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Thieffry S, Aubert J, Devers-Lamrani M, Martin-Laurent F, Romdhane S, Rouard N, Siol M, Spor A. Engineering multi-degrading bacterial communities to bioremediate soils contaminated with pesticides residues. J Hazard Mater 2024; 471:134454. [PMID: 38688223 DOI: 10.1016/j.jhazmat.2024.134454] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 02/29/2024] [Revised: 04/09/2024] [Accepted: 04/25/2024] [Indexed: 05/02/2024]
Abstract
Parallel to the important use of pesticides in conventional agriculture there is a growing interest for green technologies to clear contaminated soil from pesticides and their degradation products. Bioaugmentation i. e. the inoculation of degrading micro-organisms in polluted soil, is a promising method still in needs of further developments. Specifically, improvements in the understanding of how degrading microorganisms must overcome abiotic filters and interact with the autochthonous microbial communities are needed in order to efficiently design bioremediation strategies. Here we designed a protocol aiming at studying the degradation of two herbicides, glyphosate (GLY) and isoproturon (IPU), via experimental modifications of two source bacterial communities. We used statistical methods stemming from genomic prediction to link community composition to herbicides degradation potentials. Our approach proved to be efficient with correlation estimates over 0.8 - between model predictions and measured pesticide degradation values. Multi-degrading bacterial communities were obtained by coalescing bacterial communities with high GLY or IPU degradation ability based on their community-level properties. Finally, we evaluated the efficiency of constructed multi-degrading communities to remove pesticide contamination in a different soil. While results are less clear in the case of GLY, we showed an efficient transfer of degrading capacities towards the receiving soil even at relatively low inoculation levels in the case of IPU. Altogether, we developed an innovative protocol for building multi-degrading simplified bacterial communities with the help of genomic prediction tools and coalescence, and proved their efficiency in a contaminated soil.
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Affiliation(s)
- Sylvia Thieffry
- INRAE, Institut Agro, Université de Bourgogne, Université de Bourgogne Franche-Comté, Agroécologie,21000 Dijon, France; Université Paris-Saclay, AgroParisTech, INRAE, UMR MIA Paris-Saclay, 91120 Palaiseau, France.
| | - Julie Aubert
- Université Paris-Saclay, AgroParisTech, INRAE, UMR MIA Paris-Saclay, 91120 Palaiseau, France
| | - Marion Devers-Lamrani
- INRAE, Institut Agro, Université de Bourgogne, Université de Bourgogne Franche-Comté, Agroécologie,21000 Dijon, France
| | - Fabrice Martin-Laurent
- INRAE, Institut Agro, Université de Bourgogne, Université de Bourgogne Franche-Comté, Agroécologie,21000 Dijon, France
| | - Sana Romdhane
- INRAE, Institut Agro, Université de Bourgogne, Université de Bourgogne Franche-Comté, Agroécologie,21000 Dijon, France
| | - Nadine Rouard
- INRAE, Institut Agro, Université de Bourgogne, Université de Bourgogne Franche-Comté, Agroécologie,21000 Dijon, France
| | - Mathieu Siol
- INRAE, Institut Agro, Université de Bourgogne, Université de Bourgogne Franche-Comté, Agroécologie,21000 Dijon, France
| | - Aymé Spor
- INRAE, Institut Agro, Université de Bourgogne, Université de Bourgogne Franche-Comté, Agroécologie,21000 Dijon, France.
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Lecomte M, Cao W, Aubert J, Sherman DJ, Falentin H, Frioux C, Labarthe S. Revealing the dynamics and mechanisms of bacterial interactions in cheese production with metabolic modelling. Metab Eng 2024; 83:24-38. [PMID: 38460783 DOI: 10.1016/j.ymben.2024.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 05/03/2023] [Revised: 09/29/2023] [Accepted: 02/22/2024] [Indexed: 03/11/2024]
Abstract
Cheese taste and flavour properties result from complex metabolic processes occurring in microbial communities. A deeper understanding of such mechanisms makes it possible to improve both industrial production processes and end-product quality through the design of microbial consortia. In this work, we caracterise the metabolism of a three-species community consisting of Lactococcus lactis, Lactobacillus plantarum and Propionibacterium freudenreichii during a seven-week cheese production process. Using genome-scale metabolic models and omics data integration, we modeled and calibrated individual dynamics using monoculture experiments, and coupled these models to capture the metabolism of the community. This model accurately predicts the dynamics of the community, enlightening the contribution of each microbial species to organoleptic compound production. Further metabolic exploration revealed additional possible interactions between the bacterial species. This work provides a methodological framework for the prediction of community-wide metabolism and highlights the added value of dynamic metabolic modeling for the comprehension of fermented food processes.
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Affiliation(s)
- Maxime Lecomte
- Univ. Rennes, INRAE, STLO, F-35042, Rennes, France; Inria, Univ. Bordeaux, INRAE, F-33400, Talence, France
| | - Wenfan Cao
- Univ. Rennes, INRAE, STLO, F-35042, Rennes, France
| | - Julie Aubert
- Univ. Paris-Saclay, AgroParisTech, INRAE, UMR MIA Paris-Saclay, 91120, Palaiseau, France
| | | | | | | | - Simon Labarthe
- Inria, Univ. Bordeaux, INRAE, F-33400, Talence, France; Univ. Bordeaux, INRAE, BIOGECO, Cestas, France.
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Abellan C, Ioakeim F, Casutt A, Balmpouzis Z, Lechartier B, Noirez L, Aubert J, Rotman S, Koutsokera A. Acute Fibrinous and Organizing Pneumonia (AFOP) in Lung Transplant Recipient: A Case Report of Successful Treatment with Infliximab® and Tocilizumab®. J Heart Lung Transplant 2023. [DOI: 10.1016/j.healun.2023.02.1427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
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Boccaccini L, Arbeiter F, Arena P, Aubert J, Bühler L, Cristescu I, Nevo AD, Eboli M, Forest L, Harrington C, Hernandez F, Knitter R, Neuberger H, Rapisarda D, Sardain P, Spagnuolo G, Utili M, Vala L, Venturini A, Vladimirov P, Zhou G. Status of maturation of critical technologies and systems design: Breeding blanket. Fusion Engineering and Design 2022. [DOI: 10.1016/j.fusengdes.2022.113116] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Romdhane S, Spor A, Aubert J, Bru D, Breuil MC, Hallin S, Mounier A, Ouadah S, Tsiknia M, Philippot L. Unraveling negative biotic interactions determining soil microbial community assembly and functioning. ISME J 2022; 16:296-306. [PMID: 34321619 PMCID: PMC8692615 DOI: 10.1038/s41396-021-01076-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [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: 08/06/2020] [Revised: 07/13/2021] [Accepted: 07/20/2021] [Indexed: 02/07/2023]
Abstract
Microbial communities play important roles in all ecosystems and yet a comprehensive understanding of the ecological processes governing the assembly of these communities is missing. To address the role of biotic interactions between microorganisms in assembly and for functioning of the soil microbiota, we used a top-down manipulation approach based on the removal of various populations in a natural soil microbial community. We hypothesized that removal of certain microbial groups will strongly affect the relative fitness of many others, therefore unraveling the contribution of biotic interactions in shaping the soil microbiome. Here we show that 39% of the dominant bacterial taxa across treatments were subjected to competitive interactions during soil recolonization, highlighting the importance of biotic interactions in the assembly of microbial communities in soil. Moreover, our approach allowed the identification of microbial community assembly rule as exemplified by the competitive exclusion between members of Bacillales and Proteobacteriales. Modified biotic interactions resulted in greater changes in activities related to N- than to C-cycling. Our approach can provide a new and promising avenue to study microbial interactions in complex ecosystems as well as the links between microbial community composition and ecosystem function.
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Affiliation(s)
- Sana Romdhane
- grid.462299.20000 0004 0445 7139Université Bourgogne Franche-Comté, INRAE, AgroSup Dijon, Agroécologie, Dijon, France
| | - Aymé Spor
- grid.462299.20000 0004 0445 7139Université Bourgogne Franche-Comté, INRAE, AgroSup Dijon, Agroécologie, Dijon, France
| | - Julie Aubert
- Université Paris-Saclay, AgroParisTech, INRAE, UMR MIA-Paris, Paris, France
| | - David Bru
- grid.462299.20000 0004 0445 7139Université Bourgogne Franche-Comté, INRAE, AgroSup Dijon, Agroécologie, Dijon, France
| | - Marie-Christine Breuil
- grid.462299.20000 0004 0445 7139Université Bourgogne Franche-Comté, INRAE, AgroSup Dijon, Agroécologie, Dijon, France
| | - Sara Hallin
- grid.6341.00000 0000 8578 2742Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Arnaud Mounier
- grid.462299.20000 0004 0445 7139Université Bourgogne Franche-Comté, INRAE, AgroSup Dijon, Agroécologie, Dijon, France
| | - Sarah Ouadah
- Université Paris-Saclay, AgroParisTech, INRAE, UMR MIA-Paris, Paris, France
| | - Myrto Tsiknia
- grid.462299.20000 0004 0445 7139Université Bourgogne Franche-Comté, INRAE, AgroSup Dijon, Agroécologie, Dijon, France ,grid.10985.350000 0001 0794 1186Soil Science and Agricultural Chemistry Lab, Department of Natural Resources and Agricultural Engineering, Agricultural University of Athens, Athens, Greece
| | - Laurent Philippot
- grid.462299.20000 0004 0445 7139Université Bourgogne Franche-Comté, INRAE, AgroSup Dijon, Agroécologie, Dijon, France
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Mistrangelo C, Bühler L, Smolentsev S, Klüber V, Maione I, Aubert J. MHD flow in liquid metal blankets: Major design issues, MHD guidelines and numerical analysis. Fusion Engineering and Design 2021. [DOI: 10.1016/j.fusengdes.2021.112795] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Villain N, Béra G, Habert MO, Kas A, Aubert J, Jaubert O, Valabregue R, Fernandez-Vidal S, Corvol JC, Mangone G, Lehéricy S, Vidailhet M, Grabli D. Dopamine denervation in the functional territories of the striatum: a new MR and atlas-based 123I-FP-CIT SPECT quantification method. J Neural Transm (Vienna) 2021; 128:1841-1852. [PMID: 34704162 DOI: 10.1007/s00702-021-02434-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 06/22/2021] [Accepted: 10/21/2021] [Indexed: 11/30/2022]
Abstract
Current quantification methods of 123I-FP-CIT SPECT rely on anatomical parcellation of the striatum. We propose here to implement a new method based on MRI segmentation and functional atlas of the basal ganglia (MR-ATLAS) that could provide a reliable quantification within the sensorimotor, associative, and limbic territories of the striatum. Patients with Parkinson's disease (PD), idiopathic rapid eye movement sleep behavioral disorder (iRBD), and healthy controls underwent 123I-FP-CIT SPECT, MRI, motor, and cognitive assessments. SPECT data were corrected for partial volume effects and registered to a functional atlas of the striatum to allow quantification in every functional region of the striatum (nucleus accumbens, limbic, associative, and sensorimotor parts of the striatum). The MR-ATLAS quantification method is proved to be reliable in every territory of the striatum. In addition, good correlations were found between cognitive dysexecutive tests and the binding within the functional (limbic) territories of the striatum using the MR-ATLAS method, slightly better than correlations found using the anatomical quantification method. This new MR-ATLAS method provides a robust and useful tool for studying the dopaminergic system in PD, particularly with respect to cognitive functions. It may also be relevant to further unravel the relationship between dopaminergic denervation and cognitive or behavioral symptoms.
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Affiliation(s)
- Nicolas Villain
- Department of Neurology, AP-HP Sorbonne Université, Hôpital Pitié-Salpêtrière, 47-83 boulevard de l'Hôpital, 75651, Paris Cedex 13, France. .,Institut du Cerveau, ICM, Sorbonne Université, INSERM U1127, CNRS 7225, Paris, France.
| | - G Béra
- Institut du Cerveau, ICM, Sorbonne Université, INSERM U1127, CNRS 7225, Paris, France.,Department of Nuclear Medicine, AP-HP Sorbonne Université, Hôpital Pitié-Salpêtrière, Paris, France
| | - M-O Habert
- Institut du Cerveau, ICM, Sorbonne Université, INSERM U1127, CNRS 7225, Paris, France.,Department of Nuclear Medicine, AP-HP Sorbonne Université, Hôpital Pitié-Salpêtrière, Paris, France.,Laboratoire d'Imagerie Biomédicale, LIB, Sorbonne Université, CNRS, INSERM, Paris, France
| | - A Kas
- Institut du Cerveau, ICM, Sorbonne Université, INSERM U1127, CNRS 7225, Paris, France.,Department of Nuclear Medicine, AP-HP Sorbonne Université, Hôpital Pitié-Salpêtrière, Paris, France.,Laboratoire d'Imagerie Biomédicale, LIB, Sorbonne Université, CNRS, INSERM, Paris, France
| | - J Aubert
- Institut du Cerveau, ICM, Sorbonne Université, INSERM U1127, CNRS 7225, Paris, France
| | - O Jaubert
- Institut du Cerveau, ICM, Sorbonne Université, INSERM U1127, CNRS 7225, Paris, France
| | - R Valabregue
- Institut du Cerveau, ICM, Sorbonne Université, INSERM U1127, CNRS 7225, Paris, France
| | - S Fernandez-Vidal
- Institut du Cerveau, ICM, Sorbonne Université, INSERM U1127, CNRS 7225, Paris, France
| | - J-C Corvol
- Department of Neurology, AP-HP Sorbonne Université, Hôpital Pitié-Salpêtrière, 47-83 boulevard de l'Hôpital, 75651, Paris Cedex 13, France.,Institut du Cerveau, ICM, Sorbonne Université, INSERM U1127, CNRS 7225, Paris, France
| | - G Mangone
- Department of Neurology, AP-HP Sorbonne Université, Hôpital Pitié-Salpêtrière, 47-83 boulevard de l'Hôpital, 75651, Paris Cedex 13, France.,Institut du Cerveau, ICM, Sorbonne Université, INSERM U1127, CNRS 7225, Paris, France
| | - S Lehéricy
- Institut du Cerveau, ICM, Sorbonne Université, INSERM U1127, CNRS 7225, Paris, France.,Department of Neuroradiology, AP-HP Sorbonne Université, Hôpital Pitié-Salpêtrière, Paris, France
| | - M Vidailhet
- Department of Neurology, AP-HP Sorbonne Université, Hôpital Pitié-Salpêtrière, 47-83 boulevard de l'Hôpital, 75651, Paris Cedex 13, France.,Institut du Cerveau, ICM, Sorbonne Université, INSERM U1127, CNRS 7225, Paris, France
| | - D Grabli
- Department of Neurology, AP-HP Sorbonne Université, Hôpital Pitié-Salpêtrière, 47-83 boulevard de l'Hôpital, 75651, Paris Cedex 13, France.,Institut du Cerveau, ICM, Sorbonne Université, INSERM U1127, CNRS 7225, Paris, France
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Cao W, Aubert J, Maillard MB, Boissel F, Leduc A, Thomas JL, Deutsch SM, Camier B, Kerjouh A, Parayre S, Harel-Oger M, Garric G, Thierry A, Falentin H. Fine-Tuning of Process Parameters Modulates Specific Metabolic Bacterial Activities and Aroma Compound Production in Semi-Hard Cheese. J Agric Food Chem 2021; 69:8511-8529. [PMID: 34283609 DOI: 10.1021/acs.jafc.1c01634] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The formation of cheese flavor mainly results from the production of volatile compounds by microorganisms. We investigated how fine-tuning cheese-making process parameters changed the cheese volatilome in a semi-hard cheese inoculated with Lactococcus (L.) lactis, Lactiplantibacillus (L.) plantarum, and Propionibacterium (P.) freudenreichii. A standard (Std) cheese was compared with three variants of technological itineraries: a shorter salting time (7 h vs 10 h, Salt7h), a shorter stirring time (15 min vs 30 min, Stir15min), or a higher ripening temperature (16 °C vs 13 °C, Rip16°C). Bacterial counts were similar in the four cheese types, except for a 1.4 log10 reduction of L. lactis counts in Rip16°C cheeses after 7 weeks of ripening. Compared to Std, Stir15min and Rip16°C increased propionibacterial activity, causing higher concentrations of acetic, succinic, and propanoic acids and lower levels of lactic acid. Rip16°C accelerated secondary proteolysis and volatile production. We thus demonstrated that fine-tuning process parameters could modulate the cheese volatilome by influencing specific bacterial metabolisms.
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Affiliation(s)
- Wenfan Cao
- UMR STLO, INRAE, Institut Agro, 35042 Rennes, France
| | - Julie Aubert
- Université Paris-Saclay, AgroParisTech, INRAE, MIA-Paris, 75005 Paris, France
| | | | | | - Arlette Leduc
- UMR STLO, INRAE, Institut Agro, 35042 Rennes, France
| | | | | | | | - Ali Kerjouh
- UMR STLO, INRAE, Institut Agro, 35042 Rennes, France
| | | | | | - Gilles Garric
- UMR STLO, INRAE, Institut Agro, 35042 Rennes, France
| | - Anne Thierry
- UMR STLO, INRAE, Institut Agro, 35042 Rennes, France
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Lejal E, Chiquet J, Aubert J, Robin S, Estrada-Peña A, Rue O, Midoux C, Mariadassou M, Bailly X, Cougoul A, Gasqui P, Cosson JF, Chalvet-Monfray K, Vayssier-Taussat M, Pollet T. Temporal patterns in Ixodes ricinus microbial communities: an insight into tick-borne microbe interactions. Microbiome 2021; 9:153. [PMID: 34217365 PMCID: PMC8254910 DOI: 10.1186/s40168-021-01051-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 03/17/2021] [Indexed: 06/01/2023]
Abstract
BACKGROUND Ticks transmit pathogens of medical and veterinary importance and are an increasing threat to human and animal health. Assessing disease risk and developing new control strategies requires identifying members of the tick-borne microbiota as well as their temporal dynamics and interactions. METHODS Using high-throughput sequencing, we studied the Ixodes ricinus microbiota and its temporal dynamics. 371 nymphs were monthly collected during three consecutive years in a peri-urban forest. After a Poisson lognormal model was adjusted to our data set, a principal component analysis, sparse network reconstruction, and differential analysis allowed us to assess seasonal and monthly variability of I. ricinus microbiota and interactions within this community. RESULTS Around 75% of the detected sequences belonged to five genera known to be maternally inherited bacteria in arthropods and to potentially circulate in ticks: Candidatus Midichloria, Rickettsia, Spiroplasma, Arsenophonus and Wolbachia. The structure of the I. ricinus microbiota varied over time with interannual recurrence and seemed to be mainly driven by OTUs commonly found in the environment. Total network analysis revealed a majority of positive partial correlations. We identified strong relationships between OTUs belonging to Wolbachia and Arsenophonus, evidence for the presence of the parasitoid wasp Ixodiphagus hookeri in ticks. Other associations were observed between the tick symbiont Candidatus Midichloria and pathogens belonging to Rickettsia. Finally, more specific network analyses were performed on TBP-infected samples and suggested that the presence of pathogens belonging to the genera Borrelia, Anaplasma and Rickettsia may disrupt microbial interactions in I. ricinus. CONCLUSIONS We identified the I. ricinus microbiota and documented marked shifts in tick microbiota dynamics over time. Statistically, we showed strong relationships between the presence of specific pathogens and the structure of the I. ricinus microbiota. We detected close links between some tick symbionts and the potential presence of either pathogenic Rickettsia or a parasitoid in ticks. These new findings pave the way for the development of new strategies for the control of ticks and tick-borne diseases. Video abstract.
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Affiliation(s)
- E Lejal
- UMR BIPAR, Animal Health Laboratory, INRAE, ANSES, Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est, Maisons-Alfort, France
| | - J Chiquet
- Université Paris-Saclay, AgroParisTech, INRAE, UMR MIA-Paris, 75005, Paris, France
| | - J Aubert
- Université Paris-Saclay, AgroParisTech, INRAE, UMR MIA-Paris, 75005, Paris, France
| | - S Robin
- Université Paris-Saclay, AgroParisTech, INRAE, UMR MIA-Paris, 75005, Paris, France
| | - A Estrada-Peña
- Faculty of Veterinary Medicine, University of Zaragoza, Zaragoza, Spain
| | - O Rue
- INRAE, MaIAGE, Université Paris-Saclay, Jouy-en-Josas, France
- INRAE, BioinfOmics, MIGALE Bioinformatics Facility, Université Paris-Saclay, Jouy-en-Josas, France
| | - C Midoux
- INRAE, MaIAGE, Université Paris-Saclay, Jouy-en-Josas, France
- INRAE, BioinfOmics, MIGALE Bioinformatics Facility, Université Paris-Saclay, Jouy-en-Josas, France
- INRAE, PROSE, Université Paris-Saclay, Antony, France
| | - M Mariadassou
- INRAE, MaIAGE, Université Paris-Saclay, Jouy-en-Josas, France
- INRAE, BioinfOmics, MIGALE Bioinformatics Facility, Université Paris-Saclay, Jouy-en-Josas, France
| | - X Bailly
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, 63122, Saint Genes Champanelle, France
- Université de Lyon, INRAE, VetAgro Sup, UMR EPIA, 69280, Marcy l'Etoile, France
| | - A Cougoul
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, 63122, Saint Genes Champanelle, France
- Université de Lyon, INRAE, VetAgro Sup, UMR EPIA, 69280, Marcy l'Etoile, France
| | - P Gasqui
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, 63122, Saint Genes Champanelle, France
- Université de Lyon, INRAE, VetAgro Sup, UMR EPIA, 69280, Marcy l'Etoile, France
| | - J F Cosson
- UMR BIPAR, Animal Health Laboratory, INRAE, ANSES, Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est, Maisons-Alfort, France
| | - K Chalvet-Monfray
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, 63122, Saint Genes Champanelle, France
- Université de Lyon, INRAE, VetAgro Sup, UMR EPIA, 69280, Marcy l'Etoile, France
| | | | - T Pollet
- UMR ASTRE, CIRAD, INRAE, Campus de Baillarguet, Montpellier, France.
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Affiliation(s)
- Julie Aubert
- Université Paris‐SaclayAgroParisTechINRAEMIA‐Paris Paris France
| | | | - Stéphane Robin
- Université Paris‐SaclayAgroParisTechINRAEMIA‐Paris Paris France
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Aubert J, Aiello G, Alonso D, Batal T, Boullon R, Burles S, Cantone B, Cismondi F, Del Nevo A, Maqueda L, Morin A, Rodríguez E, Rueda F, Soldaini M, Vallory J. Design and preliminary analyses of the new Water Cooled Lithium Lead TBM for ITER. Fusion Engineering and Design 2020. [DOI: 10.1016/j.fusengdes.2020.111921] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Painchart L, Drancourt P, Aubert J, Inghels Y, Boyer J. [Interest and difficulties in setting up pharmaceutical reconciliations for patients with dressings for complex wounds]. Ann Pharm Fr 2019; 77:516-531. [PMID: 31255240 DOI: 10.1016/j.pharma.2019.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 01/02/2019] [Revised: 03/23/2019] [Accepted: 06/03/2019] [Indexed: 11/29/2022]
Abstract
OBJECTIVES The management of wounds is a commonplace activity in a patient's healthcare pathway. The involvement of the pharmacist in the management of complex dressings can help strengthen the continuity of this care thanks to the pharmaceutical reconciliation. The objective of this study was to improve the quality of information transmitted between the city and the hospital regarding complex wound dressings. METHODS This is a prospective study consisting of two groups in three services (medicine, diabetology, vascular surgery): the control group corresponded to a classic patient care and in the intervention group, the pharmacists performed dressing reconciliations. A follow-up of the patients after coming back home was realized with healthcare professionals of city involved. RESULTS Twenty patients were included in the control group and 19 in the intervention group. Entry conciliation has improved the quality and quantity of information on wounds transmitted between the city and the hospital. Exit conciliation has increased from 60 to 100% wound and dressing output prescriptions. One hundred percent of nurses surveyed were satisfied with the patients care. CONCLUSIONS Reconciliation would improve information transmitted between the city and the hospital and avoid a break in the continuity of complex wounds cares. However, the time dedicated and the adhesion of the care services were difficulties encountered. This study is the first highlighting the interest of medical device reconciliation and could allow reconciliation extension toward other medical devices.
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Affiliation(s)
- L Painchart
- Service dispositifs médicaux, pôle pharmacie, centre hospitalier de Valenciennes, 59000 Valenciennes, France.
| | - P Drancourt
- Service dispositifs médicaux, pôle pharmacie, centre hospitalier de Valenciennes, 59000 Valenciennes, France
| | - J Aubert
- Service dispositifs médicaux, pôle pharmacie, centre hospitalier de Valenciennes, 59000 Valenciennes, France
| | - Y Inghels
- Service dispositifs médicaux, pôle pharmacie, centre hospitalier de Valenciennes, 59000 Valenciennes, France
| | - J Boyer
- Service dispositifs médicaux, pôle pharmacie, centre hospitalier de Valenciennes, 59000 Valenciennes, France
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Wang X, Lebarbier E, Aubert J, Robin S. Variational Inference for Coupled Hidden Markov Models Applied to the Joint Detection of Copy Number Variations. Int J Biostat 2019; 15:/j/ijb.ahead-of-print/ijb-2018-0023/ijb-2018-0023.xml. [PMID: 30779702 DOI: 10.1515/ijb-2018-0023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 02/22/2018] [Accepted: 11/21/2018] [Indexed: 02/04/2023]
Abstract
Hidden Markov models provide a natural statistical framework for the detection of the copy number variations (CNV) in genomics. In this context, we define a hidden Markov process that underlies all individuals jointly in order to detect and to classify genomics regions in different states (typically, deletion, normal or amplification). Structural variations from different individuals may be dependent. It is the case in agronomy where varietal selection program exists and species share a common phylogenetic past. We propose to take into account these dependencies inthe HMM model. When dealing with a large number of series, maximum likelihood inference (performed classically using the EM algorithm) becomes intractable. We thus propose an approximate inference algorithm based on a variational approach (VEM), implemented in the CHMM R package. A simulation study is performed to assess the performance of the proposed method and an application to the detection of structural variations in plant genomes is presented.
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Affiliation(s)
- Xiaoqiang Wang
- School of Mathematics and Statistics, Shandong University (Weihai), Weihai,Shandong, China
| | - Emilie Lebarbier
- UMR MIA-Paris, AgroParisTech, INRA, Université Paris-Saclay, Paris, France
| | - Julie Aubert
- UMR MIA-Paris, AgroParisTech, INRA, Université Paris-Saclay, Paris, France
| | - Stéphane Robin
- UMR MIA-Paris, AgroParisTech, INRA, Université Paris-Saclay, Paris, France
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15
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Aubert J, Court B. Traumatic Ruptures of the Urethra in Children. Eur Urol 2019. [DOI: 10.1159/000455601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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16
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Bongiovì G, Aiello G, Aubert J, Di Maio P. On the thermal and thermomechanical assessment of the “Optimized Conservative” helium-cooled lithium lead breeding blanket concept for DEMO. Fusion Engineering and Design 2018. [DOI: 10.1016/j.fusengdes.2018.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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17
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Cismondi F, Boccaccini L, Aiello G, Aubert J, Bachmann C, Barrett T, Barucca L, Bubelis E, Ciattaglia S, Del Nevo A, Diegele E, Gasparotto M, Di Gironimo G, Di Maio P, Hernandez F, Federici G, Fernández-Berceruelo I, Franke T, Froio A, Gliss C, Keep J, Loving A, Martelli E, Maviglia F, Moscato I, Mozzillo R, Poitevin Y, Rapisarda D, Savoldi L, Tarallo A, Utili M, Vala L, Veres G, Zanino R. Progress in EU Breeding Blanket design and integration. Fusion Engineering and Design 2018. [DOI: 10.1016/j.fusengdes.2018.04.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Aubert J, Bertino B, Blanchét-Rethore S, Carlavan I, Deret S, Dréno B, Luzy A, Mounier C, Pascau J, Pelisson I, Portal T, Rivier M, Rosso P, Thoreau E, Vial E, Voegel J. LB1569 Non-clinical and human pharmacology of the potent and selective topical RARγ agonist trifarotene. J Invest Dermatol 2018. [DOI: 10.1016/j.jid.2018.06.106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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19
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Aubert J, Piwnica D, Bertino B, Blanchet-Réthoré S, Carlavan I, Déret S, Dreno B, Gamboa B, Jomard A, Luzy AP, Mauvais P, Mounier C, Pascau J, Pelisson I, Portal T, Rivier M, Rossio P, Thoreau E, Vial E, Voegel JJ. Nonclinical and human pharmacology of the potent and selective topical retinoic acid receptor-γ agonist trifarotene. Br J Dermatol 2018; 179:442-456. [PMID: 29974453 DOI: 10.1111/bjd.16719] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2018] [Indexed: 12/28/2022]
Abstract
BACKGROUND First- and third-generation retinoids are the main treatment for acne. Even though efficacious, they lack full selectivity for retinoic acid receptor (RAR) γ, expressed in the epidermis and infundibulum. OBJECTIVES To characterize the in vitro metabolism and the pharmacology of the novel retinoid trifarotene. MATERIALS AND METHODS In vitro assays determined efficacy, potency and selectivity on RARs, as well as the activity on the expression of retinoid target genes in human keratinocytes and ex vivo cultured skin. In vivo studies investigated topical comedolytic, anti-inflammatory and depigmenting properties. The trifarotene-induced gene expression profile was investigated in nonlesional skin of patients with acne and compared with ex vivo and in vivo models. Finally, the metabolic stability in human keratinocytes and hepatic microsomes was established. RESULTS Trifarotene is a selective RARγ agonist with > 20-fold selectivity over RARα and RARβ. Trifarotene is active and stable in keratinocytes but rapidly metabolized by human hepatic microsomes, predicting improved safety. In vivo, trifarotene 0·01% applied topically is highly comedolytic and has anti-inflammatory and antipigmenting properties. Gene expression studies indicated potent activation of known retinoid-modulated processes (epidermal differentiation, proliferation, stress response, retinoic acid metabolism) and novel pathways (proteolysis, transport/skin hydration, cell adhesion) in ex vivo and in vivo models, as well as in human skin after 4 weeks of topical application of trifarotene 0·005% cream. CONCLUSIONS Based on its RARγ selectivity, rapid degradation in human hepatic microsomes and pharmacological properties including potent modulation of epidermal processes, topical treatment with trifarotene could result in good efficacy and may present a favourable safety profile in acne and ichthyotic disorders.
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Affiliation(s)
- J Aubert
- Research Department, Galderma R&D, Les Templiers, 2400 Route des Colles, 06410, Biot, France
| | - D Piwnica
- Research Department, Galderma R&D, Les Templiers, 2400 Route des Colles, 06410, Biot, France
| | - B Bertino
- Research Department, Galderma R&D, Les Templiers, 2400 Route des Colles, 06410, Biot, France
| | - S Blanchet-Réthoré
- Research Department, Galderma R&D, Les Templiers, 2400 Route des Colles, 06410, Biot, France
| | - I Carlavan
- Research Department, Galderma R&D, Les Templiers, 2400 Route des Colles, 06410, Biot, France
| | - S Déret
- Research Department, Galderma R&D, Les Templiers, 2400 Route des Colles, 06410, Biot, France
| | - B Dreno
- Department of Dermatology, Nantes University Hospital, Nantes, France
- CIC, Inserm U892-CNRS 6299, Nantes, France
| | - B Gamboa
- Research Department, Galderma R&D, Les Templiers, 2400 Route des Colles, 06410, Biot, France
| | - A Jomard
- Research Department, Galderma R&D, Les Templiers, 2400 Route des Colles, 06410, Biot, France
| | - A P Luzy
- Research Department, Galderma R&D, Les Templiers, 2400 Route des Colles, 06410, Biot, France
| | - P Mauvais
- Pharma & Life Sciences Xpert, Antibes, France
| | - C Mounier
- Research Department, Galderma R&D, Les Templiers, 2400 Route des Colles, 06410, Biot, France
| | - J Pascau
- Research Department, Galderma R&D, Les Templiers, 2400 Route des Colles, 06410, Biot, France
| | - I Pelisson
- Research Department, Galderma R&D, Les Templiers, 2400 Route des Colles, 06410, Biot, France
| | - T Portal
- Research Department, Galderma R&D, Les Templiers, 2400 Route des Colles, 06410, Biot, France
| | - M Rivier
- Research Department, Galderma R&D, Les Templiers, 2400 Route des Colles, 06410, Biot, France
| | - P Rossio
- Research Department, Galderma R&D, Les Templiers, 2400 Route des Colles, 06410, Biot, France
| | - E Thoreau
- Research Department, Galderma R&D, Les Templiers, 2400 Route des Colles, 06410, Biot, France
| | - E Vial
- Research Department, Galderma R&D, Les Templiers, 2400 Route des Colles, 06410, Biot, France
| | - J J Voegel
- Research Department, Galderma R&D, Les Templiers, 2400 Route des Colles, 06410, Biot, France
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Pellegrin M, Bouzourene K, Aubert J, Mazzolai L. Role of CD4+ T cells in angiotensin II-induced atherosclerosis and plaque vulnerability in 2-kidney, 1-clip APOE-/-MICE. Atherosclerosis 2018. [DOI: 10.1016/j.atherosclerosis.2018.06.317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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21
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Delory T, Jeanmougin P, Le Bel J, Aubert J, Caseris M, Lesprit P, Lariven S, Lescure FX, Bouvet E. Antibioclic+ : intentions de prescriptions et données microbiologiques pour les infections urinaires communautaires. Med Mal Infect 2018. [DOI: 10.1016/j.medmal.2018.04.133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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22
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Chassé H, Aubert J, Boulben S, Le Corguillé G, Corre E, Cormier P, Morales J. Translatome analysis at the egg-to-embryo transition in sea urchin. Nucleic Acids Res 2018; 46:4607-4621. [PMID: 29660001 PMCID: PMC5961321 DOI: 10.1093/nar/gky258] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [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: 07/26/2017] [Revised: 03/09/2018] [Accepted: 03/28/2018] [Indexed: 11/12/2022] Open
Abstract
Early embryogenesis relies on the translational regulation of maternally stored mRNAs. In sea urchin, fertilization triggers a dramatic rise in translation activity, necessary for the onset of cell division. Here, the full spectrum of the mRNAs translated upon fertilization was investigated by polysome profiling and sequencing. The translatome of the early sea urchin embryo gave a complete picture of the polysomal recruitment dynamics following fertilization. Our results indicate that only a subset of maternal mRNAs were selectively recruited onto polysomes, with over-represented functional categories in the translated set. The increase in translation upon fertilization depends on the formation of translation initiation complexes following mTOR pathway activation. Surprisingly, mTOR pathway inhibition differentially affected polysomal recruitment of the newly translated mRNAs, which thus appeared either mTOR-dependent or mTOR-independent. Therefore, our data argue for an alternative to the classical cap-dependent model of translation in early development. The identification of the mRNAs translated following fertilization helped assign translational activation events to specific mRNAs. This translatome is the first step to a comprehensive analysis of the molecular mechanisms governing translation upon fertilization and the translational regulatory networks that control the egg-to-embryo transition as well as the early steps of embryogenesis.
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Affiliation(s)
- Héloïse Chassé
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff Cedex, France
- Sorbonne Université, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff Cedex, France
| | - Julie Aubert
- UMR MIA-Paris, AgroParisTech, INRA, Université Paris-Saclay, 75005 Paris, France
| | - Sandrine Boulben
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff Cedex, France
- Sorbonne Université, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff Cedex, France
| | - Gildas Le Corguillé
- CNRS, Sorbonne Université, FR2424, ABiMS, Station Biologique, 29680 Roscoff, France
| | - Erwan Corre
- CNRS, Sorbonne Université, FR2424, ABiMS, Station Biologique, 29680 Roscoff, France
| | - Patrick Cormier
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff Cedex, France
- Sorbonne Université, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff Cedex, France
| | - Julia Morales
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff Cedex, France
- Sorbonne Université, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688 Roscoff Cedex, France
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23
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Lachaise T, Ourry M, Lebreton L, Guillerm-Erckelboudt AY, Linglin J, Paty C, Chaminade V, Marnet N, Aubert J, Poinsot D, Cortesero AM, Mougel C. Can soil microbial diversity influence plant metabolites and life history traits of a rhizophagous insect? A demonstration in oilseed rape. Insect Sci 2017; 24:1045-1056. [PMID: 28544806 DOI: 10.1111/1744-7917.12478] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [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: 12/06/2016] [Revised: 03/15/2017] [Accepted: 04/19/2017] [Indexed: 05/18/2023]
Abstract
Interactions between plants and phytophagous insects play an important part in shaping the biochemical composition of plants. Reciprocally plant metabolites can influence major life history traits in these insects and largely contribute to their fitness. Plant rhizospheric microorganisms are an important biotic factor modulating plant metabolites and adaptation to stress. While plant-insects or plant-microorganisms interactions and their consequences on the plant metabolite signature are well-documented, the impact of soil microbial communities on plant defenses against phytophagous insects remains poorly known. In this study, we used oilseed rape (Brassica napus) and the cabbage root fly (Delia radicum) as biological models to tackle this question. Even though D. radicum is a belowground herbivore as a larva, its adult life history traits depend on aboveground signals. We therefore tested whether soil microbial diversity influenced emergence rate and fitness but also fly oviposition behavior, and tried to link possible effects to modifications in leaf and root metabolites. Through a removal-recolonization experiment, 3 soil microbial modalities ("high," "medium," "low") were established and assessed through amplicon sequencing of 16S and 18S ribosomal RNA genes. The "medium" modality in the rhizosphere significantly improved insect development traits. Plant-microorganism interactions were marginally associated to modulations of root metabolites profiles, which could partly explain these results. We highlighted the potential role of plant-microbial interaction in plant defenses against Delia radicum. Rhizospheric microbial communities must be taken into account when analyzing plant defenses against herbivores, being either below or aboveground.
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Affiliation(s)
- Tom Lachaise
- IGEPP, Agrocampus Ouest, INRA, Université de Rennes 1, Le Rheu, France
| | - Morgane Ourry
- IGEPP, Agrocampus Ouest, INRA, Université de Rennes 1, Le Rheu, France
| | - Lionel Lebreton
- IGEPP, Agrocampus Ouest, INRA, Université de Rennes 1, Le Rheu, France
| | | | - Juliette Linglin
- IGEPP, Agrocampus Ouest, INRA, Université de Rennes 1, Le Rheu, France
| | - Chrystelle Paty
- IGEPP, Agrocampus Ouest, INRA, Université de Rennes 1, Université Bretagne-Loire, Rennes, France
| | - Valérie Chaminade
- IGEPP, Agrocampus Ouest, INRA, Université de Rennes 1, Université Bretagne-Loire, Rennes, France
| | - Nathalie Marnet
- IGEPP, Agrocampus Ouest, INRA, Université de Rennes 1, Le Rheu, France
- INRA, UR1268 BIA-Le Rheu, France
| | - Julie Aubert
- INRA-AgroParisTech, UMR 518 Applied Mathematics and Computer Sciences-Paris, France
| | - Denis Poinsot
- IGEPP, Agrocampus Ouest, INRA, Université de Rennes 1, Université Bretagne-Loire, Rennes, France
| | - Anne-Marie Cortesero
- IGEPP, Agrocampus Ouest, INRA, Université de Rennes 1, Université Bretagne-Loire, Rennes, France
| | - Christophe Mougel
- IGEPP, Agrocampus Ouest, INRA, Université de Rennes 1, Le Rheu, France
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Aubert J, Aiello G, Arena P, Boullon R, Jaboulay JC, Morin A. Thermo-mechanical analyses and ways of optimization of the helium cooled DEMO First Wall under RCC-MRx rules. Fusion Engineering and Design 2017. [DOI: 10.1016/j.fusengdes.2016.12.040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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25
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Malek R, Bonnarme P, Irlinger F, Frey-Klett P, Onésime D, Aubert J, Loux V, Beckerich JM. Transcriptomic response of Debaryomyces hansenii during mixed culture in a liquid model cheese medium with Yarrowia lipolytica. Int J Food Microbiol 2017; 264:53-62. [PMID: 29111498 DOI: 10.1016/j.ijfoodmicro.2017.10.026] [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: 03/18/2017] [Revised: 10/17/2017] [Accepted: 10/23/2017] [Indexed: 12/31/2022]
Abstract
Yeasts play a crucial role in cheese ripening. They contribute to the curd deacidification, the establishment of acid-sensitive bacterial communities, and flavour compounds production via proteolysis and catabolism of amino acids (AA). Negative yeast-yeast interaction was observed between the yeast Yarrowia lipolytica 1E07 (YL1E07) and the yeast Debaryomyces hansenii 1L25 (DH1L25) in a model cheese but need elucidation. YL1E07 and DH1L25 were cultivated in mono and co-cultures in a liquid synthetic medium (SM) mimicking the cheese environment and the growth inhibition of DH1L25 in the presence of YL1E07 was reproduced. We carried out microbiological, biochemical (lactose, lactate, AA consumption and ammonia production) and transcriptomic analyses by microarray technology to highlight the interaction mechanisms. We showed that the DH1L25 growth inhibition in the presence of YL1E07 was neither due to the ammonia production nor to the nutritional competition for the medium carbon sources between the two yeasts. The transcriptomic study was the key toward the comprehension of yeast-yeast interaction, and revealed that the inhibition of DH1L25 in co-culture is due to a decrease of the mitochondrial respiratory chain functioning.
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Affiliation(s)
- Reine Malek
- UMR 1319 MICALIS, INRA, AgroParisTech, CBAI, BP01, 78850 Thiverval Grignon, France.
| | - Pascal Bonnarme
- INRA, AgroParisTech, UMR 782 Génie et Microbiologie des Procédés Alimentaires, Centre de Biotechnologies Agro-Industrielles, 78850 Thiverval-Grignon, France
| | - Françoise Irlinger
- INRA, AgroParisTech, UMR 782 Génie et Microbiologie des Procédés Alimentaires, Centre de Biotechnologies Agro-Industrielles, 78850 Thiverval-Grignon, France
| | - Pascale Frey-Klett
- UMR 1136 INRA-Université de Lorraine Interactions Arbres/Microorganismes, 54280 Champenoux, France
| | - Djamila Onésime
- UMR 1319 MICALIS, INRA, AgroParisTech, CBAI, BP01, 78850 Thiverval Grignon, France
| | - Julie Aubert
- UMR 518 Mathématiques et Informatiques Appliquées, AgroParisTech, INRA, 16 rue Claude Bernard, 75231 Paris Cedex 05, France
| | - Valentin Loux
- INRA, Unité Mathématique, Informatique et Génome UR1077, 78352 Jouy-en-Josas, France
| | - Jean-Marie Beckerich
- UMR 1319 MICALIS, INRA, AgroParisTech, CBAI, BP01, 78850 Thiverval Grignon, France
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Abdelnour-Berchtold E, Gonzalez M, Bellier J, Wurlod D, Ris H, Piquilloud-Imboden L, Marcucci C, Gronchi F, Nicod L, Aubert J, Krueger T. P-214OUTCOME OF PATIENTS WITH LUNG RE-TRANSPLANTATION REQUIRING PREOPERATIVE EXTRACORPOREAL MEMBRANE OXYGENATION. Interact Cardiovasc Thorac Surg 2017. [DOI: 10.1093/icvts/ivx280.214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Boccaccini L, Aiello G, Aubert J, Bachmann C, Barrett T, Del Nevo A, Demange D, Forest L, Hernandez F, Norajitra P, Porempovic G, Rapisarda D, Sardain P, Utili M, Vala L. Objectives and status of EUROfusion DEMO blanket studies. Fusion Engineering and Design 2016. [DOI: 10.1016/j.fusengdes.2015.12.054] [Citation(s) in RCA: 147] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Aubert J, Aiello G, Jaboulay JC, Kiss B, Morin A. Status on DEMO Helium Cooled Lithium Lead breeding blanket thermo-mechanical analyses. Fusion Engineering and Design 2016. [DOI: 10.1016/j.fusengdes.2016.01.037] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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29
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Di Maio P, Arena P, Aubert J, Bongiovì G, Chiovaro P, Giammusso R, Li Puma A, Tincani A. Analysis of the thermo-mechanical behaviour of the DEMO Water-Cooled Lithium Lead breeding blanket module under normal operation steady state conditions. Fusion Engineering and Design 2015. [DOI: 10.1016/j.fusengdes.2015.03.051] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Bachmann C, Aiello G, Albanese R, Ambrosino R, Arbeiter F, Aubert J, Boccaccini L, Carloni D, Federici G, Fischer U, Kovari M, Li Puma A, Loving A, Maione I, Mattei M, Mazzone G, Meszaros B, Palermo I, Pereslavtsev P, Riccardo V, Sardain P, Taylor N, Villari S, Vizvary Z, Vaccaro A, Visca E, Wenninger R. Initial DEMO tokamak design configuration studies. Fusion Engineering and Design 2015. [DOI: 10.1016/j.fusengdes.2015.05.027] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Dugat-Bony E, Straub C, Teissandier A, Onésime D, Loux V, Monnet C, Irlinger F, Landaud S, Leclercq-Perlat MN, Bento P, Fraud S, Gibrat JF, Aubert J, Fer F, Guédon E, Pons N, Kennedy S, Beckerich JM, Swennen D, Bonnarme P. Overview of a surface-ripened cheese community functioning by meta-omics analyses. PLoS One 2015; 10:e0124360. [PMID: 25867897 PMCID: PMC4395090 DOI: 10.1371/journal.pone.0124360] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [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: 12/20/2014] [Accepted: 03/02/2015] [Indexed: 11/18/2022] Open
Abstract
Cheese ripening is a complex biochemical process driven by microbial communities composed of both eukaryotes and prokaryotes. Surface-ripened cheeses are widely consumed all over the world and are appreciated for their characteristic flavor. Microbial community composition has been studied for a long time on surface-ripened cheeses, but only limited knowledge has been acquired about its in situ metabolic activities. We applied metagenomic, metatranscriptomic and biochemical analyses to an experimental surface-ripened cheese composed of nine microbial species during four weeks of ripening. By combining all of the data, we were able to obtain an overview of the cheese maturation process and to better understand the metabolic activities of the different community members and their possible interactions. Furthermore, differential expression analysis was used to select a set of biomarker genes, providing a valuable tool that can be used to monitor the cheese-making process.
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Affiliation(s)
- Eric Dugat-Bony
- INRA, UMR 782 Génie et Microbiologie des Procédés Alimentaires, F-78850, Thiverval-Grignon, France
- AgroParisTech, UMR 782 Génie et microbiologie des procédés alimentaires, F-78850, Thiverval-Grignon, France
| | - Cécile Straub
- INRA, UMR 782 Génie et Microbiologie des Procédés Alimentaires, F-78850, Thiverval-Grignon, France
- AgroParisTech, UMR 782 Génie et microbiologie des procédés alimentaires, F-78850, Thiverval-Grignon, France
| | - Aurélie Teissandier
- AgroParisTech, UMR 518 Mathématiques et Informatiques Appliquées, F-75231, Paris, France
- INRA, UMR 518 Mathématiques et Informatiques Appliquées, F-75231, Paris, France
| | - Djamila Onésime
- INRA, Institut Micalis, F-78352, Jouy-en-Josas, France
- AgroParisTech, Institut Micalis, F-78352, Jouy-en-Josas, France
| | - Valentin Loux
- INRA, UR1404 Mathématiques et Informatique Appliquées du Génome à l’Environnement, F-78352, Jouy-en-Josas, France
| | - Christophe Monnet
- INRA, UMR 782 Génie et Microbiologie des Procédés Alimentaires, F-78850, Thiverval-Grignon, France
- AgroParisTech, UMR 782 Génie et microbiologie des procédés alimentaires, F-78850, Thiverval-Grignon, France
| | - Françoise Irlinger
- INRA, UMR 782 Génie et Microbiologie des Procédés Alimentaires, F-78850, Thiverval-Grignon, France
- AgroParisTech, UMR 782 Génie et microbiologie des procédés alimentaires, F-78850, Thiverval-Grignon, France
| | - Sophie Landaud
- INRA, UMR 782 Génie et Microbiologie des Procédés Alimentaires, F-78850, Thiverval-Grignon, France
- AgroParisTech, UMR 782 Génie et microbiologie des procédés alimentaires, F-78850, Thiverval-Grignon, France
| | - Marie-Noëlle Leclercq-Perlat
- INRA, UMR 782 Génie et Microbiologie des Procédés Alimentaires, F-78850, Thiverval-Grignon, France
- AgroParisTech, UMR 782 Génie et microbiologie des procédés alimentaires, F-78850, Thiverval-Grignon, France
| | - Pascal Bento
- INRA, UR1404 Mathématiques et Informatique Appliquées du Génome à l’Environnement, F-78352, Jouy-en-Josas, France
| | | | - Jean-François Gibrat
- INRA, UR1404 Mathématiques et Informatique Appliquées du Génome à l’Environnement, F-78352, Jouy-en-Josas, France
| | - Julie Aubert
- AgroParisTech, UMR 518 Mathématiques et Informatiques Appliquées, F-75231, Paris, France
- INRA, UMR 518 Mathématiques et Informatiques Appliquées, F-75231, Paris, France
| | - Frédéric Fer
- INRA, UMR 782 Génie et Microbiologie des Procédés Alimentaires, F-78850, Thiverval-Grignon, France
- AgroParisTech, UMR 782 Génie et microbiologie des procédés alimentaires, F-78850, Thiverval-Grignon, France
- AgroParisTech, UMR 518 Mathématiques et Informatiques Appliquées, F-75231, Paris, France
- INRA, UMR 518 Mathématiques et Informatiques Appliquées, F-75231, Paris, France
| | - Eric Guédon
- INRA, Institut Micalis, F-78352, Jouy-en-Josas, France
- AgroParisTech, Institut Micalis, F-78352, Jouy-en-Josas, France
| | - Nicolas Pons
- INRA, US 1367 Metagenopolis, F-78352, Jouy-en-Josas, France
| | - Sean Kennedy
- INRA, US 1367 Metagenopolis, F-78352, Jouy-en-Josas, France
| | - Jean-Marie Beckerich
- INRA, UMR 782 Génie et Microbiologie des Procédés Alimentaires, F-78850, Thiverval-Grignon, France
- AgroParisTech, UMR 782 Génie et microbiologie des procédés alimentaires, F-78850, Thiverval-Grignon, France
| | - Dominique Swennen
- INRA, UMR 782 Génie et Microbiologie des Procédés Alimentaires, F-78850, Thiverval-Grignon, France
- AgroParisTech, UMR 782 Génie et microbiologie des procédés alimentaires, F-78850, Thiverval-Grignon, France
| | - Pascal Bonnarme
- INRA, UMR 782 Génie et Microbiologie des Procédés Alimentaires, F-78850, Thiverval-Grignon, France
- AgroParisTech, UMR 782 Génie et microbiologie des procédés alimentaires, F-78850, Thiverval-Grignon, France
- * E-mail:
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Marret H, Simon E, Beucher G, Dreyfus M, Gaudineau A, Vayssière C, Lesavre M, Pluchon M, Winer N, Fernandez H, Aubert J, Bejan-Angoulvant T, Jonville-Bera A, Clouqueur E, Houfflin-Debarge V, Garrigue A, Pierre F. Overview and expert assessment of off-label use of misoprostol in obstetrics and gynaecology: review and report by the Collège national des gynécologues obstétriciens français. Eur J Obstet Gynecol Reprod Biol 2015; 187:80-4. [DOI: 10.1016/j.ejogrb.2015.01.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 12/26/2014] [Accepted: 01/23/2015] [Indexed: 11/29/2022]
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Aiello G, Aubert J, Jonquères N, Li Puma A, Morin A, Rampal G. Development of the Helium Cooled Lithium Lead blanket for DEMO. Fusion Engineering and Design 2014. [DOI: 10.1016/j.fusengdes.2013.12.036] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Marret H, Simon E, Beucher G, Dreyfus M, Gaudineau A, Vayssière C, Lesavre M, Pluchon M, Winer N, Fernandez H, Aubert J, Bejan-Angoulvant T, Jonville-Bera AP, Clouqueur É, Houfflin-Debarge V, Garrigue A, Pierre F. État des lieux et expertise de l’usage hors AMM du misoprostol en gynécologie-obstétrique : travail du CNGOF (texte court). ACTA ACUST UNITED AC 2014; 43:107-13. [DOI: 10.1016/j.jgyn.2013.11.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Aubert J, Delalande JP, Skowronski P. [Aneurysm of abdominal aorta rupture in a patient on dabigatran treatment]. Ann Fr Anesth Reanim 2013; 32:271-272. [PMID: 23490462 DOI: 10.1016/j.annfar.2013.02.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 02/01/2013] [Indexed: 06/01/2023]
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Renaud A, Duprès M, Aubert J, Moinard V, Wibaux A, Gressier J. GRP-176 Study of the Importance of the Pharmaceutical Contribution in the Detection of Non Conformity (NC) in the Medication Process in Chemotherapy. Eur J Hosp Pharm 2013. [DOI: 10.1136/ejhpharm-2013-000276.176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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Gicquel T, Aubert J, Lepage S, Fromenty B, Morel I. Quantitative Analysis of Acetaminophen and its Primary Metabolites in Small Plasma Volumes by Liquid Chromatography-Tandem Mass Spectrometry. J Anal Toxicol 2013; 37:110-6. [DOI: 10.1093/jat/bks139] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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Dillies MA, Rau A, Aubert J, Hennequet-Antier C, Jeanmougin M, Servant N, Keime C, Marot G, Castel D, Estelle J, Guernec G, Jagla B, Jouneau L, Laloë D, Le Gall C, Schaëffer B, Le Crom S, Guedj M, Jaffrézic F. A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis. Brief Bioinform 2012; 14:671-83. [PMID: 22988256 DOI: 10.1093/bib/bbs046] [Citation(s) in RCA: 764] [Impact Index Per Article: 63.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
During the last 3 years, a number of approaches for the normalization of RNA sequencing data have emerged in the literature, differing both in the type of bias adjustment and in the statistical strategy adopted. However, as data continue to accumulate, there has been no clear consensus on the appropriate normalization method to be used or the impact of a chosen method on the downstream analysis. In this work, we focus on a comprehensive comparison of seven recently proposed normalization methods for the differential analysis of RNA-seq data, with an emphasis on the use of varied real and simulated datasets involving different species and experimental designs to represent data characteristics commonly observed in practice. Based on this comparison study, we propose practical recommendations on the appropriate normalization method to be used and its impact on the differential analysis of RNA-seq data.
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Affiliation(s)
- Marie-Agnès Dillies
- Institut Pasteur, PF2 Plate-forme Transcriptome et Epigénome, 28 rue du Dr Roux, Paris CEDEX 15, F-75724 France. Tel.: +33 (0) 145688651; Fax: +33 (0) 145688406;
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Bischoff T, Herzig L, Aubert J, Sommer J, Haller DM. [Tomorrow's family doctor]. Rev Med Suisse 2012; 8:1038-1041. [PMID: 22730638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The profession of family doctor will undergo profound changes in the coming decade due to external, political, demographic and societal developments. Changes will also occur from within the profession affecting its content and its functioning. Other influences, in addition to generational developments (reduced working hours, feminisation, revaluation of the work-life balance), will come from collaboration with new professions, news structures as well as technical and human progress. In this transitional period it is important to uphold core values of family medicine, in particular coordination, continuity of care and the global approach to patients. In training future family doctors we must both prepare them for new skills and roles, and continue to share the core values with them.
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Affiliation(s)
- T Bischoff
- Institut universitaire de médecine générale (IUMG), PMU, 1011 Lausanne.
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Gilgien W, Aubert J, Bischoff T, Herzig L, Perdrix J. [Benefits of using rapid HIV testing at the PMU-FLON walk-in clinic in Lausanne]. Rev Med Suisse 2012; 8:1067-1070. [PMID: 22730643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Lab tests are frequently used in primary care to guide patient care. This is particularly the case when a severe disorder, or one that will affect patients' initial care, needs to be excluded rapidly. At the PMU-FLON walk-in clinic the use of HIV testing as recommended by the Swiss Office of Public Health was hampered by the delay in obtaining test results. This led us to introduce rapid HIV testing which provides results within 30 minutes. Following the first 250 tests the authors discuss the results as well as the benefits of rapid HIV testing in an urban walk-in clinic.
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Aubert J, Begriche K, Knockaert L, Robin MA, Fromenty B. Increased expression of cytochrome P450 2E1 in nonalcoholic fatty liver disease: mechanisms and pathophysiological role. Clin Res Hepatol Gastroenterol 2011; 35:630-7. [PMID: 21664213 DOI: 10.1016/j.clinre.2011.04.015] [Citation(s) in RCA: 203] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Accepted: 04/20/2011] [Indexed: 02/07/2023]
Abstract
Due to the worldwide surge in obesity and type 2 diabetes, the increased incidence of nonalcoholic fatty liver disease (NAFLD) is a major concern for the public health. Indeed, NAFLD encompasses a large spectrum of conditions ranging from fatty liver to nonalcoholic steatohepatitis (NASH), which can progress to cirrhosis in some patients. A better understanding of the mechanisms involved in fatty liver and its progression into NASH is important in order to develop efficient drugs able to alleviate these liver diseases. Although numerous investigations pointed to reactive oxygen species (ROS) as key players in the progression of fatty liver to NASH, their exact source is still uncertain. Besides the mitochondrial respiratory chain, cytochrome P450 2E1 (CYP2E1) has recently emerged as another potentially important cause of ROS overproduction. Indeed, higher hepatic CYP2E1 expression and activity have been frequently observed in the context of obesity and NAFLD. It is currently unknown why CYP2E1 is enhanced in these dysmetabolic diseases, although increased hepatic levels of fatty acids and insulin resistance might play a role. Nonetheless, higher hepatic CYP2E1 could play a significant role in the pathophysiology of NASH by inducing lipid peroxidation and oxidative damage of key cellular components. Moreover, CYP2E1-mediated overproduction of ROS could promote hepatic insulin resistance, which can further aggravate fatty liver. Since a significant amount of CYP2E1 can be located within liver mitochondria, higher levels of CYP2E1 in NAFLD could also have detrimental effects on mitochondrial function. Finally, increased CYP2E1 activity during NAFLD could enhance the susceptibility of some patients to the hepatotoxicity of different xenobiotics through the CYP2E1-mediated generation of harmful reactive metabolites.
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Affiliation(s)
- J Aubert
- Inserm, U991, Université de Rennes 1, 35000 Rennes, France
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Dunlop J, Lauck S, Brown B, Rogers D, Aubert J. N012 Transcatheter heart valve procedures: Bridging cardiac surgery and interventional cardiology nursing to facilitate practice in a ‘hybrid' setting. Can J Cardiol 2011. [DOI: 10.1016/j.cjca.2011.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022] Open
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Lédée N, Munaut C, Aubert J, Sérazin V, Rahmati M, Chaouat G, Sandra O, Foidart JM. Specific and extensive endometrial deregulation is present before conception in IVF/ICSI repeated implantation failures (IF) or recurrent miscarriages. J Pathol 2011; 225:554-64. [PMID: 22025212 DOI: 10.1002/path.2948] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Revised: 04/10/2011] [Accepted: 05/25/2011] [Indexed: 11/07/2022]
Abstract
The objective was to examine if IVF/ICSI repeated implantation failures (IF) or recurrent miscarriages (RM) could be related to preconceptional endometrial deregulations. IF was defined as the absence of pregnancy despite the transfer of at least ten IVF/ICSI good quality embryos, and RM as having at least three unexplained miscarriages. Fertile controls (FC) were women who had given birth at least once. Endometrial biopsy was performed in the mild luteal phase of a non-conceptual cycle (five women were selected in each group). Affymetrix chips (GeneChip Human Genome U133 Plus2.0 Array) were used for hybridization. Data were normalized by the gcRMA method, and raw p values adjusted by the Bonferroni procedure (1%). Differential expression of selected genes was analysed using real-time PCR. Gene networks and biological functions were explored using the Ingenuity Pathways Analysis software. Endometrial gene expression profiles at the time of uterine receptivity differ dramatically in the endometrium among FC, RM, and IF patients. Compared to FC, 2126 and 2477 genes are differentially expressed in IF and RM groups, respectively, and 2363 between IF and RM. In both conditions, differential gene expression referred mainly to DNA transcription and expression. Other main cellular functions deregulated in IF conditions correspond to cell morphology, cellular development, cell cycle, and cellular assembly, while in RM conditions, deregulated cellular functions relate to cell signalling (degradation of cyclic AMP and calcium metabolism) and cellular maintenance. In both conditions, there is an over-representation of deregulations related to the haematological system. In the IF condition, cell-mediated immune response and nervous system development and function are highly deregulated, while in RM patients, main deregulations are in organ and tissue development, humoral immune response, and muscular system development and function. Extensive endometrial deregulations are present before conception in patients who experienced IF or RM with both distinct and common deregulation.
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Abdelkarim M, Vintonenko N, Starzec A, Robles A, Aubert J, Martin ML, Mourah S, Podgorniak MP, Rodrigues-Ferreira S, Nahmias C, Couraud PO, Doliger C, Sainte-Catherine O, Peyri N, Chen L, Mariau J, Etienne M, Perret GY, Crepin M, Poyet JL, Khatib AM, Di Benedetto M. Invading basement membrane matrix is sufficient for MDA-MB-231 breast cancer cells to develop a stable in vivo metastatic phenotype. PLoS One 2011; 6:e23334. [PMID: 21858074 PMCID: PMC3156115 DOI: 10.1371/journal.pone.0023334] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [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: 03/28/2011] [Accepted: 07/14/2011] [Indexed: 12/14/2022] Open
Abstract
INTRODUCTION The poor efficacy of various anti-cancer treatments against metastatic cells has focused attention on the role of tumor microenvironment in cancer progression. To understand the contribution of the extracellular matrix (ECM) environment to this phenomenon, we isolated ECM surrogate invading cell populations from MDA-MB-231 breast cancer cells and studied their genotype and malignant phenotype. METHODS We isolated invasive subpopulations (INV) from non invasive populations (REF) using a 2D-Matrigel assay, a surrogate of basal membrane passage. INV and REF populations were investigated by microarray assay and for their capacities to adhere, invade and transmigrate in vitro, and to form metastases in nude mice. RESULTS REF and INV subpopulations were stable in culture and present different transcriptome profiles. INV cells were characterized by reduced expression of cell adhesion and cell-cell junction genes (44% of down regulated genes) and by a gain in expression of anti-apoptotic and pro-angiogenic gene sets. In line with this observation, in vitro INV cells showed reduced adhesion and increased motility through endothelial monolayers and fibronectin. When injected into the circulation, INV cells induced metastases formation, and reduced injected mice survival by up to 80% as compared to REF cells. In nude mice, INV xenografts grew rapidly inducing vessel formation and displaying resistance to apoptosis. CONCLUSION Our findings reveal that the in vitro ECM microenvironment per se was sufficient to select for tumor cells with a stable metastatic phenotype in vivo characterized by loss of adhesion molecules expression and induction of pro-angiogenic and survival factors.
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Affiliation(s)
- Mohamed Abdelkarim
- Université Paris 13, CNRS FRE CSPBAT, Laboratoire de Chimie Structurale Biomoléculaire, UFR SMBH, Bobigny, France
- INSERM 553 Endothélium et Angiogénèse Laboratoire d'Hémostase, Paris, France
| | - Nadejda Vintonenko
- Université Paris 13, CNRS FRE CSPBAT, Laboratoire de Chimie Structurale Biomoléculaire, UFR SMBH, Bobigny, France
- INSERM 553 Endothélium et Angiogénèse Laboratoire d'Hémostase, Paris, France
| | - Anna Starzec
- Université Paris 13, EA4222, Li2P, Bobigny, France
| | - Aniela Robles
- Université Paris 13, CNRS FRE CSPBAT, Laboratoire de Chimie Structurale Biomoléculaire, UFR SMBH, Bobigny, France
- Université Paris 7, UMRS 940. Equipe Avenir, IGM, Paris, France
| | - Julie Aubert
- AgroParisTech, UMR 518, Mathématiques et Informatique Appliquées, Paris, France
| | - Marie-Laure Martin
- AgroParisTech, UMR 518, Mathématiques et Informatique Appliquées, Paris, France
- URGV UMR INRA 1165-CNRS 8114-UEVE, Evry, France
| | - Samia Mourah
- Université Paris 7, UMRS 940. Equipe Avenir, IGM, Paris, France
| | | | - Sylvie Rodrigues-Ferreira
- Inserm, U1016, Institut Cochin, Paris, France
- CNRS UMR 8104, Paris, France, Université Paris Descartes, Paris, France
| | - Clara Nahmias
- Inserm, U1016, Institut Cochin, Paris, France
- CNRS UMR 8104, Paris, France, Université Paris Descartes, Paris, France
| | - Pierre-Olivier Couraud
- Inserm, U1016, Institut Cochin, Paris, France
- CNRS UMR 8104, Paris, France, Université Paris Descartes, Paris, France
| | - Christelle Doliger
- Service Commun d'Imagerie, Institut d'Hématologie, Hôpital Saint Louis, Paris, France
| | - Odile Sainte-Catherine
- Université Paris 13, CNRS FRE CSPBAT, Laboratoire de Chimie Structurale Biomoléculaire, UFR SMBH, Bobigny, France
| | - Nicole Peyri
- Université Paris 13, CNRS FRE CSPBAT, Laboratoire de Chimie Structurale Biomoléculaire, UFR SMBH, Bobigny, France
- Université Paris 7, UMRS 940. Equipe Avenir, IGM, Paris, France
| | - Lei Chen
- INSERM 553 Endothélium et Angiogénèse Laboratoire d'Hémostase, Paris, France
| | - Jérémie Mariau
- INSERM 553 Endothélium et Angiogénèse Laboratoire d'Hémostase, Paris, France
| | - Monique Etienne
- Université Paris 13, Laboratoire d'Histologie, Bobigny, France
| | | | - Michel Crepin
- INSERM 553 Endothélium et Angiogénèse Laboratoire d'Hémostase, Paris, France
| | - Jean-Luc Poyet
- Université Paris 7, UMRS 940. Equipe Avenir, IGM, Paris, France
| | - Abdel-Majid Khatib
- Université Paris 7, UMRS 940. Equipe Avenir, IGM, Paris, France
- INSERM U1029 Université Bordeaux 1, Bordeaux, France
| | - Mélanie Di Benedetto
- Université Paris 13, CNRS FRE CSPBAT, Laboratoire de Chimie Structurale Biomoléculaire, UFR SMBH, Bobigny, France
- Université Paris 7, UMRS 940. Equipe Avenir, IGM, Paris, France
- * E-mail:
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Aubert J, Pajaud J, Robin M, Ribault C, Aninat C, Fromenty B. Comparative assessment of acetaminophen-induced hepatotoxicity in lean and obese mice. Toxicol Lett 2011. [DOI: 10.1016/j.toxlet.2011.05.406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Hébert A, Forquin-Gomez MP, Roux A, Aubert J, Junot C, Loux V, Heilier JF, Bonnarme P, Beckerich JM, Landaud S. Exploration of sulfur metabolism in the yeast Kluyveromyces lactis. Appl Microbiol Biotechnol 2011; 91:1409-23. [DOI: 10.1007/s00253-011-3481-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 06/29/2011] [Accepted: 07/13/2011] [Indexed: 10/17/2022]
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Abstract
AbstractMicrocellular polymer foams are of interest as biomaterials for uses such as artificial skin, synthetic vascular replacements, artificial organs, and for use in permeable drug delivery systems. We wish to report the use of thermally - induced phase separation as a technology by which a variety of polymer foams can be prepared. This process permits control of foam morphology, cell size, and density. Importantly, the phase separation process results in fully open-celled foam structures. Additives such as small molecules and functionalized polymers have been incorporated into these microcellular foams resulting in polymer surfaces with controlled porosity and chemical modification. Microcellular polyurethane foams, with chemically modified surfaces, have potential application as small-diameter vascular replacements.
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Aubert J, Reiniche P, Fogel P, Poulin Y, Lui H, Lynde C, Shapiro J, Villemagne H, Soto P, Voegel JJ. Gene expression profiling in psoriatic scalp hair follicles: clobetasol propionate shampoo 0.05% normalizes psoriasis disease markers. J Eur Acad Dermatol Venereol 2011; 24:1304-11. [PMID: 20337827 DOI: 10.1111/j.1468-3083.2010.03637.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND Clobetasol propionate shampoo is effective and safe in treatment of scalp psoriasis (SP). Gene expression profiling of psoriatic skin biopsies led to the identification of numerous disease-related genes. However, it remained unknown whether the gene expression profile of hair follicles of SP patients was also affected. OBJECTIVES To determine whether psoriasis-related genes are differentially regulated in the hair follicles of SP patients and whether the modulation of these genes can be correlated with clinical severity scores. METHODS A single arm, open study was conducted in three centres. SP patients received daily treatment with clobetasol propionate shampoo. At Baseline, Weeks 2 and 4, investigators assessed clinical severity parameters and collected scalp hair follicles in anagen phase. Total RNA extracted from hair follicles was used to determine the expression level of 44 genes, which were reported previously to be upregulated in the skin of psoriasis patients. RESULTS RNA of good quality and sufficient quantity was obtained from hair follicles of psoriasis patients and healthy volunteers (HV). The expression level of 10 inflammation-related genes was significantly increased in psoriatic hair follicles. The patient's exploratory transcriptomic score, defined as the mean fold modulation of these 10 genes compared with HV, correlated with clinical severity scores. Clobetasol propionate shampoo was effective in decreasing both the exploratory transcriptomics and the clinical severity scores. CONCLUSION Hair follicles of SP patients are affected by the inflammatory process. The change in the expression level of inflammation-related genes correlates with the severity of the disease.
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Affiliation(s)
- J Aubert
- Galderma R&D, Sophia Antipolis, France.
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Forquin MP, Hébert A, Roux A, Aubert J, Proux C, Heilier JF, Landaud S, Junot C, Bonnarme P, Martin-Verstraete I. Global regulation of the response to sulfur availability in the cheese-related bacterium Brevibacterium aurantiacum. Appl Environ Microbiol 2011; 77:1449-59. [PMID: 21169450 PMCID: PMC3067248 DOI: 10.1128/aem.01708-10] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Accepted: 12/05/2010] [Indexed: 11/20/2022] Open
Abstract
In this study, we combined metabolic reconstruction, growth assays, and metabolome and transcriptome analyses to obtain a global view of the sulfur metabolic network and of the response to sulfur availability in Brevibacterium aurantiacum. In agreement with the growth of B. aurantiacum in the presence of sulfate and cystine, the metabolic reconstruction showed the presence of a sulfate assimilation pathway, thiolation pathways that produce cysteine (cysE and cysK) or homocysteine (metX and metY) from sulfide, at least one gene of the transsulfuration pathway (aecD), and genes encoding three MetE-type methionine synthases. We also compared the expression profiles of B. aurantiacum ATCC 9175 during sulfur starvation or in the presence of sulfate. Under sulfur starvation, 690 genes, including 21 genes involved in sulfur metabolism and 29 genes encoding amino acids and peptide transporters, were differentially expressed. We also investigated changes in pools of sulfur-containing metabolites and in expression profiles after growth in the presence of sulfate, cystine, or methionine plus cystine. The expression of genes involved in sulfate assimilation and cysteine synthesis was repressed in the presence of cystine, whereas the expression of metX, metY, metE1, metE2, and BL613, encoding a probable cystathionine-γ-synthase, decreased in the presence of methionine. We identified three ABC transporters: two operons encoding transporters were transcribed more strongly during cysteine limitation, and one was transcribed more strongly during methionine depletion. Finally, the expression of genes encoding a methionine γ-lyase (BL929) and a methionine transporter (metPS) was induced in the presence of methionine in conjunction with a significant increase in volatile sulfur compound production.
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Affiliation(s)
- Marie-Pierre Forquin
- INRA-AgroParisTech, UMR 782 Génie et Microbiologie des Procédés Alimentaires, Centre de Biotechnologies Agro-Industrielles, 78850 Thiverval-Grignon, France, Institut Pasteur, Laboratoire Pathogenèse des Bactéries Anaérobies, 25-28 Rue du Docteur Roux, 75724 Paris Cedex 15, France, INRA-AgroParisTech, UMR 1319 Micalis, Centre de Biotechnologies Agro-Industrielles, 78850 Thiverval-Grignon, France, CEA, Service de Pharmacologie et d'Immunoanalyse, DSV/iBiTec-S, CEA/Saclay, 91191 Gif-sur-Yvette Cedex, France, INRA-AgroParisTech, UMR 518 Mathématiques et Informatiques Appliquées, Paris, France, Institut Pasteur, Plate-forme Puces à ADN, 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France, Université Catholique de Louvain, Louvain Centre for Toxicology and Applied Pharmacology, Brussels, Belgium, Université Paris 7-Denis Diderot, 75205 Paris, France
| | - Agnès Hébert
- INRA-AgroParisTech, UMR 782 Génie et Microbiologie des Procédés Alimentaires, Centre de Biotechnologies Agro-Industrielles, 78850 Thiverval-Grignon, France, Institut Pasteur, Laboratoire Pathogenèse des Bactéries Anaérobies, 25-28 Rue du Docteur Roux, 75724 Paris Cedex 15, France, INRA-AgroParisTech, UMR 1319 Micalis, Centre de Biotechnologies Agro-Industrielles, 78850 Thiverval-Grignon, France, CEA, Service de Pharmacologie et d'Immunoanalyse, DSV/iBiTec-S, CEA/Saclay, 91191 Gif-sur-Yvette Cedex, France, INRA-AgroParisTech, UMR 518 Mathématiques et Informatiques Appliquées, Paris, France, Institut Pasteur, Plate-forme Puces à ADN, 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France, Université Catholique de Louvain, Louvain Centre for Toxicology and Applied Pharmacology, Brussels, Belgium, Université Paris 7-Denis Diderot, 75205 Paris, France
| | - Aurélie Roux
- INRA-AgroParisTech, UMR 782 Génie et Microbiologie des Procédés Alimentaires, Centre de Biotechnologies Agro-Industrielles, 78850 Thiverval-Grignon, France, Institut Pasteur, Laboratoire Pathogenèse des Bactéries Anaérobies, 25-28 Rue du Docteur Roux, 75724 Paris Cedex 15, France, INRA-AgroParisTech, UMR 1319 Micalis, Centre de Biotechnologies Agro-Industrielles, 78850 Thiverval-Grignon, France, CEA, Service de Pharmacologie et d'Immunoanalyse, DSV/iBiTec-S, CEA/Saclay, 91191 Gif-sur-Yvette Cedex, France, INRA-AgroParisTech, UMR 518 Mathématiques et Informatiques Appliquées, Paris, France, Institut Pasteur, Plate-forme Puces à ADN, 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France, Université Catholique de Louvain, Louvain Centre for Toxicology and Applied Pharmacology, Brussels, Belgium, Université Paris 7-Denis Diderot, 75205 Paris, France
| | - Julie Aubert
- INRA-AgroParisTech, UMR 782 Génie et Microbiologie des Procédés Alimentaires, Centre de Biotechnologies Agro-Industrielles, 78850 Thiverval-Grignon, France, Institut Pasteur, Laboratoire Pathogenèse des Bactéries Anaérobies, 25-28 Rue du Docteur Roux, 75724 Paris Cedex 15, France, INRA-AgroParisTech, UMR 1319 Micalis, Centre de Biotechnologies Agro-Industrielles, 78850 Thiverval-Grignon, France, CEA, Service de Pharmacologie et d'Immunoanalyse, DSV/iBiTec-S, CEA/Saclay, 91191 Gif-sur-Yvette Cedex, France, INRA-AgroParisTech, UMR 518 Mathématiques et Informatiques Appliquées, Paris, France, Institut Pasteur, Plate-forme Puces à ADN, 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France, Université Catholique de Louvain, Louvain Centre for Toxicology and Applied Pharmacology, Brussels, Belgium, Université Paris 7-Denis Diderot, 75205 Paris, France
| | - Caroline Proux
- INRA-AgroParisTech, UMR 782 Génie et Microbiologie des Procédés Alimentaires, Centre de Biotechnologies Agro-Industrielles, 78850 Thiverval-Grignon, France, Institut Pasteur, Laboratoire Pathogenèse des Bactéries Anaérobies, 25-28 Rue du Docteur Roux, 75724 Paris Cedex 15, France, INRA-AgroParisTech, UMR 1319 Micalis, Centre de Biotechnologies Agro-Industrielles, 78850 Thiverval-Grignon, France, CEA, Service de Pharmacologie et d'Immunoanalyse, DSV/iBiTec-S, CEA/Saclay, 91191 Gif-sur-Yvette Cedex, France, INRA-AgroParisTech, UMR 518 Mathématiques et Informatiques Appliquées, Paris, France, Institut Pasteur, Plate-forme Puces à ADN, 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France, Université Catholique de Louvain, Louvain Centre for Toxicology and Applied Pharmacology, Brussels, Belgium, Université Paris 7-Denis Diderot, 75205 Paris, France
| | - Jean-François Heilier
- INRA-AgroParisTech, UMR 782 Génie et Microbiologie des Procédés Alimentaires, Centre de Biotechnologies Agro-Industrielles, 78850 Thiverval-Grignon, France, Institut Pasteur, Laboratoire Pathogenèse des Bactéries Anaérobies, 25-28 Rue du Docteur Roux, 75724 Paris Cedex 15, France, INRA-AgroParisTech, UMR 1319 Micalis, Centre de Biotechnologies Agro-Industrielles, 78850 Thiverval-Grignon, France, CEA, Service de Pharmacologie et d'Immunoanalyse, DSV/iBiTec-S, CEA/Saclay, 91191 Gif-sur-Yvette Cedex, France, INRA-AgroParisTech, UMR 518 Mathématiques et Informatiques Appliquées, Paris, France, Institut Pasteur, Plate-forme Puces à ADN, 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France, Université Catholique de Louvain, Louvain Centre for Toxicology and Applied Pharmacology, Brussels, Belgium, Université Paris 7-Denis Diderot, 75205 Paris, France
| | - Sophie Landaud
- INRA-AgroParisTech, UMR 782 Génie et Microbiologie des Procédés Alimentaires, Centre de Biotechnologies Agro-Industrielles, 78850 Thiverval-Grignon, France, Institut Pasteur, Laboratoire Pathogenèse des Bactéries Anaérobies, 25-28 Rue du Docteur Roux, 75724 Paris Cedex 15, France, INRA-AgroParisTech, UMR 1319 Micalis, Centre de Biotechnologies Agro-Industrielles, 78850 Thiverval-Grignon, France, CEA, Service de Pharmacologie et d'Immunoanalyse, DSV/iBiTec-S, CEA/Saclay, 91191 Gif-sur-Yvette Cedex, France, INRA-AgroParisTech, UMR 518 Mathématiques et Informatiques Appliquées, Paris, France, Institut Pasteur, Plate-forme Puces à ADN, 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France, Université Catholique de Louvain, Louvain Centre for Toxicology and Applied Pharmacology, Brussels, Belgium, Université Paris 7-Denis Diderot, 75205 Paris, France
| | - Christophe Junot
- INRA-AgroParisTech, UMR 782 Génie et Microbiologie des Procédés Alimentaires, Centre de Biotechnologies Agro-Industrielles, 78850 Thiverval-Grignon, France, Institut Pasteur, Laboratoire Pathogenèse des Bactéries Anaérobies, 25-28 Rue du Docteur Roux, 75724 Paris Cedex 15, France, INRA-AgroParisTech, UMR 1319 Micalis, Centre de Biotechnologies Agro-Industrielles, 78850 Thiverval-Grignon, France, CEA, Service de Pharmacologie et d'Immunoanalyse, DSV/iBiTec-S, CEA/Saclay, 91191 Gif-sur-Yvette Cedex, France, INRA-AgroParisTech, UMR 518 Mathématiques et Informatiques Appliquées, Paris, France, Institut Pasteur, Plate-forme Puces à ADN, 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France, Université Catholique de Louvain, Louvain Centre for Toxicology and Applied Pharmacology, Brussels, Belgium, Université Paris 7-Denis Diderot, 75205 Paris, France
| | - Pascal Bonnarme
- INRA-AgroParisTech, UMR 782 Génie et Microbiologie des Procédés Alimentaires, Centre de Biotechnologies Agro-Industrielles, 78850 Thiverval-Grignon, France, Institut Pasteur, Laboratoire Pathogenèse des Bactéries Anaérobies, 25-28 Rue du Docteur Roux, 75724 Paris Cedex 15, France, INRA-AgroParisTech, UMR 1319 Micalis, Centre de Biotechnologies Agro-Industrielles, 78850 Thiverval-Grignon, France, CEA, Service de Pharmacologie et d'Immunoanalyse, DSV/iBiTec-S, CEA/Saclay, 91191 Gif-sur-Yvette Cedex, France, INRA-AgroParisTech, UMR 518 Mathématiques et Informatiques Appliquées, Paris, France, Institut Pasteur, Plate-forme Puces à ADN, 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France, Université Catholique de Louvain, Louvain Centre for Toxicology and Applied Pharmacology, Brussels, Belgium, Université Paris 7-Denis Diderot, 75205 Paris, France
| | - Isabelle Martin-Verstraete
- INRA-AgroParisTech, UMR 782 Génie et Microbiologie des Procédés Alimentaires, Centre de Biotechnologies Agro-Industrielles, 78850 Thiverval-Grignon, France, Institut Pasteur, Laboratoire Pathogenèse des Bactéries Anaérobies, 25-28 Rue du Docteur Roux, 75724 Paris Cedex 15, France, INRA-AgroParisTech, UMR 1319 Micalis, Centre de Biotechnologies Agro-Industrielles, 78850 Thiverval-Grignon, France, CEA, Service de Pharmacologie et d'Immunoanalyse, DSV/iBiTec-S, CEA/Saclay, 91191 Gif-sur-Yvette Cedex, France, INRA-AgroParisTech, UMR 518 Mathématiques et Informatiques Appliquées, Paris, France, Institut Pasteur, Plate-forme Puces à ADN, 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France, Université Catholique de Louvain, Louvain Centre for Toxicology and Applied Pharmacology, Brussels, Belgium, Université Paris 7-Denis Diderot, 75205 Paris, France
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Pierre S, Coupé S, Prévot-d'Alvise N, Gaillard S, Richard S, Gouze E, Aubert J, Grillasca J. Cloning of Wap65 in sea bass (Dicentrarchus labrax) and sea bream (Sparus aurata) and expression in sea bass tissues. Comp Biochem Physiol B Biochem Mol Biol 2010; 155:396-402. [DOI: 10.1016/j.cbpb.2010.01.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2009] [Revised: 01/06/2010] [Accepted: 01/07/2010] [Indexed: 10/20/2022]
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