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43 results on '"UMR CNRS-ULP"'

1. The siRNA suppressor RTL1 is redox-regulated through glutathionylation of a conserved cysteine in the double-stranded-RNA-binding domain

Author

Charbonnel, Cyril, Niazi, Adnan, ELVIRA-MATELOT, Emilie, Nowak, Elżbieta, Zytnicki, Matthias, de Bures, Anne, Jobet, Edouard, Opsomer, Alisson, Shamandi, Nahid, Nowotny, Marcin, Carapito, Christine, Reichheld, Jean-Philippe, Vaucheret, Herve, Sáez-Vasquez, Julio, Génétique, Reproduction et Développement (GReD), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Spectrométrie de Masse BioOrganique [Strasbourg] (LSMBO), Département Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Génétique, Reproduction et Développement - Clermont Auvergne (GReD), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne (UCA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Spectrométrie de masse Bio-organique, UMR CNRS-ULP, Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), and Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Models, Molecular, RNA Cleavage, Ribonuclease III, Base Sequence, Nucleic Acid Enzymes, Arabidopsis Proteins, [SDV]Life Sciences [q-bio], Arabidopsis, Glutathione, Repressor Proteins, Protein Domains, RNA, Plant, Sequence Homology, Nucleic Acid, RNA-Binding Motifs, Nucleic Acid Conformation, Amino Acid Sequence, Cysteine, RNA, Small Interfering, 3' Untranslated Regions, Oxidation-Reduction, ComputingMilieux_MISCELLANEOUS, RNA, Double-Stranded
Abstract

International audience; RNase III enzymes cleave double stranded (ds)RNA. This is an essential step for regulating the processing of mRNA, rRNA, snoRNA and other small RNAs, including siRNA and miRNA. Arabidopsis thaliana encodes nine RNase III: four DICER-LIKE (DCL) and five RNASE THREE LIKE (RTL). To better understand the molecular functions of RNase III in plants we developed a biochemical assay using RTL1 as a model. We show that RTL1 does not degrade dsRNA randomly, but recognizes specific duplex sequences to direct accurate cleavage. Furthermore, we demonstrate that RNase III and dsRNA binding domains (dsRBD) are both required for dsRNA cleavage. Interestingly, the four DCL and the three RTL that carry dsRBD share a conserved cysteine (C230 in Arabidopsis RTL1) in their dsRBD. C230 is essential for RTL1 and DCL1 activities and is subjected to posttranscriptional modification. Indeed, under oxidizing conditions, glutathionylation of C230 inhibits RTL1 cleavage activity in a reversible manner involving glutaredoxins. We conclude that the redox state of the dsRBD ensures a fine-tune regulation of dsRNA processing by plant RNase III.

Published
2017

2. Ortho-proteogenomics: Multiple proteomes investigation through orthology and a new MS-based protocol

Author

Christine Carapito, Christine Schaeffer, Jean-Marc Reyrat, Alain Van Dorsselaer, Emmanuel Perrodou, Caroline Deshayes, Sebastien Gallien, Odile Lecompte, Olivier Poch, Institut Pluridisciplinaire Hubert Curien (IPHC), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Institut de génétique et biologie moléculaire et cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Louis Pasteur - Strasbourg I, Laboratoire de Spectrométrie de Masse BioOrganique [Strasbourg] (LSMBO), Département Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Pathogénie des infections systémiques (UMR_S 570), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Louis Pasteur - Strasbourg I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Peney, Maité, Institut Pluridisciplinaire Hubert Curien ( IPHC ), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique ( CNRS ), Institut de génétique et biologie moléculaire et cellulaire ( IGBMC ), Université Louis Pasteur - Strasbourg I-Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Spectrométrie de masse Bio-organique, UMR CNRS-ULP, Pathogénie des infections systémiques ( UMR_S 570 ), and Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS )

Subjects
Proteomics, Proteome, In silico, Mycobacterium smegmatis, Codon, Initiator, Genomics, Computational biology, Genome, Mass Spectrometry, Mycobacterium, 03 medical and health sciences, Bacterial Proteins, Species Specificity, Methods, Genetics, Genetics (clinical), 030304 developmental biology, Comparative genomics, 0303 health sciences, biology, 030302 biochemistry & molecular biology, [SDV.ETH] Life Sciences [q-bio]/Ethics, biology.organism_classification, Proteogenomics, Peptide Fragments, [SDV.ETH]Life Sciences [q-bio]/Ethics, RNA, Bacterial, [ SDV.ETH ] Life Sciences [q-bio]/Ethics, Sequence Alignment, Genome, Bacterial
Abstract

The progress in sequencing technologies irrigates biology with an ever-increasing number of genome sequences. In most cases, the gene repertoire is predicted in silico and conceptually translated into proteins. As recently highlighted, the predicted genes exhibit frequent errors, particularly in start codons, with a serious impact on subsequent biological studies. A new “ortho-proteogenomic” approach is presented here for the annotation refinement of multiple genomes at once. It combines comparative genomics with an original proteomic protocol that allows the characterization of both N-terminal and internal peptides in a single experiment. This strategy was applied to the Mycobacterium genus with Mycobacterium smegmatis as the reference, and identified 946 distinct proteins, including 443 characterized N termini. These experimental data allowed the correction of 19% of the characterized start codons, the identification of 29 proteins missed during the annotation process, and the curation, thanks to comparative genomics, of 4328 sequences of 16 other Mycobacterium proteomes.

Published
2008

3. Proteome analysis of the culture environment supporting undifferentiated mouse embryonic stem and germ cell growth

Author

Christine Carapito, Nicolas Buhr, Agnès Hovasse, Stéphane Viville, Alain Van Dorsselaer, Christine Schaeffer, Institut de génétique et biologie moléculaire et cellulaire (IGBMC), Université Louis Pasteur - Strasbourg I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Spectrométrie de masse Bio-organique, UMR CNRS-ULP, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Louis Pasteur - Strasbourg I, Laboratoire de Spectrométrie de Masse BioOrganique [Strasbourg] (LSMBO), Département Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), and Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Proteomics, Clinical Biochemistry, Cell, Bioinformatics, Biochemistry, Analytical Chemistry, Mice, 0302 clinical medicine, MESH: Animals, Electrophoresis, Gel, Two-Dimensional, MESH: Embryonic Stem Cells, Cells, Cultured, reproductive and urinary physiology, 0303 health sciences, Ethical issues, Culture environment, MESH: Proteomics, Reference Standards, Cell biology, medicine.anatomical_structure, embryonic structures, Proteome, MESH: Pluripotent Stem Cells, MESH: Reference Standards, MESH: Gelatin, biological phenomena, cell phenomena, and immunity, Germ cell, MESH: Cells, Cultured, Pluripotent Stem Cells, Biology, Mouse embryonic fibroblast, MESH: Coculture Techniques, 03 medical and health sciences, MESH: Cell Proliferation, medicine, Animals, Fibroblast, MESH: Mice, Embryonic Stem Cells, Cell Proliferation, 030304 developmental biology, urogenital system, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Fibroblasts, MESH: Electrophoresis, Gel, Two-Dimensional, Embryonic stem cell, Coculture Techniques, Culture Media, MESH: Germ Cells, Germ Cells, MESH: Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, MESH: Fibroblasts, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, MESH: Culture Media, Gelatin, 030217 neurology & neurosurgery
Abstract

The therapeutical interest of pluripotent cells and ethical issues related to the establishment of human embryonic stem cell (ESC) or embryonic germ cell (EGC) lines raise the understanding of the mechanism underlying pluripotency to a fundamental issue. Establishing a protein pluripotency signature for these cells can be complicated by the presence of unrelated proteins produced by the culture environment. Here, we have analyzed the environment supporting ESC and EGC growth, and established 2-D reference maps for each constituent present in this culture environment: mouse embryonic fibroblast feeder cells, culture medium (CM) and gelatin. The establishment of these reference maps is essential prior to the study of ESC and EGC specific proteomes. Indeed, these maps can be subtracted from ESC or EGC maps to allow focusing on spots specific for ESCs or EGCs. Our study led to the identification of 110 unique proteins from fibroblast feeder cells and 23 unique proteins from the CM, which represent major contaminants of ESC and EGC proteomes. For gelatin, no collagen-specific proteins were identified, most likely due to difficulties in resolution and low quantities. Furthermore, no differences were observed between naive and conditioned CM. Finally, we compared these reference maps to ESC 2-D gels and isolated 17 ESC specific spots. Among these spots, proteins that had already been identified in previous human and mouse ESC proteomes were identified but no apparent ESC-specific pluripotency marker could be identified. This work represents an essential step in furthering the knowledge of environmental factors supporting ESC and EGC growth.

Published
2007

4. Self-Assembly of a Diferrous Triple-Stranded Helicate with Bis(2,2‘-Bipyridine) Ligands: Thermodynamic and Kinetic Intermediates

Author

Fatin-Rouge , N., Blanc , Sylvie, Leize , E., Van Dorsselaer , A., Baret , P., Pierre , J.-L., Albrecht-Gary , A.-M., Meyer , Michel, Institut UTINAM (Univers, transport, interfaces, nanostructures, atmosphère et environnement, molécules) (Besançon), Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux ( IPREM ), Université de Pau et des Pays de l'Adour ( UPPA ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de spectrométrie de masse des interactions et des systèmes, Chimie de la matière complexe ( CMC ), Université de Strasbourg ( UNISTRA ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Strasbourg ( UNISTRA ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Spectrométrie de masse Bio-organique, UMR CNRS-ULP, Laboratoire de Chimie Biomimétique , LEDSS, Université Joseph Fourier - Grenoble 1 ( UJF ) -Centre National de la Recherche Scientifique ( CNRS ), Institut de Chimie Moléculaire de l'Université de Bourgogne [Dijon] ( ICMUB ), Université de Bourgogne ( UB ) -Centre National de la Recherche Scientifique ( CNRS ), Univers, Transport, Interfaces, Nanostructures, Atmosphère et environnement, Molécules (UMR 6213) (UTINAM), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Chimie de la matière complexe (CMC), Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Spectrométrie de Masse BioOrganique [Strasbourg] (LSMBO), Département Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'études dynamiques et structurales de la sélectivité (LEDSS), Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF), Institut de Chimie Moléculaire de l'Université de Bourgogne [Dijon] (ICMUB), and Université de Bourgogne (UB)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Models, Molecular, Magnetic Resonance Spectroscopy, Spin states, Stereochemistry, Molecular Conformation, Protonation, Ligands, 010402 general chemistry, [ CHIM ] Chemical Sciences, 01 natural sciences, 2,2'-Bipyridine, Dissociation (chemistry), Ferrous, Inorganic Chemistry, chemistry.chemical_compound, 2,2'-Dipyridyl, [CHIM]Chemical Sciences, Physical and Theoretical Chemistry, nuclear magnetic resonance spectroscopy, mass spectrometry, allosterism, Molecular Structure, 010405 organic chemistry, Chemistry, Ligand, Nucleic Acid Hybridization, Nuclear magnetic resonance spectroscopy, 0104 chemical sciences, Kinetics, Crystallography, iron complex, Spectrophotometry, Potentiometry, Proton NMR, Thermodynamics, 2 2' bipyridine derivative
Abstract

cited By 40; International audience; The protonation and iron(II) coordination properties of a bis(2,2′-bipyridine) ligand L were investigated in methanol. The protonated forms showed allosteric effects due to the flexibility of the strand. Speciation studies of the corresponding ferrous complexes were carried out as a function of pH and iron(II) concentrations. A combination of electrospray mass spectroscopy, potentiometry, and spectrophotometry allowed the determination in solution of three ferrous complexes, one mononuclear (L2Fe2+) and two dinuclear (L2Fe24+ and L3Fe24+) species. Their structure was deduced from the metal spin state and confirmed by 1H NMR measurements and molecular modeling. The dissociation process of the triple-stranded diferrous helicate L3Fe24+ by OH- revealed two rate-limiting steps. The former leads to the formation of a monoferrous triple-stranded compound via a classical mechanism, which involves hydroxy-ferrous complexes. A similar process was observed in the latter step for the release of the ferrous cation from the mononuclear intermediate. Taking into account the structural, thermodynamic, and kinetic features provided by the present study, we could propose a self-assembling mechanism of the triple-stranded diferrous helicate.

Published
2000

5. Enhanced structural and functional genome elucidation of the arsenite-oxidizing strain Herminiimonas arsenicoxydans by proteomics data

Author

Christine Carapito, Michaël Heymann, Sandrine Koechler, Philippe N. Bertin, Evelyne Turlin, Claudine Médigue, Alain Van Dorsselaer, Valérie Kugler, Florence Arsène-Ploetze, Stéphanie Weiss, Stéphane Cruveiller, Magalie Stauffert, Jessica Cleiss, Jean-Yves Coppée, Génétique moléculaire, génomique, microbiologie (GMGM), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Spectrométrie de Masse BioOrganique [Strasbourg] (LSMBO), Département Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Génétique des Génomes Bactériens, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Puces à ADN (Plate-Forme 2) (PF2), Institut Pasteur [Paris] (IP), Institut de biologie et chimie des protéines [Lyon] (IBCP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Institut Gilbert-Laustriat : Biomolécules, Biotechnologie, Innovation Thérapeutique, 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), Structure et évolution des génomes (SEG), CNS-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Génomique métabolique (UMR 8030), 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 Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Compartimentation et dynamique cellulaires (CDC), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Curie [Paris]-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Institut Pasteur [Paris], 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, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Centre National de la Recherche Scientifique (CNRS)-Institut Curie [Paris]-Université Pierre et Marie Curie - Paris 6 (UPMC), Laboratoire de Spectrométrie de masse Bio-organique, UMR CNRS-ULP, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), and Centre National de la Recherche Scientifique (CNRS)-Institut Curie-Université Pierre et Marie Curie - Paris 6 (UPMC)

Subjects
Proteomics, Proteome, Arsenites, Biology, Tandem mass spectrometry, Models, Biological, Biochemistry, Transcriptome, 03 medical and health sciences, chemistry.chemical_compound, Oxalobacteraceae, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Herminiimonas arsenicoxydans, 030304 developmental biology, Arsenite, Genetics, Gel electrophoresis, 0303 health sciences, 030306 microbiology, General Medicine, Genome project, biology.organism_classification, chemistry, Oxidation-Reduction, Genome, Bacterial
Abstract

International audience; The arsenite-oxidizing strain Herminiimonas arsenicoxydans proteome was investigated with gel electrophoresis and tandem mass spectrometry analyses. The comparison of experimental and theoretical M(r) and pI, as well as that of peptide sequences identified by MS and predicted protein sequences, allowed the correction of five protein annotations. More importantly, the functional analysis of SDS- and 2D-PAGE proteome maps obtained in the presence of arsenic, combined with partial transcriptomic results indicate that H. arsenicoxydans expressed genes and proteins required not only for arsenic detoxification or stress response but also involved in motility, exopolysaccharide synthesis, phosphate import or energetic metabolism. This study provides therefore new insights into the adaptation processes of H. arsenicoxydans in response to arsenic.

Published
2009

6. Proteomic and glycomic analyses of N-glycosylated structures involved in toxoplasma gondii-host cell interactions

Author

Willy Morelle, Christine Schaeffer, Christian Slomianny, Audrey Bednarczyk, Sylvain Fauquenoy, Alain Van Dorsselaer, Stanislas Tomavo, Agnès Hovasse, Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Laboratoire de Spectrométrie de masse Bio-organique, UMR CNRS-ULP, Rôle des canaux ioniques membranaires et du calcium intracellulaire dans la physiopathologie de la prostate, Université de Lille, Sciences et Technologies-Institut National de la Santé et de la Recherche Médicale (INSERM), Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 (UGSF), Institut National de la Recherche Agronomique (INRA)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Spectrométrie de Masse BioOrganique [Strasbourg] (LSMBO), Département Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), and Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Proteomics, Glycan, Glycosylation, Gliding motility, Molecular Sequence Data, Protozoan Proteins, Oligosaccharides, Biology, Biochemistry, Analytical Chemistry, Host-Parasite Interactions, Glycomics, 03 medical and health sciences, Polysaccharides, Myosin, parasitic diseases, Animals, Humans, Peptide-N4-(N-acetyl-beta-glucosaminyl) Asparagine Amidase, Molecular Biology, Actin, Cells, Cultured, 030304 developmental biology, Glycoproteins, chemistry.chemical_classification, 0303 health sciences, Microscopy, Confocal, 030302 biochemistry & molecular biology, Toxoplasma gondii, biology.organism_classification, Cell biology, carbohydrates (lipids), [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, chemistry, Carbohydrate Sequence, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, biology.protein, Plant Lectins, Glycoprotein, Toxoplasma
Abstract

International audience; The apicomplexan parasite Toxoplasma gondii recognizes, binds and penetrates virtually any kind of mammalian cell using a repertoire of proteins released from late secretory organelles and a unique form of gliding motility (also named glideosome) that critically depends on actin filaments and myosin. How T. gondii glycosylated proteins mediate host-parasite interactions remains elusive. To date, only limited evidence is available concerning N-glycosylation in apicomplexans. Here, we report comprehensive proteomic and glycomic analyses showing that several key components required for host cell-T. gondii interactions are N-glycosylated. Detailed structural characterization confirmed that N-glycans from T. gondii total protein extracts consist of oligomannosidic (Man5-9GlcNAc2) and paucimannosidic (Man3-4GlcNAc2) sugars, which are rarely present on mature eukaryotic glycoproteins. In situ fluorescence using Concanavalin A (Con A) and Pisum sativum agglutinin (PSA) predominantly stained the entire parasite body. Visualization of Toxoplasma glycoproteins purified by affinity chromatography followed by detailed proteomic and glycan analyses identified components involved in gliding motility, moving junction and other additional functions implicated in intracellular development. Importantly, tunicamycin-treated parasites are considerably reduced in motility, host cell invasion and growth. Collectively, these results indicate that N-glycosylation probably participates in modifying key proteins that are essential for host cell invasion by T. gondii.

Published
2008

7. Interrupted coding sequences in Mycobacterium smegmatis: authentic mutations or sequencing errors?

Author

Deshayes, Caroline, Perrodou, Emmanuel, Gallien, Sebastien, Euphrasie, Daniel, Schaeffer, Christine, Van-Dorsselaer, Alain, Poch, Olivier, Lecompte, Odile, Reyrat, Jean-Marc, Laboratoire de Spectrométrie de masse Bio-organique, UMR CNRS-ULP, Institut de génétique et biologie moléculaire et cellulaire (IGBMC), Université Louis Pasteur - Strasbourg I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Génétique mycobactérienne, Institut Pasteur [Paris], Pathogénie des infections systémiques (UMR_S 570), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Spectrométrie de Masse BioOrganique [Strasbourg] (LSMBO), Département Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Louis Pasteur - Strasbourg I, Génétique mycobactérienne - Mycobacterial genetics, Institut de génétique et biologie moléculaire et cellulaire ( IGBMC ), Université Louis Pasteur - Strasbourg I-Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Pathogénie des infections systémiques ( UMR_S 570 ), Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur [Paris] (IP)

Subjects
MESH: Sequence Analysis, DNA, MESH : Mycobacterium smegmatis, Mycobacterium smegmatis, MESH : Chromatography, Liquid, [ SDV.BBM.BM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, MESH : Frameshift Mutation, Tandem Mass Spectrometry, Electrophoresis, Gel, Two-Dimensional, Frameshift Mutation, MESH: Mycobacterium smegmatis, Research, MESH: Genomics, MESH : Genomics, MESH: Research Design, MESH: Frameshift Mutation, Computational Biology, MESH: Tandem Mass Spectrometry, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, MESH : Electrophoresis, Gel, Two-Dimensional, Genomics, Sequence Analysis, DNA, MESH : Research Design, MESH: Electrophoresis, Gel, Two-Dimensional, Research Design, MESH : Tandem Mass Spectrometry, MESH: Chromatography, Liquid, MESH : Computational Biology, MESH : Sequence Analysis, DNA, Chromatography, Liquid, MESH: Computational Biology
Abstract

The question of whether bacterial interrupted coding sequences (ICDS) should be individually verified to produce an informative genome sequence is raised after bioinformatic, proteomic and sequencing analyses reveal that a significant proportion of ICDSs in the deposited genome sequence of Mycobacterium smegmatis are a result of sequencing errors., Background In silico analysis has shown that all bacterial genomes contain a low percentage of ORFs with undetected frameshifts and in-frame stop codons. These interrupted coding sequences (ICDSs) may really be present in the organism or may result from misannotation based on sequencing errors. The reality or otherwise of these sequences has major implications for all subsequent functional characterization steps, including module prediction, comparative genomics and high-throughput proteomic projects. Results We show here, using Mycobacterium smegmatis as a model species, that a significant proportion of these ICDSs result from sequencing errors. We used a resequencing procedure and mass spectrometry analysis to determine the nature of a number of ICDSs in this organism. We found that 28 of the 73 ICDSs investigated correspond to sequencing errors. Conclusion The correction of these errors results in modification of the predicted amino acid sequences of the corresponding proteins and changes in annotation. We suggest that each bacterial ICDS should be investigated individually, to determine its true status and to ensure that the genome sequence is appropriate for comparative genomics analyses.

Published
2007

8. Identification of genes and proteins involved in the pleiotropic response to arsenic stress in Caenibacter arsenoxydans, a metalloresistant beta-proteobacterium with an unsequenced genome

Author

Emmanuelle Leize-Wagner, Sandrine Koechler, Evelyne Turlin, Christine Carapito, Philippe N. Bertin, Alain Van Dorsselaer, Antoine Danchin, Marie-Claire Lett, Daniel Muller, Laboratoire de Spectrométrie de Masse BioOrganique [Strasbourg] (LSMBO), Département Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Laboratoire de Biologie Tumorale, CRLCC Paul Strauss, XLIM (XLIM), Université de Limoges (UNILIM)-Centre National de la Recherche Scientifique (CNRS), Génétique des Génomes Bactériens, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Génétique moléculaire, génomique, microbiologie (GMGM), Régulation de l'Expression Génétique (REG), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Compartimentation et dynamique cellulaires (CDC), Centre National de la Recherche Scientifique (CNRS)-Institut Curie [Paris]-Université Pierre et Marie Curie - Paris 6 (UPMC), Substances naturelles/chimie moléculaire, Université Louis Pasteur - Strasbourg I-Ecole européenne de chimie, polymères et matériaux [Strasbourg]-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Spectrométrie de masse Bio-organique, UMR CNRS-ULP, Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Centre National de la Recherche Scientifique (CNRS)-Institut Curie-Université Pierre et Marie Curie - Paris 6 (UPMC), Institut Pluridisciplinaire Hubert Curien ( IPHC ), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique ( CNRS ), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), XLIM ( XLIM ), Université de Limoges ( UNILIM ) -Centre National de la Recherche Scientifique ( CNRS ), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique ( CNRS ), Génétique moléculaire, génomique, microbiologie ( GMGM ), Régulation de l'Expression Génétique ( REG ), Sciences Analytiques et Interactions Ioniques et Biomoléculaires ( DSA-IPHC ), Compartimentation et dynamique cellulaires ( CDC ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -INSTITUT CURIE-Centre National de la Recherche Scientifique ( CNRS ), Université Louis Pasteur - Strasbourg I-Ecole européenne de chimie, polymères et matériaux [Strasbourg]-Centre National de la Recherche Scientifique ( CNRS ), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Curie [Paris]-Centre National de la Recherche Scientifique (CNRS)

Subjects
MESH : Molecular Sequence Data, MESH : RNA, Messenger, Messenger, Drug Resistance, MESH: Amino Acid Sequence, MESH : Drug Resistance, Bacterial, MESH: Genome, Bacterial, Biochemistry, Genome, chemistry.chemical_compound, MESH : Bacterial Proteins, MESH: Betaproteobacteria, Peptide sequence, MESH: Bacterial Proteins, MESH : Betaproteobacteria, Arsenite, Genetics, 0303 health sciences, MESH : Amino Acid Sequence, MESH : Genes, Bacterial, Bacterial, Betaproteobacteria, General Medicine, MESH : Arsenic, Metals, MESH: Genes, Bacterial, MESH : Genome, Bacterial, Molecular Sequence Data, chemistry.chemical_element, Biology, Arsenic, 03 medical and health sciences, Bacterial Proteins, Drug Resistance, Bacterial, MESH: Arsenic, MESH: Drug Resistance, Bacterial, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, RNA, Messenger, Amino Acid Sequence, Gene, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, 030304 developmental biology, MESH: RNA, Messenger, Two-dimensional gel electrophoresis, MESH: Metals, MESH: Molecular Sequence Data, 030306 microbiology, MESH : Metals, Arsenate, RNA, chemistry, Genes, Genes, Bacterial, Genome, Bacterial
Abstract

International audience; The effect of high concentrations of arsenic has been investigated in Caenibacter arsenoxydans, a beta-proteobacterium isolated from an arsenic contaminated environment and able to oxidize arsenite to arsenate. As the genome of this bacterium has not yet been sequenced, the use of a specific proteomic approach based on nano-high performance liquid chromatography tandem mass spectrometry (nanoLC-MS/MS) studies and de novo sequencing to perform cross-species protein identifications was necessary. In addition, a random mutational analysis was performed. Twenty-two proteins and 16 genes were shown to be differentially accumulated and expressed, respectively, in cells grown in the presence of arsenite. Two genes involved in arsenite oxidation and one in arsenite efflux as well as two proteins responsible for arsenate reduction were identified. Moreover, numerous genes and proteins belonging to various functional classes including information and regulation pathways, intermediary metabolism, cell envelope and cellular processes were also up- or down-regulated, which demonstrates that bacterial response to arsenic is pleiotropic.

Published
2006

9. Structural characterization of 2-aminobenzamide-derivatized oligosaccharides using a matrix-assisted laser desorption/ionization two-stage time-of-flight tandem mass spectrometer

Author

Christine Schaeffer, Willy Morelle, Alain Van Dorsselaer, Jean-Claude Michalski, Marie-Christine Slomianny, Hélène Diemer, Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Laboratoire de Spectrométrie de masse Bio-organique, UMR CNRS-ULP, Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 (UGSF), Institut National de la Recherche Agronomique (INRA)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Spectrométrie de Masse BioOrganique [Strasbourg] (LSMBO), Département Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Institut Pluridisciplinaire Hubert Curien (IPHC), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), and Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Glycan, glycosylation, Molecular Sequence Data, Analytical chemistry, 010402 general chemistry, Mass spectrometry, Tandem mass spectrometry, 01 natural sciences, Reductive amination, Analytical Chemistry, Fragmentation (mass spectrometry), oligosaccharides, ortho-Aminobenzoates, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Spectroscopy, chemistry.chemical_classification, biology, Chemistry, 010401 analytical chemistry, Organic Chemistry, Glycosidic bond, Oligosaccharide, structure analysis, 0104 chemical sciences, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Matrix-assisted laser desorption/ionization, Carbohydrate Sequence, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, biology.protein, glycans
Abstract

Oligosaccharides were derivatized by reductive amination using 2-aminobenzamide (2-AB) and analyzed by matrix-assisted laser desorption/ionization two-stage time-of-flight (MALDI-TOF/TOF) tandem mass spectrometry (MS/MS) in the positive ion mode. The major signals were obtained under these conditions from the [M+Na]+ ions for all 2-AB-derivatized oligosaccharides. A systematic study was conducted on a series of 2-AB-derivatized oligosaccharides to allow rationalization of the fragmentation processes. The MALDI-TOF/TOF-MS/MS spectra of the [M+Na]+ ions of 2-AB-derivatized oligosaccharides were dominated by glycosidic cleavages. These fragments originating both from the reducing and the non-reducing ends of the oligosaccharide yield information on sequence and branching. Moreover, the MALDI-TOF/TOF-MS/MS spectra were also characterized by abundant cross-ring fragments which are very informative on the linkages of the monosaccharide residues constituting these oligosaccharides. MALDI-TOF/TOF-MS/MS analysis of 2-AB-derivatized oligosaccharides, by providing structural information at the low-picomole level, appears to be a powerful tool for carbohydrate structural analysis.

Published
2005

10. Anhydrobacteriohopanetetrol: an unusual bacteriohopane-polyol widespread in recent and past environments

Author

Audrey Bednarczyk, Tc Hernandez, Schaeffer, P., Adam, P., Hm Talbot, Farrimond, P., Armelle Riboulleau, Largeau, C., Derenne, S., Rohmer, M., Albrecht, P., Laboratoire de Spectrométrie de Masse BioOrganique [Strasbourg] (LSMBO), Département Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Institut Pluridisciplinaire Hubert Curien (IPHC), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Stratigraphie et Laboratoire de Chimie Bioorganique et Organique Physique, Université Pierre et Marie Curie - Paris 6 (UPMC), Synthèses sélective organique et produits naturels (SSOPN), Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Biogéochimie et écologie des milieux continentaux (Bioemco), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Fédération de recherche de l'ECPM (FRE), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Spectrométrie de masse Bio-organique, UMR CNRS-ULP, Ecole Nationale Supérieure de Chimie de Paris- Chimie ParisTech-PSL (ENSCP)-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Paris (ENS-PSL), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2005

11. Copurification of the FpvA ferric pyoverdin receptor of Pseudomonas aeruginosa with its iron-free ligand: implications for siderophore-mediated iron transport

Author

Schalk Ij, Prome D, Poole K, Abdallah Ma, Van Dorsselaer A, Pattus F, Pavel Kyslík, Institut Gilbert-Laustriat : Biomolécules, Biotechnologie, Innovation Thérapeutique, Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Laboratory of Enzyme Technology, Czech Academy of Sciences [Prague] (CAS), Institut de pharmacologie et de biologie structurale (IPBS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Laboratoire de Spectrométrie de Masse BioOrganique [Strasbourg] (LSMBO), Département Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Department of Microbiology and Immunology (D MICROBIOLOGY IMMUNOLOGY), Queen's University [Kingston, Canada], Czech Academy of Sciences [Prague] (ASCR), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Spectrométrie de masse Bio-organique, UMR CNRS-ULP, Queen's University [Kingston], Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), and Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Circular dichroism, Siderophore, Siderophores, MESH: Amino Acid Sequence, Ligands, 7. Clean energy, Biochemistry, Copurification, MESH: Circular Dichroism, FepA, MESH: Ligands, MESH: Endopeptidases, MESH: Bacterial Proteins, 0303 health sciences, Chemistry, Circular Dichroism, Hydrolysis, Ligand (biochemistry), Transport protein, MESH: Oligopeptides, MESH: Pseudomonas aeruginosa, Pseudomonas aeruginosa, Bacterial outer membrane, Oligopeptides, MESH: Hydrolysis, medicine.drug, Bacterial Outer Membrane Proteins, Protein Binding, MESH: Pigments, Biological, MESH: Biological Transport, Molecular Sequence Data, Iron Chelating Agents, 03 medical and health sciences, Bacterial Proteins, Endopeptidases, medicine, MESH: Protein Binding, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Amino Acid Sequence, MESH: Siderophores, 030304 developmental biology, MESH: Molecular Sequence Data, 030306 microbiology, MESH: Bacterial Outer Membrane Proteins, Biological Transport, Pigments, Biological, biochemical phenomena, metabolism, and nutrition, MESH: Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, MESH: Iron Chelating Agents, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Ferric
Abstract

The Pseudomonas aeruginosa FpvA receptor is a TonB-dependent outer membrane transport protein that catalyzes uptake of ferric pyoverdin across the outer membrane. Surprisingly, FpvA expressed in P. aeruginosa grown in an iron-deficient medium copurifies with a ligand X that we have characterized by UV, fluorescence, and mass spectrometry as being iron-free pyoverdin (apo-PaA). PaA was absent from FpvA purified from a PaA-deficient P. aeruginosa strain. The properties of ligand binding in vitro revealed very similar affinities of apo-PaA and ferric-PaA to FpvA. Fluorescence resonance energy transfer was used to study in vitro the formation of the FpvA-PaA-Fe complex in the presence of PaA-Fe or citrate-Fe. The circular dichroism spectrum of FpvA indicated a 57% beta-structure content typical of porins and in agreement with the 3D structures of the siderophore receptors FhuA and FepA. In the absence of the protease's inhibitors, a truncated form of FpvA lacking 87 amino acids at its N-terminus was purified. This truncated form still bound PaA, and its beta-sheet content was conserved. This N-terminal region displays significant homology to the N-terminal periplasmic extensions of FecA from Escherichia coli and PupB from Pseudomonas putida, which were previously shown to be involved in signal transduction. This suggests a similar function for FpvA. The mechanism of iron transport in P. aeruginosa via the pyoverdin pathway is discussed in the light of all these new findings.

Published
1999

12. Differential display of peptides induced during the immune response of Drosophila: A matrix-assisted laser desorption ionization time-of-flight mass spectrometry study

Author

Philippe BULET, Uttenweiler-Joseph, S., Moniatte, M., Dorsselaer, A., Hoffmann, J. A., Réponse immunitaire et developpement chez les insectes (RIDI - UPR 9002), Université de Strasbourg (UNISTRA)-Institut de biologie moléculaire et cellulaire (IBMC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de biologie moléculaire et cellulaire (IBMC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Spectrométrie de masse Bio-organique, UMR CNRS-ULP, Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Spectrométrie de Masse BioOrganique [Strasbourg] (LSMBO), Département Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Institut Pluridisciplinaire Hubert Curien (IPHC), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), and Uttenweiler, Sandrine

Subjects
Peptide Biosynthesis, MESH: Drosophila, MESH: Peptides, [SDV]Life Sciences [q-bio], MESH: Anti-Infective Agents, [SDV] Life Sciences [q-bio], MESH: Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Anti-Infective Agents, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Animals, MESH: Animals, MESH: Peptide Biosynthesis, Drosophila, Peptides, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

13. Essential molecular functions associated with the circular code evolution.

Author

Ahmed A, Frey G, and Michel CJ

Subjects
Algorithms, Animals, Base Sequence, Computational Biology methods, Eukaryotic Cells metabolism, Humans, Prokaryotic Cells metabolism, Codon genetics, Evolution, Molecular, Genetic Code genetics, Models, Genetic
Abstract

A circular code is a set of trinucleotides allowing the reading frames in genes to be retrieved locally, i.e. anywhere in genes and in particular without start codons, and automatically with a window of few nucleotides. In 1996, a common circular code, called X, was identified in large populations of eukaryotic and prokaryotic genes. Hence, it is believed to be an ancestral structural property of genes. A new computational approach based on comparative genomics is developed to identify essential molecular functions associated with circular codes. It is based on a quantitative and sensitive statistical method (FPTF) to identify three permuted trinucleotide sets in the three frames of genes, a flower automaton algorithm to determine if a trinucleotide set is a circular code or not, and an integrated Gene Ontology and Taxonomy (iGOT) database. By carrying out automatic circular code analyses on a huge number of gene populations where each population is associated with a particular molecular function, it identifies 266 gene populations having circular codes close to X. Surprisingly, their molecular functions include 98% of those covered by the essential genes of the DEG database (Database of Essential Genes). Furthermore, three trinucleotides GTG, AAG and GCG, replacing three trinucleotides of the code X and called "evolutionary" trinucleotides, significantly occur in these 266 gene populations. Finally, a new method developed to analyse and quantify the stability of a set of trinucleotides demonstrates that these evolutionary trinucleotides are associated with a significant increase of the stability of the common circular code X. Indeed, its stability increases from the 1502th rank to the 16th rank after the replacement of the three evolutionary trinucleotides among 9920 possible trinucleotide replacement sets., (Copyright (c) 2010 Elsevier Ltd. All rights reserved.)

Published
2010
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14. Identification of all trinucleotide circular codes.

Author

Michel CJ and Pirillo G

Subjects
Algorithms, Base Pairing, Reading Frames, Genetic Code, Models, Genetic
Abstract

A new trinucleotide proposition is proved here and allows all the trinucleotide circular codes on the genetic alphabet to be identified (their numbers and their sets of words). This new class of genetic motifs, i.e. circular codes (or synchronizing genetic motifs), may be involved in the structure and the origin of the genetic code, and in reading frames of genes., (Copyright 2010 Elsevier Ltd. All rights reserved.)

Published
2010
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15. Infanticide risk and infant defence in multi-male free-ranging sooty mangabeys, Cercocebus atys.

Author

Fruteau C, Range F, and Noë R

Subjects
Aggression, Animals, Cercocebus atys, Female, Male, Paternal Behavior, Sex Factors, Behavior, Animal, Maternal Behavior, Social Behavior
Abstract

For years, infanticide by males was thought to be unlikely in multi-male primate species. Recent studies have, however, presented evidence of infanticide in such species and a recent model by Broom and colleagues predicts that males' age and rank influence the occurrence of infanticide: youngest and highest-ranking immigrant males are more likely to commit infanticide than their older and lower-ranking counterparts if putative fathers fail to protect infants. I collected data on adult free-ranging sooty mangabey females in the Taï National Park, Ivory Coast, over 11 months including a birth and a mating season. Infanticide had been previously reported in captivity for this species, but not in the wild. Several males entered the group prior to and during the mating season. As predicted by the model, only the more dominant immigrant ones attacked mother-infant pairs significantly more often than did other males. Mothers often reacted with counter-attacks. Potential fathers guarded and supported infants and mothers throughout the period of infant vulnerability. Furthermore, as only one of seven infants died despite 136 observed attacks on mother-infant pairs and unattended infants by immigrant males, we conclude that cooperation between putative fathers and mothers represents an effective protection against infanticide., (2009 Elsevier B.V. All rights reserved.)

Published
2010
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16. Phylogenetic inference with weighted codon evolutionary distances.

Author

Criscuolo A and Michel CJ

Subjects
Algorithms, Candida genetics, Computer Simulation, Saccharomyces genetics, Sequence Alignment, Codon genetics, Evolution, Molecular, Models, Genetic, Models, Statistical, Phylogeny
Abstract

We develop a new approach to estimate a matrix of pairwise evolutionary distances from a codon-based alignment based on a codon evolutionary model. The method first computes a standard distance matrix for each of the three codon positions. Then these three distance matrices are weighted according to an estimate of the global evolutionary rate of each codon position and averaged into a unique distance matrix. Using a large set of both real and simulated codon-based alignments of nucleotide sequences, we show that this approach leads to distance matrices that have a significantly better treelikeness compared to those obtained by standard nucleotide evolutionary distances. We also propose an alternative weighting to eliminate the part of the noise often associated with some codon positions, particularly the third position, which is known to induce a fast evolutionary rate. Simulation results show that fast distance-based tree reconstruction algorithms on distance matrices based on this codon position weighting can lead to phylogenetic trees that are at least as accurate as, if not better, than those inferred by maximum likelihood. Finally, a well-known multigene dataset composed of eight yeast species and 106 codon-based alignments is reanalyzed and shows that our codon evolutionary distances allow building a phylogenetic tree which is similar to those obtained by non-distance-based methods (e.g., maximum parsimony and maximum likelihood) and also significantly improved compared to standard nucleotide evolutionary distance estimates.

Published
2009
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17. Development of a dendritic manganese-enhanced magnetic resonance imaging (MEMRI) contrast agent: synthesis, toxicity (in vitro) and relaxivity (in vitro, in vivo) studies.

Author

Bertin A, Steibel J, Michou-Gallani AI, Gallani JL, and Felder-Flesch D

Subjects
Animals, Contrast Media pharmacokinetics, Contrast Media toxicity, Dendrimers pharmacokinetics, Dendrimers toxicity, Hydrophobic and Hydrophilic Interactions, Magnetic Resonance Imaging, Magnetics, Molecular Weight, Pentetic Acid chemistry, Rats, Sensitivity and Specificity, Solubility, Tissue Distribution, Contrast Media chemistry, Dendrimers chemistry, Manganese chemistry
Abstract

A new dendritic manganese(II) chelate 1 has been evaluated by in vivo (relaxivity) and in vitro (toxicity and relaxivity) experiments as a manganese enhanced magnetic resonance imaging (MEMRI) contrast agent. Also, a comparison with its corresponding gadolinium(III) homologue 2 and the commercially available MEMRI agent MnDPDP (Teslascan, Amersham Health) was achieved in order to determine respectively the real influence of the paramagnetic ion in terms of toxicity and relaxivity for this precise treelike structure and the potential of 1 to be a favorable candidate for brain-targeting MRI. Complexes 1 and 2 displayed high hydrosolubility (0.1 M) and revealed no in vitro neuronal toxicity at concentrations as high as 1 mM. Considering manganese(II) complex 1, the in vivo nontoxicity at 20 mM (100% rats survival) is very likely due to a slow diffusion of the compound, meaning a controlled release of the paramagnetic ions. Finally, T(1) relaxivity of 4.2 mM(-1).s(-1) for 2 and T(2) relaxivity of 17.4 mM(-1).s(-1) for 1 at 4.7 T were measured and are higher than that of the commercial MRI contrast agents GdDTPA and MnDPDP, respectively.

Published
2009
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18. Kisspeptin and the seasonal control of reproduction in hamsters.

Author

Simonneaux V, Ansel L, Revel FG, Klosen P, Pévet P, and Mikkelsen JD

Subjects
Animals, Cricetinae, Cricetulus, Female, Iodide Peroxidase genetics, Iodide Peroxidase metabolism, Isoenzymes genetics, Isoenzymes metabolism, Male, Melatonin metabolism, Photoperiod, Rats, Sheep, Tumor Suppressor Proteins genetics, Reproduction physiology, Seasons, Tumor Suppressor Proteins metabolism
Abstract

Reproduction is a complex and energy demanding function. When internal and external conditions might impair reproductive success (negative energy balance, stress, harsh season) reproductive activity has to be repressed. Recent evidence suggests that these inhibitory mechanisms operate on Kiss1-expressing neurons, which were recently shown to be implicated in the regulation of GnRH release. Hamsters are seasonal rodents which are sexually active in long photoperiod and quiescent in short photoperiod. The photoperiodic information is transmitted to the reproductive system by melatonin, a pineal hormone whose secretion is adjusted to night length. The photoperiodic variation in circulating melatonin has been shown to synchronize reproductive activity with seasons, but the mechanisms involved in this effect of melatonin were so far unknown. Recently we have observed that Kiss1 mRNA level in the arcuate nucleus of the Syrian hamster is lower in short photoperiod, when animals are sexually quiescent. Notably, intracerebroventricular infusion of Kiss1 gene product, kisspeptin, in hamsters kept in short photoperiod is able to override the inhibitory photoperiod and to reactivate sexual activity. The inhibition of Kiss1 expression in short photoperiod is driven by melatonin because pinealectomy prevents decrease in Kiss1 mRNA level in short photoperiod and melatonin injection in long photoperiod down regulates Kiss1 expression. Whether melatonin acts directly on arcuate Kiss1 expressing neurons or mediates its action via interneurons is the subject of the current investigations.

Published
2009
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19. Plant microRNA detection using the circular code information.

Author

Ahmed A and Michel CJ

Subjects
Base Sequence, Models, Genetic, Genetic Code, MicroRNAs analysis, Plants genetics
Abstract

In this paper we present a new computational method leading to the identification of a new property in the plant microRNAs. This property which is based on the circular code information is then used to detect microRNAs in plants. The common C(3) circular code X is a set of 20 trinucleotides identified in the reading frames of both eukaryotic and prokaryotic genes allowing retrieval of any frame in genes, locally anywhere in the three frames (reading frame and its two shifted frames) and automatically with the same window length of 13 nucleotides in each frame. This code X is detected around the beginning of microRNAs. This method based only on the internal structure of genes, i.e. the circular code, allows sensible and precise microRNA site identification in precursor microRNAs with a sliding window of only 14 nucleotides.

Published
2008
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20. Synthesis of highly pure oxyphytosterols and (oxy)phytosterol esters Part I. Regioselective hydrogenation of stigmasterol: an easy access to oxyphytosterols.

Author

Geoffroy P, Julien-David D, Marchioni E, Raul F, Aoudé-Werner D, and Miesch M

Subjects
Drug Design, Hydrogenation, Phytosterols chemistry, Stigmasterol chemistry, Phytosterols chemical synthesis, Stigmasterol chemical synthesis
Abstract

The synthesis of several oxyphytosterols is described starting from stigmasterol, the key step being the regioselective hydrogenation of the 22-23 double bond of the latter.

Published
2008
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21. A Bayesian approach for polarimetric data reduction: the Mueller imaging case.

Author

Zallat J, Heinrich C, and Petremand M

Subjects
Algorithms, Bayes Theorem, Cluster Analysis, Computer Simulation, Diagnostic Imaging methods, Markov Chains, Models, Statistical, Pattern Recognition, Automated methods, Reproducibility of Results, Stochastic Processes, Microscopy, Polarization methods, Optics and Photonics
Abstract

In this paper, we extend to the Mueller imaging framework a formerly introduced Bayesian approach dealing with polarimetric data reduction and robust clustering of polarization encoded images in the piecewise constant case. The extension was made possible thanks to a suitable writing of the observation model in the Mueller context that relies on the system's coherency matrix and Cholesky decomposition such that the admissibility constraints are easily captured. This generalization comes at the cost of nonlinearity with respect to the parameters that have to be estimated. This estimation-clustering problem is tackled in a Bayesian framework where a hierarchical stochastic model based on a Markov random field proposed by Potts is used. This fully unsupervised approach is extensively tested over synthetic data as well as real Mueller images.

Published
2008
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22. Symmetric nonrigid image registration: application to average brain templates construction.

Author

Noblet V, Heinrich C, Heitz F, and Armspach JP

Subjects
Humans, Image Enhancement methods, Reproducibility of Results, Sensitivity and Specificity, Algorithms, Artificial Intelligence, Brain anatomy & histology, Image Interpretation, Computer-Assisted methods, Imaging, Three-Dimensional methods, Magnetic Resonance Imaging methods, Pattern Recognition, Automated methods, Subtraction Technique
Abstract

Image registration aims at estimating a consistent mapping between two images. Common techniques consist in choosing arbitrarily one image as a reference image and the other one as a floating image, thus leading to the estimation of inconsistent mappings. We present a symmetric formulation of the registration problem that maps the two images in a common coordinate system halfway between them. This framework has been considered to devise an efficient strategy for mapping a large set of images in a common coordinate system. Some results are presented in the context of 3-D nonrigid brain MR image registration for the construction of average brain templates.

Published
2008
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23. Evolution probabilities and phylogenetic distance of dinucleotides.

Author

Michel CJ

Subjects
Mutation, Phylogeny, Stochastic Processes, Dinucleotide Repeats genetics, Evolution, Molecular, Models, Genetic
Abstract

We develop here an analytical evolution model based on a dinucleotide mutation matrix 16 x 16 with six substitution parameters associated with the three types of substitutions in the two dinucleotide sites. It generalizes the previous models based on the nucleotide mutation matrices 4 x 4. It determines at some time t the exact occurrence probabilities of dinucleotides mutating randomly according to these six substitution parameters. Furthermore, several properties and two applications of this model allow to derive 16 evolutionary analytical solutions of dinucleotides and also a dinucleotide phylogenetic distance. Finally, based on this mathematical model, the SED (Stochastic Evolution of Dinucleotides) web server has been developed for deriving evolutionary analytical solutions of dinucleotides.

Published
2007
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24. Transport of quercetin di-sodium salt in the human intestinal epithelial Caco-2 cell monolayer 139.

Author

Milane HA, Al Ahmad A, Naitchabane M, Vandamme TF, Jung L, and Ubeaud G

Subjects
Biological Transport, Caco-2 Cells, Cations, Monovalent, Cell Membrane Permeability, Epithelial Cells metabolism, Humans, Hydrogen-Ion Concentration, In Vitro Techniques, Intestinal Absorption, Salts metabolism, Sodium metabolism, Sodium-Glucose Transporter 1 metabolism, Solubility, Antioxidants metabolism, Free Radical Scavengers metabolism, Intestinal Mucosa metabolism, Quercetin metabolism
Abstract

Quercetin di-sodium salt (QDS), a water-soluble derivative of quercetin (Q), is a potent free radical scavenger. The aim of this study was to examine the in vitro intestinal transport of QDS compared to that of Q using the Caco-2 human intestinal epithelial cell line. The apical (A) to basolateral (B) transport of QDS was found to be higher than the B to A transport of this compound. This polarized transport involved the presence of a carrier protein system. The involvement of the sodium/glucose transporter-1 (SGLT-1) was shown by using phloridzin, a selective inhibitor of this conveyor system. However, the transport of Q was not affected by this inhibitor. Moreover, the influx of QDS was pH-sensitive and decreased at pH 5.5 compared with that observed at pH 7.4 and 6.5. The permeability of QDS was 10-fold higher than that of Q. This could be explained by the involvement of SLGT-1 and the absence of an active efflux pump in the absorption of QDS in comparison with Q. This finding was supported by comparing the solubility of Q with that of QDS. This study indicates that both the higher solubility of QDS and its dependence on the SGLT-1 transport system resulted in more efficient permeability compared to Q.

Published
2007
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25. An analytical model of gene evolution with 9 mutation parameters: an application to the amino acids coded by the common circular code.

Author

Michel CJ

Subjects
Eukaryotic Cells, Prokaryotic Cells, Amino Acids genetics, Codon genetics, Evolution, Molecular, Models, Genetic
Abstract

We develop here an analytical evolutionary model based on a trinucleotide mutation matrix 64 x 64 with nine substitution parameters associated with the three types of substitutions in the three trinucleotide sites. It generalizes the previous models based on the nucleotide mutation matrices 4 x 4 and the trinucleotide mutation matrix 64 x 64 with three and six parameters. It determines at some time t the exact occurrence probabilities of trinucleotides mutating randomly according to these nine substitution parameters. An application of this model allows an evolutionary study of the common circular code [Formula: see text] of eukaryotes and prokaryotes and its 12 coded amino acids. The main property of this code [Formula: see text] is the retrieval of the reading frames in genes, both locally, i.e. anywhere in genes and in particular without a start codon, and automatically with a window of a few nucleotides. However, since its identification in 1996, amino acid information coded by [Formula: see text] has never been studied. Very unexpectedly, this evolutionary model demonstrates that random substitutions in this code [Formula: see text] and with particular values for the nine substitutions parameters retrieve after a certain time of evolution a frequency distribution of these 12 amino acids very close to the one coded by the actual genes.

Published
2007
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26. Codon phylogenetic distance.

Author

Michel CJ

Subjects
Evolution, Molecular, Mutation, Sequence Analysis, DNA, Codon, Models, Genetic, Phylogeny
Abstract

We develop here an analytical evolution model based on a trinucleotide mutation matrix 64x64 with nine substitution parameters associated with the three types of substitutions in the three trinucleotide sites and with non-zero elements on its main diagonal. It generalizes the previous models based on the nucleotide mutation matrices 4x4 and the trinucleotide mutation matrices 64x64 with zero elements on its main diagonal. It determines at some time t the exact occurrence probabilities of trinucleotides mutating randomly according to these nine substitution parameters. Furthermore, applications of this model allow to generalize an evolutionary analytical solution of the common circular code of eukaryotes and prokaryotes and also to derive a codon phylogenetic distance.

Published
2007
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27. Hidden Markov multiple event sequence models: A paradigm for the spatio-temporal analysis of fMRI data.

Author

Faisan S, Thoraval L, Armspach JP, and Heitz F

Subjects
Adolescent, Adult, Computer Simulation, Evoked Potentials, Auditory physiology, Female, Humans, Image Enhancement methods, Imaging, Three-Dimensional methods, Magnetic Resonance Imaging instrumentation, Male, Markov Chains, Models, Neurological, Models, Statistical, Phantoms, Imaging, Reproducibility of Results, Sensitivity and Specificity, Algorithms, Artificial Intelligence, Brain anatomy & histology, Brain physiology, Image Interpretation, Computer-Assisted methods, Magnetic Resonance Imaging methods, Pattern Recognition, Automated methods
Abstract

This paper presents a novel, completely unsupervised fMRI brain mapping method that addresses the three problems of hemodynamic response function (HRF) variability, hemodynamic event timing, and fMRI response non-linearity. Spatial and temporal information are directly taken into account into the core of the activation detection process. In practice, activation detection at voxel v is formulated in terms of temporal alignment between sequences of hemodynamic response onsets (HROs) detected in the fMRI signal at v and in the spatial neighborhood of v, and the input sequence of stimuli or stimulus onsets. Event-related and epoch paradigms are considered. The multiple event sequence alignment problem is solved within the probabilistic framework of hidden Markov multiple event sequence models (HMMESMs), a new class of hidden Markov models. Results obtained on real and synthetic data significantly outperform those obtained with the popular statistical parametric mapping (SPM2) method without requiring any prior definition of the expected activation patterns, the HMMESM mapping approach being completely unsupervised.

Published
2007
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28. An a contrario approach for change detection in 3D multimodal images: application to multiple sclerosis in MRI.

Author

Rousseau F, Faisan S, Heitz F, Armspach JP, Chevalier Y, Blanc F, de Seze J, and Rumbach L

Subjects
Algorithms, Humans, Imaging, Three-Dimensional methods, Magnetic Resonance Imaging methods, Models, Statistical, Models, Theoretical, Probability, Software, Brain pathology, Image Processing, Computer-Assisted, Imaging, Three-Dimensional instrumentation, Magnetic Resonance Imaging instrumentation, Multiple Sclerosis diagnosis, Multiple Sclerosis pathology
Abstract

Estimating significant changes between two images remains a challenging problem in medical image processing. This paper proposes a non-parametric region based method to detect significant changes in 3D multimodal Magnetic Resonance (MR) sequences. The proposed approach relies on an a contrario model which defines significant changes as events with very low probability. We adapt the a contrario framework to deal with multimodal images from which are extracted measures related to intensity and volume changes. Two fusion rules are carefully designed to handle a set of decision thresholds and a set of image measures. The final decision is taken using multiple testing procedures. The efficiency of the algorithm is demonstrated in the context of multiple sclerosis (MS) lesion analysis over time in multimodal MR sequences. We evaluate the proposed method on synthetic images using the Brainweb simulator. Finally, promising results on multimodal sequences on clinical data are presented.

Published
2007
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29. Frameshift signals in genes associated with the circular code.

Author

Ahmed A, Frey G, and Michel CJ

Subjects
Animals, Codon genetics, DNA genetics, Humans, Models, Genetic, Eukaryotic Cells physiology, Frameshifting, Ribosomal, Genes physiology, Genetic Code, Prokaryotic Cells physiology
Abstract

Three sets of 20 trinucleotides are preferentially associated with the reading frames and their 2 shifted frames of both eukaryotic and prokaryotic genes. These 3 sets are circular codes. They allow retrieval of any frame in genes (containing these circular code words), locally anywhere in the 3 frames and in particular without start codons in the reading frame, and automatically with the reading of a few nucleotides. The circular code in the reading frame, noted X, which can deduce the 2 other circular codes in the shifted frames by permutation, is the information used for analysing frameshift genes, i. e. genes with a change of reading frame during translation. This work studies the circular code signal around their frameshift sites. Two scoring methods are developed, a function P based on this code X and a function Q based both on this code X and the 4 trinucleotides with identical nucleotides. They detect a significant correlation between the code X and the -1 frameshift signals in both eukaryotic and prokaryotic genes, and the +1 frameshift signals in eukaryotic genes.

Published
2007

30. Cardiolock: an active cardiac stabilizer. First in vivo experiments using a new robotized device.

Author

Bachta W, Renaud P, Laroche E, Gangloff J, and Forgione A

Subjects
Animals, Coronary Artery Bypass, Off-Pump methods, Equipment Design, Equipment Failure Analysis, Humans, Immobilization methods, Physical Stimulation methods, Pilot Projects, Robotics methods, Stress, Mechanical, Swine, Therapy, Computer-Assisted methods, Transducers, Coronary Artery Bypass, Off-Pump instrumentation, Immobilization instrumentation, Physical Stimulation instrumentation, Robotics instrumentation, Therapy, Computer-Assisted instrumentation
Abstract

Off-pump Coronary Artery Bypass Grafting (CABG) is still today a technically difficult procedure. In fact, the mechanical stabilizers used to locally suppress the heart excursion have been demonstrated to exhibit significant residual motion. We therefore propose a novel active stabilizer which is able to compensate for this residual motion. The interaction between the heart and a mechanical stabilizer is first assessed in vivo on an animal model. Then, the principle of active stabilization, based on the high speed vision-based control of a compliant mechanism, is presented. In vivo experimental results are given using a prototype which structure is compatible with a minimally invasive approach.

Published
2007

31. Retrospective evaluation of a topology preserving non-rigid registration method.

Author

Noblet V, Heinrich C, Heitz F, and Armspach JP

Subjects
Computer Simulation, Elasticity, Humans, Information Storage and Retrieval methods, Models, Biological, Reproducibility of Results, Retrospective Studies, Sensitivity and Specificity, Algorithms, Artificial Intelligence, Image Enhancement methods, Image Interpretation, Computer-Assisted methods, Imaging, Three-Dimensional methods, Pattern Recognition, Automated methods, Subtraction Technique
Abstract

This paper proposes a comprehensive evaluation of a monomodal B-spline-based non-rigid registration algorithm allowing topology preservation in 3-D. This article is to be considered as the companion of [Noblet, V., Heinrich, C., Heitz, F., Armspach, J.-P., 2005. 3-D deformable image registration: a topology preservation scheme based on hierarchical deformation models and interval analysis optimization. IEEE Transactions on Image Processing, 14 (5), 553-566] where this algorithm, based on the minimization of an objective function, was introduced and detailed. Overall assessment is based on the estimation of synthetic deformation fields, on average brain construction, on atlas-based segmentation and on landmark mapping. The influence of the model parameters is characterized. Comparison between several objective functions is carried out and impact of their symmetrization is pointed out. An original intensity normalization scheme is also introduced, leading to significant improvements of the registration quality. The comparison benchmark is the popular demons algorithm [Thirion, J.-P., 1998. Image matching as a diffusion process: an analogy with Maxwell's demons. Medical Image Analysis, 2 (3), 243-260], that exhibited best results in a recent comparison between several non-rigid 3-D registration methods [Hellier, P., Barillot, C., Corouge, I., Gibaud, B., Le Goualher, G., Collins, D.L., Evans, A., Malandain, G., Ayache, N., Christensen, G.E., Johnson, H.J., 2003. Retrospective evaluation of intersubject brain registration. IEEE Transactions on Medical Imaging, 22 (9), 1120-1130]. The topology preserving B-spline-based method proved to outperform the commonly available ITK implementation of the demons algorithms on many points. Some limits of intensity-based registration methods are also highlighted through this work.

Published
2006
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32. Identification of circular codes in bacterial genomes and their use in a factorization method for retrieving the reading frames of genes.

Author

Frey G and Michel CJ

Subjects
Base Sequence, Computational Biology, Genes, Bacterial, Models, Genetic, Models, Statistical, Reading Frames, Genome, Bacterial, Genomics statistics & numerical data
Abstract

We developed a statistical method that allows each trinucleotide to be associated with a unique frame among the three possible ones in a (protein coding) gene. An extensive gene study in 175 complete bacterial genomes based on this statistical approach resulted in identification of 72 new circular codes. Finding a circular code enables an immediate retrieval of the reading frame locally anywhere in a gene. No knowledge of location of the start codon is required and a short window of only a few nucleotides is sufficient for automatic retrieval. We have therefore developed a factorization method (that explores previously found circular codes) for retrieving the reading frames of bacterial genes. Its principle is new and easy to understand. Neither complex treatment nor specific information on the nucleotide sequences is necessary. Moreover, the method can be used for short regions in nucleotide sequences (less than 25 nucleotides in protein coding genes). Selected additional properties of circular codes and their possible biological consequences are also discussed.

Published
2006
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33. An analytical model of gene evolution with six mutation parameters: an application to archaeal circular codes.

Author

Frey G and Michel CJ

Subjects
Mutation, Trinucleotide Repeats, Archaea genetics, DNA, Circular, Evolution, Molecular, Genetic Code, Genome, Archaeal, Models, Genetic
Abstract

We develop here an analytical evolutionary model based on a trinucleotide mutation matrix 64 x 64 with six substitution parameters associated with the transitions and transversions in the three trinucleotide sites. It generalizes the previous models based on the nucleotide mutation matrices 4 x 4 and the trinucleotide mutation matrix 64 x 64 with three parameters. It determines at some time t the exact occurrence probabilities of trinucleotides mutating randomly according to six substitution parameters. An application of this model allows an evolutionary study of the common circular code COM and the 15 archaeal circular codes X which have been recently identified in several archaeal genomes. The main property of a circular code is the retrieval of the reading frames in genes, both locally, i.e. anywhere in genes and in particular without a start codon, and automatically with a window of a few nucleotides. In genes, the circular code is superimposed on the traditional genetic one. Very unexpectedly, the evolutionary model demonstrates that the archaeal circular codes can derive from the common circular code subjected to random substitutions with particular values for six substitutions parameters. It has a strong correlation with the statistical observations of three archaeal codes in actual genes. Furthermore, the properties of these substitution rates allow proposal of an evolutionary classification of the 15 archaeal codes into three main classes according to this model. In almost all the cases, they agree with the actual degeneracy of the genetic code with substitutions more frequent in the third trinucleotide site and with transitions more frequent that transversions in any trinucleotide site.

Published
2006
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34. The state of water in living systems: from the liquid to the jellyfish.

Author

Henry M

Subjects
Animals, Entropy, History, 17th Century, History, 18th Century, History, 19th Century, History, 20th Century, History, 21st Century, History, Ancient, History, Medieval, Humans, Knowledge, Models, Biological, Muscle Contraction, Mythology, Philosophy history, Science history, Scyphozoa chemistry, Scyphozoa physiology, Thermodynamics, Cell Physiological Phenomena, Life, Water analysis, Water chemistry, Water physiology
Abstract

The status of water in living systems is reviewed both from philosophical and scientific viewpoints. Starting from antique Mediterranean civilizations (Sumerian, Egyptian, Hebrew, Greek), a world trip is proposed through Norse myths, Siberian Shamanism, Hinduism, Taoism, Buddhism, Shinto, Mayan, Aztec, Inca, Aboriginal and African philosophies in order to convince that all humans share the same qualitative idea that water was a pre-requisite for life apparition. The quantitative aspect of the problem is further analyzed at the light of the scientific contributions from two leading scientists: R.A. Gortner and E.T. Jaynes. With Gortner's work it is demonstrated using the concrete example of the Jellyfish submitted at a Faraday discussion held in London in 1930, how a paradigm shift has occurred in the thirties concerning the status of bound water in the living cell. With Jaynes' work, the disastrous consequences of the entrenchment of diffusion theory in biology are critically examined and the exact meaning of the second law of thermodynamics for biological systems is given using the concrete example of muscle contraction. In conclusion, the importance of distinguishing between an ontological and epistemological level of knowledge is stressed and suggestions for reconciling scientific and philosophical approaches are given.

Published
2005

35. On the use of nonfluorescent dye labeled ligands in FRET-based receptor binding studies.

Author

Tahtaoui C, Guillier F, Klotz P, Galzi JL, Hibert M, and Ilien B

Subjects
Benzenesulfonates chemistry, Benzodiazepinones chemistry, Boron Compounds, Cell Line, Coloring Agents chemistry, Fluorescence Resonance Energy Transfer, Green Fluorescent Proteins genetics, Humans, Ligands, Pirenzepine chemistry, Quinolinium Compounds chemistry, Radioligand Assay, Receptor, Muscarinic M1 genetics, Recombinant Fusion Proteins genetics, Benzenesulfonates chemical synthesis, Benzodiazepinones chemical synthesis, Coloring Agents chemical synthesis, Green Fluorescent Proteins metabolism, Pirenzepine analogs & derivatives, Pirenzepine chemical synthesis, Quinolinium Compounds chemical synthesis, Receptor, Muscarinic M1 metabolism, Recombinant Fusion Proteins metabolism
Abstract

The efficiency of fluorescence resonance energy transfer (FRET) is dependent upon donor-acceptor proximity and spectral overlap, whether the acceptor partner is fluorescent or not. We report here on the design, synthesis, and characterization of two novel pirenzepine derivatives that were coupled to patent blue VF and pinacyanol dyes. These nonfluorescent compounds, when added to cells stably expressing enhanced green fluorescent protein (EGFP)-fused muscarinic M1 receptors, promote EGFP fluorescence extinction in a time-, concentration-, and atropine-dependent manner. They display nanomolar affinity for the muscarinic receptor, determined using either FRET or classical radioligand binding conditions. We provide evidence that these compounds behave as potent acceptors of energy from excited EGFP with quenching efficiencies comparable to those of analogous fluorescent bodipy or rhodamine red pirenzepine derivatives. The advantages they offer over fluorescent ligands are illustrated and discussed in terms of reliability, sensitivity, and wider applicability of FRET-based receptor binding assays.

Published
2005
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36. Ginsenoside-Rd from Panax notoginseng enhances astrocyte differentiation from neural stem cells.

Author

Shi Q, Hao Q, Bouissac J, Lu Y, Tian S, and Luu B

Subjects
Animals, Astrocytes cytology, Cells, Cultured, Mice, Panax chemistry, Stem Cells cytology, Astrocytes drug effects, Cell Differentiation drug effects, Ginsenosides pharmacology, Neurons cytology, Stem Cells drug effects
Abstract

Neural stem cells cultured as neurospheres were used to assess the effects of P. notoginseng on the production of neurons and glia. The crude saponins (PNS) and ginsenoside-Rd promote the differentiation of neurospheres into astrocytes. Ginsenoside-Rd increases the production of astrocytes in a dose-dependent manner. On the other hand, both PNS and ginsenoside-Rd induce a weak but significant effect by decreasing the number of neurons. The other ginsenosides do not induce any differentiation on both neurons and astrocytes.

Published
2005
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37. Toward robotized beating heart TECABG: assessment of the heart dynamics using high-speed vision.

Author

Cuvillon L, Gangloff J, de Mathelin M, and Forgione A

Subjects
Algorithms, Animals, Heart anatomy & histology, Image Interpretation, Computer-Assisted methods, Myocardial Contraction, Swine, Artificial Intelligence, Coronary Artery Bypass methods, Electrocardiography methods, Endoscopy methods, Heart physiology, Robotics methods, Surgery, Computer-Assisted methods
Abstract

Active robotic filtering is a promising solution for beating heart Totally Endoscopic Coronary Artery Bypass Grafting (TECABG). n this work, we assess the heart motion dynamics using simultaneously igh speed imaging of optical markers attached to the heart, ECG signals and ventilator airflow acquisitions. Our goal is to make an assessment of the heart motion (shape, velocity, acceleration) in order to be able to make more accurate specifications for a dedicated robot that could follow this motion in real-time. Furthermore, using the 2 additional inputs (ECG, airflow), we propose a prediction algorithm of the motion that could be used with a predictive control algorithm to improve the tracking accuracy.

Published
2005
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38. Fluorescent pirenzepine derivatives as potential bitopic ligands of the human M1 muscarinic receptor.

Author

Tahtaoui C, Parrot I, Klotz P, Guillier F, Galzi JL, Hibert M, and Ilien B

Subjects
Allosteric Regulation, Binding Sites, Binding, Competitive, Boron Compounds chemistry, Fluorescence Resonance Energy Transfer methods, Fluorescent Dyes pharmacology, Green Fluorescent Proteins, Humans, Kinetics, Ligands, Luminescent Proteins genetics, Pirenzepine pharmacology, Radioligand Assay, Receptor, Muscarinic M1 genetics, Receptor, Muscarinic M1 metabolism, Recombinant Fusion Proteins metabolism, Rhodamines chemistry, Structure-Activity Relationship, Strychnine pharmacology, Fluorescent Dyes chemical synthesis, Pirenzepine analogs & derivatives, Pirenzepine chemical synthesis, Receptor, Muscarinic M1 drug effects, Strychnine analogs & derivatives
Abstract

Following a recent description of fluorescence resonance energy transfer between enhanced green fluorescent protein (EGFP)-fused human muscarinic M1 receptors and Bodipy-labeled pirenzepine, we synthesized seven fluorescent derivatives of this antagonist in order to further characterize ligand-receptor interactions. These compounds carry Bodipy [558/568], Rhodamine Red-X [560/580], or Fluorolink Cy3 [550/570] fluorophores connected to pirenzepine through various linkers. All molecules reversibly bind with high affinity to M1 receptors (radioligand and energy transfer binding experiments) provided that the linker contains more than six atoms. The energy transfer efficiency exhibits modest variations among ligands, indicating that the distance separating EGFP from the fluorophores remains almost constant. This also supports the notion that the fluorophores may bind to the receptor protein. Kinetic analyses reveal that the dissociation of two Bodipy derivatives (10 or 12 atom long linkers) is sensitive to the presence of the allosteric modulator brucine, while that of all other molecules (15-24 atom long linkers) is not. The data favor the idea that these analogues might interact with both the acetylcholine and the brucine binding domains., (Copyright 2004 American Chemical Society)

Published
2004
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39. Mechanical properties of mono-domain side chain nematic elastomers.

Author

Martinoty P, Stein P, Finkelmann H, Pleiner H, and Brand HR

Subjects
Anisotropy, Models, Chemical, Scattering, Radiation, Temperature, Thermodynamics, Time Factors, Water chemistry, X-Rays, Biophysics methods, Polymers chemistry
Abstract

We investigate the behavior of the shear rigidity modulus G = G' + iG" of three mono-domain side chain liquid-crystalline elastomers composed of side chain polysiloxanes cross-linked by either flexible or rigid cross-linkers. The measurements were taken in a frequency domain ranging from approximately 0.02 Hz to approximately 10(4) Hz applying the shear in a plane perpendicular to or containing the director. The measurements as a function of temperature show an anisotropy of G' which appears around T(NI), when decreasing the temperature, and which is due to the expected lowering of G'(//) coming from the coupling between the shear and the director. The measurements as a function of frequency show that G has two components for both geometries, in both the isotropic phase and in the nematic phase around the phase transition. One reflects the network behavior in its hydrodynamic regime ( G' is constant and G'' is approximately f, where f is the frequency), the other which appears at higher frequencies is characterized by a scaling law behavior (G' is approximately G" is approximately f(0.5)) of the Rouse type. We discuss the results in the framework of available theories and show that the three elastomers present a non-soft behavior, even for the elastomer for which the contrary was claimed, and that there is no separation of time scales between the director and the network. We also present data on a poly-domain sample and a non-mesomorphic one which complement these results.

Published
2004
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40. Expression of tetrodotoxin-sensitive and resistant sodium channels by rat melanotrophs.

Author

Schwab Y, Jahke R, and Jover E

Subjects
Animals, Cells, Cultured, Gene Expression Regulation drug effects, Pituitary Gland drug effects, Rats, Gene Expression Regulation physiology, Pituitary Gland cytology, Pituitary Gland metabolism, Sodium Channels biosynthesis, Tetrodotoxin pharmacology
Abstract

Rat melanotrophs fire Na+ and Ca2(+)-dependent action potentials. Whereas the molecular identity of Ca2+ channels expressed by these cells is well documented, less is known about Na channels. We characterize the expression of seven sodium channel alpha-subunit and the beta1- and beta2-subunit mRNAs. The tetrodotoxin-resistant Nav1.8 and Nav1.9 alpha subunit mRNAs are detected in the newborn intermediate lobe and in cultured melanotrophs. Electrophysiological recordings further demonstrate the expression of both tetrodotoxin-sensitive and tetrodotoxin-resistant currents by dissociated melanotrophs. Moreover, activated sodium channels are able to elicit intracellular calcium waves, both in the absence or in the presence of tetrodotoxin. This work shows that rat melanotrophs express functional tetrodotoxin-resistant sodium channels, whose activation can lead to the generation of intracellular calcium waves., (Copyright 2004 Lippincott Williams and Wilkins)

Published
2004
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41. A computer method for identifying patterns in electroencephalogram signals.

Author

Michel CJ

Subjects
Humans, Pattern Recognition, Automated, Algorithms, Audiometry, Evoked Response methods, Brain physiology, Diagnosis, Computer-Assisted methods, Models, Neurological, Models, Statistical, Periodicity, Sleep physiology
Abstract

A computer method is developed for identifying patterns in electroencephalogram (EEG) signals. An EEG numerical signal is transformed into a symbolic series. The simple transformation used here studies the variations between two successive values of the signal. Then, this series is analysed with a symbolic correlation function based on probabilities without bias. The use of large windows, e.g. 1 hour, allows the identification of weak signals hidden by the specific ones. An application of this method to the sleep analysis of a healthy adult shows a periodicity modulo 10 in all derivations. A possible neurophysiological meaning is presented in the discussion.

Published
2003
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42. Circular codes in archaeal genomes.

Author

Frey G and Michel CJ

Subjects
Archaea genetics, Archaeal Proteins genetics, Reading Frames, Trinucleotide Repeats, DNA, Circular, Genetic Code, Genome, Archaeal, Models, Genetic
Abstract

A new statistical method associating each trinucleotide with a frame is developed for identifying circular codes. Its sensibility allows the detection of several circular codes in the (protein coding) genes of archaeal genomes. Several properties of these circular codes are described, in particular the lengths of the minimal windows to retrieve the construction frames, a new definition of a parameter for measuring some probabilities of words generated by the circular codes, and the types of nucleotides in the trinucleotide sites. Some biological consequences are presented in Discussion.

Published
2003
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43. Molecular modeling of the GABA/GABA(B) receptor complex.

Author

Bernard P, Guedin D, and Hibert M

Subjects
Amino Acid Sequence, Ligands, Models, Molecular, Molecular Sequence Data, Receptors, GABA-B metabolism, Receptors, GABA-B chemistry
Abstract

A three-dimensional model of the extracellular domain of the GABA(B) receptor has been built by homology with the leucine/isoleucine/valine-binding protein. The complete putative GABA-binding site in the extracellular domain is described in both the open and closed states. The dynamics of the "Venus flytrap" mechanism has been studied, suggesting that the molecular dipole moments play a key role in GABA binding and receptor activation. Important residues putatively implicated either in ligand binding or in the dynamics of the receptor are pinpointed, thus highlighting target residues for mutagenesis experiments and model validation.

Published
2001
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