesting a pleiotropic effect of the gene on production versus health traits. Results gave strong evidence of the role of SOCS2 in the host’s inflammation of the udder and provided new insights into the key mechanisms underlying the genetic control of mastitis.
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Affiliation(s)
- Rachel Rupp
- INRA, UMR 1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR 1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR 1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
- * E-mail:
| | - Pavel Senin
- INRA, Sigenae, Castanet-Tolosan, France
- INRA, UR 0875, Mathématiques et Intelligence Artificielle Toulouse, Castanet-Tolosan, France
| | - Julien Sarry
- INRA, UMR 1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR 1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR 1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Charlotte Allain
- INRA, UMR 1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR 1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR 1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Christian Tasca
- Université de Toulouse, Institut National Polytechnique (INP), École Nationale Vétérinaire de Toulouse (ENVT), Unité Mixte de Recherche (UMR) 1225, Interactions Hôtes—Agents Pathogènes (IHAP), Toulouse, France
- INRA, UMR1225, Interactions Hôtes—Agents Pathogènes (IHAP), Toulouse, France
| | - Laeticia Ligat
- INSERM UMR1037, Centre Recherches en Cancérologie de Toulouse, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - David Portes
- INRA, UE0321 Domaine de La Fage, Saint Jean et Saint Paul, France
| | - Florent Woloszyn
- INRA, UMR 1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR 1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR 1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | | | - Guillaume Tabouret
- Université de Toulouse, Institut National Polytechnique (INP), École Nationale Vétérinaire de Toulouse (ENVT), Unité Mixte de Recherche (UMR) 1225, Interactions Hôtes—Agents Pathogènes (IHAP), Toulouse, France
- INRA, UMR1225, Interactions Hôtes—Agents Pathogènes (IHAP), Toulouse, France
| | - Mathieu Lebastard
- Université de Toulouse, Institut National Polytechnique (INP), École Nationale Vétérinaire de Toulouse (ENVT), Unité Mixte de Recherche (UMR) 1225, Interactions Hôtes—Agents Pathogènes (IHAP), Toulouse, France
- INRA, UMR1225, Interactions Hôtes—Agents Pathogènes (IHAP), Toulouse, France
| | - Cécile Caubet
- Université de Toulouse, Institut National Polytechnique (INP), École Nationale Vétérinaire de Toulouse (ENVT), Unité Mixte de Recherche (UMR) 1225, Interactions Hôtes—Agents Pathogènes (IHAP), Toulouse, France
- INRA, UMR1225, Interactions Hôtes—Agents Pathogènes (IHAP), Toulouse, France
| | - Gilles Foucras
- Université de Toulouse, Institut National Polytechnique (INP), École Nationale Vétérinaire de Toulouse (ENVT), Unité Mixte de Recherche (UMR) 1225, Interactions Hôtes—Agents Pathogènes (IHAP), Toulouse, France
- INRA, UMR1225, Interactions Hôtes—Agents Pathogènes (IHAP), Toulouse, France
| | - Gwenola Tosser-Klopp
- INRA, UMR 1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR 1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR 1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
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Pringault O, Aube J, Bouchez O, Klopp C, Mariette J, Escudie F, Senin P, Goni-Urriza M. Contrasted effects of natural complex mixtures of PAHs and metals on oxygen cycle in a microbial mat. Chemosphere 2015; 135:189-201. [PMID: 25957138 DOI: 10.1016/j.chemosphere.2015.04.037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 03/18/2015] [Accepted: 04/14/2015] [Indexed: 06/04/2023]
Abstract
The contamination of polluted environments is often due to a complex mixture of pollutants sometimes at trace levels which nevertheless may have significant effects on the diversity and functioning of organisms. The aim of this study was to assess the functional responses of a microbial mat exposed to a natural complex mixture of PAHs and metals as a function of the maturation stage of the biofilm. Microbial mats sampled in a slightly polluted environment were exposed to contaminated water of a retention basin of an oil refinery. The responses of the microbial mats differed according to season. In spring 2012, strong inhibition of both oxygen production and respiration was observed relative to the control, with rates representing less than 5% of the control after 72 h of incubation. A decrease of microbial activities was followed by a decrease of the coupling between autotrophs and heterotrophs. In contrast, in autumn 2012, no significant changes for oxygen production and respiration were observed and the coupling between autotrophs and heterotrophs was not altered. The differences observed between the spring and autumn mats might be explained by the maturity of the microbial mat with dominance of heterotrophic bacteria in spring, and diatoms and cyanobacteria in autumn, as well as by the differences in the chemical composition of the complex mixture of PAHs and metals.
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Affiliation(s)
- Olivier Pringault
- UMR 9190 MARBEC IRD-Ifremer-CNRS-Université de Montpellier, Place Eugène Bataillon, case 093, 34095 Montpellier cedex 5, France
| | - Johanne Aube
- Equipe Environnement et Microbiologie, UMR IPREM 5254, IBEAS BP 1155, Université de Pau et des Pays de l'Adour, 64013 Pau cedex, France
| | - Olivier Bouchez
- Plateforme Génomique Campus INRA, 24 chemin de borde rouge, 31326 Castanet-Tolosan Cedex, France
| | - Christophe Klopp
- Plateforme Génomique Campus INRA, 24 chemin de borde rouge, 31326 Castanet-Tolosan Cedex, France
| | - Jérome Mariette
- Plateforme Génomique Campus INRA, 24 chemin de borde rouge, 31326 Castanet-Tolosan Cedex, France
| | - Frédéric Escudie
- Plateforme Génomique Campus INRA, 24 chemin de borde rouge, 31326 Castanet-Tolosan Cedex, France
| | - Pavel Senin
- Plateforme Génomique Campus INRA, 24 chemin de borde rouge, 31326 Castanet-Tolosan Cedex, France
| | - Marisol Goni-Urriza
- Equipe Environnement et Microbiologie, UMR IPREM 5254, IBEAS BP 1155, Université de Pau et des Pays de l'Adour, 64013 Pau cedex, France
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Maza E, Frasse P, Senin P, Bouzayen M, Zouine M. Comparison of normalization methods for differential gene expression analysis in RNA-Seq experiments: A matter of relative size of studied transcriptomes. Commun Integr Biol 2013; 6:e25849. [PMID: 26442135 PMCID: PMC3918003 DOI: 10.4161/cib.25849] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 07/22/2013] [Accepted: 07/22/2013] [Indexed: 11/19/2022] Open
Abstract
In recent years, RNA-Seq technologies became a powerful tool for transcriptome studies. However, computational methods dedicated to the analysis of high-throughput sequencing data are yet to be standardized. In particular, it is known that the choice of a normalization procedure leads to a great variability in results of differential gene expression analysis. The present study compares the most widespread normalization procedures and proposes a novel one aiming at removing an inherent bias of studied transcriptomes related to their relative size. Comparisons of the normalization procedures are performed on real and simulated data sets. Real RNA-Seq data sets analyses, performed with all the different normalization methods, show that only 50% of significantly differentially expressed genes are common. This result highlights the influence of the normalization step on the differential expression analysis. Real and simulated data sets analyses give similar results showing 3 different groups of procedures having the same behavior. The group including the novel method named “Median Ratio Normalization” (MRN) gives the lower number of false discoveries. Within this group the MRN method is less sensitive to the modification of parameters related to the relative size of transcriptomes such as the number of down- and upregulated genes and the gene expression levels. The newly proposed MRN method efficiently deals with intrinsic bias resulting from relative size of studied transcriptomes. Validation with real and simulated data sets confirmed that MRN is more consistent and robust than existing methods.
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Affiliation(s)
- Elie Maza
- Université de Toulouse; INP-ENSA Toulouse; Laboratoire Génomique et Biotechnologie des Fruits; Castanet-Tolosan, France ; INRA; Laboratoire Génomique et Biotechnologie des Fruits; Auzeville, Castanet-Tolosan, France
| | - Pierre Frasse
- Université de Toulouse; INP-ENSA Toulouse; Laboratoire Génomique et Biotechnologie des Fruits; Castanet-Tolosan, France ; INRA; Laboratoire Génomique et Biotechnologie des Fruits; Auzeville, Castanet-Tolosan, France
| | - Pavel Senin
- Université de Toulouse; INP-ENSA Toulouse; Laboratoire Génomique et Biotechnologie des Fruits; Castanet-Tolosan, France ; INRA; Laboratoire Génomique et Biotechnologie des Fruits; Auzeville, Castanet-Tolosan, France
| | - Mondher Bouzayen
- Université de Toulouse; INP-ENSA Toulouse; Laboratoire Génomique et Biotechnologie des Fruits; Castanet-Tolosan, France ; INRA; Laboratoire Génomique et Biotechnologie des Fruits; Auzeville, Castanet-Tolosan, France
| | - Mohamed Zouine
- Université de Toulouse; INP-ENSA Toulouse; Laboratoire Génomique et Biotechnologie des Fruits; Castanet-Tolosan, France ; INRA; Laboratoire Génomique et Biotechnologie des Fruits; Auzeville, Castanet-Tolosan, France
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9
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Woyke T, Xie G, Copeland A, González JM, Han C, Kiss H, Saw JH, Senin P, Yang C, Chatterji S, Cheng JF, Eisen JA, Sieracki ME, Stepanauskas R. Assembling the marine metagenome, one cell at a time. PLoS One 2009; 4:e5299. [PMID: 19390573 PMCID: PMC2668756 DOI: 10.1371/journal.pone.0005299] [Citation(s) in RCA: 282] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2009] [Accepted: 03/25/2009] [Indexed: 11/18/2022] Open
Abstract
The difficulty associated with the cultivation of most microorganisms and the complexity of natural microbial assemblages, such as marine plankton or human microbiome, hinder genome reconstruction of representative taxa using cultivation or metagenomic approaches. Here we used an alternative, single cell sequencing approach to obtain high-quality genome assemblies of two uncultured, numerically significant marine microorganisms. We employed fluorescence-activated cell sorting and multiple displacement amplification to obtain hundreds of micrograms of genomic DNA from individual, uncultured cells of two marine flavobacteria from the Gulf of Maine that were phylogenetically distant from existing cultured strains. Shotgun sequencing and genome finishing yielded 1.9 Mbp in 17 contigs and 1.5 Mbp in 21 contigs for the two flavobacteria, with estimated genome recoveries of about 91% and 78%, respectively. Only 0.24% of the assembling sequences were contaminants and were removed from further analysis using rigorous quality control. In contrast to all cultured strains of marine flavobacteria, the two single cell genomes were excellent Global Ocean Sampling (GOS) metagenome fragment recruiters, demonstrating their numerical significance in the ocean. The geographic distribution of GOS recruits along the Northwest Atlantic coast coincided with ocean surface currents. Metabolic reconstruction indicated diverse potential energy sources, including biopolymer degradation, proteorhodopsin photometabolism, and hydrogen oxidation. Compared to cultured relatives, the two uncultured flavobacteria have small genome sizes, few non-coding nucleotides, and few paralogous genes, suggesting adaptations to narrow ecological niches. These features may have contributed to the abundance of the two taxa in specific regions of the ocean, and may have hindered their cultivation. We demonstrate the power of single cell DNA sequencing to generate reference genomes of uncultured taxa from a complex microbial community of marine bacterioplankton. A combination of single cell genomics and metagenomics enabled us to analyze the genome content, metabolic adaptations, and biogeography of these taxa.
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Affiliation(s)
- Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, United States of America
| | - Gary Xie
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Alex Copeland
- DOE Joint Genome Institute, Walnut Creek, California, United States of America
| | - José M. González
- Department of Microbiology, University of La Laguna, La Laguna, Tenerife, Spain
| | - Cliff Han
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Hajnalka Kiss
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Jimmy H. Saw
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Pavel Senin
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Department of Information and Computer Sciences, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Chi Yang
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Institute of Bioinformatics, National Yang-Ming University, Taipei, Taiwan
| | - Sourav Chatterji
- Department of Evolution and Ecology, University of California Davis, Davis, United States of America
| | - Jan-Fang Cheng
- DOE Joint Genome Institute, Walnut Creek, California, United States of America
| | - Jonathan A. Eisen
- DOE Joint Genome Institute, Walnut Creek, California, United States of America
- Department of Evolution and Ecology, University of California Davis, Davis, United States of America
| | - Michael E. Sieracki
- Bigelow Laboratory for Ocean Sciences, West Boothbay Harbor, Maine, United States of America
| | - Ramunas Stepanauskas
- Bigelow Laboratory for Ocean Sciences, West Boothbay Harbor, Maine, United States of America
- * E-mail:
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Hou S, Makarova KS, Saw JHW, Senin P, Ly BV, Zhou Z, Ren Y, Wang J, Galperin MY, Omelchenko MV, Wolf YI, Yutin N, Koonin EV, Stott MB, Mountain BW, Crowe MA, Smirnova AV, Dunfield PF, Feng L, Wang L, Alam M. Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia. Biol Direct 2008; 3:26. [PMID: 18593465 PMCID: PMC2474590 DOI: 10.1186/1745-6150-3-26] [Citation(s) in RCA: 134] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2008] [Accepted: 07/01/2008] [Indexed: 12/31/2022] Open
Abstract
Background The phylum Verrucomicrobia is a widespread but poorly characterized bacterial clade. Although cultivation-independent approaches detect representatives of this phylum in a wide range of environments, including soils, seawater, hot springs and human gastrointestinal tract, only few have been isolated in pure culture. We have recently reported cultivation and initial characterization of an extremely acidophilic methanotrophic member of the Verrucomicrobia, strain V4, isolated from the Hell's Gate geothermal area in New Zealand. Similar organisms were independently isolated from geothermal systems in Italy and Russia. Results We report the complete genome sequence of strain V4, the first one from a representative of the Verrucomicrobia. Isolate V4, initially named "Methylokorus infernorum" (and recently renamed Methylacidiphilum infernorum) is an autotrophic bacterium with a streamlined genome of ~2.3 Mbp that encodes simple signal transduction pathways and has a limited potential for regulation of gene expression. Central metabolism of M. infernorum was reconstructed almost completely and revealed highly interconnected pathways of autotrophic central metabolism and modifications of C1-utilization pathways compared to other known methylotrophs. The M. infernorum genome does not encode tubulin, which was previously discovered in bacteria of the genus Prosthecobacter, or close homologs of any other signature eukaryotic proteins. Phylogenetic analysis of ribosomal proteins and RNA polymerase subunits unequivocally supports grouping Planctomycetes, Verrucomicrobia and Chlamydiae into a single clade, the PVC superphylum, despite dramatically different gene content in members of these three groups. Comparative-genomic analysis suggests that evolution of the M. infernorum lineage involved extensive horizontal gene exchange with a variety of bacteria. The genome of M. infernorum shows apparent adaptations for existence under extremely acidic conditions including a major upward shift in the isoelectric points of proteins. Conclusion The results of genome analysis of M. infernorum support the monophyly of the PVC superphylum. M. infernorum possesses a streamlined genome but seems to have acquired numerous genes including those for enzymes of methylotrophic pathways via horizontal gene transfer, in particular, from Proteobacteria. Reviewers This article was reviewed by John A. Fuerst, Ludmila Chistoserdova, and Radhey S. Gupta.
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Affiliation(s)
- Shaobin Hou
- Advance Studies in Genomics, Proteomics and Bioinformatics, College of Natural Sciences, University of Hawaii, Keller Hall #319, Honolulu, Hawaii, 96822, USA.
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Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, Saw JH, Senin P, Wang W, Ly BV, Lewis KLT, Salzberg SL, Feng L, Jones MR, Skelton RL, Murray JE, Chen C, Qian W, Shen J, Du P, Eustice M, Tong E, Tang H, Lyons E, Paull RE, Michael TP, Wall K, Rice DW, Albert H, Wang ML, Zhu YJ, Schatz M, Nagarajan N, Acob RA, Guan P, Blas A, Wai CM, Ackerman CM, Ren Y, Liu C, Wang J, Wang J, Na JK, Shakirov EV, Haas B, Thimmapuram J, Nelson D, Wang X, Bowers JE, Gschwend AR, Delcher AL, Singh R, Suzuki JY, Tripathi S, Neupane K, Wei H, Irikura B, Paidi M, Jiang N, Zhang W, Presting G, Windsor A, Navajas-Pérez R, Torres MJ, Feltus FA, Porter B, Li Y, Burroughs AM, Luo MC, Liu L, Christopher DA, Mount SM, Moore PH, Sugimura T, Jiang J, Schuler MA, Friedman V, Mitchell-Olds T, Shippen DE, dePamphilis CW, Palmer JD, Freeling M, Paterson AH, Gonsalves D, Wang L, Alam M. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 2008; 452:991-6. [PMID: 18432245 PMCID: PMC2836516 DOI: 10.1038/nature06856] [Citation(s) in RCA: 608] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2007] [Accepted: 02/22/2008] [Indexed: 11/09/2022]
Abstract
Papaya, a fruit crop cultivated in tropical and subtropical regions, is known for its nutritional benefits and medicinal applications. Here we report a 3x draft genome sequence of 'SunUp' papaya, the first commercial virus-resistant transgenic fruit tree to be sequenced. The papaya genome is three times the size of the Arabidopsis genome, but contains fewer genes, including significantly fewer disease-resistance gene analogues. Comparison of the five sequenced genomes suggests a minimal angiosperm gene set of 13,311. A lack of recent genome duplication, atypical of other angiosperm genomes sequenced so far, may account for the smaller papaya gene number in most functional groups. Nonetheless, striking amplifications in gene number within particular functional groups suggest roles in the evolution of tree-like habit, deposition and remobilization of starch reserves, attraction of seed dispersal agents, and adaptation to tropical daylengths. Transgenesis at three locations is closely associated with chloroplast insertions into the nuclear genome, and with topoisomerase I recognition sites. Papaya offers numerous advantages as a system for fruit-tree functional genomics, and this draft genome sequence provides the foundation for revealing the basis of Carica's distinguishing morpho-physiological, medicinal and nutritional properties.
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Affiliation(s)
- Ray Ming
- Hawaii Agriculture Research Center, Aiea, Hawaii 96701, USA
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12
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Dunfield PF, Yuryev A, Senin P, Smirnova AV, Stott MB, Hou S, Ly B, Saw JH, Zhou Z, Ren Y, Wang J, Mountain BW, Crowe MA, Weatherby TM, Bodelier PLE, Liesack W, Feng L, Wang L, Alam M. Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia. Nature 2007; 450:879-82. [DOI: 10.1038/nature06411] [Citation(s) in RCA: 423] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2007] [Accepted: 10/24/2007] [Indexed: 11/09/2022]
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13
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Arigoni R, Chisté R, Drovanti A, Makovec F, Senin P, Setnikar I. Pharmacokinetics of tiropramide after single doses in man. Arzneimittelforschung 1986; 36:738-44. [PMID: 3718598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The plasma levels and urinary excretions of (+/-) alpha-(benzoylamino)-4-[2-(diethylamino)ethoxy]-N, N-dipropyl-benzenepropanamide (tiropramide) and of some of its metabolites were studied in healthy volunteers after the following single-dose administrations of tiropramide hydrochloride: a) i.v. 50 mg, oral 100 mg or rectal 200 mg; b) i.v. 50 mg or i.m. 50 mg; c) oral 100, 200 or 400 mg. After i.v. bolus the plasma levels of tiropramide are consistent with a three-compartment open pharmacokinetic model. The steady-state volume of distribution is 221 l. The terminal elimination constant is 0.279 h-1 (t1/2 = 2.5 h). After i.m. injection the plasma levels increase rapidly (invasion t1/2 = 2 min) and then are similar to those found after i.v. bolus. After oral administration appreciable plasma levels are found after lag times of 18-27 min. They increase with an invasion t1/2 of 14-22 min. The peak is reached 1-1.7 h after administration and the elimination occurs with a constant of 0.20-0.23 h-1. After rectal administration appreciable plasma levels are found after a lag time of 11 min and increase with an invasion t1/2 of 6 min. The peak is reached at 2.2 h. The elimination constant is 0.21 h-1. Tiropramide and some of its metabolites can be determined in the urine by gas-liquid chromatography. The following percentages of the administered dose of tiropramide and tiropramide-related substances can be found in the 24-h urines. After i.v. bolus: 16.2; after i.m. injection: 17.0; after oral administration: 19.6; after rectal administration 13.1.(ABSTRACT TRUNCATED AT 250 WORDS)
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Setnikar I, Senin P, Arigoni R. Validation of assay methods in pharmaceutical QC. Studies on tiropramide hydrochloride. Boll Chim Farm 1984; 123:263-74. [PMID: 6497975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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