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1. Deciphering Plant Chromatin Regulation via CRISPR/dCas9-Based Epigenome Engineering

Author

Annick Dubois and François Roudier

Subjects
CRISPR-dCas9, epigenome editing, epigenome engineering, chromatin, plant, Genetics, QH426-470, Biotechnology, TP248.13-248.65
Abstract

CRISPR-based epigenome editing uses dCas9 as a platform to recruit transcription or chromatin regulators at chosen loci. Despite recent and ongoing advances, the full potential of these approaches to studying chromatin functions in vivo remains challenging to exploit. In this review we discuss how recent progress in plants and animals provides new routes to investigate the function of chromatin regulators and address the complexity of associated regulations that are often interconnected. While efficient transcriptional engineering methodologies have been developed and can be used as tools to alter the chromatin state of a locus, examples of direct manipulation of chromatin regulators remain scarce in plants. These reports also reveal pitfalls and limitations of epigenome engineering approaches that are nevertheless informative as they are often associated with locus- and context-dependent features, which include DNA accessibility, initial chromatin and transcriptional state or cellular dynamics. Strategies implemented in different organisms to overcome and even take advantage of these limitations are highlighted, which will further improve our ability to establish the causality and hierarchy of chromatin dynamics on genome regulation.

Published
2021
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2. A mechanosensitive Ca2+ channel activity is dependent on the developmental regulator DEK1

Author

Daniel Tran, Roberta Galletti, Enrique D. Neumann, Annick Dubois, Reza Sharif-Naeini, Anja Geitmann, Jean-Marie Frachisse, Olivier Hamant, and Gwyneth C. Ingram

Subjects
Science
Abstract

A rise in cytoplasmic Ca2+ concentration is a well-described response of plant cells to mechanical stimulation. Here the authors show that the DEK1 protein, which is essential for epidermis specification and development in plants, is required for triggering a mechanically-activated Ca2+ channel.

Published
2017
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3. Genomic approach to study floral development genes in Rosa sp.

Author

Annick Dubois, Arnaud Remay, Olivier Raymond, Sandrine Balzergue, Aurélie Chauvet, Marion Maene, Yann Pécrix, Shu-Hua Yang, Julien Jeauffre, Tatiana Thouroude, Véronique Boltz, Marie-Laure Martin-Magniette, Stéphane Janczarski, Fabrice Legeai, Jean-Pierre Renou, Philippe Vergne, Manuel Le Bris, Fabrice Foucher, and Mohammed Bendahmane

Subjects
Medicine, Science
Abstract

Cultivated for centuries, the varieties of rose have been selected based on a number of flower traits. Understanding the genetic and molecular basis that contributes to these traits will impact on future improvements for this economically important ornamental plant. In this study, we used scanning electron microscopy and sections of meristems and flowers to establish a precise morphological calendar from early rose flower development stages to senescing flowers. Global gene expression was investigated from floral meristem initiation up to flower senescence in three rose genotypes exhibiting contrasted floral traits including continuous versus once flowering and simple versus double flower architecture, using a newly developed Affymetrix microarray (Rosa1_Affyarray) tool containing sequences representing 4765 unigenes expressed during flower development. Data analyses permitted the identification of genes associated with floral transition, floral organs initiation up to flower senescence. Quantitative real time PCR analyses validated the mRNA accumulation changes observed in microarray hybridizations for a selection of 24 genes expressed at either high or low levels. Our data describe the early flower development stages in Rosa sp, the production of a rose microarray and demonstrate its usefulness and reliability to study gene expression during extensive development phases, from the vegetative meristem to the senescent flower.

Published
2011
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4. Tinkering with the C-function: a molecular frame for the selection of double flowers in cultivated roses.

Author

Annick Dubois, Olivier Raymond, Marion Maene, Sylvie Baudino, Nicolas B Langlade, Véronique Boltz, Philippe Vergne, and Mohammed Bendahmane

Subjects
Medicine, Science
Abstract

BACKGROUND: Roses have been cultivated for centuries and a number of varieties have been selected based on flower traits such as petal form, color, and number. Wild-type roses have five petals (simple flowers), whereas high numbers of petals (double flowers) are typical attributes of most of the cultivated roses. Here, we investigated the molecular mechanisms that could have been selected to control petal number in roses. METHODOLOGY/PRINCIPAL FINDINGS: We have analyzed the expression of several candidate genes known to be involved in floral organ identity determination in roses from similar genetic backgrounds but exhibiting contrasting petal numbers per flower. We show that the rose ortholog of AGAMOUS (RhAG) is differentially expressed in double flowers as compared to simple flowers. In situ hybridization experiments confirm the differential expression of RhAG and demonstrate that in the double-flower roses, the expression domain of RhAG is restricted toward the center of the flower. Conversely, in simple-flower roses, RhAG expression domain is wider. We further show that the border of RhAG expression domain is labile, which allows the selection of rose flowers with increased petal number. Double-flower roses were selected independently in the two major regions for domestication, China and the peri-Mediterranean areas. Comparison of RhAG expression in the wild-type ancestors of cultivated roses and their descendants both in the European and Chinese lineages corroborates the correlation between the degree of restriction of RhAG expression domain and the number of petals. Our data suggests that a restriction of RhAG expression domain is the basis for selection of double flowers in both the Chinese and peri-Mediterranean centers of domestication. CONCLUSIONS/SIGNIFICANCE: We demonstrate that a shift in RhAG expression domain boundary occurred in rose hybrids, causing double-flower phenotype. This molecular event was selected independently during rose domestication in Europe/Middle East and in China.

Published
2010
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5. Genome-wide analysis of gene expression during early Arabidopsis flower development.

Author

Frank Wellmer, Márcio Alves-Ferreira, Annick Dubois, José Luis Riechmann, and Elliot M Meyerowitz

Subjects
Genetics, QH426-470
Abstract

Detailed information about stage-specific changes in gene expression is crucial for the understanding of the gene regulatory networks underlying development. Here, we describe the global gene expression dynamics during early flower development, a key process in the life cycle of a plant, during which floral patterning and the specification of floral organs is established. We used a novel floral induction system in Arabidopsis, which allows the isolation of a large number of synchronized floral buds, in conjunction with whole-genome microarray analysis to identify genes with differential expression at distinct stages of flower development. We found that the onset of flower formation is characterized by a massive downregulation of genes in incipient floral primordia, which is followed by a predominance of gene activation during the differentiation of floral organs. Among the genes we identified as differentially expressed in the experiment, we detected a significant enrichment of closely related members of gene families. The expression profiles of these related genes were often highly correlated, indicating similar temporal expression patterns. Moreover, we found that the majority of these genes is specifically up-regulated during certain developmental stages. Because co-expressed members of gene families in Arabidopsis frequently act in a redundant manner, these results suggest a high degree of functional redundancy during early flower development, but also that its extent may vary in a stage-specific manner.

Published
2006
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6. Dynamique de la Chromatine , développement des plantes, ingéniérie épigénomique

Author

François Roudier, Annick Dubois, 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), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), and ANR-18-CE12-0014,ChromAuxi,Décodage de la réponse auxine à l'interface ARFs-chromatine(2018)

Subjects
0106 biological sciences, QH301-705.5, Computer science, [SDV]Life Sciences [q-bio], Health, Toxicology and Mutagenesis, plant, Computational biology, Review, 01 natural sciences, Biochemistry, Genetics and Molecular Biology (miscellaneous), Biochemistry, 03 medical and health sciences, Genome regulation, Genetics, Epigenome editing, CRISPR, Cellular dynamics, Biology (General), epigenome engineering, 030304 developmental biology, 0303 health sciences, CRISPR-dCas9, Epigenome, Chromatin, CRISPR-dC9as9, epigenome editing, Medicine, chromatin, Transcription (software), Function (biology), 010606 plant biology & botany
Abstract

International audience; CRISPR-based epigenome editing uses dCas9 as a platform to recruit transcription or chromatin regulators at chosen loci. Despite recent and ongoing advances, the full potential of these approaches to studying chromatin functions in vivo remains challenging to exploit. In this review we discuss how recent progress in plants and animals provides new routes to investigate the function of chromatin regulators and address the complexity of associated regulations that are often interconnected. While efficient transcriptional engineering methodologies have been developed and can be used as tools to alter the chromatin state of a locus, examples of direct manipulation of chromatin regulators remain scarce in plants. These reports also reveal pitfalls and limitations of epigenome engineering approaches that are nevertheless informative as they are often associated with locus- and context-dependent features, which include DNA accessibility, initial chromatin and transcriptional state or cellular dynamics. Strategies implemented in different organisms to overcome and even take advantage of these limitations are highlighted, which will further improve our ability to establish the causality and hierarchy of chromatin dynamics on genome regulation.

Published
2021

7. Rose floral scent

Author

Sylvie Baudino, Mohammed Bendahmane, J. Clotault, Sandrine Moja, Annick Dubois, B. Nairaud, L. Hibrand-Saint Oyant, Fabrice Foucher, Jean-Louis Magnard, Aurélie Rius Bony, Bernard Blerot, Tatiana Thouroude, Jean-Claude Caissard, Frédéric Jullien, Robert C. Schuurink, Philippe Vergne, Julien Jeauffre, Pulu Sun, and Olivier Raymond

Subjects
fungi, Stamen, food and beverages, Horticulture, Biology, biology.organism_classification, Terpenoid, law.invention, Terpene, chemistry.chemical_compound, chemistry, law, Pollinator, Botany, Queen (butterfly), Petal, Essential oil, Geraniol
Abstract

The rose is the queen of flowers and is widely used as a garden plant and for the cut flower market. Roses are also used for the production of essential oil for the cosmetic and perfume industries. A lot of botanical roses are scented and use their volatiles to attract pollinators. Fragrances in garden roses are very diverse and scent has always been an important character in the selection process. Breeders have recently tried to introduce new fragrances, for instance reminiscent of fruit or spice odors. But despite their efforts, some roses on the market are not very fragrant, especially the ones selected for the cut flower market. The cause of this lack of scent is not known. In modern roses or Hybrid Tea roses, scent is mainly produced by petals, although stamens can also contribute to the emission of volatiles. Scent compounds are concentrated in rose petal epidermis, probably in small lipid droplets. In spite of numerous chemical studies, the biosynthetic pathways of many rose scent compounds are unknown. We are studying several genes involved in the biosynthesis of scent in rose. For example, we recently characterized the enzymes responsible for the so-called “tea scent” emitted by Chinese roses. Apart from “tea scent”, terpenoids, especially monoterpenes, are also major constituents of rose flowers, mostly responsible for the “typical rose scent”. Generally, terpenoid biosynthesis in plants is achieved by various terpene synthases. However, with a combination of transcriptomic and genetic approaches, our research group recently discovered a terpene synthase-independent pathway. A key enzyme of this pathway is RhNUDX1, belonging to the Nudix protein family. It has geranyl diphosphate diphosphohydrolase activity in vitro. A positive correlation was found between the expression levels of RhNUDX1 gene and the production of the monoterpene geraniol, indicating its essential role in scent production in roses.

Published
2019

9. Biosynthesis of 2-Phenylethanol in Rose Petals Is Linked to the Expression of One Allele of RhPAAS

Author

Fabrice Foucher, Philippe Vergne, Mohammed Bendahmane, Emilie Cavel, Aymeric Roccia, Laurence Hibrand-Saint Oyant, Judit Szécsi, Sylvie Baudino, Tatiana Thouroude, Aurélie Rius Bony, Jean-Claude Caissard, Annick Dubois, Julien Jeauffre, Jana Machenaud, Laboratoire BVpam, Université Jean Monnet [Saint-Étienne] (UJM), Institut de Recherche en Horticulture et Semences (IRHS), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales (BVPAM), Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), Reproduction et développement des plantes (RDP), 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 de Lyon-Centre National de la Recherche Scientifique (CNRS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Region Auvergne-Rhone-Alpes, INRA, France, CNRS GDR MediatEC 3658, ANR Rosascent, Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales (LBVPAM), Université Jean Monnet [Saint-Étienne] (UJM)-Centre National de la Recherche Scientifique (CNRS), and 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)

Subjects
0106 biological sciences, Candidate gene, Physiology, Population, Quantitative Trait Loci, Plant Science, Flowers, Quantitative trait locus, Biology, Rosa, 01 natural sciences, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Botany, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Cultivar, Allele, education, Alleles, Hybrid, Plant Proteins, 2. Zero hunger, education.field_of_study, Vase life, food and beverages, Articles, Phenylethyl Alcohol, Biosynthetic Pathways, Odorants, Petal, 010606 plant biology & botany
Abstract

International audience; Floral scent is one of the most important characters in horticultural plants. Roses (Rosa spp.) have been cultivated for their scent since antiquity. However, probably by selecting for cultivars with long vase life, breeders have lost the fragrant character in many modern roses, especially the ones bred for the cut flower market. The genetic inheritance of scent characters has remained elusive so far. In-depth knowledge of this quantitative trait is thus very much needed to breed more fragrant commercial cultivars. Furthermore, rose hybrids harbor a composite genomic structure, which complexifies quantitative trait studies. To understand rose scent inheritance, we characterized a segregating population from two diploid cultivars, Rosa × hybrida cv H190 and Rosa wichurana, which have contrasting scent profiles. Several quantitative trait loci for the major volatile compounds in this progeny were identified. One among these loci contributing to the production of 2-phenylethanol, responsible for the characteristic odor of rose, was found to be colocalized with a candidate gene belonging to the 2-phenylethanol biosynthesis pathway: the PHENYLACETALDEHYDE SYNTHASE gene RhPAAS. An in-depth allele-specific expression analysis in the progeny demonstrated that only one allele was highly expressed and was responsible for the production of 2-phenylethanol. Unexpectedly, its expression was found to start early during flower development, before the production of the volatile 2-phenylethanol, leading to the accumulation of glycosylated compounds in petals.; Analyse des composés du parfum dans une population en ségrégation qui montre que la synthèse du2-phenylethanol est liée à l'expression d'un allèle deu gène de laphenylacetaldehyde synthase dans les pétales

Published
2019

10. Production of homozygous rose line derived from heterozygous genotype

Author

Mohammed Bendahmane, Philippe Vergne, Jeremy Just, Judit Szécsi, Annick Dubois, and Olivier Raymond

Subjects
0301 basic medicine, Rose (mathematics), Heterozygous genotype, 03 medical and health sciences, 030104 developmental biology, General Earth and Planetary Sciences, Line (text file), Biology, Molecular biology, General Environmental Science
Published
2018

11. The Rosa genome provides new insights into the domestication of modern roses

Author

Sylvie Baudino, Caroline Pont, Arnaud Lemainque, Michiel Vandenbussche, Jean-Claude Caissard, Teva Vernoux, Patrick Wincker, Florence Piola, Chang Liu, Hélène Badouin, Adnane Boualem, Mohammed-Amin Madoui, Moussa Benhamed, Jean-Marc Aury, Jérôme Salse, Abdelhafid Bendahmane, Manuel Le Bris, Benjamin Govetto, Hadi Quesneville, Olivier Raymond, Jérôme Gouzy, Mohammed Bendahmane, Sandrine Moja, Annick Dubois, Judit Szécsi, Priscilla Villand, Claudia Bardoux, Shu-Hua Yang, Céline Lopez-Roques, Ludovic Cottret, Pascal Heitzler, Antoine Larrieu, Véronique Boltz, Nathalie Choisne, Yoan Labrousse, Léa François, David Latrasse, Marion Verdenaud, Lauriane Perrier, Philippe Vergne, Sébastien Carrère, Magali Perez, Karine Labadie, Arnaud Couloux, Xiaopeng Fu, Jérémy Just, 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 des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), 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), Centre National de Génotypage (CNG), 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), Institut National de la Recherche Agronomique (INRA), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), 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 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)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés (LEHNA), Centre National de la Recherche Scientifique (CNRS)-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), 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), Institut de biologie moléculaire des plantes (IBMP), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Zentrum für Molekularbiologie der Pflanzen (ZMBP), Eberhard Karls Universität Tübingen, ANR-13-BSV7-0014,DODO,Identification et caractérisation des mutations DOMINANT DOUBLE (DODO) and DOUBLE FLOWER (DF) chez le pétunia et la rose(2013), ANR-12-BSV6-0005,AuxiFlo,Couplage entre le réseau transcriptionnel de l'auxine et l'identité florale(2012), ANR-11-IDEX-02/10-LABX-0040,SPS,Saclay Plant Sciences(2011), European Project: 341076,EC:FP7:ERC,ERC-2013-ADG,SEXYPARTH(2014), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Université Jean Monnet [Saint-Étienne] (UJM)-Centre National de la Recherche Scientifique (CNRS), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Recherche Agronomique (INRA), 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), 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), Équipe 2 - Écologie Végétale et Zones Humides (EVZH), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS)-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 National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, GET-PACBIO program (programme operationnel FEDER-FSE MIDI-PYRENEES ET GARONNE), French National Institute of Agronomic Research (INRA), program Fonds Recherche of Ecole Normale Superieure-Lyon-France, Genoscope, French National Research Agency program DODO : ANR-16CE20-0024-03, French National Research Agency program AUXIFLO : ANR-12-BSV6-0005, Labex Saclay Plant Sciences-SPS : ANR-10- LABX-0040-SPS, ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), 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 de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales (BVPAM), Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), and Huazhong Agricultural University [Wuhan] (HZAU)

Subjects
0301 basic medicine, Candidate gene, Genotype, Flowers, Biology, Genes, Plant, Rosa, Genome, Article, Domestication, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Gene Expression Regulation, Plant, Genetic variation, Genetics, rosaceae, Rosa chinensis, Gene, odeur, couleur, Hybrid, Plant Proteins, Vegetal Biology, Whole Genome Sequencing, génome, Genetic Variation, Genomics, Sequence Analysis, DNA, biology.organism_classification, 030104 developmental biology, Evolutionary biology, [SDE]Environmental Sciences, gène candidat, Ploidy, séquençage adn, Biologie végétale, Genome, Plant
Abstract

Epub ahead of print; International audience; Roses have high cultural and economic importance as ornamental plants and in the perfume industry. We report the rose whole-genome sequencing and assembly and resequencing of major genotypes that contributed to rose domestication. We generated a homozygous genotype from a heterozygous diploid modern rose progenitor, Rosa chinensis ‘Old Blush’. Using single-molecule real-time sequencing and a meta-assembly approach, we obtained one of the most comprehensive plant genomes to date. Diversity analyses highlighted the mosaic origin of ‘La France’, one of the first hybrids combining the growth vigor of European species and the recurrent blooming of Chinese species. Genomic segments of Chinese ancestry identified new candidate genes for recurrent blooming. Reconstructing regulatory and secondary metabolism pathways allowed us to propose a model of interconnected regulation of scent and flower color. This genome provides a foundation for understanding the mechanisms governing rose traits and should accelerate improvement in roses, Rosaceae and ornamentals.

Published
2018

12. ROSE GENOMICS: CHALLENGES AND PERSPECTIVES

Author

Olivier Raymond, Mohammed Bendahmane, Annick Dubois, Judit Szécsi, Jérémy Just, Philippe Vergne, 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), Flanders Research Institute for Agriculture, Fisheries and Food (ILVO). BEL., École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Rose (mathematics), 0303 health sciences, [SDV]Life Sciences [q-bio], food and beverages, Genomics, Horticulture, Biology, 01 natural sciences, 03 medical and health sciences, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Domestication, genome, Rosaceae, 030304 developmental biology, 010606 plant biology & botany
Abstract

International audience; Cultivated roses have a very ancient history. Artificial crossing led to what is today perceived as modern rose cultivars. Impressively, these modern rose cultivars were established from less than 10 species, which have contributed to the origin of the about 35,000 existing rose cultivars. Roses exhibit an extraordinary diversity of traits, both of economic and scientific importance. Several recent studies have been marked as important milestones on the journey towards deeply understanding the molecular and genetic mechanisms that govern these traits, yet we still lack information on the genome sequences of rose species and cultivars, especially those that heavily participated to rose domestication and breeding programs.

Published
2015

13. Genetics and genomics of flower initiation and development in roses

Author

Manuel Le Bris, Olivier Raymond, Mohammed Bendahmane, Annick Dubois, 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), Avignon Université (AU), Biologie Vegetale Department of the French 'Institut National de la Recherche Agronomique, École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Time Factors, Physiology, [SDV]Life Sciences [q-bio], Quantitative Trait Loci, Color, Plant Development, morphogenesis, POWDERY MILDEW RESISTANCE, Genomics, Flowers, Plant Science, Cut flowers, Biology, Genes, Plant, Rosa, 01 natural sciences, HYBRIDA L, DIPLOROSES, Anthocyanins, 03 medical and health sciences, Gene Expression Regulation, Plant, Flowering Newsletter Review, Ornamental plant, Botany, genomics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Arabidopsis thaliana, MOLECULAR CHARACTERIZATION, Domestication, Plant Proteins, rose, 030304 developmental biology, BUD BURST, Volatile Organic Compounds, 0303 health sciences, FLORAL IDENTITY GENES, fungi, food and beverages, FLAVONOBIOSYNTHETIC-PATHWAY, AGROBACTERIUM-TUMEFACIENS, biology.organism_classification, O-METHYLTRANSFERASES, Plant development, Phenotype, Flower, Petal, MADS-BOX GENES, 010606 plant biology & botany
Abstract

International audience; Roses hold high symbolic value and great cultural importance in different societies throughout human history. They are widely used as garden ornamental plants, as cut flowers, and for the production of essential oils for the perfume and cosmetic industries. Domestication of roses has a long and complex history, and the rose species have been hybridized across vast geographic areas such as Europe, Asia, and the Middle East. The domestication processes selected several flower characters affecting floral quality, such as recurrent flowering, double flowers, petal colours, and fragrance. The molecular and genetic events that determine some of these flower characters cannot be studied using model species such as Arabidopsis thaliana, or at least only in a limited manner. In this review, we comment on the recent development of genetic, genomic, and transcriptomic tools for roses, and then focus on recent advances that have helped unravel the molecular mechanisms underlying several rose floral traits.

Published
2013

14. PLANT VOLATILES. Biosynthesis of monoterpene scent compounds in roses

Author

Jean-Louis, Magnard, Aymeric, Roccia, Jean-Claude, Caissard, Philippe, Vergne, Pulu, Sun, Romain, Hecquet, Annick, Dubois, Laurence, Hibrand-Saint Oyant, Frédéric, Jullien, Florence, Nicolè, Olivier, Raymond, Stéphanie, Huguet, Raymonde, Baltenweck, Sophie, Meyer, Patricia, Claudel, Julien, Jeauffre, Michel, Rohmer, Fabrice, Foucher, Philippe, Hugueney, Mohammed, Bendahmane, and Sylvie, Baudino

Subjects
Volatile Organic Compounds, Terpenes, Acyclic Monoterpenes, Molecular Sequence Data, Odorants, Monoterpenes, Plastids, Pyrophosphatases, Rosa, Transcriptome
Abstract

The scent of roses (Rosa x hybrida) is composed of hundreds of volatile molecules. Monoterpenes represent up to 70% percent of the scent content in some cultivars, such as the Papa Meilland rose. Monoterpene biosynthesis in plants relies on plastid-localized terpene synthases. Combining transcriptomic and genetic approaches, we show that the Nudix hydrolase RhNUDX1, localized in the cytoplasm, is part of a pathway for the biosynthesis of free monoterpene alcohols that contribute to fragrance in roses. The RhNUDX1 protein shows geranyl diphosphate diphosphohydrolase activity in vitro and supports geraniol biosynthesis in planta.

Published
2015

15. A mechanosensitive Ca

Author

Daniel, Tran, Roberta, Galletti, Enrique D, Neumann, Annick, Dubois, Reza, Sharif-Naeini, Anja, Geitmann, Jean-Marie, Frachisse, Olivier, Hamant, and Gwyneth C, Ingram

Subjects
Phenotype, Arabidopsis Proteins, Calpain, Arabidopsis, Calcium, Stress, Mechanical, Article
Abstract

Responses of cells to mechanical stress are thought to be critical in coordinating growth and development. Consistent with this idea, mechanically activated channels play important roles in animal development. For example, the PIEZO1 channel controls cell division and epithelial-layer integrity and is necessary for vascular development in mammals. In plants, the actual contribution of mechanoperception to development remains questionable because very few putative mechanosensors have been identified and the phenotypes of the corresponding mutants are rather mild. Here, we show that the Arabidopsis Defective Kernel 1 (DEK1) protein, which is essential for development beyond early embryogenesis, is associated with a mechanically activated Ca2+ current in planta, suggesting that perception of mechanical stress plays a critical role in plant development., A rise in cytoplasmic Ca2+ concentration is a well-described response of plant cells to mechanical stimulation. Here the authors show that the DEK1 protein, which is essential for epidermis specification and development in plants, is required for triggering a mechanically-activated Ca2+ channel.

Published
2015

16. Biosynthesis of monoterpene scent compounds in roses

Author

Stéphanie Huguet, Julien Jeauffre, Sophie Meyer, Raymonde Baltenweck, Sylvie Baudino, Michel Rohmer, Annick Dubois, Aymeric Roccia, Mohammed Bendahmane, Fabrice Foucher, Romain Hecquet, Patricia Claudel, Laurence Hibrand-Saint Oyant, Philippe Hugueney, Jean-Claude Caissard, Florence Nicolè, Pulu Sun, Frédéric Jullien, Jean-Louis Magnard, Olivier Raymond, Philippe Vergne, Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales (LBVPAM), Université Jean Monnet [Saint-Étienne] (UJM), 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), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), 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), Santé de la vigne et qualité du vin (SVQV), Institut National de la Recherche Agronomique (INRA)-Université de Strasbourg (UNISTRA), Institut Le Bel, Region Rhone-Alpes, CNRS [GDR 2827], ENS Lyon, INRA, Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales (BVPAM), Université Jean Monnet - Saint-Étienne (UJM)-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), Laboratoire BVpam, 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)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université Louis Pasteur - Strasbourg I, AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11), 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
0106 biological sciences, Rose, pyrophosphatase, Monoterpene, [SDV]Life Sciences [q-bio], Biology, plastide, Biosynthesis, 01 natural sciences, Nudix hydrolase, Terpene, 03 medical and health sciences, chemistry.chemical_compound, Botany, donnée de séquence moléculaire, Cultivar, odeur, 2-phenylethanol, Geranyl diphosphate, biosynthesis, rose, monoterpene, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, Multidisciplinary, fungi, food and beverages, Metabolic pathway, Enzyme, Biochemistry, chemistry, transcriptome, Geraniol, 010606 plant biology & botany
Abstract

Stop to smell the roses Some roses smell beautiful, yet others only look beautiful. Magnard et al. leveraged this distinction to study the biosynthesis of geraniol, a monoterpene alcohol in rose scent (see the Perspective by Tholl and Gershenzon). Enzymes known for geraniol synthesis in other plants, such as basil, did not seem to provide that function for roses. Instead, a diphosphohydrolase, which functions in the cytoplasm of cells in rose petals, generates the geraniol emitted by fragrant roses. Identification of the enzyme and its gene enables marker-assisted breeding to put the perfume back into beauty. Science , this issue p. 81 ; see also p. 28

Published
2015

17. Functional analysis via standardized whole-blood stimulation systems defines the boundaries of a healthy immune response to complex stimuli

Author

Ivo Gomperts-Boneca, Ludovic Deriano, Spencer L. Shorte, Annick Dubois, Anavaj Sakuntabhai, Claude Leclerc, Caroline Demangel, Ana Cumano, Lluis Quintana-Murci, Matthew L. Albert, Antonio A. Freitas, Antoine Toubert, Lars Rogge, Manfred Schmolz, Gérard Eberl, Vincent Rouilly, Valentina Libri, Alejandra Urrutia, James P. Di Santo, Eric Tartour, Marie-Noëlle Ungeheuer, Françoise Dromer, Hugo Mouquet, Olivier Schwartz, Benoit Beitz, Mikael David, Olivier Lantz, Stéphanie Thomas, Ivo G. Boneca, Philippe Bousso, Laurent Abel, Vassili Soumelis, Cécile Delval, Darragh Duffy, Benno Schwikowski, Frédéric Tangy, Serge Hercberg, Jost Enninga, Milena Hasan, Samuel S.T. LaBrie, Sandra Pellegrini, Aurélie Bisiaux, Stanislas Pol, Marc Daëron, Andrés Alcover, Immunobiologie des Cellules dendritiques, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de Recherche Translationnelle - Center for Translational Science (CRT), Institut Pasteur [Paris] (IP), Centre d'Immunologie Humaine (CIH), Substances Lichéniques et Photoprotection, Université de Rennes (UR), Centre d'Immunologie et de Maladies Infectieuses (CIMI), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Immunobiologie des Cellules Dendritiques, Myriad rules based medicine, Chambre Régionale d'Agriculture des Pays de la Loire, Biologie et Génétique de la Paroi bactérienne - Biology and Genetics of Bacterial Cell Wall (BGPB), Laboratoire de géographie physique : Environnements Quaternaires et Actuels (LGP), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Département d'Immunologie - Department of Immunology, Immunorégulation, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Génétique Evolutive Humaine - Human Evolutionary Genetics, Laboratory of Cellular Physiology and Immunology and Chris Browne Center, Rockefeller University [New York], St. Giles Laboratory of Human Genetics of Infectious Diseases, Laboratory of Human Genetics of Infectious Diseases, Institut National de la Santé et de la Recherche Médicale (INSERM), Imagine - Institut des maladies génétiques (IMAGINE - U1163), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Biologie Cellulaire des Lymphocytes - Lymphocyte Cell Biology, Dynamiques des Réponses Immunes, Lymphopoïèse (Lymphopoïèse (UMR_1223 / U1223 / U-Pasteur_4)), Institut Pasteur [Paris] (IP)-Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM), Cellule Pasteur, Université Paris Diderot - Paris 7 (UPD7)-PRES Sorbonne Paris Cité, Centre d'Immunologie de Marseille - Luminy (CIML), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Immunobiologie de l'Infection - Immunobiology of Infection, Département de Génomes et Génétique - Department of Genomes and Genetics, Mycologie moléculaire, Centre National de Référence Mycologie et Antifongiques-Mycologie Moléculaire (CNRMA), Microenvironnement et Immunité - Microenvironment and Immunity, Dynamique des Interactions Hôte-Pathogène - Dynamics of Host-Pathogen Interactions, Equipe 3: EREN- Equipe de Recherche en Epidémiologie Nutritionnelle (CRESS - U1153), Université Paris 13 (UP13)-Institut National de la Recherche Agronomique (INRA)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS (U1153 / UMR_A_1125 / UMR_S_1153)), Institut National de la Recherche Agronomique (INRA)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris Descartes - Paris 5 (UPD5)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Recherche Agronomique (INRA)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris Descartes - Paris 5 (UPD5)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de formation en masso-kinésithérapie (IFMK Brest), Université de Brest (UBO)-Centre Hospitalier Régional Universitaire de Brest (CHRU Brest), Réponse humorale aux pathogènes, Signalisation des Cytokines - Cytokine Signaling, Service d'hépatologie médicale [CHU Cochin], Hôpital Cochin [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Génétique fonctionnelle des Maladies infectieuses - Functional Genetics of Infectious Diseases, Centre de recherche sur les liens sociaux (CERLIS - UMR 8070), Université Sorbonne Nouvelle - Paris 3-Université Paris Descartes - Paris 5 (UPD5)-Centre National de la Recherche Scientifique (CNRS), Biologie systémique - Systems Biology, Imagopole (CITECH), Laboratoire d'Immunologie Clinique, Institut Curie [Paris], Génomique virale et vaccination, Cytokines et Immunologie des Tumeurs Humaines (U753), Université Paris-Sud - Paris 11 (UP11)-Institut Gustave Roussy (IGR)-Institut National de la Santé et de la Recherche Médicale (INSERM), Hôpital Saint-Louis, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Diderot - Paris 7 (UPD7), Investigation Clinique et d’Accès aux Ressources Biologiques (Plate-forme) - Clinical Investigation and Access to BioResources (ICAReB), This work benefited from support of the French government’s Invest in the Future Program, managed by the Agence Nationale de la Recherche (ANR, reference 10-LABX-69-01). We also acknowledge A. Pugsley for his support in obtaining funding and the logistical aspects of initiating the project, Milieu Intérieur Consortium (32 collaborateurs) : Abel L, Alcover A, Bousso P, Cumano A, Daëron M, Delval C, Demangel C, Deriano L, Di Santo J, Dromer F, Eberl G, Enninga J, Freitas A, Gomperts-Boneca I, Hercberg S, Lantz O, Leclerc C, Mouquet H, Pellegrini S, Pol S, Rogge L, Sakuntabhai A, Schwartz O, Schwikowski B, Shorte S, Soumelis V, Tangy F, Tartour E, Toubert A, Ungeheuer MN, Quintana-Murci L, Albert ML., ANR-10-LABX-0069,MILIEU INTERIEUR,GENETIC & ENVIRONMENTAL CONTROL OF IMMUNE PHENOTYPE VARIANCE: ESTABLISHING A PATH TOWARDS PERSONALIZED MEDICINE(2010), Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Pasteur [Paris], Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris]-Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Institut National de la Recherche Agronomique (INRA)-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Université Paris 13 (UP13)-Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS (U1153 / UMR_A_1125 / UMR_S_1153)), Université Paris Diderot - Paris 7 (UPD7)-Université Sorbonne Paris Cité (USPC)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Recherche Agronomique (INRA)-Université Paris Diderot - Paris 7 (UPD7)-Université Sorbonne Paris Cité (USPC)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Recherche Agronomique (INRA), Centre Hospitalier Régional Universitaire de Brest (CHRU Brest)-Université de Brest (UBO), Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale ( INSERM ), Centre de Recherche Translationnelle ( CRT ), Centre d'Immunologie Humaine ( CIH ), Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ), Centre d'Immunologie et de Maladies Infectieuses ( CIMI ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Biologie et Génétique de la Paroi bactérienne, Laboratoire de géographie physique ( LGP ), Université Panthéon-Sorbonne ( UP1 ) -Université Paris-Est Créteil Val-de-Marne - Paris 12 ( UPEC UP12 ) -Centre National de la Recherche Scientifique ( CNRS ), Département d'Immunologie, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique ( CNRS ), rockefeller university, St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Institut National de la Santé et de la Recherche Médicale ( INSERM ), Imagine - Institut des maladies génétiques ( IMAGINE - U1163 ), Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Biologie Cellulaire des Lymphocytes, Lymphopoïèse, Université Paris Diderot - Paris 7 ( UPD7 ) -PRES Sorbonne Paris Cité, Centre d'Immunologie de Marseille - Luminy ( CIML ), Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Aix Marseille Université ( AMU ) -Centre National de la Recherche Scientifique ( CNRS ), Immunobiologie de l'Infection, Département de Génomes et Génétique, Centre National de Référence Mycologie et Antifongiques-Mycologie Moléculaire ( CNRMA ), Microenvironnement et Immunité, Dynamique des Interactions Hôte-Pathogène, Equipe 3: EREN- Equipe de Recherche en Epidémiologie Nutritionnelle ( CRESS - U1153 ), Université Paris 13 ( UP13 ) -Institut National de la Recherche Agronomique ( INRA ) -Conservatoire National des Arts et Métiers [CNAM] ( CNAM ) -Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité ( CRESS (U1153 / UMR_A 1125) ), Institut National de la Recherche Agronomique ( INRA ) -Université Sorbonne Paris Cité ( USPC ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Institut National de la Recherche Agronomique ( INRA ) -Université Sorbonne Paris Cité ( USPC ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Institut de formation en masso-kinésithérapie ( IFMK Brest ), Université de Brest ( UBO ) -Centre Hospitalier Régional Universitaire de Brest ( CHRU Brest ), Signalisation des Cytokines, Assistance publique - Hôpitaux de Paris (AP-HP)-CHU Cochin [AP-HP], Génétique fonctionnelle des Maladies infectieuses, CERLIS - Centre de recherche sur les liens sociaux - UMR 8070 ( CERLIS - UMR 8070 ), Centre National de la Recherche Scientifique ( CNRS ) -Université Paris Descartes - Paris 5 ( UPD5 ) -Université Sorbonne Nouvelle - Paris 3, Biologie systémique, Imagopole ( CITECH ), Institut Curie, Institut Curie-Institut Curie, Cytokines et Immunologie des Tumeurs Humaines ( U753 ), Université Paris-Sud - Paris 11 ( UP11 ) -Institut Gustave Roussy ( IGR ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Assistance publique - Hôpitaux de Paris (AP-HP)-Université Paris Diderot - Paris 7 ( UPD7 ), Investigation Clinique et d’Accès aux Ressources Biologiques (Plate-forme) - Clinical Investigation and Access to BioResources ( ICAReB ), ANR : 10-LABX-0069,MILIEU INTERIEUR,GENETIC & ENVIRONMENTAL CONTROL OF IMMUNE PHENOTYPE VARIANCE: ESTABLISHING A PATH TOWARDS PERSONALIZED MEDICINE ( 2010 ), Centre de Recherche Translationnelle (CRT), Centre National de la Recherche Scientifique (CNRS)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Université Panthéon-Sorbonne (UP1), Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris 13 (UP13)-Institut National de la Recherche Agronomique (INRA)-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS (U1153 / UMR_A_1125 / UMR_S_1153)), CHU Cochin [AP-HP]-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP), Université Paris Diderot - Paris 7 (UPD7)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP), and ANR: 10-LABX-0069,MILIEU INTERIEUR,GENETIC & ENVIRONMENTAL CONTROL OF IMMUNE PHENOTYPE VARIANCE: ESTABLISHING A PATH TOWARDS PERSONALIZED MEDICINE(2010)

Subjects
Chemokine, MESH : Cytokines, MESH : Antigens, Disease, MESH : Monitoring, Immunologic, Adaptive Immunity, 0302 clinical medicine, Immunophenotyping, Reference Values, [ SDV.IMM ] Life Sciences [q-bio]/Immunology, Immunology and Allergy, MESH: Monitoring, Immunologic, MESH: Healthy Volunteers, 0303 health sciences, MESH: Cytokines, biology, MESH: Reference Values, MESH : Immunity, Innate, Healthy Volunteers, 3. Good health, MESH: Reproducibility of Results, Infectious Diseases, Cytokines, [SDV.IMM]Life Sciences [q-bio]/Immunology, MESH: Antigens, MESH: Immunity, Innate, Inflammation Mediators, Functional analysis (psychology), Whole blood stimulation, MESH : Adaptive Immunity, Immunology, MESH: Inflammation Mediators, MESH : Reference Values, MESH : Inflammation Mediators, 03 medical and health sciences, Immune system, Immunity, Monitoring, Immunologic, Humans, Antigens, 030304 developmental biology, MESH : Healthy Volunteers, MESH: Humans, MESH : Reproducibility of Results, MESH : Humans, Reproducibility of Results, Immunity, Innate, Reference values, biology.protein, MESH: Adaptive Immunity, 030215 immunology
Abstract

International audience; Standardization of immunophenotyping procedures has become a high priority. We have developed a suite of whole-blood, syringe-based assay systems that can be used to reproducibly assess induced innate or adaptive immune responses. By eliminating preanalytical errors associated with immune monitoring, we have defined the protein signatures induced by (1) medically relevant bacteria, fungi, and viruses; (2) agonists specific for defined host sensors; (3) clinically employed cytokines; and (4) activators of T cell immunity. Our results provide an initial assessment of healthy donor reference values for induced cytokines and chemokines and we report the failure to release interleukin-1α as a common immunological phenotype. The observed naturally occurring variation of the immune response may help to explain differential susceptibility to disease or response to therapeutic intervention. The implementation of a general solution for assessment of functional immune responses will help support harmonization of clinical studies and data sharing.

Published
2014

18. Transcriptome database resource and gene expression atlas for the rose

Author

Rossitza Atanassova, Sylvie Baudino, Ludovic Cottret, Aymeric Roccia, Soulaiman Sakr, Annick Dubois, Olivier Raymond, Jérôme Gouzy, Manuel Le Bris, Fabrice Foucher, Jean-Paul Onesto, Benjamin Pouvreau, Sébastien Carrère, Mohammed Bendahmane, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Institut de Recherches Historiques du Septentrion (IRHiS) - UMR 8529 (IRHiS), Université de Lille-Centre National de la Recherche Scientifique (CNRS), AIP-Bioressources programme, 'Biologie Vegetale' Department of the French 'Institut National de la Recherche Agronomique', 'Genetique et Amelioration des Plantes' Department of the French 'Institut National de la Recherche Agronomique', and Centre National de la Recherche Scientifique (CNRS)-Université de Lille

Subjects
0106 biological sciences, Gene Expression, Polymerase Chain Reaction, 01 natural sciences, Genome, scent compound, Transcriptome, Gene Expression Regulation, Plant, functional-characterization, Arabidopsis, Databases, Genetic, Gene expression, [SDV.SA.HORT]Life Sciences [q-bio]/Agricultural sciences/Horticulture, Plant Proteins, rose, Expressed Sequence Tags, 2. Zero hunger, Regulation of gene expression, Genetics, 0303 health sciences, Expressed sequence tag, biology, o-methyltransferases, High-Throughput Nucleotide Sequencing, BIOTECHNOLOGY & APPLIED MICROBIOLOGY, homolog, product-moment correlation, phenylacetaldehyde reductase, Multigene Family, Rose, Gene expression atlas, PRODUCT-MOMENT CORRELATION, POLLEN DEVELOPMENT, PHENYLACETALDEHYDE REDUCTASE, FUNCTIONAL-CHARACTERIZATION, O-METHYLTRANSFERASES, SCENT COMPOUND, ARABIDOPSIS, BIOSYNTHESIS, EVOLUTION, HOMOLOG, Prunus, DNA microarray, Genome, Plant, Plant Shoots, Research Article, Biotechnology, lcsh:QH426-470, lcsh:Biotechnology, Rosa, Fragaria, 03 medical and health sciences, lcsh:TP248.13-248.65, evolution, RNA, Messenger, Gene, 030304 developmental biology, pollen development, biology.organism_classification, lcsh:Genetics, arabidopsis, biosynthesis, transcriptome, Software, 010606 plant biology & botany
Abstract

Background For centuries roses have been selected based on a number of traits. Little information exists on the genetic and molecular basis that contributes to these traits, mainly because information on expressed genes for this economically important ornamental plant is scarce. Results Here, we used a combination of Illumina and 454 sequencing technologies to generate information on Rosa sp. transcripts using RNA from various tissues and in response to biotic and abiotic stresses. A total of 80714 transcript clusters were identified and 76611 peptides have been predicted among which 20997 have been clustered into 13900 protein families. BLASTp hits in closely related Rosaceae species revealed that about half of the predicted peptides in the strawberry and peach genomes have orthologs in Rosa dataset. Digital expression was obtained using RNA samples from organs at different development stages and under different stress conditions. qPCR validated the digital expression data for a selection of 23 genes with high or low expression levels. Comparative gene expression analyses between the different tissues and organs allowed the identification of clusters that are highly enriched in given tissues or under particular conditions, demonstrating the usefulness of the digital gene expression analysis. A web interface ROSAseq was created that allows data interrogation by BLAST, subsequent analysis of DNA clusters and access to thorough transcript annotation including best BLAST matches on Fragaria vesca, Prunus persica and Arabidopsis. The rose peptides dataset was used to create the ROSAcyc resource pathway database that allows access to the putative genes and enzymatic pathways. Conclusions The study provides useful information on Rosa expressed genes, with thorough annotation and an overview of expression patterns for transcripts with good accuracy.

Published
2012

19. Genomic approach to study floral development genes in Rosa sp

Author

Philippe Vergne, Sandrine Balzergue, Fabrice Legeai, Julien Jeauffre, Mohammed Bendahmane, Arnaud Remay, Jean-Pierre Renou, Tatiana Thouroude, Aurelie Chauvet, Annick Dubois, Fabrice Foucher, Marie-Laure Martin-Magniette, Yann Pecrix, Shu-Hua Yang, Véronique Boltz, Stéphane Janczarski, Olivier Raymond, Manuel Le Bris, Marion Maene, Reproduction et développement des plantes (RDP), 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 de Lyon-Centre National de la Recherche Scientifique (CNRS), Génétique et Horticulture (GenHort), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, 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), 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), 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), Génétique et Horticulture (GENHORT), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-Institut National d'Horticulture, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Scalable, Optimized and Parallel Algorithms for Genomics (GenScale), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Service de Gynécologie et Obstétrique [Rennes] = Gynaecology [Rennes], CHU Pontchaillou [Rennes], This work was funded by the 'Biologie Vegetale' and the 'Genetique et Amelioration des Plantes' Departments of the French Institut National de la Recherche Agronomique, and by the Region Rhones-Alpes. Dr. Maene, Dr. Pecrix and Dr. Remay were supported by funds from the Region Rhone Alpes (Dr. Maene), The Region PACA (Dr. Pecrix) and by a joint grant from Region Pays de la Loire and the French 'Institut National de la Recherche Agronomique' (Dr. Remay). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript., Bendahmane, Mohammed, École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Institut National d'Horticulture-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Service de Gynécologie et Obstétrique [Rennes], Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-CHU Pontchaillou [Rennes]-Hôpital Sud, 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'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), Université Paul Cézanne - Aix-Marseille 3-Centre National de la Recherche Scientifique (CNRS)-Avignon Université (AU)-Université de Provence - Aix-Marseille 1, Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), and Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1)

Subjects
0106 biological sciences, initiation florale, Floral development, Microarrays, Plant genetics, Gene Identification and Analysis, lcsh:Medicine, F62 - Physiologie végétale - Croissance et développement, Plant Science, 01 natural sciences, microscopie électronique à balayage, F30 - Génétique et amélioration des plantes, Transcriptomes, Meristems, Transcriptome, rosa, Gene Expression Regulation, Plant, Floraison, Databases, Genetic, lcsh:Science, rosa genetics, molecular sequence annotation, meristem genetics, genes, developmental genetics, multidisciplinary sciences, science and technology, Flowering Plants, Roses, Oligonucleotide Array Sequence Analysis, Plant Growth and Development, Expressed Sequence Tags, Genetics, 0303 health sciences, Expressed sequence tag, Multidisciplinary, Vegetal Biology, mrna, phytogénétique, Gene Expression Regulation, Developmental, food and beverages, Genomics, Plants, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], ABC model of flower development, stade de développement, Meristem initiation, analyse microarray, puce à adn, rosier, Méristème, Sequence databases, DNA microarray, Research Article, expression des gènes, Meristem, Flowers, Biology, Genes, Plant, Real-Time Polymerase Chain Reaction, génomique, Molecular Genetics, 03 medical and health sciences, Genome Analysis Tools, Botany, Transcription factors, Gene Regulation, Genes, Developmental, Stade de développement végétal, Gene Networks, Gene, 030304 developmental biology, lcsh:R, stade de floraison, fungi, méristème floral, Molecular Sequence Annotation, lcsh:Q, Gene expression, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Biologie végétale, Developmental Biology, 010606 plant biology & botany
Abstract

International audience; Cultivated for centuries, the varieties of rose have been selected based on a number of flower traits. Understanding the genetic and molecular basis that contributes to these traits will impact on future improvements for this economically important ornamental plant. In this study, we used scanning electron microscopy and sections of meristems and flowers to establish a precise morphological calendar from early rose flower development stages to senescing flowers. Global gene expression was investigated from floral meristem initiation up to flower senescence in three rose genotypes exhibiting contrasted floral traits including continuous versus once flowering and simple versus double flower architecture, using a newly developed Affymetrix microarray (Rosa1_Affyarray) tool containing sequences representing 4765 unigenes expressed during flower development. Data analyses permitted the identification of genes associated with floral transition, floral organs initiation up to flower senescence. Quantitative real time PCR analyses validated the mRNA accumulation changes observed in microarray hybridizations for a selection of 24 genes expressed at either high or low levels. Our data describe the early flower development stages in Rosa sp, the production of a rose microarray and demonstrate its usefulness and reliability to study gene expression during extensive development phases, from the vegetative meristem to the senescent flower.

Published
2011

20. Tinkering with the C-function : a molecular frame for the selection of double flowers in cultivated roses

Author

Sylvie Baudino, Véronique Boltz, Philippe Vergne, Nicolas B. Langlade, Olivier Raymond, Mohammed Bendahmane, Marion Maene, Annick Dubois, 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 de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales (LBVPAM), Université Jean Monnet [Saint-Étienne] (UJM), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), 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), and Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon)

Subjects
0106 biological sciences, Models, Anatomic, Gynoecium, Stamen, lcsh:Medicine, Plant Biology, MADS Domain Proteins, Flowers, Rosa, 01 natural sciences, 03 medical and health sciences, Plant Biology/Plant Genetics and Gene Expression, Plant Biology/Plant Growth and Development, Gene Expression Regulation, Plant, Botany, Arabidopsis thaliana, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, lcsh:Science, Domestication, Molecular Biology, In Situ Hybridization, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Hybrid, Plant Proteins, 0303 health sciences, Volatile Organic Compounds, Vegetal Biology, Multidisciplinary, biology, Agamous, Reverse Transcriptase Polymerase Chain Reaction, Gene Expression Profiling, lcsh:R, fungi, food and beverages, Gene Expression Regulation, Developmental, Genetic Variation, biology.organism_classification, Phenotype, Developmental Biology/Plant Growth and Development, RHAG, biology.protein, Hybridization, Genetic, lcsh:Q, Petal, Biologie végétale, 010606 plant biology & botany, Research Article
Abstract

Background Roses have been cultivated for centuries and a number of varieties have been selected based on flower traits such as petal form, color, and number. Wild-type roses have five petals (simple flowers), whereas high numbers of petals (double flowers) are typical attributes of most of the cultivated roses. Here, we investigated the molecular mechanisms that could have been selected to control petal number in roses. Methodology/Principal Findings We have analyzed the expression of several candidate genes known to be involved in floral organ identity determination in roses from similar genetic backgrounds but exhibiting contrasting petal numbers per flower. We show that the rose ortholog of AGAMOUS (RhAG) is differentially expressed in double flowers as compared to simple flowers. In situ hybridization experiments confirm the differential expression of RhAG and demonstrate that in the double-flower roses, the expression domain of RhAG is restricted toward the center of the flower. Conversely, in simple-flower roses, RhAG expression domain is wider. We further show that the border of RhAG expression domain is labile, which allows the selection of rose flowers with increased petal number. Double-flower roses were selected independently in the two major regions for domestication, China and the peri-Mediterranean areas. Comparison of RhAG expression in the wild-type ancestors of cultivated roses and their descendants both in the European and Chinese lineages corroborates the correlation between the degree of restriction of RhAG expression domain and the number of petals. Our data suggests that a restriction of RhAG expression domain is the basis for selection of double flowers in both the Chinese and peri-Mediterranean centers of domestication. Conclusions/Significance We demonstrate that a shift in RhAG expression domain boundary occurred in rose hybrids, causing double-flower phenotype. This molecular event was selected independently during rose domestication in Europe/Middle East and in China.

Published
2010

21. Genome-wide analysis of gene expression during early Arabidopsis flower development

Author

Elliot M. Meyerowitz, José Luis Riechmann, Annick Dubois, Marcio Alves-Ferreira, Frank Wellmer, Division of Biology [Pasadena], California Institute of Technology (CALTECH), and NIGMS NIH HHS [GM45697], [R01 GM045697]

Subjects
0106 biological sciences, Cancer Research, Time Factors, Transcription, Genetic, Arabidopsis, génome végétal, Plant Science, QH426-470, 01 natural sciences, Gene Expression Regulation, Plant, Arabidopsis thaliana, Genetics (clinical), Oligonucleotide Array Sequence Analysis, Plant Proteins, Genetics/Genomics, Regulation of gene expression, Genetics, régulation de l'expression génique, 0303 health sciences, Vegetal Biology, biology, Gene Expression Regulation, Developmental, food and beverages, ABC model of flower development, Genome, Plant, Research Article, Transcriptional Activation, lcsh:QH426-470, Evolution, Flowers, Development, Genes, Plant, protéine végétale, 03 medical and health sciences, activation de la transcription, Gene family, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, transcription génétique, Gene, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, développement de la fleur, Gene Expression Profiling, fungi, biology.organism_classification, floral development, Gene expression profiling, lcsh:Genetics, Arabidopsis (Thale Cress), profilage génétique, Genetics/Gene Expression, Flower formation, Caltech Library Services, Biologie végétale, 010606 plant biology & botany
Abstract

Detailed information about stage-specific changes in gene expression is crucial for the understanding of the gene regulatory networks underlying development. Here, we describe the global gene expression dynamics during early flower development, a key process in the life cycle of a plant, during which floral patterning and the specification of floral organs is established. We used a novel floral induction system in Arabidopsis, which allows the isolation of a large number of synchronized floral buds, in conjunction with whole-genome microarray analysis to identify genes with differential expression at distinct stages of flower development. We found that the onset of flower formation is characterized by a massive downregulation of genes in incipient floral primordia, which is followed by a predominance of gene activation during the differentiation of floral organs. Among the genes we identified as differentially expressed in the experiment, we detected a significant enrichment of closely related members of gene families. The expression profiles of these related genes were often highly correlated, indicating similar temporal expression patterns. Moreover, we found that the majority of these genes is specifically up-regulated during certain developmental stages. Because co-expressed members of gene families in Arabidopsis frequently act in a redundant manner, these results suggest a high degree of functional redundancy during early flower development, but also that its extent may vary in a stage-specific manner., Synopsis The development of flowers is one of the characteristic features of higher plants. In an effort to gain detailed insights into the molecular processes underlying flower development, the authors have analyzed the expression of the genes of the small plant Arabidopsis thaliana, which is widely used by biologists for the study of plant development, during the early stages of flower formation. To this end, they used DNA microarray analysis, a technology that allows the simultaneous detection of thousands of gene transcripts in a single experiment. Because young floral buds of Arabidopsis are minute and are difficult to dissect, the authors established a system that allows the simultaneous induction of a large number of flowers on a single plant. Using this system, they identified groups of genes, many of them novel or uncharacterized, that are highly active during distinct stages of flower development. These genes are likely involved in controlling the various developmental changes that take place during the formation of flowers. The authors also found that many of these genes are closely related in sequence, suggesting that they might be involved in similar or identical processes, and thus uncovering a large degree of potential functional redundancy during flower development.

Published
2006

22. The AP-1 clathrin-adaptor is required for lysosomal enzymes sorting and biogenesis of the contractile vacuole complex in Dictyostelium Cells

Author

Yaya Lefkir, Aleksandra Bogdanovic, Franz Bruckert, Theresa J. O'Halloran, Annick Dubois, Rebecca J. Brady, Benoît de Chassey, François Letourneur, Pierre Cosson, Olivier Destaing, Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, Laboratoire de Biochimie et Biophysique des Systèmes Intégrés, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), University of Texas at Austin, Laboratoire de Biologie Moléculaire et Cellulaire, École normale supérieure de Lyon (ENS de Lyon)-Centre National de la Recherche Scientifique (CNRS), Université de Genève = University of Geneva (UNIGE), Institut de biologie et chimie des protéines [Lyon] (IBCP), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Lyon (ENS Lyon)-Centre National de la Recherche Scientifique (CNRS), Université de Genève (UNIGE), and Deleage, Gilbert

Subjects
alignement de séquences, Vacuole, Protein Transport/physiology, Genes, Reporter, clathrine, donnée de séquence moléculaire, Dictyostelium, ComputingMilieux_MISCELLANEOUS, 0303 health sciences, biology, Clathrin/metabolism, 030302 biochemistry & molecular biology, Signal transducing adaptor protein, Articles, Dictyostelium/genetics/physiology, Enzymes/metabolism, Transport protein, Cell biology, Contractile vacuole, Enzymes, Protein Transport, Biochemistry, symbols, Autre (Sciences du Vivant), [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], Endosome, intracellular trafficking, Protein subunit, Adaptor Protein Complex 1, Molecular Sequence Data, gène rapporteur, Clathrin, 03 medical and health sciences, symbols.namesake, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Animals, Humans, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Adaptor Protein Complex 1/genetics/physiology, Amino Acid Sequence, séquence d'acides aminés, ddc:612, Molecular Biology, microscope électronique, 030304 developmental biology, complexe protéique, transport de protéine, Lysosomes/enzymology, Vacuoles/metabolism/ultrastructure, Cell Biology, Golgi apparatus, Microscopy, Electron, Vacuoles, biology.protein, Lysosomes, Sequence Alignment
Abstract

International audience; Adaptor protein complexes (AP) are major components of the cytoplasmic coat found on clathrin-coated vesicles. Here, we report the molecular and functional characterization of Dictyostelium clathrin-associated AP-1 complex, which in mammalian cells, participates mainly in budding of clathrin-coated vesicles from the trans-Golgi network (TGN). The gamma-adaptin AP-1 subunit was cloned and shown to belong to a Golgi-localized 300-kDa protein complex. Time-lapse analysis of cells expressing gamma-adaptin tagged with the green-fluorescent protein demonstrates the dynamics of AP-1-coated structures leaving the Golgi apparatus and rarely moving toward the TGN. Targeted disruption of the AP-1 medium chain results in viable cells displaying a severe growth defect and a delayed developmental cycle compared with parental cells. Lysosomal enzymes are constitutively secreted as precursors, suggesting that protein transport between the TGN and lysosomes is defective. Although endocytic protein markers are correctly localized to endosomal compartments, morphological and ultrastructural studies reveal the absence of large endosomal vacuoles and an increased number of small vacuoles. In addition, the function of the contractile vacuole complex (CV), an osmoregulatory organelle is impaired and some CV components are not correctly targeted.Adaptor protein complexes (AP) are major components of the cytoplasmic coat found on clathrin-coated vesicles. Here, we report the molecular and functional characterization of Dictyostelium clathrin-associated AP-1 complex, which in mammalian cells, participates mainly in budding of clathrin-coated vesicles from the trans-Golgi network (TGN). The gamma-adaptin AP-1 subunit was cloned and shown to belong to a Golgi-localized 300-kDa protein complex. Time-lapse analysis of cells expressing gamma-adaptin tagged with the green-fluorescent protein demonstrates the dynamics of AP-1-coated structures leaving the Golgi apparatus and rarely moving toward the TGN. Targeted disruption of the AP-1 medium chain results in viable cells displaying a severe growth defect and a delayed developmental cycle compared with parental cells. Lysosomal enzymes are constitutively secreted as precursors, suggesting that protein transport between the TGN and lysosomes is defective. Although endocytic protein markers are correctly localized to endosomal compartments, morphological and ultrastructural studies reveal the absence of large endosomal vacuoles and an increased number of small vacuoles. In addition, the function of the contractile vacuole complex (CV), an osmoregulatory organelle is impaired and some CV components are not correctly targeted.

Published
2003

23. Two members of the beige/CHS (BEACH) family are involved at different stages in the organization of the endocytic pathway in Dictyostelium

Author

Yaya Lefkir, Anna Marchetti, Pierre Cosson, Mohammed Benghezal, Arturo De Lozanne, Sophie Cornillon, François Letourneur, Franz Bruckert, Annick Dubois, Institut de biologie et chimie des protéines [Lyon] (IBCP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Deleage, Gilbert, Université de Genève (UNIGE), Université de Lyon, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), University of Texas, Institute for Cellular and Molecular Biology, Université de Genève = University of Geneva (UNIGE), and ProdInra, Migration

Subjects
Phagocytic cup, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], Vacuolar Proton-Translocating ATPases, intracellular trafficking, Endocytic cycle, Mutant, Protozoan Proteins, Biology, 03 medical and health sciences, Phagocytosis, Lysosome, Phagosomes, hemic and lymphatic diseases, medicine, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Cell Adhesion, Animals, Dictyostelium, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Gene, 030304 developmental biology, Genetics, 0303 health sciences, [SDV.OT] Life Sciences [q-bio]/Other [q-bio.OT], 030302 biochemistry & molecular biology, Proteins, Cell Biology, BEACH domain, biology.organism_classification, Phenotype, Endocytosis, Cell biology, Protein Structure, Tertiary, Kinetics, medicine.anatomical_structure, Chediak-Higashi, Mutation, lysosome, beige, Signal transduction, Lysosomes
Abstract

International audience; Proteins of the Chediak-Higashi/Beige (BEACH) family have been implicated in the function of lysosomes, as well as in signal transduction, but their molecular role is still poorly understood. In Dictyostelium, at least six members of the family can be identified. Here cells with mutations in two of these genes, LVSA and LVSB, were analyzed. Interestingly both mutants exhibited defects in the organization of the endocytic pathway, albeit at distinct stages. In lvsB mutant cells, the regulated secretion of lysosomal enzymes was enhanced, a phenotype reminiscent of the Chediak-Higashi syndrome. LvsA mutant cells exhibited alterations in the organization and function of the early endocytic and phagocytic pathway. The LvsA protein may participate in the signaling pathway, which links adhesion of a particle to the subsequent formation of a phagocytic cup. Further genetic analysis will be necessary to determine whether other members of the BEACH family of proteins are also involved in controlling the organization of the endocytic pathway.Proteins of the Chediak-Higashi/Beige (BEACH) family have been implicated in the function of lysosomes, as well as in signal transduction, but their molecular role is still poorly understood. In Dictyostelium, at least six members of the family can be identified. Here cells with mutations in two of these genes, LVSA and LVSB, were analyzed. Interestingly both mutants exhibited defects in the organization of the endocytic pathway, albeit at distinct stages. In lvsB mutant cells, the regulated secretion of lysosomal enzymes was enhanced, a phenotype reminiscent of the Chediak-Higashi syndrome. LvsA mutant cells exhibited alterations in the organization and function of the early endocytic and phagocytic pathway. The LvsA protein may participate in the signaling pathway, which links adhesion of a particle to the subsequent formation of a phagocytic cup. Further genetic analysis will be necessary to determine whether other members of the BEACH family of proteins are also involved in controlling the organization of the endocytic pathway.

Published
2002

24. ERGIC-53 KKAA signal mediates endoplasmic reticulum retrieval in yeast

Author

Yaya Lefkir, Benoît de Chassey, Dagmar Dogic, Annick Dubois, François Letourneur, Institut de biologie et chimie des protéines [Lyon] (IBCP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), and Deleage, Gilbert

Subjects
Histology, Mutant, Golgi Apparatus, Saccharomyces cerevisiae, Biology, Protein Sorting Signals, medicine.disease_cause, Endoplasmic Reticulum, Pathology and Forensic Medicine, 03 medical and health sciences, Protein targeting, medicine, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Secretory pathway, 030304 developmental biology, 0303 health sciences, Endoplasmic reticulum, 030302 biochemistry & molecular biology, Membrane Proteins, ER retention, Cell Biology, General Medicine, COPI, Yeast, Cell biology, Mannose-Binding Lectins, Biochemistry, Carbohydrate Metabolism, Function (biology)
Abstract

International audience; Studies on the ERGIC-53 KKAA signal have revealed a new mechanism for static retention of mammalian proteins in the endoplasmic reticulum (Andersson, H., Kappeler, F., Hauri, H. P. (1999): Protein targeting to endoplasmic reticulum by dilysine signals involves direct retention in addition to retrieval. J. Biol. Chem. 274,15080 - 15084). To test if this mechanism was conserved in yeast, the ERGIC-53 KKAA signal was transferred on two different yeast reporter proteins. Making use of a genetic assay, we demonstrate that this signal induces COPI-dependent ER retrieval. ER retention of KKAA-tagged proteins was impaired in yeast mutants affected in COPI subunits. Furthermore, biochemical analysis of post-ER carbohydrate modifications detected on reporter proteins indicated that KKAA-tagged proteins recycle continuously within early compartments of the secretory pathway. Therefore in yeast, the KKAA signal might only function as a classical dilysine ER retrieval signal.Studies on the ERGIC-53 KKAA signal have revealed a new mechanism for static retention of mammalian proteins in the endoplasmic reticulum (Andersson, H., Kappeler, F., Hauri, H. P. (1999): Protein targeting to endoplasmic reticulum by dilysine signals involves direct retention in addition to retrieval. J. Biol. Chem. 274,15080 - 15084). To test if this mechanism was conserved in yeast, the ERGIC-53 KKAA signal was transferred on two different yeast reporter proteins. Making use of a genetic assay, we demonstrate that this signal induces COPI-dependent ER retrieval. ER retention of KKAA-tagged proteins was impaired in yeast mutants affected in COPI subunits. Furthermore, biochemical analysis of post-ER carbohydrate modifications detected on reporter proteins indicated that KKAA-tagged proteins recycle continuously within early compartments of the secretory pathway. Therefore in yeast, the KKAA signal might only function as a classical dilysine ER retrieval signal.

Published
2001

25. Identification of clathrin-adaptor medium chains in Dictyostelium discoideum : differential expression during development

Author

Benoît de Chassey, Annick Dubois, Yaya Lefkir, François Letourneur, Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, Institut de biologie et chimie des protéines [Lyon] (IBCP), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), and Deleage, Gilbert

Subjects
[SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], intracellular trafficking, Cellular differentiation, Adaptor Protein Complex 1, Molecular Sequence Data, Adaptor Protein Complex 2, Protozoan Proteins, Nerve Tissue Proteins, Clathrin, Dictyostelium discoideum, 03 medical and health sciences, 0302 clinical medicine, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Genetics, Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Dictyostelium, Amino Acid Sequence, Cloning, Molecular, Tyrosine, Gene, 030304 developmental biology, chemistry.chemical_classification, adaptin, 0303 health sciences, Sequence Homology, Amino Acid, biology, Reverse Transcriptase Polymerase Chain Reaction, Vesicle, Vesicle coat, Gene Expression Regulation, Developmental, Clathrin-Coated Vesicles, General Medicine, Phosphoproteins, biology.organism_classification, Molecular biology, Adaptor Protein Complex mu Subunits, Amino acid, Cell biology, Adaptor Proteins, Vesicular Transport, chemistry, biology.protein, cellular slime mold, 030217 neurology & neurosurgery
Abstract

International audience; Clathrin-adaptor complexes (APs) are vesicle coat components that participate in cargo selectivity and transport vesicle formation. Here we cloned and characterized apm1, apm3 and apm4 cDNAs encoding AP medium chains (mu) in D. discoideum. Amino acid comparison suggested that predicted proteins were homologous to known mu1, mu3 and mu4 subunits of mammalian APs as they shared 69, 51, and 26% identity with mouse mu1A, human mu3A and human mu4, respectively. In all chains, amino acid residues predicted to interact with tyrosine based sorting signals were conserved. Southern blot analysis indicated only one copy of each gene in D. discoideum genome. Expression of apm1 and apm3 mRNAs stayed relatively constant during vegetative growth and throughout development. In contrast, apm4 was poorly expressed in amoebae but became well detectable by RT-PCR upon cell differentiation. This regulated expression of coat proteins enlightens the importance of intracellular membrane transport vesicles during development in D. discoideum and strengthens this attractive model organism for studying the function of coat complexes in vivo.Clathrin-adaptor complexes (APs) are vesicle coat components that participate in cargo selectivity and transport vesicle formation. Here we cloned and characterized apm1, apm3 and apm4 cDNAs encoding AP medium chains (mu) in D. discoideum. Amino acid comparison suggested that predicted proteins were homologous to known mu1, mu3 and mu4 subunits of mammalian APs as they shared 69, 51, and 26% identity with mouse mu1A, human mu3A and human mu4, respectively. In all chains, amino acid residues predicted to interact with tyrosine based sorting signals were conserved. Southern blot analysis indicated only one copy of each gene in D. discoideum genome. Expression of apm1 and apm3 mRNAs stayed relatively constant during vegetative growth and throughout development. In contrast, apm4 was poorly expressed in amoebae but became well detectable by RT-PCR upon cell differentiation. This regulated expression of coat proteins enlightens the importance of intracellular membrane transport vesicles during development in D. discoideum and strengthens this attractive model organism for studying the function of coat complexes in vivo.

Published
2001

26. Two members of the beige/CHS (BEACH) family are involved at different stages in the organization of the endocytic pathway in Dictyostelium.

Author

Sophie, Cornillon, Annick, Dubois, Franz, Brckert, Yaya, Lefkir, Anna, Marchetti, Mohammed, Benghezal, Arturo, De Lozanne, Franois, Letourneur, and Pierre, Cosson

Abstract

Proteins of the Chediak-Higashi/Beige (BEACH) family have been implicated in the function of lysosomes, as well as in signal transduction, but their molecular role is still poorly understood. In Dictyostelium, at least six members of the family can be identified. Here cells with mutations in two of these genes, LVSA and LVSB, were analyzed. Interestingly both mutants exhibited defects in the organization of the endocytic pathway, albeit at distinct stages. In lvsB mutant cells, the regulated secretion of lysosomal enzymes was enhanced, a phenotype reminiscent of the Chediak-Higashi syndrome. LvsA mutant cells exhibited alterations in the organization and function of the early endocytic and phagocytic pathway. The LvsA protein may participate in the signaling pathway, which links adhesion of a particle to the subsequent formation of a phagocytic cup. Further genetic analysis will be necessary to determine whether other members of the BEACH family of proteins are also involved in controlling the organization of the endocytic pathway.

Published
2002

27. The Milieu Intérieur study — An integrative approach for study of human immunological variance

Author

Stéphanie Thomas, Vincent Rouilly, Etienne Patin, Cécile Alanio, Annick Dubois, Cécile Delval, Louis-Guillaume Marquier, Nicolas Fauchoux, Seloua Sayegrih, Muriel Vray, Darragh Duffy, Lluis Quintana-Murci, Matthew L. Albert, Laurent Abel, Andres Alcover, Philippe Bousso, Pierre Bruhns, Ana Cumano, Marc Daëron, Caroline Demangel, Ludovic Deriano, James Di Santo, Françoise Dromer, Gérard Eberl, Jost Enninga, Antonio Freitas, Odile Gelpi, Ivo Gomperts-Boneca, Serge Hercberg, Olivier Lantz, Claude Leclerc, Hugo Mouquet, Sandra Pellegrini, Stanislas Pol, Lars Rogge, Anavaj Sakuntabhai, Olivier Schwartz, Benno Schwikowski, Spencer Shorte, Vassili Soumelis, Frédéric Tangy, Eric Tartour, Antoine Toubert, Marie-Noëlle Ungeheuer, Immunobiologie des Cellules Dendritiques, Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Génétique Evolutive Humaine - Human Evolutionary Genetics, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Pôle Intégré de Recherche Clinique (PIRC), Institut Pasteur [Paris], Biotrial, Biotrial, Rennes, France, Epidémiologie des Maladies Emergentes - Emerging Diseases Epidemiology, Pasteur-Cnam Risques infectieux et émergents (PACRI), Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM), This work benefited from the support of the French government's 'Invest in the Future program', managed by the Agence Nationale de la Recherche (ANR, reference 10-LABX-69-01). We acknowledge the advice of the 'healthy donor' working group that helped us to define the inclusion/exclusion criteria: Laurent Abel, François Aubin, Raphaëlle Bourdet-Sicard, Ingrid Callies, Miguel Fenoy, Bridget Holmes, Laurence Mathivet, Cédric Ménager, Stéphane Reynier, Manfred Schmoltz, Muriel Vray). Scientific advisory board members that supported the trial design discussions included: Hyam Levitsky, Philip Greenberg, John Marioni, Jonathan Braun, Adrian Hayday and Thomas Joos. We also thank Dusko Ehrlich and Joël Doré for advice on stool sample collection procedures. We would like to acknowledge all the Biotrial team of doctors, nurses, technicians and project managers for their expertise and professionalism. We also thank the donors for their contribution to the study., Consortium 'Milieu Intérieur' (34 collaborateurs) : Abel L, Alcover A, Bousso P, Bruhns P, Cumano A, Daëron M, Delval C, Demangel C, Deriano L, Di Santo J, Dromer F, Eberl G, Enninga J, Freitas A, Gelpi O, Gomperts-Boneca I, Hercberg S, Lantz O, Leclerc C, Mouquet H, Pellegrini S, Pol S, Rogge L, Sakuntabhai A, Schwartz O, Schwikowski B, Shorte S, Soumelis V, Tangy F, Tartour E, Toubert A, Ungeheuer MN, Quintana-Murci L, Albert ML., ANR-10-LABX-0069,MILIEU INTERIEUR,GENETIC & ENVIRONMENTAL CONTROL OF IMMUNE PHENOTYPE VARIANCE: ESTABLISHING A PATH TOWARDS PERSONALIZED MEDICINE(2010), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP), Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), RIBIERRE, Helene, and Laboratoires d'excellence - GENETIC & ENVIRONMENTAL CONTROL OF IMMUNE PHENOTYPE VARIANCE: ESTABLISHING A PATH TOWARDS PERSONALIZED MEDICINE - - MILIEU INTERIEUR2010 - ANR-10-LABX-0069 - LABX - VALID

Subjects
Gerontology, Adult, Male, medicine.medical_specialty, [SDV.IMM] Life Sciences [q-bio]/Immunology, Cohort design, Population, Immunology, Disease, Immune phenotypes, Bioinformatics, Cohort Studies, Young Adult, Sex Factors, Risk Factors, Epidemiology, Medicine, SNP, Immunology and Allergy, Humans, Milieu intérieur, education, Aged, education.field_of_study, business.industry, Smoking, Age Factors, CMV, Variance (accounting), Healthy donor, Middle Aged, Baseline serologic data, Metabolic syndrome, 3. Good health, Cross-Sectional Studies, Socioeconomic Factors, Immune System, Cytomegalovirus Infections, [SDV.IMM]Life Sciences [q-bio]/Immunology, Female, Sample collection, France, business, Cohort study
Abstract

International audience; The Milieu Intérieur Consortium has established a 1000-person healthy population-based study (stratified according to sex and age), creating an unparalleled opportunity for assessing the determinants of human immunologic variance. Herein, we define the criteria utilized for participant enrollment, and highlight the key data that were collected for correlative studies. In this report, we analyzed biological correlates of sex, age, smoking-habits, metabolic score and CMV infection. We characterized and identified unique risk factors among healthy donors, as compared to studies that have focused on the general population or disease cohorts. Finally, we highlight sex-bias in the thresholds used for metabolic score determination and recommend a deeper examination of current guidelines. In sum, our clinical design, standardized sample collection strategies, and epidemiological data analyses have established the foundation for defining variability within human immune responses.

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