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3. GCN5 modulates salicylic acid homeostasis by regulating H3K14ac levels at the 5′ and 3′ ends of its target genes

Author

Ruggieri, Valentino, Alexiou, Konstantinos, Morata, Jordi, Argyris, Jason, Pujol, Marta, Yano, Ryoichi, Nonaka, Satoko, Ezura, Hiroshi, Cigliano, Riccardo Aiese, Sanseverino, Walter, Puigdomenech, Pere, Casacuberta, Josep, Kirienko, Anna, Porozov, Yuri, Malkov, Nikita, Akhtemova, Gulnara, Le Signor, Christine, Thompson, Richard, Saffray, Christine, Dalmais, Marion, Tikhonovich, Igor, Dolgikh, Elena, Boucheham, Anouar, Sommard, Vivien, Zehraoui, Farida, Batouche, Mohamed, Israeli, David, Tahi, Fariza, Jacob, Pierre, Avni, Adi, Ligerot, Yasmine, De Saint Germain, Alexandre, Waldie, Tanya, Kadakia, Nikita, Pillot, Jean-Paul, Prigge, Michael, Aubert, Gregoire, Leyser, Ottoline, Estelle, Mark, Debellé, Frederic, Rameau, Catherine, GOUZY, Jerome, Badouin, Hélène, Lemainque, Arnaud, Vergne, Philippe, Moja, Sandrine, Choisne, Nathalie, Pont, Caroline, Carrere, Sebastien, Caissard, Jean-Claude, Couloux, Arnaud, Cottret, Ludovic, Aury, Jean-Marc, Szécsi, Judit, Madoui, Mohammed-Amin, Yang, Shu-Hua, Piola, Florence, Larrieu, Antoine, Perez, Magali, Labadie, Karine, Perrier, Lauriane, govetto, Benjamin, LABROUSSE, Yoan, Villand, Priscilla, Bardoux, Claudia, Boltz, Véronique, Lopez-Roques, Celine, Heitzler, Pascal, Vernoux, Teva, Quesneville, Hadi, Boualem, Adnane, Liu, Chang, Le Bris, Manuel, Salse, Jerome, Baudino, Sylvie, Wincker, Patrick, François, Léa, Verdenaud, Marion, Fu, Xiaopeng, Ruleman, Darcy, Dubois, Annick, Vandenbussche, Michiel, Raymond, Olivier, Just, Jérémy, Bendahmane, Mohammed, Giner, Ana, Pascual, Laura, Bourgeois, Michael, Gyetvai, Gabor, Rios, Pablo, Picó, Belén, Troadec, Christelle, Bendahmane, Abdel, Garcia-Mas, Jordi, MARTIN-HERNANDEZ, Ana Montserrat, Kim, Soonkap, Piquerez, Sophie, Ramirez-Prado, Juan, Mastorakis, Emmanouil, Veluchamy, Alaguraj, Latrasse, David, Manza-Mianza, Deborah, Brik-Chaouche, Rim, Huang, Ying, Rodriguez-Granados, Natalia, Concia, Lorenzo, Blein, Thomas, Citerne, Sylvie, Bendahmane, Abdelhafid, Bergounioux, Catherine, Crespi, Martin, Mahfouz, Magdy, Raynaud, Cécile, Hirt, Heribert, Ntoukakis, Vardis, BENHAMED, Moussa, Centre for Research in Agricultural Genomics (CRAG), IRTA, Center for Research in Agricultural Genomics, University of Tsukuba, Sequentia Biotech SL, LAboratoire PLasma et Conversion d'Energie (LAPLACE), 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, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), All-Russia Research Institute for Agricultural Microbiology, University Salah Boubnider Constantine 3, Laboratoire d'Informatique de Paris-Nord (LIPN), Université Sorbonne Paris Cité (USPC)-Institut Galilée-Université Paris 13 (UP13)-Centre National de la Recherche Scientifique (CNRS), LIRE laboratory, Constantine, University of Constantine, GENETHON 3, Université Paris Saclay (COmUE), Tel Aviv University [Tel Aviv], Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Sainsbury Laboratory, University of Cambridge [UK] (CAM), University of California [San Diego] (UC San Diego), University of California, Laboratoire de chimie organique et organométallique (LCOO), Université Sciences et Technologies - Bordeaux 1-Centre National de la Recherche Scientifique (CNRS), Division of Biology [La Jolla], University of California-University of California, UMR 0441 INRA / CNRS : Laboratoire de Biologie moléculaire des relations plantes-microorganismes, Institut National de la Recherche Agronomique (INRA), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Sexe et évolution, Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), 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), Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales (LBVPAM), Université Jean Monnet [Saint-Étienne] (UJM), Unité de Recherche Génomique Info (URGI), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Département de chirurgie, CRLCC Val d'Aurelle - Paul Lamarque, Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Reproduction et développement des plantes (RDP), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés (LEHNA), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS), Centre for Plant Integrative Biology [Nothingham] (CPIB), University of Nottingham, UK (UON), Institut de Génomique d'Evry (IG), Institut de Biologie François JACOB (JACOB), 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 Paris-Saclay, Institut Sophia Agrobiotech [Sophia Antipolis] (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 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), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), GeT PlaGe, Genotoul, Institut de génétique et biologie moléculaire et cellulaire (IGBMC), Université Louis Pasteur - Strasbourg I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Sun Yat-Sen University [Guangzhou] (SYSU), Institut Méditerranéen d'Ecologie et de Paléoécologie (IMEP), Université Paul Cézanne - Aix-Marseille 3-Université de Provence - Aix-Marseille 1-Avignon Université (AU)-Centre National de la Recherche Scientifique (CNRS), Huazhong Agricultural University, Division of Biology [Pasadena], California Institute of Technology (CALTECH), Unité de recherche Génétique et amélioration des fruits et légumes (GAFL), Génétique et Ecophysiologie des Légumineuses à Graines (UMRLEG) (UMR 102), Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Universitat Politecnica de Valencia (UPV), Institute of Agrifood Research and Technology (IRTA), Institut de Recerca i Tecnologia Agroalimentaries, King Abdullah University of Science and Technology (KAUST), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), School of Economics and Management [Beijing] (BUAA), Beihang University, Institut de biotechnologie des plantes (IBP), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Warwick [Coventry], AgroParisTech, and ANR-18-CE20-0015,EPICLIPSE,Dynamique des marques épigénétiques dans les cellules hôtes infectées et subversion de l'épigénome par le pathogène.(2018)

Subjects
0106 biological sciences, Transcription, Genetic, AcademicSubjects/SCI00010, [SDV]Life Sciences [q-bio], Arabidopsis, Biology, Genes, Plant, 01 natural sciences, Histones, 03 medical and health sciences, Gene Expression Regulation, Plant, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, Homeostasis, Plant Immunity, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Epigenetics, Promoter Regions, Genetic, QH426, ComputingMilieux_MISCELLANEOUS, Histone Acetyltransferases, 030304 developmental biology, Regulation of gene expression, 0303 health sciences, Arabidopsis Proteins, Lysine, Gene regulation, Chromatin and Epigenetics, Acetylation, Biotic stress, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Cell biology, Chromatin, enzymes and coenzymes (carbohydrates), Histone, Acetyltransferase, Transcription Coactivator, biology.protein, 5' Untranslated Regions, Salicylic Acid, 010606 plant biology & botany
Abstract

The modification of histones by acetyl groups has a key role in the regulation of chromatin structure and transcription. The Arabidopsis thaliana histone acetyltransferase GCN5 regulates histone modifications as part of the Spt-Ada-Gcn5 Acetyltransferase (SAGA) transcriptional coactivator complex. GCN5 was previously shown to acetylate lysine 14 of histone 3 (H3K14ac) in the promoter regions of its target genes even though GCN5 binding did not systematically correlate with gene activation. Here, we explored the mechanism through which GCN5 controls transcription. First, we fine-mapped its GCN5 binding sites genome-wide and then used several global methodologies (ATAC-seq, ChIP-seq and RNA-seq) to assess the effect of GCN5 loss-of-function on the expression and epigenetic regulation of its target genes. These analyses provided evidence that GCN5 has a dual role in the regulation of H3K14ac levels in their 5′ and 3′ ends of its target genes. While the gcn5 mutation led to a genome-wide decrease of H3K14ac in the 5′ end of the GCN5 down-regulated targets, it also led to an increase of H3K14ac in the 3′ ends of GCN5 up-regulated targets. Furthermore, genome-wide changes in H3K14ac levels in the gcn5 mutant correlated with changes in H3K9ac at both 5′ and 3′ ends, providing evidence for a molecular link between the depositions of these two histone modifications. To understand the biological relevance of these regulations, we showed that GCN5 participates in the responses to biotic stress by repressing salicylic acid (SA) accumulation and SA-mediated immunity, highlighting the role of this protein in the regulation of the crosstalk between diverse developmental and stress-responsive physiological programs. Hence, our results demonstrate that GCN5, through the modulation of H3K14ac levels on its targets, controls the balance between biotic and abiotic stress responses and is a master regulator of plant-environmental interactions.

Published
2020

4. OGC Borehole Interoperability Experiment Engineering Report

Author

Grellet, Sylvain, Boisvert, Eric, Simons, Bruce, Rainaud, Jean-François, Lorenz, Henning, Haener, Rainer, Beaufils, Mickaël, Hollingsworth, Jay, Lieberman, Josh, Liu, Yan, Nayembil, Martin, Raymond, Olivier, Sharples, John, Warren, Peter, and LALOEUF-BLANCHARD, Sabine

Subjects
use case, spatial reference system, Geoteknik, data, conceptual model, [SDU.STU] Sciences of the Universe [physics]/Earth Sciences, borehole, Geosciences, Multidisciplinary, Geotechnical Engineering, Multidisciplinär geovetenskap, Interoperability, GML/XML encoding schema, vocabulary
Abstract

This document reports on an exercise involving several government organizations, private companies, and academics trying to harmonize various representations of boreholes into acommon model. Boreholes are widely used in geoscience and engineering to probe and assess the underground, and all those communities (custodians, vendors, distributors, etc.) model this information differently. This heterogeneity becomes a problem when information from various sources needs to be aggregated. On the other hand, different communities use boreholes,therefore, different models are expected to address different use cases. This experiment looked at solutions to harmonize core aspects of boreholes while recognizing domain specific models. This exercise resulted in a tentative model, examples and recommendations for next steps. Those steps include the recommendation for OGC to support the creation of a Borehole Standards Working Group (SWG) to formalize the core borehole model (BoreholeML (BhML)) as anofficial standard. Future work should include expanding the scope of the draft borehole model presented here and co-ordinate with ongoing OGC Geoscience standards for geology and hydrogeology to ensure that those standards can operate together. It also includes working with existing standard custodians to produce BhML-compliant version of their existing borehole standards. Generic information describing the Borehole (who, how, when, etc.) and the other aspects that describe a Borehole (e.g. construction, monitoring, management areas, etc.) are required butwere excluded from this IE. Many of these are already summarized in pre-existing models. This semantic enrichment should be undertaken by a second Borehole IE or a SWG. This report includes several XML Instance Documents that conform to a draft BhML XML Schema. These are contained in the various ER Annexes as well as from the Borehole IE GitHub repository (https://github.com/opengeospatial/boreholeie/). Where appropriate, the report references the corresponding GitHub content.

Published
2020

5. macSUP - un écho de «l’art comme expérience»

Author

Lonardoni, Francoise, Boutonnier, Thierry, Carole, Davy, Coltice, Nicolas, Dubos, Arnaud, Freud, Nicolas, Goutaland, Carine, Kopp, Jan, Lachaize, Felix, Lathuiliere, Sylvianne, Le Luyer, Cécile, Loeve, Sacha, Marandin, Clarisse, Pillonnet, Anne, Pomiès, Anissa, Raymond, Olivier, Ramos-Canut, Stella, Sahli, Naël, Thaller, Fanny, Trepoz-Vielle, Alicia, Valois, Fabrice, Yvonnet, Bruno, Musée d'Art Contemporain de Lyon (MAC Lyon), Laboratoire des Multimatériaux et Interfaces (LMI), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université de Lyon, Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL), École Centrale de Lyon (ECL), Institut National des Sciences Appliquées (INSA), Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA), Matériaux et nanostructures photoniques (MNP), Institut Lumière Matière [Villeurbanne] (ILM), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), emlyon business school, Reproduction et développement des plantes (RDP), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Liquides et interfaces (L&I), Ecole Nationale Superieure de Lyon, Ecole Nationale Supérieure des Beaux-Arts de Lyon (ENSBA), Eric Dayre et David Gauthier, CAROLE, Davy, emlyon business school (EM), and École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL)

Subjects
Arts Sciences, [SHS.ART] Humanities and Social Sciences/Art and art history, [SHS.ART]Humanities and Social Sciences/Art and art history, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2020

6. A miR172 target-deficient AP2-like gene correlates with the double flower phenotype in roses

Author

François, Léa, Verdenaud, Marion, Fu, Xiaopeng, Ruleman, Darcy, Dubois, Annick, Vandenbussche, Michiel, Bendahmane, Abdelhafid, Raymond, Olivier, Just, Jérémy, Bendahmane, Mohammed, Reproduction et développement des plantes (RDP), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Huazhong Agricultural University [Wuhan] (HZAU), INRA, ENS lYON, ANR (Program DODO) [ANR-16CE20-0024-03], ANR-16-CE20-0024,ROSASCENT,Biosynthèse des terpènes du parfum chez la rose(2016), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon)

Subjects
[SDV]Life Sciences [q-bio], lcsh:R, fungi, Gene Expression Regulation, Developmental, lcsh:Medicine, food and beverages, Flowers, Plants, Genetically Modified, Rosa, Article, MicroRNAs, Gene Expression Regulation, Plant, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, lcsh:Q, lcsh:Science, [SDV.BDD]Life Sciences [q-bio]/Development Biology, Phylogeny, ComputingMilieux_MISCELLANEOUS, Plant Proteins
Abstract

International audience; One of the well-known floral abnormalities in flowering plants is the double-flower phenotype, which corresponds to flowers that develop extra petals, sometimes even containing entire flowers within flowers. Because of their highly priced ornamental value, spontaneous double-flower variants have been found and selected for in a wide range of ornamental species. Previously, double flower formation in roses was associated with a restriction of AGAMOUS expression domain toward the centre of the meristem, leading to extra petals. Here, we characterized the genomic region containing the mutation associated with the switch from simple to double flowers in the rose. An APETALA2-like gene (RcAP2L), a member of the Target Of EAT-type (TOE-type) subfamily, lies within this interval. In the double flower rose, two alleles of RcAP2L are present, one of which harbours a transposable element inserted into intron 8. This insertion leads to the creation of a miR172 resistant RcAP2L variant. Analyses of the presence of this variant in a set of simple and double flower roses demonstrate a correlation between the presence of this allele and the double flower phenotype. These data suggest a role of this miR172 resistant RcAP2L variant in regulating RcAGAMOUS expression and double flower formation in Rosa sp.

Published
2018

7. Integration of ground-penetrating radar and microgravimetric methods to map shallow caves

Author

Raymond Olivier, Marc Luetscher, and Milan Beres

Subjects
geography, Geophysics, geography.geographical_feature_category, Cave, law, Ground-penetrating radar, Radar, Karst, Geomorphology, Geology, law.invention
Abstract

Ground-penetrating radar (GPR) and microgravimetric surveys have been conducted in the southern Jura mountains of western Switzerland in order to map subsurface karstic features. The study site, La Grande Rolaz cave, is an extensive system in which many portions have been mapped. By using small station spacing and careful processing for the geophysical data, and by modeling these data with topographic information from within the cave, accurate interpretations have been achieved. The constraints on the interpreted geologic models are better when combining the geophysical methods than when using only one of the methods, despite the general limitations of two-dimensional (2D) profiling. For example, microgravimetry can complement GPR methods for accurately delineating a shallow cave section approximately 10×10 m2 in size. Conversely, GPR methods can be complementary in determining cavity depths and in verifying the presence of off-line features and numerous areas of small cavities and fractures, which may be difficult to resolve in microgravimetric data.

Published
2001

8. Rosa

Author

Smulders, M. J. M., Arens, P., Koning-Boucoiran, C. F. S., Gitonga, V. W., Krens, F. A., Atanassov, A., Atanassov, I., Rusanov, K. E., Bendahmane, Mohammed, Dubois, Annick, Raymond, Olivier, Caissard, J. C., Baudino, S., Crespel, Laurent, Gudin, S., Ricci, S. C., Kovatcheva, N., van Huylenbroeck, J., Leus, L., Wissemann, V., Zimmermann, H., Hensen, I., Werlemark, G., Nybom, H., Plant Breeding, Wageningen University and Research [Wageningen] (WUR), AgroBioInstitute, Reproduction et développement des plantes (RDP), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Université Jean Monnet [Saint-Étienne] (UJM), Unité mixte de recherche génétique et horticulture Genhort, Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-Institut National d'Horticulture, Université Paul Cézanne - Aix-Marseille 3, Amélioration génétique d'espèces à multiplication végétative (UPR Multiplication végétative), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institute for Roses, Aromatic and Medicinal plants, Partenaires INRAE, Research Institute for Agricultural, Fisheries and Food (ILVO), Institut fur Botanik, Justus-Liebig-Universität Gießen (JLU), Department of Geobotany and Botanical Garden, Martin-Luther-Universität Halle Wittenberg (MLU), Swedish University of Agricultural Sciences (SLU), DAAD, DFG, TTI Green Genetics, National Science Fund of the Ministry of Education and Science (Bulgaria), M.J.M. smulders, Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Institut National d'Horticulture-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Justus-Liebig-Universität Gießen = Justus Liebig University (JLU), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), and Université Jean Monnet - Saint-Étienne (UJM)

Subjects
0106 biological sciences, 0303 health sciences, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, food and beverages, F70 - Taxonomie végétale et phytogéographie, 01 natural sciences, F30 - Génétique et amélioration des plantes, Plant Breeding, 03 medical and health sciences, Laboratorium voor Plantenveredeling, Life Science, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, 030304 developmental biology, 010606 plant biology & botany
Abstract

Chapter 12; International audience; Presently, about 100–250 species are usually recognized in the genus Rosa. The low levels of DNA sequence divergence found across the genus suggest that it is a young genus with much speciation taking place after the last glaciation. Poor phylogenetic resolution and commonly occurring contradictions between chloroplast and nuclear gene phylogenies suggest that hybridization has been a strong driving force in the evolution of roses, often accompanied by polyploidization. In addition, extensive anthropogenic impact has led to the development of many new semi-wild and/or cultivated rose varieties. Some wild species have become invasive. This chapter describes the taxonomy of roses. It presents examples of interesting traits in wild species that may valuable to broaden the genetic base of cultivated roses, such as thornlessness, winter hardiness, drought resistance, and improved shelf-life. Also fragrance and compounds with possible health effects are discussed. The highest priority in rose breeding research is the development of disease resistant roses. Different resistance mechanisms have been found for black spot and powdery mildew in various wild rose species. We describe how resistance genes are being mapped using crosses between wild, diploid rose species, and how other genes for traits of interest are being identified. We proceed with a discussion of various ways to overcome the taxonomic and ploidy level barriers for introgression of traits into cultivated hybrid rose or garden rose germplasm, including dihaploidization, polyploidization, and transgenics. Even so, breeding programs with wild species are usually time-consuming. For garden roses, the genetic and morphological distance between modern cultivars and the wild species is smaller, which makes the use of wild species easier than in the case of cut roses.

Published
2011
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9. Scent evolution in Chinese roses

Author

Scalliet, Gabriel, Piola, Florence, Douady, Christophe Jean, Réty, Stéphane, Raymond, Olivier, Baudino, Sylvie, Bordji, Karim, Bendahmane, Mohammed, Dumas, Christian, Cock, Mark, Hugueney, Philippe, Cock, J. Mark, BioSciences Lyon-Gerland (BLG), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Hospices Civils de Lyon (HCL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Reproduction et développement des plantes (RDP), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Syngenta Crop Protection Münschwillen AG (SCPM), SUISSE, Génome et Evolution des Plantes Supérieures (GEPS (EA3731)), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, Laboratoire d'Ecologie des Hydrosystèmes Fluviaux (EHF), Laboratoire de cristallographie et RMN biologiques (LCRB - UMR 8015), Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5), Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales (LBVPAM), Université Jean Monnet [Saint-Étienne] (UJM), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Santé de la vigne et qualité du vin (SVQV), Institut National de la Recherche Agronomique (INRA)-Université de Strasbourg (UNISTRA), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, Université Paris Descartes - Paris 5 (UPD5)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales (BVPAM), Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Université de Strasbourg (UNISTRA)-Institut National de la Recherche Agronomique (INRA), BioSciences Lyon-Gerland ( BLG ), École normale supérieure - Lyon ( ENS Lyon ) -Institut National de la Recherche Agronomique ( INRA ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Hospices Civils de Lyon ( HCL ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Reproduction et développement des plantes ( RDP ), Centre National de la Recherche Scientifique ( CNRS ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -École normale supérieure - Lyon ( ENS Lyon ), Syngenta Crop Protection Münschwillen AG ( SCPM ), Génome et Evolution des Plantes Supérieures ( GEPS (EA3731) ), Université Claude Bernard Lyon 1 ( UCBL ), Laboratoire d'Ecologie des Hydrosystèmes Fluviaux ( EHF ), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de cristallographie et RMN biologiques ( LCRB - UMR 8015 ), Université Paris Descartes - Paris 5 ( UPD5 ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales ( LBVPAM ), Université Jean Monnet [Saint-Étienne] ( UJM ), Station biologique de Roscoff [Roscoff] ( SBR ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ), Santé de la vigne et qualité du vin ( SVQV ), Université de Strasbourg ( UNISTRA ) -Institut National de la Recherche Agronomique ( INRA ), and Université Paris Descartes - Paris 5 (UPD5)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, China, Molecular Sequence Data, Flowers, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Anisoles, Biology, Rosa, Orcinol, Methylation, 01 natural sciences, Genome, Substrate Specificity, 03 medical and health sciences, chemistry.chemical_compound, Biosynthesis, hybrid tea, dimethoxytoluene, Botany, Gene family, Rosa chinensis, Gene, 030304 developmental biology, chemistry.chemical_classification, Genetics, ROSE, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, 0303 health sciences, Polymorphism, Genetic, Multidisciplinary, Base Sequence, OOMT, Methyltransferases, Biological Sciences, biology.organism_classification, Biological Evolution, flower, Europe, Enzyme, volatiles, chemistry, CHINESE ROSES, Odorants, ORCINOL O-METHYLTRANSFERASE, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, 010606 plant biology & botany
Abstract

The phenolic methyl ether 3,5-dimethoxytoluene (DMT) is a major scent compound of many modern rose varieties, and its fragrance participates in the characteristic “tea scent” that gave their name to Tea and Hybrid Tea roses. Among wild roses, phenolic methyl ether (PME) biosynthesis is restricted to Chinese rose species, but the progenitors of modern roses included both European and Chinese species (e.g., Rosa chinensis cv Old Blush), so this trait was transmitted to their hybrid progeny. The last steps of the biosynthetic pathways leading to DMT involve two methylation reactions catalyzed by the highly similar orcinol O -methyltransferases (OOMT) 1 and 2. OOMT1 and OOMT2 enzymes exhibit different substrate specificities that are consistent with their operating sequentially in DMT biosynthesis. Here, we show that these different substrate specificities are mostly due to a single amino acid polymorphism in the phenolic substrate binding site of OOMTs. An analysis of the OOMT gene family in 18 species representing the diversity of the genus Rosa indicated that only Chinese roses possess both the OOMT2 and the OOMT1 genes. In addition, we provide evidence that the Chinese-rose-specific OOMT1 genes most probably evolved from an OOMT2 -like gene that has homologues in the genomes of all extant roses. We propose that the emergence of the OOMT1 gene may have been a critical step in the evolution of scent production in Chinese roses.

Published
2008

10. A Subway Project In Lausanne, Switzerland, As An Urban Microgravimetry Test Site: Acquisition, Correction Of Buildings Influence And Modeling

Author

Pier Vittorio Radogna, Raymond Olivier, and Philippe Logean

Subjects
Shore, Engineering, geography, geography.geographical_feature_category, business.industry, Lithology, Bedrock, Elevation, Drilling, Geodesy, Overburden, Altitude, business, Digital elevation model, Cartography
Abstract

A new subway will be constructed within the next decade in Lausanne. The geology involved constitutes alpine molassic bedrock and an overlaying quaternary glacial fill. The choice of the subway corridor (6 km) had to consider the exact thickness of these geological units. The availability of mechanical logging data offered the opportunity for testing a microgravimetry survey. The distance from nearby constructions determined whether corrections had to be made for these volumes or could be omitted. We calculated, with an in house program, the effect of different buildings to choose architectural styles with similar gravimetric responses. We are using then a geographic information system (GIS) to group these buildings by typology based on cadastral records and correct all the buildings with simplified architectural styles. The voids of the basements were included in the digital elevation model to take account of the complexity of the Lausanne morphology. All these corrections could be calculated before the acquisition in order to chose the best gravity stations location. The residual gravity map is adjusted to only some drillings, in order to regionalize this punctual data and to compare the results of the bedrock modeling with the drillings not taken into account. The microgravity objective The objective is to regionalize isolated drilling information to the entire test zone. The goal of the microgravity survey would be to reduce the number of drillings and to enlarge the knowledge of the modeled bedrock surface along the project corridor. Geographical and geological situation A new underground railway, named M2, will be constructed within the next decade in Lausanne, the fifth populated city of Switzerland, from the shore of Lake Geneva at 375 m altitude to the suburb Epalinges further north at 698 m altitude. The choice of the six-kilometer-long corridor (fig. 1) had to consider the tertiary lithology to be excavated for the construction of the tunnel . The involved geology is constituted by the alpine molassic formation (a local tertiary sandstone), overlaying quaternary glacial fill and an overburden of loose soil. According to drills the bedrock is situated at a depth varying from 1.5 m to 25 m. The density contrast and the depth of the bedrock are sufficient for a micro-gravity investigation. Average densities obtained by sampling were 2.4 g/cm for the molassic bedrock, 2.1 g/cm for the glacial fill and 1.8 g/cm for the backfill. Figure 1.: The six-kilometer-long corridor of the planned “Lausanne Metro” from Ouchy on the bank of Lake Geneva to Epalinges. Microgravity Survey zone I In summer 2001 and 2002 the first micro-gravity site I was chosen in the northern part of the town to carry out preliminary tests. In summer 2002, the measurements campaign was continued in the same site along the highway running parallel to the future underground. The buildings, regularly spaced, have a repetitive shape and the correction of their effect seemed quite easy. Micro-gravity acquisitions were carried out with an electronic readout Lacoste & Romberg D89 (ETHZ) in two 200 m long parallel profiles (Fig. 2) along the Avenue of Berne (zone I). Average station spacing was 5 m and in some cases 1 m. The position was determined by GPS or laser theodolite with a GPS location accuracy better than 5 cm and a relative elevation better than 3 cm. For the close topographic corrections (Hammer, 1939) average relief elevation was measured within 22 m and with an accuracy of 10 cm. Measurements were executed late at night so as to minimize traffic noise. Standard corrections and adjustment to drillings allowed the determination of a residual anomaly. 2D modeling We modeled two surfaces of the bedrock using the residual anomaly calculated from this data. A geologic section from the cantonal transportation service was available plus four drillings; one along the profile and three laterally shifted at 15 m intervals. The comparison of the calculated surfaces and the geologic section (Figure 3) shows a good coherence and the general trend is similar. The calculated profiles were fitted only with the crossed drillings, unlike the geologic section 0 50 100 150 200 distance (m) -0.5 -0.4 -0.3 -0.2 -0.1 0

Published
2004

11. Evaluation of a Precipitation Map Using a Smoothed Elevation-Precipitation Relationship and Optimal Estimates (Kriging)

Author

Raymond Olivier, F.A. de Montmollin, R. G. Simard, and F. Zwahlen

Subjects
Altitude, Meteorology, Kriging, Anomaly (natural sciences), Linear regression, Elevation, Precipitation, Spatial dependence, Geodesy, Variogram, Geology, Water Science and Technology
Abstract

Using 45 rain gauges, located in the center of French-speaking Switzerland (approx. 1,600 sq. km), we evaluate an annual mean precipitation map for the years 1974, 1975 and 1976. This estimate is based mainly on the anomaly method. For the index elevation, we selected an average altitude over an area of optimized size. This was evaluated from the best linear regression between index elevation of different areas and the precipitations. An anomaly map was estimated using universal kriging: the structural analysis of the anomaly values permitted the adjustment of a variogram which made it possible to evaluate the spatial dependence of the anomaly variable. In order to obtain the precipitation map, not only was an anomaly map used but also a smoothed altitude map. This was calculated with the aid of an altimetric data bank covering the west part of Switzerland

Published
1980

12. Utilisation d'une grille d'altitudes digitalisées pour la cartographie d'éléments du bilan hydrique

Author

François Zwahlen, Raymond Olivier, and François De Montmollin

Subjects
Hydrology, Water balance, geography, geography.geographical_feature_category, Elevation, Evaporation, Drainage basin, Environmental science, Precipitation, Surface runoff, Water Science and Technology
Abstract

The authors tried to determine the various elements of the water balance in a Swiss middleland typical water basin. To obtain this result they correlated pluviometry and elevation on a digitalized grid, which elements are 50 m 2 . This allows the elaboration of coordinated maps of the kind as proposed by Nordenson. This requires the establishment of precipitation and evaporation maps (the Turc formula or any other can be used), and it also requires a knowledge of the runoff. To illustrate the possibilities of the models constructed, the authors studied the various characteristics of the Mentue, a river located north of Lausanne (Switzerland).

Published
1979

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