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10 results on '"Pierre Ezanno"'

1. Single molecule sequencing of the M13 virus genome without amplification.

Author

Luyang Zhao, Liwei Deng, Gailing Li, Huan Jin, Jinsen Cai, Huan Shang, Yan Li, Haomin Wu, Weibin Xu, Lidong Zeng, Renli Zhang, Huan Zhao, Ping Wu, Zhiliang Zhou, Jiao Zheng, Pierre Ezanno, Andrew X Yang, Qin Yan, Michael W Deem, and Jiankui He

Subjects
Medicine, Science
Abstract

Next generation sequencing (NGS) has revolutionized life sciences research. However, GC bias and costly, time-intensive library preparation make NGS an ill fit for increasing sequencing demands in the clinic. A new class of third-generation sequencing platforms has arrived to meet this need, capable of directly measuring DNA and RNA sequences at the single-molecule level without amplification. Here, we use the new GenoCare single-molecule sequencing platform from Direct Genomics to sequence the genome of the M13 virus. Our platform detects single-molecule fluorescence by total internal reflection microscopy, with sequencing-by-synthesis chemistry. We sequenced the genome of M13 to a depth of 316x, with 100% coverage. We determined a consensus sequence accuracy of 100%. In contrast to GC bias inherent to NGS results, we demonstrated that our single-molecule sequencing method yields minimal GC bias.

Published
2017
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2. Single molecule sequencing of M13 virus genome without amplification

Author

Zhou Zhiliang, Huan Jin, Haomin Wu, Lidong Zeng, Pierre Ezanno, Zhao Luyang, Michael W. Deem, Yan Li, Yan Qin, Huan Shang, Deng Liwei, Jinsen Cai, Jiankui He, Wu Ping, Xu Weibin, Renli Zhang, Zheng Jiao, Huan Zhao, and Li Gailing

Subjects
Genetics, DNA nanoball sequencing, DNA sequencer, Massive parallel sequencing, Shotgun sequencing, Multiple displacement amplification, Transmission electron microscopy DNA sequencing, Biology, Deep sequencing, Single molecule real time sequencing
Abstract

Third generation sequencing is a direct measurement of DNA/RNA sequences at the single molecule level without amplification. In this study, we report sequencing of the genome of the M13 virus by a new single molecule sequencing platform. Our platform detects single molecule fluorescence by the total internal reflection microscope technique, with sequencing-by-synthesis chemistry. We sequenced the genome of M13 to a depth of 316x and 100% coverage. The consensus sequence accuracy is 100%. We demonstrated that single molecule sequencing has no significant GC bias.

Published
2017
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3. Author Correction: The oxidative inactivation of FeFe hydrogenase reveals the flexibility of the H-cluster

Author

Kateryna Sybirna, Carole Baffert, Pierre Ezanno, Luca De Gioia, Isabelle Meynial-Salles, Maurizio Bruschi, Hervé Bottin, Philippe Soucaille, Jochen Blumberger, C Greco, Po-hung Wang, Christophe Léger, Vincent Fourmond, and Marco Montefiori

Subjects
Hydrogenase, Flexibility (anatomy), medicine.anatomical_structure, Chemistry, Stereochemistry, General Chemical Engineering, medicine, Cluster (physics), General Chemistry, Oxidative phosphorylation
Published
2019
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4. Single molecule sequencing of the M13 virus genome without amplification

Author

Michael W. Deem, Huan Jin, Li Gailing, Lidong Zeng, Jiankui He, Wu Ping, Huan Shang, Renli Zhang, Xu Weibin, Jinsen Cai, Pierre Ezanno, Zheng Jiao, Deng Liwei, Haomin Wu, Zhao Luyang, Yan Qin, Yan Li, Huan Zhao, Andrew X. Yang, and Zhou Zhiliang

Subjects
0301 basic medicine, Molecular biology, lcsh:Medicine, Artificial Gene Amplification and Extension, Genome, Polymerase Chain Reaction, law.invention, Database and Informatics Methods, Sequencing techniques, law, Genomic library, DNA sequencing, Genome Sequencing, lcsh:Science, Polymerase chain reaction, Base Composition, Multidisciplinary, High-Throughput Nucleotide Sequencing, RNA sequencing, Genomics, Transcriptome Analysis, Sequence Analysis, Nucleic Acid Amplification Techniques, Research Article, Next-Generation Sequencing, Bioinformatics, Sequence alignment, Computational biology, Genome, Viral, 03 medical and health sciences, Genomic Medicine, Consensus sequence, Genetics, Biology and life sciences, Base Sequence, lcsh:R, Computational Biology, Nucleic acid amplification technique, Vector Cloning, Genome Analysis, Genomic Libraries, Research and analysis methods, 030104 developmental biology, Molecular biology techniques, lcsh:Q, Sequence Alignment, Cloning, Bacteriophage M13
Abstract

Next generation sequencing (NGS) has revolutionized life sciences research. However, GC bias and costly, time-intensive library preparation make NGS an ill fit for increasing sequencing demands in the clinic. A new class of third-generation sequencing platforms has arrived to meet this need, capable of directly measuring DNA and RNA sequences at the single-molecule level without amplification. Here, we use the new GenoCare single-molecule sequencing platform from Direct Genomics to sequence the genome of the M13 virus. Our platform detects single-molecule fluorescence by total internal reflection microscopy, with sequencing-by-synthesis chemistry. We sequenced the genome of M13 to a depth of 316x, with 100% coverage. We determined a consensus sequence accuracy of 100%. In contrast to GC bias inherent to NGS results, we demonstrated that our single-molecule sequencing method yields minimal GC bias.

Published
2017

5. Arginine171 of Chlamydomonas reinhardtii [Fe–Fe] hydrogenase HydA1 plays a crucial role in electron transfer to its catalytic center

Author

Christophe Léger, Pierre Ezanno, Carole Baffert, Hervé Bottin, and Kateryna Sybirna

Subjects
Hydrogenase, biology, Renewable Energy, Sustainability and the Environment, Chemistry, Mutant, Tryptophan, Energy Engineering and Power Technology, Chlamydomonas reinhardtii, Condensed Matter Physics, Photochemistry, biology.organism_classification, Electron transport chain, Catalysis, Electron transfer, Fuel Technology, Hydrogen production
Abstract

[Fe–Fe] hydrogenases, with hydrogen evolution activities outperforming [Ni–Fe] hydrogenases by 3–4 orders of magnitude, are still the most promising enzyme class for hydrogen production purposes. For Chlamydomonas reinhardtii [Fe–Fe] hydrogenase HydA1 the question of catalytic activity and electron transport is of main importance. Here we report the characterization of two mutant forms of C. reinhardtii HydA1. An aspartic acid in place of arginine 171 leads to a six-fold increase of the catalytic activity in comparison to the wild type protein during methyl viologen-dependent hydrogen production. Tryptophan in position 171 does not result in any change in methyl viologen-induced activity. At the same time these mutations lead to a strong decrease in ferredoxin-dependent hydrogen production while the catalytic center of mutant forms stays intact. The localization of this amino acid (arginine 171 ) in the environment of Cr HydA1 H-cluster indicates that the limitation of the catalytic activity of this hydrogenase is due to the electron transfer step to the catalytic center where the reduction of protons takes place.

Published
2013
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6. The efficient hemostatic effect of Antarctic krill chitosan is related to its hydration property

Author

Haobo Pan, Jianhui Yue, Pierre Ezanno, Ting Wang, William W. Lu, Wu Shuai, Di Liu, Changshun Ruan, Huang Zhuoyao, and Xiaoli Zhao

Subjects
Erythrocyte Aggregation, Polymers and Plastics, Hemorrhage, macromolecular substances, Erythrocyte aggregation, Hemostatics, Chitosan, chemistry.chemical_compound, Materials Chemistry, Animals, Platelet activation, Food science, Blood coagulation test, Hemostatic Agent, biology, Organic Chemistry, technology, industry, and agriculture, Water, equipment and supplies, biology.organism_classification, Platelet Activation, carbohydrates (lipids), Mice, Inbred C57BL, Antarctic krill, Biochemistry, chemistry, Hemostasis, Blood Coagulation Tests, Water binding, Euphausiacea
Abstract

Antarctic krill chitosan (A-Chitosan) was first evaluated in its hemostatic effect in this study. The prepared A-Chitosan powder showed low level of crystallinity and significantly high water binding capacity as 1293% (w/w). By mice tail amputation model and blood coagulation timing experiment, it is showed that this chitosan accelerated the tail hemostasis by 55% and shortened the blood clotting time by 38%. This efficacy was better than two other commercial chitosans investigated and was corresponding to their water binding capacities. Through examining the effect of chitosan on blood components, it could be found that platelets adhesion was mainly affected by the water binding capacity, and red blood cells aggregation was dependent on their deacetylation degree. The physicochemical properties resulted in better hydration property of chitosan would improve its hemostatic effect. These results suggested that Antarctic krill chitosan is a good candidate for hemostatic application.

Published
2015

7. The oxidative inactivation of FeFe hydrogenase reveals the flexibility of the H-cluster

Author

Isabelle Meynial-Salles, Jochen Blumberger, Vincent Fourmond, Carole Baffert, Marco Montefiori, Luca De Gioia, Pierre Ezanno, Claudio Greco, Philippe Soucaille, Kateryna Sybirna, Po-hung Wang, Hervé Bottin, Christophe Léger, Maurizio Bruschi, Bioénergétique et Ingénierie des Protéines (BIP ), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Department of Earth and Environmental Sciences [Milano], Università degli Studi di Milano-Bicocca = University of Milano-Bicocca (UNIMIB), Service de Bioénergétique, Biologie Stucturale, et Mécanismes (SB2SM), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie et de Technologies de Saclay (IBITECS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Department of Physics and Astronomy [UCL London], University College of London [London] (UCL), Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Department of Biotechnologies and Biosciences, Centre National de la Recherche Scientifique, Aix-Marseille Universite, Agence Nationale de la Recherche [ANR-12-BS08-0014, ANR-2010-BIOE-004], Ministero dell'Istruzione, dell'Universita e della Ricerca [Prin 2010M2JARJ], Ministry of Education, Republic of China (Taiwan), Engineering and Physical Sciences Research Council [EP/J015571/1, EP/F067496], Royal Society, Università degli Studi di Milano-Bicocca [Milano] (UNIMIB), Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), University of Milano-Bicocca, Fourmond, V, Greco, C, Sybirna, K, Baffert, C, Wang, P, Ezanno, P, Montefiori, M, Bruschi, M, Meynial Salles, I, Soucaille, P, Blumberger, J, Bottin, H, DE GIOIA, L, Léger, C, Bioénergétique et Ingénierie des Protéines ( BIP ), Aix Marseille Université ( AMU ) -Centre National de la Recherche Scientifique ( CNRS ), Department of Earth and Environmental Sciences ( DEES ), Service de Bioénergétique, Biologie Stucturale, et Mécanismes ( SB2SM ), Centre National de la Recherche Scientifique ( CNRS ) -Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Institut de Biologie et de Technologies de Saclay ( IBITECS ), Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), University College of London [London] ( UCL ), Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés ( LISBP ), Institut National de la Recherche Agronomique ( INRA ) -Institut National des Sciences Appliquées - Toulouse ( INSA Toulouse ), and Institut National des Sciences Appliquées ( INSA ) -Institut National des Sciences Appliquées ( INSA ) -Centre National de la Recherche Scientifique ( CNRS )

Subjects
Iron-Sulfur Proteins, Hydrogenase, Coordination sphere, Protein Conformation, General Chemical Engineering, Phenylalanine, Oxidative phosphorylation, Hydrogenase mimic, Photochemistry, Electrocatalyst, [ CHIM ] Chemical Sciences, Catalysis, Oxidizing agent, [CHIM]Chemical Sciences, chemistry.chemical_classification, General Chemistry, Combinatorial chemistry, Kinetics, Enzyme, chemistry, Mutation, Enzyme mechanisms, Tyrosine, hydrogenases, hydrogen, density functional theory, molecular dynamics, Electrocatalysis, Oxidation-Reduction, Hydrogen
Abstract

Nature is a valuable source of inspiration in the design of catalysts, and various approaches are used to elucidate the mechanism of hydrogenases, the enzymes that oxidize or produce H 2. In FeFe hydrogenases, H 2 oxidation occurs at the H-cluster, and catalysis involves H 2 binding on the vacant coordination site of an iron centre. Here, we show that the reversible oxidative inactivation of this enzyme results from the binding of H 2 to coordination positions that are normally blocked by intrinsic CO ligands. This flexibility of the coordination sphere around the reactive iron centre confers on the enzyme the ability to avoid harmful reactions under oxidizing conditions, including exposure to O 2. The versatile chemistry of the diiron cluster in the natural system might inspire the design of novel synthetic catalysts for H 2 oxidation. © 2014 Macmillan Publishers Limited.

Published
2014
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8. The quest for a functional substrate access tunnel in FeFe hydrogenase

Author

Philippe Soucaille, Laurent Cournac, Vincent Fourmond, Christophe Léger, Juan C. Fontecilla-Camps, Carole Baffert, Pierre Ezanno, Thomas Lautier, Patrick Bertrand, Isabelle Meynial-Salles, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), UMR 5504, Centre National de la Recherche Scientifique (CNRS), Université de la Méditerranée - Aix-Marseille 2, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université Joseph Fourier - Grenoble 1 (UJF), CNRS, ANR, INSA, CEA, Universite de Provence, pole de competitivite Capenergies, City of Marseilles, Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), and Toulouse Biotechnology Institute (TBI)

Subjects
Iron-Sulfur Proteins, Models, Molecular, Hydrogenase, Clostridium acetobutylicum, CYTOCHROME-C-OXIDASE, Stereochemistry, [SDV]Life Sciences [q-bio], NIFE HYDROGENASE, 010402 general chemistry, 01 natural sciences, CARBAMOYL-PHOSPHATE SYNTHETASE, PROTEIN FILM VOLTAMMETRY, 03 medical and health sciences, [SDV.IDA]Life Sciences [q-bio]/Food engineering, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Physical and Theoretical Chemistry, CARBON-MONOXIDE, SYNTHASE/CARBON MONOXIDE DEHYDROGENASE, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, Carbon Monoxide, biology, Chemistry, ACTIVE-SITE, Mutagenesis, Active site, Substrate (chemistry), Nitrogenase, biology.organism_classification, 0104 chemical sciences, Oxygen, Kinetics, Enzyme, X-RAY CRYSTALLOGRAPHY, MOLECULAR-DYNAMICS, Intramolecular force, biology.protein, Mutagenesis, Site-Directed, DESULFOVIBRIO-DESULFURICANS, Hydrogen
Abstract

International audience; We investigated di-hydrogen transport between the solvent and the active site of FeFe hydrogenases. Substrate channels supposedly exist and serve various functions in certain redox enzymes which use or produce O(2), H(2), NO, CO, or N(2), but the preferred paths have not always been unambiguously identified, and whether a continuous, permanent channel is an absolute requirement for transporting diatomic molecules is unknown. Here, we review the literature on gas channels in proteins and enzymes and we report on the use of site-directed mutagenesis and various kinetic methods, which proved useful for characterizing substrate access to the active site of NiFe hydrogenase to test the putative "static'' H(2) channel of FeFe hydrogenases. We designed 8 mutations in attempts to interfere with intramolecular diffusion by remodeling this putative route in Clostridium acetobutylicum FeFe hydrogenase, and we observed that none of them has a strong effect on any of the enzyme's kinetic properties. We suggest that H(2) may diffuse either via transient cavities, or along a conserved water-filled channel. Nitrogenase sets a precedent for the involvement of a hydrophilic channel to conduct hydrophobic molecules.

Published
2011
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9. CO Disrupts the Reduced H-Cluster of FeFe Hydrogenase. A Combined DFT and Protein Film Voltammetry Study

Author

Emilien Etienne, Claudio Greco, Philippe Soucaille, Kateryna Sybirna, Christophe Léger, Luca Bertini, Thomas Lautier, Patrick Bertrand, Hervé Bottin, Luca De Gioia, Pierre Ezanno, Isabelle Meynial-Salles, Carole Baffert, Centre National de la Recherche Scientifique (CNRS), Università degli Studi di Milano [Milano] (UNIMI), Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), ANR, Pole de competitivite Capenergies, European Commission [SolarH2 212508], Università degli Studi di Milano = University of Milan (UNIMI), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Baffert, C, Bertini, L, Lautier, T, Greco, C, Sybirna, K, Ezanno, P, Etienne, E, Philippe Soucaille, P, Bertrand, P, Bottin, H, Meynial Salles, I, DE GIOIA, L, and Leger, C

Subjects
Hydrogenase, Stereochemistry, In silico, [SDV]Life Sciences [q-bio], Chlamydomonas reinhardtii, 010402 general chemistry, 01 natural sciences, Biochemistry, Catalysis, CHLAMYDOMONAS-REINHARDTII, CARBON-MONOXIDE BINDING, chemistry.chemical_compound, Colloid and Surface Chemistry, ONLY HYDROGENASE, Catalytic Domain, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Electrochemistry, Cluster (physics), Protein Film Voltammetry, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Density Functional theory, CO binding, CHIM/03 - CHIMICA GENERALE E INORGANICA, Carbon Monoxide, ANALOGS, biology, 010405 organic chemistry, ACTIVE-SITE, Active site, General Chemistry, biology.organism_classification, 0104 chemical sciences, CHIM/02 - CHIMICA FISICA, chemistry, Iron-hydrogenasi, Protein film voltammetry, biology.protein, Quantum Theory, Carbon monoxide binding, CLOSTRIDIUM-PASTEURIANUM, Oxidation-Reduction, ENZYMES, Carbon monoxide
Abstract

International audience; Carbon monoxide is often described as a competitive inhibitor of FeFe hydrogenases, and it is used for probing H-2 binding to synthetic or in silico models of the active site H-cluster. Yet it does not always behave as a simple inhibitor. Using an original approach which combines accurate electrochemical measurements and theoretical calculations, we elucidate the mechanism by which, under certain conditions, CO binding can cause permanent damage to the H-cluster. Like in the case of oxygen inhibition, the reaction with CO engages the entire H-cluster, rather than only the Fe-2 subsite.

Published
2011
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10. Asymmetrical stress generated by the erythrocyte lipid flippase triggers multiple bud formation on the surface of spherical giant liposomes

Author

Pierre Ezanno, Sophie Cribier, Philippe F. Devaux, Institut de biologie physico-chimique (IBPC (FR_550)), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC), Institut de Biologie Physico-Chimique (Centre National de la Recherche Scientifique UPR 1929), and Université Paris Diderot - Paris 7 (UPD7)

Subjects
Erythrocytes, food.ingredient, Biophysics, Membrane biology, Biology, 01 natural sciences, Lecithin, Fluorescence, Membrane bending, 03 medical and health sciences, Adenosine Triphosphate, food, Lecithins, 0103 physical sciences, Monolayer, Flippase activity, Surface Tension, Magnesium, Unilamellar Liposomes, 030304 developmental biology, 0303 health sciences, Liposome, 010304 chemical physics, [CHIM.ORGA]Chemical Sciences/Organic chemistry, Vesicle, Sodium, General Medicine, Flippase, Cell biology, Microscopy, Fluorescence, lipids (amino acids, peptides, and proteins), Stress, Mechanical
Abstract

International audience; Proteo-giant liposomes were electroformed from a mixture of lecithin vesicles and inside-out vesicles from erythrocytes. After addition of Mg-ATP in the vicinity of the proteo-giant liposomes, small buds appeared on the liposome surfaces, which--via an increase in lipids in the outer monolayer--demonstrated the active transport of lipids from the inner to the outer monolayer, indicating flippase activity.

Published
2010
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