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14 results on '"Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP)"'

1. Genome editing in diatoms: achievements and goals

Author

Marianne Jaubert, Carolina Río Bártulos, Andrés Ritter, Angela Falciatore, Marianne Nymark, Peter G. Kroth, Misha Kolot, Monia Teresa Russo, Manuel Serif, Per Winge, Atle M. Bones, Maria Immacolata Ferrante, Fayza Daboussi, Fachbereich Biologie, University of Konstanz, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), 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), Integrative Marine Ecology, Stazione Zoologica Anton Dohrn (SZN), Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (LCQB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Paris Seine (IBPS), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-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), Gordon and Betty Moore Foundation [GBMF 4966], European Assemble plus (Association of European Marine Biological Research Laboratories Expanded) consortium [H2020-INFRAIA-1-2016-2017], Stazione Zoologica Anton Dohrn, Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), 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), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-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), and ANR-16-CE05-0006,SynDia,Conception d'une plateforme d'ingénierie génomique pour les microalgues(2016)

Subjects
0301 basic medicine, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Ecology (disciplines), Thalassiosira pseudonana, Genomics, diatomée, Plant Science, mutant screening, 03 medical and health sciences, ingénierie métabolique, TALEN, Genome editing, Transcription Activator-Like Effector Nucleases, ddc:570, aquatic ecosystem, mutagénèse chimique, genome editing, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, 14. Life underwater, Phaeodactylum tricornutum, Diatoms, Gene Editing, Marine biology, promoter, modification génétique, Genome, biology, Cas9, fungi, General Medicine, biology.organism_classification, diatom, écosystème aquatique, 030104 developmental biology, Diatom, algue, Evolutionary biology, CRISPR, criblage génétique, CRISPR-Cas Systems, metabolic engineering, Agronomy and Crop Science, conjugation
Abstract

Diatoms are major components of phytoplankton and play a key role in the ecology of aquatic ecosystems. These algae are of great scientific importance for a wide variety of research areas, ranging from marine ecology and oceanography to biotechnology. During the last 20 years, the availability of genomic information on selected diatom species and a substantial progress in genetic manipulation, strongly contributed to establishing diatoms as molecular model organisms for marine biology research. Recently, tailored TALEN endonucleases and the CRISPR/Cas9 system were utilized in diatoms, allowing targeted genetic modifications and the generation of knockout strains. These approaches are extremely valuable for diatom research because breeding, forward genetic screens by random insertion, and chemical mutagenesis are not applicable to the available model species Phaeodactylum tricornutum and Thalassiosira pseudonana, which do not cross sexually in the lab. Here, we provide an overview of the genetic toolbox that is currently available for performing stable genetic modifications in diatoms. We also discuss novel challenges that need to be addressed to fully exploit the potential of these technologies for the characterization of diatom biology and for metabolic engineering. © Springer-Verlag GmbH Germany, part of Springer Nature 2018. This is a post-peer-review, pre-copyedit version of an article published in Plant Cell Reports. The final authenticated version is available online at: http://dx.doi.org/10.1007/s00299-018-2334-1. Locked until 23.08.2019 due to the copyright restrictions.

Published
2018

2. Study of phase separation in an InGaN alloy by electron energy loss spectroscopy in an aberration corrected monochromated scanning transmission electron microscope

Author

X. Wang, Pierre Ruterana, Toshihiro Aoki, Veerendra C. Angadi, Thomas Walther, Paolo Longo, University of Sheffield [Sheffield], Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research - Chinese Academy of Sciences, Centre de recherche sur les Ions, les MAtériaux et la Photonique (CIMAP - UMR 6252), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), LeRoy Eyring Center for Solid State Science, Normandie Université (NU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche sur les Matériaux Avancés (IRMA), Normandie Université (NU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Rouen Normandie (UNIROUEN), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), 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), Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Normandie Université (NU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Caen Normandie (UNICAEN), Normandie Université (NU), and Messing, G

Subjects
Materials science, Band gap, 02 engineering and technology, Electron, 01 natural sciences, Molecular physics, Optics, 0103 physical sciences, Scanning transmission electron microscopy, [CHIM.CRIS]Chemical Sciences/Cristallography, General Materials Science, Spectroscopy, ComputingMilieux_MISCELLANEOUS, Plasmon, 010302 applied physics, [PHYS.PHYS]Physics [physics]/Physics [physics], Scattering, business.industry, Mechanical Engineering, Electron energy loss spectroscopy, [CHIM.MATE]Chemical Sciences/Material chemistry, 021001 nanoscience & nanotechnology, Condensed Matter Physics, Mechanics of Materials, Density of states, 0210 nano-technology, business
Abstract

Phase separation of InxGa1−xN into Ga-rich and In-rich regions has been studied by electron energy-loss spectroscopy (EELS) in a monochromated, aberration corrected scanning transmission electron microscope (STEM). We analyze the full spectral information contained in EELS of InGaN, combining for the first time studies of high-energy and low-energy ionization edges, plasmon, and valence losses. Elemental maps of the N K, In M4,5 and Ga L2,3 edges recorded by spectrum imaging at 100 kV reveal sub-nm fluctuations of the local indium content. The low energetic edges of Ga M4,5 and In N4,5 partially overlap with the plasmon peaks. Both have been fitted iteratively to a linear superimposition of reference spectra for GaN, InN, and InGaN, providing a direct measurement of phase separation at the nm-scale. Bandgap measurements are limited in real space by scattering delocalization rather than the electron beam size to ∼10 nm for small bandgaps, and their energetic accuracy by the method of fitting the onset of the joint density of states rather than energy resolution. For an In0.62Ga0.38N thin film we show that phase separation occurs on several length scales.

Published
2016

3. A critical analysis of Powell’s results on the interdivision time distribution

Author

Jérôme Morchain, Vincent Quedeville, Rodney O. Fox, Philippe Villedieu, Fédération de Recherche Fluides, Energie, Réacteurs, Matériaux et Transferts (FERMAT), 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)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT), 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), Institut de Mathématiques de Toulouse UMR5219 (IMT), Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT)-Université de Toulouse (UT)-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 Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), ONERA / DMPE, Université de Toulouse [Toulouse], ONERA-PRES Université de Toulouse, Iowa State University (ISU), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, 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), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse 1 Capitole (UT1)-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, POPULATION BALANCE MODEL, Population balance model, BIOCHEMICAL REACTOR, lcsh:Medicine, Time distribution, Probability density function, Unobservable, Article, First relationship, [SPI]Engineering Sciences [physics], 03 medical and health sciences, 0302 clinical medicine, medicine, Computational models, Statistical physics, lcsh:Science, Cellular Senescence, Cell Proliferation, Mathematics, Confusion, REACTEUR BIOCHIMIQUE, [PHYS]Physics [physics], Multidisciplinary, lcsh:R, Cell Cycle, MODELE DE BILAN DE POPULATION, Observable, Models, Theoretical, Applied mathematics, 030104 developmental biology, Cell cycle genetics, lcsh:Q, medicine.symptom, Cell Division, 030217 neurology & neurosurgery
Abstract

The cell-age and interdivision-time probability density functions (PDFs) have been extensively investigated since the 1940s due to their fundamental role in cell growth. The pioneering work of Powell established the first relationship between the interdivision-time and cell-age PDFs. In the literature, two definitions for the interdivision-time PDF have been proposed. One stands for the age-at-rupture PDF and is experimentally observable, whereas the other is the probability density that a cell divides at a certain age and is unobservable. From Powell’s results pertaining to the unobservable interdivision-time PDF, Painter and Marr derived an inequality that is true but is incorrectly used by experimentalists to analyse single-cell data. Unfortunately, the confusion between these two PDFs persists. To dissipate this confusion, exact relationships between the cell-age and the interdivision-time PDFs are derived in this work from an age-structured model, which can be used by experimentalists to analyse cell growth in batch and continuous culture modes.

Published
2019

4. Mechanism of O2 diffusion and reduction in FeFe hydrogenases

Author

Philippe Soucaille, Matteo Sensi, Christophe Léger, Isabelle Meynial-Salles, Charles Gauquelin, Carole Baffert, Jochen Blumberger, Laure Saujet, Robert B. Best, David De Sancho, Adam Kubas, Christophe Orain, Hervé Bottin, Vincent Fourmond, Kubas, A, Orain, C, Sancho, D, Saujet, L, Sensi, M, Gauquelin, C, Meynial-Salles, I, Soucaille, P, Bottin, H, Baffert, C, Fourmond, V, Best, R, Blumberger, J, Léger, C, Department of Physics and Astronomy [UCL London], University College of London [London] ( UCL ), Bioénergétique et Ingénierie des Protéines ( BIP ), Aix Marseille Université ( AMU ) -Centre National de la Recherche Scientifique ( CNRS ), Department of Chemistry [Cambridge, UK], University of Cambridge [UK] ( CAM ), 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 ), Institut de Biologie et de Technologies de Saclay ( IBITECS ), Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), 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 ), and Institut de Microbiologie de la Méditerranée ( IMM )

Subjects
Hydrogenase, General Chemical Engineering, Mutant, Nanotechnology, Molecular Dynamics Simulation, Molecular Dynamics, 010402 general chemistry, Electrochemistry, [ CHIM ] Chemical Sciences, 01 natural sciences, Catalysis, Diffusion, Molecular dynamics, Metalloproteins, Site-Directed, Clostridium, CHIM/03 - CHIMICA GENERALE E INORGANICA, chemistry.chemical_classification, biology, 010405 organic chemistry, Chemistry, Mutagenesis, Active site, Electrochemical Techniques, General Chemistry, 0104 chemical sciences, Oxygen, CHIM/02 - CHIMICA FISICA, Enzyme mecanisms, Enzyme, Hydrogen, Mutagenesis, Site-Directed, Oxidation-Reduction, Quantum Theory, Density functional theory, Electrocatalysis, Enzyme mechanisms, Metalloproteins, Molecular dynamics, Density functional theory, Biophysics, biology.protein, Electrocatalysis, Cysteine
Abstract

International audience; FeFe hydrogenases are the most efficient H2-producing enzymes. However, inactivation by O2 remains an obstacle that prevents them being used in many biotechnological devices. Here, we combine electrochemistry, site-directed mutagenesis, molecular dynamics and quantum chemical calculations to uncover the molecular mechanism of O2 diffusion within the enzyme and its reactions at the active site. We propose that the partial reversibility of the reaction with O2 results from the four-electron reduction of O2 to water. The third electron/proton transfer step is the bottleneck for water production, competing with formation of a highly reactive OH radical and hydroxylated cysteine. The rapid delivery of electrons and protons to the active site is therefore crucial to prevent the accumulation of these aggressive species during prolonged O2 exposure. These findings should provide important clues for the design of hydrogenase mutants with increased resistance to oxidative damage.

Published
2016

5. Characterization and mutagenesis of two novel iron–sulphur cluster pentonate dehydratases

Author

Paul Carlson, Martina Andberg, Merja Oja, Anu Koivula, Merja Penttilä, Sophie Bozonnet, Niina Hakulinen, Niina Aro-Kärkkäinen, Mervi Toivari, Michael J. O’Donohue, VTT Technical Research Centre of Finland (VTT), 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 Chemistry, Sookmyung Women's University , Seoul 04310, Korea., Academy of Finland through the Centre of Excellence in White Biotechnology-Green Chemistry [118573], ANR-08-CP2D-0017,PENTOVAL,Production par voie biotechnologique d'acides pentanoiques à partir de co-produits de bioraffineries - Biotechnological production of pentanoic acids from sidestreams of agrobiomass biorefineries(2008), 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), Pentoval project [129174], and Pentoval project - Agence Nationale de la Recherche [ANR-08-CP2D-0017]

Subjects
0301 basic medicine, EC 4.2.1.25, [SDV]Life Sciences [q-bio], EC 4.2.1.82, IlvD/ EDDfamily, L-arabonate dehydratase, medicine.disease_cause, Gluconates, Applied Microbiology and Biotechnology, Rhizobium leguminosarum, Sugar acids, 03 medical and health sciences, chemistry.chemical_compound, Bacterial Proteins, Caulobacter crescentus, Escherichia coli, medicine, Amino Acid Sequence, Cloning, Molecular, Peptide sequence, Hydro-Lyases, chemistry.chemical_classification, D-xylonate dehydratase, Xylose, 030102 biochemistry & molecular biology, biology, Enolase superfamily, General Medicine, Arabinose, 030104 developmental biology, Enzyme, chemistry, Biochemistry, Dehydratase, Aldonic acid, biology.protein, IlvD/EDD family, Sequence Alignment, Biotechnology, Cysteine
Abstract

We describe here the identification and characterization of two novel enzymes belonging to the IlvD/EDD protein family, the D-xylonate dehydratase from Caulobacter crescentus, Cc XyDHT, (EC 4.2.1.82), and the L-arabonate dehydratase from Rhizobium leguminosarum bv. trifolii, Rl ArDHT (EC 4.2.1.25), that produce the corresponding 2-keto-3-deoxy-sugar acids. There is only a very limited amount of characterization data available on pentonate dehydratases, even though the enzymes from these oxidative pathways have potential applications with plant biomass pentose sugars. The two bacterial enzymes share 41 % amino acid sequence identity and were expressed and purified from Escherichia coli as homotetrameric proteins. Both dehydratases were shown to accept pentonate and hexonate sugar acids as their substrates and require Mg2+ for their activity. Cc XyDHT displayed the highest activity on D-xylonate and D-gluconate, while Rl ArDHT functioned best on D-fuconate, L-arabonate and D-galactonate. The configuration of the OH groups at C2 and C3 position of the sugar acid were shown to be critical, and the C4 configuration also contributed substantially to the substrate recognition. The two enzymes were also shown to contain an iron-sulphur [Fe-S] cluster. Our phylogenetic analysis and mutagenesis studies demonstrated that the three conserved cysteine residues in the aldonic acid dehydratase group of IlvD/EDD family members, those of C60, C128 and C201 in Cc XyDHT, and of C59, C127 and C200 in Rl ArDHT, are needed for coordination of the [Fe-S] cluster. The iron-sulphur cluster was shown to be crucial for the catalytic activity (k(cat)) but not for the substrate binding (K-m) of the two pentonate dehydratases.

Published
2016

6. Evaluation of dough rheological properties and bread texture of pearl millet-wheat flour mix

Author

Sameh Maktouf, Khawla Ben Jeddou, Claire Moulis, Magali Remaud-Simeon, Hejer Hajji, Raoudha Ellouz-Ghorbel, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), 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), Faculty of Sciences of Tunis, Laboratory Microorganismes and Biomol Act, Université de Sfax - University of Sfax, Unite Enzymes et Bioconvers, ENIS, Faculty of Science of Tunis, Laboratory Microorganismes and Biomol Act, Faculty of Sciences Tunis, Laboratory Microorganismes & Biomol Act, Unite Enzymes & Bioconvers, ENIS, Faculty of Sciences of Tunis, Lab Microorganismes & Biomol Act, French Institute of Cooperation (Campus France), 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), and 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)

Subjects
GRAINS, PROTEINS, [SDV]Life Sciences [q-bio], Wheat flour, engineering.material, FUNCTIONAL-PROPERTIES, 0404 agricultural biotechnology, Rheology, Millet flour, QUALITY, Rheological properties, RETENTION, Texture (crystalline), Food science, OPTIMIZATION, Bread making, Mathematics, biology, 04 agricultural and veterinary sciences, FAT BINDING-CAPACITY, biology.organism_classification, Bread volume, 040401 food science, Texture analysis, engineering, STARCH, Original Article, METHODOLOGY, Pennisetum, Pearl, SYSTEM, Food Science
Abstract

This study was undertaken with the objective of formulating composite bread using pearl millet (Pennisetum glaucum) and wheat (Triticum aestivum) flours . Rheological and bread making properties of composite flours were evaluated. Mixolab results revealed torque increased and dough stability time decreased upon incorporation of pearl millet flour in wheat flour. The incorporation of millet flour at optimum level (5 %) led to an increase of the dough strength (W) and the elasticity-to-extensibility ratio (P/L) by 31 % and 65 % respectively. The bread texture and volume were also improved. These findings indicated the potentiality of using millet flour in bread making.

Published
2016

7. Rational engineering of a native hyperthermostable lactonase into a broad spectrum phosphotriesterase

Author

Julien Hiblot, Celine Bergonzi, Nicholas Armstrong, Eric Chabrière, Mikael Elias, Pauline Jacquet, Guillaume Gotthard, David Daudé, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS), Ecole Polytechnique Fédérale de Lausanne (EPFL), 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 Biochemistry [St. Paul, MN, USA], University of Minnesota [Twin Cities] (UMN), University of Minnesota System-University of Minnesota System-Molecular Biology and Biophysics & Biotechnology Institute, European Synchrotron Radiation Facility (ESRF), This work was granted by DGA, France (REI. 2009 34 0045). G.G. and P.J. are PhD students granted by DGA. Financial support was also obtained from the MnDrive Initiative (M.E.) to support this work. This work was supported by 'Investissements d’avenir' program (Méditerranée Infection 10-IAHU-03) of the French Agence Nationale de la Recherche (ANR)., ANR-10-IAHU-0003,Méditerranée Infection,I.H.U. Méditerranée Infection(2010), INSB-INSB-Centre National de la Recherche Scientifique (CNRS), 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), Molecular Biology and Biophysics & Biotechnology Institute-University of Minnesota [Twin Cities], University of Minnesota System-University of Minnesota System, ANR-10-IAHU-0003/10-IAHU-0003,Méditerranée Infection,Méditerranée Infection(2010), COMBE, Isabelle, Instituts Hospitalo-Universitaires - I.H.U. Méditerranée Infection - - Méditerranée Infection2010 - ANR-10-IAHU-0003 - IAHU - VALID, Institut National des Sciences Appliquées (INSA)-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées (INSA)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), and Molecular Biology and Biophysics & Biotechnology Institute-University of Minnesota [Twin Cities] (UMN)

Subjects
Models, Molecular, 0301 basic medicine, Protein Conformation, ved/biology.organism_classification_rank.species, lcsh:Medicine, Protein Engineering, Article, Substrate Specificity, Structure-Activity Relationship, 03 medical and health sciences, Enzyme activator, Catalytic Domain, Hydrolase, Lactonase, Pesticides, Binding site, lcsh:Science, Binding Sites, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, Multidisciplinary, Molecular Structure, 030102 biochemistry & molecular biology, biology, Chemistry, ved/biology, lcsh:R, Sulfolobus solfataricus, Temperature, Active site, Substrate (chemistry), Protein engineering, Enzyme Activation, Biodegradation, Environmental, Phosphoric Triester Hydrolases, 030104 developmental biology, Amino Acid Substitution, Biochemistry, Mutation, biology.protein, lcsh:Q, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, Protein Binding
Abstract

The redesign of enzyme active sites to alter their function or specificity is a difficult yet appealing challenge. Here we used a structure-based design approach to engineer the lactonase SsoPox from Sulfolobus solfataricus into a phosphotriesterase. The five best variants were characterized and their structure was solved. The most active variant, αsD6 (V27A-Y97W-L228M-W263M) demonstrates a large increase in catalytic efficiencies over the wild-type enzyme, with increases of 2,210-fold, 163-fold, 58-fold, 16-fold against methyl-parathion, malathion, ethyl-paraoxon, and methyl-paraoxon, respectively. Interestingly, the best mutants are also capable of degrading fensulfothion, which is reported to be an inhibitor for the wild-type enzyme, as well as others that are not substrates of the starting template or previously reported W263 mutants. The broad specificity of these engineered variants makes them promising candidates for the bioremediation of organophosphorus compounds. Analysis of their structures reveals that the increase in activity mainly occurs through the destabilization of the active site loop involved in substrate binding, and it has been observed that the level of disorder correlates with the width of the enzyme specificity spectrum. This finding supports the idea that active site conformational flexibility is essential to the acquisition of broader substrate specificity.

Published
2017

8. A French multicenter study of over 700 patients with 22q11 deletions diagnosed using FISH or aCGH

Author

François Vialard, Eva Pipiras, Pascale Kleinfinger, Dominique Martin-Coignard, Marie Catty, Elisabeth Flori, Emilie Landais, Mylène Valduga, Marie-France Portnoï, Aline Receveur, Agnès Choiset, Ghislaine Plessis, Nathalie Le Meur, Audrey Basinko, Justine Besseau-Ayasse, James Lespinasse, Radu Harbuz, Céline Poirsier, Martine Doco-Fenzy, Pascaline Letard, Caroline Schluth-Bolard, Anne Bazin, Jérôme Toutain, Fabienne Prieur, Florence Amblard, Cédric Le Caignec, Tiffany Busa, Marie Christine de Blois, Melanie Jimenez, Patrick Callier, Chantal Missirian, Céline Pebrel-Richard, Paul Kuentz, Catherine Yardin, François Cartault, Hakima Lallaoui, Service de génétique [Reims], Centre Hospitalier Universitaire de Reims (CHU Reims), UVSQ - Département de maïeutique (UVSQ Maïeutique), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Centre de recherche en neurosciences de Lyon (CRNL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet [Saint-Étienne] (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), CHU Bordeaux [Bordeaux], Département de génétique médicale [Hôpital de la Timone - APHM], Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE)-Institut National de la Santé et de la Recherche Médicale (INSERM), Génétique Médicale et Génomique Fonctionnelle (GMGF), Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre hospitalier universitaire de Nantes (CHU Nantes), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Service de Génétique [CHU Caen], CHU Caen, Normandie Université (NU)-Tumorothèque de Caen Basse-Normandie (TCBN)-Normandie Université (NU)-Tumorothèque de Caen Basse-Normandie (TCBN)-Université de Caen Normandie (UNICAEN), Normandie Université (NU), Génétique moléculaire et génétique épidémiologique, Université de Brest (UBO)-Institut National de la Santé et de la Recherche Médicale (INSERM), Neuroprotection du Cerveau en Développement / Promoting Research Oriented Towards Early Cns Therapies (PROTECT), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpital Robert Debré-Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM), Service de cytogénétique, CHU Strasbourg-Hôpital de Hautepierre [Strasbourg], Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), 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), Laboratoire de cytogénétique et génétique moléculaire [CHRU Nancy], Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), Service de Génétique, Centre Hospitalier Universitaire de Reims (CHU Reims)-Hôpital Maison Blanche-IFR 53, Université de Reims Champagne-Ardenne (URCA)-Université de Reims Champagne-Ardenne (URCA), Service de génétique, Centre hospitalier Félix Guyon, Bellepierre, Département de Génétique Chromosomique, Bâtiment Hôtel Dieu - Centre Hospitalier de Chambéry, Laboratoire de génétique médicale et cytogénétique [Le Mans], Centre Hospitalier Le Mans (CH Le Mans), Centre de génétique - Centre de référence des maladies rares, anomalies du développement et syndromes malformatifs (CHU de Dijon), CHU Clermont-Ferrand, Service de Génétique et d'Embryologie Médicales [CHU Trousseau], Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Trousseau [APHP], Service d'histologie, embryologie et cytogénétique [Béclère], Université Paris-Sud - Paris 11 (UP11)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpital Antoine Béclère, Département de génétique et procréation, Université Joseph Fourier - Grenoble 1 (UJF)-Hôpital Couple-Enfant, Service d'Histologie, cytologie, cytogénétique, biologie cellulaire [CHU Limoges], CHU Limoges, Activité Motrice et Adaptation PsychoPhysiologique (AMAPP), Université d'Orléans (UO), Service de génétique [Rouen], CHU Rouen, Normandie Université (NU)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Service Histologie-embryologie-cytogénétique, Université Paris 13 (UP13)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpital Jean Verdier [Bondy], Assistance publique - Hôpitaux de Paris (AP-HP) (APHP), Laboratoire Pasteur Cerba, Laboratoire de Cytogénétique, CHI Poissy-Saint-Germain, Service de gynécologie et obstétrique [CHI Poissy-Saint Germain], Université de Versailles Saint-Quentin-en-Yvelines - UFR Sciences de la santé Simone Veil (UVSQ Santé), Centre de recherche en neurosciences de Lyon - Lyon Neuroscience Research Center (CRNL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Laboratoire CERBA [Saint Ouen l'Aumône], Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-CHU Caen, Normandie Université (NU)-Tumorothèque de Caen Basse-Normandie (TCBN)-Tumorothèque de Caen Basse-Normandie (TCBN), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Robert Debré-Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM), 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), CHU Trousseau [APHP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Université Paris-Sud - Paris 11 (UP11)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-AP-HP - Hôpital Antoine Béclère [Clamart], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Université Paris 13 (UP13)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Jean Verdier [AP-HP], Association des Cytogénéticiens de Langue Française, Gamètes, implantation, gestation (GIG), Institut National de la Santé et de la Recherche Médicale (INSERM)- Hôpital de la Timone [CHU - APHM] (TIMONE)-Assistance Publique - Hôpitaux de Marseille (APHM)-Aix Marseille Université (AMU), Institut Pasteur [Paris]-Laboratoire CERBA [Saint Ouen l'Aumône], Service de génétique et embryologie médicales [CHU Trousseau], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris 13 (UP13)-Hôpital Jean Verdier [AP-HP], and Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Université Paris 13 (UP13)-Hôpital Jean Verdier [Bondy]

Subjects
Adult, Male, 0301 basic medicine, Pediatrics, medicine.medical_specialty, 22q11 Deletion Syndrome, Adolescent, [SDV]Life Sciences [q-bio], Population, Article, 03 medical and health sciences, Intellectual disability, Genetics, medicine, Humans, Genetic Testing, Child, education, ComputingMilieux_MISCELLANEOUS, In Situ Hybridization, Fluorescence, Genetics (clinical), Comparative Genomic Hybridization, Fetus, education.field_of_study, business.industry, Incidence (epidemiology), Infant, Newborn, Cytogenetics, Infant, Microdeletion syndrome, medicine.disease, 3. Good health, 030104 developmental biology, Child, Preschool, Cohort, Paternal Inheritance, Female, France, business, Comparative genomic hybridization
Abstract

Although 22q11.2 deletion syndrome (22q11.2DS) is the most recurrent human microdeletion syndrome associated with a highly variable phenotype, little is known about the condition's true incidence and the phenotype at diagnosis. We performed a multicenter, retrospective analysis of postnatally diagnosed patients recruited by members of the Association des Cytogénéticiens de Langue Française (the French-Speaking Cytogeneticists Association). Clinical and cytogenetic data on 749 cases diagnosed between 1995 and 2013 were collected by 31 French cytogenetics laboratories. The most frequent reasons for referral of postnatally diagnosed cases were a congenital heart defect (CHD, 48.6%), facial dysmorphism (49.7%) and developmental delay (40.7%). Since 2007 (the year in which array comparative genomic hybridization (aCGH) was introduced for the routine screening of patients with intellectual disability), almost all cases have been diagnosed using FISH (96.1%). Only 15 cases (all with an atypical phenotype) were diagnosed with aCGH; the deletion size ranged from 745 to 2904 kb. The deletion was inherited in 15.0% of cases and was of maternal origin in 85.5% of the latter. This is the largest yet documented cohort of patients with 22q11.2DS (the most commonly diagnosed microdeletion) from the same population. French cytogenetics laboratories diagnosed at least 108 affected patients (including fetuses) per year from among a national population of ∼66 million. As observed for prenatal diagnoses, CHDs were the most frequently detected malformation in postnatal diagnoses. The most common CHD in postnatal diagnoses was an isolated septal defect.

Published
2015

9. Conferring cellulose-degrading ability to Yarrowia lipolytica to facilitate a consolidated bioprocessing approach

Author

Gianluca Cioci, Sophie Duquesne, Sophie Bozonnet, Jean-Marc Nicaud, Zhong Peng Guo, Alain Marty, Michael J. O’Donohue, Toulouse White Biotechnology (TWB), 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), 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), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Institut National de la Recherche Agronomique, ANR-11-BTBR-0003,PROBIO3,Production biocatalytique de bioproduits lipidiques à partir de matières premières renouvelables et(2011), Agence Nationale de la Recherche (Investissements d'Avenir program) [ANR-11-BTBR-0003], Guo, Zhongpeng, Marty, Alain, O'Donohue, Michael, and 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)

Subjects
Yarrowia lipolytica, 0301 basic medicine, bioprocédé, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, lcsh:Biotechnology, Biotechnologies, Cellulase, Management, Monitoring, Policy and Law, Applied Microbiology and Biotechnology, lcsh:Fuel, Neurospora crassa, Consolidated bioprocessing, 03 medical and health sciences, chemistry.chemical_compound, beta-glucosidase, lcsh:TP315-360, lcsh:TP248.13-248.65, Cellulolytic biocatalyst, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Endoglucanase, Bioprocess, Cellulose, Génie des procédés, chemistry.chemical_classification, cellulolytic biocatalyst, cellulase, endoglucanase, cellobiohydrolase, consolidated bioprocessing, cellulose, biology, Renewable Energy, Sustainability and the Environment, Beta-glucosidase, Research, Yarrowia, biology.organism_classification, Yeast, β-Glucosidase, enzyme, 030104 developmental biology, General Energy, Enzyme, Process Engineering, Biochemistry, chemistry, protéine, biology.protein, Cellobiohydrolase, protein, neurospora crassa, Biotechnology
Abstract

Background Yarrowia lipolytica, one of the most widely studied “nonconventional” oleaginous yeast species, is unable to grow on cellulose. Recently, we identified and overexpressed two endogenous β-glucosidases in Y. lipolytica, thus enabling this yeast to use cello-oligosaccharides as a carbon source for growth. Using this engineered yeast platform, we have now gone further toward building a fully cellulolytic Y. lipolytica for use in consolidated bioprocessing of cellulose. Results Initially, different essential enzyme components of a cellulase cocktail (i.e,. cellobiohydrolases and endoglucanases) were individually expressed in Y. lipolytica in order to ascertain the viability of the strategy. Accordingly, the Trichoderma reesei endoglucanase I (TrEG I) and II (TrEG II) were secreted as active proteins in Y. lipolytica, with the secretion yield of EG II being twice that of EG I. Characterization of the purified His-tagged recombinant EG proteins (rhTrEGs) revealed that rhTrEG I displayed higher specific activity than rhTrEG II on both cellotriose and insoluble cellulosic substrates, such as Avicel, β-1, 3 glucan, β-1, 4 glucan, and PASC. Similarly, cellobiohydrolases, such as T. reesei CBH I and II (TrCBH I and II), and the CBH I from Neurospora crassa (NcCBH I) were successfully expressed in Y. lipolytica. However, the yield of the expressed TrCBH I was low, so work on this was not pursued. Contrastingly, rhNcCBH I was not only well expressed, but also highly active on PASC and more active on Avicel (0.11 U/mg) than wild-type TrCBH I (0.065 U/mg). Therefore, work was pursued using a combination of NcCBH I and TrCBH II. The quantification of enzyme levels in culture supernatants revealed that the use of a hybrid promoter instead of the primarily used TEF promoter procured four and eight times more NcCBH I and TrCBH II expressions, respectively. Finally, the coexpression of the previously described Y. lipolytica β-glucosidases, the CBH II, and EG I and II from T. reesei, and the N. crassa CBH I procured an engineered Y. lipolytica strain that was able to grow both on model cellulose substrates, such as highly crystalline Avicel, and on industrial cellulose pulp, such as that obtained using an organosolv process. Conclusions A Y. lipolytica strain coexpressing six cellulolytic enzyme components has been successfully developed. In addition, the results presented show how the recombinant strain can be optimized, for example, using artificial promoters to tailor expression levels. Most significantly, this study has provided a demonstration of how the strain can grow on a sample of industrial cellulose as sole carbon source, thus revealing the feasibility of Yarrowia-based consolidated bioprocess for the production of fuel and chemical precursors. Further, enzyme and strain optimization, coupled to appropriate process design, will undoubtedly lead to much better performances in the future. Electronic supplementary material The online version of this article (doi:10.1186/s13068-017-0819-8) contains supplementary material, which is available to authorized users.

Published
2017

10. An integrated 'process modelling-life cycle assessment' tool for the assessment and design of water treatment processes

Author

Isabelle Baudin, Enrico Benetto, Ligia Tiruta-Barna, Yoann Mery, 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), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA), Suez Environm CIRSEE, Partenaires INRAE, French National Research Agency (ANR), Public Research Centre Henri Tudor, Luxembourg, 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), Université de Toulouse (UT), and Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)

Subjects
Engineering, Process modeling, Relation (database), Process (engineering), [SDV]Life Sciences [q-bio], High variability, Life cycle inventory, 02 engineering and technology, 010501 environmental sciences, 01 natural sciences, 12. Responsible consumption, Unit (housing), Life cycle assessment, 020401 chemical engineering, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Drinking water, Process modelling, Water treatment, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, 0204 chemical engineering, OPTIMIZATION, Life-cycle assessment, 0105 earth and related environmental sciences, General Environmental Science, Eco-design, business.industry, 6. Clean water, 13. Climate action, Systems engineering, IMPACT ASSESSMENT, Water quality, Sensitivity analysis, business, METHODOLOGY, POTABLE WATER
Abstract

International audience; The application of Life Cycle Assessment (LCA) to the design of water treatment plants is hampered by: (1) a large diversity of unit processes, (2) the high variability of the operation conditions in relation with the water quality input, and (3) the range of possible technical solutions to fulfil the treatment needs. For a consistent prospective assessment, the LCA should be based on the simulated functioning of the unit processes rather than on average data, as it is most often the case when no real data are available. Here, a novel, integrated and flexible process modelling-life cycle assessment (PM-LCA) tool for design and LCA of water treatment technologies is presented. The tool (EVALEAU) was developed in UmbertoA (R) (v5.5) using the Python language for code scripting. A library of unit process (UP) modules was built. Each module is a detailed and highly parameterized model of a specific water treatment process, which is further linked with the software PHREEQCA (R) for water chemistry calculation. Input data are: water composition, design, operation parameters, including literature or user-defined values. The modules are linked to Ecoinvent datasets (v2.2) for background processes. By combining the modules, water treatment chains can be designed and evaluated in UmbertoA (R) with a high level of detail and specifications. A sensitivity analysis toolbox (Morris method) was included for the identification of the process parameters mainly affecting the impact results. The tool was successfully applied to the test bed case of an existing drinking water plant located in the Paris region. The conventional LCA results, based on average recorded data, were compared with the results obtained using the PM-LCA tool. Modelling results for technical parameters were also compared with data collected on site. An overall good agreement between simulations and real data was obtained, proving the relevance of the developed tool. Sensitivity analysis indicated that ozone production and transfer into water are the main technological parameters influencing climate change (taken as example since it is of high interest for stakeholders), which have therefore to be fine-tuned. The EVALEAU tool successfully solves the challenge of linking LCA results to the related engineering design choices, from the assessment and eco-design perspectives. The concepts and methodologies embedded within the tool provide the user with complementary views of the designed system, in terms of potable water quality, design and operation parameters and environmental impacts generated over its life cycle.

Published
2013

11. Relating diffusion along the substrate tunnel and oxygen sensitivity in hydrogenase

Author

Marc Rousset, Christophe Léger, Bruno Guigliarelli, Sébastien Dementin, Thomas Lautier, Patrick Bertrand, Christine Cavazza, Juan C. Fontecilla-Camps, Fanny Leroux, Pierre-Pol Liebgott, Isabelle Meynial-Salles, Carole Baffert, Bénédicte Burlat, Pierre Ceccaldi, Philippe Soucaille, Vincent Fourmond, Bioénergétique et Ingénierie des Protéines (BIP ), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), 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), Institut de biologie structurale et microbiologie (IBSM), Université de la Méditerranée - Aix-Marseille 2-Université Paul Cézanne - Aix-Marseille 3-Université de Provence - Aix-Marseille 1-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Chimie et Biologie des Métaux (LCBM - UMR 5249), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Microbiologie de la Méditerranée (IMM), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), 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), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Azzopardi, Laure, and Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Models, Molecular, Hydrogenase, Diffusion, Inorganic chemistry, Molecular Conformation, chemistry.chemical_element, Molecular Dynamics Simulation, Crystallography, X-Ray, Oxygen, Catalytic Domain, Electrochemistry, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Amino Acids, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Molecular Biology, ComputingMilieux_MISCELLANEOUS, chemistry.chemical_classification, Carbon Monoxide, Electron Spin Resonance Spectroscopy, Substrate (chemistry), Cell Biology, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Amino acid, Kinetics, chemistry, Biophysics, Desulfovibrio, Hydrogen
Abstract

In hydrogenases and many other redox enzymes, the buried active site is connected to the solvent by a molecular channel whose structure may determine the enzyme's selectivity with respect to substrate and inhibitors. The role of these channels has been addressed using crystallography and molecular dynamics, but kinetic data are scarce. Using protein film voltammetry, we determined and then compared the rates of inhibition by CO and O2 in ten NiFe hydrogenase mutants and two FeFe hydrogenases. We found that the rate of inhibition by CO is a good proxy of the rate of diffusion of O2 toward the active site. Modifying amino acids whose side chains point inside the tunnel can slow this rate by orders of magnitude. We quantitatively define the relations between diffusion, the Michaelis constant for H2 and rates of inhibition, and we demonstrate that certain enzymes are slowly inactivated by O2 because access to the active site is slow.

Published
2009

12. Dynamic microbial response under ethanol stress to monitor Saccharomyces cerevisiae activity in different initial physiological states

Author

G. Goma, Sandrine Alfenore, Carole Molina-Jouve, Y. Sanchez-Gonzalez, Xavier Cameleyre, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), 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), CRITT Bio-Industrie, Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-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), 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), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Ecole d'Ingénieurs de Purpan (INP - PURPAN), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), and Université de Toulouse (UT)

Subjects
Cell viability, Cell regeneration, [SDV]Life Sciences [q-bio], Saccharomyces cerevisiae, Biomedical Engineering, Stress tolerance, Bioengineering, Microbiology, 03 medical and health sciences, chemistry.chemical_compound, Bioreactors, Stress, Physiological, Bioreactor, Yeast Saccharomyces cerevisiae, Ethanol fuel, Food science, Viability assay, Bioprocess, 030304 developmental biology, 0303 health sciences, Ethanol, biology, 030306 microbiology, General Medicine, biology.organism_classification, Yeast, Kinetics, Ethanol production, chemistry, Fermentation, Biotechnology
Abstract

Dynamic Saccharomyces cerevisiae responses to increasing ethanol stresses were investigated to monitor yeast viability and to optimize bioprocess performance when gradients occurred due to the specific configuration of multi-stage bioreactors with cell recycling or of large volume industrial bioreactors inducing chemical heterogeneities. Twelve fed-batch cultures were carried out with initial ethanol concentrations (P in) ranging from 5 g l−1 to 110 g l−1 with three different inoculums in different physiological states in terms of viability and quantity of ethanol produced (P o). For a given initial cell viability of 50%, the time to reach the maximum growth rate and maximum ethanol production rate was dependent on the difference P in − P o. Whatever the initial physiological state, when the initial ethanol concentration P in reached 100 g l−1, the yeasts died. Experimental results showed that the initial physiological state of the yeast was the major parameter to determine, the microorganisms’ capacities to adapt and resist environmental changes.

Published
2008

13. Very high ethanol productivity in an innovative continuous two-stage bioreactor with cell recycle

Author

Sandrine Alfenore, F. Ben Chaabane, Gilles Roux, Carole Molina-Jouve, Xavier Cameleyre, C. Bideaux, Stéphane E. Guillouet, A. Aldiguier, Philippe Blanc, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), 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), Laboratoire de Génie Chimique (LGC), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, CRITT Bio-Industrie, Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-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), Équipe DIagnostic, Supervision et COnduite (LAAS-DISCO), Laboratoire d'analyse et d'architecture des systèmes (LAAS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse 1 Capitole (UT1)-Université Toulouse - Jean Jaurès (UT2J)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse 1 Capitole (UT1)-Université Toulouse - Jean Jaurès (UT2J), Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse 1 Capitole (UT1), 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), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Ecole d'Ingénieurs de Purpan (INP - PURPAN), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT)-Université de Toulouse (UT)-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 Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), and Université de Toulouse (UT)-Université Toulouse Capitole (UT Capitole)

Subjects
0106 biological sciences, [SDV]Life Sciences [q-bio], Cell Culture Techniques, Ultrafiltration, Biomass, Cell Count, Bioengineering, Saccharomyces cerevisiae, Biology, Models, Biological, 01 natural sciences, 7. Clean energy, 03 medical and health sciences, chemistry.chemical_compound, Bioreactors, 010608 biotechnology, Bioreactor, Two-stage bioreactor, Computer Simulation, Ethanol fuel, Cell Proliferation, 0303 health sciences, Ethanol, Chromatography, Waste management, 030306 microbiology, Cell recycle, Equipment Design, General Medicine, Equipment Failure Analysis, Glucose, chemistry, Fermentation, Computer-Aided Design, Steady state (chemistry), Industrial and production engineering, Biotechnology
Abstract

The performance of an innovative two-stage continuous bioreactor with cell recycle-potentially capable of giving very high ethanol productivity-was investigated. The first stage was dedicated to cell growth, whereas the second stage was dedicated to ethanol production. A high cell density was obtained by an ultrafiltration module coupled to the outlet of the second reactor. A recycle loop from the second stage to the first one was tested to improve cell viability and activity. Cultivations of Saccharomyces cerevisiae in mineral medium on glucose were performed at 30 degrees Celsius and pH 4. At steady state, total biomass concentrations of 59 and 157 gDCW l(-1) and ethanol concentrations of 31 and 65 g l(-1) were obtained in the first and second stage, respectively. The residual glucose concentration was 73 g l(-1) in the first stage and close to zero in the second stage. The present study shows that a very high ethanol productivity (up to 41 g l(-1) h(-1)) can indeed be obtained with complete conversion of the glucose and with a high ethanol titre (8.3 degrees GL) in the two-stage system.

Published
2006

14. Direct microcontact printing of oligonucleotides for biochip applications

Author

Jean Marie François, Christophe Thibault, Christophe Vieu, Emmanuelle Trevisiol, S Casimirius, V. Le berre, Équipe Ingénierie pour les sciences du vivant (LAAS-ELIA), Laboratoire d'analyse et d'architecture des systèmes (LAAS), Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT)-Université de Toulouse (UT)-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 Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT), 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), Biochip and Bionanotechnogy, 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)-Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse 1 Capitole (UT1)-Université Toulouse - Jean Jaurès (UT2J)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse 1 Capitole (UT1)-Université Toulouse - Jean Jaurès (UT2J), 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), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées, Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), and Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse)

Subjects
microcontact printing, lcsh:Medical technology, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Materials science, Fabrication, Contact time, lcsh:Biotechnology, Biomedical Engineering, biochips, Pharmaceutical Science, Medicine (miscellaneous), Bioengineering, Nanotechnology, 02 engineering and technology, 010402 general chemistry, 01 natural sciences, Applied Microbiology and Biotechnology, lcsh:TP248.13-248.65, DNA immobilisation, [SPI.NANO]Engineering Sciences [physics]/Micro and nanotechnologies/Microelectronics, Biochip, elastomeric stamp, Oligonucleotide, Research, detection of mutations, Spotting, Stamping, 021001 nanoscience & nanotechnology, 0104 chemical sciences, lcsh:R855-855.5, Microcontact printing, Molecular Medicine, Surface modification, 0210 nano-technology
Abstract

Background A critical step in the fabrication of biochips is the controlled placement of probes molecules on solid surfaces. This is currently performed by sequential deposition of probes on a target surface with split or solid pins. In this article, we present a cost-effective procedure namely microcontact printing using stamps, for a parallel deposition of probes applicable for manufacturing biochips. Results Contrary to a previous work, we showed that the stamps tailored with an elastomeric poly(dimethylsiloxane) material did not require any surface modification to be able to adsorb oligonucleotides or PCR products. The adsorbed DNA molecules are subsequently printed efficiently on a target surface with high sub-micron resolution. Secondly, we showed that successive stamping is characterized by an exponential decay of the amount of transferred DNA molecules to the surface up the 4th print, then followed by a second regime of transfer that was dependent on the contact time and which resulted in reduced quality of the features. Thus, while consecutive stamping was possible, this procedure turned out to be less reproducible and more time consuming than simply re-inking the stamps between each print. Thirdly, we showed that the hybridization signals on arrays made by microcontact printing were 5 to 10-times higher than those made by conventional spotting methods. Finally, we demonstrated the validity of this microcontact printing method in manufacturing oligonucleotides arrays for mutations recognition in a yeast gene. Conclusion The microcontact printing can be considered as a new potential technology platform to pattern DNA microarrays that may have significant advantages over the conventional spotting technologies as it is easy to implement, it uses low cost material to make the stamp, and the arrays made by this technology are 10-times more sensitive in term of hybridization signals than those manufactured by conventional spotting technology.

Published
2005

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