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1. Yamadazyma barbieri f.a. sp. nov., an ascomycetous anamorphic yeast isolated from a Mid-Atlantic Ridge hydrothermal site (−2300 m) and marine coastal waters

Author

Stella Debaets, Mário Gadanho, Carlos A. Rosa, Gaëtan Burgaud, Serge Casaregola, Noémie Jacques, José Paulo Sampaio, Monika Coton, Natália O. P. Maciel, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne (LUBEM), Université de Brest (UBO), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, CIRM-Levures, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Biosystems and Integrative Sciences Institute (BioISI), University of Lisbon, Unidade de Ciencias Biomoleculares Aplicadas (UCIBIO), Requimte, Departamento de Química (DQ), Faculdade de Ciências e Tecnologia (FCT NOVA), Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA)-Faculdade de Ciências e Tecnologia (FCT NOVA), Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA)-Universidade do Porto [Porto]-Departamento de Química (DQ), Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA)-Universidade do Porto [Porto], FCT Portugal [UID/Multi/04378/2013, UID/Multi/04046/2013], European Project: 311975, Universidade de Lisboa = University of Lisbon (ULISBOA), Universidade do Porto = University of Porto-Departamento de Química (DQ), Faculdade de Ciências e Tecnologia = School of Science & Technology (FCT NOVA), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Faculdade de Ciências e Tecnologia = School of Science & Technology (FCT NOVA), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade do Porto = University of Porto-Departamento de Química (DQ), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Universidade do Porto [Porto]-Departamento de Química (DQ), Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA), Universidade de Lisboa (ULISBOA), Universidade do Porto-Departamento de Química (DQ), and Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade do Porto-Departamento de Química (DQ)

Subjects
0301 basic medicine, [SDV]Life Sciences [q-bio], Yamadazyma, Mid-Atlantic Ridge, Biology, Microbiology, 03 medical and health sciences, Hydrothermal Vents, Genus, Phylogenetics, Botany, 14. Life underwater, Internal transcribed spacer, DNA, Fungal, Mycological Typing Techniques, milieu marin, Atlantic Ocean, Phylogeny, Ecology, Evolution, Behavior and Systematics, caractérisation de souche, MycoBank, flore levurienne, Sequence Analysis, DNA, General Medicine, biology.organism_classification, Yeast, identification d'espèce, 030104 developmental biology, RNA, Ribosomal, ocean environment, Saccharomycetales, Brazil, Hydrothermal vent
Abstract

Two yeast strains that are members of the same species were isolated from different marine habitats, i.e. one from Mid-Atlantic Ridge ocean water samples located in the direct vicinity of black smokers near the Rainbow deep-sea hydrothermal vent and one from Brazilian marine water samples off the Ipanema beach. Strains CLIB 1964(T) and CLIB 1965 are anamorphic ascomycetous yeasts affiliated to the Yamadazyma clade of Saccharomycetales. Interestingly, these strains were phylogenetically and distinctly positioned into a group of species comprising all species of the genus Yamadazyma isolated from marine habitats including deep-sea hydrothermal vents, i.e. Candida atmosphaerica, C. spencermartinsiae, C. atlantica, C. oceani and C. taylorii. These strains differed significantly in their D1/D2 domain sequences of the LSU rRNA gene from the closely related species mentioned above, by 2.6, 3.0, 3.4, 3.8 and 6.0 %, respectively. Internal transcribed spacer region sequence divergence was also significant and corresponded to 4.6, 4.7, 4.7, 12.0 and 24.7% with C. atlantica, C. atmosphaerica, C. spencermartinsiae, C. oceani and C. taylorii, respectively. Phenotypically, strains CLIB 1964(T) and CLIB 1965 could be distinguished from closely related species by their inability to assimilate L-sorbose. CLIB 1964(T) (= CBS 14301(T) = UBOCC-A-214001(T)) is the designated type strain for Yamadazyma barbieri sp. nov. The MycoBank number is MB 815884.

Published
2016
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2. Adaptation of S. cerevisiae to Fermented Food Environments Reveals Remarkable Genome Plasticity and the Footprints of Domestication

Author

Legras, Jean-Luc, Galeote, Virginie, Bigey, Frédéric, Camarasa, Carole, Marsit, Souhir, Nidelet, Thibault, Sanchez, Isabelle, Couloux, Arnaud, Guy, Julie, Franco-Duarte, Ricardo, Marcet Houben, Marina, Gabaldón Estevan, Juan Antonio, 1973, Schuller, Dorit, Sampaio, José Paulo, Dequin, Sylvie, Sciences Pour l'Oenologie (SPO), Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie])-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), CBMA, Department of Biology, University of Minho, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra [Barcelona], Unidade de Ciencias Biomoleculares Aplicadas (UCIBIO), Requimte, Departamento de Química (DQ), Faculdade de Ciências e Tecnologia (FCT NOVA), Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA)-Faculdade de Ciências e Tecnologia (FCT NOVA), Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA)-Universidade do Porto [Porto]-Departamento de Química (DQ), Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA)-Universidade do Porto [Porto], Université Montpellier 1 (UM1)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), University of Minho [Braga], Universitat Pompeu Fabra [Barcelona] (UPF), Universidade do Porto = University of Porto-Departamento de Química (DQ), Faculdade de Ciências e Tecnologia = School of Science & Technology (FCT NOVA), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Faculdade de Ciências e Tecnologia = School of Science & Technology (FCT NOVA), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade do Porto = University of Porto-Departamento de Química (DQ), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), GIS IBiSA-AO 2010-2011, France, AIP Bioressources from the National Institute for Agricultural Research, Franc, Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, 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), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Institut National de la Recherche Agronomique (INRA), Universidade do Porto-Departamento de Química (DQ), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade do Porto-Departamento de Química (DQ), Universidade Nova de Lisboa = NOVA University of Lisboa (NOVA)-Universidade Nova de Lisboa = NOVA University of Lisboa (NOVA)-Faculdade de Ciências e Tecnologia (FCT NOVA), Universidade Nova de Lisboa = NOVA University of Lisboa (NOVA)-Universidade Nova de Lisboa = NOVA University of Lisboa (NOVA)-Universidade do Porto [Porto]-Departamento de Química (DQ), and Universidade Nova de Lisboa = NOVA University of Lisboa (NOVA)-Universidade Nova de Lisboa = NOVA University of Lisboa (NOVA)-Universidade do Porto [Porto]

Subjects
DNA Copy Number Variations, Gene Transfer, Horizontal, [SDV]Life Sciences [q-bio], Adaptation, Biological, Saccharomyces cerevisiae, Horizontal gene transfer, human activity, adaptation, yeast, brewer s, Biological Evolution, Domestication, domestication, séquençage du génome, activité humaine, Sweep, horizontal gene transfer, saccharomyces cerevisiae, sweep, Adaptation, Fermented Foods, Genome, Fungal, Selection, Genetic, fermentation, Discoveries
Abstract

The budding yeast Saccharomyces cerevisiae can be found in the wild and is also frequently associated with human activities. Despite recent insights into the phylogeny of this species, much is still unknown about how evolutionary processes related to anthropogenic niches have shaped the genomes and phenotypes of S. cerevisiae. To address this question, we performed population-level sequencing of 82 S. cerevisiae strains from wine, flor, rum, dairy products, bakeries, and the natural environment (oak trees). These genomic data enabled us to delineate specific genetic groups corresponding to the different ecological niches and revealed high genome content variation across the groups. Most of these strains, compared with the reference genome, possessed additional genetic elements acquired by introgression or horizontal transfer, several of which were population-specific. In addition, several genomic regions in each population showed evidence of nonneutral evolution, as shown by high differentiation, or of selective sweeps including genes with key functions in these environments (e.g., amino acid transport for wine yeast). Linking genetics to lifestyle differences and metabolite traits has enabled us to elucidate the genetic basis of several niche-specific population traits, such as growth on galactose for cheese strains. These data indicate that yeast has been subjected to various divergent selective pressures depending on its niche, requiring the development of customized genomes for better survival in these environments. These striking genome dynamics associated with local adaptation and domestication reveal the remarkable plasticity of the S. cerevisiae genome, revealing this species to be an amazing complex of specialized populations.

Published
2018
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3. Subproteomic signature comparison of in vitro selected fluoroquinolone resistance and ciprofloxacin stress in Salmonella Typhimurium DT104B

Author

Patrícia Poeta, Gilberto Igrejas, Carmen Torres, Manuela Caniça, Ingrid Chafsey, José Luis Capelo, Susana Correia, Christophe Chambon, Didier Viala, Michel Hébraud, department of neurology, clinical dementia center and DZNE, University Medical Centre Goettingen, Microbiologie Environnement Digestif Santé - Clermont Auvergne ( MEDIS ), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne ( UCA ), Qualité des Produits Animaux ( QUAPA ), Institut National de la Recherche Agronomique ( INRA ), Unité Mixte de Recherches sur les Herbivores ( UMR 1213 Herbivores ), VetAgro Sup ( VAS ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique ( INRA ), Universidad de La Rioja ( UR ), National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections (NRL-AMR-HAI), Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, I.P, UCIBIO-REQUIMTE, Faculty of Science and Technology, Universidade Nova de Lisboa, Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro, Department of Genetics and Biotechnology, Department of Genetics and Biotechnology, Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (Portugal), Veterinary Science Department, Unidade de Ciencias Biomoleculares Aplicadas (UCIBIO), Requimte, Universidade do Porto [Porto]-Departamento de Química (DQ), Faculdade de Ciências e Tecnologia (FCT NOVA), Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA)-Faculdade de Ciências e Tecnologia (FCT NOVA), Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA)-Universidade do Porto [Porto]-Departamento de Química (DQ), Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA), Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix, Qualité des Produits Animaux (QuaPA), Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherches 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)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique (INRA), Área de Bioquímica y Biología Molecular, Universidad de La Rioja (UR), Faculty of Sciences and Technology (FCT NOVA), Universidade Nova de Lisboa (NOVA), Departamento de Química (DQ), Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA)-Universidade do Porto [Porto], Faculty of Sciences and Technology, ProteoMass Scientific Society, Universidade do Porto = University of Porto-Departamento de Química (DQ), Faculdade de Ciências e Tecnologia = School of Science & Technology (FCT NOVA), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Faculdade de Ciências e Tecnologia = School of Science & Technology (FCT NOVA), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade do Porto = University of Porto-Departamento de Química (DQ), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Microbiologie Environnement Digestif Santé (MEDIS), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Instituto Nacional de Saùde Dr Ricardo Jorge [Portugal] (INSA), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Portuguese Foundation for Science and Technology (FCT) SFRH/BD/75160/2010, European Social Fund Ministry of Education and Science (MEC), national funds from FCT/MEC UID/Multi/04378/2013, ERDF under the PT Partnership Agreement POCI-01-0145-FEDER-007728, Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade do Porto-Departamento de Química (DQ), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade do Porto, INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Universidade do Porto-Departamento de Química (DQ), and Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement

Subjects
0301 basic medicine, Salmonella, Proteome, [SDV]Life Sciences [q-bio], [ SDV.AEN ] Life Sciences [q-bio]/Food and Nutrition, education, Shotgun Proteomics, Salmonella Typhimurium DT104B, Biology, [ SDV.MP.BAC ] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, medicine.disease_cause, fluoroquinolone, Biochemistry, Microbiology, ciprofloxacine, 03 medical and health sciences, stress, Antibiotic resistance, Stress, Physiological, ciprofloxacin, Lc ms ms, Drug Resistance, Bacterial, medicine, antimicrobial resistance, Selection, Genetic, LC-MS/MS, Shotgun proteomics, Molecular Biology, ComputingMilieux_MISCELLANEOUS, Comparative Subproteomics, [ SDV ] Life Sciences [q-bio], Resistência aos Antimicrobianos, comparative subproteomics, in vitro, 2-DE, salmonella Typhimurium DT104B, In vitro, Fluoroquinolone resistance, 3. Good health, Anti-Bacterial Agents, Ciprofloxacin, 030104 developmental biology, shotgun proteomics, Antimicrobial Resistance, salmonella typhimurium, medicine.drug, Fluoroquinolones
Abstract

Background: Fluoroquinolone resistance in nontyphoidal Salmonella is a situation of serious and international concern, particularly in S. Typhimurium DT104B multiresistant strains. Although known to be multifactorial, fluoroquinolone resistance is still far from a complete understanding. Methods: Subproteome changes between an experimentally selected fluoroquinolone-resistant strain (Se6-M) and its parent strain (Se6), and also in Se6-M under ciprofloxacin (CIP) stress, were evaluated in order to give new insights into the mechanisms involved. Proteomes were compared at the intracellular and membrane levels by a 2-DE~LC-MS/MS and a shotgun LC-MS/MS approach, respectively. Results: In total, 35 differentially abundant proteins were identified when comparing Se6 with Se6-M (25 more abundant in Se6 and 10 more abundant in Se6-M) and 82 were identified between Se6-M and Se6-M+CIP (51 more abundant in Se6-M and 31 more abundant under ciprofloxacin stress). Conclusion: Several proteins with known and possible roles in quinolone resistance were identified which provide important information about mechanism-related differential protein expression, supporting the current knowledge and also leading to new testable hypotheses on the mechanism of action of fluoroquinolone drugs. info:eu-repo/semantics/publishedVersion

Published
2017
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4. Wheat glutenin: the 'tail' of the 1By protein subunits

Author

Emmanuelle Bancel, Gilberto Igrejas, Gérard Branlard, José Luis Capelo, J. D. Nunes-Miranda, Christophe Chambon, Didier Viala, Catherine Ravel, Functional Genomics and Proteomics Unit, Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (Portugal), UCIBIO-REQUIMTE, Faculty of Science and Technology, Universidade Nova de Lisboa, Génétique Diversité et Ecophysiologie des Céréales ( GDEC ), Institut National de la Recherche Agronomique ( INRA ) -Université Blaise Pascal - Clermont-Ferrand 2 ( UBP ), Unité Mixte de Recherches sur les Herbivores ( UMR 1213 Herbivores ), VetAgro Sup ( VAS ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique ( INRA ), Qualité des Produits Animaux ( QUAPA ), Institut National de la Recherche Agronomique ( INRA ), Faculty of Sciences and Technology, Universidade Nova de Lisboa ( UNINOVA ), Unidade de Ciencias Biomoleculares Aplicadas (UCIBIO), Requimte, Universidade do Porto-Departamento de Química (DQ), Faculdade de Ciências e Tecnologia = School of Science & Technology (FCT NOVA), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Faculdade de Ciências e Tecnologia = School of Science & Technology (FCT NOVA), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade do Porto-Departamento de Química (DQ), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Qualité des Produits Animaux (QuaPA), Institut National de la Recherche Agronomique (INRA), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Portuguese Foundation for Science and Technology (FCT) SFRH/BD/80496/2011, European Social Fund, Ministry of Education and Science (MEC), FCT/MEC UID/Multi/04378/2013, ERDF POCI-01-0145-FEDER-007728, Departamento de Química (DQ), Faculdade de Ciências e Tecnologia (FCT NOVA), Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA)-Faculdade de Ciências e Tecnologia (FCT NOVA), Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA)-Universidade do Porto [Porto]-Departamento de Química (DQ), Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA)-Universidade do Porto [Porto], Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Unité Mixte de Recherches 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)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique (INRA), Faculty of Sciences and Technology (FCT NOVA), Universidade Nova de Lisboa (NOVA), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade do Porto, Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Recherche Agronomique (INRA), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Universidade do Porto = University of Porto-Departamento de Química (DQ), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade do Porto = University of Porto-Departamento de Química (DQ), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Universidade do Porto [Porto]-Departamento de Química (DQ), and Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA)

Subjects
0106 biological sciences, 0301 basic medicine, gluténine, Glutens, [SDV]Life Sciences [q-bio], Protein subunit, Biophysics, proteolytic cleavage, 01 natural sciences, Biochemistry, 1By HMW-GS, Polymerization, 03 medical and health sciences, Glutenin, clivage proteolytique, blé, wheat, Immunochemistry, Food Quality, Storage protein, Asparagine, Cysteine, Triticum, wheat glutenin, 2. Zero hunger, chemistry.chemical_classification, C-terminal domain maturation, biology, [ SDV ] Life Sciences [q-bio], asparaginyl endopeptidase, Seed Storage Proteins, food and beverages, asparagine, Gluten, Molecular Weight, Protein Subunits, 030104 developmental biology, Enzyme, chemistry, protéine, biology.protein, protein, Protein Processing, Post-Translational, 010606 plant biology & botany, glutenin
Abstract

Epub ahead of print; Gluten-forming storage proteins play a major role in the viscoelastic properties of wheat dough through the formation of a continuous proteinaceous network. The high-molecular-weight glutenin subunits represent a functionally important subgroup of gluten proteins by promoting the formation of large glutenin polymers through interchain disulphide bonds between glutenin subunits. Here, we present evidences that y-type glutenin subunits encoded at the Glu-B1 locus are prone to proteolytic processing at the C-terminus tail, leading to the loss of the unique cysteine residue present at the C-terminal domain. Results obtained by intact mass measurement and immunochemistry for each proteoform indicate that the proteolytic cleavage appears to occur at the carboxyl-side of two conserved asparagine residues at the C-terminal domain start. Hence, we hypothesize that the responsible enzymes are a class of cysteine endopeptidases - asparaginyl endopeptidases - described in post-translational processing of other storage proteins in wheat. Biological significance The reported study provides new insights into wheat storage protein maturation. In view of the importance of gluten proteins on dough viscoelastic properties and end-product quality, the reported C-terminal domain cleavage of high-molecular-weight glutenin subunits is of particular interest, since this domain possesses a unique conserved cysteine residue which is assumed to participate in gluten polymerization.

Published
2017
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5. Binding of the five multistate species of the anthocyanin analog 7- β -D-glucopyranosyloxy-4′-hydroxyflavylium to the β -cyclodextrin derivative captisol

Author

Nathalie Mora, Olivier Dangles, Nuno Basílio, Johan Mendoza, Sheiraz Al Bittar, Fernando Pina, Laboratorio Associado para a Quimica Verde (LAQV), Requimte, Universidade do Porto-Departamento de Química (DQ), Faculdade de Ciências e Tecnologia = School of Science & Technology (FCT NOVA), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Faculdade de Ciências e Tecnologia = School of Science & Technology (FCT NOVA), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade do Porto-Departamento de Química (DQ), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Sécurité et Qualité des Produits d'Origine Végétale (SQPOV), Avignon Université (AU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Universidade do Porto [Porto]-Departamento de Química (DQ), Faculdade de Ciências e Tecnologia (FCT NOVA), Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA)-Faculdade de Ciências e Tecnologia (FCT NOVA), Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA)-Universidade do Porto [Porto]-Departamento de Química (DQ), Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA), Institut National de la Recherche Agronomique (INRA)-Avignon Université (AU), Dangles, Olivier, Pina, Fernando, Departamento de Química (DQ), Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA)-Universidade do Porto [Porto], and Avignon Université (AU)-Institut National de la Recherche Agronomique (INRA)

Subjects
Anthocyanin, Circular dichroism, Multistate, General Chemical Engineering, [SDV]Life Sciences [q-bio], Quantum yield, 010402 general chemistry, Photochemistry, 01 natural sciences, cyclodextrine, chemistry.chemical_compound, Reaction rate constant, anthocyanine, photolyse, Equilibrium constant, chemistry.chemical_classification, calorimétrie isothermique, Cyclodextrin, 010405 organic chemistry, Process Chemistry and Technology, Isothermal titration calorimetry, Host-guest, 0104 chemical sciences, chemistry, cyclodextrin, photolysis, Flavylium, spectrométrie ultra violet visible, Physical chemistry, Flash photolysis, Derivative (chemistry)
Abstract

The host-guest chemistry of the anthocyanin analog 7-β-D-glucopyranosyloxy-4′-hydroxyflavylium (GHF) was studied in the presence of the β-cyclodextrin derivative captisol by stopped flow, UV–visible spectroscopy, flash photolysis, circular dichroism and isothermal titration calorimetry. The equilibrium and rate constants of the multistate of chemical species derived from the flavylium ion were calculated and compared with those in the absence of the host. A new procedure to obtain the host-guest association constants of the multistate (including the transient species) by superimposing the two energy level diagrams, in the presence and absence of the cyclodextrin, was developed. The results indicate that the magnitude of the association constants follows the order, trans-chalcone ≈ cis-chalcone ≈ hemiketal > quinoidal base > flavylium cation. The hydration equilibrium constant increases ca. 42 times in the presence of captisol as the hydration and dehydration rate constants respectively increases and decreases. The other equilibrium constants are modestly affected: the rate constants of ring closure and opening are significantly decreased in the complex and the isomerization rate constants increase in both directions. The quantum yield of the photochromic system in the presence of captisol is 0.3, i.e. 3 times higher than in the absence of the host.

Published
2017
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6. Comparative subproteomic analysis of clinically acquired fluoroquinolone resistance and ciprofloxacin stress in Salmonella Typhimurium DT104B

Author

José Luis Capelo, Susana Correia, Christophe Chambon, Michel Hébraud, Yolanda Sáenz, Gilberto Igrejas, Didier Viala, Ingrid Chafsey, Patrícia Poeta, Functional Genomics and Proteomics Unit, Universidade de Trás-os-Montes e Alto Douro, Department of Genetics and Biotechnology, University of Tras-os-Montes and Alto Douro, Veterinary Science Department, University of Trás-os-Montes and Alto Douro (Portugal), Unidade de Ciencias Biomoleculares Aplicadas (UCIBIO), Requimte, Departamento de Química (DQ), Faculdade de Ciências e Tecnologia (FCT NOVA), Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA)-Faculdade de Ciências e Tecnologia (FCT NOVA), Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA)-Universidade do Porto [Porto]-Departamento de Química (DQ), Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA)-Universidade do Porto [Porto], Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix, Qualité des Produits Animaux (QuaPA), Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherches 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)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique (INRA), Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), Faculty of Sciences and Technology (FCT NOVA), Universidade Nova de Lisboa (NOVA), Portuguese Foundation for Science and Technology (FCT) SFRH/BD/75160/2010, European Social Fund, Ministry of Education and Science (MEC), FCT/MEC UID/Multi/04378/2013, ERDF POCI-01-0145-FEDER-007728, Universidade do Porto = University of Porto-Departamento de Química (DQ), Faculdade de Ciências e Tecnologia = School of Science & Technology (FCT NOVA), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Faculdade de Ciências e Tecnologia = School of Science & Technology (FCT NOVA), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade do Porto = University of Porto-Departamento de Química (DQ), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Microbiologie Environnement Digestif Santé (MEDIS), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), department of neurology, clinical dementia center and DZNE, University Medical Centre Goettingen, Microbiologie Environnement Digestif Santé - Clermont Auvergne ( MEDIS ), Université Clermont Auvergne ( UCA ) -INRA Clermont-Ferrand-Theix, Qualité des Produits Animaux ( QUAPA ), Institut National de la Recherche Agronomique ( INRA ), Unité Mixte de Recherches sur les Herbivores ( UMR 1213 Herbivores ), VetAgro Sup ( VAS ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique ( INRA ), Centro de Investigación Biomédica de La Rioja, UCIBIO-REQUIMTE, Faculty of Science and Technology, Universidade Nova de Lisboa, Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro, Universidade do Porto [Porto]-Departamento de Química (DQ), Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne ( UCA ), Faculty of Sciences and Technology, Universidade Nova de Lisboa ( UNINOVA ), Universidade do Porto-Departamento de Química (DQ), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade do Porto-Departamento de Química (DQ), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade do Porto, and VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement

Subjects
0301 basic medicine, Serotype, Salmonella, fluoroquinolone resistance, salmonella typhimurium DT104B, [ SDV.AEN ] Life Sciences [q-bio]/Food and Nutrition, [SDV]Life Sciences [q-bio], Clinical Biochemistry, [ SDV.MP.BAC ] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, medicine.disease_cause, fluoroquinolone, Microbiology, ciprofloxacine, 03 medical and health sciences, Antibiotic resistance, Stress, Physiological, ciprofloxacin, Drug Resistance, Bacterial, medicine, Humans, antimicrobial resistance, ciprofloxacin stress, ComputingMilieux_MISCELLANEOUS, résistance antimicrobienne, biology, Strain (chemistry), [ SDV ] Life Sciences [q-bio], comparative subproteomics, biology.organism_classification, 3. Good health, Ciprofloxacin, 030104 developmental biology, Mechanism of action, Salmonella enterica, Proteome, medicine.symptom, salmonella typhimurium, medicine.drug
Abstract

PURPOSE Antimicrobial resistance is a worldwide public health threat and Salmonella enterica subsp. enterica serotype Typhimurium phage type DT104B multiresistant strains with additional quinolone resistance have been responsible for global outbreaks and high mortality. Quinolone resistance is known to be multifactorial but is still far from a complete understanding. To give new insights about the resistance mechanisms involved, this work aimed to evaluate subproteome changes between an S. Typhimurium DT104B clinical strain that acquired fluoroquinolone resistance after treatment (Se20) and its pretreatment parental strain (Se6), and also subproteome variations in Se20 under ciprofloxacin (CIP) stress (Se20+CIP). EXPERIMENTAL DESIGN The proteomes were compared at the intracellular and membrane levels by a 2-DE∼LC-MS/MS and a shotgun LC-MS/MS approach, respectively. RESULTS In total, 14 differentially abundant proteins were identified when comparing Se6 with Se20 and 91 were identified between Se20 and Se20+CIP. Several proteins with known and possible roles in quinolone resistance (AAC(6')-Ib-cr4, OmpD, OmpX, GlmS, GlmU, H-NS, etc.) were identified and discussed. CONCLUSIONS AND CLINICAL RELEVANCE The great number of proteins identified in this study provides important information about mechanism-related differential protein expression which supports the current knowledge and might lead to new testable hypotheses on the mechanism of action of fluoroquinolone drugs.

Published
2017
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7. New insights into wheat toxicity: Breeding did not seem to contribute to a prevalence of potential celiac disease's immunostimulatory epitopes

Author

Gilberto Igrejas, Gérard Branlard, Fernando M. Nunes, Miguel Ribeiro, José A. Carrillo, Marta Rodríguez-Quijano, Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (Portugal), Department of Genetics and Biotechnology, CQ-VR, Chemistry Research Centre, Chemistry Department, Unidad de Genética y Mejora de plantas Departamento de Biotecnología-Biología Vegetal, E.T.S. Ingenieros Agrónomos, Universidad Politécnica de Madrid (UPM), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Unidade de Ciencias Biomoleculares Aplicadas (UCIBIO), Requimte, Universidade do Porto-Departamento de Química (DQ), Faculdade de Ciências e Tecnologia = School of Science & Technology (FCT NOVA), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Faculdade de Ciências e Tecnologia = School of Science & Technology (FCT NOVA), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade do Porto-Departamento de Química (DQ), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Foundation for Science and Technology (FCT) - Portugal and European Social Fund (ESF) [SFRH/BD/82334/2011], Unidade de Ciencias Biomoleculares Aplicadas-UCIBIO - national funds from FCT/MEC [UID/Multi/04378/2013], ERDF under the PT2020 Partnership [POCI-01-0145-FEDER-007728], FCT [PTDC/QUI-QUI/100044/2008, PEst-OE/QUI/UI0616/2014], COMPETE, Universidade do Porto = University of Porto-Departamento de Química (DQ), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade do Porto = University of Porto-Departamento de Química (DQ), Departamento de Química (DQ), Faculdade de Ciências e Tecnologia (FCT NOVA), Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA)-Faculdade de Ciências e Tecnologia (FCT NOVA), Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA)-Universidade do Porto [Porto]-Departamento de Química (DQ), Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA)-Universidade do Porto [Porto], Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Universidade do Porto [Porto]-Departamento de Química (DQ), and Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA)

Subjects
0301 basic medicine, Hot Temperature, Glutens, [SDV]Life Sciences [q-bio], Prevalence, Gliadins, Enzyme-Linked Immunosorbent Assay, Disease, Epitope, Gliadin, Analytical Chemistry, 03 medical and health sciences, Epitopes, Immune system, Toxic epitopes, Humans, Chromatography, High Pressure Liquid, Triticum, 2. Zero hunger, Genetics, chemistry.chemical_classification, 030109 nutrition & dietetics, biology, business.industry, nutritional and metabolic diseases, food and beverages, General Medicine, Gluten Proteins, Gluten, digestive system diseases, Biotechnology, Tetraploidy, Celiac Disease, Plant Breeding, 030104 developmental biology, chemistry, RP-HPLC, Toxicity, biology.protein, Food Technology, business, Food Science
Abstract

Gluten proteins, namely gliadins, are the primary trigger of the abnormal immune response in celiac disease. It has been hypothesised that modern wheat breeding practices may have contributed to the increase in celiac disease prevalence during the latter half of the 20th century. Our results do not support this hypothesis as Triticum aestivum spp. vulgare landraces, which were not subjected to breeding practices, presented higher amounts of potential celiac disease's immunostimulatory epitopes when compared to modern varieties. Furthermore, high variation between wheat varieties concerning the toxic epitopes amount was observed. We carried out quantitative analysis of gliadin types by RP-HPLC to verify its correlation with the amount of toxic epitopes: x-type gliadins content explain about 40% of the variation of toxic epitopes in tetraploid wheat varieties. This research provides new insights regarding wheat toxicity and into the controversial idea that human practices may have conducted to an increased exposure to toxic epitopes.

Published
2016
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8. Analogs of Natural 3-Deoxyanthocyanins: O-Glucosides of the 4′,7-Dihydroxyflavylium Ion and the Deep Influence of Glycosidation on Color

Author

Sheiraz Al Bittar, Nathalie Mora, Fernando Pina, Nuno Basílio, Olivier Dangles, Laboratorio Associado para a Quimica Verde (LAQV), Requimte, Universidade do Porto [Porto]-Departamento de Química (DQ), Faculdade de Ciências e Tecnologia (FCT NOVA), Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA)-Faculdade de Ciências e Tecnologia (FCT NOVA), Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA)-Universidade do Porto [Porto]-Departamento de Química (DQ), Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA), Faculty of Sciences, Technology & Health, INRA UMR 408, Avignon Université (AU), Sécurité et Qualité des Produits d'Origine Végétale (SQPOV), Institut National de la Recherche Agronomique (INRA)-Avignon Université (AU), Universidade do Porto-Departamento de Química (DQ), Faculdade de Ciências e Tecnologia = School of Science & Technology (FCT NOVA), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Faculdade de Ciências e Tecnologia = School of Science & Technology (FCT NOVA), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade do Porto-Departamento de Química (DQ), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Avignon Université (AU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Dangles, Olivier, Pina, Fernando, Departamento de Química (DQ), Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA)-Universidade do Porto [Porto], and Avignon Université (AU)-Institut National de la Recherche Agronomique (INRA)

Subjects
3-deoxyanthocyanidin, [SDV]Life Sciences [q-bio], Photochemistry, 01 natural sciences, stabilité de la couleur, Anthocyanins, lcsh:Chemistry, chemistry.chemical_compound, multistate, Glucosides, Apigenin, lcsh:QH301-705.5, Spectroscopy, Aqueous solution, irradiation, Quinones, General Medicine, Hydrogen-Ion Concentration, photochromism, Computer Science Applications, visual_art, visual_art.visual_art_medium, Isomerization, chalkone, flavylium, glucoside, chalcone, 010402 general chemistry, Article, Catalysis, Reversible reaction, Inorganic Chemistry, Pigment, Photochromism, Reaction rate constant, Isomerism, ultrasonic treatment, Physical and Theoretical Chemistry, Molecular Biology, 010405 organic chemistry, Organic Chemistry, Pigments, Biological, Chromophore, 0104 chemical sciences, kafir, Aglycone, chemistry, lcsh:Biology (General), lcsh:QD1-999, pigment naturel, sorghum
Abstract

3-Deoxyanthocyanidins and their O-β-d-glucosides are natural pigments abundant in black sorghum. O-glycosidation can perturb the acid-base properties of the chromophore and lower its electron density with a large impact on the distribution of colored and colorless forms in aqueous solution. In this work, the influence of O-glycosidation on color is systematically studied from a series of 3-deoxyanthocyanin analogs. The pH- and light-dependent reversible reactions of 7-β-d-glucopyranosyloxy-4′-hydroxyflavylium (P3) and 4′-β-d-glucopyranosyloxy-7-hydroxyflavylium (P5) were completely characterized in mildly acidic solution and compared with the parent aglycone 4′,7-dihydroxyflavylium ion and the O-methylethers of P3 and P5. Except P5, the chalcone forms of the pigments exhibit a high cis-trans isomerization barrier that allows a pseudo-equilibrium involving all species except the trans-chalcone. At equilibrium, only the flavylium cation and trans-chalcone are observed. With all pigments, the colored flavylium ion can be generated by irradiation of the trans-chalcone (photochromism). Glycosidation of C7–OH accelerates hydration and strongly slows down cis-trans isomerization with the pH dependence of the apparent isomerization rate constant shifting from a bell-shaped curve to a sigmoid. The color of P5 is much more stable than that of its regioisomer P3 in near-neutral conditions.

Published
2016
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9. A population genomics insight into the Mediterranean origins of wine yeast domestication

Author

Douda Bensasson, Jean Luc Legras, Yumi Imanishi, Marta Serra, Polona Zalar, Benedetta Turchetti, Paula Gonçalves, José Paulo Sampaio, Kiminori Shimizu, Raquel Barbosa, Pedro Almeida, Julie Guy, Arnaud Couloux, Sylvie Dequin, Unidade de Ciencias Biomoleculares Aplicadas (UCIBIO), Requimte, Universidade do Porto = University of Porto-Departamento de Química (DQ), Faculdade de Ciências e Tecnologia = School of Science & Technology (FCT NOVA), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Faculdade de Ciências e Tecnologia = School of Science & Technology (FCT NOVA), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade do Porto = University of Porto-Departamento de Química (DQ), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Department of Biology, Biotechnical Faculty, University of Ljubljana, Department of Applied Material and Life Science, College of Engineering, Kanto Gakuin University, Medical Mycology Research Center, Chiba University, Dipartimento di Scienze Agrarie, Alimentari e Ambientali & Industrial Yeasts Collection DBVPG, Università degli Studi di Perugia = University of Perugia (UNIPG), Sciences Pour l'Oenologie (SPO), Université Montpellier 1 (UM1)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Faculty of Life Sciences, Bar-Ilan University [Israël], FCT Portugal [PTDC/BIA-EVF/118618/2010, PTDC/AGR-ALI/118590/2010, UID/Multi/04378/2013, SFRH/BD/77390/2011], Natural Environment Research Council UK [NE/D008824/1], Universidade do Porto-Departamento de Química (DQ), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade do Porto-Departamento de Química (DQ), Università degli Studi di Perugia (UNIPG), 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), Universidade do Porto [Porto]-Departamento de Química (DQ), Faculdade de Ciências e Tecnologia (FCT NOVA), Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA)-Faculdade de Ciências e Tecnologia (FCT NOVA), Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA)-Universidade do Porto [Porto]-Departamento de Química (DQ), Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA), Universita degli Studi di Perugia, Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie])-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Departamento de Química (DQ), and Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA)-Universidade do Porto [Porto]

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, comparative genomics, domestication fingerprints, microbe domestication, microbe population genomics, yeast molecular ecology, Ecology, Evolution, Behavior and Systematics, Genetics, yeast, brewer s, phylogeny, Mediterranean Basin, Population genomics, Quercus, vin, saccharomyces cerevisiae, DNA, Fungal, Winemaking, Fermentation in winemaking, 0303 health sciences, education.field_of_study, Ecology, Mediterranean Region, food and beverages, Europe, Yeast in winemaking, oenologie, Genome, Fungal, Evolution, Population, Biology, Polymorphism, Single Nucleotide, bassin méditerranéen, Evolution, Molecular, 03 medical and health sciences, Behavior and Systematics, DNA, Ribosomal Spacer, phylogénie, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, analyse génomique, wine, education, Domestication, levure, 030304 developmental biology, Wine, Models, Genetic, 030306 microbiology, Genetic Variation, Sequence Analysis, DNA, Genetics, Population, Microsatellite Repeats
Abstract

The domestication of the wine yeast Saccharomyces cerevisiae is thought to be contemporary with the development and expansion of viticulture along the Mediterranean basin. Until now, the unavailability of wild lineages prevented the identification of the closest wild relatives of wine yeasts. Here, we enlarge the collection of natural lineages and employ whole-genome data of oak-associated wild isolates to study a balanced number of anthropic and natural S. cerevisiae strains. We identified industrial variants and new geographically delimited populations, including a novel Mediterranean oak population. This population is the closest relative of the wine lineage as shown by a weak population structure and further supported by genomewide population analyses. A coalescent model considering partial isolation with asymmetrical migration, mostly from the wild group into the Wine group, and population growth, was found to be best supported by the data. Importantly, divergence time estimates between the two populations agree with historical evidence for winemaking. We show that three horizontally transmitted regions, previously described to contain genes relevant to wine fermentation, are present in the Wine group but not in the Mediterranean oak group. This represents a major discontinuity between the two populations and is likely to denote a domestication fingerprint in wine yeasts. Taken together, these results indicate that Mediterranean oaks harbour the wild genetic stock of domesticated wine yeasts.

Published
2015
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10. Detection of two glass transitions on triton X-100 under confinement

Author

Florence Danede, Madalena Dionísio, Carlos J. Dias, Esther G. Merino, Abdenacer Idrissi, Natália T. Correia, Isabel Fonseca, Paulo Duarte Neves, Centro de Química Fina e Biotecnologia (CQFB), Requimte, Universidade do Porto-Departamento de Química (DQ), Faculdade de Ciências e Tecnologia = School of Science & Technology (FCT NOVA), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Faculdade de Ciências e Tecnologia = School of Science & Technology (FCT NOVA), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade do Porto-Departamento de Química (DQ), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), CENIMAT/I3N, Departemento de Ciencia dos Materiais, Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Unité Matériaux et Transformations - UMR 8207 (UMET), Institut de Chimie du CNRS (INC)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Ecole Nationale Supérieure de Chimie de Lille (ENSCL), Laboratoire Avancé de Spectroscopie pour les Intéractions la Réactivité et l'Environnement - UMR 8516 (LASIRE), Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Centrale Lille Institut (CLIL), Departamento de Química (DQ), Faculdade de Ciências e Tecnologia (FCT NOVA), Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA)-Faculdade de Ciências e Tecnologia (FCT NOVA), Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA)-Universidade do Porto [Porto]-Departamento de Química (DQ), Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA)-Universidade do Porto [Porto], Departemento de Ciencia dos Materiais-Faculdade de Ciências e Tecnologia (FCT NOVA), Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA), Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Ecole Nationale Supérieure de Chimie de Lille (ENSCL)-Institut National de la Recherche Agronomique (INRA), Laboratoire de Spectrochimie Infrarouge et Raman - UMR 8516 (LASIR), Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Universidade do Porto = University of Porto-Departamento de Química (DQ), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade do Porto = University of Porto-Departamento de Química (DQ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure de Chimie de Lille (ENSCL)-Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Universidade do Porto [Porto]-Departamento de Química (DQ), and Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure de Chimie de Lille (ENSCL)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)

Subjects
Confined systems, X ray diffraction, Analytical chemistry, Supercooled state, 02 engineering and technology, Dielectric, Dielectric relaxation spectroscopy, 010402 general chemistry, 01 natural sciences, law.invention, Interfacial polarization, chemistry.chemical_compound, Differential scanning calorimetry, Molecular population, law, Two glass transition, Physical and Theoretical Chemistry, Crystallization, Supercooling, Calorimetric analysis, Chemistry, Thermogravimetric analysis, Molecules, 021001 nanoscience & nanotechnology, 0104 chemical sciences, Surfaces, Coatings and Films, Electronic, Optical and Magnetic Materials, Amorphous solid, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, loading, General Energy, Temperature dependence, Triton X-100, Relaxation (physics), Glass, differential scanning calorimetry, 0210 nano-technology, Glass transition
Abstract

Because of the strong tendency of Triton X-100 to crystallize, inclusion in a SBA-15 matrix of 5.7 nm in pore diameter was used as a means to suppress crystallization. Clear evidence that Triton X-100 exists under confinement in the amorphous and supercooled state is given by X-ray diffraction supported by differential scanning calorimetry and dielectric relaxation spectroscopy. From the thermogravimetric analysis, a loading degree of 50% (wt) was estimated; the decomposition of confined Triton X-100 follows a two-step profile, indicating that molecules are partitioned between bulklike and adsorbed, the latter fraction being in a higher proportion. This allowed the unequivocal detection by DSC of two well-resolved glass transitions (∼ 20 K apart), which is a remarkable result obtained by conventional calorimetric analysis in confined systems. The two molecular populations have different mobilities giving rise to two different dielectric relaxation processes: an αTr/SBA bulklike process associated with molecules located more in the center of the pores, slightly slowed down relative to bulk α-relaxation, and an S-process due to molecules absorbed at the walls with significantly hindered mobility. Moreover, an MWS process is detected due to interfacial polarization that builds up between the adsorbed Triton X-100 molecules and SBA pore walls whose temperature dependence seems to be correlated with the one of the S-process. The inclusion in SBA-15 revealed to be a good strategy to simultaneously avoid crystallization and achieve a long-term stabilization of the disordered form.

Published
2013
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