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1,468 results on '"Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA)"'

1. Modulation of helicobacter pylori transcriptional profile by subinhibitory concentrations of rifampicin

Author: Véronique Le Berre, A. Larin, T. Akopian, Jean-Marie François, V. Chelysheva, Kuvat Momynaliev, Serguei Sokol, O. Selezneva, V. Govorun, D. Alexeev, Biochip and Bionanotechnogy, 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)-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), 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)-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)-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), 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: 0303 health sciences, Helicobacter pylori, biology, 030306 microbiology, [SDV]Life Sciences [q-bio], selection, bacterial infections and mycoses, biology.organism_classification, Microbiology, 03 medical and health sciences, Psychiatry and Mental health, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], medicine, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, microarray, rpoB, Rifampicin, 030304 developmental biology, medicine.drug
Abstract: International audience; Subinhibitory concentrations (sub-MICs) of antibiotics do not kill bacteria, but they are able to interfere with important aspects of bacterial cell function, such as adhesion to host cells, surface bacterial energy, susceptibility to host defense mechanisms, inhibition of enzyme function and toxin production. In order to understand how H. pylori copes with environmental stress and what facilitates the emergence of RIF mutants in H. pylori, we used DNA microarrays to compare the gene expression profiles of H. pylori in the presence and absence of subinhibitory concentrations of rifampicin (1/16 MIC (0.1 mg/L), 1/8 MIC (0,2mg/L), ¼ MIC (0,4 mg/L), and ½ MIC (0,8 mg/L). We found that еhe expression of 57 genes (of the 1,576 genes analyzed) was increased more than ≥ 1,5-fold, and the expression of only 29 genes was decreased more than ≤ 1,5-fold in significant way (p-value < 0,05), when H. pylori was treated with sub-MICs of RIF. No correlation was found between the sub-MICs of RIF and gene expression. We conclude that the alteration in the transcriptional pattern of H. pylori after the exposure to sub-MICs of RIF is mainly due to a direct interaction between rifampicin and the RNA polymerase β-subunit. Finally, we propose that subinhibitory concentrations of rifampicin may lead to an increase in the number of hypermutable cells in the H. pylori population.
Published: 2013

2. Porcine pancreatic α-amylase inhibition by the kidney bean (Phaseolus vulgaris) inhibitor (α-AI1) and structural changes in the α-amylase inhibitor complex

Author: Roger Koukiekolo, Guy Marchis-Mouren, Marius Santimone, Véronique Le Berre, Véronique Desseaux, Pierre Rougé, Yann Moreau, Institut méditerranéen de Recherche en Nutrition : Biochimie et Biologie de la Nutrition (IMRN), Université Paul Cézanne - Aix-Marseille 3-Institut National de la Recherche Agronomique (INRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Biochip and Bionanotechnogy, 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)-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), Surfaces Cellulaires et Signalisation chez les Végétaux (SCSV), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut Méditerranéen de Biochimie et Biologie de la Nutrition (IMRN), Institut National de la Recherche Agronomique (INRA), 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)-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 pharmacologie et de biologie structurale (IPBS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Université Paul Cézanne - Aix-Marseille 3-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), 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 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 Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Models, Molecular, 0106 biological sciences, Protein Conformation, Swine, [SDV]Life Sciences [q-bio], Oligosaccharides, Plasma protein binding, 01 natural sciences, Biochemistry, Analytical Chemistry, Protein structure, Amylase, Enzyme Inhibitors, Plant Proteins, Inhibition, 0303 health sciences, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], biology, Chemistry, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Intercellular Signaling Peptides and Proteins, lipids (amino acids, peptides, and proteins), Plant Lectins, Maltopentaose, Stereochemistry, Biophysics, Phaseolus vulgaris, 03 medical and health sciences, Animals, a-Amylase, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Enzyme kinetics, Phytohemagglutinins, Binding site, Pancreas, Molecular Biology, Glycoproteins, 030304 developmental biology, Binding Sites, Models, Statistical, Subtilisin, Active site, Substrate (chemistry), Kinetics, biology.protein, Amylose, alpha-Amylases, 010606 plant biology & botany
Abstract: Porcine pancreatic alpha-amylase (PPA) is inhibited by the red kidney bean (Phaseolus vulgaris) inhibitor alpha-AI1 [Eur. J. Biochem. 265 (1999) 20]. Inhibition kinetics were carried out using DP 4900-amylose and maltopentaose as substrate. As shown by graphical and statistical analysis of the kinetic data, the inhibitory mode is of the mixed noncompetitive type whatever the substrate thus involving the EI, EI2, ESI and ESI2 complexes. This contrast with the E2I complex obtained in the crystal and with biophysical studies. Such difference very likely depends on the [I]/[E] ratio. At low ratio, the E2I complex is favoured; at high ratio the EI, ESI and EI2 complexes are formed. The inhibition model also differs from those previously proposed for acarbose [Eur. J. Biochem. 241 (1996) 787 and Eur. J. Biochem. 252 (1998) 100]. In particular, with alpha-AI1, the inhibition takes place only when PPA and alpha-AI are preincubated together before adding the substrate. This indicates that the abortive PPA-alphaAI1 complex is formed during the preincubation period. One additional carbohydrate binding site is also demonstrated yielding the ESI complex. Also, a second protein binding site is found in EI2 and ESI2 abortive complexes. Conformational changes undergone by PPA upon alpha-AI1 binding are shown by higher sensitivity to subtilisin attack. From X-ray analysis of the alpha-AI1-PPA complex (E2I), the major interaction occurs with two hairpin loops L1 (residues 29-46) and L2 (residues 171-189) of alpha-AI1 protruding into the V-shaped active site of PPA. The hydrolysis of alpha-AI1 that accounts for the inhibitory activity is reported.
Published: 2004

3. Prevalence, identification by a DNA microarray-based assay of human and food isolates Listeria spp. from Tunisia

Author: V. Le berre, H. Smaoui, A. Kechrid, I. Barkallah, Alexandre Leclercq, Marc Lecuit, Abdellatif Boudabous, S. Helel, F. Hmaied, Jean Marie François, Microbiologie et biologie moléculaire, CNSTN, pôle technologique, Biopuces du génopôle, 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)-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 des Listeria, Centre National de Référence des Listeria, et Centre collaborateur de l’OMS pour la listériose d’origine alimentaire (CNR - CCMOS), Institut Pasteur [Paris], Laboratoire de bactériologie, Hôpital d'enfant de Tunis-Bab Saadoun, Microbiologie et biomolécules actives, Faculté de sciences, campus universitaire, This research was supported by National Centre of Nuclear Sciences and technologies., Laboratoire de microbiologie et biologie moléculaire ( CNSTN ), Technopôle Sidi-Thabet, 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 ), Littoral, Environnement, Télédétection, Géomatique ( LETG - Caen ), Littoral, Environnement, Télédétection, Géomatique UMR 6554 ( LETG ), Université de Caen Normandie ( UNICAEN ), Normandie Université ( NU ) -Normandie Université ( NU ) -Université d'Angers ( UA ) -Université de Nantes ( UN ) -École pratique des hautes études ( EPHE ) -Université de Brest ( UBO ) -Université de Rennes 2 ( UR2 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Caen Normandie ( UNICAEN ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de microbiologie, Hôpital d'enfants de Tunis, Laboratoire d'électronique et des technologies de l'Information [Sfax] ( LETI ), École Nationale d'Ingénieurs de Sfax | National School of Engineers of Sfax ( ENIS ), 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)-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), Laboratoire des Listeria, Centre National de Référence des Listeria, et Centre collaborateur de l’OMS pour la listériose d’origine alimentaire (CNR - CCOMS), 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 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 Institut Pasteur [Paris] (IP)
Subjects: Serotype, Male, Microarray, [SDV]Life Sciences [q-bio], medicine.disease_cause, Listeria species, Disease Outbreaks, Food Supply, Pregnancy, [ SDV.MP ] Life Sciences [q-bio]/Microbiology and Parasitology, Prevalence, Listeriosis, ComputingMilieux_MISCELLANEOUS, Cerebrospinal Fluid, Oligonucleotide Array Sequence Analysis, 2. Zero hunger, Aged, 80 and over, 0303 health sciences, Cross Infection, biology, Virulence, Fishes, General Medicine, PFGE, Tunis, 3. Good health, Bacterial Typing Techniques, Electrophoresis, Gel, Pulsed-Field, Female, DNA microarray, DNA, Bacterial, Meat, Tunisia, Listeria, Lipoproteins, iap, Microbiology, 03 medical and health sciences, Listeria monocytogenes, Bacterial Proteins, Multiplex polymerase chain reaction, Pulsed-field gel electrophoresis, medicine, Animals, Humans, Serotyping, 030304 developmental biology, [ SDV ] Life Sciences [q-bio], 030306 microbiology, Puce à ADN, Infant, Newborn, Urban Health, Infant, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Genes, Bacterial, Food Microbiology, Microarray-based assay
Abstract: International audience; Buts de l’étudeL’objectif de ce travail est d’évaluer la prévalence de Listeria spp. dans différentes matrices alimentaires et de caractériser des isolats alimentaires et humains.Matériel et méthodesEntre 2005 et 2007, 100 échantillons alimentaires prélevés dans les marchés de Tunis ont été analysés ; cinq souches humaines de Listeria monocytogenes ont été étudiées. La caractérisation des isolats de L. monocytogenes a été réalisée par multiplex PCR sérogroupage et par électrophorèse sur gel en champ pulsé (PFGE) appliquant l’enzyme Ascl et Apal. Nous avons développé une puce à ADN afin de différencier les espèces au sein du genre Listeria.RésultatsLa prévalence de Listeria spp. dans les échantillons alimentaires a été estimée à 14 %. Deux isolats ont été identifiés L. monocytogenes et 12 L. innocua. La méthode de puce à ADN par sa précision a permis de distinguer entre les différentes espèces de Listeria spp. Les résultats étaient conformes à l’identification biochimique. Les isolats alimentaires de L. monocytogenes ont été assignés au sérogroupe IIa (sérovar 1/2a). Cependant, les isolats humains ont été assignés au sérogroupe IVb (sérovars 4b). Ces isolats ont présenté une similarité importante par PFGE. Les isolats alimentaires de L. monocytogenes ont été classés en deux pulsotypes différents. Ces pulsotypes étaient différents de celui des souches humaines.ConclusionNos résultats confirment la présence de Listeria spp. dans différentes matrices alimentaires collectées à Tunis. Des efforts supplémentaires devraient être déployés afin de prendre en considération le risque de toxi-infections alimentaires liées à L. monocytogenes et d’identifier les sources potentielles d’infection.
Published: 2014

4. Celecoxib activates Stat5 and restores or increases the expression of growth hormone-regulated genes in hepatocarcinogenesis

Author: Olga Beltrán-Ramírez, Serguei Sokol, Jean Marie François, Jaime Arellanes-Robledo, Rebeca García-Román, Véronique Le Berre, Saúl Villa-Treviño, Adriana Márquez-Quiñones, Martha Estela Salcido-Neyoy, Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV-IPN), Institut de médecine moléculaire de Rangueil (I2MR), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-IFR150-Institut National de la Santé et de la Recherche Médicale (INSERM), Biochip and Bionanotechnogy, 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)-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), Université de Toulouse (UT)-Université de Toulouse (UT)- Institut Fédératif de Recherche Bio-médicale Institution (IFR150)-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)-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)-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), and Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Male, Cancer Research, [SDV]Life Sciences [q-bio], Gene Expression, medicine.disease_cause, Rats, Sprague-Dawley, Liver Neoplasms, Experimental, 0302 clinical medicine, Gene expression, STAT5 Transcription Factor, Cytochrome P-450 CYP3A, Pharmacology (medical), STAT5, ComputingMilieux_MISCELLANEOUS, Oligonucleotide Array Sequence Analysis, Sulfonamides, 0303 health sciences, biology, 3. Good health, Real-time polymerase chain reaction, Oncology, 030220 oncology & carcinogenesis, Aryl Hydrocarbon Hydroxylases, medicine.drug, musculoskeletal diseases, Antineoplastic Agents, [SDV.CAN]Life Sciences [q-bio]/Cancer, 03 medical and health sciences, Alpha-Globulins, medicine, Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Cytochrome P450 Family 2, Transcription factor, 030304 developmental biology, Pharmacology, Gene Expression Profiling, Molecular biology, Rats, Gene expression profiling, Celecoxib, Growth Hormone, Cytochrome P-450 CYP2B1, Steroid Hydroxylases, biology.protein, Cancer research, STAT protein, Pyrazoles, Carcinogenesis
Abstract: We have previously evaluated the chemopreventive effect of celecoxib on preneoplastic lesions in rat liver. However, though the effects of celecoxib have been tested in a variety of carcinomas, there has not been a study on the modulation of gene expression in response to this drug. Here, we evaluated the effect of celecoxib on the gene expression profile associated with hepatocarcinogenesis. Male Sprague-Dawley rats underwent the modified resistant hepatocyte model and were fed a diet containing 1500 ppm of celecoxib. Gene expression profiles were evaluated using DNA microarrays and further validations were performed using quantitative PCR, western blotting and immunohistochemical staining. Celecoxib modulated the expression of 46 genes, and those regulated by growth hormone were selected for further analysis. Celecoxib significantly upregulated the expression of the Cyp2b1/2, Cyp3a1, and alpha2-urinary globulin (alpha2uG) genes and restored the expression of Cyp2b3 to normal. The protein expression of Cyp2b1/2 was increased, but the expressions of Cyp3a1 and alpha2uG were only restored to normal levels. The increased Cyp2b1/2 expression in response to celecoxib was mainly confined to preneoplastic lesions. A search for the upstream mediator of these genetic alterations found that carcinogenesis inactivated by 87% the signal transducer and activator of transcription 5 (Stat5), a transcription factor that is activated by growth hormone signaling, but celecoxib treatment restored its activation. In conclusion, these results suggest that celecoxib exerts anticancer effects on altered hepatic cells by restoring mRNA and the protein expression levels of specific genes, in part through the reactivation of Stat5.
Published: 2010

5. Comparative transcriptome analysis between original and evolved recombinant lactose-consuming Saccharomyces cerevisiae strains

Author: Jean Marie François, Pedro M. R. Guimarães, José A. Teixeira, Serguei Sokol, Lucília Domingues, Véronique Le Berre, Institute for Systems and Computer Engineering, Technology and Science [Braga] (INESC TEC), Biochip and Bionanotechnogy, 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)-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), ITAV, Université Fédérale Toulouse Midi-Pyrénées, Laboratoire Léon Brillouin (LLB - UMR 12), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Institute for Biotechnology and Bioengineering (IBB), Technical University of Lisbon, Universidade do Minho, Institut des Technologies Avancées en sciences du Vivant (ITAV), 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 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 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), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Evolutionary engineering, Saccharomyces cerevisiae Proteins, [SDV]Life Sciences [q-bio], Saccharomyces cerevisiae, Lactose, Ethanol fermentation, 01 natural sciences, Applied Microbiology and Biotechnology, law.invention, Transcriptome, Evolution, Molecular, 03 medical and health sciences, chemistry.chemical_compound, Species Specificity, law, 010608 biotechnology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Lactose fermentation, Gene, 030304 developmental biology, 2. Zero hunger, Genetics, Recombination, Genetic, 0303 health sciences, biology, Ethanol, Microarray analysis techniques, Recombinant Saccharomyces cerevisiae, General Medicine, biology.organism_classification, Biological Evolution, Genetic Enhancement, chemistry, Recombinant DNA, Metabolome, Molecular Medicine, Fermentation, cDNA microarrays, Transcription Factors
Abstract: The engineering of Saccharomyces cerevisiae strains for lactose utilization has been attempted with the intent of developing high productivity processes for alcoholic fermentation of cheese whey. A recombinant S. cerevisiae flocculent strain that efficiently ferments lactose to ethanol was previously obtained by evolutionary engineering of an original recombinant that displayed poor lactose fermentation performance. We compared the transcriptomes of the original and the evolved recombinant strains growing in lactose, using cDNA microarrays. Microarray data revealed 173 genes whose expression levels differed more than 1.5-fold. About half of these genes were related to RNA-mediated transposition. We also found genes involved in DNA repair and recombination mechanisms, response to stress, chromatin remodeling, cell cycle control, mitosis regulation, glycolysis and alcoholic fermentation. These transcriptomic data are in agreement with some of the previously identified physiological and molecular differences between the recombinants, and point to further hypotheses to explain those differences., (undefined)
Published: 2008

6. Proteasome Activity Deregulation in LEC Rat Hepatitis: Following the Insights of Transcriptomic Analysis

Author: Saúl Villa-Treviño, Jean Marie François, Julio Isael Pérez-Carreón, Véronique Le Berre, Françoise Guéraud, Alain Paris, Balbine Roussel, Adriana Márquez-Quiñones, Institut de médecine moléculaire de Rangueil (I2MR), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-IFR150-Institut National de la Santé et de la Recherche Médicale (INSERM), Xénobiotiques, Ecole Nationale Vétérinaire de Toulouse (ENVT), 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-Institut National de la Recherche Agronomique (INRA), Sérine protéases et physiopathologie de l'unité neurovasculaire, Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), CINVESTAV del IPN, 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), Biochip and Bionanotechnogy, 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), Ctr Invest & Estudios Avanzados, Dept Biol Celular, Instituto Politecnico Nacional [Mexico] (IPN), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-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)-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)-Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université de Toulouse (UT)-Université de Toulouse (UT)- Institut Fédératif de Recherche Bio-médicale Institution (IFR150)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), 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 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)
Subjects: Male, Proteasome Endopeptidase Complex, biotechnology et applied microbiology, heredity, [SDV]Life Sciences [q-bio], Hepatitis, Animal, Biology, medicine.disease_cause, Biochemistry, génétique, Transcriptome, 03 medical and health sciences, 0302 clinical medicine, Downregulation and upregulation, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], medicine, Animals, genetics, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Least-Squares Analysis, Molecular Biology, Gene, ComputingMilieux_MISCELLANEOUS, Oligonucleotide Array Sequence Analysis, 030304 developmental biology, Rats, Inbred LEC, Hepatitis, 0303 health sciences, biotechnologie et applications, Gene Expression Profiling, Proteasome complex, medicine.disease, Molecular biology, Rats, 3. Good health, Oxidative Stress, Gene Expression Regulation, Proteasome, 030220 oncology & carcinogenesis, Multivariate Analysis, Molecular Medicine, DNA microarray, Oxidative stress, Biotechnology
Abstract: International audience; LEC rats show spontaneous hepatitis and hepatocarcinoma development related to oxidative stress due to abnormal copper accumulation in the liver. We used DNA microarrays bearing 22,012 genes to investigate at the transcriptomic level the progression of the hepatitis in LEC rats in comparison to a control obtained from LEC rats treated with D-penicillamine, a copper chelating agent known to block hepatitis development. Multivariate statistical analyses as partial least square (PLS) regression between transcriptomic data and hepatitis markers in plasma led us to select 483 genes related to hepatitis development in these rats. After a complementary discriminant analysis (PLS-DA), 239 important genes for the separation between the different rat groups were selected. Gene ontology classification revealed an over-representation of genes involved in protein metabolism-related functions. More importantly, some genes implicated in proteasome pathway were upregulated. However, analysis of 20S proteasome activity showed that trypsin-like and peptidylglutamyl peptide hydrolase activities were diminished during hepatitis. Because oxidative stress is known to promote the inactivation of the proteasome complex, we propose the deregulation of the proteasome genes expression as a result of oxidative inactivation of proteasome activity during hepatitis in LEC rats. These results bring new insights in the hepatitis and the hepatocarcinogenesis development
Published: 2007

7. Early transcriptional response of wine yeast after rehydration: osmotic shock and metabolic activation

Author: Jean Marie François, Maite Novo, Gemma Beltran, Serguei Sokol, Véronique Anton Leberre, Nicolas Rozès, José Manuel Guillamón, Alberto Mas, Departament de Bioquímica i Biotecnologia, Facultat d’Enologia, Universitat Rovira i Virgili, 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), Biochip and Bionanotechnogy, 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), 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), 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), 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 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)
Subjects: Saccharomyces cerevisiae Proteins, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Proteome, Osmotic shock, Saccharomyces cerevisiae, Wine, Cycloheximide, Pentose phosphate pathway, Applied Microbiology and Biotechnology, Microbiology, 03 medical and health sciences, chemistry.chemical_compound, Osmotic Pressure, Gene Expression Regulation, Fungal, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.IDA]Life Sciences [q-bio]/Food engineering, Osmotic pressure, cycloheximide, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Oligonucleotide Array Sequence Analysis, 030304 developmental biology, 0303 health sciences, ribosomal proteins, biology, 030306 microbiology, Gene Expression Profiling, Water, General Medicine, biology.organism_classification, Yeast, Culture Media, Yeast in winemaking, chemistry, Biochemistry, Fermentation, osmotic stress, Genome, Fungal, transcription, Heat-Shock Response
Abstract: International audience; The inoculation of active dry wine yeast (ADWY) is one of the most common practices in winemaking. We have used DNA microarray technology to examine the genetic expression patterns of a commercial ADWY strain after rehydration. After rehydration of ADWY for 30 min, a further hour in water after rehydration did not lead to any relevant changes in global gene expression. Expression changes in rehydrated cells upon incubation in a sorbitol solution at the same osmotic pressure as in complete must were rather limited, whereas the presence of fermentable carbon sources or the complete medium (synthetic must) produced very similar transcriptional responses. The main responses were the activation of some genes of the fermentation pathway and of the nonoxidative branch of the pentose phosphate pathway, and the induction of a huge cluster of genes related to ribosomal biogenesis and protein synthesis. The presence of cycloheximide in fermentable medium produced a similar but stronger transcriptional response. Whereas the viabilities of rehydrated cells incubated for 1 h in these different media were similar, yeast vitality, which represents the fermentative capacity of the yeast, showed a positive correlation with the availability of a fermentable carbon source.
Published: 2007

8. Integration of transcriptomic and metabolic analyses for understanding the global responses of low-temperature winemaking fermentations

Author: Maite Novo, Jean Marie François, Véronique Anton Leberre, Nicolas Rozès, Alberto Mas, Gemma Beltran, José Manuel Guillamón, Serguei Sokol, Delphine Labourdette, Departament de Bioquímica i Biotecnologia, Facultat d’Enologia, Universitat Rovira i Virgili, 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), Biotecnologia Enològica, Departament de Bioquimica i Biotecnologia, Facultat d’Enologia, Biochip and Bionanotechnogy, 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), 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), 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 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)
Subjects: [SDV]Life Sciences [q-bio], Wine, Industrial fermentation, Saccharomyces cerevisiae, Biology, yeast, Applied Microbiology and Biotechnology, Microbiology, Esterase, 03 medical and health sciences, chemistry.chemical_compound, transcript profiling, Gene Expression Regulation, Fungal, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Viability assay, Phospholipids, Fatty acid synthesis, Oligonucleotide Array Sequence Analysis, 030304 developmental biology, Winemaking, Fermentation in winemaking, 0303 health sciences, 030306 microbiology, Gene Expression Profiling, Fatty Acids, Temperature, flavours, General Medicine, Yeast, Up-Regulation, Cold Temperature, wine fermentation, chemistry, Biochemistry, Fermentation, metabolic regulation
Abstract: Wine produced at low temperature is often considered to have improved sensory qualities. To investigate the effects of temperature on winemaking, the expression patterns during the industrial fermentation process carried out at 13 degrees C and 25 degrees C were compared, and correlated with physiological and biochemical data, including viability, fermentation byproducts and lipid content of the cells. From a total of 535 ORFs that were significantly differentially expressed between the 13 degrees C and 25 degrees C fermentations, two significant transcription programmes were identified. A cold-stress response was expressed at the initial stage of the fermentation, and this was followed by a transcription pattern of upregulated genes concerned with the cell cycle, growth control and maintenance in the middle and late stages of the process at 13 degrees C with respect to 25 degrees C. These expression patterns were correlated with higher cell viability at low temperature. The other relevant transcriptomic difference was that several genes implicated in cytosolic fatty acid synthesis were downregulated, while those involved in mitochondrial short-chain fatty acid synthesis were upregulated in the fermentation process conducted at 13 degrees C with respect to that at 25 degrees C. These transcriptional changes were qualitatively correlated with improved resistance to ethanol and increased production of short-chain (C(4)-C(8)) fatty acids and their corresponding esters at 13 degrees C as compared to 25 degrees C. While this increase of ethyl esters may account in part for the improved sensory quality of wine fermented at 13 degrees C, it is still unclear how the esterification of the short-chain fatty acids takes place. On the basis of its strong upregulation at 13 degrees C, we propose a possible role of IAH1 encoding an esterase/ester synthase in this process.
Published: 2006

9. Gene Expression Profile Related to the Progression of Preneoplastic Nodules toward Hepatocellular Carcinoma in Rats

Author: Evelia Arce-Popoca, Véronique Le Berre, Leticia Alemán-Lazarini, Serguei Sokol, Jean Marie François, Saúl Villa-Treviño, Samia Fattel-Fazenda, Cristina López-García, Julio Isael Pérez-Carreón, Sergio Hernández-García, Centro de Investigacion y de Estudios Avanzados del IPN, CINVESTAV., Biochip and Bionanotechnogy, 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 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), Ctr Invest & Estudios Avanzados, Dept Biol Celular, Instituto Politecnico Nacional [Mexico] (IPN), 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)-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)-Centre National de la Recherche Scientifique (CNRS)-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: Cancer Research, Hepatocarcinogenesis, redox control, cancer markers, [SDV]Life Sciences [q-bio], Biology, lcsh:RC254-282, Transcriptome, 03 medical and health sciences, 0302 clinical medicine, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Gene expression, medicine, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Gene, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Cancer, transcriptomic, glutathione metabolism, lcsh:Neoplasms. Tumors. Oncology. Including cancer and carcinogens, medicine.disease, Molecular biology, 3. Good health, Gene expression profiling, 030220 oncology & carcinogenesis, Hepatocellular carcinoma, Immunohistochemistry, Liver cancer
Abstract: In this study, we investigated the time course gene expression profile of preneoplastic nodules and hepatocellular carcinomas (HCC) to define the genes implicated in cancer progression in a resistant hepatocyte model. Tissues that included early nodules (1 month, ENT-1), persistent nodules (5 months, ENT-5), dissected HCC (12 months), and normal livers (NL) from adult rats were analyzed by cDNA arrays including 1185 rat genes. Differential genes were derived in each type of sample (n = 3) by statistical analysis. The relationship between samples was described in a Venn diagram for 290 genes. From these, 72 genes were shared between tissues with nodules and HCC. In addition, 35 genes with statistical significance only in HCC and with extreme ratios were identified. Differential expression of 11 genes was confirmed by comparative reverse transcription–polymerase chain reaction, whereas that of 2 genes was confirmed by immunohistochemistry. Members involved in cytochrome P450 and second-phase metabolism were downregulated, whereas genes involved in glutathione metabolism were upregulated, implicating a possible role of glutathione and oxidative regulation. We provide a gene expression profile related to the progression of nodules into HCC, which contributes to the understanding of liver cancer development and offers the prospect for chemoprevention strategies or early treatment of HCC. Neoplasia (2006) 8, 373‐383
Published: 2006

10. Microstructured liposome array

Author: Barnabé Chaize, Mathias Winterhalter, Tristan Ruysschaert, Véronique Le Berre, Michel Nguyen, Didier Fournier, Anne-Marie Caminade, Jean-Pierre Majoral, Bernard Meunier, Emmanuelle Trévisiol, Geneviève Pratviel, Institut de pharmacologie et de biologie structurale (IPBS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Laboratoire de chimie de coordination (LCC), 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 de Chimie de Toulouse (ICT-FR 2599), Institut de Recherche pour le Développement (IRD)-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-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Biochip and Bionanotechnogy, 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)-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), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie de Toulouse (ICT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), 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 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 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 de Toulouse (ICT-FR 2599), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut de Recherche pour le Développement (IRD)-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-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Plateforme Biopuces, Génopôle Toulouse Midi-Pyrénées, Institut de pharmacologie et de biologie structurale ( IPBS ), Centre National de la Recherche Scientifique ( CNRS ) -Université Toulouse III - Paul Sabatier ( UPS ), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, 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 ) -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 ), ITAV, Université Fédérale Toulouse Midi-Pyrénées, Laboratoire de chimie de coordination ( LCC ), Centre National de la Recherche Scientifique ( CNRS ), Service de Chirurgie Hépatobiliaire et Digestive, Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Hôpital Pontchaillou-CHU Pontchaillou [Rennes], Laboratoire de Chimie de Coordination, Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDV.BIO]Life Sciences [q-bio]/Biotechnology, [SDV]Life Sciences [q-bio], Biomedical Engineering, Oligonucleotides, Pharmaceutical Science, Bioengineering, Nanotechnology, 02 engineering and technology, 010402 general chemistry, 01 natural sciences, MESH: Oligonucleotides, Molecule, A-DNA, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH: Nanotechnology, ComputingMilieux_MISCELLANEOUS, Oligonucleotide Array Sequence Analysis, Pharmacology, Liposome, Amphiphilic molecule, [ SDV ] Life Sciences [q-bio], Oligonucleotide, Chemistry, Organic Chemistry, 021001 nanoscience & nanotechnology, Grafting, Fluorescence, 0104 chemical sciences, MESH: Oligonucleotide Array Sequence Analysis, Liposomes, Biophysics, MESH: Liposomes, 0210 nano-technology, Biotechnology
Abstract: Conversion of a DNA chip to a nanocapsule array was performed by grafting on a liposome an oligonucleotide complementary to an oligonucleotide bound to the array. Each liposome may be loaded by a soluble molecule or may present a hydrophobic or amphiphilic molecule inserted in its wall. To detect liposomes on the chip, we used fluorescent dyes encapsulated in the liposome internal volume or fluorescent lipids. We observed that an oligonucleotide-grafted liposome containing a defined dye specifically accumulated on the area where its complementary oligonucleotide had been spotted on the array. The virtually unlimited amount of addresses allows the specific binding of large amounts of liposomes in one single batch.
Published: 2006

11. 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

12. Dendrimeric coating of glass slides for sensitive DNA microarrays analysis

Author: Anne-Marie Caminade, Véronique Le Berre, Adilia Dagkessamanskaia, Serguei Sokol, Bernard Meunier, Jean Marie François, Emmanuelle Trevisiol, Jean-Pierre Majoral, Biochip and Bionanotechnogy, 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)-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 chimie de coordination (LCC), 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 de Chimie de Toulouse (ICT-FR 2599), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-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-Institut de Recherche pour le Développement (IRD)-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 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 de Toulouse (ICT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Plateforme Biopuces, Génopôle Toulouse Midi-Pyrénées, Institut de Chimie de Toulouse (ICT-FR 2599), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut de Recherche pour le Développement (IRD)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)
Subjects: DNA, Complementary, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Polymers, Surface Properties, [SDV]Life Sciences [q-bio], 02 engineering and technology, Biology, 010402 general chemistry, 01 natural sciences, Polymorphism, Single Nucleotide, Sensitivity and Specificity, chemistry.chemical_compound, Dendrimer, Complementary DNA, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, [CHIM]Chemical Sciences, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, ComputingMilieux_MISCELLANEOUS, NAR Methods Online, Oligonucleotide Array Sequence Analysis, Propylamines, Oligonucleotide, Hybridization probe, Phosphorus, Silanes, 021001 nanoscience & nanotechnology, Molecular biology, 0104 chemical sciences, chemistry, Protein microarray, Gene chip analysis, Biophysics, DNA microarray, 0210 nano-technology, Oligonucleotide Probes, DNA
Abstract: International audience; Successful use and reliability of microarray technology is highly dependent on several factors, including surface chemistry parameters and accessibility of cDNA targets to the DNA probes fixed onto the surface. Here, we show that functionalisation of glass slides with homemade dendrimers allow production of more sensitive and reliable DNA microarrays. The dendrimers are nanometric structures of size-controlled diameter with aldehyde function at their periphery. Covalent attachment of these spherical reactive chemical structures on amino-silanised glass slides generates a reactive approximately 100 A layer onto which amino-modified DNA probes are covalently bound. This new grafting chemistry leads to the formation of uniform and homogenous spots. More over, probe concentration before spotting could be reduced from 0.2 to 0.02 mg/ml with PCR products and from 20 to 5 micro M with 70mer oligonucleotides without affecting signal intensities after hybridisation with Cy3- and Cy5-labelled targets. More interestingly, while the binding capacity of captured probes on dendrimer-activated glass surface (named dendrislides) is roughly similar to other functionalised glass slides from commercial sources, detection sensitivity was 2-fold higher than with other available DNA microarrays. This detection limit was estimated to 0.1 pM of cDNA targets. Altogether, these features make dendrimer-activated slides ideal for manufacturing cost-effective DNA arrays applicable for gene expression and detection of mutations.
Published: 2003

13. Isopropanol production from carbon dioxide in Cupriavidus necator in a pressurized bioreactor

Author: Louna Maignien, Jasbir Singh, Eric Lombard, Lucile Garrigues, Stéphane E. Guillouet, 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), H.E.L Group, Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), 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: Ralstonia eutropha, 0106 biological sciences, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Cupriavidus necator, Bioengineering, Isopropanol, Laboratory scale, 01 natural sciences, 2-Propanol, 03 medical and health sciences, chemistry.chemical_compound, Bioreactors, 010608 biotechnology, Carbon source, Pressure, Bioreactor, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Autotroph, Molecular Biology, 030304 developmental biology, 0303 health sciences, Strain (chemistry), biology, Chemistry, Bioreactor design, General Medicine, biology.organism_classification, Pulp and paper industry, Carbon dioxide, 13. Climate action, Autotrophy, Gas fermentation, Bacteria, Hydrogen, Biotechnology
Abstract: International audience; A bioreactor was designed to provide high gas mass transfer to reach cell and product titres in the g L-1 level from CO2 for realistic, laboratory scale, engineered autotrophic strain evaluation. The design was based on independent CO2, H-2 and air inputs and the ability to operate at high pressures. The bioreactor configuration and cultivation strategy enabled growth of Cupriavidus necator strains for long periods, to reach over 3 g L-1 dry cell weight. No negative impact of the high pressure was observed on viability of the strains up to more than 4 bar overpressure. The cultivation was then carried out using an engineered isopropanol producing strain; in this case, 3.5 g L-1 isopropanol was obtained from CO2 as the sole carbon source. This is the first reported demonstration of a successful production from engineered bacteria of product in the g L-1 range on CO2 , raising the prospect of future development of CO2-based bioprocesses.
Published: 2020

14. A metrics-based approach to preparing sustainable membranes: application to ultrafiltration

Author: Ligia Barna, Flavie Prézélus, Christelle Guigui, Jean-Christophe Remigy, Dihia Chabni, Centre National de la Recherche Scientifique - CNRS (FRANCE), Institut National Polytechnique de Toulouse - INPT (FRANCE), Institut National de la Recherche Agronomique - INRA (FRANCE), Institut National des Sciences Appliquées de Toulouse - INSA (FRANCE), Université Toulouse III - Paul Sabatier - UT3 (FRANCE), 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, 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 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 de Liège, Universite Federale de Toulouse (PRES), Region Occitanie/Pyrenees-Mediterranee, France, 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)-Centre National de la Recherche Scientifique (CNRS), and Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE)
Subjects: [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Materials science, Ultrafiltration, membrane polymérique, solvant, 02 engineering and technology, 010402 general chemistry, 01 natural sciences, chemistry.chemical_compound, polymère, [CHIM.GENI]Chemical Sciences/Chemical engineering, Sustainable development, Génie chimique, Environmental Chemistry, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Génie des procédés, Process engineering, Flammability, Cellulose diacetate, Phase separation process, business.industry, Methyl lactate, 021001 nanoscience & nanotechnology, Pollution, 6. Clean water, 0104 chemical sciences, Solvent, Membrane, chemistry, 13. Climate action, 0210 nano-technology, business, Ecodesign
Abstract: International audience; The purpose of the research is to make a first step towards rationalizing green polymeric membrane preparation. A holistic methodological approach based on metrics that consider technical, environmental, health and safety issues have been suggested to assess sustainability of membrane preparation. Metrics have been applied to solvent substitution in a non-solvent induced phase separation process. The flammability hazard of three shortlisted alternative solvents has substituted the reprotoxicity hazard of common solvents. The ultrafiltration cellulose diacetate membranes prepared with methyl lactate as solvent have a greater renewable intensity and require a lower number of solvents for their preparation. Trade-offs between use of resources (polymer, solvent, energy…) and membrane properties are inevitable. Further socio-economic, risk and life cycle analysis are crucial to fully integrate ecodesign in membrane preparation.
Published: 2019

15. Neutral genetic drift-based engineering of a sucrose-utilizing enzyme toward glycodiversification

Author: David Daudé, Alizée Vergès, Magali Remaud-Simeon, Stéphane Emond, Isabelle André, Emmanuelle Cambon, Samuel Tranier, 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), Inst Pharmacol & Biol Struct, Dept Biophys Struct,CNRS, Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, French National Research Agency (ANR Project GLUCODESIGN) ANR-08-PCVI-002-02, French Ministry of Research, ANR-08-PCVI-0002,GLUCODESIGN,Ingénierie à façon de glycoenzymes par des outils de criblage virtuel innovants pour le design de vaccins entériques(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), 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 pharmacologie et de biologie structurale (IPBS), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Mutation rate, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, glycodiversification, macromolecular substances, neutral drift, 010402 general chemistry, 01 natural sciences, amylosucrase, Catalysis, Negative selection, Amylosucrase, Genetic drift, Hydrolase, transglucosylase engineering, chemistry.chemical_classification, biology, 010405 organic chemistry, Substrate (chemistry), General Chemistry, Protein engineering, 0104 chemical sciences, carbohydrates (lipids), enzyme engineering, Enzyme, Biochemistry, chemistry, biology.protein
Abstract: Neutral drift (also called purifying selection) is an attractive approach to generate polymorphic variant libraries for enzyme engineering. Here, we have applied this strategy to modify the substrate specificity of a transglucosylase. Our model enzyme, the amylosucrase from Neisseria polysaccharea, is a glucosylation biocatalyst of prime interest because it uses the widespread substrate sucrose as a glucosyl donor and shows broad acceptor promiscuity. A library of 440 functional amylosucrase variants was generated after four rounds of neutral drift at a low mutation rate. The functional variations present in this library were investigated by assaying the ability of these variants to use an alternative glucosyl donor (p-nitrophenyl-α-d-glucopyranoside, pNP-Glc) and to glucosylate a range of acceptors (including methyl-α-l-rhamnopyranoside, which is not naturally recognized by the parental enzyme). The impact of these mutations on the thermal stability of the variants was also assessed. Large variations of acceptor promiscuity were observed, ranging from the complete loss of detectable activity to a 2-fold increase relative to the parental enzyme. Variants showing increased catalytic efficiency toward the alternative pNP-Glc donor were also identified. Specifically, one variant combining four unprecedented amino acid changes was 25-fold more efficient at utilizing pNP-Glc than the parental enzyme and acquired glucosylation activity toward methyl-α-l-rhamnopyranoside. Enzymes with improved thermal stability were also identified. Overall, our work demonstrates that neutral drift is an effective and powerful strategy to engineer transglycosylases with enhanced or even acquired substrate specificities from small-sized functional libraries compatible with accurate low-throughput multi-parameter analyses.
Published: 2019

16. Variable Neighborhood Search with Cost Function Networks To Solve Large Computational Protein Design Problems

Author: David Mignon, Sophie Barbe, Thomas Schiex, Juan Cortés, Thomas Simonson, David Allouche, Antoine Charpentier, ATOS Origin, Laboratoire de Biochimie de l'Ecole polytechnique (BIOC), École polytechnique (X)-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), Équipe Robotique et InteractionS (LAAS-RIS), Laboratoire d'analyse et d'architecture des systèmes (LAAS), 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), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), 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 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), ANR-16-CE40-0028,DE-MO-GRAPH,Décomposition de Modèles Graphiques(2016), 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), and Université Fédérale Toulouse Midi-Pyrénées
Subjects: Models, Molecular, Mathematical optimization, Protein Conformation, PREDICTION, Computer science, General Chemical Engineering, Protein design, Monte Carlo method, SOFTWARE, Library and Information Sciences, Protein Engineering, Energy minimization, 01 natural sciences, [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI], Software, MONTE-CARLO, 0103 physical sciences, DEAD-END ELIMINATION, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], OPTIMIZATION, 010304 chemical physics, business.industry, REDESIGN, ALGORITHMS, Probabilistic logic, Computational Biology, Proteins, General Chemistry, Protein engineering, FRAMEWORK, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], 0104 chemical sciences, Computer Science Applications, 010404 medicinal & biomolecular chemistry, Dead-end elimination, LIBRARY, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], SIDE-CHAIN, business, Monte Carlo Method, Variable neighborhood search
Abstract: International audience; Computational protein design (CPD) aims to predict amino acid sequences that fold to specific structures and perform desired functions. CPD depends on a rotamer library, an energy function, and an algorithm to search the sequence/conformation space. Variable neighborhood search (VNS) with cost function networks is a powerful framework that can provide tight upper bounds on the global minimum energy. We propose a new CPD heuristic based on VNS in which a subset of the solution space (a “neighborhood”) is explored, whose size is gradually increased with a dedicated probabilistic heuristic. The algorithm was tested on 99 protein designs with fixed backbones involving nine proteins from the SH2, SH3, and PDZ families. The number of mutating positions was 20, 30, or all of the amino acids, while the rest of the protein explored side-chain rotamers. VNS was more successful than Monte Carlo (MC), replica-exchange MC, and a heuristic steepest-descent energy minimization, providing solutions with equal or lower best energies in most cases. For complete protein redesign, it gave solutions that were 2.5 to 11.2 kcal/mol lower in energy than those obtained with the other approaches. VNS is implemented in the toulbar2 software. It could be very helpful for large and/or complex design problems.
Published: 2018

17. Modelling PAH partitioning during sludge disintegration: The key role of dissolved and colloidal matter

Author: Mansour Bounouba, Evrard Mengelle, Mathieu Spérandio, Yolaine Bessiere, I. Mozo, Nicolas Lesage, 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), Centre scientifique et Technique Jean Feger (CSTJF), TOTAL FINA ELF, ANRT (CIFRE) [1261/2009], 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), CSTJF, TOTAL SA, and Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: sonication, Environmental Engineering, Health, Toxicology and Mutagenesis, 0208 environmental biotechnology, Fraction (chemistry), 02 engineering and technology, 010501 environmental sciences, modèle, 01 natural sciences, modelling, active sludge, chemistry.chemical_compound, Colloid, boue activée, partitioning, Environmental Chemistry, biological treatment, Polycyclic Aromatic Hydrocarbons, 0105 earth and related environmental sciences, Naphthalene, DCM, numerical models, Aqueous solution, Sewage, Public Health, Environmental and Occupational Health, Aqueous two-phase system, Sorption, PAH, General Medicine, General Chemistry, hydrocarbone aromatique, Pollution, traitement biologique, 6. Clean water, 020801 environmental engineering, Activated sludge, chemistry, Environmental chemistry, Pyrene, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, transfer, Water Pollutants, Chemical
Abstract: The partitioning between solids and the aqueous phase largely controls the fate of PAH compounds in biological treatment. The prediction of PAH sorption behaviour into activated sludge was investigated here. The suitability of a three-compartment model to describe partitioning in such a complex matrix was first evaluated by adding increasing quantities of dissolved and colloidal matter (DCM) (from 0 to 34.9% of the total matter). In a range of DCM concentrations varying from 0 to 1.4 g L−1, the PAH aqueous fraction, including both freely dissolved and sorbed to DCM molecules, increased from 9.9% to 33% for naphthalene (the most soluble PAH) and from 0.29% to 13.3% for indeno(1,2,3,c,d)pyrene (the least soluble PAH tested). The sorption of PAHs on dissolved and colloidal matter (DCM) was assessed by determining two partitioning constants (KPART and KDCM) for the 16 PAHs listed by the US EPA. New experiments were carried out for model validation and show that the model properly predicts the PAH partitioning following sludge disintegration by sonication.
Published: 2018

18. An operational methodology for applying dynamic Life Cycle Assessment to buildings

Author: Ligia Tiruta-Barna, Jacques Chevalier, Koji Negishi, Alexandra Lebert, Nicoleta Schiopu, 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 Scientifique et Technique du Bâtiment, French National Research Agency [ANR-13-IS09-0007-01/DyPLCA], Centre Scientifique et Technique du Bâtiment (CSTB), ANR-13-IS09-0007,DyPLCA,Evaluation environnementale des procédés en fonctionnement dynamique – prise en compte du temps dans la méthode d'Analyse du Cycle de Vie(2013), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), 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: dynamic life cycle impact assessment, Environmental Engineering, Computer science, 020209 energy, Geography, Planning and Development, 02 engineering and technology, 010501 environmental sciences, 01 natural sciences, 7. Clean energy, performance environnementale, Field (computer science), [SPI.MAT]Engineering Sciences [physics]/Materials, Software, Multiple time dimensions, building, batiment, 11. Sustainability, 0202 electrical engineering, electronic engineering, information engineering, Life-cycle assessment, 0105 earth and related environmental sciences, Civil and Structural Engineering, construction industry, 9. Industry and infrastructure, business.industry, Energy mix, Building and Construction, Technical performance, dynamic life cycle inventory, Work (electrical), 13. Climate action, Systems engineering, Architectural technology, business
Abstract: While the Life Cycle Assessment (LCA) method is a powerful tool for environmental performance evaluation, the current LCA methodology faces some limitations in evaluating environmental performances of systems with a long time scales, such as buildings. Building systems have particularly long lifetimes as compared to other products or services. They are composed of elements that evolve over time and are characterized by time-dependent parameters. A literature review was performed in the aim of identifying the time-dependent characteristics of a building system at different levels: building technology level (e.g. technical performance degradations and technological innovations), end-user level (e.g. occupant behaviour) and external system level (e.g. infrastructures, energy mix, regulations). A new LCA framework including the time dimension, applied to a building system, is proposed. It involves operational and reproducible tools (computational software and databases) to perform effective temporal evaluations and incorporates dynamic Life Cycle Inventory (LCI, including the temporal evolution of a building system and of the related environment interventions, i.e. emissions and resource consumption) and dynamic Life Cycle Impact Assessment (LCIA, climate change and toxicity). To integrate the specificities of buildings in dynamic LCI modelling, different existing assets (at national and international level) in the field of LCA are analysed. This work proposes an original methodology for performing a dynamic LCA of buildings using new tools still under development.
Published: 2018

19. On single bubble mass transfer in a volatile liquid

Author: Arnaud Cockx, Pascal Guiraud, Dominique Legendre, Damien Colombet, Ulrich Nieken, Sophie Galinat, Claude Daniel, Ute Tuttlies, 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 mécanique des fluides de Toulouse (IMFT), 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, Fédération de Recherche Fluides, Energie, Réacteurs, Matériaux et Transferts (FERMAT), 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), Solvay, Institut für Chemische Verfahrenstechnik, University of Stuttgart, Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), 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)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Centre National de la Recherche Scientifique - CNRS (FRANCE), Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), Institut National de la Recherche Agronomique - INRA (FRANCE), Institut National des Sciences Appliquées de Toulouse - INSA (FRANCE), SOLVAY (FRANCE), Université Toulouse III - Paul Sabatier - UT3 (FRANCE), Universität Stuttgart (GERMANY), Institut für Chemische Verfahrenstechnik - ICVT (GERMANY), and Institut National Polytechnique de Toulouse - INPT (FRANCE)
Subjects: transfert de masse, réacteur, cyclohexane, Materials science, Mécanique des fluides, Bubble, Evaporation, Thermodynamics, 02 engineering and technology, particule - surface interactions, interaction particule surface, 01 natural sciences, reactor, Isothermal process, 010305 fluids & plasmas, méthode de suivi, Physics::Fluid Dynamics, thermodynamics, 020401 chemical engineering, Phase (matter), Mass transfer, 0103 physical sciences, Fluid mechanics, [PHYS.MECA.MEFL]Physics [physics]/Mechanics [physics]/Fluid mechanics [physics.class-ph], thermodynamique, 0204 chemical engineering, phase liquide, Fluid Flow and Transfer Processes, liquid phase, [PHYS.MECA.MEFL]Physics [physics]/Mechanics [physics]/Mechanics of the fluids [physics.class-ph], Mechanical Engineering, Condensed Matter Physics, Lewis number, Volume (thermodynamics), 13. Climate action, Particle
Abstract: International audience; We consider single bubble mass transfer of an non-condensible gas into a volatile liquid phase in indus- trial conditions, as observed for example in hydrocarbons liquid phase oxidation processes. Instantaneous bubble size, shape and velocity are measured using image processing with a particle tracking method. The mass transfer rate nitrogen into hot and pressurized liquid cyclohexane is deduced from the bubble volume decrease rate and is compared to literature correlations valid under isothermal conditions. Experiments are performed in a pressurized reactor for P = 20 bar, 30° ≤ T ≤ 150°C and bubble Reynolds number Re = O(10—100). The analysis of bubble rise dynamics shows that the gas-liquid system studied can be considered as a clean system. The mass transfer results are found to follow isothermal correlations predictions excepted for ambient temperature for which liquid evaporation in bubbles is shown to be coupled with mass transfer. This phenomena seems to be a consequence of having a high Lewis number.
Published: 2018

20. The art of adapting to extreme environments: The model system Pseudoalteromonas

Author: Marco Fondi, Ermenegilda Parrilli, Donatella de Pascale, Maria Luisa Tutino, Pietro Tedesco, Angelina Lo Giudice, Renato Fani, University of Naples Federico II, 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), Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Institute of Polar Sciences [Venezia-Mestre] (CNR-ISP), Consiglio Nazionale delle Ricerche [Roma] (CNR), Consiglio Nazionale delle Ricerche (CNR), University of Naples Federico II = Università degli studi di Napoli Federico II, 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), Università degli Studi di Firenze = University of Florence (UniFI), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Parrilli, Ermenegilda, Pietro, Tedesco, Marco, Fondi, Tutino, MARIA LUISA, Angelina Lo Giudice, Donatella de Pascale, and Renato, Fani
Subjects: [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Acclimatization, General Physics and Astronomy, Genomics, Context (language use), Model system, Biology, 03 medical and health sciences, 0302 clinical medicine, Phenomics, Pseudoalteromonas, Artificial Intelligence, Extreme environment, 14. Life underwater, Adaptation, 030304 developmental biology, Ecological niche, 0303 health sciences, Ecology, Extreme environments, biology.organism_classification, Adaptation, Physiological, Cold Temperature, 13. Climate action, Antarctica, General Agricultural and Biological Sciences, 030217 neurology & neurosurgery
Abstract: International audience; Extremophilic microbes have adapted to thrive in ecological niches characterized by harsh chemical/physical conditions such as, for example, very low/high temperature. Living organisms inhabiting these environments have developed peculiar mechanisms to cope with extreme conditions, in such a way that they mark the chemical-physical boundaries of life on Earth. Studying such mechanisms is stimulating from a basic research viewpoint and because of biotechnological applications.Pseudoalteromonas species are a group of marine gamma-proteobacteria frequently isolated from a range of extreme environments, including cold habitats and deep-sea sediments. Since deep-sea floors constitute almost 60% of the Earth's surface and cold temperatures represent the most common of the extreme conditions, the genus Pseudoalteromonas can be considered one of the most important model systems for studying microbial adaptation. Particularly, among all Pseudoalteromonas representatives, P. haloplanktis TAC125 has recently gained a central role. This bacterium was isolated from seawater sampled along the Antarctic ice-shell and is considered one of the model organisms of cold-adapted bacteria. It is capable of thriving in a wide temperature range and it has been suggested as an alternative host for the soluble overproduction of heterologous proteins, given its ability to rapidly multiply at low temperatures.In this review, we will present an overview of the recent advances in the characterization of Pseudoalteromonas strains and, more importantly, in the understanding of their evolutionary and chemical-physical strategies to face such a broad array of extreme conditions. A particular attention will be given to systems-biology approaches in the study of the above-mentioned topics, as genome-scale datasets (e.g. genomics, proteomics, phenomics) are beginning to expand for this group of organisms. In this context, a specific section dedicated to P. haloplanktis TAC125 will be presented to address the recent efforts in the elucidation of the metabolic rewiring of the organisms in its natural environment (Antarctica).
Published: 2021

21. Development and validation of a UHPLC-ESI-QTOF mass spectrometry method to analyze opines, plant biomarkers of crown gall or hairy root diseases

Author: Isabelle Kerzaon, Yves Dessaux, David Chapulliot, Rosa Padilla, Floriant Bellvert, Xavier Nesme, Vincent Gaillard, Ludovic Vial, Thao Nhi Le, Céline Lavire, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université d'Orléans (UO), 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), MetaToul-MetaboHUB, Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), 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-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), 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-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), French national program EC2CO (project IBAD) BioEnviS Research Federation French Ministere de l'Education Nationale, de l'Enseignement Superieur et de la Recherche Consejo Nacional de Ciencia y Tecnologia (CONACyT)CVU 397515Rhone-Alpes international cooperation and mobility program (CMIRA), Institut de Chimie Organique et Analytique (ICOA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Orléans (UO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), MetaToul FluxoMet (TBI-MetaToul), MetaboHUB-MetaToul, MetaboHUB-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-MetaboHUB-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Toulouse Biotechnology Institute (TBI), 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 Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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 Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Toulouse Biotechnology Institute (TBI), 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 de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), and CCSD, Accord Elsevier
Subjects: Spectrometry, Mass, Electrospray Ionization, Opines, Agrobacterium, Clinical Biochemistry, Opine, Arginine, Mass spectrometry, Plant Roots, 030226 pharmacology & pharmacy, 01 natural sciences, Biochemistry, Analytical Chemistry, Matrix (chemical analysis), 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Plant Tumors, Quantification, Diagnosis, Gall, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, Mannitol, Chromatography, High Pressure Liquid, Plant Diseases, Octopine, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Chromatography, biology, 010401 analytical chemistry, Crown (botany), Reproducibility of Results, food and beverages, Cell Biology, General Medicine, biology.organism_classification, 0104 chemical sciences, [SDV.EE] Life Sciences [q-bio]/Ecology, environment, Detection, chemistry, UHPLC-ESI-MS-QTOF, Nopaline, Biomarkers
Abstract: International audience; Opines are low-molecular-weight metabolites specifically biosynthesized by agrobacteria-transformed plant cells when plants are struck by crown gall and hairy root diseases, which cause uncontrolled tissue overgrowth. Transferred DNA is sustainably incorporated into the genomes of the transformed plant cells, so that opines constitute a persistent biomarker of plant infection by pathogenic agrobacteria and can be targeted for crown gall/hairy root disease diagnosis. We developed a general, rapid, specific and sensitive analytical method for overall opine detection using ultra-high-performance liquid chromatography-electrospray ionization quadrupole time-of-flight mass spectrometry (UHPLC-ESI-MS-QTOF), with easy preparation of samples. Based on MS, MS/MS and chromatography data, the detection selectivity of a wide range of standard opines was validated in pure solution and in different plant extracts. The method was successfully used to detect different structural types of opines, including opines for which standard compounds are unavailable, in tumors or hairy roots induced by pathogenic strains. As the method can detect a wide range of opines in a single run, it represents a powerful tool for plant gall analysis and crown gall/hairy root disease diagnosis. Using an appropriate dilution of plant extract and a matrix-based calibration curve, the quantification ability of the method was validated for three opines belonging to different families (nopaline, octopine, mannopine), which were accurately quantified in plant tissue extracts.
Published: 2021

22. Development of modified airlift reactor (MALR) for improving oxygen transfer: optimize design and operation condition using ‘design of experiment’ methodology

Author: Phaly Ham, Nattawin Chawaloesphonsiya, Pisut Painmanakul, Kritchart Wongwailikhit, Saret Bun, Jenyuk Lohwacharin, Chulalongkorn University [Bangkok], Institute of Technology of Cambodia [Cambodge] (KHM), 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), ASEAN University Network/Southeast Asia Engineering Education Development Network (AUN/SEED-Net) Program of Japan International Cooperation Agency (JICA) through Collaborative Research (CR) Program JFY 2015, Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), and Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA)
Subjects: Oxygen transfer, Oxygen mass transfer, 0208 environmental biotechnology, design of experiment, chemistry.chemical_element, 02 engineering and technology, 010501 environmental sciences, response surface design, 7. Clean energy, 01 natural sciences, Oxygen, Bioreactors, Aqueous solubility, Environmental Chemistry, Response surface methodology, Process engineering, K(L)acoefficient, Waste Management and Disposal, airlift reactor, 0105 earth and related environmental sciences, Water Science and Technology, business.industry, Design of experiments, Airlift reactor, General Medicine, 6. Clean water, 020801 environmental engineering, 2(k)factorial design, chemistry, 13. Climate action, Environmental science, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, optimization
Abstract: International audience; Oxygen scarcity may significantly affect the process performance since it has low aqueous solubility and high demand by chemical and biological processes. The oxygen mass transfer is therefore necessary to enhance. This work aimed to develop the gas-liquid reactor, named Modified Airlift Reactor (MALR) for improving the oxygen transfer efficiency in terms of internal configurations and aeration parameters by equipping a vertical baffle for creating liquid circulation phenomena, and installing slanted baffles in the reactor riser to extend air-bubbles retention time and to improve their distributions. Since extremum conditions of the investigated factors may inefficient, optimum levels are required to identify. 2(k)factorial and response surface design of Design of Experiment (DOE) methodology were applied to optimize these complex variables in terms of overall liquid mass transfer coefficient (K(L)a) of clean water. As a result, the main effective factors of MALR with their optimum value are amount of baffles (N-b similar to 3 baffles), baffle angle (alpha similar to 50 degrees), position of base area (Y-r similar to 10 cm), open space on baffle (A(s)similar to 90 cm(2)), and gas flow (Qg). Increasing Qg resulted betterK(L)afor the studied ranges (2-18 LPM). At the optimum condition, the improvement of MALR in terms ofK(L)acoefficient was increased up to 97% and 28% compared to the regular bubble column and airlift reactor, respectively, at a certain gas flow without any extra energy. The correlation models ofK(L)acoefficient with significant variables and power consumption were constructed for future estimation purposes.
Published: 2020

23. Hydrodynamics and gas-liquid mass transfer around a confined sliding bubble

Author: Abderrahmane Kherbeche, Mei Mei, Nicolas Dietrich, Marie-Jean Thoraval, Gilles Hébrard, State Key Laboratory for strength and vibration of mechanical structures, Xi'an Jiaotong University (Xjtu), 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), 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 (FRANCE), Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), Institut National de la Recherche Agronomique - INRA (FRANCE), Institut National des Sciences Appliquées de Toulouse - INSA (FRANCE), Université Toulouse III - Paul Sabatier - UT3 (FRANCE), Xi'an Jiaotong University - XJTU (CHINA), and Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés - LISBP (Toulouse, France)
Subjects: Mass flux, Materials science, Mass transfer coefficient, General Chemical Engineering, Bubble, 02 engineering and technology, Wake, 010402 general chemistry, Archimedes number, 01 natural sciences, Sherwood number, Industrial and Manufacturing Engineering, Physics::Fluid Dynamics, Sliding bubble, Mass transfer, Génie chimique, Environmental Chemistry, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Génie des procédés, Gas/liquid/solid reactors, Visualization, VisualizationHydrodynamics, General Chemistry, Mechanics, 021001 nanoscience & nanotechnology, 0104 chemical sciences, Vortex, Gas/Liquid/Solid reactors, Hydrodynamics, 0210 nano-technology
Abstract: International audience; An experimental investigation of gas-liquid mass transfer in the wake of a confined air bubble sliding under an inclined wall in a 2D Hele-Shaw cell is reported. A colorimetric technique based on an oxygen-sensitive dye was used to visualize the oxygen transfer. Bubble velocities, shape eccentricities, interfacial areas and, for the first time, the instantaneous spatio-temporal distribution of oxygen concentration fields in the bubble wake, have been investigated for upper wall inclination angles of 10° ≤ α ≤ 60° and Archimedes numbers of 783 ≤ Ar ≤ 3221. Image processing has allowed, through a specific approach, a quantification of mass transfer. The calculation of the mass flux allowed the deduction of the liquid-side mass transfer coefficient kL. Experiments reveals that, at low angles of inclination, bubble velocities decelerates, shape eccentricities increased, and the instantaneous spatial and temporal distribution of oxygen concentration fields illustrated two distinct regions underneath the sliding bubble: a single vortex loop enclosing the near wake where oxygen is transferred, and a far wake containing oxygen in the form of a single long strip. When inclination angles and bubble sizes were increasing, velocities were increasing, the vortex elongated gradually until it disappears at high angles where total mass fluxes increased. This increase of bubble velocities has increased liquid-side mass transfer coefficient kL allowing a scaling law between the Sherwood number and the modified Archimedes number Ar.sin(α) to be proposed.
Published: 2020

24. NMR metabolomics for understanding the role of alkaline phosphatase in neurotransmission and inflammation processesEuropean RFMF Metabomeeting

Author: Guidetti, Brigitte, Fabing, Isabelle, Baltas, Michel, Ballereau, Stéphanie, Castellan, Tessa, Génisson, Yves, Remaud Simeon, Magali, Bozonnet, Sophie, Nahoum, Virginie, Mourey, Lionel, Demange, Pascal, Milon, Alain, Maveyraud, Laurent, Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique (SPCMIB), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie de Toulouse (ICT-FR 2599), Institut de Recherche pour le Développement (IRD)-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-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, 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 pharmacologie et de biologie structurale (IPBS), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)
Subjects: [CHIM]Chemical Sciences, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2020

25. Towards transparent valorization of food surplus, waste and loss:Clarifying definitions, food waste hierarchy, and role in the circular economy

Author: Dominika Alexa Teigiserova, Lorie Hamelin, Marianne Thomsen, Research Group on EcoIndustrial System Analysis, Department of Environmental Science, Aarhus University [Aarhus], Centre for Circular Bioeconomy, 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), Horizon 2020 project DECISIVE (Decentralised valorisation of biowaste) [689229], Aarhus University's Centre for Circular Bioeconomy, Aarhus University Graduate School of Science and Technology, Cambioscop project, French National Research Agency (ANR) [ANR-17-MGPA-0006], Aarhus University, 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), 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: Environmental Engineering, 010504 meteorology & atmospheric sciences, Circular economy, Natural resource economics, Supply chain, Food surplus, Context (language use), Definitions, 010501 environmental sciences, 01 natural sciences, 12. Responsible consumption, Food Supply, strong sustainability, circular bioeconomy, 11. Sustainability, économie circulaire, Environmental Chemistry, Recycling, food waste hierarchy, Waste Management and Disposal, 0105 earth and related environmental sciences, gestion des déchets, biorefinery, Food waste, circular economy, Food loss, Minimization of residues, Pollution, Refuse Disposal, Policy, Work (electrical), food waste, 13. Climate action, Food, Management system, Sustainability, gaspillage alimentaire, Whole food, waste management, Business, minimization of residues, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, policy, Circular bioeconomy
Abstract: In this study, the key gaps of food waste prevention have been addressed in the context of the emerging circular economy. First, current terminology related to food waste was reviewed and clarified, in particular, the terms food surplus, waste and losses. This work highlights why the clarity of these definitions is crucial for the sustainability of future food waste management systems, especially in the context of circular economy. Through a simple matrix, definitions are linked to the concepts of edibility and possibility of avoidance, leading to six distinct categories of food waste: i) edible, ii) naturally inedible (pits), iii) industrial residue, iv) inedible due to natural causes (pests), v) inedible due to ineffective management and vi) not accounted for. Category I encompasses surplus food only; category II-V food waste and category VI food losses. Based on this, an updated pyramid for food waste hierarchy is proposed, distinguishing surplus food and a new category for material recycling, in order to reflect the future food waste biorefineries in the circular bioeconomy. Nutrient and energy recovery are two separate categories and the terms recovery and recycling are clarified. Finally, a circular economy framework is presented for food surplus and waste, considering closing the loop throughout the whole food supply chain, in connection with the concept of strong and weak sustainability. This is presented along with a review of key EU policies related to food waste and examples of initiatives from the Member States.
Published: 2020

26. Increasing field strength versus advanced isotope labeling for NMR based fluxomics

Author: Fabien Létisse, Edern Cahoreau, Pierre Millard, Guy Lippens, Mickael Dinclaux, 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), Unité de Glycobiologie Structurale et Fonctionnelle (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), MetaboHUB-AR-11-INBS-0010, Region Provence-Alpes-Cote d'Azur Region Occitanie, European Union (EU), SICOVAL, Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), 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), MetaToul FluxoMet (TBI-MetaToul), MetaboHUB-MetaToul, MetaboHUB-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-MetaboHUB-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Toulouse Biotechnology Institute (TBI), 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 Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Université de Lille-Centre National de la Recherche Scientifique (CNRS)
Subjects: deuteration, [PHYS]Physics [physics], Resolution (mass spectrometry), Field (physics), Isotope, 010405 organic chemistry, Chemistry, [SDV]Life Sciences [q-bio], Field strength, General Chemistry, 010402 general chemistry, 01 natural sciences, fluxomics, metabolomics, 0104 chemical sciences, Metabolomics, Heteronuclear molecule, Deuterium, high field NMR, Computational chemistry, General Materials Science, Fluxomics, ComputingMilieux_MISCELLANEOUS
Abstract: International audience; Nuclear magnetic resonance (NMR)-based fluxomics seeks to measure the incorporation of isotope labels in selected metabolites to follow kinetically the synthesis of the latter. It can however equally be used to understand the biosynthetic origin of the same metabolites. We investigate here different NMR approaches to optimize such experiments in terms of resolution and time requirement. Using the isoleucine biosynthesis as an example, we explore the use of different field strengths ranging from 500 MHz to 1.1 GHz. Because of the different field dependence of chemical shift and heteronuclear J couplings, the spectra change at different field strengths. We equally explore the approach to silence the leucine/valine methyl signals through the use of a suitable deuterated precursor, thereby allowing selective observation of the Ile C-13 labeling pattern. Combining both approaches, we arrive at an efficient procedure for the NMR-based exploration of Ile biosynthesis.
Published: 2020

27. Harvesting of Prebiotic Fructooligosaccharides by Nonbeneficial Human Gut Bacteria

Author: Gabrielle Potocki-Véronèse, Elisabeth Laville, Nicolas Terrapon, Pascale Lepercq, Zhi Wang, Pietro Tedesco, Fabien Létisse, Myriam Mercade, Alexandra S. Tauzin, 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), Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Region Provence-Alpes-Cote d'Azur Region Occitanie, Institut National de la Recherche Agronomique (INRA), INSA Toulouse, China Scholarship Council, European Project: 685474,H2020,H2020-LEIT-BIO-2015-1,METAFLUIDICS(2016), 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), and Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0301 basic medicine, Molecular Biology and Physiology, medicine.medical_treatment, Dorea, chronic gut diseases, fructooligosaccharides, microbiome, phosphotransferase system, prebiotique, lcsh:QR1-502, Oligosaccharides, Gut flora, phosphotransférase, lcsh:Microbiology, protéine transmembranaire, Phosphotransferase, Transporter Classification Database, biology, Microbiology and Parasitology, PEP group translocation, Microbiologie et Parasitologie, QR1-502, 3. Good health, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Biochemistry, Carbohydrate Metabolism, Research Article, Firmicutes, 030106 microbiology, Microbiology, 03 medical and health sciences, Metabolomics, microbiote, transmembrane protein, Escherichia coli, medicine, Humans, oligosaccharide, Microbiome, Molecular Biology, ingénierie du génome, métagénomique, metagenomics, Bacteria, Prebiotic, Phosphotransferases, biology.organism_classification, Gastrointestinal Microbiome, Prebiotics, 030104 developmental biology, Fermentation, genome engineering
Abstract: Prebiotics are increasingly used as food supplements, especially in infant formulas, to modify the functioning and composition of the microbiota. However, little is currently known about the mechanisms of prebiotic recognition and transport by gut bacteria, while these steps are crucial in their metabolism. In this study, we established a new strategy to profile the specificity of oligosaccharide transporters, combining microbiomics, genetic locus and strain engineering, and state-of-the art metabolomics. We revisited the transporter classification database and proposed a new way to classify these membrane proteins based on their structural and mechanistic similarities. Based on these developments, we identified and characterized, at the molecular level, a fructooligosaccharide transporting phosphotransferase system, which constitutes a biomarker of diet and gut pathology. The deciphering of this prebiotic metabolization mechanism by a nonbeneficial bacterium highlights the controversial use of prebiotics, especially in the context of chronic gut diseases., Prebiotic oligosaccharides, such as fructooligosaccharides, are increasingly being used to modulate the composition and activity of the gut microbiota. However, carbohydrate utilization analyses and metagenomic studies recently revealed the ability of deleterious and uncultured human gut bacterial species to metabolize these functional foods. Moreover, because of the difficulties of functionally profiling transmembrane proteins, only a few prebiotic transporters have been biochemically characterized to date, while carbohydrate binding and transport are the first and thus crucial steps in their metabolization. Here, we describe the molecular mechanism of a phosphotransferase system, highlighted as a dietary and pathology biomarker in the human gut microbiome. This transporter is encoded by a metagenomic locus that is highly conserved in several human gut Firmicutes, including Dorea species. We developed a generic strategy to deeply analyze, in vitro and in cellulo, the specificity and functionality of recombinant transporters in Escherichia coli, combining carbohydrate utilization locus and host genome engineering and quantification of the binding, transport, and growth rates with analysis of phosphorylated carbohydrates by mass spectrometry. We demonstrated that the Dorea fructooligosaccharide transporter is specific for kestose, whether for binding, transport, or phosphorylation. This constitutes the biochemical proof of effective phosphorylation of glycosides with a degree of polymerization of more than 2, extending the known functional diversity of phosphotransferase systems. Based on these new findings, we revisited the classification of these carbohydrate transporters. IMPORTANCE Prebiotics are increasingly used as food supplements, especially in infant formulas, to modify the functioning and composition of the microbiota. However, little is currently known about the mechanisms of prebiotic recognition and transport by gut bacteria, while these steps are crucial in their metabolism. In this study, we established a new strategy to profile the specificity of oligosaccharide transporters, combining microbiomics, genetic locus and strain engineering, and state-of-the art metabolomics. We revisited the transporter classification database and proposed a new way to classify these membrane proteins based on their structural and mechanistic similarities. Based on these developments, we identified and characterized, at the molecular level, a fructooligosaccharide transporting phosphotransferase system, which constitutes a biomarker of diet and gut pathology. The deciphering of this prebiotic metabolization mechanism by a nonbeneficial bacterium highlights the controversial use of prebiotics, especially in the context of chronic gut diseases.
Published: 2020

28. Trends in Systems Biology for the Analysis and Engineering of Clostridium acetobutylicum Metabolism

Author: Ngoc-Phuong-Thao Nguyen, Minyeong Yoo, Philippe Soucaille, BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, UK (UON), School of Medicine, Tan Duc e-City, Duc Hoa, Tan Tao University (TTU), 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), Metabolic Explorer Company, European Project: 237942,EC:FP7:PEOPLE,FP7-PEOPLE-ITN-2008,CLOSTNET(2009), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), 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: Microbiology (medical), biologie des systèmes, Clostridium acetobutylicum, Primary metabolism, approche transcriptomique, Commodity chemicals, Systems biology, fluxomique, Proteomics, Microbiology, Metabolic engineering, Industrial Microbiology, 03 medical and health sciences, proteomics, ingénierie métabolique, Virology, Metabolomics, protéomique, Genetic Association Studies, Fluxomics, 030304 developmental biology, 0303 health sciences, biology, 030306 microbiology, fungi, systems biology, Gene Expression Regulation, Bacterial, biology.organism_classification, equipment and supplies, clostridium acetobutylicum, Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Metabolic regulation, biocarburant, Biofuels, Mutation, biofuel, Biochemical engineering, Genetic Engineering, metabolic engineering, Metabolic Networks and Pathways
Abstract: Clostridium acetobutylicum has received renewed interest worldwide as a promising producer of biofuels and bulk chemicals such as n-butanol, 1,3-propanediol, 1,3-butanediol, isopropanol, and butyrate. To develop commercial processes for the production of bulk chemicals via a metabolic engineering approach it is necessary to better characterize both the primary metabolism and metabolic regulation of C. acetobutylicum. Here, we review the history of the development of omics studies of C. acetobutylicum, summarize the recent application of quantitative/integrated omics approaches to the physiological analysis and metabolic engineering of this bacterium, and provide directions for future studies to address current challenges.
Published: 2020

29. Synthetic Biology Applied to Carbon Conservative and Carbon Dioxide Recycling Pathways

Author: François, Jean marie, Lachaux, Cléa, Morin, Nicolas, 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), Toulouse White Biotechnology (TWB), French National Research Agency (ANR), Ministry of Research and Education (MENRT), 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), and Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: petroleum, changement climatique, analyse microbiologique, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, émission de gaz carbonique, Microbiology and Parasitology, Bioengineering and Biotechnology, carbon dioxide, chemicals, Biotechnologies, Review, Microbiologie et Parasitologie, microbial physiology, metabolic engineering, synthetic biology, bio-based products, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, pétrole, microbiological analysis, réchauffement climatique, global change
Abstract: The global warming conjugated with our reliance to petrol derived processes and products have raised strong concern about the future of our planet, asking urgently to find sustainable substitute solutions to decrease this reliance and annihilate this climate change mainly due to excess of CO2 emission. In this regard, the exploitation of microorganisms as microbial cell factories able to convert non-edible but renewable carbon sources into biofuels and commodity chemicals appears as an attractive solution. However, there is still a long way to go to make this solution economically viable and to introduce the use of microorganisms as one of the motor of the forthcoming bio-based economy. In this review, we address a scientific issue that must be challenged in order to improve the value of microbial organisms as cell factories. This issue is related to the capability of microbial systems to optimize carbon conservation during their metabolic processes. This initiative, which can be addressed nowadays using the advances in Synthetic Biology, should lead to an increase in products yield per carbon assimilated which is a key performance indice in biotechnological processes, as well as to indirectly contribute to a reduction of CO2 emission.
Published: 2020

30. A catalog of microbial genes from the bovine rumen unveils a specialized and diverse biomass-degrading environment

Author: Fang Li, Xun Xu, Cécile Martin, Weineng Chen, Diego P. Morgavi, Karsten Kristiansen, Fangming Yang, Huanming Yang, Milka Popova, Huanzi Zhong, Jiyang Li, Gabrielle Potocki-Véronèse, Vincent Lombard, Hui Zhang, Bernard Henrissat, Jing Wang, Bing Chen, Lise Madsen, Junhua Li, Emmanuelle Maguin, Nicolas Terrapon, Jing Guo, Yuliaxis Ramayo-Caldas, Ziyi Yang, Jordi Estellé, Shanmei Tang, Stanislav D Ehrlich, National University of Singapore (NUS), Beijing Genomics Institute [Shenzhen] (BGI), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Architecture et fonction des macromolécules biologiques (AFMB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), 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), Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Harbin Institute of Technology (HIT), Laboratoire de photonique et de nanostructures (LPN), China University of Mining and Technology (CUMT), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), University of Auckland [Auckland], Huazhong University of Science and Technology [Wuhan] (HUST), University of Copenhagen = Københavns Universitet (UCPH), Unité de recherche Génétique Microbienne (UGM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), European Union's Seventh Framework Program (FP/2007/2013)/European Research Council (ERC) Grant (322820), ANR-11-DPBS-0001,MGP,MetaGenoPolis(2011), Microbiota Interaction with Human and Animal (MIHA), Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay-AgroParisTech-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Méthodes et Algorithmes pour la Bioinformatique (MAB), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Conception et commande de robots pour la manipulation (DEXTER), University of Copenhagen = Københavns Universitet (KU), 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), Producció Animal, and Genètica i Millora Animal
Subjects: animal structures, Swine, [SDV]Life Sciences [q-bio], AcademicSubjects/SCI02254, Health Informatics, Computational biology, Genome, metagenome, 03 medical and health sciences, Rumen, Mice, Ruminant, Animals, Humans, Microbiome, Biomass, KEGG, Gene, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, rumen, biology, 030306 microbiology, herbivory, Research, Microbiota, bovine, Prokaryote, Drug Resistance, Microbial, 15. Life on land, biology.organism_classification, Computer Science Applications, Diet, Gastrointestinal Microbiome, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Metagenomics, carbohydrate-active enzymes, AcademicSubjects/SCI00960, Cattle, Digestion
Abstract: Background The rumen microbiota provides essential services to its host and, through its role in ruminant production, contributes to human nutrition and food security. A thorough knowledge of the genetic potential of rumen microbes will provide opportunities for improving the sustainability of ruminant production systems. The availability of gene reference catalogs from gut microbiomes has advanced the understanding of the role of the microbiota in health and disease in humans and other mammals. In this work, we established a catalog of reference prokaryote genes from the bovine rumen. Results Using deep metagenome sequencing we identified 13,825,880 non-redundant prokaryote genes from the bovine rumen. Compared to human, pig, and mouse gut metagenome catalogs, the rumen is larger and richer in functions and microbial species associated with the degradation of plant cell wall material and production of methane. Genes encoding enzymes catalyzing the breakdown of plant polysaccharides showed a particularly high richness that is otherwise impossible to infer from available genomes or shallow metagenomics sequencing. The catalog expands the dataset of carbohydrate-degrading enzymes described in the rumen. Using an independent dataset from a group of 77 cattle fed 4 common dietary regimes, we found that only Conclusions These data bring new insights into functions, carbohydrate-degrading enzymes, and microbes of the rumen to complement the available information on microbial genomes. The catalog is a significant biological resource enabling deeper understanding of phenotypes and biological processes and will be expanded as new data are made available.
Published: 2020

31. An optical in-situ tool for visualizing and understanding wetting dynamics in membrane distillation

Author: Paul Jacob, Corinne Cabassud, Baptiste Dejean, Stéphanie Laborie, Toulouse Biotechnology Institute (TBI), 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-14-CE04-0008,WETMEM,Nouvelles membranes et outils pour une meilleure compréhension, modélisation et contrôle du mouillage de pores en distillation membranaire pour le dessalement des eaux(2014), 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), UMR TBI, CNRS, INRA, INSA, Université de Toulouse, French National Research Agency (ANR) [ANR-14-CE04-0008], 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: Materials science, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Scanning electron microscope, membrane distillation, Filtration and Separation, 02 engineering and technology, 010402 general chemistry, Membrane distillation, 01 natural sciences, Biochemistry, microscopie électronique à balayage, [SPI]Engineering Sciences [physics], TRACER, tensioactif, General Materials Science, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Physical and Theoretical Chemistry, Spectroscopy, optical tool, transmission lumineuse, wetting, in situ, Laminar flow, 021001 nanoscience & nanotechnology, 0104 chemical sciences, in-situ detection, Membrane, [CHIM.POLY]Chemical Sciences/Polymers, Chemical engineering, SEM, [SPI.OPTI]Engineering Sciences [physics]/Optics / Photonic, Wetting, 0210 nano-technology, Dispersion (chemistry)
Abstract: This paper describes the development of a new optical tool to detect in-situ wetting in membrane distillation. The principle of the detection tool is based on the phenomenon of light transmission. A dedicated experimental setup was developed. The proof of concept of this optical tool is validated using in parallel the Detection of Dissolved Tracer Intrusion (DDTI) method that was previously developed, and which is based on the detection of remaining salt traces in wetted pores by scanning electron microscopy and x-ray dispersion spectroscopy. The in-situ tool was used in standard operating conditions (feed temperature 40 °C, laminar flow and vacuum pressure 6 kPa) for vacuum membrane distillation with deionized water, a synthetic saline solution, and seawaters. Controlled wetting was then induced by adding a surfactant in the feed after 30 min of operation and wetting dynamics could be effectively visualized. Additionally, the scalability (macro and mesoscales) of this tool was verified and wetting was visualized at different locations on the membrane surface and compared with the wetting observations made at a global scale. A definition of pore wetting is also proposed.
Published: 2020

32. Demonstration of Electrically Injected Semipolar Laser Diodes Grown on Low-Cost and Scalable Sapphire Substrates

Author: Bastien Bonef, Daniel Cohen, James S. Speck, Philippe De Mierry, Matthew S. Wong, Feng Wu, Shuji Nakamura, Philippe Vennéguès, Haojun Zhang, Michel Khoury, Steven P. DenBaars, Hongjian Li, Department of Computer Science and Engineering [Hong Kong, China], The Chinese University of Hong Kong [Hong Kong], 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 d'Etude des Matériaux par Microscopie Avancée (LEMMA), Modélisation et Exploration des Matériaux (MEM), 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)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université Panthéon-Assas (UP2), Centre de recherche sur l'hétéroepitaxie et ses applications (CRHEA), Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), University of California, COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), 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), University of California (UC), and Université Nice Sophia Antipolis (1965 - 2019) (UNS)
Subjects: 010302 applied physics, [PHYS]Physics [physics], Materials science, business.industry, Slope efficiency, 02 engineering and technology, 021001 nanoscience & nanotechnology, Laser, Polarization (waves), 7. Clean energy, 01 natural sciences, law.invention, Lidar, law, 0103 physical sciences, Scalability, Sapphire, Optoelectronics, General Materials Science, [PHYS.COND]Physics [physics]/Condensed Matter [cond-mat], 0210 nano-technology, business, Science, technology and society, ComputingMilieux_MISCELLANEOUS, Diode
Abstract: The last two decades have shown an increasing need for GaN-based laser diodes (LDs), which are currently only grown on bulk GaN substrates, which remain to date very expensive and/or only available in small sizes. The ever growing laser market will expand in the coming years, thanks to the development of automotive laser lighting, high-speed Li-Fi optical data transmission, LiDAR sensing for autonomous vehicles and smart cities, head-up displays, and AR/VR systems, in addition to biomedical and further industrial applications. These emerging technologies demand for mass-production of GaN-based lasers to be produced on large-size, low-cost, and industrially compatible substrates. To address this issue, we demonstrate the first electrically injected semipolar 440 nm LD on high-quality and low-defect-density (11-22) GaN templates grown on scalable and low-cost sapphire substrates. The LDs exhibit a threshold current density of 17 kA/cm2, a single facet output power of more than 200 mW at 2 A with a slope efficiency of 0.85 W/A, and a TE polarization having a ratio of 97.6%. These results enable the advancement of ultra-low-cost LDs while benefiting from the inherent advantages of semipolar GaN properties.
Published: 2019

33. Dynamic simulation of N2O emissions from a full-scale partial nitritation reactor

Author: Mathieu Spérandio, Mark C.M. van Loosdrecht, Eveline Volcke, K. E. Mampaey, Universiteit Gent = Ghent University [Belgium] (UGENT), 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), Delft University of Technology (TU Delft), Ghent University [Belgium] (UGENT), Symbiose : Ecosystèmes microbiens et bioprocédés d’épuration et de valorisation (TBI-SYMBIOSE), Toulouse Biotechnology Institute (TBI), 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Biotechnology, Department of Biosystems Engineering [Ghent], Universiteit Gent = Ghent University (UGENT), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), 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: 0106 biological sciences, Environmental Engineering, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, [SDV]Life Sciences [q-bio], Biomedical Engineering, Heterotroph, Digester effluent, Bioengineering, Wastewater treatment, 01 natural sciences, Greenhouse gas emission, 03 medical and health sciences, chemistry.chemical_compound, Denitrifying bacteria, 010608 biotechnology, Ammonium, Biological nitrogen removal, Effluent, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Nitrous oxide, Pulp and paper industry, equipment and supplies, Anoxic waters, 6. Clean water, Wastewater, chemistry, 13. Climate action, Environmental science, Aeration, Dynamic simulation, Biotechnology
Abstract: International audience; This study deals with the potential and the limitations of dynamic models for describing and predicting nitrous oxide (N2O) emissions associated with biological nitrogen removal from wastewater. The results of a three-week monitoring campaign on a full-scale partial nitritation reactor were reproduced through a state-of-the-art model including different biological N2O formation pathways. The partial nitritation reactor under study was a SHARON reactor treating the effluent from a municipal wastewater treatment plant sludge digester. A qualitative and quantitative comparison between experimental data and simulation results was performed to identify N2O formation pathways as well as for model identification. Heterotrophic denitrifying bacteria and ammonium oxidizing bacteria (AOB) were responsible for N2O formation under anoxic conditions, whereas under aerated conditions the AOB were the most important N2O producers. Relative to previously proposed models, hydroxylamine (NH2OH) had to be included as a state variable in the AOB conversions in order to describe potential N2O formation by AOB under anoxic conditions. An oxygen inhibition term in the corresponding reaction kinetics was required to fairly represent the relative contribution of the different AOB pathways for N2O production. Nevertheless, quantitative prediction of N2O emissions with models remains a challenge, which is discussed.
Published: 2019

34. 3D analysis of the whole subcutaneous adipose tissue reveals a complex spatial network of interconnected lobules with heterogeneous browning ability

Author: Audrey Carrière, Yves Martinez, Luc Pénicaud, Franck Plouraboué, Jacques Rouquette, Anne Lorsignol, Christophe Guissard, Louis Casteilla, Jules Dichamp, Xavier Descombes, Corinne Barreau, Institut de mécanique des fluides de Toulouse (IMFT), 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, STROMALab, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), 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-Institut National de la Santé et de la Recherche Médicale (INSERM)-Etablissement Français du Sang-Centre National de la Recherche Scientifique (CNRS), Neurobiologie, plasticité tissulaire et métabolisme énergétique (NPTME), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Fédération de Recherche Agrobiosciences, Interactions et Biodiversité (FR AIB), Morphologie et Images (MORPHEME), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut de Biologie Valrose (IBV), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Signal, Images et Systèmes (Laboratoire I3S - SIS), Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis (I3S), Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis (I3S), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National de la Santé et de la Recherche Médicale (INSERM)-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 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 des Technologies Avancées en sciences du Vivant (ITAV), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Signal, Images et Systèmes (Laboratoire I3S - SIS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis (I3S), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), BIGNAU, Suzy, Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Etablissement Français du Sang-Institut National de la Santé et de la Recherche Médicale (INSERM), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)-Signal, Images et Systèmes (Laboratoire I3S - SIS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), 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)-Université Toulouse III - Paul Sabatier (UT3), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Centre National de la Recherche Scientifique - CNRS (FRANCE), Etablissement Français du Sang - EFS Midi-Pyrénées (FRANCE), Ecole Nationale Vétérinaire de Toulouse - ENVT (FRANCE), Institut National Polytechnique de Toulouse - INPT (FRANCE), Institut National de la Santé et de la Recherche Médicale - INSERM (FRANCE), Université Nice Sophia Antipolis (FRANCE), Université Toulouse III - Paul Sabatier - UT3 (FRANCE), Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), 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), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Etablissement Français du Sang-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), and Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: 0301 basic medicine, Cell type, 3D analysis, [SDV.MHEP.PHY] Life Sciences [q-bio]/Human health and pathology/Tissues and Organs [q-bio.TO], Confocal, [SDV]Life Sciences [q-bio], Subcutaneous Fat, Adipose tissue, Fluorescent Antibody Technique, lcsh:Medicine, Network, Lobules, heterogeneous browning ability, Biology, Fat pad, Article, law.invention, whole subcutaneous adipose tissue, 03 medical and health sciences, 0302 clinical medicine, Imaging, Three-Dimensional, Image processing, Confocal microscopy, law, Adipocytes, Image Processing, Computer-Assisted, [SDV.MHEP.PHY]Life Sciences [q-bio]/Human health and pathology/Tissues and Organs [q-bio.TO], Humans, lcsh:Science, Process (anatomy), Multidisciplinary, Microscopy, Confocal, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, Mesenchymal stem cell, lcsh:R, Soft tissue, Lipid Metabolism, Cell biology, [SDV] Life Sciences [q-bio], 030104 developmental biology, Biologie cellulaire, lcsh:Q, Browning, Fat metabolism, 030217 neurology & neurosurgery, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, 3D
Abstract: Adipose tissue, as the main energy storage organ and through its endocrine activity, is interconnected with all physiological functions. It plays a fundamental role in energy homeostasis and in the development of metabolic disorders. Up to now, this tissue has been analysed as a pool of different cell types with very little attention paid to the organization and putative partitioning of cells. Considering the absence of a complete picture of the intimate architecture of this large soft tissue, we developed a method that combines tissue clearing, acquisition of autofluorescence or lectin signals by confocal microscopy, segmentation procedures based on contrast enhancement, and a new semi-automatic image analysis process, allowing accurate and quantitative characterization of the whole 3D fat pad organization. This approach revealed the unexpected anatomic complexity of the murine subcutaneous fat pad. Although the classical picture of adipose tissue corresponds to a superposition of simple and small ellipsoidal lobules of adipose cells separated by mesenchymal spans, our results show that segmented lobules display complex 3D poly-lobular shapes. Despite differences in shape and size, the number of these poly-lobular subunits is similar from one fat pad to another. Finally, investigation of the relationships of these subunits between each other revealed a never-described organization in two clusters with distinct molecular signatures and specific vascular and sympathetic nerve densities correlating with different browning abilities. This innovative procedure reveals that subcutaneous adipose tissue exhibits a subtle functional heterogeneity with partitioned areas, and opens new perspectives towards understanding its functioning and plasticity.
Published: 2019

35. 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

36. A tool to operationalize dynamic LCA, including time differentiation on the complete background database

Author: Tomás Navarrete Gutiérrez, Yoann Pigné, Ligia Tiruta-Barna, Emil Popovici, Thomas Schaubroeck, Enrico Benetto, Allan Hayato Shimako, Thomas Gibon, Equipe Réseaux d'interactions et Intelligence Collective (RI2C - LITIS), Laboratoire d'Informatique, de Traitement de l'Information et des Systèmes (LITIS), 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)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Normandie Université (NU), Luxembourg Institute of Science and Technology (LIST), 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), ANR-13-IS09-0007,DyPLCA,Evaluation environnementale des procédés en fonctionnement dynamique – prise en compte du temps dans la méthode d'Analyse du Cycle de Vie(2013), Université Le Havre Normandie (ULH), Normandie Université (NU)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Université Le Havre Normandie (ULH), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), 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: Temporal database, Computer science, 020209 energy, [INFO.INFO-DS]Computer Science [cs]/Data Structures and Algorithms [cs.DS], 02 engineering and technology, 010501 environmental sciences, computer.software_genre, Graph search, 7. Clean energy, 01 natural sciences, Graph traversal, 0202 electrical engineering, electronic engineering, information engineering, Production (economics), Dynamic LCA, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, General Environmental Science, Upstream (petroleum industry), Discounting, Operationalization, Database, [SDE.IE]Environmental Sciences/Environmental Engineering, Integrated software, Temporally differentiated, LCI, LCIA, Electricity generation, 13. Climate action, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, computer, Dynamic modeling
Abstract: Purpose The objective is to demonstrate an operational tool for dynamic LCA, based on the model by Tiruta-Barna et al. (J Clean Prod 116:198-206, Tiruta-Barna et al. 2016). The main innovation lies in the combination of full temporalization of the background inventory and a graph search algorithm leading to full dynamic LCI, further coupled to dynamic LCIA. The following objectives were addressed: (1) development of a database with temporal parameters for all processes of ecoinvent 3.2, (2) implementation of the model and the database in integrated software, and (3) demonstration on a case study comparing a conventional internal combustion engine car to an electric one. Methods Calculation of dynamic LCA (including temporalization of background and foreground system) implies (i) a dynamic LCI model, (ii) a temporal database including temporal characterization of ecoinvent 3.2, (iii) a graph search algorithm, and (iv) dynamic LCIA models, in this specific case for climate change. The dynamic LCI model relies on a supply chain modeling perspective, instead of an accounting one. Unit processes are operations showing a specific functioning over time. Mass and energy exchanges depend on specific supply models. Production and supply are described by temporal parameters and functions. The graph search algorithm implements the dynamic LCI model, using the temporal database, to derive the life cycle environmental interventions scaled to the functional unit and distributed over time. The interventions are further combined with the dynamic LCIA models to obtain the temporally differentiated LCA results. Results and discussion A web-based tool for dynamic LCA calculations (DyPLCA) implementing the dynamic LCI model and temporal database was developed. The tool is operational and available for testing (http://dyplca.univ-lehavre.fr/). The case study showed that temporal characterization of background LCI can change significantly the LCA results. It is fair to say that temporally differentiated LCI in the background offers little interest for activities with high downstream emissions. It can provide insightful results when applied to life cycle systems where significant environmental interventions occur upstream. Those systems concern, for example, renewable electricity generation, for which most emissions are embodied in an infrastructure upstream. It is also observed that a higher degree of infrastructure contribution leads to higher spreading of impacts over time. Finally, a potential impact of the time window choice and discounting was observed in the case study, for comparison and decision-making. Time differentiation as a whole may thus influence the conclusions of a study. Conclusions The feasibility of dynamic LCA, including full temporalization of background system, was demonstrated through the development of a web-based tool and temporal database. It was showed that considering temporal differentiation across the complete life cycle, especially in the background system, can significantly change the LCA results. This is particularly relevant for product systems showing significant environmental interventions and material exchanges over long time periods upstream to the functional unit. A number of inherent limitations were discussed and shall be considered as opportunities for further research. This requires a collegial effort, involving industrial experts from different sectors.
Published: 2019

37. Guaranteed Diversity & Quality for the Weighted CSP

Author: Jelena Vucinic, Sophie Barbe, Simon de Givry, George Katsirelos, Thomas Schiex, Manon Ruffini, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Mathématiques et Informatique Appliquées (MIA-Paris), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-AgroParisTech-Université Paris-Saclay, 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), Funded by the Agence Nationale de la Recherche, ANR-16-CE40-002, ANR-19-PIA3-0004, ANR-16-CE40-0028,DE-MO-GRAPH,Décomposition de Modèles Graphiques(2016), ANR-19-P3IA-0004,ANITI,Artificial and Natural Intelligence Toulouse Institute(2019), Institut National de la Recherche Agronomique (INRA), Toulouse Biotechnology Institute (TBI), 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), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, contrat REGION doctorant TOULOUZETA n° 00000950-CT15000449, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE), Mathématiques et Informatique Appliquées (MIA Paris-Saclay), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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: Protein Design, Mathematical optimization, Computer science, Bioinformatics, [SDV]Life Sciences [q-bio], 02 engineering and technology, 010501 environmental sciences, 01 natural sciences, Constraint Programming, Set (abstract data type), CONSISTENCY, [SDV.IDA]Life Sciences [q-bio]/Food engineering, 0202 electrical engineering, electronic engineering, information engineering, Constraint programming, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, [INFO]Computer Science [cs], COMPUTATIONAL PROTEIN DESIGN, [MATH]Mathematics [math], OPTIMIZATION, Constraint satisfaction problem, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, Soft Arc Consistency, Diversity, Bayesian network, Function (mathematics), CONSTRAINT, Dual and Hidden representation, Weighted Constraint Satisfaction Problem, Semi-metric, Bounded function, [SDE]Environmental Sciences, 020201 artificial intelligence & image processing
Abstract: International audience; In many applications of constraint programming, it is often impossible to capture all the relevant information in one numerical criterion. In this case, it is useful to produce a set of high quality yet diverse solutions. In this paper, motivated by a Computational Protein Design application, we consider the general problem of producing a diverse set of high-quality solutions of a given Weighted Constraint Satisfaction Problem, with guarantees both on solution quality and diversity. We use weighted automata decomposed in functions of bounded arity, incremental CFN solving, a simple form of predictive bounding and compressed representations of distance constraints for improved efficiency. We show that this approach can be successfully applied to a variety of problems that include both Protein Design Problems but also large Bayesian networks represented as Cost Function Networks. We also show that our approach has the capacity to enumerate so-called local delta-modes and that it does provide improved protein designs.
Published: 2019

38. Flow investigation in an innovating dynamic filtration module using tracing methods

Author: Christophe Andre, Xiaomin Xie, Luc Fillaudeau, Nicolas Dietrich, Philippe Schmitz, 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), Toulouse Biotechnology Institute (TBI), China Scholarship Council, 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), and Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: residence time distribution, Turbulence, Flow (psychology), Filtration and Separation, Laminar flow, 02 engineering and technology, Mechanics, systemic approach, 021001 nanoscience & nanotechnology, Residence time distribution, [SDE.ES]Environmental Sciences/Environmental and Society, Analytical Chemistry, Volumetric flow rate, law.invention, modelling, Impeller, Distribution function, [CHIM.GENI]Chemical Sciences/Chemical engineering, 020401 chemical engineering, law, Environmental science, 0204 chemical engineering, dynamic filtration, 0210 nano-technology, Filtration
Abstract: International audience; Residence Time Distribution (RTD) experiments were carried out under laminar and turbulent 43regimesin a complex dynamic filtration module, named Rotating and Vibrating Filtration (RVF). 44This filtration module,dedicated to bioprocess intensification and downstream processing,45consists of two filtration cells in series in which a three-blade impeller rotates between twoflat46membranes.47Ourobjectivesareto improve filtration and overall industrial bioprocess performancesby (i) 48deeply understandingthe flow behaviourwithin RVF modulesand (ii) characterizing and 49modellingthe RTD througha systemic analysisand (iii) identifying critical operating conditions 50with microbial cells.51Analytical study of distribution functions was conductedand statistical moments were calculated 52and discussed. This study providesuseful recommendations, guidelines byidentifyingefficient 53volume (functioning area), dead zone volume (dysfunctioningarea). The influence of operating 54parameters (mixing rateNand flow rate Qf) on the mean residence time,tswerehighlighted. The 55systemic analysis led to compare threemodelswith analytical solutions. Finally, a simple model 56allowing the description of the evolution of the RTD of the studied filtration module was 57 proposed.
Published: 2019

39. Adaptive response of yeast cells to triggered toxicity of phosphoribulokinase

Author: Catherine Rouzeau, Jean Baudry, Krzysztof Langer, Véronique Anton-Leberre, Jérôme Bibette, Denis Pompon, Adilya Dagkesamanskaya, 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 Colloïdes et Matériaux Divisés (LCMD), ESPCI ParisTech-Centre National de la Recherche Scientifique (CNRS), ANR-14-CE08-0008,DYNAMETAFLUID,Analyse dynamique de l’adaptation génétique d’un microbe à une ingénierie à l’aide d’un dispositif micro-fluidique d’analyse métabolique(2014), Centre National de la Recherche Scientifique (CNRS)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), ANR-14-CE08-0008,DYNAMETAFLUID,Analyse dynamique de l'adaptation génétique d'un microbe à une ingénierie à l'aide d'un dispositif micro-fluidique d'analyse métabolique(2014), 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), Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, cell toxicity response, [SDV]Life Sciences [q-bio], Gene Dosage, Saccharomyces cerevisiae, Microbiology, Metabolic engineering, Amino Acids, Aromatic, 03 medical and health sciences, Plasmid, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, plasmid burden, Molecular Biology, Gene, population heterogeneity, biology, Phosphoribulokinase, RuBisCO, General Medicine, Adaptation, Physiological, Yeast, Anti-Bacterial Agents, Cell biology, Complementation, Phosphotransferases (Alcohol Group Acceptor), 030104 developmental biology, Metabolic Engineering, Doxycycline, biology.protein, Expression cassette, Plasmids
Abstract: Adjustment of plasmid copy number resulting from the balance between positive and negative impacts of borne synthetic genes, plays a critical role in the global efficiency of multistep metabolic engineering. Differential expression of co-expressed engineered genes is frequently observed depending on growth phases, metabolic status and triggered adjustments of plasmid copy numbers, constituting a dynamic process contributing to minimize global engineering burden. A yeast model involving plasmid based expression of phosphoribulokinase (PRKp), a key enzyme for the reconstruction of synthetic Calvin cycle, was designed to gain further insights into such a mechanism. A conditional PRK expression cassette was cloned either onto a low (ARS-CEN based) or a high (2-micron origin based) copy number plasmid using complementation of a trp1 genomic mutation as constant positive selection. Evolution of plasmid copy numbers, PRKp expressions, and cell growth rates were dynamically monitored following gene de-repression through external doxycycline concentration shifts. In the absence of RubisCO encoding gene permitting metabolic recycling, PRKp expression that led to depletion of ribulose phosphate, a critical metabolite for aromatic amino-acids biosynthesis, and accumulation of the dead-end diphosphate product contribute to toxicity. Triggered copy number adjustment was found to be a dynamic process depending both on plasmid types and levels of PRK induction. With the ARS-CEN plasmid, cell growth was abruptly affected only when level PRKp expression exceeded a threshold value. In contrast, a proportional relationship was observed with the 2-micron plasmid consistent with large copy number adjustments. Micro-compartment partitioning of bulk cultures by embedding individual cells into inverse culture medium/oil droplets, revealed the presence of slow and fast growing subpopulations that differ in relative proportions for low and high copy number plasmids.
Published: 2018

40. Efficient in vivo synthesis of lasso peptide pseudomycoidin proceeds in the absence of both the leader and the leader peptidase

Author: Zyubko, Tatyana, Serebryakova, Marina, Andreeva, Julia, Metelev, Mikhail, Lippens, Guy, Dubiley, Svetlana, Severinov, Konstantin, 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), Institutes of Molecular Genetics and Gene Biology, Russian Academy of Sciences [Moscow] (RAS), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), 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: [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2019

41. Modelling PAHs removal in activated sludge process: effect of disintegration

Author: Yolaine Bessiere, Evrard Mengelle, I. Mozo, Nicolas Lesage, Mathieu Spérandio, Mansour Bounouba, Centre scientifique et Technique Jean Feger (CSTJF), TOTAL FINA ELF, 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 National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), 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: sonication, Environmental Engineering, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, 0208 environmental biotechnology, 02 engineering and technology, 010501 environmental sciences, micropollutants, 01 natural sciences, biodegradation, bioreactor, Adsorption, Bioreactors, polycyclic aromatic hydrocarbon, Polycyclic Aromatic Hydrocarbons, 0105 earth and related environmental sciences, Water Science and Technology, Pollutant, Sewage, Chemistry, Biodegradation, 020801 environmental engineering, Waste treatment, wastewater treatment, Activated sludge, Wastewater, Environmental chemistry, Water treatment, Sewage treatment
Abstract: The removal of polycyclic aromatic hydrocarbons (PAHs) in activated sludge was evaluated using two laboratory-scale bioreactors, coupled or not with a disintegration system (sonication). Mass balances performed on each system underlined that PAHs removal was significantly improved after sludge disintegration, especially for the higher molecular weight PAHs studied, which tended to adsorb to suspended matter. A model was developed in order to study the effect of sludge disintegration on the content of dissolved and colloidal matter (DCM), and to predict the potential impacts on PAHs availability and degradation. Results showed that this new model was efficient for capturing apparent degradation improvement trends and for discriminating between the involved mechanisms. This study showed that DCM content increased after sludge disintegration, and proved to be the main driver for improving PAHs apparent degradation.
Published: 2019

42. Performance of a monofiber optical probe in determining the droplet size and velocity in spray systems comparing with a high-speed camera

Author: Gilles Hébrard, Kritchart Wongwailikhit, Nicolas Dietrich, Pisut Painmanakul, Department of Environmental Engineering, Faculty of Engineering, Chulalongkorn University [Bangkok], Toulouse Biotechnology Institute (TBI), 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), 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), 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: Work (thermodynamics), Materials science, Liquid fraction, business.industry, General Chemical Engineering, 02 engineering and technology, General Chemistry, 021001 nanoscience & nanotechnology, Collision, Optical fiber probe, [SDE.ES]Environmental Sciences/Environmental and Society, Industrial and Manufacturing Engineering, Spray nozzle, Physics::Fluid Dynamics, Droplet coalescence, Optics, [CHIM.GENI]Chemical Sciences/Chemical engineering, 020401 chemical engineering, 0204 chemical engineering, 0210 nano-technology, business, Size determination, Droplet size, ComputingMilieux_MISCELLANEOUS
Abstract: Optical fiber probe has been recently developed for characterizing the liquid dispersed in gas in droplet form, but its performance has yet been identified for an actual spray system. This work aims to compare the performance of a monofiber optical probe in characterizing the hydrodynamics in spray systems with that of a high-speed camera. Initially, both techniques determined the same series of droplets produced by a syringe. The droplet velocities and sizes obtained from the optical probe were in accordance with the high-speed camera when the droplet coalescence was filtered out from the data. Second, a full-cone spray nozzle was used and the average velocities from the two techniques were close, but the off-center collision on the probe and the difference in size limits caused the discrepancy in the size determination. However, the probe is still beneficial to determine the droplet hydrodynamics and local liquid fraction, the essential characteristics of a spray system.
Published: 2019

43. Effet de la température sur les interactions et le comportement rhéologique de dispersions de micelles de caséines concentrées

Author: Doudies, Floriane, Arsene, Anne-Sophie, Famelart, Marie-Hélène, Lambrouin, Fabienne, Bouchoux, Antoine, Pignon, F., Gesan-Guiziou, Genevieve, Science et Technologie du Lait et de l'Oeuf (STLO), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Laboratoire Rhéologie et Procédés (LRP), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), 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), 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), Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Université Grenoble Alpes (UGA), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), and Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA)
Subjects: protéine de lait, sol gel transition, température, [SDV.IDA]Life Sciences [q-bio]/Food engineering, compressibilité, elastic modulus, rhéologie, micelle de caséine, transition sol-gel, rheology, transition sol gel, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition
Abstract: Les caséines sont présentes dans le lait sous forme de micelles qui s'apparentent à des agrégats colloïdaux poreux, déformables et compressibles [1,2]. La compréhension des propriétés de ces objets et des interactions qu’ils bâtissent (i.e. compressibilité, transition sol-gel, cohésion des gels) en fonction de leur concentration est nécessaire à la compréhension des phénomènes de colmatage qui gouvernent les performances des opérations de filtration du lait largement utilisées industriellement. En effet, lors de la mise en œuvre du procédé de séparation membranaire destiné à séparer les micelles de caséines des protéines sériques et d'autres espèces moléculaires, les micelles se concentrent au voisinage de la membrane. Cette accumulation de matière entraîne une diminution du flux de perméation et de la transmission des protéines sériques. Les propriétés de compressibilité des micelles et de viscoélasticité de leur dispersion concentrée en relation avec les mécanismes de structuration induits lors de l'augmentation de leur concentration, ont été étudiées par compression osmotique et par rhéométrie à 20°C [3-5]. Les dispersions de micelles de caséines présentent une transition sol-gel à une concentration de gélification (Cgel) de 170-180 g/L à 20°C [3-5]. Déterminer cette Cgel permet de définir des conditions de filtration limitant le colmatage des membranes [6]. Actuellement, l’utilisation de membranes organiques spiralées à basse température (≈8-12°C) pour la filtration de lait rencontre un succès grandissant. Il est connu que la dynamique, la structure et la composition chimique des micelles de caséines évoluent avec la température [2], mais peu d’études de son comportement à basse température en milieu concentré ont été réalisées [7]. Il est donc nécessaire d’élucider l’influence des basses températures sur la compression, la structure et la transition sol-gel des dispersions de micelles de caséines concentrées afin d'améliorer notre connaissance des conditions optimales de filtration du lait à basse température. Le but de ce travail est d’analyser l’influence de la température sur les interactions et le comportement rhéologique (i.e. compressibilité, comportement d’écoulement, transition sol-gel, cohésion des gels) des dispersions de micelles de caséines concentrées. Les expériences ont été menées à 7°C et 20°C. Des dispersions de micelles de caséines à différentes concentrations (de 25 à 700 g/L) ont été préparées, soit par dispersion de poudre d’isolat de micelles de caséines, soit par compression osmotique. La compressibilité des micelles de caséines a été caractérisée par des expériences de compression osmotique (de 0.01 à 13 bar). La transition sol-gel a été caractérisée par rhéométrie via des mesures d’écoulement et de cisaillement harmonique. Les deux techniques utilisées apportent également des informations sur les interactions micelle-micelle. Une équation d’état de la pression osmotique en fonction de la concentration en caséine a été déterminée à 7°C : il a été mis en évidence que la compressibilité, c’est-à-dire la concentration atteinte à une pression osmotique donnée des micelles de caséines augmente quand la température augmente de 7°C à 20°C. Par exemple pour atteindre une concentration de 450 g/L, il faut appliquer une pression osmotique de 2.6 bar à 7°C contre 1 bar à 20°C. De plus, la transition sol-gel à 7°C est observée à 150 g/L (correspondant à une compression de 0.18 bar) contre 170 g/L (correspondant à une compression de 0.073 bar) à 20°C. Les micelles de caséines sont plus hydratées et ont donc une plus forte voluminosité [7] à basse température, elles s’opposent davantage à la compression, mais elles interagissent et gélifient à plus faible concentration qu’à 20°C. Ces résultats mettent en avant la nécessité d'une modification de la conduite des protocoles de filtration appliqués lors du fonctionnement de ce procédé à basse température, afin de maintenir des performances équivalentes à celles actuellement obtenues à température élevées.
Published: 2019

44. A computational study of the molecular basis of antibiotic resistance in a DXR mutant

Author: Fanny S. Krebs, Jérémy Esque, Roland H. Stote, Institut de Chimie de Strasbourg, Université de Strasbourg (UNISTRA)-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 Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), 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: Protein Conformation, Mutant, Molecular Dynamics Simulation, Ligands, 010402 general chemistry, medicine.disease_cause, 01 natural sciences, Molecular mechanics, Mycobacterium tuberculosis, 03 medical and health sciences, Fosfomycin, [SDV.SP.MED]Life Sciences [q-bio]/Pharmaceutical sciences/Medication, Mutant protein, Drug Discovery, Escherichia coli, medicine, Physical and Theoretical Chemistry, Aldose-Ketose Isomerases, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Pentosephosphates, 0303 health sciences, Mutation, Binding Sites, biology, Chemistry, Point mutation, Drug Resistance, Microbial, Models, Theoretical, biology.organism_classification, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Fosmidomycin, Anti-Bacterial Agents, 0104 chemical sciences, 3. Good health, Computer Science Applications, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Biochemistry, Mevalonate pathway, medicine.drug
Abstract: Proteins of the independent mevalonate pathway for isoprenoid biosynthesis are important targets for the development of new antibacterial compounds as this pathway is present in most pathogenic organisms such as Mycobacterium tuberculosis, DPlasmodium falciparum and Escherichia coli, but is not present in mammalian species, including humans. Deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) is an important target in this pathway and the most effective DXR inhibitor to date is fosmidomycin, which is used to treat malaria and, more recently, tuberculosis. Recently, Armstrong C. M. et al. showed that a mutant of DXR, S222T, induces a loss of the fosmidomycin inhibition efficiency, even though the bacteria culture is still viable and able to produce isoprenoids. As this represents a potential fosmidomycin-resistant mutation, it is important to understand the mechanism of this apparent mutation-induced resistance to fosmidomycin. Here, we used molecular dynamics simulations and Molecular Mechanics/Poisson Boltzmann Surface Area analysis to understand the structural and energetic basis of the resistance. Our results suggest that the point mutation results in changes to the structural dynamics of an active site loop that probably protects the active site and facilitates enzymatic reaction. From the simulation analysis, we also showed that the mutation results in changes in the interaction energy profiles in a way that can explain the observed activity of the mutant protein toward the natural inhibitor deoxy-D-xylulose 5-phosphate. These results should be taken into consideration in future efforts to develop new therapeutic antibiotic compounds that target DXR.
Published: 2019

45. Multivalent Metallosupramolecular Assemblies as Effective DNA Binding Agents

Author: Sébastien Ulrich, Xiao-Yu Cao, Yannick Bessin, Wojciech Drożdż, Jean-Marie Lehn, Virginie Gervais, Artur R. Stefankiewicz, Anna Walczak, Centre de Biochimie Structurale [Montpellier] (CBS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire 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 Science et d'ingénierie supramoléculaires (ISIS), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Adam Mickiewicz University in Poznań (UAM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut des Biomolécules Max Mousseron [Pôle Chimie Balard] (IBMM), Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Institut de Chimie du CNRS (INC)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), 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 Strasbourg (UNISTRA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et Nanosciences Grand-Est (MNGE), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), and Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS)
Subjects: chemistry.chemical_element, Antineoplastic Agents, Zinc, Calorimetry, Crystallography, X-Ray, 010402 general chemistry, 01 natural sciences, Catalysis, Coordination complex, chemistry.chemical_compound, Cations, [CHIM]Chemical Sciences, ComputingMilieux_MISCELLANEOUS, chemistry.chemical_classification, Gel electrophoresis, 010405 organic chemistry, Organic Chemistry, Cationic polymerization, Isothermal titration calorimetry, DNA, General Chemistry, Nuclear magnetic resonance spectroscopy, Combinatorial chemistry, 0104 chemical sciences, 3. Good health, chemistry, Self-assembly
Abstract: We report the implementation of coordination chemistry onto the generation of new types of metallosupramolecular complexes with laterally appended cationic moieties for DNA binding in buffered aqueous media. Utilization of an N,N,O-type coordination pocket along with an octahedral zinc(II) metal ion allowed us to obtain mono- and tetranuclear complexes in both solution and solid state, as confirmed by NMR spectroscopy and single-crystal X-ray diffraction, respectively. By using isothermal titration calorimetry and gel electrophoresis, multiply charged cationic assemblies were observed to effectively bind to DNA through multivalent electrostatic interactions. Furthermore, we observed a correlation between the multivalency of the compounds employed and the effectiveness of DNA binding.
Published: 2018

46. Local hydrodynamics investigation within a dynamic filtration unit under laminar flow

Author: Nicolas Dietrich, Alain Liné, Xiaomin Xie, Philippe Schmitz, Luc Fillaudeau, C. Le Men, 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), China Scholarship Council [201304490066], 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: [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Materials science, General Chemical Engineering, Proper Orthogonal Decomposition, hydrodynamique, 02 engineering and technology, Viscous liquid, law.invention, Physics::Fluid Dynamics, Impeller, 020401 chemical engineering, law, Shear stress, Newtonian fluid, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Mean flow, 0204 chemical engineering, Filtration, Wall shear stress and torque, filtration, seepage, Laminar flow, General Chemistry, Mechanics, 021001 nanoscience & nanotechnology, 6. Clean water, Particle Image Velocimetry, Particle image velocimetry, 0210 nano-technology, Hydrodynamics of Dynamic Filtration Unit
Abstract: Conference: 9th International Symposium on Mixing in Industrial ProcessesLocation: Birmingham, ENGLANDDate: JUN 25-28, 2017; A dynamic filtration module, called a Rotating and Vibrating Filtration (R.V.F.) module, was designed and dedicated to the treatment of highly viscous fluid, such as fermentation broth or liquid food. To this end, an experimental study was undertaken, using a laminar flow regime with a viscous Newtonian model fluid in a dynamic filtration module in order to quantify the effect of local hydrodynamics on filtration. Instantaneous velocity fields can be measured and analyzed within an R.V.F. by using Particle Image Velocimetry (P.I.V.). In this study, we applied P.I.V. to study the laminar local hydrodynamics in 3 different slices within the 3 mm gap between the membrane and the impeller and 3 vertical slices at different radial positions, with rotation speeds from 0 to 10 Hz. Radial and vertical profiles of tangential velocity were then plotted. Proper Orthogonal Decomposition (P.O.D.) was applied to the P.I.V. data to discriminate between mean flow and fluctuating velocities induced by the periodic motion of the impeller. Thus, viscous shear stress profiles were deduced in terms of both mean shear stress profile and root mean squared (r.m.s.) fluctuating shear stress profile; wall values were then deduced. With this approach, we were able to quantify the distribution of viscous shear stress at the wall (membrane), in terms of mean value and r.m.s. contribution. Dynamic filtration efficiency was thus enlightened by local hydrodynamics. (C) 2018 Institution of Chemical Engineers.
Published: 2018

47. B Cells Producing Type I IFN Modulate Macrophage Polarization in Tuberculosis

Author: Andre G. Loxton, Pablo Schierloh, Ingrid Mercier, Jan Rehwinkel, Brigitte Gicquel, Véronique Anton-Leberre, Talal Al-Saati, María del Carmen Sasiain, Anne O'Garra, Pierre Boudinot, Ludovic Tailleux, Olivier Neyrolles, Roland Lang, André Colom, Stefan H. E. Kaufmann, Simon Fillatreau, Alan Bénard, Denis Hudrisier, Luc Jouneau, Imme Sakwa, Institut de pharmacologie et de biologie structurale (IPBS), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Immunometabolism and Macrophages in Tuberculosis/Human Immunodeficiency Virus-1 Co-infection (LIA IM-TB/HIV), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Academia Nacional de Medicina, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Deutsches Rheuma-ForschungsZentrum, Academia Nacional de Medicina, 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), Pathogénomique mycobactérienne intégrée, Institut Pasteur [Paris] (IP), Unité de recherche Virologie et Immunologie Moléculaires (VIM (UR 0892)), Institut National de la Recherche Agronomique (INRA), Centre Régional d'Exploration Fonctionnelle et Ressources Expérimentales (CREFRE), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), University of Oxford, Stellenbosch University, Max Planck Institute for Infection Biology (MPIIB), Max-Planck-Gesellschaft, Nationale Institute for Medical Research, Imperial College London, Deutsches RheumaForschungszentrum, Leibniz Institute - German Rheumatism Research Centre (DRFZ), Supported by Centre National de la Recherche Scientifique, University of Toulouse–Université Paul Sabatier, Institut Pasteur, Agence Nationale de la Recherche grants B-TB ANR-12-BSV3-0002 and ANR-11-EQUIPEX-0003 (O.N.), the European Union grants NEWTBVAC 241745 and TBVAC2020 643381 (O.N. and S.H.E.K.), grant ERA-INFECT ABIR (S.F. and S.H.E.K), the Bettencourt-Schueller Foundation, the Fondation pour la Recherche Médicale grant DEQ20160334902 (O.N.), and Deutsche Forschungsgemeinschaft grants SFB 796 and TP B6 (R.L.) and SFB TRR10 (S.F.). A.O’G. is funded by the Francis Crick Institute, which receives its core funding from Cancer Research UK (FC001126), the UK Medical Research Council (FC001126), and the Wellcome Trust (FC001126), by the UK Medical Research Council (MR/U117565642/1), and by the European Research Council (294682-TB-PATH). A.B. held a fellowship from the Fondation pour la Recherche Médicale., ANR-12-BSV3-0002,B-TB,Rôle des lymphocytes B dans l'immunité et l'inflammation tuberculeuse(2012), ANR-11-EQPX-0011,CRITEX,Parc national d'équipements innovants pour l'étude spatiale et temporelle de la Zone Critique des Bassins Versants(2011), European Project: 241745,EC:FP7:HEALTH,FP7-HEALTH-2009-single-stage,NEWTBVAC(2010), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Immunometabolism and Macrophages in Tuberculosis/Human Immunodeficiency Virus-1 Co-infection (IM-TB/HIV), 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 Pasteur [Paris], Unité de recherche Virologie et Immunologie Moléculaires (VIM), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Hôpital Purpan [Toulouse], CHU Toulouse [Toulouse], University of Oxford [Oxford], Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées
Subjects: 0301 basic medicine, Pulmonary and Respiratory Medicine, CIENCIAS MÉDICAS Y DE LA SALUD, Tuberculosis, [SDV]Life Sciences [q-bio], Inmunología, Macrophage polarization, TUBERCULOSIS, IFN, Critical Care and Intensive Care Medicine, Mice, 03 medical and health sciences, 0302 clinical medicine, medicine, Animals, Humans, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, MACROPHAGES, Lung, B-Lymphocytes, business.industry, Editorials, food and beverages, Mycobacterium tuberculosis, B LYMPHOCYTES, medicine.disease, Virology, macrophages, 3. Good health, Mice, Inbred C57BL, B-1 cell, Disease Models, Animal, Medicina Básica, 030104 developmental biology, tuberculosis, Interferon Type I, Immunology, business, Spleen, Function (biology), Signal Transduction, B lymphocytes, 030215 immunology
Abstract: In addition to their well-known function as antibody-producing cells, B lymphocytes can markedly influence the course of infectious or noninfectious diseases via antibody-independent mechanisms. In tuberculosis (TB), B cells accumulate in lungs, yet their functional contribution to the host response remains poorly understoo Fil: Bénard, Alan. Centre National de la Recherche Scientifique; Francia Fil: Sakwa, Imme. Leibniz - Institute Of Freshwater Ecology And Inland Fisheries; Alemania Fil: Schierloh, Luis Pablo. Instituto National de Recherches Agronomiques. Centre de Recherches de Toulouse; Francia. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Medicina Experimental. Academia Nacional de Medicina de Buenos Aires. Instituto de Medicina Experimental; Argentina Fil: Colom, André. Centre National de la Recherche Scientifique; Francia Fil: Mercier, Ingrid. Instituto National de Recherches Agronomiques. Centre de Recherches de Toulouse; Francia Fil: Tailleux, Ludovic. Instituto Pasteur; Francia Fil: Jouneau, Luc. Institut National de la Recherche Agronomique; Francia Fil: Boudinot, Pierre. Institut National de la Recherche Agronomique; Francia Fil: Al Saati, Talal. Université Paul Sabatier; Francia Fil: Lang, Roland. Universitat Erlangen-Nuremberg; Alemania Fil: Rehwinkel, Jan. University of Oxford; Reino Unido Fil: Loxton, Andre G.. Stellenbosch University; Sudáfrica Fil: Kaufmann, Stefan H. E.. Max Planck Institut für Infektionsbiologie; Alemania Fil: Anton Leberre, Veronique. Institut National de la Recherche Agronomique; Francia Fil: O'Garra, Anne. National Institute for Medical Research; Reino Unido Fil: Sasiain, María del Carmen. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Medicina Experimental. Academia Nacional de Medicina de Buenos Aires. Instituto de Medicina Experimental; Argentina Fil: Gicquel, Brigitte. Institut National de la Recherche Agronomique; Francia Fil: Fillatreau, Simon. Centre National de la Recherche Scientifique; Francia Fil: Neyrolles, Olivier. Centre National de la Recherche Scientifique; Francia Fil: Hudrisier, Denis. Centre National de la Recherche Scientifique; Francia
Published: 2018

48. Enrichment and adaptation yield high anammox conversion rates under low temperatures

Author: M. Caligaris, Guillermina Hernandez-Raquet, G. Gaval, Siegfried E. Vlaeminck, Mathieu Spérandio, B. Barillon, S. Dubos, Yolaine Bessiere, I. Mozo, P. De Cocker, 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), CIRSEE, Suez, Center for Microbial Ecology and Technology (CMET), Ghent University, Treatment Infrastructures, Research Group of Sustainable Energy, Air and Water Technology, University of Antwerp, ANRT (CIFRE) [2014/0754], 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), Centre International de Recherche Sur l'Eau et l'Environnement [Suez] (CIRSEE), SUEZ ENVIRONNEMENT (FRANCE), Universiteit Gent = Ghent University (UGENT), University of Antwerp (UA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), and Universiteit Gent = Ghent University [Belgium] (UGENT)
Subjects: [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Environmental Engineering, Denitrification, Nitrogen, Microorganism, 0208 environmental biotechnology, chemistry.chemical_element, bioréacteur, Bioengineering, 02 engineering and technology, 010501 environmental sciences, Biology, 01 natural sciences, chemistry.chemical_compound, Bioreactors, Ammonium Compounds, séquençage, Bioreactor, Ammonium, biological nitrogen removal, Waste Management and Disposal, shortcut nitrogen removal, 0105 earth and related environmental sciences, bactérie, Renewable Energy, Sustainability and the Environment, Physics, Temperature, Environmental engineering, General Medicine, bacterium, cold anammox, Anoxic waters, réacteur anaérobie, 020801 environmental engineering, Activated sludge, chemistry, microbial community structure, Anammox, Oxidation-Reduction, Engineering sciences. Technology, Nuclear chemistry
Abstract: This study compared two anammox sequencing batch reactors (SBR) for one year. SBRconstantT was kept at 30 degrees C while temperature in SBRloweringT was decreased step-wise from 30 degrees C to 20 degrees C and 15 degrees C followed by over 140 days at 12.5 degrees C and 10 degrees C. High retention of anammox bacteria (AnAOB) and minimization of competition with AnAOB were key. 5-L anoxic reactors with the same inoculum were fed synthetic influent containing 25.9 mg NH4+-N/L and 34.1 mg NO2--N/L (no COD). Specific ammonium removal rates continuously increased in SBRconstantT, reaching 785 mg NH4+-N/gVSS/d, and were maintained in SBRloweringT, reaching 82.2 and 91.8 mg NH4+-N/gVSS/d at 12.5 and 10 degrees C respectively. AnAOB enrichment (increasing hzsA and 16S rDNA gene concentrations) and adaptation (shift from Ca. Brocadia to Ca. Kuenenia in SBRloweringT) contributed to these high rates. Rapidly settling granules developed, with average diameters of 1.2 (SBRconstantT) and 1.6 mm (SBRloweringT). Results reinforce the potential of anammox for mainstream applications.
Published: 2018

49. Potential of snake fruit (Salacca zalacca (Gaerth.) Voss) for the development of a beverage through fermentation with the Kombucha consortium

Author: Fitria Rizki Novitasari, Elok Zubaidah, Philippe Blanc, Ignatius Srianta, Firka Julian Dewantari, Department of Food Science and Technology, Faculty of Agricultural Technology, Brawijaya University (UB), Department of Food Technology, Faculty of Agricultural Technology, Widya Mandala Catholic University Surabaya, 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), 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), and Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Kombucha, antioxidant, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, food.ingredient, DPPH, Bioengineering, activité anti-oxydante, 01 natural sciences, Applied Microbiology and Biotechnology, tannin, chemistry.chemical_compound, 0404 agricultural biotechnology, food, Functional food, caractérisation sensorielle, 010608 biotechnology, phénol, sensory properties, flavonoid, Food science, snake fruit, Acetic acid bacteria, Sugar, fermentation, Aroma, 2. Zero hunger, bioactive compounds, tanin, biology, Chemistry, food and beverages, 04 agricultural and veterinary sciences, biology.organism_classification, 040401 food science, antibacterial, Kombucha consortium, Salacca zalacca, flavonoïde, Fermentation, Agronomy and Crop Science, Food Science, Biotechnology
Abstract: Sugared snake fruit juices were fermented for 14 days with the Kombucha consortium containing yeasts and acetic acid bacteria. Five Indonesian cultivars (Salak Doyong, Salak Madu, Salak Pondoh, Salak Segaran and Salak Suwaru) of the fruit were studied. The physicochemical and sensory properties of the fermented products revealed the snake fruit Kombucha from the Salak Suwaru cultivar as the most acceptable with color indices L* and b* respectively 30.5 and 13.2; total sugar, 7.54%; total soluble solids, 11.3%; total acidity, 1.65%; pH, 3.15; and sensory scores (out of 5) of 3.90 for color, 3.70 for taste and 3.80 for aroma. The fermentation enhanced antioxidant activity of the snake fruit Kombucha, as assessed by 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity, and consistent with increases in phenolics, tannins and flavonoids. Acetic acid was the major organic acid of the fermented product that showed an enhanced antibacterial activity by inhibiting Gram-positive (Staphylococcus aureus) and Gram-negative (Escherichia coli) bacteria. Snake fruits can be used to develop functional food beverages and foods through the Kombucha fermentation.
Published: 2018

50. An assessment of methods of moments for the simulation of population dynamics in large-scale bioreactors

Author: Jérôme Morchain, Geoffrey Laronze, Maxime Pigou, Pascal Fede, Marie-Isabelle Penet, 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 Mécanique des Fluides et des Solides, Sanofi, Sanofi Chimie - C&BD Biochemistry Vit, 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)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique - CNRS (FRANCE), Institut National Polytechnique de Toulouse - INPT (FRANCE), Institut National des Sciences Appliquées de Toulouse - INSA (FRANCE), Sanofi Aventis (FRANCE), Université Toulouse III - Paul Sabatier - UT3 (FRANCE), and Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE)
Subjects: 0106 biological sciences, 0301 basic medicine, Mathematical optimization, physiologie des microorganismes, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Mécanique des fluides, General Chemical Engineering, Population, Method of moments, Population balance equation, Method, hydrodynamique, distribution des populations, Population balance model, Method of moments (statistics), (E)QMOM, population distribution, 01 natural sciences, Stability (probability), Industrial and Manufacturing Engineering, vertical integration, entropie, méthode des moments, Biological dynamics, 03 medical and health sciences, 010608 biotechnology, population dynamics, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, intégration, education, Maximum Entropy, Simulation, Mathematics, education.field_of_study, Applied Mathematics, Scale (chemistry), Principle of maximum entropy, adaptation des espèces, General Chemistry, équation d'équilibre, of moments, Quadrature (mathematics), dynamique des populations, 030104 developmental biology, Method of classes, entropy, modélisation des systèmes complexes, Predictive modelling
Abstract: A predictive modelling for the simulation of bioreactors must account for both the biological and hydrodynamics complexities. Population balance models (PBM) are the best approach to conjointly describe these complexities, by accounting for the adaptation of inner metabolism for microorganisms that travel in a large-scale heterogeneous bioreactor. While being accurate for solving the PBM, the Class and Monte-Carlo methods are expensive in terms of calculation and memory use. Here, we apply Methods of Moments to solve a population balance equation describing the dynamic adaptation of a biological population to its environment. The use of quadrature methods (Maximum Entropy, QMOM or EQMOM) is required for a good integration of the metabolic behavior over the population. We then compare the accuracy provided by these methods against the class method which serves as a reference. We found that the use of 5 moments to describe a distribution of growth-rate over the population gives satisfactory accuracy against a simulation with a hundred classes. Thus, all methods of moments allow a significant decrease of memory usage in simulations. In terms of stability, QMOM and EQMOM performed far better than the Maximum Entropy method. The much lower memory impact of the methods of moments offers promising perspectives for the coupling of biological models with a fine hydrodynamics depiction.
Published: 2017

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