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1,533 results on '"Max Planck Institute for Developmental Biology"'

1. Petabase-scale sequence alignment catalyses viral discovery

Author: Robert C. Edgar, Jeff Taylor, Victor Lin, Tomer Altman, Pierre Barbera, Dmitry Meleshko, Dan Lohr, Gherman Novakovsky, Benjamin Buchfink, Basem Al-Shayeb, Jillian F. Banfield, Marcos de la Peña, Anton Korobeynikov, Rayan Chikhi, Artem Babaian, Sans affiliation, Altman Analytics LLC, Heidelberg Institute for Theoretical Studies (HITS ), St Petersburg State University (SPbU), Weill Medical College of Cornell University [New York], University of British Columbia (UBC), Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft, University of California [Berkeley] (UC Berkeley), University of California (UC), Consejo Superior de Investigaciones Científicas [Spain] (CSIC), Algorithmes pour les séquences biologiques - Sequence Bioinformatics, Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), PB was financially supported by the Klaus Tschira Foundation, RC by ANR Transipedia, Inception and PRAIRIE grants (PIA/ANR-16-CONV-0005, ANR-18-CE45-0020, ANR-19-P3IA-0001), MdlP by Ministerio de Econom ́ıa y Competitividad of Spain and FEDER grant (BFU2017-87370-P), AK and DM were supported by the Russian Science Foundation (grant 19-14-00172) and computation was carried out in part by Resource Centre 'Computer Centre of SPbU'., ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), ANR-18-CE45-0020,Transipedia,Signatures transcriptionnelles pour une analyse RNA-seq globale(2018), ANR-19-P3IA-0001,PRAIRIE,PaRis Artificial Intelligence Research InstitutE(2019), sans affiliation, University of California [Berkeley], University of California, and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: Models, Molecular, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Sequencing data, Sequence alignment, Computational biology, Biology, Genome, Evolution, Molecular, 03 medical and health sciences, Data sequences, Virology, Databases, Genetic, Pandemic, Animals, Humans, RNA Viruses, Bacteriophages, 030304 developmental biology, Sequence (medicine), 0303 health sciences, Multidisciplinary, Archives, Virome, 030306 microbiology, Biodiversity, Cloud Computing, RNA-Dependent RNA Polymerase, Coronavirus, Cloud computing architecture, Hepatitis Delta Virus, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Sequence Alignment, Software
Abstract: Public sequence data represents a major opportunity for viral discovery, but its exploration has been inhibited by a lack of efficient methods for searching this corpus, which is currently at the petabase scale and growing exponentially. To address the ongoing pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 and expand the known sequence diversity of viruses, we aligned pangenomes for coronaviruses (CoV) and other viral families to 5.6 petabases of public sequencing data from 3.8 million biologically diverse samples. To implement this strategy, we developed a cloud computing architecture, Serratus, tailored for ultra-high throughput sequence alignment at the petabase scale. From this search, we identified and assembled thousands of CoV and CoV-like genomes and genome fragments ranging from known strains to putatively novel genera. We generalise this strategy to other viral families, identifying several novel deltaviruses and huge bacteriophages. To catalyse a new era of viral discovery we made millions of viral alignments and family identifications freely available to the research community. Expanding the known diversity and zoonotic reservoirs of CoV and other emerging pathogens can accelerate vaccine and therapeutic developments for the current pandemic, and help us anticipate and mitigate future ones.
Published: 2022

2. Evolution of life cycles and reproductive traits: Insights from the brown algae

Author: Christophe Destombe, Josué Barrera-Redondo, Svenja Heesch, Myriam Valero, Remy Luthringer, Denis Roze, Akira F. Peters, J. Mark Cock, Nicolas Salamin, Martha L. Serrano-Serrano, Susana M. Coelho, Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), University of Rostock, University of Lausanne (UNIL), Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft, Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Bezhin Rosko, Evolutionary Biology and Ecology of Algae (EBEA), and Pontificia Universidad Católica de Chile (UC)-Sorbonne Université (SU)-Universidad Austral de Chile-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR)
Subjects: 0106 biological sciences, 0301 basic medicine, Phaeophyceae, Isogamy, sex determination, Asexual reproduction, Phaeophyta, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Phylogenetics, Animals, gamete size, parthenogenesis, Evolutionary dynamics, Ecology, Evolution, Behavior and Systematics, Life Cycle Stages, biology, Reproduction, ploidy, Bayes Theorem, biology.organism_classification, Biological Evolution, Sexual reproduction, Sexual dimorphism, Brown algae, 030104 developmental biology, Anisogamy, Evolutionary biology, [SDE]Environmental Sciences
Abstract: International audience; A vast diversity of types of life cycles exists in nature, and several theories have been advanced to explain how this diversity has evolved and how each type of life cycle is retained over evolutionary time. Here, we exploited the diversity of life cycles and reproductive traits of the brown algae (Phaeophyceae) to test several hypotheses on the evolution of life cycles. We investigated the evolutionary dynamics of four life-history traits: life cycle, sexual system, level of gamete dimorphism and gamete parthenogenetic capacity. We assigned states to up to 77 representative species of the taxonomic diversity of the brown algal group, in a multi-gene phylogeny. We used maximum likelihood and Bayesian analyses of correlated evolution, while taking the phylogeny into account, to test for correlations between traits, and to investigate the chronological sequence of trait acquisition. Our analyses are consistent with the prediction that diploid growth evolves when sexual reproduction is preferred over asexual reproduction, possibly because it allows the complementation of deleterious mutations. We also found that haploid sex determination is ancestral in relation to diploid sex determination. However, our results could not address whether increased zygotic and diploid growth are associated with increased sexual dimorphism. Our analyses suggest that in the brown algae, isogamous species evolved from anisogamous ancestors, contrary to the commonly reported pattern where evolution proceeds from isogamy to anisogamy.
Published: 2021

3. A partially sex‐reversed giant kelp sheds light into the mechanisms of sexual differentiation in a UV sexual system

Author: Susana M. Coelho, Akira F. Peters, Wilhelm Boland, J. M. Cock, Maritta Kunert, E. Gachet, D. Mueller, Olivier Godfroy, Agnieszka P. Lipinska, G. Cossard, Renato Westermeier, J. Gueno, Universität Konstanz, Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Max Planck Institute for Chemical Ecology, Max-Planck-Gesellschaft, Bezhin Rosko, Universidad Austral de Chile, and Max Planck Institute for Developmental Biology
Subjects: 0106 biological sciences, 0301 basic medicine, Sex Differentiation, Physiology, Feminization (biology), [SDV]Life Sciences [q-bio], Male sex determination, sexual differentiation, Plant Science, Biology, Haploidy, Phaeophyta, brown algae, 01 natural sciences, 03 medical and health sciences, autosomes, Gene, development, 030304 developmental biology, Genetics, 0303 health sciences, Sexual differentiation, Autosome, feminisation, sex chromosomes, Chromosome, Ectocarpus, Sex determination, biology.organism_classification, Phenotype, Sexual dimorphism, 030104 developmental biology, Macrocystis, Ploidy, 010606 plant biology & botany
Abstract: SummaryIn UV sexual systems, sex is determined during the haploid phase of the life cycle and males have a V chromosome whereas females have a U chromosome. Previous work in the brown algal model Ectocarpus revealed that the V chromosome has a dominant role in male sex determination and suggested that the female developmental program may occur by ‘default’, triggered in the absence of the male master sex determination gene(s). Here, we describe the identification of a genetically male giant kelp strain presenting phenotypic features typical of a female, despite lacking the U-specific region. The conversion to the female developmental program is however incomplete, because gametes of this feminised male are unable to produce the sperm-attracting pheromone lamoxirene. We identify the transcriptomic patterns underlying the male and female specific developmental programs, and reveal the faster evolutionary rates of male-biased genes compared to female-biased and unbiased genes. Moreover, we show that the phenotypic feminisation of the variant strain is associated with both feminisation and de-masculinisation of gene expression patterns. Importantly, the feminisation phenotype was associated with the dramatic downregulation of two V-specific genes including a candidate sex-determining gene on the V-specific region. Our results reveal the transcriptional changes associated with sexual differentiation in a UV system with marked sexual dimorphism, and contribute to disentangling the role of sex-linked genes and autosomal gene expression in the initiation of the male and female developmental programs. Overall, the data presented here imply that the U-specific region in the giant kelp is not required to initiate the female developmental program, but is critical to produce fully functional eggs, arguing against the idea that female is the ‘default’ sex in this species.
Published: 2021

4. Global distribution patterns of marine nitrogen-fixers by imaging and molecular methods

Author: Colomban de Vargas, Madeline Carsique, Patrick Wincker, Marc Picheral, Fabien Lombard, Rainer Pepperkok, Etienne Dvorak, Silvia G. Acinas, Francisco M. Cornejo-Castillo, Sébastien Colin, Chris Bowler, Eric Karsenti, Juan José Pierella Karlusich, Rachel A. Foster, Eric Pelletier, Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Tara Oceans-GOSEE (FR2022), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), European Molecular Biology Laboratory [Heidelberg] (EMBL), Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), ECOlogy of MArine Plankton (ECOMAP), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft, Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Stockholm University, Fonds Français pour l'Environnement Mondial, Knut and Alice Wallenberg Foundation, European Research Council, European Commission, Agence Nationale de la Recherche (France), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), HAL-SU, Gestionnaire, Global Oceans Systems Ecology & Evolution - Tara Oceans (GOSEE), Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Aix Marseille Université (AMU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Université de Toulon (UTLN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche pour le Développement (IRD [France-Nord])-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay)-European Molecular Biology Laboratory (EMBL)-École Centrale de Nantes (Nantes Univ - ECN), Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Université australe du Chili, ANR-16-CE01-0008,PHYTOMET,Étude métallomique du phytoplancton: effet de l'acidification des océans sur la séquestration du fer(2016), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Aquatic Organisms, Nitrogen, Mesopelagic zone, Oceans and Seas, Science, General Physics and Astronomy, Cyanobacteria, [SDU.STU.OC] Sciences of the Universe [physics]/Earth Sciences/Oceanography, Article, General Biochemistry, Genetics and Molecular Biology, Molecular Imprinting, 03 medical and health sciences, Microbial ecology, Nitrogen Fixation, Element cycles, Seawater, 14. Life underwater, Symbiosis, Nitrogen cycle, Phylogeny, Microbial biooceanography, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, 030304 developmental biology, Ecological niche, Marine biology, 0303 health sciences, Deep chlorophyll maximum, Multidisciplinary, Bacteria, Environmental microbiology, 030306 microbiology, Ecology, [SDE.IE]Environmental Sciences/Environmental Engineering, Bacterioplankton, General Chemistry, New production, Plankton, 3. Good health, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, Global distribution, 13. Climate action, Metagenomics, Nitrogen fixation, Environmental science, [SDE.IE] Environmental Sciences/Environmental Engineering, Diazotroph, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: This article is contribution number 118 of Tara Oceans.-- 18 pages, 10 figures, supplementary information https://doi.org/10.1038/s41467-021-24299-y.-- Data availability: The authors declare that all the data supporting the findings of this study are publicly available in the following repositories and in the supplementary information files of this paper. The contextual data are available in Pangaea (www.pangaea.de)21 with the identifier https://doi.org/10.1594/PANGAEA.875582. Flow cytometry data23,108 are available in Mendeley Data (https://data.mendeley.com) with the identifier https://doi.org/10.17632/p9r9wttjkm.2. The confocal microscopy30 and UVP533 images annotated as diazotrophs in the current work and their corresponding metadata were submitted to the EMBL-EBI repository BioStudies (www.ebi.ac.uk/biostudies) under accession S-BSST529; while the whole image databases and their metadata are available at Ecotaxa (confocal microscopy of 5–20 µm sized-fractionated samples: https://ecotaxa.obs-vlfr.fr/prj/3365; confocal microscopy of 20–180 μm sized-fractionated samples: https://ecotaxa.obs-vlfr.fr/prj/2274; UVP5: https://ecotaxa.obs-vlfr.fr/prj/579). Tara Oceans metagenomes22,24,25 are archived at ENA under the accession numbers: PRJEB1787, PRJEB1788, PRJEB4352, PRJEB4419, PRJEB9691, PRJEB9740, and PRJEB9742. The nifH and recA catalogs were compiled from Integrated Microbial Genomes (IMG, https://img.jgi.doe.gov/); Marine Microbial Eukaryotic Transcriptome Sequencing Project (MMETSP; https://github.com/dib-lab/dib-MMETSP); OM-Reference Gene Catalog version 2 (OM-RGC-v2, https://www.ocean-microbiome.org/); Tara Oceans assemblies (Supplementary Table 8 from ref. 16); and the nifH database (version April 2014) curated and hosted at Zehr Lab, University of California, Santa Cruz, CA, USA (https://www.jzehrlab.com/nifh). The 10 nifH sequences generated in the clone libraries of the current work were submitted to ENA under the accession numbers: MW590317–MW590326. Source data are provided with this paper, Nitrogen fixation has a critical role in marine primary production, yet our understanding of marine nitrogen-fixers (diazotrophs) is hindered by limited observations. Here, we report a quantitative image analysis pipeline combined with mapping of molecular markers for mining >2,000,000 images and >1300 metagenomes from surface, deep chlorophyll maximum and mesopelagic seawater samples across 6 size fractions (20 µm). Using imaging and molecular data, we estimate that polyploidy can substantially affect gene abundances of symbiotic versus colony-forming diazotrophs. Our results support the canonical view that larger diazotrophs (>10 μm) dominate the tropical belts, while unicellular cyanobacterial and non-cyanobacterial diazotrophs are globally distributed in surface and mesopelagic layers. We describe co-occurring diazotrophic lineages of different lifestyles and identify high-density regions of diazotrophs in the global ocean. Overall, we provide an update of marine diazotroph biogeographical diversity and present a new bioimaging-bioinformatic workflow, This work has been supported by the FFEM - French Facility for Global Environment, French Government ‘Investissements d’Avenir’ programs OCEANOMICS (ANR-11-BTBR-0008), FRANCE GENOMIQUE (ANR-10-INBS-09-08), MEMO LIFE (ANR-10-LABX-54), and PSL Research University (ANR-11-IDEX-0001-02). R.A.F. acknowledges funding from Knut and Alice Wallenberg foundation. C.B. acknowledges funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Diatomic; grant agreement No. 835067) and Agence Nationale de la Recherche “Phytomet” (ANR-16-CE01-0008) projects. F.M.C.-C. acknowledges funding from the European Union’s Horizon 2020 research program under the Marie Sklodowska-Curie grant agreement No. 749380 (UCYN2PLAST). S.G.A. acknowledges funding from the project “MAGGY” (CTM2017-87736-R) from the Spanish Ministry of Economy and Competitiveness and the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S). J.J.P.K. acknowledges postdoctoral funding from the Fonds Français pour l’Environnement Mondial
Published: 2021

5. Meeting Report

Author: Leitner, Alexander, Bonvin, Alexandre M J J, Borchers, Christoph H, Chalkley, Robert J, Chamot-Rooke, Julia, Combe, Colin W, Cox, Jürgen, Dong, Meng-Qiu, Fischer, Lutz, Götze, Michael, Gozzo, Fabio C, Heck, Albert J R, Hoopmann, Michael R, Huang, Lan, Ishihama, Yasushi, Jones, Andrew R, Kalisman, Nir, Kohlbacher, Oliver, Mechtler, Karl, Moritz, Robert L, Netz, Eugen, Novak, Petr, Petrotchenko, Evgeniy, Sali, Andrej, Scheltema, Richard A, Schmidt, Carla, Schriemer, David, Sinz, Andrea, Sobott, Frank, Stengel, Florian, Thalassinos, Konstantinos, Urlaub, Henning, Viner, Rosa, Vizcaíno, Juan A, Wilkins, Marc R, Rappsilber, Juri, Sub NMR Spectroscopy, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Biomolecular Mass Spectrometry and Proteomics, NMR Spectroscopy, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Utrecht University [Utrecht], University of Victoria [Canada] (UVIC), Lady Davis Institute for Medical Research [Montréal], McGill University = Université McGill [Montréal, Canada]-Jewish General Hospital, Skolkovo Institute of Science and Technology [Moscow] (Skoltech), University of California [San Francisco] (UCSF), University of California, Spectrométrie de Masse pour la Biologie – Mass Spectrometry for Biology (UTechS MSBio), Institut Pasteur [Paris]-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), University of Edinburgh, Max Planck Institute of Biochemistry (MPIB), Max-Planck-Gesellschaft, National Institute of Biological Sciences [Beijing, China] (Number 7 Science Park Road), Zhongguancun Life Science Park [Beijing, China], Technische Universität Berlin (TU), University of Campinas [Campinas] (UNICAMP), Institute for Systems Biology [Seattle] (ISB), University of California [Irvine] (UCI), Kyoto University [Kyoto], University of Liverpool, The Hebrew University of Jerusalem (HUJ), University of Tübingen, Max Planck Institute for Developmental Biology, Research Institute of Molecular Pathology (IMP), Charles University [Prague] (CU), Martin-Luther-University Halle-Wittenberg, University of Calgary, University of Leeds, University of Antwerp (UA), University of Konstanz, Birkbeck College [University of London], University College of London [London] (UCL), Max-Planck-Institut für Biophysikalische Chemie - Max Planck Institute for Biophysical Chemistry [Göttingen], Thermo Fisher Scientific (Bremen) GmbH, European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, University of New South Wales [Sydney] (UNSW), This work was supported by the Wellcome Trust through a Senior Research Fellowship to J.R. (103139) and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation, project 329673113). Funded by the DFG under Germany's Excellence Strategy, EXC 2008/1-390540038. The Wellcome Centre for Cell Biology is supported by core funding from the Wellcome Trust (203149)., We thank the participants of the meetings mentioned throughout the text for their many different contributions. Although we made an effort to include all labs that may feel a belonging to the field of Cross-linking MS, we apologize to all those that we missed. Developing standards in Cross-linking MS is to be viewed as an inclusive activity, so please feel warmly invited to join our efforts, University of California [San Francisco] (UC San Francisco), University of California (UC), Institut Pasteur [Paris] (IP)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Max-Planck-Institut für Biochemie = Max Planck Institute of Biochemistry (MPIB), Technical University of Berlin / Technische Universität Berlin (TU), Universidade Estadual de Campinas = University of Campinas (UNICAMP), University of California [Irvine] (UC Irvine), Kyoto University, Sub NMR Spectroscopy, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Biomolecular Mass Spectrometry and Proteomics, and NMR Spectroscopy
Subjects: 0303 health sciences, Computer science, Physics, 030302 biochemistry & molecular biology, Mass spectrometry, Other Quantitative Biology (q-bio.OT), Data science, Quantitative Biology - Other Quantitative Biology, 03 medical and health sciences, Chemistry, White paper, Structural Biology, Transparency (graphic), FOS: Biological sciences, ddc:570, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Human medicine, Molecular Biology, Biology, Reliability (statistics), 030304 developmental biology
Abstract: Crosslinking mass spectrometry (Crosslinking MS) has substantially matured as a method over the last two decades through parallel development in multiple labs, demonstrating its applicability for protein structure determination, conformation analysis and mapping protein interactions in complex mixtures. Crosslinking MS has become a much-appreciated and routinely applied tool especially in structural biology. Therefore, it is timely that the community commits to the development of methodological and reporting standards. This white paper builds on an open process comprising a number of events at community conferences since 2015 and identifies aspects of Crosslinking MS for which guidelines should be developed as part of a Crosslinking MS standards initiative., Comment: 26 pages, 1 figure
Published: 2020

6. Genetic and genomic approaches for adaptation of grapevine to climate change

Author: Silvia Vezzulli, Eric Duchêne, Ludger Hausmann, Lorenza Dalla Costa, Nathalie Ollat, Pablo Carbonell-Bejerano, Anna Schwandner, Jérôme Grimplet, Pierre-François Bert, Mario Pecile, Luigi Bavaresco, Gabriele Di Gaspero, Mickael Malnoy, Michele Morgante, Serge Delrot, Ecophysiologie et Génomique Fonctionnelle de la Vigne (UMR EGFV), Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1-Université Victor Segalen - Bordeaux 2-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro), Centro de Investigacion y Tecnologia Agroalimentaria de Aragon (CITA), Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft, Julius Kühn-Institut (JKI), Santé de la vigne et qualité du vin (SVQV), Université de Strasbourg (UNISTRA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Università cattolica del Sacro Cuore [Roma] (Unicatt), Fondazione Edmund Mach - Edmund Mach Foundation [Italie] (FEM), Istituto di Genomica Applicata (IGA), Istituto di Genomica Applicata, Università degli Studi di Udine - University of Udine [Italie], Consiglio per la Ricerca in Agricoltura e l’analisi dell’economia agraria (CREA), Chittaranjan Kole, and KOLE, Chittaranjan
Subjects: 0106 biological sciences, Genotyping, Vitis vinifera L, Climate change, Biology, Terroir, 01 natural sciences, Vineyard, 03 medical and health sciences, Effects of global warming, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Regeneration (ecology), Vitis spp, Genetic resources, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Genetic diversity, business.industry, 15. Life on land, Data bases, Biotechnology, Settore AGR/07 - GENETICA AGRARIA, 13. Climate action, Phenotyping, Settore AGR/03 - ARBORICOLTURA GENERALE E COLTIVAZIONI ARBOREE, Rootstock, Adaptation, Viticulture, business, 010606 plant biology & botany
Abstract: International audience; The necessity to adapt to climate change is even stronger for grapevine than for other crops, because grape berry composition—a key determinant of fruit and wine quality, typicity and market value— highly depends on “terroir” (complete natural environment), on vintage (annual climate variability), and on their interactions. In the same time, there is a strong demand to reduce the use of pesticides. Thus, the equation that breeders and grape growers must solve has three entries that cannot be dissociated: adaptation to climate change, reduction of pesticides, and maintenance of wine typicity. Although vineyard management may cope to some extent to the short–medium-term effects of climate change, genetic improvement is necessary to provide long-term sustainable solutions to these problems. Most vineyards over the world are planted using vines that harbor two grafted plants’ genomes. Although this makes the range of interactions (scion-atmosphere, rootstock-soil, scion-rootstock) more complex, it also opens up wider possibilities for the genetic improvement of either or both the grafted genotypes. Positive aspects related to grapevine breeding are as follows: (a) a wide genetic diversity of rootstocks and scions that has not been thoroughly explored yet; (b) progress in sequencing technologies that allows high-throughput sequencing of entire genomes, faster mapping of targeted traits and easier determination of genetic relationships; (c) progress in new breeding technologies that potentially permit precise modifications on resident genes; (d) automation of phenotyping that allows faster and more complete monitoring of many traits on relatively large plant populations; (e) functional characterization of an increasing number of genes involved in the control of development, berry metabolism, disease resistance, and adaptation to environment. Difficulties involve: (a) the perennial nature and the large size of the plant that makes field testing long and demanding in manpower; (b) the low efficiency of transformation, regeneration and small size of breeding populations; (c) the complexity of the adaptive traits and the need to define more clearly future ideotypes; (d) the lack of shared and integrative platforms allowing a complete appraisal of the genotype-phenotype-environmental links; (e) legal, market and consumer acceptance of new genotypes. The present chapter provides an overview of suitable strategies and challenges linked to the adaptation of viticulture to a changing environment.
Published: 2020

7. Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases

Author: Tørresen, Ole K., Star, Bastiaan, Mier, Pablo, Andrade-Navarro, Miguel A., Bateman, Alex, Jarnot, Patryk, Gruca, Aleksandra, Grynberg, Marcin, Kajava, Andrey V., Promponas, Vasilis J., Anisimova, Maria, Jakobsen, Kjetill S., Linke, Dirk, Centre de recherche en Biologie Cellulaire (CRBM), Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1), Promponas, Vasilis J. [0000-0003-3352-4831], European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Silesian University of Technology, Biophysics and Bioinformatics Laboratory, Zürich University of Applied Sciences (ZHAW), Max Planck Institute for Developmental Biology, and Max-Planck-Gesellschaft
Subjects: FOS: Computer and information sciences, Bioinformatics, [SDV]Life Sciences [q-bio], Sequence assembly, Genomics, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Computational biology, Biology, Genome, 03 medical and health sciences, Annotation, 0302 clinical medicine, Tandem repeat, Genetics, Animals, Survey and Summary, Databases, Protein, Gene, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, End user, 572: Biochemie, DNA, Sequence Analysis, DNA, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Workflow, ComputingMethodologies_PATTERNRECOGNITION, Gadus morhua, Tandem Repeat Sequences, Scientific Experimental Error, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Databases, Nucleic Acid, 030217 neurology & neurosurgery
Abstract: The widespread occurrence of repetitive stretches of DNA in genomes of organisms across the tree of life imposes fundamental challenges for sequencing, genome assembly, and automated annotation of genes and proteins. This multi-level problem can lead to errors in genome and protein databases that are often not recognized or acknowledged. As a consequence, end users working with sequences with repetitive regions are faced with ‘ready-to-use’ deposited data whose trustworthiness is difficult to determine, let alone to quantify. Here, we provide a review of the problems associated with tandem repeat sequences that originate from different stages during the sequencing-assembly-annotation-deposition workflow, and that may proliferate in public database repositories affecting all downstream analyses. As a case study, we provide examples of the Atlantic cod genome, whose sequencing and assembly were hindered by a particularly high prevalence of tandem repeats. We complement this case study with examples from other species, where mis-annotations and sequencing errors have propagated into protein databases. With this review, we aim to raise the awareness level within the community of database users, and alert scientists working in the underlying workflow of database creation that the data they omit or improperly assemble may well contain important biological information valuable to others.
Published: 2019

8. Arabidopsis proteins with a transposon-related domain act in gene silencing

Author: Yoko, Ikeda, Thierry, Pélissier, Pierre, Bourguet, Claude, Becker, Marie-Noëlle, Pouch-Pélissier, Romain, Pogorelcnik, Magdalena, Weingartner, Detlef, Weigel, Jean-Marc, Deragon, Olivier, Mathieu, Génétique, Reproduction et Développement (GReD), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Santé et de la Recherche Médicale (INSERM), Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Université de Perpignan Via Domitia (UPVD), Laboratoire d'Informatique, de Modélisation et d'optimisation des Systèmes (LIMOS), SIGMA Clermont (SIGMA Clermont)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Ecole Nationale Supérieure des Mines de St Etienne-Centre National de la Recherche Scientifique (CNRS)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Department of Molecular Biology, Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-SIGMA Clermont (SIGMA Clermont)-Ecole Nationale Supérieure des Mines de St Etienne (ENSM ST-ETIENNE)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Retroelements, Arabidopsis Proteins, [SDV]Life Sciences [q-bio], Science, Centromere, Arabidopsis, Nuclear Proteins, food and beverages, DNA Methylation, Article, Evolution, Molecular, Protein Domains, Heterochromatin, DNA Transposable Elements, Gene Silencing, RNA, Small Interfering, ComputingMilieux_MISCELLANEOUS
Abstract: Transposable elements (TEs) are prevalent in most eukaryotes, and host genomes have devised silencing strategies to rein in TE activity. One of these, transcriptional silencing, is generally associated with DNA methylation and short interfering RNAs. Here we show that the Arabidopsis genes MAIL1 and MAIN define an alternative silencing pathway independent of DNA methylation and short interfering RNAs. Mutants for MAIL1 or MAIN exhibit release of silencing and appear to show impaired condensation of pericentromeric heterochromatin. Phylogenetic analysis suggests not only that MAIL1 and MAIN encode a retrotransposon-related plant mobile domain, but also that host plant mobile domains were captured by DNA transposons during plant evolution. Our results reveal a role for Arabidopsis proteins with a transposon-related domain in gene silencing., Host genomes have evolved multiple silencing mechanisms to repress transposable element activity. Here Ikeda et al. show that the Arabidopsis MAIL1 and MAIN genes encode a retrotransposon-related plant mobile domain and define an alternative silencing pathway largely independent of DNA methylation and siRNAs.
Published: 2017

9. A G-protein-coupled receptor mediates neuropeptide-induced oocyte maturation in the jellyfish Clytia

Author: Sandra Chevalier, Gonzalo Quiroga Artigas, Lucas Leclère, Gáspár Jékely, Philipp Bauknecht, Tsuyoshi Momose, Pascal Lapébie, Evelyn Houliston, Julie Uveira, Centre d'océanologie de Marseille (COM), Université de la Méditerranée - Aix-Marseille 2-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie du Développement de Villefranche sur mer (LBDV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft, Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-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), University of Exeter, Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de la Méditerranée - Aix-Marseille 2, and Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Male, Receptors, Neuropeptide, Sexual Reproduction, 0301 basic medicine, Somatic cell, Peptide Hormones, Xenopus, [SDV]Life Sciences [q-bio], Gene Expression, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], Biochemistry, Receptors, G-Protein-Coupled, Animals, Genetically Modified, 0302 clinical medicine, Animal Cells, Cyclic AMP, Medicine and Health Sciences, Biology (General), Receptor, [SDV.BDD]Life Sciences [q-bio]/Development Biology, Phylogeny, [SDV.BDD.GAM]Life Sciences [q-bio]/Development Biology/Gametogenesis, G alpha subunit, 0303 health sciences, General Neuroscience, Eukaryota, Neurochemistry, Animal Models, Neuropeptide Y receptor, Cell biology, medicine.anatomical_structure, Experimental Organism Systems, OVA, Xenopus Oocytes, Vertebrates, Frogs, Gamete, Female, Cellular Types, Anatomy, Neurochemicals, General Agricultural and Biological Sciences, Genital Anatomy, Research Article, Signal Transduction, Gs alpha subunit, Transmembrane Receptors, Spawning, QH301-705.5, Modes of Reproduction, Neuropeptide, Biology, Research and Analysis Methods, General Biochemistry, Genetics and Molecular Biology, [SDV.BDLR.RS]Life Sciences [q-bio]/Reproductive Biology/Sexual reproduction, Amphibians, Cnidaria, 03 medical and health sciences, Model Organisms, medicine, Animals, Gonads, 030304 developmental biology, G protein-coupled receptor, General Immunology and Microbiology, Neuropeptides, Reproductive System, Organisms, Wild type, Biology and Life Sciences, Proteins, Cell Biology, Oocyte, Invertebrates, Hormones, Hydrozoa, Germ Cells, 030104 developmental biology, Mutation, Oocytes, Animal Studies, Jellyfish, CRISPR-Cas Systems, G Protein Coupled Receptors, 030217 neurology & neurosurgery, Neuroscience, Developmental Biology
Abstract: The reproductive hormones that trigger oocyte meiotic maturation and release from the ovary vary greatly between animal species. Identification of receptors for these maturation-inducing hormones (MIHs) and understanding how they initiate the largely conserved maturation process remain important challenges. In hydrozoan cnidarians including the jellyfish Clytia hemisphaerica, MIH comprises neuropeptides released from somatic cells of the gonad. We identified the receptor (MIHR) for these MIH neuropeptides in Clytia using cell culture–based “deorphanization” of candidate oocyte-expressed G protein–coupled receptors (GPCRs). MIHR mutant jellyfish generated using CRISPR-Cas9 editing had severe defects in gamete development or in spawning both in males and females. Female gonads, or oocytes isolated from MIHR mutants, failed to respond to synthetic MIH. Treatment with the cAMP analogue Br-cAMP to mimic cAMP rise at maturation onset rescued meiotic maturation and spawning. Injection of inhibitory antibodies to the alpha subunit of the Gs heterodimeric protein (GαS) into wild-type oocytes phenocopied the MIHR mutants. These results provide the molecular links between MIH stimulation and meiotic maturation initiation in hydrozoan oocytes. Molecular phylogeny grouped Clytia MIHR with a subset of bilaterian neuropeptide receptors, including neuropeptide Y, gonadotropin inhibitory hormone (GnIH), pyroglutamylated RFamide, and luqin, all upstream regulators of sexual reproduction. This identification and functional characterization of a cnidarian peptide GPCR advances our understanding of oocyte maturation initiation and sheds light on the evolution of neuropeptide-hormone systems., A study of jellyfish oocytes identifies the receptor for Maturation-Inducing Hormone, the neuropeptide hormone that triggers oocyte maturation and spawning via GαS and cyclic AMP. This receptor defines a superfamily of hormone-receptor systems involved in regulating sexual reproduction across animal species.
Published: 2019

10. Predicting kidney failure from longitudinal kidney function trajectory: A comparison of models

Author: Ron T. Gansevoort, Bénédicte Stengel, Marie Metzger, Hiddo J.L. Heerspink, Jack F.M. Wetzels, Jan A.J.G. van den Brand, Peter J. Blankestijn, Tjeerd M. H. Dijkstra, Department of nephrology [Nimègue, Pays-Bas], Radboud Institute for Health Sciences [Nimègue, Pays-Bas], Radboud University Medical Center [Nijmegen]-Radboud University Medical Center [Nijmegen], Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft, Center for Integrative Neuroscience [Tubingue, Allemagne], University of Tübingen, Centre de recherche en épidémiologie et santé des populations (CESP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris-Sud - Paris 11 (UP11)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Department of Nephrology [Utrecht, Pays-Bas], University Medical Center [Utrecht], Department of Clinical Pharmacy and Pharmacology [Groningue, Pays-Bas], University Medical Center Groningen [Groningen] (UMCG), Department of Nephrology [Groningue, Pays-Bas], JAJGvdB is supported by grant DKF14OKG07 from the Dutch Kidney Foundation (www.nierstichting.nl), TD was supported by CogIMon H2020 ICT-644727. (https://ec.europa.eu/programmes/horizon2020/en/). The MASTERPLAN Study was supported by grant number PV01 from the Dutch Kidney Foundation (www.nierstichting.nl) and grant 2003B261 from the Netherlands Heart Foundation (Nederlandse Hartstichting, (www.hartstichting.nl). In addition, unrestricted grants were provided by Amgen, Genzyme, Pfizer and Sanofi-Aventis for the MASTERPLAN study. The NephroTest cohort study was supported by the following grants: INSERM (www.inserm.fr) GIS-IReSP AO 8113LS TGIR (B.S.), French Ministry of Health AOM 09114 (M.Fr.), INSERM AO 8022LS (B.S.), Agence de la Biomédecine R0 8156LL (B.S.), AURA (M.Fr.) and Roche 2009-152-447G (M.Fr.)., Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Paris-Sud - Paris 11 (UP11)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM), Bodescot, Myriam, Groningen Kidney Center (GKC), Real World Studies in PharmacoEpidemiology, -Genetics, -Economics and -Therapy (PEGET), and Cardiovascular Centre (CVC)
Subjects: Oncology, Male, Physiology, 030232 urology & nephrology, Blood Pressure, Kidney Function Tests, Vascular Medicine, Biochemistry, [SDV.MHEP.UN]Life Sciences [q-bio]/Human health and pathology/Urology and Nephrology, 0302 clinical medicine, Mathematical and Statistical Techniques, Skeletal Joints, Chronic Kidney Disease, Medicine and Health Sciences, 030212 general & internal medicine, Prospective Studies, Prospective cohort study, Musculoskeletal System, Multidisciplinary, Agricultural and Biological Sciences(all), Statistics, Middle Aged, Prognosis, Nephrology, Creatinine, Cohort, Physical Sciences, Disease Progression, Medicine, Female, medicine.symptom, Anatomy, Research Article, Glomerular Filtration Rate, medicine.medical_specialty, Science, Renal function, Research and Analysis Methods, Risk Assessment, 03 medical and health sciences, Diagnostic Medicine, Internal medicine, medicine, Journal Article, Humans, Statistical Methods, Renal Insufficiency, Chronic, General, Survival analysis, Renal Physiology, Models, Statistical, Proportional hazards model, business.industry, Biochemistry, Genetics and Molecular Biology(all), Data Science, Repeated measures design, Biology and Life Sciences, Kidneys, Renal System, medicine.disease, [SDV.MHEP.UN] Life Sciences [q-bio]/Human health and pathology/Urology and Nephrology, Albuminuria, Kidney Failure, Chronic, Renal disorders Radboud Institute for Health Sciences [Radboudumc 11], business, Biomarkers, Mathematics, Kidney disease, Forecasting, Genetics and Molecular Biology(all)
Abstract: Contains fulltext : 205516.pdf (Publisher’s version ) (Open Access) RATIONALE & OBJECTIVE: Early prediction of chronic kidney disease (CKD) progression to end-stage kidney disease (ESKD) currently use Cox models including baseline estimated glomerular filtration rate (eGFR) only. Alternative approaches include a Cox model that includes eGFR slope determined over a baseline period of time, a Cox model with time varying GFR, or a joint modeling approach. We studied if these more complex approaches may further improve ESKD prediction. STUDY DESIGN: Prospective cohort. SETTING & PARTICIPANTS: We re-used data from two CKD cohorts including patients with baseline eGFR >30ml/min per 1.73m2. MASTERPLAN (N = 505; 55 ESKD events) was used as development dataset, and NephroTest (N = 1385; 72 events) for validation. PREDICTORS: All models included age, sex, eGFR, and albuminuria, known prognostic markers for ESKD. ANALYTICAL APPROACH: We trained the models on the MASTERPLAN data and determined discrimination and calibration for each model at 2 years follow-up for a prediction horizon of 2 years in the NephroTest cohort. We benchmarked the predictive performance against the Kidney Failure Risk Equation (KFRE). RESULTS: The C-statistics for the KFRE was 0.94 (95%CI 0.86 to 1.01). Performance was similar for the Cox model with time-varying eGFR (0.92 [0.84 to 0.97]), eGFR (0.95 [0.90 to 1.00]), and the joint model 0.91 [0.87 to 0.96]). The Cox model with eGFR slope showed the best calibration. CONCLUSION: In the present studies, where the outcome was rare and follow-up data was highly complete, the joint models did not offer improvement in predictive performance over more traditional approaches such as a survival model with time-varying eGFR, or a model with eGFR slope.
Published: 2019

11. Article Multiple C2 domains and transmembrane region proteins (MCTPs) tether membranes at plasmodesmata

Author: Max E. Kraner, Mathieu Fouché, Timothy J. Hawkins, Jean-Marc Crowet, Magali Deleu, Amèlia Gaston, Véronique Germain, Françoise Immel, Jens Tilsner, Vikram Alva, Laurence Lins, Marie Glavier, Yrjö Helariutta, Marion Rocher, Marie L Brault, Jules D. Petit, Stéphane Claverol, William J Nicolas, Andrea Paterlini, Lysiane Brocard, Emmanuelle Bayer, Magali S. Grison, Laboratoire de biogenèse membranaire (LBM), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), Université de Liège, Bordeaux Imaging Center (BIC), Université de Bordeaux (UB)-Institut François Magendie-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Durham University, Laboratoire de Biophysique Moléculaire aux Interfaces, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft, Plateforme génomique fonctionnelle (PGFB), Université Bordeaux Segalen - Bordeaux 2, University of Cambridge [UK] (CAM), University of St Andrews [Scotland], The James Hutton Institute, BBSRC, University of St Andrews. Biomedical Sciences Research Complex, University of St Andrews. School of Biology, Petit, Jules D [0000-0003-4652-2843], Immel, Françoise [0000-0002-2028-902X], Nicolas, William J [0000-0001-5970-8626], Glavier, Marie [0000-0002-7100-7045], Gaston, Amèlia [0000-0001-9974-8083], Crowet, Jean-Marc [0000-0002-9252-2396], Grison, Magali S [0000-0002-3080-3686], Alva, Vikram [0000-0003-1188-473X], Paterlini, Andrea [0000-0002-1777-3160], Helariutta, Ykä [0000-0002-7287-8459], Deleu, Magali [0000-0001-8255-2965], Lins, Laurence [0000-0001-7772-6748], Tilsner, Jens [0000-0003-3873-0650], Bayer, Emmanuelle M [0000-0001-8642-5293], and Apollo - University of Cambridge Repository
Subjects: multiple C2 domains and transmembrane region proteins, QH301 Biology, Mutant, Arabidopsis, Plant Biology, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], Endoplasmic Reticulum, Biochemistry, intercellular communication in plants, 0302 clinical medicine, Gene Expression Regulation, Plant, Genes, Reporter, Membrane & Intracellular Transport, plasmo-desmata, Cells, Cultured, Phospholipids, R2C, 0303 health sciences, Vegetal Biology, ER-PM membrane contact sites, plasmodesmata, Tethering, Chemistry, ~DC~, Plasmodesmata, Gene Expression Regulation, Developmental, Articles, Plants, Genetically Modified, Intracellular communication in plants, Cell biology, Membrane, plante, BDC, Intracellular, Signal Transduction, Multiple C2 domains transmembrane region proteins, Green Fluorescent Proteins, Plasmodesma, Saccharomyces cerevisiae, ER‐PM membrane contact sites, Article, physiologie végétale, 03 medical and health sciences, QH301, Protein Domains, développement de la plante, Plant Cells, Organelle, Tobacco, Genetics, Humans, Molecular Biology, 030304 developmental biology, Arabidopsis Proteins, Endoplasmic reticulum, Gene Expression Profiling, Cell Membrane, Glycosyltransferases, Membrane Proteins, DAS, Luminescent Proteins, Biologie végétale, 030217 neurology & neurosurgery, Function (biology)
Abstract: Funding: Work in J.T, lab is supported by grant BB/M007200/1 from the U.K. Biotechnology and Biomedical Sciences Research Council (BBSRC) and by the Scottish Government's Rural and Environment Science and Analytical Services Division (RESAS). In eukaryotes, membrane contact sites (MCS) allow direct communication between organelles. Plants have evolved a unique type of MCS, inside intercellular pores, the plasmodesmata, where endoplasmic reticulum (ER)–plasma membrane (PM) contacts coincide with regulation of cell‐to‐cell signalling. The molecular mechanism and function of membrane tethering within plasmodesmata remain unknown. Here, we show that the multiple C2 domains and transmembrane region protein (MCTP) family, key regulators of cell‐to‐cell signalling in plants, act as ER‐PM tethers specifically at plasmodesmata. We report that MCTPs are plasmodesmata proteins that insert into the ER via their transmembrane region while their C2 domains dock to the PM through interaction with anionic phospholipids. A Atmctp3/Atmctp4 loss of function mutant induces plant developmental defects, impaired plasmodesmata function and composition, while MCTP4 expression in a yeast Δtether mutant partially restores ER‐PM tethering. Our data suggest that MCTPs are unique membrane tethers controlling both ER‐PM contacts and cell‐to‐cell signalling. Publisher PDF
Published: 2019

12. Non-linear phenotypic variation uncovers the emergence of heterosis in Arabidopsis thaliana

Author: Dominique de Vienne, Detlef Weigel, Louise Fouqueau, Cyrille Violle, François Vasseur, Thibault Nidelet, Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Max Planck Institute for Developmental Biology, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud]), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Paris-Sud - Paris 11 (UP11)-Institut National de la Recherche Agronomique (INRA), Sciences Pour l'Oenologie (SPO), 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 Montpellier 1 (UM1)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA), French Agency for Research (ANR) [ANR-17-CE020-0018-01], European Research Council (ERC) (AdG IMMUNEMESIS) [340602], European Research Council (ERC) (StG CONSTRAINTS) [639706], Agreenskills fellowship programme - EU's Seventh Framework Programme [3215 FP7-609398], ANR-17-CE02-0018,AraBreed,Exploration des réponses évolutives des plantes à des changements environnementaux à la lumière des théories écologiques : un test expérimental chez l'espèce modèle Arabidopsis thaliana(2017), European Project: 609398,EC:FP7:PEOPLE,FP7-PEOPLE-2013-COFUND,AGREENSKILLSPLUS(2014), European Project: 639706,H2020,ERC-2014-STG,CONSTRAINTS(2015), Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Université Montpellier 1 (UM1)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie])-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Vasseur, François, and Weigel, Detlef
Subjects: 0301 basic medicine, Animal breeding, Genotype, QH301-705.5, Heterosis, Population, Arabidopsis, Biology, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, 0302 clinical medicine, Hybrid Vigor, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Biology (General), Allele, education, Crosses, Genetic, Hybrid, 2. Zero hunger, education.field_of_study, Vegetal Biology, General Immunology and Microbiology, Models, Genetic, General Neuroscience, 15. Life on land, Phenotype, Primer, 030104 developmental biology, Genetic distance, Biological Variation, Population, Evolutionary biology, Hybridization, Genetic, hétérosis, Allometry, General Agricultural and Biological Sciences, Biologie végétale, 030217 neurology & neurosurgery
Abstract: Recognition and exploitation of hybrid vigor or heterosis among individual crosses of plants and animals has a long and distinguished history. Its manifestation is influenced by a combination of genetic, epigenetic, phenotypic, and environmental factors. Although heterosis is known to be governed by both dominant and epistatic gene action, its expression is greatly influenced by nonlinear interaction among epigenetic and phenotypic (phenomic) components. The magnitude of heterosis is generally inferred post hoc by the phenotypic performance of hybrids among laboriously made individual crosses. The expression of dominance, however, is nonlinear at the cellular level and obeys the principles underlying metabolic flux. Then, is it possible to exploit these relationships to predict heterosis? Vasseur and colleagues have indeed demonstrated the feasibility of such an approach in a series of experiments taking integrated biochemical and computational approaches, as well as testing these results on large samples of model organisms. The results offer promise toward phenomic prediction of heterosis across a wide array of organisms., A recent study applies allometric models to test Sewall Wright’s 85 year-old conjecture on the expression of dominance among traits that contribute to productivity and Darwinian fitness in Arabidopsis thaliana. This Primer explores the wide-ranging implications for agriculture and human health.
Published: 2019

13. Adaptive diversification of growth allometry in the plant Arabidopsis thaliana

Author: Oscar Javier Ayala-Garay, Cyrille Violle, Brian J. Enquist, Denis Vile, George Wang, François Vasseur, Moises Exposito-Alonso, Detlef Weigel, Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Division of Geriatric Medicine and Gerontology, Johns Hopkins University School of Medicine, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud]), Department of Molecular Biology [Tübingen], Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, European Research Council (ERC-StG-CONSTRAINTS), European Project: 340602,EC:FP7:ERC,ERC-2013-ADG,IMMUNEMESIS(2014), Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3)
Subjects: 0301 basic medicine, 0106 biological sciences, croissance végétale, Evolution, Climate Change, Local adaptation, Metabolic theory of ecology, Tree allometry, Arabidopsis, modèle allométrique, Biology, Balancing selection, 010603 evolutionary biology, 01 natural sciences, Intraspecific competition, 03 medical and health sciences, Stress, Physiological, GWAS, analyse génomique, Stabilizing selection, Scaling, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Multidisciplinary, Vegetal Biology, Fitness trade-off, Abiotic stress, Arabidopsis Proteins, arabidopsis thaliana, food and beverages, 15. Life on land, Biological Sciences, Models, Theoretical, Metabolic scaling theory, Adaptation, Physiological, Biological Evolution, 030104 developmental biology, Evolutionary biology, [SDE]Environmental Sciences, équation allométrique, Allometry, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, human activities, Biologie végétale
Abstract: Significance Are there biological constants unifying phenotypic diversity across scales? Metabolic scaling theory (MST) predicts mathematical regularity and constancy in the allometric scaling of growth rate with body size across species. Here we show that adaptation to climate in Arabidopsis thaliana is associated with local strains that substantially deviate from the values predicted by MST. This deviation can be linked to increased stress tolerance at the expense of seed production, and it occurs through selection on genes that are involved in the abiotic stress response and are geographically correlated with climatic conditions. This highlights the evolutionary role of allometric diversification and helps establish the physiological bases of plant adaptation to contrasting environments., Seed plants vary tremendously in size and morphology; however, variation and covariation in plant traits may be governed, at least in part, by universal biophysical laws and biological constants. Metabolic scaling theory (MST) posits that whole-organismal metabolism and growth rate are under stabilizing selection that minimizes the scaling of hydrodynamic resistance and maximizes the scaling of resource uptake. This constrains variation in physiological traits and in the rate of biomass accumulation, so that they can be expressed as mathematical functions of plant size with near-constant allometric scaling exponents across species. However, the observed variation in scaling exponents calls into question the evolutionary drivers and the universality of allometric equations. We have measured growth scaling and fitness traits of 451 Arabidopsis thaliana accessions with sequenced genomes. Variation among accessions around the scaling exponent predicted by MST was correlated with relative growth rate, seed production, and stress resistance. Genomic analyses indicate that growth allometry is affected by many genes associated with local climate and abiotic stress response. The gene with the strongest effect, PUB4, has molecular signatures of balancing selection, suggesting that intraspecific variation in growth scaling is maintained by opposing selection on the trade-off between seed production and abiotic stress resistance. Our findings suggest that variation in allometry contributes to local adaptation to contrasting environments. Our results help reconcile past debates on the origin of allometric scaling in biology and begin to link adaptive variation in allometric scaling to specific genes.
Published: 2018

14. High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell

Author: Stanley Motley, Joseph R. Ecker, Florian Jupe, Olivier Loudet, Todd P. Michael, Detlef Weigel, Christa Lanz, Justin P. Sandoval, Felix Bemm, J. Craig Venter Institute [La Jolla, USA] (JCVI), Salk Institute for Biological Studies, Plant Molecular and Cellular Biology Laboratory, Monsanto Company, Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, European Project: 340602,EC:FP7:ERC,ERC-2013-ADG,IMMUNEMESIS(2014), and Michael, Todd P.
Subjects: 0301 basic medicine, 0106 biological sciences, short-read, Computer science, Science, [SDV]Life Sciences [q-bio], Arabidopsis, General Physics and Astronomy, Sequence assembly, Hybrid genome assembly, Genomics, Computational biology, long-read, Biology, 01 natural sciences, Genome, Chromosomes, Plant, Article, General Biochemistry, Genetics and Molecular Biology, DNA sequencing, diversity, Structural variation, 03 medical and health sciences, [SDV.IDA]Life Sciences [q-bio]/Food engineering, chromosome, arrays, tool, Arabidopsis thaliana, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, lcsh:Science, 030304 developmental biology, Genetics, 0303 health sciences, Multidisciplinary, Contig, Arabidopsis Proteins, High-Throughput Nucleotide Sequencing, General Chemistry, biology.organism_classification, 030104 developmental biology, Minion, lcsh:Q, Nanopore sequencing, Genome, Plant, 010606 plant biology & botany
Abstract: The handheld Oxford Nanopore MinION sequencer generates ultra-long reads with minimal cost and time requirements, which makes sequencing genomes at the bench feasible. Here, we sequence the gold standard Arabidopsis thaliana genome (KBS-Mac-74 accession) on the bench with the MinION sequencer, and assemble the genome using typical consumer computing hardware (4 Cores, 16 Gb RAM) into chromosome arms (62 contigs with an N50 length of 12.3 Mb). We validate the contiguity and quality of the assembly with two independent single-molecule technologies, Bionano optical genome maps and Pacific Biosciences Sequel sequencing. The new A. thaliana KBS-Mac-74 genome enables resolution of a quantitative trait locus that had previously been recalcitrant to a Sanger-based BAC sequencing approach. In summary, we demonstrate that even when the purpose is to understand complex structural variation at a single region of the genome, complete genome assembly is becoming the simplest way to achieve this goal., Long-read sequencing technologies facilitate efficient and high quality genome assembly. Here Michael et al. achieve a fast reference assembly for Arabidopsis thaliana KBS-Mac-74 accession using the handheld Oxford Nanopore MinION sequencer and consumer computing hardware, and demonstrate its usefulness in resolving complex structural variation.
Published: 2018

15. Dynamics of H3K4me3 Chromatin Marks Prevails over H3K27me3 for Gene Regulation during Flower Morphogenesis in Arabidopsis thaliana

Author: Robert Blanvillain, Markus Schmid, David Posé, Christian Kroner, Hugues Parrinello, Felix Ott, Marine Rohmer, Julia Engelhorn, Cristel C. Carles, Physiologie cellulaire et végétale (LPCV), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Optical Engineering Group, Institut de Génomique Fonctionnelle - Montpellier GenomiX (IGF MGX), Institut de Génomique Fonctionnelle (IGF), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Department of Molecular Biology [Tübingen], Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, ANR-10-JCJC-1206,ChromFlow,Dynamique de l'activation de la chromatine au cours de la morphogenèse florale(2010), European Project: 327377,EC:FP7:PEOPLE,FP7-PEOPLE-2012-IEF,CHROMACT(2013), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-BioCampus (BCM), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, Epigenomics, Arabidopsis thaliana, Health, Toxicology and Mutagenesis, Organogenesis, SEP3, Floral induction, chromatin and expression dynamics, reproductive development, differentiation, ChIP-seq, RNA-seq, macromolecular substances, 01 natural sciences, Biochemistry, Genetics and Molecular Biology (miscellaneous), Biochemistry, Chromatin remodeling, 03 medical and health sciences, Genetics, Histone code, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Chromatin dynamics, Reproductive development, ComputingMilieux_MISCELLANEOUS, AP3, Regulation of gene expression, MADS floral gene, biology, ULTRAPETALA1, fungi, AG, Plant, Chromatin, 030104 developmental biology, Histone, Flower development, Differentiation, biology.protein, H3K4me3, Utvecklingsbiologi, sense organs, Gene expression, Flower morphogenesis, Developmental Biology, 010606 plant biology & botany
Abstract: International audience; Plant life-long organogenesis involves sequential, time and tissue specific expression of developmental genes. This requires activities of Polycomb Group (PcG) and trithorax Group complexes (trxG), respectively responsible for repressive Histone 3 trimethylation at lysine 27 (H3K27me3) and activation-related Histone 3 trimethylation at lysine 4 (H3K4me3). However, the genome-wide dynamics in histone modifications that occur during developmental processes have remained elusive. Here, we report the distributions of H3K27me3 and H3K4me3 along with expression changes, in a developmental series including Arabidopsis thaliana leaf and three stages of flower development. We found that chromatin mark levels are highly dynamic over the time series on nearly half of all Arabidopsis genes. Moreover, during early flower morphogenesis, changes in H3K4me3 prevail over changes in H3K27me3 and quantitatively correlate with expression changes, while H3K27me3 changes occur later. Notably, we found that H3K4me3 increase during the early activation of PcG target genes while H3K27me3 level remain relatively constant at the locus. Our results reveal that H3K4me3 predicts changes in gene expression better than H3K27me3, unveil unexpected chromatin mechanisms at gene activation and underline the relevance of tissue-specific temporal epigenomics.
Published: 2017

16. Solid-State NMR H-N-(C)-H and H-N-C-C 3D/4D Correlation Experiments for Resonance Assignment of Large Proteins

Author: Maxime J. C. Audin, Vilius Kurauskas, Remco Sprangers, Pavel Macek, Carsten Krichel, Diego F. Gauto, Hugo Pacheco de Freitas Fraga, Charles-Adrien Arnaud, Jia-Ying Guan, Paul Schanda, Cécile Breyton, Jérôme Boisbouvier, Institut de biologie structurale (IBS - UMR 5075 ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft, ANR-16-CE11-0027,PerfoBac,Comment les bactériophages perforent-ils la paroi des bactéries ?(2016), European Project: 311318,EC:FP7:ERC,ERC-2012-StG_20111109,PROTDYN2FUNCTION(2013), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDV]Life Sciences [q-bio], 010402 general chemistry, 01 natural sciences, Article, chemistry.chemical_compound, Protein structure, Amide, Atomic model, Triple-resonance nuclear magnetic resonance spectroscopy, [CHIM]Chemical Sciences, protein quality control machinery, Physical and Theoretical Chemistry, Spectroscopy, NMR methods, Nuclear Magnetic Resonance, Biomolecular, 010405 organic chemistry, Chemistry, phage proteins, protein assemblies, Proteins, Nuclear magnetic resonance spectroscopy, Amides, Atomic and Molecular Physics, and Optics, 0104 chemical sciences, 3. Good health, Crystallography, Heteronuclear molecule, Solid-state nuclear magnetic resonance, NMR pulse sequences
Abstract: International audience; Solid-state NMR can provide insight into protein structure and dynamics at the atomic level without inherent protein size limitations. However, a major hurdle to studying large proteins by solid-state NMR spectroscopy is related to spectral complexity and resonance overlap, which increase with molecular weight and severely hamper the assignment process. Here we show the use of two sets of experiments that expand the tool kit of 1H-detected assignment approaches, and which correlate a given amide pair either to the two adjacent CO-CA pairs (4D hCOCANH/hCOCAcoNH), or to the amide 1H of the neighboring residue (3D HcocaNH/HcacoNH, which can be extended to up to 5D). The experiments are based on efficient coherence transfers between backbone atoms using INEPT transfers between carbons and cross-polarization for heteronuclear transfers. We exemplify the usefulness of these experiments with applications to assemblies of deuterated, fully amide-protonated proteins from ca. 20 to 60 kDa monomer, at MAS frequencies from ca. 40 to 55 kHz. These experiments will also be applicable to protonated proteins at higher MAS frequencies. We report the resonance assignment of a domain within the 50.4 kDa bacteriophage T5 tube protein pb6, and compare these to solution-state NMR assignments of the isolated domain in solution. This comparison reveals contacts of this domain to the core of the polymeric tail tube assembly. Solid‐state NMR H‐N‐(C)‐H and H‐N‐C‐C 3D/4D correlation experiments for resonance assignment of large proteins. Available from: https://www.researchgate.net/publication/319020315_Solid-state_NMR_H-N-C-H_and_H-N-C-C_3D4D_correlation_experiments_for_resonance_assignment_of_large_proteins.
Published: 2017

17. A circRNA from SEPALLATA3 regulates splicing of its cognate mRNA through R-loop formation

Author: Chloe Zubieta, Markus Schmid, Vanessa M. Conn, Aditya Nayak, Véronique Hugouvieux, Agnès Jourdain, Simon J. Conn, Gökhan Cildir, Giovanna Capovilla, Vinay Tergaonkar, Stephanie A. Conos, Centre for Cancer Biology, Hanson Institute, Adelaide, Physiologie cellulaire et végétale (LPCV), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Department of Molecular Biology [Tübingen], Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Department of Biochemistry, Yong Loo Lin School of Medicine and Department of Biological Sciences, National University of Singapore (NUS), Laboratory of NF-κB Signaling, Institute of Molecular and Cell Biology, Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, ANR (FLOPINET), CNRS, NHMRC [GNT1089167], Australian Research Council [FT160100318], ATIP-Avenir, LabEx GRAL [ANR-10-LABX-49-01], South Australian Government Department of State Development, CEA Irtelis fellowship, ANR-16-CE92-0023,FLOPINET,Floral Pioneer Factors(2016), ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Conn, Vanessa M, Hugouvieux, Véronique, Nayak, Aditya, Conos, Stephanie A, Capovilla, Giovanna, Cildir, Gökhan, Jourdain, Agnés, Tergaonkar, Vinay, Schmid, Markus, Zubieta, Chloe, Conn, Simon J, Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), ANR-16-CE92-0023,FLOPINET,Floral Pioneer Factors, and ANR-10-LABX-49-01,Labex GRAL
Subjects: 0106 biological sciences, 0301 basic medicine, circular RNAs (circRNAs), DNA, Plant, RNA Splicing, SEP3, Arabidopsis, Plant Science, Biology, 01 natural sciences, Flowering, 03 medical and health sciences, Splicing factor, Exon, alternative splicing, Circular RNA, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, RNA, Messenger, Gene, SEPALLATA3, Homeodomain Proteins, Genetics, Arabidopsis Proteins, Alternative splicing, RNA, Plant, Gene regulation, 030104 developmental biology, back-splicing, RNA splicing, DNA, Circular, Transcription factor, Homeotic gene, Transcription Factors, 010606 plant biology & botany
Abstract: Simon J. Conn (simon.conn@unisa.edu.au); International audience; Circular RNAs (circRNAs) are a diverse and abundant class of hyper-stable, non-canonical RNAs that arise through a form of alternative splicing (AS) called back-splicing. These single-stranded, covalently-closed circRNA molecules have been identified in all eukaryotic kingdoms of life(1), yet their functions have remained elusive. Here, we report that circRNAs can be used as $bona\ fide$ biomarkers of functional, exon-skipped AS variants in $Arabidopsis$, including in the homeotic MADS-box transcription factor family. Furthermore, we demonstrate that circRNAs derived from exon 6 of the SEPALLATA3 (SEP3) gene increase abundance of the cognate exon-skipped AS variant (SEP3.3 which lacks exon 6), in turn driving floral homeotic phenotypes. Toward demonstrating the underlying mechanism, we show that the SEP3 exon 6 circRNA can bind strongly to its cognate DNA locus, forming an RNA:DNA hybrid, or R-loop, whereas the linear RNA equivalent bound significantly more weakly to DNA. R-loop formation results in transcriptional pausing, which has been shown to coincide with splicing factor recruitment and AS(2-4). This report presents a novel mechanistic insight for how at least a subset of circRNAs probably contribute to increased splicing efficiency of their cognate exon-skipped messenger RNA and provides the first evidence of an organismal-level phenotype mediated by circRNA manipulation.
Published: 2017

18. The future of metabolomics in ELIXIR

Author: van Rijswijk, M, Beirnaert, C, Caron, C, Cascante, M, Dominguez, V, Dunn, WB, Ebbels, TMD, Giacomoni, F, Gonzalez-Beltran, A, Hankemeier, T, Haug, K, Izquierdo-Garcia, JL, Jimenez, RC, Jourdan, F, Kale, N, Klapa, MI, Kohlbacher, O, Koort, K, Kultima, K, Le Corguillé, G, Moreno, P, Moschonas, NK, Neumann, S, O'Donovan, C, Reczko, M, Rocca-Serra, P, Rosato, A, Salek, RM, Sansone, S-A, Satagopam, V, Schober, D, Shimmo, R, Spicer, RA, Spjuth, O, Thévenot, EA, Viant, MR, Weber, RJM, Willighagen, EL, Zanetti, G, Steinbeck, C, Dutch Techcentre for Life Sciences [Utrecht], Netherlands Metabolomics Centre, Department of Mathematics and Computer Science, ADReM, University of Antwerp (UA), French Institute of Bioinformatics (ELIXIR-FR), Department of Biochemistry and Molecular Biomedicine, Faculty of Science and Technology, Biochemistry and Molecular Biology, University of Barcelona, Birmingham Metabolomics Training Centre, University of Birmingham, Department of Surgery and Cancer, Imperial College London, Unité de Nutrition Humaine (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), MetaboHUB, Oxford e-Research Centre, University of Oxford, Leiden Academic Centre for Drug Research (LACDR), Universiteit Leiden, European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Centro Nacional de Investigaciones Cardiovasculares, Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), ELIXIR Hub [Cambridge], Métabolisme et Xénobiotiques (ToxAlim-MeX), ToxAlim (ToxAlim), Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Ecole d'Ingénieurs de Purpan (INP - PURPAN), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT), Forth ICE-HT, Institute of Chemical Engineering Sciences, Foundation for Research and Technology - Hellas (FORTH), Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft, Department of Computer Science, Duke University [Durham], Center for Bioinformatics, University of Tübingen, The Centre of Excellence in Neural and Behavioural Sciences, Tallinn University, School of Natural Sciences and Health, Department of Medical Sciences (University of Miyasaki), University of Miyasaki, ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science (ABIMS), Fédération de recherche de Roscoff (FR2424), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC), Centre National de la Recherche Scientifique (CNRS), Department of General Biology, Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), University of Patras, Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry (IPB), BSRC 'Alexander Fleming', Magnetic Resonance Center/Interuniversity Consortium of Magnetic Resonance Metalloproteins, Università degli Studi di Firenze = University of Florence (UniFI), Luxembourg Centre For Systems Biomedicine (LCSB), University of Luxembourg [Luxembourg], Université du Luxembourg (Uni.lu), Department of Pharmaceutical Biosciences, Uppsala University, Laboratoire Sciences des Données et de la Décision (LS2D), Département Métrologie Instrumentation & Information (DM2I), Laboratoire d'Intégration des Systèmes et des Technologies (LIST (CEA)), Direction de Recherche Technologique (CEA) (DRT (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Technologique (CEA) (DRT (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Laboratoire d'Intégration des Systèmes et des Technologies (LIST (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Department of Bioinformatics, BiGCaT, Maastricht University [Maastricht], NUTRIM, Data-Intensive Computing, CRS4 Bioinformat, Friedrich-Schiller-Universität = Friedrich Schiller University Jena [Jena, Germany], ANR-11-INBS-0010,METABOHUB,Développement d'une infrastructure française distribuée pour la métabolomique dédiée à l'innovation(2011), European Project: 654241,H2020,H2020-EINFRA-2014-2,PhenoMeNal(2015), European Commission, Unité de Nutrition Humaine - Clermont Auvergne (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Leiden University, Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science (FR2424), Université Pierre et Marie Curie (Paris 6), Federal University of Minas Gerais Belo Horizonte, University of Patras [Patras], University of Florence (UNIFI), Laboratoire d'analyse des données et d'intelligence des systèmes (LADIS), Laboratoire d'Intégration des Systèmes et des Technologies (LIST), Université Paris-Saclay-Direction de Recherche Technologique (CEA) (DRT (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Technologique (CEA) (DRT (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Laboratoire d'Intégration des Systèmes et des Technologies (LIST), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Maastricht University, Friedrich-Schiller-Universität Jena, ANR-11-INBS-0010/11-INBS-0010,METABOHUB,Développement d’une infrastructure française distribuée pour la métabolomique dédiée à l’innovation(2011), Commission of the European Communities, European Molecular Biology Laboratory, Apollo-University Of Cambridge Repository, van Rijswijk, Merlijn [0000-0002-1067-7766], Beirnaert, Charlie [0000-0003-3007-2569], Gonzalez-Beltran, Alejandra [0000-0003-3499-8262], Haug, Kenneth [0000-0003-3168-4145], Jimenez, Rafael C [0000-0001-5404-7670], Kale, Namrata [0000-0002-4255-8104], Klapa, Maria I [0000-0002-2047-3185], Moschonas, Nicholas K [0000-0002-2556-537X], Rosato, Antonio [0000-0001-6172-0368], Salek, Reza M [0000-0001-8604-1732], Sansone, Susanna-Assunta [0000-0001-5306-5690], Schober, Daniel [0000-0001-8014-6648], Spicer, Rachel A [0000-0002-2807-8796], Spjuth, Ola [0000-0002-8083-2864], Thévenot, Etienne A [0000-0003-1019-4577], Willighagen, Egon L [0000-0001-7542-0286], Steinbeck, Christoph [0000-0001-6966-0814], Apollo - University of Cambridge Repository, RS: NUTRIM - R1 - Obesity, diabetes and cardiovascular health, Bioinformatica, RS: NUTRIM - R4 - Gene-environment interaction, University of Oxford [Oxford], Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Laboratoire d'Intégration des Systèmes et des Technologies (LIST), Università degli Studi di Firenze = University of Florence [Firenze], Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Ecole d'Ingénieurs de Purpan (INPT - EI Purpan), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées
Subjects: 0301 basic medicine, databases, Data management, computational workflows, infrastructure en ligne, Cloud computing, Computational biology, Biology, General Biochemistry, Genetics and Molecular Biology, Chemical Biology of the Cell, analyse métabolomique, 03 medical and health sciences, statistical analysis, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [INFO.INFO-DL]Computer Science [cs]/Digital Libraries [cs.DL], Use case, General Pharmacology, Toxicology and Pharmaceutics, signal processing, computer.programming_language, bioinformatics infrastructure, training, 030102 biochemistry & molecular biology, General Immunology and Microbiology, metabolomics, bioinformatics, distributed computing, cloud, business.industry, cloud computing, pipeline, Articles, General Medicine, Opinion Article, Data science, metabolomics, Open data, Identification (information), 030104 developmental biology, Workflow, multi-omics approaches, Elixir (programming language), [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], business, data standards, computer, Omics technologies
Abstract: We are grateful to the proteomics community for sharing their experiences from their meeting “The future of proteomics in ELIXIR” on March 1–2 2017 in Tübingen, allowing us to build on this and organise our workshop as a one-day event.The meeting was funded by PhenoMeNal, European Commission's Horizon2020 programme, grant agreement number 654241; Metabolomics, the youngest of the major omics technologies, is supported by an active community of researchers and infrastructure developers across Europe. To coordinate and focus efforts around infrastructure building for metabolomics within Europe, a workshop on the "Future of metabolomics in ELIXIR" was organised at Frankfurt Airport in Germany. This one-day strategic workshop involved representatives of ELIXIR Nodes, members of the PhenoMeNal consortium developing an e-infrastructure that supports workflow-based metabolomics analysis pipelines, and experts from the international metabolomics community. The workshop established metabolite identification as the critical area, where a maximal impact of computational metabolomics and data management on other fields could be achieved. In particular, the existing four ELIXIR Use Cases, where the metabolomics community - both industry and academia - would benefit most, and which could be exhaustively mapped onto the current five ELIXIR Platforms were discussed. This opinion article is a call for support for a new ELIXIR metabolomics Use Case, which aligns with and complements the existing and planned ELIXIR Platforms and Use Cases
Published: 2017

19. Enterotypes in the landscape of gut microbial community composition

Author: Curtis Huttenhower, Ian B. Jeffery, Howard Ochman, George M. Weinstock, Fredrik Bäckhed, S. Dusko Ehrlich, Paul W. O'Toole, David A. Relman, Martin J. Blaser, Georg Zeller, Jun Wang, Christopher Quince, Rob Knight, Liping Zhao, Masahira Hattori, Dan Knights, Fergus Shanahan, Ruth E. Ley, Gary D. Wu, Falk Hildebrand, Jeroen Raes, Peer Bork, Paul I. Costea, Claire M. Fraser, Willem M. de Vos, James D. Lewis, Frederic D. Bushman, Shinichi Sunagawa, Manimozhiyan Arumugam, European Molecular Biology Laboratory (EMBL), Vrije Universiteit Brussel (VUB), Flanders Institute for Biotechnology, Novo Nordisk Foundation Center for Basic Metabolic Research (CBMR), Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), University of Copenhagen = Københavns Universitet (KU), University of Gothenburg (GU), New York University Langone Medical Center (NYU Langone Medical Center), NYU System (NYU), University of Pennyslvania, University of Helsinki, Laboratory of Microbiology, Wageningen University and Research [Wageningen] (WUR), MetaGenoPolis, Institut National de la Recherche Agronomique (INRA), Centre for Host-Microbiome Interactions, Dental Institute Central Office, Guy’s Hospital, King‘s College London, University of Maryland School of Medicine, University of Maryland System, Waseda University, Harvard School of Public Health, APC Microbiome Institute [Cork], University College Cork (UCC), University of Minnesota [Twin Cities] (UMN), University of Minnesota System, Department of Computer Science and Engineering, University of Minnesota System-University of Minnesota System, Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft, Department of Integrative Biology [Berkeley] (IB), University of California [Berkeley], University of California-University of California, Warwick Medical School, University of Warwick [Coventry], Stanford University, Veterans Affairs Palo Alto Health Care System, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Department of Biology, Northern Arizona University [Flagstaff], Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Macau University of Science and Technology (MUST), Department of Medicine and State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong (HKU), The Jackson Laboratory [Bar Harbor] (JAX), Shanghai Jiao Tong University School of Medicine, Université Catholique de Louvain = Catholic University of Louvain (UCL), University of Colorado, University of Colorado [Boulder], Department of Chemistry and Biochemistry [Boulder], University of Colorado Anschutz [Aurora], Molecular Medicine Partnership Unit, Heidelberg University, Max Delbrück Center for Molecular Medicine [Berlin] (MDC), Helmholtz-Gemeinschaft = Helmholtz Association, EMBL, VIB, Rega institute for Medical Research, MicrobesInside [250172], European Community's Seventh Framework Programme via the MetaHIT [HEALTH-F4-2007-201052], METACARDIS project [FP7-HEALTH-2012-INNOVATION-I-305312], European Union's Horizon research and innovation programme (Marie Sklodowska-Curie grant) [600375], Metagenopolis grant [ANR-11-DPBS-0001], IHMS project [FP7-HEALTH-2010-single-stage-261376], European Project: 268985,EC:FP7:ERC,ERC-2010-AdG_20100317,CANCERBIOME(2011), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), University of Copenhagen = Københavns Universitet (UCPH), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Waseda University [Tokyo, Japan], University of California [Berkeley] (UC Berkeley), and University of California (UC)-University of California (UC)
Subjects: 0301 basic medicine, Microbiology (medical), 16S, [SDV]Life Sciences [q-bio], 030106 microbiology, Immunology, Applied Microbiology and Biotechnology, Microbiology, Article, diversity, 03 medical and health sciences, Human health, Human gut, bacteroides, Clinical Research, Microbiologie, RNA, Ribosomal, 16S, Genetics, Life Science, Animals, Humans, Microbiome, genes, VLAG, Ribosomal, human intestinal microbiota, Bacteria, Human Genome, association, Environmental ethics, Biodiversity, Cell Biology, infection, Bacterial Typing Techniques, Gastrointestinal Microbiome, Gastrointestinal Tract, Clinical Practice, Geography, age, Community composition, Medical Microbiology, Metagenomics, prevotella, RNA, Metagenome, Enterotype, diet, metabolism
Abstract: International audience; Population stratification is a useful approach for a better understanding of complex biological problems in human health and wellbeing. The proposal that such stratification applies to the human gut microbiome, in the form of distinct community composition types termed enterotypes, has been met with both excitement and controversy. In view of accumulated data and re-analyses since the original work, we revisit the concept of enterotypes, discuss different methods of dividing up the landscape of possible microbiome configurations, and put these concepts into functional, ecological and medical contexts. As enterotypes are of use in describing the gut microbial community landscape and may become relevant in clinical practice, we aim to reconcile differing views and encourage a balanced application of the concept.
Published: 2017

20. Fine genetic mapping of RXopJ4, a bacterial spot disease resistance locus from Solanum pennellii LA716

Author: Robert E. Stall, Julin N. Maloof, Lily Liu, D. Dahlbeck, Joshua Chiu, Brian J. Staskawicz, Molly Sharlach, Seisuke Kimura, Neelima Sinha, Jeffrey B. Jones, Daniel Koenig, Gerald V. Minsavage, José M. Jiménez-Gómez, Department of Plant and Microbial Biology, University of California, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Max Planck Institute for Plant Breeding Research (MPIPZ), Department of Bioresource and Environmental Sciences, Kyoto Sangyo University, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Department of Plant Biology, Plant Pathology Department, University of Florida [Gainesville], Two Blades Foundation, National Science Foundation, and University of Florida [Gainesville] (UF)
Subjects: Genetic Markers, 0106 biological sciences, Candidate gene, Xanthomonas, DNA, Plant, [SDV]Life Sciences [q-bio], Quantitative Trait Loci, Population, Introgression, Locus (genetics), Quantitative trait locus, Plant disease resistance, Biology, Genes, Plant, Solanum, 01 natural sciences, Chromosomes, Plant, 03 medical and health sciences, Gene mapping, Genetics, education, Disease Resistance, Plant Diseases, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, education.field_of_study, Chromosome Mapping, Sequence Analysis, DNA, General Medicine, Phenotype, Genetic marker, Agronomy and Crop Science, 010606 plant biology & botany, Biotechnology
Abstract: The RXopJ4 resistance locus from the wild accession Solanum pennellii (Sp) LA716 confers resistance to bacterial spot disease of tomato (S. lycopersicum, Sl) caused by Xanthomonas perforans (Xp). RXopJ4 resistance depends on recognition of the pathogen type III effector protein XopJ4. We used a collection of Sp introgression lines (ILs) to narrow the RXopJ4 locus to a 4.2-Mb segment on the long arm of chromosome 6, encompassed by the ILs 6-2 and 6-2-2. We then adapted or developed a collection of 14 molecular markers to map on a segregating F(2) population from a cross between the susceptible parent Sl FL8000 and the resistant parent RXopJ4 8000 OC(7). In the F(2) population, a 190-kb segment between the markers J350 and J352 cosegregated with resistance. This fine mapping will enable both the identification of candidate genes and the detection of resistant plants using cosegregating markers. The RXopJ4 resistance gene(s), in combination with other recently characterized genes and a quantitative trait locus (QTL) for bacterial spot disease resistance, will likely be an effective tool for the development of durable resistance in cultivated tomato.
Published: 2012

21. mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes

Author: Alexander Stark, Isabelle Behm-Ansmant, Peer Bork, Tobias Doerks, Elisa Izaurralde, Jan Rehwinkel, European Molecular Biology Laboratory [Heidelberg] (EMBL), Massachusetts Institute of Technology (MIT), Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft, and MDC Library
Subjects: RNA Caps, Repetitive Sequences, Amino Acid, RNA Stability, Piwi-interacting RNA, 570 Life Sciences, Biology, 610 Medical Sciences, Medicine, 03 medical and health sciences, 0302 clinical medicine, Ribonucleases, mRNA decay, P-bodies, microRNA, Gene expression, Genetics, CCR4-NOT complex, Gene silencing, Animals, Drosophila Proteins, Amino Acid Sequence, Gene Silencing, RNA, Messenger, Eukaryotic Initiation Factors, Conserved Sequence, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Effector, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Deadenylation, Argonaute, GW182, Molecular biology, MicroRNAs, Drosophila melanogaster, Cardiovascular and Metabolic Diseases, 030220 oncology & carcinogenesis, Caspases, Multiprotein Complexes, Argonaute Proteins, Decapping, Developmental Biology, Research Paper, Transcription Factors
Abstract: MicroRNAs (miRNAs) silence the expression of target genes post-transcriptionally. Their function is mediated by the Argonaute proteins (AGOs), which colocalize to P-bodies with mRNA degradation enzymes. Mammalian P-bodies are also marked by the GW182 protein, which interacts with the AGOs and is required for miRNA function. We show that depletion of GW182 leads to changes in mRNA expression profiles strikingly similar to those observed in cells depleted of the essential Drosophila miRNA effector AGO1, indicating that GW182 functions in the miRNA pathway. When GW182 is bound to a reporter transcript, it silences its expression, bypassing the requirement for AGO1. Silencing by GW182 is effected by changes in protein expression and mRNA stability. Similarly, miRNAs silence gene expression by repressing protein expression and/or by promoting mRNA decay, and both mechanisms require GW182. mRNA degradation, but not translational repression, by GW182 or miRNAs is inhibited in cells depleted of CAF1, NOT1, or the decapping DCP1:DCP2 complex. We further show that the N-terminal GW repeats of GW182 interact with the PIWI domain of AGO1. Our findings indicate that GW182 links the miRNA pathway to mRNA degradation by interacting with AGO1 and promoting decay of at least a subset of miRNA targets.
Published: 2016

22. A SAM oligomerization domain shapes the genomic binding landscape of the LEAFY transcription factor

Author: Camille Sayou, Markus Schmid, David Posé, Max H. Nanao, Marta Peirats Llobet, Grégoire Denay, Marc Jamin, François Parcy, Renaud Dumas, Emmanuel Thévenon, Gabrielle Tichtinsky, Laura Gregoire, Felix Ott, Physiologie cellulaire et végétale (LPCV), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), European Molecular Biology Laboratory, Institut de biologie structurale (IBS - UMR 5075 ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Department of Molecular Biology [Tübingen], Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, DFG [SCHM1560/7-1], ANR [Blanc - SVSE2 - 2011- Charmful], CEA NanoProt3D programme, iRTELIS CEA PhD programme, European Community [283570], FRISBI [ANR-10-INSB-05-02], GRAL within the Grenoble Partnership for Structural Biology (PSB) [ANR-10-LABX-49-01], European Project: 227764,EC:FP7:INFRA,FP7-INFRASTRUCTURES-2008-1,PCUBE(2009), Laboratoire de physiologie cellulaire végétale (LPCV), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie structurale (IBS - UMR 5075), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS), Nanao, Max H., Dumas, Renaud, Parcy, François, Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Models, Molecular, Transcription, Genetic, Arabidopsis, General Physics and Astronomy, Gene Expression, Crystallography, X-Ray, Protein Structure, Secondary, chemistry.chemical_compound, Gene Expression Regulation, Plant, Transcriptional regulation, Cloning, Molecular, Genetics, Multidisciplinary, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Gene Expression Regulation, Developmental, food and beverages, Chromatin, Recombinant Proteins, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Genome, Plant, Protein Binding, Cellbiologi, Science, Molecular Sequence Data, Sequence alignment, Computational biology, Flowers, Biology, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, Escherichia coli, Amino Acid Sequence, Binding site, Leafy, Transcription factor, Binding Sites, Arabidopsis Proteins, fungi, Oryza, General Chemistry, Cell Biology, Protein Structure, Tertiary, 030104 developmental biology, chemistry, Protein Multimerization, Sterile alpha motif, Sequence Alignment, DNA, Transcription Factors
Abstract: Deciphering the mechanisms directing transcription factors (TFs) to specific genome regions is essential to understand and predict transcriptional regulation. TFs recognize short DNA motifs primarily through their DNA-binding domain. Some TFs also possess an oligomerization domain suspected to potentiate DNA binding but for which the genome-wide influence remains poorly understood. Here we focus on the LEAFY transcription factor, a master regulator of flower development in angiosperms. We have determined the crystal structure of its conserved amino-terminal domain, revealing an unanticipated Sterile Alpha Motif oligomerization domain. We show that this domain is essential to LEAFY floral function. Moreover, combined biochemical and genome-wide assays suggest that oligomerization is required for LEAFY to access regions with low-affinity binding sites or closed chromatin. This finding shows that domains that do not directly contact DNA can nevertheless have a profound impact on the DNA binding landscape of a TF., The LEAFY transcription factor is a master regulator of flower development in plants. Here the authors describe the structure of a LEAFY oligomerization domain and show that mutations that disrupt oligomerization alter its capacity to bind low affinity and poorly accessible target sites.
Published: 2016

23. mi RISC and the CCR 4– NOT complex silence mRNA targets independently of 43S ribosomal scanning

Author: Kuzuoğlu-Öztürk, Duygu, Bhandari, Dipankar, Huntzinger, Eric, Fauser, Maria, Helms, Sigrun, Izaurralde, Elisa, Kuzuoğlu‐Öztürk, Duygu, Max Planck Institute for Developmental Biology, and Max-Planck-Gesellschaft
Subjects: 0301 basic medicine, MESH: Drosophila Proteins, [SDV]Life Sciences [q-bio], RNA-binding protein, Biology, Ribosome, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, 0302 clinical medicine, MESH: Argonaute Proteins, microRNA, DDX6, CCR4-NOT complex, Gene silencing, MESH: DEAD-box RNA Helicases, Molecular Biology, argonaute, MESH: RNA, Messenger, Genetics, Messenger RNA, MESH: Humans, General Immunology and Microbiology, General Neuroscience, deadenylation, MESH: Transcription Factors, Argonaute, GW182, Cell biology, MESH: Cell Line, MESH: Proto-Oncogene Proteins, 030104 developmental biology, MESH: RNA-Binding Proteins, MESH: Autoantigens, eIF4A, MESH: Ribosomes, MESH: MicroRNAs, 030217 neurology & neurosurgery
Abstract: International audience; miRNAs associate with Argonaute (AGO) proteins to silence the expression of mRNA targets by inhibiting translation and promoting deadenylation, decapping, and mRNA degradation. A current model for silencing suggests that AGOs mediate these effects through the sequential recruitment of GW182 proteins, the CCR4-NOT deadenylase complex and the translational repressor and decapping activator DDX6. An alternative model posits that AGOs repress translation by interfering with eIF4A function during 43S ribosomal scanning and that this mechanism is independent of GW182 and the CCR4-NOT complex in Drosophila melanogaster Here, we show that miRNAs, AGOs, GW182, the CCR4-NOT complex, and DDX6/Me31B repress and degrade polyadenylated mRNA targets that are translated via scanning-independent mechanisms in both human and Dm cells. This and additional observations indicate a common mechanism used by these proteins and miRNAs to mediate silencing. This mechanism does not require eIF4A function during ribosomal scanning.
Published: 2016

24. Epigenome confrontation triggers immediate reprogramming of DNA methylation and transposon silencing in Arabidopsis thaliana F1 epihybrids

Author: Claude Becker, Detlef Weigel, Mélanie Rigal, Yoko Ikeda, Jane Devos, Romain Pogorelcnik, Olivier Mathieu, Thierry Pélissier, Génétique, Reproduction et Développement (GReD), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Santé et de la Recherche Médicale (INSERM), Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Department of Molecular Biology, Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Genetics, Multidisciplinary, [SDV]Life Sciences [q-bio], food and beverages, Epigenome, Biology, 03 medical and health sciences, 030104 developmental biology, Epigenetics of physical exercise, PNAS Plus, DNA methylation, Epigenetics, Reprogramming, Transposons as a genetic tool, RNA-Directed DNA Methylation, ComputingMilieux_MISCELLANEOUS, Epigenomics
Abstract: Genes and transposons can exist in variable DNA methylation states, with potentially differential transcription. How these epialleles emerge is poorly understood. Here, we show that crossing an Arabidopsis thaliana plant with a hypomethylated genome and a normally methylated WT individual results, already in the F1 generation, in widespread changes in DNA methylation and transcription patterns. Novel nonparental and heritable epialleles arise at many genic loci, including a locus that itself controls DNA methylation patterns, but with most of the changes affecting pericentromeric transposons. Although a subset of transposons show immediate resilencing, a large number display decreased DNA methylation, which is associated with de novo or enhanced transcriptional activation and can translate into transposon mobilization in the progeny. Our findings reveal that the combination of distinct epigenomes can be viewed as an epigenomic shock, which is characterized by a round of epigenetic variation creating novel patterns of gene and TE regulation.
Published: 2016

25. The Nuclear Ribonucleoprotein SmD1 Interplays with Splicing, RNA Quality Control, and Posttranscriptional Gene Silencing in Arabidopsis[OPEN]

Author: Vincent Jauvion, Federico Ariel, Martin Crespi, Ivan Le Masson, Emilie Elvira-Matelot, Florian Bardou, Hervé Vaucheret, Jun Cao, Nathalie Bouteiller, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, 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), Department of Molecular Biology, Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, and Agence Nationale de la Recherche [ANR-10-BLAN-1707, ANR-10-LABX-40]
Subjects: 0301 basic medicine, Small interfering RNA, intron, [SDV]Life Sciences [q-bio], Mutant, Plant Science, Biology, genome-wide identification, 03 medical and health sciences, RNA interference, [SDV.IDA]Life Sciences [q-bio]/Food engineering, MRNA transport, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, thaliana, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, plant transformation, Research Articles, Ribonucleoprotein, Genetics, fungi, transgene, Intron, turnover, RNA, Cell Biology, endogenous sirna, ago1, 030104 developmental biology, RNA splicing, interfering rnas
Abstract: International audience; RNA quality control (RQC) eliminates aberrant RNAs based on their atypical structure, whereas posttranscriptional gene silencing (PTGS) eliminates both aberrant and functional RNAs through the sequence-specific action of short interfering RNAs (siRNAs). The Arabidopsis thaliana mutant smd1b was identified in a genetic screen for PTGS deficiency, revealing the involvement of SmD1, a component of the Smith (Sm) complex, in PTGS. The smd1a and smd1b single mutants are viable, but the smd1a smd1b double mutant is embryo-lethal, indicating that SmD1 function is essential. SmD1b resides in nucleoli and nucleoplasmic speckles, colocalizing with the splicing-related factor SR34. Consistent with this, the smd1b mutant exhibits intron retention at certain endogenous mRNAs. SmD1 binds to RNAs transcribed from silenced transgenes but not nonsilenced ones, indicating a direct role in PTGS. Yet, mutations in the RQC factors UPFRAMESHIFT3, EXORIBONUCLEASE2 (XRN2), XRN3, and XRN4 restore PTGS in smd1b, indicating that SmD1 is not essential for but rather facilitates PTGS. Moreover, the smd1b mtr4 double mutant is embryo-lethal, suggesting that SmD1 is essential for mRNA TRANSPORT REGULATOR4-dependent RQC. These results indicate that SmD1 interplays with splicing, RQC, and PTGS. We propose that SmD1 facilitates PTGS by protecting transgene-derived aberrant RNAs from degradation by RQC in the nucleus, allowing sufficient amounts to enter cytoplasmic siRNA bodies to activate PTGS.
Published: 2016

26. Modulation of Fgfr1a Signaling in Zebrafish Reveals a Genetic Basis for the Aggression-Boldness Syndrome

Author: Katharina Stumpenhorst, Theresa Faus-Kessler, Matthew P. Harris, Nicolas Rohner, Laure Bally-Cuif, Anja Folchert, William H. J. Norton, Jacques Callebert, Institute of Developmental Genetics [Neuherberg], Helmholtz-Zentrum München (HZM), Neurobiologie & Développement (N&D), Centre National de la Recherche Scientifique (CNRS), Institut de Neurobiologie Alfred Fessard (INAF), Department of Zebrafish Neurogenetics, Helmholtz Zentrum München, Department of Genetics [Tübingen], Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Service Biochimie et Biologie Moleculaire, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Lariboisière-Fernand-Widal [APHP], and Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)
Subjects: Male, media_common.quotation_subject, Molecular Sequence Data, Motor Activity, Fibroblast growth factor, histamine h-3 receptor, fish danio-rerio, behavioral syndromes, gasterosteus-aculeatus, 3-spined stickleback, therapeutic target, betta-splendens, brain, expression, system, Animals, Genetically Modified, 03 medical and health sciences, Behavioral syndrome, 0302 clinical medicine, medicine, Animals, Amino Acid Sequence, Receptor, Fibroblast Growth Factor, Type 1, Zebrafish, 030304 developmental biology, media_common, Genetics, 0303 health sciences, biology, Mechanism (biology), Boldness, Aggression, General Neuroscience, Syndrome, Articles, Zebrafish Proteins, biology.organism_classification, Fibroblast growth factor receptor, Female, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], Signal transduction, medicine.symptom, 030217 neurology & neurosurgery, Signal Transduction
Abstract: Behavioral syndromes are suites of two or more behaviors that correlate across environmental contexts. The aggression–boldness syndrome links aggression, boldness, and exploratory activity in a novel environment. Although aggression–boldness has been described in many animals, the mechanism linking its behavioral components is not known. Here we show that mutation of the gene encoding fibroblast growth factor receptor 1a (fgfr1a) simultaneously increases aggression, boldness, and exploration in adult zebrafish. We demonstrate that altered Fgf signaling also results in reduced brain histamine levels in mutants. Pharmacological increase of histamine signaling is sufficient to rescue the behavioral phenotype offgfr1amutants. Together, we show that a single genetic locus can underlie the aggression–boldness behavioral syndrome. We also identify one of the neurotransmitter pathways that may mediate clustering of these behaviors.
Published: 2011
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27. Accurate NMR Structures Through Minimization of an Extended Hybrid Energy

Author: Michael Nilges, Michael Habeck, Wolfgang Rieping, Thérèse E. Malliavin, Aymeric Bernard, Benjamin Bardiaux, Bioinformatique Structurale, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft, Max Planck Institute for Biological Cybernetics, University of Cambridge [UK] (CAM), This work was funded by EC grants QLG2-CT-2000-01313 and QLG2–CT– 2002–00988 (to M.N.) and the ACI IMPBio ICMD-RMN (to T.M., European Project: QLG2-CT-2002-00988,SPINE(2002), and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: Models, Molecular, PROTEINS, Computer science, Bayesian probability, Structure (category theory), MESH: Algorithms, Crystallography, X-Ray, 010402 general chemistry, Models, Biological, Sensitivity and Specificity, 01 natural sciences, 03 medical and health sciences, Quality (physics), Structural Biology, MESH: Nuclear Magnetic Resonance, Biomolecular, Humans, MESH: Energy Transfer, Nuclear Magnetic Resonance, Biomolecular, Molecular Biology, 030304 developmental biology, 0303 health sciences, MESH: Humans, MESH: Molecular Weight, MESH: Models, Chemical, MESH: Models, Biological, Function (mathematics), MESH: Crystallography, X-Ray, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], MESH: Sensitivity and Specificity, 0104 chemical sciences, Term (time), Molecular Weight, Crystallography, Energy Transfer, Models, Chemical, Data quality, Minification, Algorithm, Algorithms, MESH: Models, Molecular, Energy (signal processing)
Abstract: International audience; The use of generous distance bounds has been the hallmark of NMR structure determination. However, bounds necessitate the estimation of data quality before the calculation, reduce the information content, introduce human bias, and allow for major errors in the structures. Here, we propose a new rapid structure calculation scheme based on Bayesian analysis. The minimization of an extended energy function, including a new type of distance restraint and a term depending on the data quality, results in an estimation of the data quality in addition to coordinates. This allows for the determination of the optimal weight on the experimental information. The resulting structures are of better quality and closer to the X-ray crystal structure of the same molecule. With the new calculation approach, the analysis of discrepancies from the target distances becomes meaningful. The strategy may be useful in other applications-for example, in homology modeling.
Published: 2008

28. Trends, Stasis, and Drift in the Evolution of Nematode Vulva Development

Author: Ralf J. Sommer, Irina Kolotuev, Antoine Barrière, Benjamin Podbilewicz, David H. A. Fitch, Karin Kiontke, Marie-Anne Félix, New york University, Department of Biology, New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU), Institut Jacques Monod (IJM (UMR_7592)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Israel Institute of Technology, Department of Biology, Israel Institute of Technology, Max Planck Institute for Developmental Biology, and Max-Planck-Gesellschaft
Subjects: 0106 biological sciences, EVO_ECOL, Nuclear gene, ved/biology.organism_classification_rank.species, Morphogenesis, DEVBIO, Biology, 010603 evolutionary biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, Vulva, 03 medical and health sciences, Genetic drift, Phylogenetics, Directionality, Animals, Caenorhabditis elegans, [SDV.BDD]Life Sciences [q-bio]/Development Biology, Selection (genetic algorithm), Phylogeny, 030304 developmental biology, Genetics, 0303 health sciences, Agricultural and Biological Sciences(all), ved/biology, Mechanism (biology), Biochemistry, Genetics and Molecular Biology(all), Genetic Drift, Biological Evolution, Pristionchus pacificus, Female, General Agricultural and Biological Sciences
Abstract: International audience; BACKGROUND: A surprising amount of developmental variation has been observed for otherwise highly conserved features, a phenomenon known as developmental system drift. Either stochastic processes (e.g., drift and absence of selection-independent constraints) or deterministic processes (e.g., selection or constraints) could be the predominate mechanism for the evolution of such variation. We tested whether evolutionary patterns of change were unbiased or biased, as predicted by the stochastic or deterministic hypotheses, respectively. As a model, we used the nematode vulva, a highly conserved, essential organ, the development of which has been intensively studied in the model systems Caenorhabditis elegans and Pristionchus pacificus. RESULTS: For 51 rhabditid species, we analyzed more than 40 characteristics of vulva development, including cell fates, fate induction, cell competence, division patterns, morphogenesis, and related aspects of gonad development. We then defined individual characters and plotted their evolution on a phylogeny inferred for 65 species from three nuclear gene sequences. This taxon-dense phylogeny provides for the first time a highly resolved picture of rhabditid evolution and allows the reconstruction of the number and directionality of changes in the vulva development characters. We found an astonishing amount of variation and an even larger number of evolutionary changes, suggesting a high degree of homoplasy (convergences and reversals). Surprisingly, only two characters showed unbiased evolution. Evolution of all other characters was biased. CONCLUSIONS: We propose that developmental evolution is primarily governed by selection and/or selection-independent constraints, not stochastic processes such as drift in unconstrained phenotypic space.
Published: 2007
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29. Solid-state NMR Study of the YadA Membrane-Anchor Domain in the Bacterial Outer Membrane

Author: Madhu Nagaraj, Marcella Orwick-Rydmark, Barth‐J. van Rossum, Michael Habeck, Benjamin Bardiaux, Shakeel A. Shahid, Trent W. Franks, Nandini Chauhan, Dirk Linke, Leibniz Forschungsinstitut für Molekulare Pharmakolgie = Leibniz Institute for Molecular Pharmacology [Berlin, Allemagne] (FMP), Leibniz Association, Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft, University of Oslo (UiO), Bioinformatique structurale - Structural Bioinformatics, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Max Planck Institute for Biophysical Chemistry (MPI-BPC), Georg-August-University [Göttingen], This work was supported by the Baden-Wîrttemberg-Stiftung program 'Methoden fîr die Lebenswissenschaften' to DL and MH NMR data from this work was deposited in the BMRB database (accession number : 26606), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and Georg-August-University = Georg-August-Universität Göttingen
Subjects: Models, Molecular, MESH: Yersinia enterocolitica/chemistry, MESH: Gene Expression, Yersinia Infections, Molecular Sequence Data, Gene Expression, membrane proteins, MESH: Escherichia coli/genetics, MESH: Amino Acid Sequence, medicine.disease_cause, Bacterial Adhesion, Catalysis, MESH: Protein Structure, Tertiary, Yersinia adhesin A, MESH: Yersinia enterocolitica/genetics, MESH: Nuclear Magnetic Resonance, Biomolecular, Escherichia coli, medicine, Humans, structural biology, Amino Acid Sequence, MESH: Bacterial Adhesion, Adhesins, Bacterial, Nuclear Magnetic Resonance, Biomolecular, Peptide sequence, Yersinia enterocolitica, autotransport, MESH: Molecular Sequence Data, MESH: Humans, Chemistry, MESH: Adhesins, Bacterial/chemistry, General Chemistry, Lipids, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Protein Structure, Tertiary, MESH: Yersinia Infections/microbiology, Crystallography, MESH: Adhesins, Bacterial/genetics, Membrane, Microcrystalline, Solid-state nuclear magnetic resonance, Structural biology, Membrane protein, solid-state NMR, MESH: Escherichia coli/chemistry, Bacterial outer membrane, MESH: Models, Molecular, MESH: Lipids/chemistry
Abstract: International audience; MAS-NMR was used to study the structure and dynamics at ambient temperatures of the membrane-anchor domain of YadA (YadA-M) in a pellet of the outer membrane of E. coli in which it was expressed. YadA is an adhesin from the pathogen Yersinia enterocolitica that is involved in interactions with the host cell, and it is a model protein for studying the autotransport process. Existing assignments were sucessfully transferred to a large part of the YadA-M protein in the E. coli lipid environment by using 13C-13C DARR and PDSD spectra at different mixing times. The chemical shifts in most regions of YadA-M are unchanged relative to those in microcrystalline YadA-M preparations from which a structure has previously been solved, including the ASSA region that is proposed to be involved in transition-state hairpin formation for transport of the soluble domain. Comparisons of the dynamics between the microcrystalline and membrane-embed- ded samples indicate greater flexibility of the ASSA region in the outer-membrane preparation at physiological tempera- tures. This study will pave the way towards MAS-NMR structure determination of membrane proteins, and a better understanding of functionally important dynamic residues in native membrane environments.
Published: 2015

30. Evolution. Response to Comment on 'A promiscuous intermediate underlies the evolution of LEAFY DNA binding specificity'

Author: Renaud Dumas, Detlef Weigel, Norman Warthmann, François Parcy, Yong Zhang, Gane Ka-Shu Wong, Michael Melkonian, Samuel F. Brockington, Emmanuel Thévenon, Camille Sayou, Marie Monniaux, Edwige Moyroud, Max H. Nanao, Hicham Chahtane, Department of Plant Sciences, University of Cambridge [UK] (CAM), Laboratoire de physiologie cellulaire végétale (LPCV), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Unit for Virus Host-Cell Interactions, Université Grenoble Alpes (UGA), European Molecular Biology Laboratory, Research School of Biology (Australian National University), Botanisches Institut, Universität Köln, Beijing Genomics Institute, Department of Biological Sciences [Edmonton], University of Alberta, Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft, Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Research School of Biology [Canberra, Australia], Australian National University (ANU), Universität zu Köln = University of Cologne, Beijing Genomics Institute [Shenzhen] (BGI), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Recherche Agronomique (INRA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), and Universität zu Köln
Subjects: 0106 biological sciences, DNA, Plant, Evolution, [SDV]Life Sciences [q-bio], Computational biology, DNA binding specificity, Biology, 010603 evolutionary biology, 01 natural sciences, LEAFY gene, Evolution, Molecular, 03 medical and health sciences, chemistry.chemical_compound, Phylogenetics, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Leafy, Transcription factor, Plant Proteins, 030304 developmental biology, Genetics, Technical response to a comment, 0303 health sciences, Multidisciplinary, Dna binding specificity, Plant, Evolutionary transitions, DNA-Binding Proteins, Flower development, chemistry, Identification (biology), DNA, Transcription Factors
Abstract: Brunkard et al . propose that the identification of novel LEAFY sequences contradicts our model of evolution through promiscuous intermediates. Based on the debate surrounding land plant phylogeny and on our analysis of these interesting novel sequences, we explain why there is no solid evidence to disprove our model.
Published: 2015

31. Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation

Author: Florian Maumus, Nora Bujdoso, Christiane Kiefer, I. Mateos, Claudia Chica, Korbinian Schneeberger, Claude Becker, George Coupland, Mathieu Piednoël, Maria C. Albani, Raquel Iglesias-Fernández, Martin A. Lysak, Geo Velikkakam James, Vimal Rawat, Karl Nordström, Thomas Piofczyk, Loren Castaings, Laura de Lorenzo, Cristina Barrero-Sicilia, Matthias Zytnicki, François Roudier, Javier Paz-Ares, Vincent Colot, Julieta L. Mateos, Markus C. Berns, Pilar Carbonero, Eva-Maria Willing, Sara Bergonzi, Bogna Szarzynska, Detlef Weigel, Jörg Hagmann, Norman Warthmann, Seth J. Davis, Ales Pecinka, Romy Chen-Min-Tao, Terezie Mandáková, Stephan C. Schuster, Hadi Quesneville, Carlos Alonso-Blanco, Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research (MPIPZ), Research group Plant Cytogenomics, Central European Institute of Technology [Brno] (CEITEC), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Department of Molecular Biology, Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Research School of Biology, Australian National University (ANU), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Unité de Biométrie et Intelligence Artificielle (UBIA), Department of Plant Molecular Genetics, Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Científicas [Spain] (CSIC), Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Max-Planck-Gesellschaft, Center for Comparative Genomics and Bioinformatics, Pennsylvania State University (Penn State), Penn State System-Penn State System, ANR, Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT)-Brno University of Technology [Brno] (BUT), Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Center for Comparative Genomics and Bioinformatics (CCBB), Brno University of Technology [Brno] (BUT), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Transposable element, Epigenomics, Biología, [SDV]Life Sciences [q-bio], Retrotransposon, Plant Science, Biology, 01 natural sciences, Genome, Ciencias Biológicas, 03 medical and health sciences, Plant evolution, Laboratorium voor Plantenveredeling, Life Science, Ciencias de las Plantas, Botánica, 030304 developmental biology, 2. Zero hunger, Genetics, 0303 health sciences, Arabis alpina, ARABIS ALPINA, Methylation, biology.organism_classification, Long terminal repeat, GENOME, Phylogenetics, Plant Breeding, DNA methylation, CIENCIAS NATURALES Y EXACTAS, 010606 plant biology & botany
Abstract: Despite evolutionary conserved mechanisms to silence transposable element activity, there are drastic differences in the abundance of transposable elements even among closely related plant species. We conducted a de novo assembly for the 375 Mb genome of the perennial model plant, Arabis alpina. Analysing this genome revealed long-lasting and recent transposable element activity predominately driven by Gypsy long terminal repeat retrotransposons, which extended the low-recombining pericentromeres and transformed large formerly euchromatic regions into repeat-rich pericentromeric regions. This reduced capacity for long terminal repeat retrotransposon silencing and removal in A. alpina co-occurs with unexpectedly low levels of DNA methylation. Most remarkably, the striking reduction of symmetrical CG and CHG methylation suggests weakened DNA methylation maintenance in A. alpina compared with Arabidopsis thaliana. Phylogenetic analyses indicate a highly dynamic evolution of some components of methylation maintenance machinery that might be related to the unique methylation in A. alpina. Fil: Willing, Eva Maria. Max Planck Institute for Plant Breeding Research; Alemania Fil: Rawat, Vimal. Central European Institute of Technology; República Checa Fil: Mandáková, Terezie. Central European Institute of Technology; República Checa Fil: Maumus, Florian. INRA. Research Unit in Genomics; Francia Fil: James, Geo Velikkakam. Max Planck Institute for Plant Breeding Research; Alemania Fil: Nordström, Karl J. V.. Max Planck Institute for Plant Breeding Research; Alemania Fil: Becker, Claude. Max Planck Institute for Developmental Biology; Alemania Fil: Warthmann, Norman. Max Planck Institute for Developmental Biology; Alemania. The Australian National University; Australia Fil: Chica, Claudia. Centre National de la Recherche Scientifique; Francia Fil: Szarzynska, Bogna. Centre National de la Recherche Scientifique; Francia Fil: Zytnicki, Matthias. Max Planck Institute for Developmental Biology; Alemania Fil: Albani, Maria C.. Max Planck Institute for Plant Breeding Research; Alemania Fil: Kiefer, Christiane. Max Planck Institute for Plant Breeding Research; Alemania Fil: Bergonzi, Sara. Max Planck Institute for Plant Breeding Research; Alemania Fil: Castaings, Loren. Max Planck Institute for Plant Breeding Research; Alemania Fil: Mateos, Julieta Lisa. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina. Max Planck Institute for Plant Breeding Research; Alemania Fil: Berns, Markus C.. Max Planck Institute for Plant Breeding Research; Alemania Fil: Bujdoso, Nora. Max Planck Institute for Plant Breeding Research; Alemania Fil: Piofczyk, Thomas. Max Planck Institute for Plant Breeding Research; Alemania Fil: Roudier, François. Centre National de la Recherche Scientifique; Francia Fil: Carbonero, Pilar. Universidad Politécnica de Madrid; España Fil: Paz Ares, Javier. Consejo Superior de Investigaciones Cientificas; España Fil: Davis, Seth J.. Max Planck Institute for Plant Breeding Research; Alemania Fil: Pecinka, Ales. Max Planck Institute for Plant Breeding Research; Alemania Fil: Quesneville, Hadi. INRA. Research Unit in Genomics; Francia Fil: Colot, Vincent. Centre National de la Recherche Scientifique; Francia Fil: Lysak, Martin A.. Central European Institute of Technology; República Checa Fil: Weigel, Detlef. Max Planck Institute for Developmental Biology; Alemania Fil: Coupland, George. Max Planck Institute for Plant Breeding Research; Alemania Fil: Schneeberger, Korbinian. Max Planck Institute for Plant Breeding Research; Alemania
Published: 2015

32. Phenotyping and beyond: modelling the relationships between traits

Author: Vile, Denis, Bresson, Justine, Lievre, Maryline, Vasseur, François, Balsera, Crispulo, Bediee, Alexis, Rolland, Gaelle, Dauzat, Myriam, Muller, Bertrand, Granier, Christine, Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft, Federation of European Societies of Plant Biology (FESPB). INT., and ProdInra, Migration
Subjects: [SDV] Life Sciences [q-bio], [SDE] Environmental Sciences, [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences
Abstract: International audience; Plant phenotyping technology has become more advanced with the capacity to measure many morphological and physiological traits on a given individual. With increasing automation, getting access to various traits on a high number of genotypes over time raises the need to develop systems for data storage and analyses, all congregating into plant phenotyping pipelines. Here, we highlight several studies that illustrate the latest advances in plant multi-trait phenotyping and discuss future needs to ensure the best use of all these quantitative data. We assert that the next challenge is to disentangle how plant traits are embedded in networks of dependencies (and independencies) by modelling the relationships between them and how these are affected by genetics and environment.
Published: 2014

33. A promiscuous intermediate underlies the evolution of LEAFY DNA binding specificity

Author: Camille Sayou, Norman Warthmann, Samuel F. Brockington, François Parcy, Michael Melkonian, Hicham Chahtane, Yong Zhang, Renaud Dumas, Edwige Moyroud, Max H. Nanao, Gane Ka-Shu Wong, Emmanuel Thévenon, Detlef Weigel, Marie Monniaux, Laboratoire de physiologie cellulaire végétale (LPCV), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Unit of Virus Host- Cell Interactions, Université Grenoble Alpes (UGA), European Molecular Biology Laboratory [Grenoble] (EMBL), Department of Plant Sciences, University of Cambridge [UK] (CAM), Department of Molecular Biology [Tübingen], Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Botanisches Institut, Universität Köln, Beijing Genomics Institute (BGI), Beijing Genomics Institute, Department of Biological Sciences [Edmonton], University of Alberta, funds from the Max Planck Society, Coopérations et Mobilités Internationales Rhône-Alpes, FP7 P-CUBE number 227764, Alberta Ministry of Enterprise and Advanced Education, Alberta Innovates Technology Futures, Innovates Centre of Research Excellence, Musea Ventures, and BGI-Shenzhen, Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Universität zu Köln = University of Cologne, Beijing Genomics Institute [Shenzhen] (BGI), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Recherche Agronomique (INRA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), and Universität zu Köln
Subjects: Genetics, Multidisciplinary, Cell division, Mechanism (biology), fungi, Regulator, evolutionary transitions, plant, DNA binding specificity, Biology, LEAFY gene, transcription factors, Gene duplication, evolution, flower development, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Gene, Transcription factor, Leafy, Function (biology)
Abstract: LEAFY Evolution It is generally believed that redundancy across gene copies allows for the evolution of novel function in proteins. However, it is less clear how single-copy genes with crucial function may evolve. Sayou et al. (p. 645 , published online 16 January; see the Perspective by Kovach and Lamb ) examined the evolution of the essential plant transcription factor LEAFY, which is generally found as a single-copy gene. LEAFY homologs in taxa representing the major evolutionary branches of the land plants and algae exhibited three classes of LEAFY binding sites. Structural analysis identified amino acid changes in the proteins, that were responsible for contacts with specific DNA motifs and allowed the likely effects of specific amino acid changes over the evolution of land plants to be resolved.
Published: 2014

34. Interact to survive: Phyllobacterium brassicacearum improves Arabidopsis tolerance to severe water Deficit and growth recovery

Author: Marc Labadie, Denis Vile, Bruno Touraine, François Vasseur, Myriam Dauzat, Justine Bresson, Fabrice Varoquaux, Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft, 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, Physiology, [SDV]Life Sciences [q-bio], Plant-Microbial Interactions, Arabidopsis, Plant Science, phyllobacterium, 01 natural sciences, Arabidopsis thaliana, Biomass, Photosynthesis, Phyllobacterium brassicacearum, 2. Zero hunger, 0303 health sciences, Rhizosphere, Multidisciplinary, Ecology, biology, déficit hydrique, Plant physiology, food and beverages, Adaptation, Physiological, 6. Clean water, Plant growth-promoting rhizobacteria, Medicine, Research Article, Science, Drought tolerance, Rhizobacteria, 03 medical and health sciences, Symbiosis, Stress, Physiological, Plant-Environment Interactions, inoculation, 030304 developmental biology, Drought, Plant Ecology, Ecology and Environmental Sciences, arabidopsis thaliana, fungi, Water, Biology and Life Sciences, tolérance à la sécheresse, Phyllobacteriaceae, 15. Life on land, biology.organism_classification, Agronomy, interaction plante bactérie, 010606 plant biology & botany
Abstract: Mutualistic bacteria can alter plant phenotypes and confer new abilities to plants. Some plant growth-promoting rhizobacteria (PGPR) are known to improve both plant growth and tolerance to multiple stresses, including drought, but reports on their effects on plant survival under severe water deficits are scarce. We investigated the effect of Phyllobacterium brassicacearum STM196 strain, a PGPR isolated from the rhizosphere of oilseed rape, on survival, growth and physiological responses of Arabidopsis thaliana to severe water deficits combining destructive and non-destructive high-throughput phenotyping. Soil inoculation with STM196 greatly increased the survival rate of A. thaliana under several scenarios of severe water deficit. Photosystem II efficiency, assessed at the whole-plant level by high-throughput fluorescence imaging (F v/F m), was related to the probability of survival and revealed that STM196 delayed plant mortality. Inoculated surviving plants tolerated more damages to the photosynthetic tissues through a delayed dehydration and a better tolerance to low water status. Importantly, STM196 allowed a better recovery of plant growth after rewatering and stressed plants reached a similar biomass at flowering than non-stressed plants. Our results highlight the importance of plant-bacteria interactions in plant responses to severe drought and provide a new avenue of investigations to improve drought tolerance in agriculture.
Published: 2014

35. On the origin and evolutionary history of NANOG

Author: Céline Vivien, Barbara A. Demeneix, Gabriel V. Markov, Laurent Coen, Pierluigi Scerbo, Laurent Kodjabachian, Fabrice Girardot, Institut de Biologie du Développement de Marseille (IBDM), Aix Marseille Université (AMU)-Collège de France (CdF)-Centre National de la Recherche Scientifique (CNRS), Département Régulations, Développement et Diversité Moléculaire (CNRS UMR8041 - MNHN), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Institut de Génomique Fonctionnelle de Lyon (IGFL), 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), Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, WatchFrog S.A. [Evry, France], European Project: 018652,CRESCENDO, European Project: 607142,EC:FP7:PEOPLE,FP7-PEOPLE-2013-ITN,DEVCOM(2013), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Evolution des régulations endocriniennes (ERE), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), CONTENSIN, Magali, Collaborative & Robust Engineering using Simulation Capability Enabling Next Design Optimisation - CRESCENDO - 018652 - INCOMING, European Initial Training Network on Developmental and Computational Biology - DEVCOM - - EC:FP7:PEOPLE2013-09-01 - 2017-08-31 - 607142 - VALID, Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon)
Subjects: Most recent common ancestor, Homeobox protein NANOG, Pluripotency, Hominids, Pseudogene, lcsh:Medicine, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, Synteny, Evolutionary genetics, Molecular Genetics, Evolution, Molecular, Sequence alignment, Phylogenetics, Gene Duplication, Genetics, Animals, Humans, Gene family, Evolutionary Systematics, lcsh:Science, Platypus, Genome Evolution, [SDV.BC] Life Sciences [q-bio]/Cellular Biology, Phylogeny, reproductive and urinary physiology, Human evolution, Homeodomain Proteins, Evolutionary Biology, Multidisciplinary, Phylogenetic analysis, Sequence Homology, Amino Acid, POU domain, Human evolutionary genetics, lcsh:R, Computational Biology, Genomic Evolution, Genomics, Nanog Homeobox Protein, Genetic Loci, Osteichthyes, embryonic structures, Homeobox, lcsh:Q, Research Article
Abstract: International audience; Though pluripotency is well characterized in mammals, many questions remain to be resolved regarding its evolutionary history. A necessary prerequisite for addressing this issue is to determine the phylogenetic distributions and orthology relationships of the transcription factor families sustaining or modulating this property. In mammals, the NANOG homeodomain transcription factor is one of the core players in the pluripotency network. However, its evolutionary history has not been thoroughly studied, hindering the interpretation of comparative studies. To date, the NANOG family was thought to be monogenic, with numerous pseudogenes described in mammals, including a tandem duplicate in Hominidae. By examining a wide-array of craniate genomes, we provide evidence that the NANOG family arose at the latest in the most recent common ancestor of osteichthyans and that NANOG genes are frequently found as tandem duplicates in sarcopterygians and as a single gene in actinopterygians. Their phylogenetic distribution is thus reminiscent of that recently shown for Class V POU paralogues, another key family of pluripotency-controlling factors. However, while a single ancestral duplication has been reported for the Class V POU family, we suggest that multiple independent duplication events took place during evolution of the NANOG family. These multiple duplications could have contributed to create a layer of complexity in the control of cell competence and pluripotency, which could explain the discrepancies relative to the functional evolution of this important gene family. Further, our analysis does not support the hypothesis that loss of NANOG and emergence of the preformation mode of primordial germ cell specification are causally linked. Our study therefore argues for the need of further functional comparisons between NANOG paralogues, notably regarding the novel duplicates identified in sauropsids and non-eutherian mammals.
Published: 2014

36. The genome of the stress-tolerant wild tomato species Solanum pennellii

Author: Saulo Alves Aflitos, Gabriel Lichtenstein, Linyong Mao, Alexander Vogel, Neelima Sinha, Yimin Xu, Detlef Weigel, Itai Ofner, Borjana Arsova, Marie E. Bolger, Fernando Carrari, Zhangjun Fei, Hadi Quesneville, Lauren R. Headland, Ralph Panstruga, Julin N. Maloof, Björn Usadel, Jocelyn K. C. Rose, Eric A. Fich, Christa Lanz, Seisuke Kimura, Takayuki Tohge, Korbinian Schneeberger, René Klein Lankhorst, James J. Giovannoni, Saleh Alseekh, Julia Vrebalov, Rainer Schwacke, Małgorzata Ryngajłło, Iben Sørensen, Alisdair R. Fernie, Ravi Kumar, Roeland C. H. J. van Ham, Sonia Osorio, Dani Zamir, Elio Schijlen, Daniel Koenig, José M. Jiménez-Gómez, Mariana Conte, Heike Keller, Federico Scossa, Anthony Bolger, Florian Maumus, Department of Metabolic Network [MPI-MP], Max Planck Institute of Molecular Plant Physiology (MPI-MP), Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Institute for Biology I, Institute for Botany and Molecular Genetics (IBMG), Rheinisch-Westfälische Technische Hochschule Aachen (RWTH), Max-Planck-Gesellschaft, Centro di Ricerca per l'Orticoltura, Agricultural Research Council (CRA), Department of Metabolic Networks [Potsdam-Golm], Institut for Organic and Earth Sciences, Research Centre Jülich, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Department of Molecular Physiology [Potsdam-Golm], Department of Plant Biology, Cornell University, Instituto Nacional de Investigación Agropecuaria (INIA), Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research (MPIPZ), Faculty of Agriculture, The Hebrew University of Jerusalem (HUJ), Boyce Thompson Institute [Ithaca], Instituto de Hortofructicultura Subtropical y Mediterranea 'La Mayora' - Department of Molecular Biology and Biochemistry, Universidad de Málaga [Málaga], Plant Research International (PRI), Wageningen University and Research Centre [Wageningen] (WUR), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Department of Plant Breeding and Genetics, University of California [Davis] (UC Davis), University of California-University of California, Heinrich-Heine-Universität Düsseldorf [Düsseldorf], Institute for Biology I, Unit of Plant Molecular Cell Biology, Agricultural Research Service - Robert W.Holley Center for Agriculture & Health, United States Department of Agriculture, Institute for Biology I, Institute for Botany and Molecular Genetics, Max Planck Society, Deutsche Israeli Project FE 552/12-1, Bundesministerium fur Bildung und Forschung (BMBF) FKZ 0315961, Deutsche Forschungsgemeinschaft International Research Training Groups (IRTG), 1525 CRA Young Investigator Program, INTA, Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET) grant, Agencia Nacional de Promocion Cientifica y Tecnologica (ANPCYPT) grant, NSF grant IOS-0820854, US National Science Foundation DBI-0606595 DBI-1313887, Agriculture and Food Research Initiative competitive grant ,USDA National Institute of Food and Agriculture 2011-04197, US National Science Foundation Plant Genome Program DBI-0820612 IOS-0923312, Institute of Bio- and Geosciences [Jülich] (IBG), Forschungszentrum Jülich GmbH | Centre de recherche de Juliers, Helmholtz-Gemeinschaft = Helmholtz Association-Helmholtz-Gemeinschaft = Helmholtz Association, Cornell University [New York], Instituto de Hortofruticultura Subtropical y Mediterranea 'La Mayora' (IHSM), Universidad de Málaga [Málaga] = University of Málaga [Málaga]-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Wageningen University and Research [Wageningen] (WUR), and Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf]
Subjects: Germplasm, [SDV]Life Sciences [q-bio], Plant genetics, Genome, Medical and Health Sciences, traits, Wild tomato, education.field_of_study, biology, plants, qtl, Germoplasma, BioSolar Cells, Chromosome Mapping, food and beverages, Genomics, Biological Sciences, Candidate Genes, Biosystematiek, introgression lines, Genome, Plant, Genes Candidatos, Plant molecular biology, Bioinformatics, Physiological, Population, Quantitative Trait Loci, Introgression, Solanum, Stress, Chromosomes, Plant, Article, Chromosomes, Solanum pennellii, Mapas Genéticos, BIOS Applied Bioinformatics, Tomatoes, Tomate, Stress, Physiological, ddc:570, Botany, evolution, Bioinformatica, Genetics, Genomes, education, Genomas, Estres, fungi, Genetic Maps, Plant, fruit, biology.organism_classification, gene-expression, trichomes, DNA Transposable Elements, responses, Biosystematics, EPS, accumulation, Tolerance, Tolerancia, Developmental Biology
Abstract: Björn Usadel and colleagues report the genome sequence of the wild tomato species Solanum pennellii. The authors identify genes important for stress tolerance, metabolism and fruit maturation and suggest that transposable elements have had an important role in the evolution of the S. penellii stress response. Supplementary information The online version of this article (doi:10.1038/ng.3046) contains supplementary material, which is available to authorized users., Solanum pennellii is a wild tomato species endemic to Andean regions in South America, where it has evolved to thrive in arid habitats. Because of its extreme stress tolerance and unusual morphology, it is an important donor of germplasm for the cultivated tomato Solanum lycopersicum1. Introgression lines (ILs) in which large genomic regions of S. lycopersicum are replaced with the corresponding segments from S. pennellii can show remarkably superior agronomic performance2. Here we describe a high-quality genome assembly of the parents of the IL population. By anchoring the S. pennellii genome to the genetic map, we define candidate genes for stress tolerance and provide evidence that transposable elements had a role in the evolution of these traits. Our work paves a path toward further tomato improvement and for deciphering the mechanisms underlying the myriad other agronomic traits that can be improved with S. pennellii germplasm. Supplementary information The online version of this article (doi:10.1038/ng.3046) contains supplementary material, which is available to authorized users.
Published: 2014

37. Extensive [i]cis[/i]-regulatory variation robust to environmental perturbation in [i]Arabidopsis[/i]

Author: Cubillos, Francisco A., Stegle, Oliver, Grondin, Cécile, Canut, Matthieu, Tisne, Sebastien, Gy, Isabelle, Loudet, Olivier, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft, Max Planck Institute for Intelligent Systems, European Molecular Biology Laboratory, European Bioinformatics Institute, ANR Grant 2Complex/ANR-09-BLAN-0366, Marie Curie FP7 fellowship, European Project: 243359, and Max Planck Institute for Intelligent Systems [Tübingen]
Subjects: [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], fungi, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology
Abstract: [i]cis[/i]- and trans-acting factors affect gene expression and responses to environmental conditions. However, for most plant systems, we lack a comprehensive map of these factors and their interaction with environmental variation. Here, we examined allele-specific expression (ASE) in an F1 hybrid to study how alleles from two Arabidopsis thaliana accessions affect gene expression. To investigate the effect of the environment, we used drought stress and developed a variance component model to estimate the combined genetic contributions of cis- and trans-regulatory polymorphisms, environmental factors, and their interactions. We quantified ASE for 11,003 genes, identifying 3318 genes with consistent ASE in control and stress conditions, demonstrating that cis- acting genetic effects are essentially robust to changes in the environment. Moreover, we found 1618 genes with genotype x environment (GxE) interactions, mostly cis x E interactions with magnitude changes in ASE. We found fewer trans x E interactions, but these effects were relatively less robust across conditions, showing more changes in the direction of the effect between environments; this confirms that trans-regulation plays an important role in the response to environmental conditions. Our data provide a detailed map of cis- and trans-regulation and GxE interactions in A. thaliana, laying the ground for mechanistic investigations and studies in other plants and environments.
Published: 2014

38. Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato

Author: Korbinian Schneeberger, Lauren R. Headland, Takayuki Tohge, An V. Tat, Daniel Koenig, Björn Usadel, Christa Lanz, Markus Pauly, Michael F. Covington, Anthony Bolger, Neelima Sinha, José M. Jiménez-Gómez, Ravi Kumar, Seisuke Kimura, Jie Peng, Mallorie Taylor-Teeples, Daniel Fulop, Siobhan M. Brady, Julin N. Maloof, Guangyan Xiong, Upendra K. Devisetty, Alisdair R. Fernie, Daniel H. Chitwood, Stephan Ossowski, Detlef Weigel, Department of Plant Biology, University of California, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research (MPIPZ), Kyoto Sangyo University, Department of Molecular Physiology [Potsdam-Golm], Max Planck Institute of Molecular Plant Physiology (MPI-MP), Department of Metabolic Networks [Potsdam-Golm], Department of Plant Developmental Biology, Genes and Disease Program, Centre de Regulacio´ Geno´mica-CRG-UPF, Department of Plant and Microbial Biology, RWTH Aachen University, Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ), Department of Statistics, National Science Foundation Grant (IOS-0820854), and Human Frontier Science Program Fellowship (LT000783)
Subjects: 0106 biological sciences, Nonsynonymous substitution, abiotic stress, [SDV]Life Sciences [q-bio], Genes, Plant, 01 natural sciences, Genome, 03 medical and health sciences, domestication, biotic stress, Solanum lycopersicum, Gene Expression Regulation, Plant, Wild tomato, Selection, Genetic, Domestication, Gene, Selection (genetic algorithm), 030304 developmental biology, 2. Zero hunger, Genetics, 0303 health sciences, Multidisciplinary, Natural selection, biology, food and beverages, Biotic stress, biology.organism_classification, PNAS Plus, Transcriptome, 010606 plant biology & botany
Abstract: International audience; Although applied over extremely short timescales, artificial selection has dramatically altered the form, physiology, and life history of cultivated plants. We have used RNAseq to define both gene sequence and expression divergence between cultivated tomato and five related wild species. Based on sequence differences, we detect footprints of positive selection in over 50 genes. We also document thousands of shifts in gene-expression level, many of which resulted from changes in selection pressure. These rapidly evolving genes are commonly associated with environmental response and stress tolerance. The importance of environmental inputs during evolution of gene expression is further highlighted by large-scale alteration of the light response coexpression network between wild and cultivated accessions. Human manipulation of the genome has heavily impacted the tomato transcriptome through directed admixture and by indirectly favoring nonsynonymous over synonymous substitutions. Taken together, our results shed light on the pervasive effects artificial and natural selection have had on the transcriptomes of tomato and its wild relatives.
Published: 2013

39. The Capsella rubella genome and the genomic consequences of rapid mating system evolution

Author: Stephen I. Wright, Daniel Koenig, Richard M. Clark, Mathieu Blanchette, Wei Wang, Hadi Quesneville, Yaniv Brandvain, Tanja Slotte, Terezie Mandáková, Jarrod Chapman, Joshua G. Steffen, L. Killian Newman, Lisa M. Smith, Kim A. Steige, Martin A. Lysak, Shohei Takuno, Adrian E. Platts, Peter Andolfatto, Detlef Weigel, Jeremy Schmutz, Shengqiang Shu, Emilio Vello, Brandon S. Gaut, Jerry Jenkins, Florian Maumus, Tina T. Hu, Stefan R. Henz, Graham Coop, Magnus Nordborg, Khaled M. Hazzouri, Ya-Long Guo, Jane Grimwood, Daniel S. Rokhsar, Juan S. Escobar, J. Arvid Ågren, Simon E. Prochnik, Department of Ecology and Evolutionary Biology, University of Toronto, Uppsala University, New York University [Abu Dhabi], NYU System (NYU), Department of Molecular Biology, Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Chinese Academy of Sciences (CAS), Department of Evolutionary Biology, Department of Biology, Northern Arizona University [Flagstaff], Masaryk University [Brno] (MUNI), Utah State University (USU), Colby-Sawyer College, Partenaires INRAE, University of California, Department of Plant Sciences, University of California [Davis] (UC Davis), University of California-University of California, Department of Evolution and Ecology, Princeton University, McGill University = Université McGill [Montréal, Canada], Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Hudson Alpha Institute for Biotechnology, Joint Genome Institute (JGI), U.S. Department of Energy, University of California [Berkeley], and Centre for the Analysis of Genome Evolution and Function
Subjects: 0106 biological sciences, Time Factors, [SDV]Life Sciences [q-bio], ved/biology.organism_classification_rank.species, Molecular Sequence Data, Arabidopsis, Outcrossing, Self-Fertilization, Genes, Plant, 01 natural sciences, Rubella, Genome, Evolution, Molecular, 03 medical and health sciences, Genetics, medicine, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Capsella, Pollination, Gene, 030304 developmental biology, genomic consequences, 0303 health sciences, biology, ved/biology, Selfing, Sequence Analysis, DNA, medicine.disease, biology.organism_classification, Mating system, Capsella rubella genome, mating systelm evolution, Fertilization, Capsella rubella, Genome, Plant, 010606 plant biology & botany
Abstract: International audience; The shift from outcrossing to selfing is common in flowering plants, but the genomic consequences and the speed at which they emerge remain poorly understood. An excellent model for understanding the evolution of self fertilization is provided by Capsella rubella, which became self compatible
Published: 2013

40. Emergence of clones in sexual populations

Author: Boris I. Shraiman, Richard A. Neher, Marija Vucelja, Marc Mézard, Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft, Courant Institute of Mathematical Sciences [New York] (CIMS), New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU), Laboratoire de Physique Théorique et Modèles Statistiques (LPTMS), Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11), Kavli Institute for Theoretical Physics [Santa Barbara] (KITP), University of California [Santa Barbara] (UCSB), and University of California-University of California
Subjects: Statistics and Probability, Linkage disequilibrium, Population, Population genetics, FOS: Physical sciences, Outcrossing, Biology, 01 natural sciences, 03 medical and health sciences, 0103 physical sciences, Genetic variation, Allele, [PHYS.COND.CM-SM]Physics [physics]/Condensed Matter [cond-mat]/Statistical Mechanics [cond-mat.stat-mech], 10. No inequality, 010306 general physics, education, Quantitative Biology - Populations and Evolution, Condensed Matter - Statistical Mechanics, 030304 developmental biology, 0303 health sciences, education.field_of_study, Statistical Mechanics (cond-mat.stat-mech), Genetic heterogeneity, Populations and Evolution (q-bio.PE), Statistical and Nonlinear Physics, Heritability, Evolutionary biology, FOS: Biological sciences, Statistics, Probability and Uncertainty
Abstract: In sexual population, recombination reshuffles genetic variation and produces novel combinations of existing alleles, while selection amplifies the fittest genotypes in the population. If recombination is more rapid than selection, populations consist of a diverse mixture of many genotypes, as is observed in many populations. In the opposite regime, which is realized for example in the facultatively sexual populations that outcross in only a fraction of reproductive cycles, selection can amplify individual genotypes into large clones. Such clones emerge when the fitness advantage of some of the genotypes is large enough that they grow to a significant fraction of the population despite being broken down by recombination. The occurrence of this "clonal condensation" depends, in addition to the outcrossing rate, on the heritability of fitness. Clonal condensation leads to a strong genetic heterogeneity of the population which is not adequately described by traditional population genetics measures, such as Linkage Disequilibrium. Here we point out the similarity between clonal condensation and the freezing transition in the Random Energy Model of spin glasses. Guided by this analogy we explicitly calculate the probability, Y, that two individuals are genetically identical as a function of the key parameters of the model. While Y is the analog of the spin-glass order parameter, it is also closely related to rate of coalescence in population genetics: Two individuals that are part of the same clone have a recent common ancestor., revised version
Published: 2012

41. Targeted ultramicrotomy: a valuable tool for correlated light and electron microscopy of small model organisms

Author: Kolotuev, Irina, Bumbarger, Daniel, Labouesse, Michel, Schwab, Yannick, Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), De Villemeur, Hervé, Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)
Subjects: Cryopreservation, Microscopy, Confocal, Plastic Embedding, [SDV.IB.IMA] Life Sciences [q-bio]/Bioengineering/Imaging, Microscopy, Electron, Transmission, [SDV.IB.IMA]Life Sciences [q-bio]/Bioengineering/Imaging, Sepharose, Cryoelectron Microscopy, Animals, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Caenorhabditis elegans, [SDV.BC] Life Sciences [q-bio]/Cellular Biology, Cryoultramicrotomy
Abstract: In: Correlative Light and Electron MIcroscopy. Edited by Thomas Müller-Reichert and Paul Verkade ISBN: 978-0-12-416026-2; International audience; Correlative light and electron microscopy (CLEM) is used when one needs to combine both imaging modalities on the same sample. When working on living small model organisms, such as Caenorhabditis elegans, specific CLEM protocols are required to acquire high-resolution light microscopic images of a region of interest and thereafter to relocate and study the same object at the ultrastructural level using a transmission electron microscope. In this chapter, we describe how to process living specimens from the confocal microscope to the transmission electron microscopy (TEM), focusing on an improved ultramicrotomy technique that allows a precise and reliable targeting of the object of interest. This improvement significantly reduces the time consuming and frequently frustrating search for the region of interest. Our targeted ultramicrotomy protocol is versatile enough to be applied on a variety of bulk specimens, such as fly and fish embryos, or mouse tissues.
Published: 2012

42. Genome-wide binding-site analysis of REVOLUTA reveals a link between leaf patterning and light-mediated growth responses

Author: Brandt, Ronny, Salla-Martret, Merce, Bou-Torrent, Jordi, Musielak, Thomas, Stahl, Mark, Lanz, Christa, Ott, Felix, Schmid, Markus, Greb, Thomas, Schwarz, Martina, Choi, Sang-Bong, Barton, M. Kathryn, Reinhart, Brenda J., Liu, Tie, Quint, Marcel, Palauqui, Jean-Christophe, Martinez-Garcia, Jaime F., Wenkel, Stephan, National Science Foundation (US), Generalitat de Catalunya, Ministerio de Ciencia e Innovación (España), German Research Foundation, Robert Bosch Foundation, Federal Ministry of Food and Agriculture (Germany), European Commission, Zentrum für Molekularbiologie der Pflanzen (ZMBP), Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Department of Molecular Biology [Tübingen], Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Sch Biotechnol & Environm Engn, Myongji Univ, Department of Plant Biology [Carnegie] (DPB), Carnegie Institution for Science [Washington], Dept Mol Signal Proc, D-06120 Halle, Leibniz Institute of Plant Biochemistry (IPB), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Carnegie Institution for Science, National Science Foundation (NSF) [0929413], Generalitat de Catalunya (Xarba) [2009-SGR697], MICINN - FEDER funds [BIO2005-00154, CSD2007-00036, BIO2008-00169], Deutsche Forschungsgemeinschaft (DFG) [WE4281/6-1], European Union [256502], Ministry for Agriculture (Bundesanstalt fur Landwirtschaft und Ernahrung) [CHN 13-22/12-13], Eberhard Karls Universität Tübingen, Department of Plant Biology [Carnegie Institution], Zentrum für Molekularbiologie der Pflanzen ( ZMBP ), Dept Mol Biol, Gregor Mendel Institute of Molecular Plant Biology ( GMI ), Austrian Academy of Sciences ( OeAW ), Leibniz Institute of Plant Biochemistry, Institut Jean-Pierre Bourgin ( IJPB ), and Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Arabidopsis thaliana, PLANT DEVELOPMENT, fungi, HD-ZIPIII, SHADE-AVOIDANCE RESPONSES, ARABIDOPSIS, GENE, HD-ZIPII, CELL FATE, TRANSCRIPTION, auxin, AUXIN BIOSYNTHESIS, REGULATOR, [ SDV.SA ] Life Sciences [q-bio]/Agricultural sciences, shade avoidance, ZIP, leaf development, POLARITY
Abstract: Unlike the situation in animals, the final morphology of the plant body is highly modulated by the environment. During Arabidopsis development, intrinsic factors provide the framework for basic patterning processes. CLASS III HOMEODOMAIN LEUCINE ZIPPER (HD-ZIPIII) transcription factors are involved in embryo, shoot and root patterning. During vegetative growth HD-ZIPIII proteins control several polarity set-up processes such as in leaves and the vascular system. We have identified several direct target genes of the HD-ZIPIII transcription factor REVOLUTA (REV) using a chromatin immunoprecipitation/DNA sequencing (ChIP-Seq) approach. This analysis revealed that REV acts upstream of auxin biosynthesis and affects directly the expression of several class II HD-ZIP transcription factors that have been shown to act in the shade-avoidance response pathway. We show that, as well as involvement in basic patterning, HD-ZIPIII transcription factors have a critical role in the control of the elongation growth that is induced when plants experience shade. Leaf polarity is established by the opposed actions of HD-ZIPIII and KANADI transcription factors. Finally, our study reveals that the module that consists of HD-ZIPIII/KANADI transcription factors controls shade growth antagonistically and that this antagonism is manifested in the opposed regulation of shared target genes., The Barton lab receives funding from the Carnegie Institution for Science and the National Science Foundation (NSF2010, grant #0929413). Research in the JFM-G laboratory is supported by grants from the Generalitat de Catalunya (Xarba, 2009-SGR697) and MICINN – FEDER funds (BIO2005-00154, CSD2007-00036, BIO2008-00169). Research in the SW laboratory is made possible by funding from the Deutsche Forschungsgemeinschaft (DFG, WE4281/6-1), the European Union (FP7 No. 256502), the Robert Bosch Foundation and the Ministry for Agriculture (Bundesanstalt für Landwirtschaft und Ernährung; CHN13-22/12-13) to SW.
Published: 2012

43. Prediction of regulatory interactions from genome sequences using a biophysical model for the $Arabidopsis$ LEAFY transcription factor

Author: Eugenio G. Minguet, David Posé, François Parcy, Edwige Moyroud, Olivier Bastien, Markus Schmid, Sandrine Blanchet, Marie Monniaux, Felix Ott, Detlef Weigel, Emmanuel Thévenon, Levi Yant, Laboratoire de physiologie cellulaire végétale (LPCV), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Department of Molecular Biology [Tübingen], Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Biotechnology and Biological Sciences Research Council, University J. Fourier, Grenoble, ERA-NET Plant Genomics Project BLOOM-NET [SCHM 1560/7-1], Max Planck Society, ANR-07-BLAN-0211,Plant-TFcode,Cracking the code of transcriptional regulation: the key to the past and future evolution of plants(2007), ANR-07-BSYS-0002,FLOWER MODEL,Modélisation de la croissance et de la régulation des gènes dans les organes floraux(2007), European Project: 226477,EC:FP7:KBBE,FP7-KBBE-2008-2B,AENEAS(2009), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique, Agence Nationale de la Recherche (ANR), and FP7 Collaborative Project AENEAS [KBBE-2009-226477]
Subjects: 0106 biological sciences, Arabidopsis thaliana, biophysical model, Arabidopsis, plant, Plant Science, Regulatory Sequences, Nucleic Acid, 01 natural sciences, Genome, LFY, Gene Expression Regulation, Plant, MADS-box, Research Articles, transcription factor, 0303 health sciences, biology, Agamous, food and beverages, Genome, Plant, Protein Binding, Chromatin Immunoprecipitation, DNA, Plant, Molecular Sequence Data, Computational biology, Flowers, Genes, Plant, DNA sequencing, AGAMOUS Protein, Arabidopsis, Biophysical Phenomena, Evolution, Molecular, 03 medical and health sciences, regulatory networks, AGAMOUS, Botany, evolution, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, gene, Gene, Transcription factor, 030304 developmental biology, DNA binding sites, flowering, Binding Sites, Base Sequence, Models, Genetic, Arabidopsis Proteins, fungi, Reproducibility of Results, Cell Biology, biology.organism_classification, Introns, floral development, LEAFY, DNA binding site, genomic sequences, 010606 plant biology & botany, Transcription Factors
Abstract: L'article original est publié par The American Society of Plant Biologists; International audience; Despite great advances in sequencing technologies, generating functional information for nonmodel organisms remains a challenge. One solution lies in an improved ability to predict genetic circuits based on primary DNA sequence in combination with detailed knowledge of regulatory proteins that have been characterized in model species. Here, we focus on the LEAFY (LFY) transcription factor, a conserved master regulator of floral development. Starting with biochemical and structural information, we built a biophysical model describing LFY DNA binding specificity in vitro that accurately predicts in vivo LFY binding sites in the Arabidopsis thaliana genome. Applying the model to other plant species, we could follow the evolution of the regulatory relationship between LFY and the AGAMOUS (AG) subfamily of MADS box genes and show that this link predates the divergence between monocots and eudicots. Remarkably, our model succeeds in detecting the connection between LFY and AG homologs despite extensive variation in binding sites. This demonstrates that the cis-element fluidity recently observed in animals also exists in plants, but the challenges it poses can be overcome with predictions grounded in a biophysical model. Therefore, our work opens new avenues to deduce the structure of regulatory networks from mere inspection of genomic sequences.
Published: 2011

44. The genome of Tetranychus urticae reveals herbivorous pest adaptations

Author: Fernando Roch, Johannes Mathieu, T. Ryan Gregory, René Feyereisen, Stephane Rombauts, Edward J. Osborne, Anica Bjelica, Ryan M. Pace, Manuel Martinez, Lou Verdon, Isabel Diaz, Marie Navarro, Phuong Cao Thi Ngoc, Sergej Djuranovic, Rodrigo Mancilla Villalobos, Élio Sucena, Stefan R. Henz, Sara Magalhães, Gustavo Acevedo, Maria Navajas, Jeffrey L. Hutter, Guy Smagghe, Luc Tirry, Miodrag Grbic, Eric Bonnet, Marisela Vélez, Andre Pires-daSilva, Stephen D. Hudson, Yves Van de Peer, Masatoshi Iga, Jia Zeng, Catherine Blais, Kristof Demeestere, Marc Cazaux, Richard M. Clark, Jeffrey A. Fawcett, Vojislava Grbic, Jeremy Schmutz, Jan A. Veenstra, Thomas Van Leeuwen, Lisa M. Nagy, Soojin V. Yi, Cindy Martens, Aminael Sánchez-Rodríguez, Félix Ortego, Guy Baele, Laurent Farinelli, John Ewer, Pierre Rouzé, Olivier Christiaens, Lothar Wissler, Vladimir Zhurov, Erika Lindquist, Wannes Dermauw, Pedro Hernández-Crespo, Evolutionary Biology (IBED, FNWI), Department of Biology, Northern Arizona University [Flagstaff], Instituto de Ciencias de la Vid y el Vino - Institute of Grapevine and Wine Sciences, Partenaires INRAE, Faculty of Bioscience Engineering, Universiteit Gent = Ghent University [Belgium] (UGENT), Utah State University (USU), Department of plant Biotechnology and Bioinformatics, University of Gent, Department of plant systems biology, Flanders Institute for Biotechnology, Centro de Investigaciones Biológicas (CIB), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Instituto Gulbenkian de Ciência, Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Department of Molecular and Cellular Biology, University of Arizona, School of Medicine, Johns Hopkins University (JHU)-Oncology Center, Institut de Neurosciences cognitives et intégratives d'Aquitaine (INCIA), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1-SFR Bordeaux Neurosciences-Centre National de la Recherche Scientifique (CNRS), Universidad de Valparaiso, University of Western Ontario (UWO), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Facultad de Ciencas [Madrid], Universidad Autonoma de Madrid (UAM), School of Biology, Georgia Institute of Technology [Atlanta], University of Texas, Université des Sciences Sociales (Toulouse 1), Centre National de la Recherche Scientifique (CNRS), Institute for Evolution and Biodiversity (IEB), Westfälische Wilhelms-Universität Münster (WWU), Université Catholique de Louvain = Catholic University of Louvain (UCL), Université Pierre et Marie Curie - Paris 6 (UPMC), Laboratoire de Biologie du Développement [Paris] (LBD), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft, Department of Integrative Biology (University of Guelph), University of Guelph, Boyce Thompson Institute [Ithaca], Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food [Ottawa] (AAFC), Fasteris SA, Hudson Alpha Institute for Biotechnology, Joint Genome Institute (JGI), Interactions Biotiques et Santé Végétale, Institut National de la Recherche Agronomique (INRA), Universiteit Gent = Ghent University (UGENT), Department of Molecular and Cellular Biology [University of Arizona], Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1 (UB)-SFR Bordeaux Neurosciences-Centre National de la Recherche Scientifique (CNRS), Universidad Autónoma de Madrid (UAM), Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT), Westfälische Wilhelms-Universität Münster = University of Münster (WWU), Laboratoire de Biologie du Développement [IBPS] (LBD), Agriculture and Agri-Food (AAFC), and Fasteris SA [Plan-les-Ouates, Switzerland]
Subjects: 0106 biological sciences, SEQUENCED GENOME, Gene Transfer, Horizontal, Molecular Sequence Data, Silk, Genomics, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Molting, Biology, ACARI, 01 natural sciences, Genome, Article, Evolution, Molecular, GENE TRANSFER, 03 medical and health sciences, Spider mite, DETOXICATION, Animals, Herbivory, Tetranychus urticae, 030304 developmental biology, 0303 health sciences, Parasteatoda tepidariorum, Spider, Multidisciplinary, TETRANICHUS URTICAE, Ecology, Host (biology), fungi, Genes, Homeobox, PESTICIDE RESISTANCE, Plants, biology.organism_classification, Adaptation, Physiological, Nanostructures, TRANSCRIPTOME ANALYSIS, 010602 entomology, Ecdysterone, Gene Expression Regulation, Evolutionary biology, Multigene Family, PEST analysis, SILK PRODUCTION, Fibroins, Tetranychidae, Transcriptome, GENOMICS
Abstract: 6 páginas, 5 figuras -- PAGS nros. 487-492, Grbic, Miodrag et.al., The spider mite Tetranychus urticae is a cosmopolitan agricultural pest with an extensive host plant range and an extreme record of pesticide resistance. Here we present the completely sequenced and annotated spider mite genome, representing the first complete chelicerate genome. At 90 megabases T. urticae has the smallest sequenced arthropod genome. Compared with other arthropods, the spider mite genome shows unique changes in the hormonal environment and organization of the Hox complex, and also reveals evolutionary innovation of silk production. We find strong signatures of polyphagy and detoxification in gene families associated with feeding on different hosts and in new gene families acquired by lateral gene transfer. Deep transcriptome analysis of mites feeding on different plants shows how this pest responds to a changing host environment. The T. urticae genome thus offers new insights into arthropod evolution and plant–herbivore interactions, and provides unique opportunities for developing novel plant protection strategies, M.G. and V.G. acknowledge support from NSERC Strategic Grant STPGP 322206-05, Marie Curie Incoming International Fellowship, OECD Co-operative Research Programme: Biological resource management for Sustainable Agricultural Systems JA00053351, and Ontario Research Fund–Global Leadership in Genomics and Life Sciences GL2-01-035. The genome and transcriptome sequencing projects were funded by the Government of Canada through Genome Canada and the Ontario Genomics Institute (OGI-046), JGI Community Sequencing Program grant 777506 to M.G., a University of Utah SEED grant (to R.M.C.), and National Science Foundation (NSF) grant 0820985 (to R.M.C., Principal Investigator L. Sieburth); work conducted by the US Department of Energy Joint Genome Institute is supported by the Office of Science of the US Department of Energy under contract No. DE-AC02-05CH11231
Published: 2011

45. Probing the reproducibility of leaf growth and molecular phenotypes: a comparison of three arabidopsis accessions cultivated in ten laboratories

Author: Juliette Fabre, Bernd Rinn, Josip Perkovic, Christian Meyer, Jesper T. Gronlund, Lothar Willmitzer, Christine Granier, Sean T. May, Michael W. Bevan, Vicky Buchanan-Wollaston, Gerrit T.S. Beemster, Catherine Massonnet, Camila Caldana, Gaëlle Messerli, José Luis Micol, Lars Hennig, Wilhelm Gruissem, Fabio Fiorani, Pierre Hilson, Matthew A. Hannah, Denis Vile, Sean Walsh, Silvia Rubio-Díaz, Rhonda C. Meyer, Emma Wigmore, Detlef Weigel, Jan Lisec, Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Max Planck Institute of Molecular Plant Physiology (MPI-MP), Max-Planck-Gesellschaft, Department of Plant Systems Biology, Flanders Institute for Biotechnology, Department of Plant Biotechnology and Genetics, Ghent University [Belgium] (UGENT), Department of Biology, Plant Biotechnology, Warwick Horticulture Research International, University of Warwick [Coventry], Max Planck Institute for Developmental Biology, Plant Sciences, School of Biosciences, University of Nottingham, UK (UON), Cell and Developmental Biology Department, John Innes Centre [Norwich], Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, División de Genética and Instituto de Bioingeniería, Universidad Miguel Hernández [Elche] (UMH), Department of Biosystems Science and Engineering [ETH Zürich] (D-BSSE), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), Department of Plant Biotechnology and Bioinformatics, 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), Universiteit Gent = Ghent University [Belgium] (UGENT), and Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich)
Subjects: 0106 biological sciences, feuille, Genotype, Physiology, croissance végétale, méthode de mesure, Arabidopsis, Plant Science, Computational biology, Plants genetics, 01 natural sciences, Transcriptome, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Species Specificity, RELATION GENOTYPE x ENVIRONNEMENT, métabolite, Génétique des plantes, Genetics, Transcriptome Profiles, Arabidopsis thaliana, RNA, Messenger, Biology, 030304 developmental biology, Blue light, 0303 health sciences, SIGNATURE METABOLIQUE, biology, Gene Expression Profiling, fungi, Reproducibility of Results, food and beverages, biology.organism_classification, Phenotype, environnement, Systems Biology, Molecular Biology, and Gene Regulation, Gene expression profiling, Plant Leaves, phénotype, transcriptome, 010606 plant biology & botany
Abstract: L'article original est publié par The American Society of Plant Biologists; A major goal of the life sciences is to understand how molecular processes control phenotypes. Because understanding biological systems relies on the work of multiple laboratories, biologists implicitly assume that organisms with the same genotype will display similar phenotypes when grown in comparable conditions. We investigated to what extent this holds true for leaf growth variables and metabolite and transcriptome profiles of three Arabidopsis (Arabidopsis thaliana) genotypes grown in 10 laboratories using a standardized and detailed protocol. A core group of four laboratories generated similar leaf growth phenotypes, demonstrating that standardization is possible. But some laboratories presented significant differences in some leaf growth variables, sometimes changing the genotype ranking. Metabolite profiles derived from the same leaf displayed a strong genotype x environment (laboratory) component. Genotypes could be separated on the basis of their metabolic signature, but only when the analysis was limited to samples derived from one laboratory. Transcriptome data revealed considerable plant-to-plant variation, but the standardization ensured that interlaboratory variation was not considerably larger than intralaboratory variation. The different impacts of the standardization on phenotypes and molecular profiles could result from differences of temporal scale between processes involved at these organizational levels. Our findings underscore the challenge of describing, monitoring, and precisely controlling environmental conditions but also demonstrate that dedicated efforts can result in reproducible data across multiple laboratories. Finally, our comparative analysis revealed that small variations in growing conditions (light quality principally) and handling of plants can account for significant differences in phenotypes and molecular profiles obtained in independent laboratories.
Published: 2010

46. Phytohormones and the cell wall in Arabidopsis during seedling growth

Author: Richard Sibout, Clara Sánchez-Rodríguez, Staffan Persson, Ignacio Rubio-Somoza, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Max Planck Institute of Molecular Plant Physiology (MPI-MP), Max-Planck-Gesellschaft, and Max Planck Institute for Developmental Biology
Subjects: 0106 biological sciences, Arabidopsis, plant sciences, Plant Science, seedling, Root hair initiation, 01 natural sciences, Cell wall, 03 medical and health sciences, plantes, Auxin, régulateur de croissance, plant growth regulators, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Vascular tissue, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, biology, Cell growth, fungi, food and beverages, Cell plate, biology.organism_classification, cell size, phytohormones, chemistry, Biochemistry, Seedlings, cell wall, Secondary cell wall, 010606 plant biology & botany
Abstract: Cell wall biosynthesis, and remodelling, is a prerequisite for plant growth; from cell plate formation in dividing cells, to the strengthening of the vascular tissue by secondary cell wall deposits. Many plant hormones are also essential for plant growth and development, such as auxin that controls cell proliferation and differentiation. Direct links between hormone actions and changes in cell wall structure have therefore been assumed, and long sought. While many studies during recent decades have supported such relationships, the vast majority have been inferred through indirect means. In an era that embraces cell-wall-related products, including cellulosic biofuels, we attempt to give an overview of phytohormone-mediated cell expansion, and cell wall biosynthesis in Arabidopsis during seedling growth.
Published: 2010

47. A unifying probabilistic framework for analyzing residual dipolar couplings

Author: Michael Nilges, Michael Habeck, Wolfgang Rieping, Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft, Max Planck Institute for Biological Cybernetics, Bioinformatique Structurale, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), University of Cambridge [UK] (CAM), Wolfgang Rieping thanks the European Molecular Biology Organisation for financial support., and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Models, Molecular, Rotation, MESH: Probability, MESH: Protein Structure, Secondary, Biomolecular structure, Nuclear Overhauser effect, Residual dipolar couplings, Crystallography, X-Ray, 010402 general chemistry, Residual, Inferential structure determination, 01 natural sciences, Biochemistry, Protein Structure, Secondary, Article, 03 medical and health sciences, Nuclear magnetic resonance, MESH: Rotation, Histogram, MESH: Nuclear Magnetic Resonance, Biomolecular, Statistical physics, Tensor, Nuclear Magnetic Resonance, Biomolecular, Spectroscopy, Probability, 030304 developmental biology, 0303 health sciences, Orientation (computer vision), Chemistry, MESH: Crystallography, X-Ray, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], MESH: Liquid Crystals, Liquid Crystals, 0104 chemical sciences, Markov chain Monte Carlo, Protein structure, NMR structure determination, Rotation (mathematics), Magnetic dipole–dipole interaction, MESH: Models, Molecular
Abstract: International audience; Residual dipolar couplings provide complementary information to the nuclear Overhauser effect measurements that are traditionally used in biomolecular structure determination by NMR. In a de novo structure determination, however, lack of knowledge about the degree and orientation of molecular alignment complicates the analysis of dipolar coupling data. We present a probabilistic framework for analyzing residual dipolar couplings and demonstrate that it is possible to estimate the atomic coordinates, the complete molecular alignment tensor, and the error of the couplings simultaneously. As a by-product, we also obtain estimates of the uncertainty in the coordinates and the alignment tensor. We show that our approach encompasses existing methods for determining the alignment tensor as special cases, including least squares estimation, histogram fitting, and elimination of an explicit alignment tensor in the restraint energy.
Published: 2008

48. Genomic analysis of Bartonella identifies type IV secretion systems as host adaptability factors

Author: Henri L Saenz, Günter Raddatz, Christoph Dehio, Muriel Vayssier-Taussat, Christa Lanz, Philipp Engel, Stephan C. Schuster, Michèle C Stoeckli, Richard J. Birtles, Université de Bâle, Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft, Max Planck Institute for Biological Cybernetics, Unité mixte de recherche biologie moléculaire et immunologie parasitaires et fongiques, Institut National de la Recherche Agronomique (INRA)-École nationale vétérinaire - Alfort (ENVA)-Agence Française de Sécurité Sanitaire des Aliments (AFSSA)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), University of Liverpool, Pennsylvania State University (Penn State), Penn State System, and Institut National de la Recherche Agronomique (INRA)-École nationale vétérinaire d'Alfort (ENVA)-Agence Française de Sécurité Sanitaire des Aliments (AFSSA)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)
Subjects: Bartonella, Lineage (genetic), Bartonella tribocorum, Virulence Factors, Molecular Sequence Data, HENSELAE, Genome, Evolution, Molecular, 03 medical and health sciences, TRANSPOSASE, Bartonella Infections, ERYTHROCYTES, HISTORY, Genetics, Animals, STRATEGY, NEGATIVE SELECTION, Phylogeny, 030304 developmental biology, Whole genome sequencing, SEQUENCE ALIGNMENT, 0303 health sciences, [SDV.GEN]Life Sciences [q-bio]/Genetics, Bartonella henselae, biology, Virulence, 030306 microbiology, Genomics, Sequence Analysis, DNA, biology.organism_classification, PATHOGEN BARTONELLA, Rats, GENUS BARTONELLA, Bartonella quintana, BACILLIFORMIS, bacteria, Bartonella bacilliformis, Genome, Bacterial
Abstract: International audience; The bacterial genus Bartonella comprises 21 pathogens causing characteristic intraerythrocytic infections. Bartonella bacilliformis is a severe pathogen representing an ancestral lineage, whereas the other species are benign pathogens that evolved by radial speciation. Here, we have used comparative and functional genomics to infer pathogenicity genes specific to the radiating lineage, and we suggest that these genes may have facilitated adaptation to the host environment. We determined the complete genome sequence of Bartonella tribocorum by shotgun sequencing and functionally identified 97 pathogenicity genes by signature-tagged mutagenesis. Eighty-one pathogenicity genes belong to the core genome ( 1,097 genes) of the radiating lineage inferred from genome comparison of B. tribocorum, Bartonella henselae and Bartonella quintana. Sixty-six pathogenicity genes are present in B. bacilliformis, and one has been lost by deletion. The 14 pathogenicity genes specific for the radiating lineage encode two laterally acquired type IV secretion systems, suggesting that these systems have a role in host adaptability.
Published: 2007

49. Probabilistic Structure Calculation

Author: Michael Nilges, Michael Habeck, Wolfgang Rieping, Bioinformatique Structurale, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Max Planck Institute for Biological Cybernetics, Max-Planck-Gesellschaft, Max Planck Institute for Developmental Biology, University of Cambridge [UK] (CAM), and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: Mathematical optimization, Computer science, General Chemical Engineering, Bayesian probability, Structure (category theory), Dihedral angle, 010402 general chemistry, Optimisation Mots-clés : théorème de Bayes, 01 natural sciences, 03 medical and health sciences, Probability theory, 0103 physical sciences, Nuisance parameter, Optimisation, Statistical physics, Sampling, 010306 general physics, Prior information, NOE, 030304 developmental biology, Physics, 0303 health sciences, Probabilistic logic, Experimental data, Bayes's theorem, General Chemistry, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Calculation methods, 0104 chemical sciences, Markov chain monte carlo algorithm, Data quality, Echantillonage
Abstract: International audience; AbstractMolecular structures are usually calculated from experimental data with some method of energy minimisation or non-linear optimisation. Key aims of a structure calculation are to estimate the coordinate uncertainty, and to provide a meaningful measure of the quality of the fit to the data. We discuss approaches to optimally combine prior information and experimental data and the connection to probability theory. We analyse the appropriate statistics for NOEs and NOE-derived distances, and the related question of restraint potentials. Finally, we will discuss approaches to determine the appropriate weight on the experimental evidence and to obtain in this way an estimate of the data quality from the structure calculation. Whereas objective estimates of coordinates and their uncertainties can only be obtained by a full Bayesian treatment of the problem, standard structure calculation methods continue to play an important role. To obtain the full benefit of these methods, they should be founded on a rigorous Bayesian analysis; RésuméPour calculer des structures moléculaires à partir des données expérimentales, on utilise habituellement une méthode de minimisation d'énergie, ou d'optimisation. Les objectifs majeurs d'un calcul de structure sont l'estimation de l'incertitude des coordonnées, et l'estimation d'une mesure de la qualité de l'ajustement aux données. Nous discutons des approches pour combiner d'une façon optimale l'information préalable et les données exprimentales, et le lien avec la théorie des probabilités. Nous analysons les statistiques appropriées pour les NOE et les distances dérivées, et les potentiels de contrainte. Finalement, nous discutons des approches pour un choix optimal du poids sur l'évidence expérimentale, pour obtenir de cette façon une évaluation de la qualité de données à partir du calcul de la structure. Des estimations objectives de coordonnées et de leurs incertitudes peuvent seulement être obtenues par un traitement completement bayésien du problème. Neanmoins, les méthodes standard de calcul de structure continuent à jouer un rôle important. Pour obtenir le plein avantage de ces méthodes, elles devraient être fondées sur une analyse Bayésienne rigoureuse.
Published: 2007

50. Interaction of LEAFY, AGAMOUS and TERMINAL FLOWER1 in maintaining floral meristem identity in Arabidopsis

Author: Detlef Weigel, François Parcy, Kirsten Bomblies, Plant Biology Laboratory, The Salk Institute for Biological Studies, Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Department of Molecular Biology, Max Planck Institute for Developmental Biology, and Max-Planck-Gesellschaft-Max-Planck-Gesellschaft
Subjects: 0106 biological sciences, MESH: AGAMOUS Protein, Arabidopsis, MESH: Mutation, Transcription, Genetic, Recombinant Fusion Proteins, Meristem, Arabidopsis, MESH: Arabidopsis Proteins, 01 natural sciences, AGAMOUS Protein, Arabidopsis, 03 medical and health sciences, Gene Expression Regulation, Plant, MESH: Recombinant Fusion Proteins, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, MESH: Arabidopsis, MESH: Gene Expression Regulation, Plant, Molecular Biology, Transcription factor, Leafy, Psychological repression, MESH: Meristem, Plant Proteins, 030304 developmental biology, Genetics, 0303 health sciences, biology, MESH: Plant Proteins, Arabidopsis Proteins, Agamous, MESH: Transcription, Genetic, fungi, MESH: Biological Markers, food and beverages, Herpes Simplex Virus Protein Vmw65, MESH: Transcription Factors, Plants, Genetically Modified, biology.organism_classification, Inflorescence, MESH: Plants, Genetically Modified, Mutation, MESH: Herpes Simplex Virus Protein Vmw65, Homeotic gene, Biomarkers, Transcription Factors, 010606 plant biology & botany, Developmental Biology
Abstract: The Arabidopsis transcription factor LEAFY acts upstream of homeotic genes such as AGAMOUS to confer floral identity on meristems that arise after the transition to reproductive development. Compared to the genetic circuitry regulating the establishment of floral meristem identity, little is known about its maintenance. Previous experiments with leafy heterozygous plants and agamous mutants grown in conditions that reduce the floral inductive stimulus have shown that both genes are required to prevent reversion of floral to inflorescence meristems. Here, we present evidence that LEAFY maintains floral meristem identity independently of AGAMOUS, and that the primary role of LEAFY is either direct repression of shoot identity genes or repression of an intermediate factor that activates shoot identity genes. The latter conclusions were deduced from the phenotypes conferred by a gain-of-function transgene, LEAFY:VP16, that appears to act as a dominant negative, or antimorphic, allele during maintenance of floral meristem identity. These observations contrast with previous findings that LEAFY acts as a direct activator of floral homeotic genes, supporting the hypothesis that the transcriptional activity of LEAFY is dependent on specific co-regulators.
Published: 2002

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