34 results on '"Bernard Fernandez"'
Search Results
2. Revisiting Ehrlichia ruminantium Replication Cycle Using Proteomics: The Host and the Bacterium Perspectives
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Isabel Marcelino, Philippe Holzmuller, Ana Coelho, Gabriel Mazzucchelli, Bernard Fernandez, and Nathalie Vachiéry
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Ehrlichia ruminantium ,endothelial cells ,host response ,immunomodulation ,bacterial life cycle ,differential protein expression ,Biology (General) ,QH301-705.5 - Abstract
The Rickettsiales Ehrlichia ruminantium, the causal agent of the fatal tick-borne disease Heartwater, induces severe damage to the vascular endothelium in ruminants. Nevertheless, E. ruminantium-induced pathobiology remains largely unknown. Our work paves the way for understanding this phenomenon by using quantitative proteomic analyses (2D-DIGE-MS/MS, 1DE-nanoLC-MS/MS and biotin-nanoUPLC-MS/MS) of host bovine aorta endothelial cells (BAE) during the in vitro bacterium intracellular replication cycle. We detect 265 bacterial proteins (including virulence factors), at all time-points of the E. ruminantium replication cycle, highlighting a dynamic bacterium–host interaction. We show that E. ruminantium infection modulates the expression of 433 host proteins: 98 being over-expressed, 161 under-expressed, 140 detected only in infected BAE cells and 34 exclusively detected in non-infected cells. Cystoscape integrated data analysis shows that these proteins lead to major changes in host cell immune responses, host cell metabolism and vesicle trafficking, with a clear involvement of inflammation-related proteins in this process. Our findings led to the first model of E. ruminantium infection in host cells in vitro, and we highlight potential biomarkers of E. ruminantium infection in endothelial cells (such as ROCK1, TMEM16K, Albumin and PTPN1), which may be important to further combat Heartwater, namely by developing non-antibiotic-based strategies.
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- 2021
- Full Text
- View/download PDF
3. Immunomodulatory Effects of Amblyomma variegatum Saliva on Bovine Cells: Characterization of Cellular Responses and Identification of Molecular Determinants
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Valérie Rodrigues, Bernard Fernandez, Arthur Vercoutere, Léo Chamayou, Alexandre Andersen, Oana Vigy, Edith Demettre, Martial Seveno, Rosalie Aprelon, Ken Giraud-Girard, Frédéric Stachurski, Etienne Loire, Nathalie Vachiéry, and Philippe Holzmuller
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Amblyomma variegatum ,tick saliva ,PBMC ,immuno-modulation ,proteomics ,Microbiology ,QR1-502 - Abstract
The tropical bont tick, Amblyomma variegatum, is a tick species of veterinary importance and is considered as one of major pest of ruminants in Africa and in the Caribbean. It causes direct skin lesions, transmits heartwater, and reactivates bovine dermatophilosis. Tick saliva is reported to affect overall host responses through immunomodulatory and anti-inflammatory molecules, among other bioactive molecules. The general objective of this study was to better understand the role of saliva in interaction between the Amblyomma tick and the host using cellular biology approaches and proteomics, and to discuss its impact on disease transmission and/or activation. We first focused on the immuno-modulating effects of semi-fed A. variegatum female saliva on bovine peripheral blood mononuclear cells (PBMC) and monocyte-derived macrophages in vitro. We analyzed its immuno-suppressive properties by measuring the effect of saliva on PBMC proliferation, and observed a significant decrease in ConA-stimulated PBMC lymphoproliferation. We then studied the effect of saliva on bovine macrophages using flow cytometry to analyze the expression of MHC-II and co-stimulation molecules (CD40, CD80, and CD86) and by measuring the production of nitric oxide (NO) and pro- or anti-inflammatory cytokines. We observed a significant decrease in the expression of MHC-II, CD40, and CD80 molecules, associated with decreased levels of IL-12-p40 and TNF-α and increased level of IL-10, which could explain the saliva-induced modulation of NO. To elucidate these immunomodulatory effects, crude saliva proteins were analyzed using proteomics with an Orbitrap Elite mass spectrometer. Among the 336 proteins identified in A. variegatum saliva, we evidenced bioactive molecules exhibiting anti-inflammatory, immuno-modulatory, and anti-oxidant properties (e.g., serpins, phospholipases A2, heme lipoprotein). We also characterized an intriguing ubiquitination complex that could be involved in saliva-induced immune modulation of the host. We propose a model for the interaction between A. variegatum saliva and host immune cells that could have an effect during tick feeding by favoring pathogen dissemination or activation by reducing the efficiency of host immune response to the corresponding tick-borne diseases.
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- 2018
- Full Text
- View/download PDF
4. Alliance of proteomics and genomics to unravel the specificities of Sahara bacterium Deinococcus deserti.
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Arjan de Groot, Rémi Dulermo, Philippe Ortet, Laurence Blanchard, Philippe Guérin, Bernard Fernandez, Benoit Vacherie, Carole Dossat, Edmond Jolivet, Patricia Siguier, Michael Chandler, Mohamed Barakat, Alain Dedieu, Valérie Barbe, Thierry Heulin, Suzanne Sommer, Wafa Achouak, and Jean Armengaud
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Genetics ,QH426-470 - Abstract
To better understand adaptation to harsh conditions encountered in hot arid deserts, we report the first complete genome sequence and proteome analysis of a bacterium, Deinococcus deserti VCD115, isolated from Sahara surface sand. Its genome consists of a 2.8-Mb chromosome and three large plasmids of 324 kb, 314 kb, and 396 kb. Accurate primary genome annotation of its 3,455 genes was guided by extensive proteome shotgun analysis. From the large corpus of MS/MS spectra recorded, 1,348 proteins were uncovered and semiquantified by spectral counting. Among the highly detected proteins are several orphans and Deinococcus-specific proteins of unknown function. The alliance of proteomics and genomics high-throughput techniques allowed identification of 15 unpredicted genes and, surprisingly, reversal of incorrectly predicted orientation of 11 genes. Reversal of orientation of two Deinococcus-specific radiation-induced genes, ddrC and ddrH, and identification in D. deserti of supplementary genes involved in manganese import extend our knowledge of the radiotolerance toolbox of Deinococcaceae. Additional genes involved in nutrient import and in DNA repair (i.e., two extra recA, three translesion DNA polymerases, a photolyase) were also identified and found to be expressed under standard growth conditions, and, for these DNA repair genes, after exposure of the cells to UV. The supplementary nutrient import and DNA repair genes are likely important for survival and adaptation of D. deserti to its nutrient-poor, dry, and UV-exposed extreme environment.
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- 2009
- Full Text
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5. MALDI‐MS/MS of N‐Terminal TMPP‐Acyl Peptides: A Worthwhile Tool to Decipher Protein N‐Termini
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Bernard Fernandez, Jean Armengaud, Gilles Subra, Christine Enjalbal, Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut des Biomolécules Max Mousseron [Pôle Chimie Balard] (IBMM), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM), and Université de Montpellier (UM)
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Mass spectrometry ,MALDI-Tof/Tof ,[SDV]Life Sciences [q-bio] ,Acylation ,Organic Chemistry ,TMPP-acylation ,Spectroscopie ,Protéine ,Réaction chimique ,U50 - Sciences physiques et chimie ,Peptide synthétique ,MS/MS ,Physical and Theoretical Chemistry ,Peptides - Abstract
International audience; N-terminal derivatization of proteins with permanently positive charged reagent constitutes a viable mass spectrometry bottom-up strategy for systematic confident identification of protein N-termini. Although shotgun nanoLC-ESI-MS/MS approaches are commonly applied in that context by dissociating multiply charged molecular ions upon low energy collision-induced dissociations (CID), we were keen to investigate an alternative sequencing method reckoning on more comprehensive high energy charge remote fragmentations (CRF) available with a MALDI-Tof/Tof instrument. Hence, two tunable activation methods, i. e. metastable laser-induced dissociations (LID) and high energy CID, were applied to several synthetic N-terminal tris(trimethoxyphenyl)phosphonium (TMPP) acetyl peptides and their MS/MS behaviors were compared with low energy CID MS/MS data (LC-ESI-QqTof equipment). The amino acid composition was found to play a significant role in the peptide backbone dissociation pathways of these fixed singly charged ions. Proline, arginine, aspartic acid, glutamic acid, but also surprisingly aliphatic residues were impacting the expected sequence fragmentation pattern.
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- 2022
6. Revisiting
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Isabel, Marcelino, Philippe, Holzmuller, Ana, Coelho, Gabriel, Mazzucchelli, Bernard, Fernandez, and Nathalie, Vachiéry
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infection biomarkers ,animal structures ,virulence factors ,host response ,Ehrlichia ruminantium ,immunomodulation ,Article ,endothelial cells ,bacterial life cycle ,differential protein expression - Abstract
The Rickettsiales Ehrlichia ruminantium, the causal agent of the fatal tick-borne disease Heartwater, induces severe damage to the vascular endothelium in ruminants. Nevertheless, E. ruminantium-induced pathobiology remains largely unknown. Our work paves the way for understanding this phenomenon by using quantitative proteomic analyses (2D-DIGE-MS/MS, 1DE-nanoLC-MS/MS and biotin-nanoUPLC-MS/MS) of host bovine aorta endothelial cells (BAE) during the in vitro bacterium intracellular replication cycle. We detect 265 bacterial proteins (including virulence factors), at all time-points of the E. ruminantium replication cycle, highlighting a dynamic bacterium–host interaction. We show that E. ruminantium infection modulates the expression of 433 host proteins: 98 being over-expressed, 161 under-expressed, 140 detected only in infected BAE cells and 34 exclusively detected in non-infected cells. Cystoscape integrated data analysis shows that these proteins lead to major changes in host cell immune responses, host cell metabolism and vesicle trafficking, with a clear involvement of inflammation-related proteins in this process. Our findings led to the first model of E. ruminantium infection in host cells in vitro, and we highlight potential biomarkers of E. ruminantium infection in endothelial cells (such as ROCK1, TMEM16K, Albumin and PTPN1), which may be important to further combat Heartwater, namely by developing non-antibiotic-based strategies.
- Published
- 2021
7. Crimean-Congo Hemorrhagic Fever Virus Antibodies among Livestock on Corsica, France, 2014–2016
- Author
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Noël Tordo, Sébastien Grech-Angelini, François Casabianca, Loic Comtet, Raphaëlle Métras, Philippe Holzmuller, Renaud Lancelot, Olivier Ferraris, Vincent Michaud, Laurence Vial, Christophe N. Peyrefitte, Valérie Rodrigues, Armelle Peyraud, Geneviève Libeau, Renata Servan de Almeida, Aurélie Pédarrieu, Nathalie Vachiery, Bernard Fernandez, Denise Bastron, Groupement Technique Vétérinaire de Corse, Laboratoire de Recherches sur le Développement de l'Elevage (LRDE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Institut Pasteur de Dakar, Réseau International des Instituts Pasteur (RIIP), Unité des Virus Emergents (UVE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), World Health Organisation (WHO), Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Organisation Mondiale de la Santé Animale / World Organisation Animal Health [Paris] (OIE), Institut Pasteur de Guinée, IDvet [Grabels], Laboratoire de Recherche et de Développement de l'EPITA (LRDE), Ecole Pour l'Informatique et les Techniques Avancées (EPITA), French Ministry of Agriculture General Directorate for Food, LESUR, Hélène, Institut de Recherche Biomédicale des Armées (IRBA), Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Organisation Mondiale de la Santé Animale / World Animal Health Information System (OIE-WAHIS)
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Identification ,Epidemiology ,viruses ,[SDV]Life Sciences [q-bio] ,vector-borne infections ,Corsica ,serology ,lcsh:Medicine ,Antibodies, Viral ,L73 - Maladies des animaux ,serologic survey ,Serology ,Crimean-Congo Hemorrhagic Fever Virus Antibodies among Livestock on Corsica, France, 2014–2016 ,0302 clinical medicine ,antibodies ,Caprin ,030212 general & internal medicine ,Fièvre hémorragique de Crimée-Congo ,biology ,tickborne infection ,Hemorrhagic fever virus ,3. Good health ,[SDV] Life Sciences [q-bio] ,Infectious Diseases ,Hemorrhagic Fever Virus, Crimean-Congo ,Livestock ,France ,Antibody ,L72 - Organismes nuisibles des animaux ,Crimean Congo hemorrhagic fever virus ,Microbiology (medical) ,sheep ,goats ,Ovin ,030231 tropical medicine ,Virus ,Sérologie ,lcsh:Infectious and parasitic diseases ,03 medical and health sciences ,Virus identification ,Research Letter ,Animals ,lcsh:RC109-216 ,Crimean-Congo haemorrhagic fever virus [EN] ,Maladie transmissible par tiques ,Bovin ,business.industry ,Anticorps ,lcsh:R ,Virology ,zoonoses ,Crimean-Congo hemorrhagic fever virus ,livestock ,Enquête pathologique ,cattle ,[SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie ,biology.protein ,Hemorrhagic Fever, Crimean ,[SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie ,business - Abstract
Because the NIS reports hospital discharges rather than unique patients, we were unable to identify patients with multiple hospitalizations or estimate the per-person costs of hepatitis A inpatient care. We were also not able to separately report the costs associated with liver transplantation. Even though using highly sensitive inclusion criteria might have introduced an element of cost over-estimation in some patients incidentally diagnosed with hepatitis A while admitted for other conditions, our results almost certainly underestimate hospitalization costs associated with the ongoing hepatitis A outbreaks because NIS does not include hospital-based physician fees. Moreover, the national $306.8 million estimate does not account for outpatient visits , emergency department visits that did not result in an admission to the same hospital, lost productivity , out-of-pocket costs to patients or their informal caregivers, or public health costs associated with the hepatitis A outbreaks, further reinforcing the conservative nature of this estimate. Given the high proportion of hospitalized patients during the ongoing hepatitis A outbreaks, we estimated the average hepatitis A-related hospitalization costs to highlight the preventable economic burden of these outbreaks on healthcare systems and state governments. Hepatitis A is a vaccine-preventable disease. Despite longstanding vaccination recommendations for adults at increased risk for hepatitis A virus infection or adverse consequences of infection, self-reported adult hepatitis A vaccination coverage with >2 doses was only 10.9% for persons >19 years of age in 2017 (6). Our findings underscore the importance of improving hepatitis A vaccination coverage among at-risk adults, in accordance with Advisory Committee on Immunization Practices recommendations (7).
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- 2020
8. Higher Education in Management: The Case of China
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Tianchu Lu, Zhiqiang Lu, and Bernard Fernandez
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Government ,Economic growth ,Higher education ,business.industry ,Best practice ,Political science ,Control (management) ,Cultural values ,Mindset ,China ,business - Abstract
Education is one of the most important cultural values in the Chinese mindset. Business schools have been developing rapidly in China since 1978 to the extent that they are now offering the largest number of degree programs in the world. As China was isolated for years, business schools were under great pressure to reform their model. After looking at best practices in higher education worldwide, Chinese business schools, whether public, private or corporate, developed in their own ways, building international bridges in the academic world, via international cooperation under the control of the Chinese government.
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- 2017
9. Proteomic insights into the lifestyle of an environmentally relevant marine bacterium
- Author
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Bernard Fernandez, Balbina Nogales, Joseph Alexander Christie-Oleza, Jean Armengaud, and Rafael Bosch
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Proteome ,biology ,Ecology ,Ruegeria ,Roseobacter ,biology.organism_classification ,Generalist and specialist species ,Proteomics ,Microbiology ,Bacterial Proteins ,Original Article ,Seawater ,Gene pool ,Rhodobacteraceae ,Adaptation ,Functional genomics ,Phylogeny ,Ecology, Evolution, Behavior and Systematics - Abstract
In terms of lifestyle, free-living bacteria are classified as either oligotrophic/specialist or opportunist/generalist. Heterogeneous marine environments such as coastal waters favour the establishment of marine generalist bacteria, which code for a large pool of functions. This is basically foreseen to cope with the heterogeneity of organic matter supplied to these systems. Nevertheless, it is not known what fraction of a generalist proteome is needed for house-keeping functions or what fraction is modified to cope with environmental changes. Here, we used high-throughput proteomics to define the proteome of Ruegeria pomeroyi DSS-3, a model marine generalist bacterium of the Roseobacter clade. We evaluated its genome expression under several natural environmental conditions, revealing the versatility of the bacterium to adapt to anthropogenic influence, poor nutrient concentrations or the presence of the natural microbial community. We also assayed 30 different laboratory incubations to increase proteome coverage and to dig further into the functional genomics of the bacterium. We established its core proteome and the proteome devoted to adaptation to general cellular physiological variations (almost 50%). We suggest that the other half of its theoretical proteome is the opportunist genetic pool devoted exclusively to very specific environmental conditions.
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- 2011
10. Structural insights into a new homodimeric self‐activated GTPase family
- Author
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Bernard Fernandez, Charles Pineau, Sophie Schmitt, Didier Flament, Dominique Housset, Patrick Forterre, Stephanie Gras, Jean Armengaud, Valérie Chaumont, Arnaud Hecker, Philippe Carpentier, Fabienne Charrier-Savournin, Institut de biologie structurale (IBS - UMR 5075 ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire de Biochimie des Systèmes Perturbés (LBSP), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire de microbiologie des environnements extrêmophiles (LM2E), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Groupe d'Etude de la Reproduction Chez l'Homme et les Mammiferes (GERHM), Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris] (IP), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), and Institut Pasteur [Paris]
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Pyrococcus abyssi ,MESH: Protein Structure, Secondary ,GTPase ,Crystallography, X-Ray ,Biochemistry ,Protein Structure, Secondary ,GTP Phosphohydrolases ,0302 clinical medicine ,Crystal ,Nucleotide ,MESH: Pyrococcus abyssi ,SIMIBI ,Genetics ,chemistry.chemical_classification ,0303 health sciences ,Signal recognition particle ,biology ,Nucleotides ,MESH: DNA, Archaeal ,DNA, Archaeal ,030220 oncology & carcinogenesis ,MESH: Phosphates ,Dimerization ,MESH: Enzyme Activation ,MESH: GTP Phosphohydrolases ,G protein ,Scientific Report ,Replication ,[SDV.BC]Life Sciences [q-bio]/Cellular Biology ,Phosphates ,03 medical and health sciences ,Hydrolase ,Humans ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,Binding site ,Molecular Biology ,030304 developmental biology ,Binding Sites ,MESH: Humans ,Structure ,MESH: Crystallography, X-Ray ,biology.organism_classification ,MESH: Nucleotides ,Enzyme Activation ,MESH: Binding Sites ,MESH: Dimerization ,chemistry ,G-domain - Abstract
The human XAB1/ MBDin GTPase and its close homologues form one of the ten phylogenetically distinct families of the SIMIBI ( after signal recognition particle, MinD and BioD) class of phosphate- binding loop NTPases. The genomic context and the partners identified for the archaeal and eukaryotic homologues indicate that they are involved in genome maintenance - DNA repair or replication. The crystal structure of PAB0955 from Pyrococcus abyssi shows that, unlike other SIMIBI class G proteins, these highly conserved GTPases are homodimeric, regardless of the presence of nucleotides. The nucleotide- binding site of PAB0955 is rather rigid and its conformation is closest to that of the activated SRP G domain. One insertion to the G domain bears a strictly conserved GPN motif, which is part of the catalytic site of the other monomer and stabilizes the phosphate ion formed. Owing to this unique functional feature, we propose to call this family as GPN- loop GTPase.
- Published
- 2007
11. Prioritizing targets for structural biology through the lens of proteomics: The archaeal protein TGAM_1934 from Thermococcus gammatolerans
- Author
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Valérie Aloin, Fabrice Confalonieri, Alain Dedieu, Karine de Guillen, Bernard Fernandez, Jean-Baptiste Boyer, Arnaud Lagorce, Jean Armengaud, Christian Roumestand, Yinshan Yang, Centre de Biochimie Structurale [Montpellier] (CBS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de Biochimie des Systèmes Perturbés (LBSP), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Radiorésistance des bactéries et des archées (RBA), Département Biologie des Génomes (DBG), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Centre de Biochimie Structurale [Montpellier] ( CBS ), Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Biochimie des Systèmes Perturbés ( LBSP ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), Institut de génétique et microbiologie [Orsay] ( IGM ), Université Paris-Sud - Paris 11 ( UP11 ) -Centre National de la Recherche Scientifique ( CNRS ), Radiorésistance des bactéries et des archées ( RBA ), Département Biologie des Génomes ( DBG ), Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ) -Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)
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Models, Molecular ,Proteomics ,Protein Conformation ,Archaeal Proteins ,[SDV]Life Sciences [q-bio] ,Molecular Sequence Data ,Quantitative proteomics ,High-throughput proteomics ,Computational biology ,Biochemistry ,Microbiology ,Protein structure ,Iron-Binding Proteins ,Amino Acid Sequence ,Nuclear Magnetic Resonance, Biomolecular ,Molecular Biology ,Peptide sequence ,biology ,[ SDV ] Life Sciences [q-bio] ,Genome project ,computer.file_format ,ORFan ,biology.organism_classification ,Protein Data Bank ,Molecular biology ,Thermococcus ,Structural biology ,Protein evolution ,NMR structure ,computer ,Genome annotation - Abstract
International audience; ORFans are hypothetical proteins lacking any significant sequence similarity with other proteins. Here, we highlighted by quantitative proteomics the TGAM_1934 ORFan from the hyperradioresistant Thermococcus gammatolerans archaeon as one of the most abundant hypothetical proteins. This protein has been selected as a priority target for structure determination on the basis of its abundance in three cellular conditions. Its solution structure has been determined using multidimensional heteronuclear NMR spectroscopy. TGAM_1934 displays an original fold, although sharing some similarities with the 3D structure of the bacterial ortholog of frataxin, CyaY, a protein conserved in bacteria and eukaryotes and involved in iron-sulfur cluster biogenesis. These results highlight the potential of structural proteomics in prioritizing ORFan targets for structure determination based on quantitative proteomics data. The proteomic data and structure coordinates have been deposited to the ProteomeXchange with identifier PXD000402 (http://proteomecentral.proteomexchange.org/dataset/PXD000402) and Protein Data Bank under the accession number 2mcf, respectively.
- Published
- 2015
12. Unravelling the Mystery of the Atomic Nucleus : A Sixty Year Journey 1896 — 1956
- Author
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Bernard Fernandez, Georges Ripka, Bernard Fernandez, and Georges Ripka
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- Nuclear physics--History
- Abstract
Unravelling the Mystery of the Atomic Nucleus is a history of atomic and nuclear physics. It begins in 1896 with the discovery of radioactivity, which leads to the discovery of the nucleus at the center of the atom. It follows the experimental discoveries and the theoretical developments up to the end of the Fifties.Unlike previous books regarding on history of nuclear physics, this book methodically describes how advances in technology enabled physicists to probe the physical properties of nuclei as well as how the physical laws which govern these microscopic systems were progressively discovered. The reader will gain a clear understanding of how theory is inextricably intertwined with the progress of technology. Unravelling the Mystery of the Atomic Nucleus will be of interest to physicists and to historians of physics, as well as those interested development of science.
- Published
- 2013
13. Argon broadening of the 13CO R(0) and R(7) transitions in the fundamental band at temperatures between 80 and 297K: comparison between experiment and theory
- Author
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Arlan W. Mantz, Henrik Koch, Tom Pedersen, Javier López Cacheiro, Albert Henry, Franck Thibault, Ch. Claveau, Bernard Fernandez, Alain Valentin, Daniel Hurtmans, Mantz, A. W., Thibault, F., Cacheiro, J. L., Fernandez, B., Pedersen, T. B., Koch, H., Valentin, A., Claveau, C., Henry, A., and Hurtmans, D.
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Atomic and Molecular Physics, and Optic ,Argon ,Materials science ,business.industry ,Tunable diode laser ,Ab initio ,chemistry.chemical_element ,Atomic and Molecular Physics, and Optics ,Spectral line ,Optics ,chemistry ,Potential energy surface ,Low temperature ,Line broadening ,Physical and Theoretical Chemistry ,Atomic physics ,Carbon monoxide ,Spectroscopy ,Homogeneous broadening ,business ,Line (formation) ,Doppler broadening - Abstract
We present measurements of Ar-broadening parameters for the R(0) and R(7) lines in the fundamental band of13CO at eight temperatures from 80 to 297 K. The broadening parameters are determined by simultaneous least-squares fitting of spectra recorded using a frequency stabilized diode laser spectrometer. The comparison of the broadening parameter values for R(7) derived at room temperature and different pressures from different line profiles shows that an empirical line profile, which takes into account narrowing effects (Dicke narrowing and absorber speed dependence) but neglects any correlation between collisions, is able to describe the observed lines with constant values of the narrowing and broadening parameters over a 10-500 Torr pressure range. Starting from a recent ab initio potential energy surface, theoretical thermally averaged close coupling values of the Ar broadening parameter are calculated for the same temperatures. The comparison between experimental and calculated values shows an overall agreement of 1.5%. © 2003 Elsevier Inc. All rights reserved.
- Published
- 2003
14. RNA Sequencing and Proteogenomics Reveal the Importance of Leaderless mRNAs in the Radiation-Tolerant Bacterium Deinococcus deserti
- Author
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Jean Armengaud, Bernard Fernandez, Stéphane Cruveiller, David Roche, David Pignol, Monika Ludanyi, Laurence Blanchard, David Vallenet, Arjan de Groot, Biologie végétale et microbiologie environnementale - UMR7265 (BVME), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Microbiologie Environnementale et Moléculaire (MEM), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biochimie des Systèmes Perturbés (LBSP), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire Innovations technologiques pour la Détection et le Diagnostic (LI2D), Service de Pharmacologie et Immunoanalyse (SPI), Médicaments et Technologies pour la Santé (MTS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Médicaments et Technologies pour la Santé (MTS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-07-BLAN-0106,DEINOCOCCUS,Structure of the nucleoïd and radioresistance of Deinococcus radiodurans and Deinococcus deserti(2007), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)
- Subjects
Proteomics ,desiccation tolerance ,protein protection ,[SDV]Life Sciences [q-bio] ,Molecular Sequence Data ,Biology ,genome evolution ,medicine.disease_cause ,Radiation Tolerance ,transcription start sites ,Transcriptome ,Evolution, Molecular ,Eukaryotic translation ,Start codon ,Bacterial Proteins ,Transcription (biology) ,Genetics ,medicine ,Deinococcus ,small peptides ,RNA, Messenger ,Gene ,Ecology, Evolution, Behavior and Systematics ,protein translation initiation ,ComputingMilieux_MISCELLANEOUS ,Base Sequence ,Sequence Analysis, RNA ,Deinococcus deserti ,Proteogenomics ,biology.organism_classification ,Adaptation, Physiological ,RNA, Bacterial ,Research Article - Abstract
Deinococcus deserti is a desiccation- and radiation-tolerant desert bacterium. Differential RNA sequencing (RNA-seq) was performed to explore the specificities of its transcriptome. Strikingly, for 1,174 (60%) mRNAs, the transcription start site was found exactly at (916 cases, 47%) or very close to the translation initiation codon AUG or GUG. Such proportion of leaderless mRNAs, which may resemble ancestral mRNAs, is unprecedented for a bacterial species. Proteomics showed that leaderless mRNAs are efficiently translated in D. deserti. Interestingly, we also found 173 additional transcripts with a 5'-AUG or 5'-GUG that would make them competent for ribosome binding and translation into novel small polypeptides. Fourteen of these are predicted to be leader peptides involved in transcription attenuation. Another 30 correlated with new gene predictions and/or showed conservation with annotated and nonannotated genes in other Deinococcus species, and five of these novel polypeptides were indeed detected by mass spectrometry. The data also allowed reannotation of the start codon position of 257 genes, including several DNA repair genes. Moreover, several novel highly radiation-induced genes were found, and their potential roles are discussed. On the basis of our RNA-seq and proteogenomics data, we propose that translation of many of the novel leaderless transcripts, which may have resulted from single-nucleotide changes and maintained by selective pressure, provides a new explanation for the generation of a cellular pool of small peptides important for protection of proteins against oxidation and thus for radiation/desiccation tolerance and adaptation to harsh environmental conditions.
- Published
- 2014
15. N-Terminal-oriented proteogenomics of the marine bacterium Roseobacter denitrificans Och114 using N-Succinimidyloxycarbonylmethyl tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP) labeling and diagonal chromatography
- Author
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Joseph Alexander Christie-Oleza, Céline Bland, Bernard Fernandez, Erica M. Hartmann, and Jean Armengaud
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Proteomics ,Protein digestion ,Molecular Sequence Data ,Biology ,Tandem mass spectrometry ,Mass spectrometry ,Biochemistry ,Analytical Chemistry ,QH301 ,Organophosphorus Compounds ,Bacterial Proteins ,Tandem Mass Spectrometry ,Amino Acid Sequence ,Molecular Biology ,Chromatography ,Base Sequence ,Technological Innovation and Resources ,Molecular Sequence Annotation ,Gene Annotation ,Roseobacter ,Proteogenomics ,biology.organism_classification ,Peptides ,Genome, Bacterial - Abstract
Given the ease of whole genome sequencing with next-generation sequencers, structural and functional gene annotation is now purely based on automated prediction. However, errors in gene structure are frequent, the correct determination of start codons being one of the main concerns. Here, we combine protein N termini derivatization using (N-Succinimidyloxycarbonylmethyl)tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP Ac-OSu) as a labeling reagent with the COmbined FRActional DIagonal Chromatography (COFRADIC) sorting method to enrich labeled N-terminal peptides for mass spectrometry detection. Protein digestion was performed in parallel with three proteases to obtain a reliable automatic validation of protein N termini. The analysis of these N-terminal enriched fractions by high-resolution tandem mass spectrometry allowed the annotation refinement of 534 proteins of the model marine bacterium Roseobacter denitrificans OCh114. This study is especially efficient regarding mass spectrometry analytical time. From the 534 validated N termini, 480 confirmed existing gene annotations, 41 highlighted erroneous start codon annotations, five revealed totally new mis-annotated genes; the mass spectrometry data also suggested the existence of multiple start sites for eight different genes, a result that challenges the current view of protein translation initiation. Finally, we identified several proteins for which classical genome homology-driven annotation was inconsistent, questioning the validity of automatic annotation pipelines and emphasizing the need for complementary proteomic data. All data have been deposited to the ProteomeXchange with identifier PXD000337.
- Published
- 2014
16. Unravelling the Mystery of the Atomic Nucleus: A Sixty Year Journey 1896 — 1956
- Author
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Georges Ripka and Bernard Fernandez
- Subjects
Discovery of the neutron ,Nuclear reaction ,Nuclear physics ,Physics ,symbols.namesake ,Pauli exclusion principle ,Atomic nucleus ,Particle Physics – Theory ,symbols ,Nuclear force ,Alpha particle ,Nuclear matter ,Bohr model - Abstract
Foreword.- Chapter 1. Radioactivity, the First Puzzles.- The "Uranic Rays" of Henri Becquerel.- Polonium and Radium.- Emanation from Thorium.- The Puzzle is Disentangled.- Consecrations and Mourning: the End of an Era.- Chapter 2. A Nucleus at the Heart of the Atom.- Prehistory of the Atom.- 1897: The Electrons Are in the Atom.- The Scattering of alpha Particles Makes It Possible to "See" a Nucleus in the Atom.- A Last Ingredient: Moseley Measures the Charge of the Nucleus in the Atom.- Chapter 3. Quantum Mechanics, the Unavoidable Path.- Branching Off.- An Improbable Beginning.- Niels Bohr: The Quanta Are in the Atom.- 1913-1923: Victories and Setbacks.- 1925: Spin and the Pauli Principle.- Quantum Mechanics.- Chapter 4. A Timid Infancy.- The Atomic Nucleus in 1913.- The Discovery of Isotopes and the Measurement of Masses of Nuclei.- An Enquiry Full of Surprises: ss Radioactivity.- The First Nuclear Reactions.- The Nucleus in 1920 According to Rutherford.- The Rapid Expansion of Experimental Means.- The Atomic Nucleus in 1930.- Chapter 5. 1930-1940: A Dazzling Development.- The Nucleus: A New Boundary.- The Discovery of the Neutron.- Nuclear Theory After the Discovery of the Neutron.- A New Particle: The Positron.- The Birth of Particle Accelerators.- "Charge Independence" of the Nuclear Force.- The Discovery of Artificial Radioactivity.- The School of Rome.- The Great Exodus of Jewish Scientists Under Nazism.- A Proliferation of Theories: Yukawa, Breit and Wigner, Bohr.- The Death of a Giant: Ernest Rutherford.- Hans Bethe Sums Up the Situation in 1936-1937.- The Fission of Uranium.- Chapter 6. The Upheavals of the Second World War.- A Chronology.- The New Face of Physics After the War.- Chapter 7. The Time of Maturity.- New Experimental Means.- Data Accumulate.- The "Shell" Structure of Nuclei.- Elastic Scattering and the "Optical Model".- Direct Nuclear Reactions.- A Collective Behavior.- A Unified Model of the Nucleus.- The Nuclear Force.- Nuclear Matter.- Chapter 8. Where the Narrative Ends.- Glossary.- Bibliography of Cited Books.- Index.
- Published
- 2013
17. A Nucleus at the Heart of the Atom
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Bernard Fernandez
- Subjects
Physics ,Helium atom ,Electric charge ,Spectral line ,Atomic mass ,Marie curie ,symbols.namesake ,chemistry.chemical_compound ,medicine.anatomical_structure ,chemistry ,Zinc sulphide ,Avogadro constant ,symbols ,medicine ,Atomic physics ,Nucleus - Abstract
The concept of atoms has existed for centuries, ever since the speculations of Epicurus, until the hesitations of the abbot Nollet. The first experimental manifestations and the conjectures of Dalton, Avogadro and Prout. The atom, a modest point-like object at first, becomes adorned with spectral lines and claims the right to possess an internal structure.
- Published
- 2012
18. The Time of Maturity
- Author
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Bernard Fernandez
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Computer science ,SHELL model ,Maturity (finance) ,Engineering physics - Abstract
A variety of new accelerators are aimed at creating beams of increasingly energetic particles. New means of detecting and analyzing particles are invented, mostly due to the development of electronic devices which become numerous, varied and flexible, the fruit of apparently unlimited imagination.
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- 2012
19. Radioactivity: The First Puzzles
- Author
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Bernard Fernandez
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Photographic plate ,Becquerel ,chemistry ,Philosophy ,chemistry.chemical_element ,Astronomy ,Uranium ,Radiation ,Marie curie - Abstract
Henri Becquerel, while searching for X-rays, discovers a radiation emitted by uranium. The scientific community shows no interest in such a weak and incomprehensible phenomenon with no practical applications.
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- 2012
20. Where the Narrative Ends
- Author
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Bernard Fernandez
- Subjects
media_common.quotation_subject ,Political economy ,Political science ,Narrative ,Prosperity ,media_common - Abstract
At the end of the 1950s, nuclear physics is in full bloom. The structure of nuclei is beginning to be understood, and increasingly powerful experimental means probe the nucleus as never before. The economic prosperity as well as strategic considerations, royally endow nuclear physics both humanly and financially. The early years of teeming activity are followed by a period of intensive work devoted to the consolidation and the deepening of our understanding of nuclei.
- Published
- 2012
21. A Timid Infancy
- Author
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Bernard Fernandez
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Niels bohr ,Nuclear reaction ,Physics ,Quantum mechanics ,Atomic nucleus ,Continuous spectrum ,Physics::Atomic Physics ,Nuclear Experiment ,Physics::History of Physics ,Atomic mass - Abstract
In the second of the three famous papers, which Niels Bohr wrote in 1913, and in which he described the properties of atoms in terms of quantum physics, he concluded that radioactive phenomena most likely occur in the atomic nucleus
- Published
- 2012
22. The Upheavals of the Second World War
- Author
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Bernard Fernandez
- Subjects
Refugee ,World War II ,Interwar period ,chemistry.chemical_element ,Natural uranium ,Uranium ,language.human_language ,Plutonium ,German ,chemistry ,Political science ,language ,Economic history ,Manhattan project - Abstract
Two refugees, one German, the other Austrian, show the English the extraordinary destructive power which a pure uranium 235 bomb would have. After a tedious start, the United States devote immense resources, both financial and human, in order to build a uranium or plutonium “atomic” bomb. Hiroshima and Nagasaki are destroyed by nuclear fire.
- Published
- 2012
23. Biosynthesis of wyosine derivatives in tRNA: an ancient and highly diverse pathway in Archaea
- Author
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Valérie de Crécy-Lagard, Henri Grosjean, Akiko Noma, Jean Armengaud, Céline Brochier-Armanet, Sophie Alvarez, Bernard Fernandez, Gabriela Phillips, Benjamin J. Lyons, Jaunius Urbonavičius, Louis Droogmans, Institut de génétique et microbiologie [Orsay] (IGM), and Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
Genome ,Mass Spectrometry ,03 medical and health sciences ,chemistry.chemical_compound ,Biosynthesis ,RNA, Transfer ,Crenarchaeota ,Genetics ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,Molecular Biology ,Gene ,Ecology, Evolution, Behavior and Systematics ,Research Articles ,Phylogeny ,030304 developmental biology ,0303 health sciences ,biology ,Guanosine ,030302 biochemistry & molecular biology ,biology.organism_classification ,Archaea ,[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology ,chemistry ,Biochemistry ,Transfer RNA ,Euryarchaeota ,Wybutosine ,Chromatography, Liquid ,Signal Transduction - Abstract
International audience; Wyosine (imG) and its derivatives such as wybutosine (yW) are found at position 37 of phenylalanine-specific transfer RNA (tRNA(Phe)), 3' adjacent to the anticodon in Eucarya and Archaea. In Saccharomyces cerevisiae, formation of yW requires five enzymes acting in a strictly sequential order: Trm5, Tyw1, Tyw2, Tyw3, and Tyw4. Archaea contain wyosine derivatives, but their diversity is greater than in eukaryotes and the corresponding biosynthesis pathways still unknown. To identify these pathways, we analyzed the phylogenetic distribution of homologues of the yeast wybutosine biosynthesis proteins in 62 archaeal genomes and proposed a scenario for the origin and evolution of wyosine derivatives biosynthesis in Archaea that was partly experimentally validated. The key observations were 1) that four of the five wybutosine biosynthetic enzymes are ancient and may have been present in the last common ancestor of Archaea and Eucarya, 2) that the variations in the distribution pattern of biosynthesis enzymes reflect the diversity of the wyosine derivatives found in different Archaea. We also identified 7-aminocarboxypropyl-demethylwyosine (yW-86) and its N4-methyl derivative (yW-72) as final products in tRNAs of several Archaea when these were previously thought to be only intermediates of the eukaryotic pathway. We confirmed that isowyosine (imG2) and 7-methylwyosine (mimG) are two archaeal-specific guanosine-37 derivatives found in tRNA of both Euryarchaeota and Crenarchaeota. Finally, we proposed that the duplication of the trm5 gene in some Archaea led to a change in function from N1 methylation of guanosine to C7 methylation of 4-demethylwyosine (imG-14).
- Published
- 2010
24. Proteomics-based Refinement of Deinococcus deserti Genome Annotation Reveals an Unwonted Use of Non-canonical Translation Initiation Codons
- Author
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Mathieu Baudet, Gilles Subra, Alain Dedieu, Jean-Charles Gaillard, Jean Armengaud, Mohamed Barakat, Philippe Ortet, Philippe J Guerin, Bernard Fernandez, Christine Enjalbal, Arjan de Groot, Laboratoire de Biochimie des Systèmes Perturbés, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Microbienne de la Rhizosphère et d'Environnements Extrêmes (LEMIRE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Biologie végétale et microbiologie environnementale - UMR7265 (BVME), Institut des Biomolécules Max Mousseron [Pôle Chimie Balard] (IBMM), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Montpellier (UM)-Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), and Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Institut de Chimie du CNRS (INC)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
Proteomics ,Molecular Sequence Data ,Codon, Initiator ,Protein Sorting Signals ,medicine.disease_cause ,Biochemistry ,Genome ,Analytical Chemistry ,03 medical and health sciences ,Organophosphorus Compounds ,Eukaryotic translation ,Bacterial Proteins ,medicine ,Deinococcus ,Amino Acid Sequence ,Databases, Protein ,Molecular Biology ,Gene ,030304 developmental biology ,2. Zero hunger ,Genetics ,0303 health sciences ,Base Sequence ,Sequence Homology, Amino Acid ,Staining and Labeling ,biology ,[CHIM.ORGA]Chemical Sciences/Organic chemistry ,Research ,030302 biochemistry & molecular biology ,Genome project ,biology.organism_classification ,Proteogenomics ,Deinococcus deserti ,DnaA ,Genes, Bacterial ,Protein Biosynthesis ,Peptides ,Genome, Bacterial - Abstract
International audience; Deinococcaceae are a family of extremely radiation tolerant bacteria that is currently subjected to numerous studies aimed at understanding the molecular mechanisms for such radiotolerance. To achieve a comprehensive and accurate annotation of Deinococcus deserti genome, we performed an N-terminal-oriented characterization of its proteome. For this, we used a labeling reagent, N-Tris(2,4,6-trimethoxyphenyl)phosphonium acetyl (TMPP), to selectively derivatize protein N-termini. The large scale identification of TMPP-modified Nterminal- most peptides by a shotgun liquid chromatography-tandem mass spectrometry analysis led to the validation of 278 and correction of 73 translation initiation codons in D. deserti genome. In addition, four new genes were detected, three located on the main chromosome and one on plasmid P3. Surprisingly, experimental evidences were obtained indicating that DnaA (the protein involved in the DNA replication initiation process) and RpsL (the S12 ribosomal conserved protein) translation is initiated in Deinococcaceae from non-canonical codons (ATC and CTG, respectively). Such use may be the basis of specific regulation mechanisms affecting replication and translation. We report the use of nonconventional translation initiation codons for two other genes: Deide_03051 and infC. We also analyzed signal peptide cleavages at a genome-wide scale. Based on comparative proteogenomic analysis, we propose a set of 137 corrections to improve Deinococcus radiodurans and Deinococcus geothermalis gene annotations. Some of these corrections affect important genes involved in DNA repair mechanisms such as polA, ligA, and ddrB. Our results demonstrate that predicting translation initiation codons is still difficult and that proteomic-based refinement of genome annotations is necessary. Whether such use of noncanonical translation initiation codons is much more frequent for other bacterial phyla than previously reported or restricted to Deinococcaceae remains to be investigated. Our results demonstrate that predicting translation initiation codons is still difficult for some bacteria and that proteomics-based refinement of genome annotations may be helpful in such cases.
- Published
- 2010
25. Alliance of proteomics and genomics to unravel the specificities of Sahara bacterium Deinococcus deserti
- Author
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Carole Dossat, Suzanne Sommer, Benoit Vacherie, Rémi Dulermo, Edmond Jolivet, Patricia Siguier, Laurence Blanchard, Wafa Achouak, Bernard Fernandez, Philippe Ortet, Michael Chandler, Jean Armengaud, Philippe J Guerin, Valérie Barbe, Thierry Heulin, Alain Dedieu, Arjan de Groot, Mohamed Barakat, Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Biologie végétale et microbiologie environnementale - UMR7265 (BVME), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Microbiologie Environnementale et Moléculaire (MEM), Laboratoire d'Ecologie Microbienne de la Rhizosphère et d'Environnements Extrêmes (LEMIRE), Laboratoire de Biochimie des Systèmes Perturbés (LBSP), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Génomique d'Evry (IG), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), ANR-07-BLAN-0106,DEINOCOCCUS,Structure of the nucleoïd and radioresistance of Deinococcus radiodurans and Deinococcus deserti(2007), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de microbiologie et génétique moléculaires (LMGM), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
Proteomics ,Cancer Research ,Proteomes ,Computational Biology/Comparative Sequence Analysis ,Gene prediction ,medicine.disease_cause ,Genome ,Africa, Northern ,Genetics (clinical) ,2. Zero hunger ,Genetics ,0303 health sciences ,Genetics and Genomics/Gene Expression ,Genomics ,Genome project ,Deinococcus deserti ,[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology ,Evolutionary Biology/Microbial Evolution and Genomics ,Proteome ,Genetics and Genomics/Gene Discovery ,Deinococcus ,Desert Climate ,Genetics and Genomics/Comparative Genomics ,Ecology/Environmental Microbiology ,Research Article ,lcsh:QH426-470 ,Ultraviolet Rays ,Molecular Sequence Data ,DNA repair ,DNA polymerase ,Biology ,Microbiology ,03 medical and health sciences ,Bacterial Proteins ,[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN] ,medicine ,Microbiology/Environmental Microbiology ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,Molecular Biology ,Bacterial genomics ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,Molecular Biology/Recombination ,Whole genome sequencing ,Comparative genomics ,Molecular Biology/DNA Repair ,030306 microbiology ,Database searching ,[SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology ,lcsh:Genetics ,Gamma Rays ,Biophysics/Protein Chemistry and Proteomics ,13. Climate action ,Genome, Bacterial ,Genome annotation - Abstract
To better understand adaptation to harsh conditions encountered in hot arid deserts, we report the first complete genome sequence and proteome analysis of a bacterium, Deinococcus deserti VCD115, isolated from Sahara surface sand. Its genome consists of a 2.8-Mb chromosome and three large plasmids of 324 kb, 314 kb, and 396 kb. Accurate primary genome annotation of its 3,455 genes was guided by extensive proteome shotgun analysis. From the large corpus of MS/MS spectra recorded, 1,348 proteins were uncovered and semiquantified by spectral counting. Among the highly detected proteins are several orphans and Deinococcus-specific proteins of unknown function. The alliance of proteomics and genomics high-throughput techniques allowed identification of 15 unpredicted genes and, surprisingly, reversal of incorrectly predicted orientation of 11 genes. Reversal of orientation of two Deinococcus-specific radiation-induced genes, ddrC and ddrH, and identification in D. deserti of supplementary genes involved in manganese import extend our knowledge of the radiotolerance toolbox of Deinococcaceae. Additional genes involved in nutrient import and in DNA repair (i.e., two extra recA, three translesion DNA polymerases, a photolyase) were also identified and found to be expressed under standard growth conditions, and, for these DNA repair genes, after exposure of the cells to UV. The supplementary nutrient import and DNA repair genes are likely important for survival and adaptation of D. deserti to its nutrient-poor, dry, and UV-exposed extreme environment., Author Summary D. deserti belongs to the Deinococcaceae, a family of bacteria characterized by an exceptional ability to withstand the lethal effects of DNA-damaging agents, including ionizing radiation, UV light, and desiccation. It was isolated from Sahara surface sands, an extreme and nutrient-poor environment, regularly exposed to intense UV radiation, cycles of extreme temperatures, and desiccation. The evolution of organisms that are able to survive acute irradiation doses of 15,000 Gy is difficult to explain given the apparent absence of highly radioactive habitats on Earth over geologic time. Thus, it seems more likely that the natural selection pressure for the evolution of radiation-resistant bacteria was chronic exposure to nonradioactive forms of DNA damage, in particular those promoted by desiccation. Here, we report the first complete genome sequence of a bacterium, D. deserti VCD115, isolated from hot, arid desert surface sand. Accurate genome annotation of its 3,455 genes was guided by extensive proteome analysis in which 1,348 proteins were uncovered after growth in standard conditions. Supplementary genes involved in manganese import, in nutrient import, and in DNA repair were identified and are likely important for survival and adaptation of D. deserti to its hostile environment.
- Published
- 2009
26. Les deux hypothèses d’Avogadro en 1811
- Author
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Bernard Fernandez
- Published
- 2009
27. Pigeon circovirus infection: pathological observations and suggested pathogenesis
- Author
-
F. Nguyen, Lydie Guigand, M. Wyers, Philippe Robart, Catherine Guereaud, Bernard Lefebvre, Nadia Amenna, Bernard Fernandez, Caroline Groizeleau, and Jérôme Abadie
- Subjects
Pathology ,medicine.medical_specialty ,animal structures ,General Immunology and Microbiology ,Pigeon circovirus infection ,medicine.medical_treatment ,Pigeon circovirus ,Immunosuppression ,Disease ,Biology ,Virology ,Pathogenesis ,Lymphatic system ,Food Animals ,medicine ,Animal Science and Zoology ,Bursa of Fabricius ,Pathological - Abstract
Pigeon circovirus infection (PiCV) was diagnosed by light and transmission electron microscopy in 15 birds from five lofts in western France. Histopathological findings were suggestive of primary bursotropism of pigeon circovirus, followed by secondary systemic spread from the bursa of Fabricius, particularly to non-bursal lymphoid organs. The last stage of the disease was associated with various secondary (particularly bacterial) infections. In situ detection of apoptosis in the bursa of Fabricius indicated that PiCV was concomitant with an increase in bursal lymphocytic apoptotic events related to viral infection and leading to severe acquired immunosuppression.
- Published
- 2009
28. International Executives, Identity Strategies and Mobility in France and China
- Author
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Philippe Pierre, Bernard Fernandez, Evalde Mutabazi, business school, emlyon, and emlyon business school
- Subjects
05 social sciences ,Subsidiary ,Ethnic group ,Identity (social science) ,Organizational culture ,[SHS.ECO]Humanities and Social Sciences/Economics and Finance ,nobody ,050601 international relations ,0506 political science ,Cultural learning ,Multinational corporation ,0502 economics and business ,[SHS.GESTION]Humanities and Social Sciences/Business administration ,Business ,Business and International Management ,Marketing ,China ,[SHS.ECO] Humanities and Social Sciences/Economics and Finance ,[SHS.GESTION] Humanities and Social Sciences/Business administration ,050203 business & management - Abstract
International audience; The strategies of multinational firms increasingly rely in Asia Pacific Region on processes of socialising their employees, who are seeking to develop and reinforce a “global” company culture, without endangering the cultures of local subsidiaries. Specialists have coined the term “cross-cultural management”. A role of “company ambassador” is allocated to a new generation of international executives in Asia whose mission will be to play an effective role as interface between head office its the subsidiaries - and between the subsidiaries themselves - once they have been suitably “impregnated” with the company culture and the particular features of different markets. The repeated experience of international mobility that executives live through means that the individual may well be living in conflict with previous identities. It is true to say that nobody stays long in an internationally mobile situation without running the risk of there being strong divergence between the domestic and residential worlds, the life of the community and the world of the company. This article has been written as a result of in-depth research into the way executives of a large French oil company built up their identities and as a result of a study examines intercultural learning based on French expatriates' experience in China. We consider how French expatriates experience China and what imaginary underlies their perception. Analysis of daily socialization and interaction processes shows intercultural competence develops along distinct immersion stages: immersion-adjustment, immersion-comprehension, and immersion-integration. Individually, adjustment and comprehension support intercultural practice. The ultimate immersion stage leads to enlightened pragmatism stemming from “nomadic intelligence”. Where a researcher in the social sciences or a business man might have expected to have found an homogenous international elite, international executives building an “international system”, the heterogeneous nature of the identity strategies of international executives give the lie to the myth of the large company as a space for the irreversible assimilation of its members. At an individual level, being an international executive is a unique way of living the experience abroad, or rather, several different ways of experiencing identity strategies linked to the manipulation of one's ethnicity in a context of significant geographical and functional mobility.
- Published
- 2006
29. Expression, purification, crystallization and preliminary crytallographic analysis of the PAB0955 gene product
- Author
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Dominique Housset, Jean Armengaud, Philippe Carpentier, Bernard Fernandez, Stephanie Gras, and Valérie Chaumont
- Subjects
Pyrococcus ,ATPase ,Biophysics ,GTPase ,Crystallography, X-Ray ,Biochemistry ,law.invention ,Gene product ,Bacterial Proteins ,Structural Biology ,law ,Genetics ,Nucleotide ,Amino Acid Sequence ,Crystallization ,DNA Primers ,chemistry.chemical_classification ,Base Sequence ,biology ,Condensed Matter Physics ,biology.organism_classification ,Peptide Fragments ,Acid Anhydride Hydrolases ,Crystallography ,DNA, Archaeal ,chemistry ,Crystallization Communications ,biology.protein ,Bacteria ,Pyrococcus abyssi ,Archaea - Abstract
PAB0955 from Pyrococcus abyssi is a prototype of a new Walker-type ATPase/GTPase conserved in archaea and eukaryota but not found in bacteria. PAB0955 has been expressed, purified and crystallized, and it has been shown that this thermostable protein is dimeric in reductive conditions. Crystals have been obtained either without nucleotide or in the presence of GDP or GTPgammaS. Preliminary X-ray crystallographic data up to 2.08 A resolution have been collected from these crystals.
- Published
- 2005
30. Chapitre 6. Confiance et méfiance dans le rapport à l’altérité asiatique : le cas de l’expérience d’expatriés français en Chine
- Author
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Bernard Fernandez
- Published
- 2004
31. N2-methylation of guanosine at position 10 in tRNA is catalyzed by a THUMP domain-containing, S-adenosylmethionine-dependent methyltransferase, conserved in Archaea and Eukaryota
- Author
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Jaunius Urbonavičius, Janusz Marek Bujnicki, Jean Armengaud, Henri Grosjean, Bernard Fernandez, and Guylaine Chaussinand
- Subjects
Models, Molecular ,Rossmann fold ,S-Adenosylmethionine ,Time Factors ,Molecular Sequence Data ,Guanosine ,Biochemistry ,Methylation ,Catalysis ,chemistry.chemical_compound ,RNA, Transfer ,Catalytic Domain ,Amino Acid Sequence ,Protein Structure, Quaternary ,Molecular Biology ,tRNA Methyltransferases ,biology ,Calorimetry, Differential Scanning ,Sequence Homology, Amino Acid ,C-terminus ,Temperature ,Cell Biology ,Methyltransferases ,DNA Methylation ,biology.organism_classification ,Archaea ,Recombinant Proteins ,Protein Structure, Tertiary ,Eukaryotic Cells ,chemistry ,Databases as Topic ,Transfer RNA ,Pyrococcus furiosus ,Chromatography, Gel ,RNA ,Electrophoresis, Polyacrylamide Gel ,Pyrococcus abyssi ,Plasmids - Abstract
In sequenced genomes, genes belonging to the cluster of orthologous group COG1041 are exclusively, and almost ubiquitously, found in Eukaryota and Archaea but never in Bacteria. The corresponding gene products exhibit a characteristic Rossmann fold, S-adenosylmethionine-dependent methyltransferase domain in the C terminus and a predicted RNA-binding THUMP (thiouridine synthases, RNA methyltransferases, and pseudouridine synthases) domain in the N terminus. Recombinant PAB1283 protein from the archaeon Pyrococcus abyssi GE5, a member of COG1041, was purified and shown to behave as a monomeric 39-kDa entity. This protein (EC 2.1.1.32), now renamed (Pab)Trm-G10, which is extremely thermostable, forms a 1:1 complex with tRNA and catalyzes the adenosylmethionine-dependent methylation of the exocyclic amino group (N(2)) of guanosine located at position 10. Depending on the experimental conditions used, as well as the tRNA substrate tested, the enzymatic reaction leads to the formation of either N(2)-monomethyl (m(2)G) or N(2)-dimethylguanosine (m(2)(2)G). Interestingly, (Pab)Trm-G10 exhibits different domain organization and different catalytic site architecture from another, earlier characterized, tRNA-dimethyltransferase from Pyrococcus furiosus ((Pfu)Trm-G26, also known as (Pfu)Trm1, a member of COG1867) that catalyzes an identical two-step dimethylation of guanosine but at position 26 in tRNAs and is also conserved among all sequenced Eukaryota and Archaea. The co-occurrence of these two guanosine dimethyltransferases in both Archaea and Eukaryota but not in Bacteria is a hallmark of distinct tRNAs maturation strategies between these domains of life.
- Published
- 2004
32. Muscle satellite cell heterogeneity: in vitro and in vivo evidences for populations that fuse differently
- Author
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Mickael Brault, Isabelle Leroux, Yan Cherel, Nathalie Daval, Julie Lesoeur, Karl Rouger, Lydie Guigand, Bernard Fernandez, Développement et Pathologie du Tissu Musculaire (DPTM), and Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Nantes
- Subjects
Male ,Turkeys ,Pathology ,medicine.medical_specialty ,Histology ,Satellite Cells, Skeletal Muscle ,Population ,[SDV.BC]Life Sciences [q-bio]/Cellular Biology ,Biology ,Pathology and Forensic Medicine ,Muscle hypertrophy ,CELL FUSION ,In vivo ,medicine ,Animals ,Muscle, Skeletal ,education ,Cells, Cultured ,Cell Proliferation ,Cell Nucleus ,education.field_of_study ,Cell fusion ,Cell growth ,Myogenesis ,MELEAGRIS GALLOPAVO (AVES) ,CELL TRANSPLANTATION ,Skeletal muscle ,Cell Differentiation ,Cell Biology ,beta-Galactosidase ,Coculture Techniques ,In vitro ,Clone Cells ,Cell biology ,medicine.anatomical_structure ,TURKEY ,SKELETAL MUSCLE ,CO-CULTURE ,SATELLITE CELL - Abstract
During development, muscle growth results from the proliferation of satellite cells (SC) and their fusion with fibers. Several studies revealed heterogeneity of SC population notably based on the proliferation rate. Here, we examined the SC characteristics of turkey skeletal muscles in terms of proliferation and more specifically fusion, to define if the ability of these cells to fuse may represent a distinct characteristic between them and could be directly associated with their proliferation properties. Freshly extracted SC were plated in clonal condition and their proliferation rate was assessed 11 days later. To investigate the SC fusion behavior, in vitro and in vivo approaches were developed. Highly and slowly proliferative SC were initially labeled with a nuclear beta-galactosidase (beta-Gal) activity and co-cultured with differentiated primary cultures. After 5 days, distribution of beta-Gal positive (beta-Gal+) nuclei was examined. Also, the two labeled SC types were transplanted into different muscles in autologous model. One week later, number of beta-Gal+ nuclei per fiber and diameter of fibers displaying beta-Gal+ nuclei were determined. In vitro, we showed that SC from turkey skeletal muscle are present as a heterogeneous population in terms of proliferation. Examination of their fusion properties in vitro as well as in vivo revealed that highly proliferative SC exclusively exhibited fusion with differentiated myotubes or myofibers, whereas slowly proliferative SC mainly fused together. Collectively, these data demonstrate for the first time that SC with different proliferation rate also intrinsically differ in their fusion potential, suggesting distinct roles for these sub-populations in muscle growth.
- Published
- 2004
33. Identification, purification, and characterization of an eukaryotic-like phosphopantetheine adenylyltransferase (coenzyme A biosynthetic pathway) in the hyperthermophilic archaeon Pyrococcus abyssi
- Author
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Simonetta Gribaldo, Valérie Chaumont, Claude Vidaud, Pierre Gans, Hannu Myllykallio, Patrick Forterre, Jean Armengaud, Jean-Luc Pellequer, Charles Marchetti, Bernard Fernandez, Françoise Rollin-Genetet, Stéphanie Finet, Service de Biochimie et Toxicologie Nucléaire (SBTN), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), European Synchroton Radiation Facility [Grenoble] (ESRF), Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Intéractions et Reconnaissances Moléculaires (LIRM), Institut de biologie structurale (IBS - UMR 5075 ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)
- Subjects
Pyrococcus ,Coenzyme A ,Archaeal Proteins ,Molecular Sequence Data ,Biology ,medicine.disease_cause ,Biochemistry ,Protein Structure, Secondary ,chemistry.chemical_compound ,medicine ,Escherichia coli ,Histidine ,Amino Acid Sequence ,[SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM] ,Molecular Biology ,Protein secondary structure ,Phylogeny ,chemistry.chemical_classification ,Calorimetry, Differential Scanning ,Cell Biology ,biology.organism_classification ,Nucleotidyltransferases ,Recombinant Proteins ,Protein Structure, Tertiary ,Metabolic pathway ,Enzyme ,[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology ,Eukaryotic Cells ,chemistry ,Bacteria ,Pyrococcus abyssi ,Archaea - Abstract
International audience; Although coenzymeA (CoA) is essential in numerous metabolic pathways in all living cells, molecular characterization of the CoA biosynthetic pathway in Archaea remains undocumented. Archaeal genomes contain detectable homologues for only three of the five steps of the CoA biosynthetic pathway characterized in Eukarya and Bacteria. In case of phosphopantetheine adenylyltransferase (PPAT) (EC 2.7.7.3), the putative archaeal enzyme exhibits significant sequence similarity only with its eukaryotic homologs, an unusual situation for a protein involved in a central metabolic pathway. We have overexpressed in Escherichia coli, purified, and characterized this putative PPAT from the hyperthermophilic archaeon Pyrococcus abyssi (PAB0944). Matrixassisted laser desorption ionization-time of flight mass spectrometry and high performance liquid chromatography measurements are consistent with the presence of a dephospho-CoA (dPCoA) molecule tightly bound to the polypeptide. The protein indeed catalyzes the synthesis of dPCoA from 4-phosphopantetheine and ATP, as well as the reverse reaction. The presence of dPCoA stabilizes PAB0944, as it induces a shift from 76 to 82°C of the apparent T m measured by differential scanning microcalorimetry. Potassium glutamate was found to stabilize the protein at 400 mM. The enzyme behaves as a monomeric protein. Although only distantly related, secondary structure prediction indicates that archaeal and eukaryal PPAT belong to the same nucleotidyltransferase superfamily of bacterial PPAT. The existence of operational proteins highly conserved between Archaea and Eukarya involved in a central metabolic pathway challenge evolutionary scenarios in which eukaryal operational proteins are strictly of bacterial origin.
- Published
- 2003
34. Case report and review of resolved fusariosis
- Author
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Bernard Fernandez, David L. Longworth, Thomas N. Helm, Kenneth J. Tomecki, Brian J. Bolwell, and Geraldine S. Hall
- Subjects
Fusariosis ,Male ,Pathology ,medicine.medical_specialty ,Antifungal Agents ,Dermatology ,Fusarium ,hemic and lymphatic diseases ,Acute lymphocytic leukemia ,Amphotericin B ,medicine ,Immune Tolerance ,Dermatomycoses ,Humans ,Mycosis ,Fungemia ,Myositis ,Palpable purpura ,medicine.diagnostic_test ,business.industry ,Middle Aged ,Precursor Cell Lymphoblastic Leukemia-Lymphoma ,medicine.disease ,Skin biopsy ,Drug Therapy, Combination ,medicine.symptom ,business ,Vasculitis - Abstract
Erythematous macules, nonpalpable and palpable purpura, and flaccid pustules developed in a 59-year-old man with acute lymphocytic leukemia 8 days after reinduction chemotherapy with cytosine arabinoside and daunorubicin. Tissue and blood cultures grew Fusarium proliferatum, and a skin biopsy specimen revealed fungal vasculitis. Anemia and muscle weakness accompanied the disseminated infection, for which the patient received granulocyte transfusions and amphotericin B, ketoconazole, rifampin, and griseofulvin. Skin lesions and fungemia resolved with recovery of the bone marrow, and 51 days after the completion of his chemotherapy he returned home. If promptly recognized and aggressively treated, disseminated fusariosis is responsive to therapy. Infection with Fusarium species should be suspected in profoundly neutropenic patients in whom disseminated palpable purpura and myositis develop concomitantly.
- Published
- 1990
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