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1,765 results on '"Sainsbury Laboratory"'

1. DEK influences the trade-off between growth and 1 arrest via H2A.Z-nucleosomes in Arabidopsis

Author: Brestovitsky, Anna, Ezer, Daphne, Waidmann, Sascha, Maslen, Sarah, Balcerowicz, Martin, Cortijo, Sandra, Charoensawan, Varodom, Rhodes, Daniela, Jonak, Claudia, Wigge, Philip, Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), University of Natural Resources and Life Sciences (BOKU), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, 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), 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), Nanyang Technological University [Singapour], Sainsbury Laboratory Cambridge, University of Natural Resources and Applied Life Sciences (BOKU), 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), 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, 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: stomatognathic diseases, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics
Abstract: The decision of whether to grow and proliferate or to restrict growth and develop resilience to stress is a key biological trade-off. In plants, constitutive growth results in increased sensitivity to environmental stress1,2. The underlying mechanisms controlling this decision are however not well understood. We used temperature as a cue to discover regulators of this process in plants, as it both enhances growth and development rates within a specific range and is also a stress at extremes. We found that the conserved chromatin-associated protein DEK plays a central role in balancing the response between growth and arrest in Arabidopsis, and it does this via H2A.Z-nucleosomes. DEK target genes show two distinct categories of chromatin architecture based on the distribution of H2A.Z in +1 nucleosome and gene body, and these predict induction or repression by DEK. We show that these chromatin signatures of DEK target genes are conserved in human cells, suggesting that DEK may act through an evolutionarily conserved mechanism to control the balance between growth and arrest in plants and animals.
Published: 2020

2. The Rust Fungus Melampsora larici-populina Expresses a Conserved Genetic Program and Distinct Sets of Secreted Protein Genes During Infection of Its Two Host Plants, Larch and Poplar

Author: Sébastien Duplessis, Arnaud Hecker, Jérémy Pétrowski, Stéphane Hacquard, Clemence Marchal, Cécile Lorrain, Pascal Frey, Benjamin Petre, Christine Delaruelle, Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), The Sainsbury Laboratory (TSL), Agence Nationale de la Recherche, Lab of Excellence ARBRE (Advanced Research on the Biology of FoRest Ecosystem) ANR-11-LABX-0002-01, Sainsbury Laboratory Cambridge, University of Cambridge [UK] (CAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), and The Sainsbury Laboratory [Norwich] (TSL)
Subjects: 0106 biological sciences, 0301 basic medicine, Pharmacogenomic Variants, rouille du peuplier, Physiology, [SDV]Life Sciences [q-bio], Rust (fungus), Larix, populus, champignon pathogène, 01 natural sciences, Host Specificity, COLONIZATION, Fungal Proteins, 03 medical and health sciences, mélèze, larch, Gene Expression Regulation, Fungal, CANDIDATE EFFECTORS, Heteroecious, Gene family, fungal pathogen, Gene, Plant Diseases, 030304 developmental biology, Genetics, 0303 health sciences, biology, Host (biology), Basidiomycota, food and beverages, General Medicine, Melampsora, biology.organism_classification, EVOLUTION, TRANSCRIPTOME ANALYSIS, Sexual reproduction, melampsora larici populina, 030104 developmental biology, BIOTROPHY, PATTERNS, Larch, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: SummaryMechanims required for broad spectrum or specific host colonization of plant parasites are poorly understood. As a perfect illustration, heteroecious rust fungi require two alternate host plants to complete their life cycle. Melampsora larici-populina infects two taxonomically unrelated plants, larch on which sexual reproduction is achieved and poplar on which clonal multiplication occurs leading to severe epidemics in plantations. High-depth RNA sequencing was applied to three key developmental stages of M. larici-populina infection on larch: basidia, pycnia and aecia. Comparative transcriptomics of infection on poplar and larch hosts was performed using available expression data. Secreted protein was the only significantly over-represented category among differentially expressed M. larici-populina genes in basidia, pycnia and aecia compared together, highlighting their probable involvement in the infection process. Comparison of fungal transcriptomes in larch and poplar revealed a majority of rust genes commonly expressed on the two hosts and a fraction exhibiting a host-specific expression. More particularly, gene families encoding small secreted proteins presented striking expression profiles that highlight probable candidate effectors specialized on each host. Our results bring valuable new information about the biological cycle of rust fungi and identify genes that may contribute to host specificity.
Published: 2018

3. Genomics analysis of Aphanomyces spp. identifies a new class of oomycete effector associated with host adaptation

Author: Gaulin, Elodie, Pel, Michiel, Camborde, Laurent, San Clemente, Hélène, Courbier, Sarah, Dupouy, Marie-Alexane, Lengellé, Julie, Veyssière, Marine, Le Ru, Aurélie, Grandjean, Frédéric, Cordaux, Richard, Moumen, Bouziane, Gilbert, Clément, Cano, Liliana, Aury, Jean-Marc, Guy, Julie, Wincker, Patrick, Bouchez, Olivier, Klopp, Christophe, Dumas, Bernard, Laboratoire de Recherche en Sciences Végétales (LRSV), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut Jacques Monod (IJM (UMR_7592)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Surfaces Cellulaires et Signalisation chez les Végétaux (SCSV), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Plateforme Imagerie Microscopie, Fédération de Recherche FR3450, Ecologie, Evolution, Symbiose (EES), Ecologie et biologie des interactions (EBI), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS)-Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), The Sainsbury Laboratory (TSL), Génomique métabolique (UMR 8030), 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)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire de Génétique Cellulaire (LGC), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Système d'Information des GENomes des Animaux d'Elevage (SIGENAE), Institut National de la Recherche Agronomique (INRA), HEC Paris - Recherche - Hors Laboratoire, Ecole des Hautes Etudes Commerciales (HEC Paris), Interactions Microbiennes dans la Rhizosphère et les Racines, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Utrecht University [Utrecht], Évolution, génomes, comportement et écologie (EGCE), Centre National de la Recherche Scientifique (CNRS)-IRD-Université Paris-Sud - Paris 11 (UP11), The Sainsbury Laboratory [Norwich] (TSL), University of Florida [Gainesville] (UF), Université de Toulouse, INRA, CNRS, Castanet-Tolosan, Sigenae, Projet IBISA-Genoscope APHANO-GP: AP09/10-n°19 ANR-12-JSV6-0004-01, Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Plateforme TRI FR-AIB, Fédération de Recherche Agrobiosciences, Interactions et Biodiversité (FR AIB), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Toulouse Réseau Imagerie-Genotoul ( TRI-Genotoul), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Paris-Sud - Paris 11 (UP11)-IRD-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-12-JSV6-0004,APHANO-Effect,Analyse génomique d'une nouvelle famille d'effecteurs d'oomycètes transloqués dans les cellules végétales: rôle dans l'adaptation à l'hôte et la pathogénie chez le parasite racinaire de légumineuses Aphanomyces euteiches(2012), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Laboratoire Evolution, Génomes, Comportement, Ecologie, CNRS/Université Paris-Sud UMR9191, IRD UMR247, Université Paris-Sud - Paris 11 (UP11), and University of Florida [Gainesville]
Subjects: Aphanomyces, Oomycete, Effector, Secretome, Host adaptation, SSP, POTATO FAMINE PATHOGEN, DIFFERENTIAL EXPRESSION ANALYSIS, FILAMENTOUS PLANT-PATHOGENS, CRAYFISH PLAGUE PATHOGEN, MEDICAGO-TRUNCATULA, PARTIAL RESISTANCE, ROOT-ROT, PHYTOPHTHORA-CAPSICI, IMMUNE-RESPONSE, UNITED-STATES, Acclimatization, [SDV]Life Sciences [q-bio], Animals, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, lcsh:QH301-705.5, ComputingMilieux_MISCELLANEOUS, Plant Diseases, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, fungi, food and beverages, Genomics, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, lcsh:Biology (General), Oomycetes, Research Article
Abstract: Background Oomycetes are a group of filamentous eukaryotic microorganisms that have colonized all terrestrial and oceanic ecosystems, and they include prominent plant pathogens. The Aphanomyces genus is unique in its ability to infect both plant and animal species, and as such exemplifies oomycete versatility in adapting to different hosts and environments. Dissecting the underpinnings of oomycete diversity provides insights into their specificity and pathogenic mechanisms. Results By carrying out genomic analyses of the plant pathogen A. euteiches and the crustacean pathogen A. astaci, we show that host specialization is correlated with specialized secretomes that are adapted to the deconstruction of the plant cell wall in A. euteiches and protein degradation in A. astaci. The A. euteiches genome is characterized by a large repertoire of small secreted protein (SSP)-encoding genes that are highly induced during plant infection, and are not detected in other oomycetes. Functional analysis revealed an SSP from A. euteiches containing a predicted nuclear-localization signal which shuttles to the plant nucleus and increases plant susceptibility to infection. Conclusion Collectively, our results show that Aphanomyces host adaptation is associated with evolution of specialized secretomes and identify SSPs as a new class of putative oomycete effectors. Electronic supplementary material The online version of this article (10.1186/s12915-018-0508-5) contains supplementary material, which is available to authorized users.
Published: 2018

4. Callose-Regulated Symplastic Communication Coordinates Symbiotic Root Nodule Development

Author: Gaudioso-Pedraza, R, Beck, M, Frances, L, Kirk, P, Ripodas, C, Niebel, A, Oldroyd, GED, Benitez-Alfonso, Y, de Carvalho-Niebel, F, Centre for Plant Sciences [Leeds], University of Leeds-Faculty of Biological Sciences-Institute of Integrative and Comparative Biology, Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Sainsbury Laboratory Cambridge, University of Cambridge [UK] (CAM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Sainsbury Laboratory Cambridge University (SLCU), Leeds University : 110 French Laboratoire d'Excellence (Labex) TULIP post-doctoral grant 'Young Scientists for the Future', AgreenSkills fellowship : 2013609398, BBSRC DTP : BB/M011151/1, Royal Society, EPSRC : EF/M027740/1, Leverhulme Trust : RPG-2016-136, ANR COME-IN grant : ANR-14-CE35-0007-01, TULIP grant : ANR-10-LABX-41, and European Project: 609398,EC:FP7:PEOPLE,FP7-PEOPLE-2013-COFUND,AGREENSKILLSPLUS(2014)
Subjects: [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract: International audience; The formation of nitrogen-fixing nodules in legumes involves the initiation of synchronized programs in the root epidermis and cortex to allow rhizobial infection and nodule development. In this study, we provide evidence that symplastic communication, regulated by callose turnover at plasmodesmata (PD), is important for coordinating nodule development and infection in Medicago truncatula. Here, we show that rhizobia promote a reduction in callose levels in inner tissues where nodules initiate. This downregulation coincides with the localized expression of M. truncatula beta-1,3-glucanase 2 (MtBG2), encoding a novel PD-associated callose-degrading enzyme. Spatiotemporal analyses revealed that MtBG2 expression expands from dividing nodule initials to rhizobia-colonized cortical and epidermal tissues. As shown by the transport of fluorescent molecules in vivo, symplastic-connected domains are created in rhizobia-colonized tissues and enhanced in roots constitutively expressing MtBG2. MtBG2-overexpressing roots additionally displayed reduced levels of PD-associated callose. Together, these findings suggest an active role for MtBG2 in callose degradation and in the formation of symplastic domains during sequential nodule developmental stages. Interfering with symplastic connectivity led to drastic nodulation phenotypes. Roots ectopically expressing beta-1,3-glucanases (including MtBG2) exhibited increased nodule number, and those expressing MtBG2 RNAi constructs or a hyperactive callose synthase (under symbiotic promoters) showed defective nodulation phenotypes. Obstructing symplastic connectivity appears to block a signaling pathway required for the expression of NODULE INCEPTION (NIN) and its target NUCLEAR FACTOR-YA1 (NF-YA1) in the cortex. We conclude that symplastic intercellular communication is proactively enhanced by rhizobia, and this is necessary for appropriate coordination of bacterial infection and nodule development.
Published: 2018

5. Lipo‐chitooligosaccharides promote lateral root formation and modify auxin homeostasis in Brachypodium distachyon

Author: Fabienne Maillet, Benoit Lefebvre, Luis Buendia, Devin O'Connor, Sandra Bensmihen, Quitterie van de-Kerkhove, Saïda Danoun, Clare Gough, Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Sainsbury Laboratory Cambridge, University of Cambridge [UK] (CAM), Laboratoire de Recherche en Sciences Végétales (LRSV), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Sainsbury Laboratory Cambridge University (SLCU), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), INRA/SPE project 'LCAux', French 'Ministere de l'Enseignement Superieur et de la Recherche', ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), and ANR-16-CE20-0025,WHEATSYM,ROLES DES SIGNAUX MICROBIENS LCO/CO ET DE LEURS RECEPTEURS DE PLANTES DANS DES INTERACTIONS BENEFIQUES ENTRE MONOCOTYLEDONES ET MICROORGANISMES DU SOL(2016)
Subjects: 0106 biological sciences, 0301 basic medicine, Indoles, hormone homeostasis, Physiology, Oligosaccharides, lateral root primordia, Chitin, Endogeny, Plant Science, root architecture, indole-3-butyric acid (IBA), Models, Biological, Plant Roots, 01 natural sciences, Fluorescence, 03 medical and health sciences, lipochitooligosaccharide (LCO), Auxin, Nod factors, Homeostasis, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, heterocyclic compounds, Gene, Lateral root formation, ComputingMilieux_MISCELLANEOUS, chemistry.chemical_classification, Chitosan, Indoleacetic Acids, biology, Auxin homeostasis, Chemistry, fungi, food and beverages, biology.organism_classification, Lipids, Medicago truncatula, Cell biology, auxin dosage, 030104 developmental biology, Brachypodium, Brachypodium distachyon, symbiotic signal, Signal Transduction, 010606 plant biology & botany
Abstract: International audience; . Lipo-chitooligosaccharides (LCOs) are microbial symbiotic signals that also influence root growth. In Medicago truncatula, LCOs stimulate lateral root formation (LRF) synergistically with auxin. However, the molecular mechanisms of this phenomenon and whether it is restricted to legume plants are not known. . We have addressed the capacity of the model monocot Brachypodium distachyon (Brachypodium) to respond to LCOs and auxin for LRF. For this, we used a combination of root phenotyping assays, live-imaging and auxin quantification, and analysed the regulation of auxin homeostasis genes. We show that LCOs and a low dose of the auxin precursor indole-3-butyric acid (IBA) stimulated LRF in Brachypodium, while a combination of LCOs and IBA led to different regulations. Both LCO and IBA treatments locally increased endogenous indole-3-acetic acid (IAA) content, whereas the combination of LCO and IBA locally increased the endogenous concentration of a conjugated form of IAA (IAA-Ala). LCOs, IBA and the combination differentially controlled expression of auxin homeostasis genes. . These results demonstrate that LCOs are active on Brachypodium roots and stimulate LRF probably through regulation of auxin homeostasis. The interaction between LCO and auxin treatments observed in Brachypodium on root architecture opens interesting avenues regarding their possible combined effects during the arbuscular mycorrhizal symbiosis.
Published: 2018

6. The Fourteenth Data Release of the Sloan Digital Sky Survey:First Spectroscopic Data from the Extended Baryon Oscillation Spectroscopic Survey and from the Second Phase of the Apache Point Observatory Galactic Evolution Experiment

Author: Abolfathi , Bela, Aguado , D. S., Aguilar , Gabriela, Prieto , Carlos Allende, Almeida , Andres, Ananna , Tonima Tasnim, Anders , Friedrich, Anderson , Scott F., Andrews , Brett H., Anguiano , Borja, Aragon-Salamanca , Alfonso, Argudo-Fernandez , Maria, Armengaud , Eric, Ata , Metin, Aubourg , Eric, Avila-Reese , Vladimir, Badenes , Carles, Bailey , Stephen, Balland , Christophe, Barger , Kathleen A., Barrera-Ballesteros , Jorge, Bartosz , Curtis, Bastien , Fabienne, Bates , Dominic, Baumgarten , Falk, Bautista , Julian, Beaton , Rachael, Beers , Timothy C., Belfiore , Francesco, Bender , Chad F., Bernardi , Mariangela, Bershady , Matthew A., Beutler , Florian, Bird , Jonathan C., Bizyaev , Dmitry, Blanc , Guillermo A., Blanton , Michael R., Blomqvist , Michael, Bolton , Adam S., Boquien , Médéric, Borissova , Jura, Bovy , Jo, Diaz , Christian Andres Bradna, Brandt , William Nielsen, Brinkmann , Jonathan, Brownstein , Joel R., Bundy , Kevin, Burgasser , Adam J., Burtin , Etienne, Busca , Nicolás G., Canas , Caleb I., Cano-Diaz , Mariana, Cappellari , Michele, Carrera , Ricardo, Casey , Andrew R., Sodi , Bernardo Cervantes, Chen , Yanping, Cherinka , Brian, Chiappini , Cristina, Choi , Peter Doohyun, Chojnowski , Drew, Chuang , Chia-Hsun, Chung , Haeun, Clerc , Nicolas, Cohen , Roger E., Comerford , Julia M., Comparat , Johan, Nascimento , Janaina Correa do, da Costa , Luiz, Cousinou , Marie-Claude, Covey , Kevin, Crane , Jeffrey d., Cruz-Gonzalez , Irene, Cunha , Katia, Ilha , Gabriele da Silva, Damke , Guillermo J., Darling , Jeremy, Davidson Jr. , James W., Dawson , Kyle, Lizaola , Miguel Angel C. de Icaza, de la Macorra , Axel, De La Torre , Sylvain, De Lee , Nathan, Agathe , Victoria de Sainte, Machado , Alice Deconto, Dell'Agli , Flavia, Delubac , Timothée, Diamond-Stanic , Aleksandar M., Donor , John, Downes , Juan Jose, Drory , Niv, Bourboux , Hélion du Mas des, Duckworth , Christopher J., Dwelly , Tom, Dyer , Jamie, Ebelke , Garrett, Eigenbrot , Arthur Davis, Eisenstein , Daniel J., Elsworth , Yvonne P., Emsellem , Eric, Eracleous , Mike, Erfanianfar , Ghazaleh, Escoffier , Stéphanie, Fan , Xiaohui, Alvar , Emma Fernandez, Fernandez-Trincado , J. G., Cirolini , Rafael Fernando, Feuillet , Diane, Finoguenov , Alexis, Fleming , Scott W., Font-Ribera , Andreu, Freischlad , Gordon, Frinchaboy , Peter, Fu , Hai, Chew , Yilen Gomez Maqueo, Galbany , Lluis, Perez , Ana E. Garcia, Garcia-Dias , R., García-Hernández , D. A., Oehmichen , Luis Alberto Garma, Gaulme , Patrick, Gelfand , Joseph, Gil-Marin , Hector, Gillespie , Bruce A., Goddard , Daniel, Hernandez , Jonay I. Gonzalez, Gonzalez-Perez , Violeta, Grabowski , Kathleen, Green , Paul J., Grier , Catherine J., Gueguen , Alain, Guo , Hong, Guy , Julien, Hagen , Alex, Hall , Patrick, Harding , Paul, Hasselquist , Sten, Hawley , Suzanne, Hayes , Christian R., Hearty , Fred, Hekker , Saskia, Hernández , Jesús, Toledo , Hector Hernandez, Hogg , David W., Holley-Bockelmann , Kelly, Holtzman , Jon, Hou , Jiamin, Hsieh , Bau-Ching, Hunt , Jason A. S., Hutchinson , Timothy A., Hwang , Ho Seong, Angel , Camilo Eduardo Jimenez, Johnson , Jennifer A., Jones , Amy, Jönsson , Henrik, Jullo , Eric, Khan , Fahim Sakil, Kinemuchi , Karen, Kirkby , David, Kirkpatrick IV , Charles C., Kitaura , Francisco-Shu, Knapp , Gillian R., Kneib , Jean-Paul, Kollmeier , Juna A., Lacerna , Ivan, Lane , Richard R., Lang , Dustin, Law , David R., Goff , Jean-Marc Le, Lee , Young-Bae, Li , Hongyu, Li , Cheng, Lian , Jianhui, Liang , Yu, Lima , Marcos, Lin , Lihwai, Long , Dan, Lucatello , Sara, Lundgren , Britt, Mackereth , J. Ted, MacLeod , Chelsea L., Mahadevan , Suvrath, Maia , Marcio Antonio Geimba, Majewski , Steven, Manchado , Arturo, Maraston , Claudia, Mariappan , Vivek, Marques-Chaves , Rui, Masseron , Thomas, Masters , Karen L., Mcdermid , Richard M., McGreer , Ian D., Melendez , Matthew, Meneses-Goytia , Sofia, Merloni , Andrea, Merrifield , Michael R., Meszaros , Szabolcs, Meza , Andres, Minchev , Ivan, Minniti , Dante, Prieto , Carlos, Ananna , Tonima, Anderson , Scott, Andrews , Brett, Aragón-Salamanca , Alfonso, Argudo-Fernández , Maria, Barger , Kathleen, Beers , Timothy, Bender , Chad, Bershady , Matthew, Bird , Jonathan, Blanc , Guillermo, Blanton , Michael, Bolton , Adam, Andres , Christian, Diaz , Bradna, Brandt , William, Brownstein , Joel, Burgasser , Adam, Busca , Nicolás, Cañas , Caleb, Cano-Díaz , Mariana, Casey , Andrew, Sodi , Bernardo, Choi , Peter, 10 , Davidson, Angel , Miguel, De Icaza Lizaola , C, De Sainte , Victoria, 72 , Agathe, Machado , Alice, Dell 'agli , Flavia, Diamond-Stanic , Aleksandar, Downes , Juan, du Mas des Bourboux , Hélion, Duckworth , Christopher, Davis Eigenbrot , Arthur, Eisenstein , Daniel, Elsworth , Yvonne, Fernández Alvar , Emma, Fernández-Trincado , J., Cirolini , Rafael, Fleming , Scott, Gómez , Yilen, Chew , Maqueo, Galbany , Lluís, García Pérez , Ana, Alberto , Luis, Oehmichen , Garma, Gil-Marín , Héctor, Gillespie , Bruce, González Hernández , Jonay, Green , Paul, Grier , Catherine, Hayes , Christian, Toledo , Hector, Hogg , David, Hunt , Jason, Hutchinson , Timothy, Hwang , Ho, Jimenez Angel , Camilo, Johnson , Jennifer, Fahim , Sakil, Kirkpatrick , Charles, 94 , Iv, Knapp , Gillian, Kollmeier , Juna, Lane , Richard, Law , DAvid, Le Goff , Jean-Marc, Macleod , Chelsea, Antonio , Marcio, Maia , Geimba, Masters , Karen, Mueller , Eva-Maria, Muller-Sanchez , Francisco, Muna , Demitri, Muñoz , Ricardo, Myers , Adam, Nair , Preethi, Nandra , Kirpal, Ness , Melissa, Newman , Jeffrey, Nichol , Robert, Nidever , David, Nitschelm , Christian, Noterdaeme , Pasquier, O 'connell , Julia, Oelkers , Ryan, Oravetz , Audrey, Oravetz , Daniel, Aquino Ortíz , Erik, Osorio , Yeisson, Pace , Zach, Padilla , Nelson, Palanque-Delabrouille , Nathalie, Palicio , Pedro, Pan , Hsi-An, Pan , Kaike, Parikh , Taniya, Pâris , Isabelle, Park , Changbom, Peirani , Sebastien, Pellejero-Ibanez , Marcos, Penny , Samantha, Percival , Will, Perez-Fournon , Ismael, Petitjean , Patrick, Pieri , Matthew, Pinsonneault , Marc, Pisani , Alice, Prada , Francisco, Prakash , Abhishek, Bárbara De Andrade Queiroz , Anna, Raddick , M, Raichoor , Anand, Rembold , Sandro, Richstein , Hannah, Riffel , Rogemar, Riffel , Rogério, Rix , Hans-Walter, Robin , Annie, Torres , Sergio, Román-Zúñiga , Carlos, Ross , Ashley, Rossi , Graziano, Ruan , John, Ruggeri , Rossana, Ruiz , Jose, Salvato , Mara, Sánchez , Ariel, Sanchez , Sebastian, Sanchez Almeida , Jorge, Sánchez-Gallego , José, Antonio , Felipe, Rojas , Santana, Santiago , Basílio, Schiavon , Ricardo, Schimoia , Jaderson, Schlafly , Edward, Schlegel , David, Schneider , Donald, Schuster , William, Schwope , Axel, Seo , Hee-Jong, Serenelli , Aldo, Shen , Shiyin, Shen , Yue, Shetrone , Matthew, Shull , Michael, Aguirre , Silva, Simon , Joshua, Skrutskie , Mike, Slosar , Anže, Smethurst , Rebecca, Smith , Verne, Sobeck , Jennifer, Somers , Garrett, Souter , Barbara, Souto , Diogo, Spindler , Ashley, Stark , David, Stassun , Keivan, Steinmetz , Matthias, Stello , Dennis, Storchi-Bergmann , Thaisa, Streblyanska , Alina, Stringfellow , Guy, Suárez , Genaro, Sun , Jing, Szigeti , Laszlo, Taghizadeh-Popp , Manuchehr, talbot , michael, Tang , Baitian, Tao , Charling, Tayar , Jamie, Tembe , Mita, Teske , Johanna, Aniruddha R. , Thakar, Daniel , Thomas, Tissera , Patricia, Tojeiro , Rita, Tremonti , Christy, Troup , Nicholas W., Urry , Meg, Valenzuela , O., van den Bosch , Remco, Vargas-González , Jaime, Magaña , Mariana Vargas, Vazquez , Jose Alberto, Villanova , Sandro, Vogt , Nicole, Wake , David, Wang , Yuting, Weaver , Benjamin Alan, Weijmans , Anne-Marie, Weinberg , David H., Westfall , Kyle B., Whelan , David G., Wilcots , Eric, Wild , Vivienne, Williams , Rob A., Wilson , John, Wood-Vasey , W.M., Wylezalek , Dominika, Xiao , Ting, Yan , Renbin, Yang , Meng, Ybarra , Jason E., Yèche , Christophe, Zakamska , Nadia, Zamora , Olga, Zarrouk , Pauline, Zasowski , Gail, Zhang , Kai, Zhao , Chang, Zhao , Gong-Bo, Zheng , Zheng, Zhou , Zhi-Min, Zhu , Guangtun, Zinn , Joel C., Zou , Hu, AstroParticule et Cosmologie (APC (UMR_7164)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Department of Astrophysical Sciences [Princeton], Princeton University, Laboratoire de Physique Nucléaire et de Hautes Énergies (LPNHE (UMR_7585)), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université Paris Diderot - Paris 7 (UPD7)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Department of Astronomy and Astrophysics [PennState], Pennsylvania State University (Penn State), Penn State System-Penn State System, Université Paris Diderot - Paris 7 (UPD7), Department of Physics and Astronomy [Philadelphia], University of Pennsylvania, Laboratoire d'Astrophysique de Marseille (LAM), Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS), Astrophysique Interprétation Modélisation (AIM (UMR7158 / UMR_E_9005 / UM_112)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), California Institute of Technology (CALTECH), Institut de Recherches sur les lois Fondamentales de l'Univers (IRFU), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Sub-department of Astrophysics [Oxford], Department of Physics [Oxford], University of Oxford-University of Oxford, Centre de Physique des Particules de Marseille (CPPM), Aix Marseille Université (AMU)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Département de Physique des Particules (ex SPP) (DPhP), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, European Southern Observatory (ESO), Univers, Transport, Interfaces, Nanostructures, Atmosphère et environnement, Molécules (UMR 6213) (UTINAM), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Max-Planck-Institut für Astronomie (MPIA), Max-Planck-Gesellschaft, Department of Physics and Astronomy [Irvine], University of California [Irvine] (UC Irvine), University of California (UC)-University of California (UC), Laboratoire d'études spatiales et d'instrumentation en astrophysique (LESIA (UMR_8109)), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Departamento de Matemáticas [Madrid], Universidad Autónoma de Madrid (UAM), Department of Physics and Astronomy [Nashville], Vanderbilt University [Nashville], Korea Institute for Advanced Study (KIAS), Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), Wuhan University [China], Equipe de Recherche sur l’Utilisation des Données Individuelles en lien avec la Théorie Economique (ERUDITE), Université Paris-Est Marne-la-Vallée (UPEM)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Institute of Astronomy [Cambridge], Max-Planck-Institut für Astrophysik (MPA), Department of Physics and Astronomy [Rochester], University of Rochester [USA], Institut d'Astrophysique de Paris (IAP), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Inflammation, Tissus épithéliaux et Cytokines (LITEC), Université de Poitiers, Recherches Epistémologiques et Historiques sur les Sciences Exactes et les Institutions Scientifiques (REHSEIS (UMR_7596)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Galaxies, Etoiles, Physique, Instrumentation (GEPI), Laboratoire d'astrophysique de l'observatoire de Besançon (UMR 6091) (LAOB), Universidad Politécnica de Madrid (UPM), Universidad de Jaén (UJA), Institute of Space Sciences [Barcelona] (ICE-CSIC), Spanish National Research Council [Madrid] (CSIC), University of Edinburgh, Stellar Astrophysics Centre [Aarhus] (SAC), Aarhus University [Aarhus], Alfred P. Sloan Foundation, Department of Energy (US), University of Utah, AVL, AstroParticule et Cosmologie ( APC - UMR 7164 ), Centre National de la Recherche Scientifique ( CNRS ) -Institut National de Physique Nucléaire et de Physique des Particules du CNRS ( IN2P3 ) -Observatoire de Paris-Université Paris Diderot - Paris 7 ( UPD7 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), Institut d'astrophysique spatiale ( IAS ), Université Paris-Sud - Paris 11 ( UP11 ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Centre National de la Recherche Scientifique ( CNRS ), Department of Astronomy and Astrophysics ( PENNSYLVANIA STATE UNIVERSITY ), PennState University [Pennsylvania] ( PSU ), Université Paris Diderot - Paris 7 ( UPD7 ), University of Pennsylvania [Philadelphia], Laboratoire d'Astrophysique de Marseille ( LAM ), Centre National de la Recherche Scientifique ( CNRS ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Aix Marseille Université ( AMU ) -Centre National d'Etudes Spatiales ( CNES ), Astrophysique Interactions Multi-échelles ( AIM - UMR 7158 - UMR E 9005 ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Paris Diderot - Paris 7 ( UPD7 ), California Institute of Technology ( CALTECH ), Institut de Recherches sur les lois Fondamentales de l'Univers ( IRFU ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay, University of Oxford [Oxford]-University of Oxford [Oxford], Imaging Diagnostic Center, Nanfang Hospital Guangzhou, Departamento de FisicaTeorica e IFT-UAM/CSIC, Universidad Autonoma de Madrid ( UAM ), Centre de Physique des Particules de Marseille ( CPPM ), Centre National de la Recherche Scientifique ( CNRS ) -Institut National de Physique Nucléaire et de Physique des Particules du CNRS ( IN2P3 ) -Aix Marseille Université ( AMU ), Carnegie Institution of Washington, AUTRES, Département de Physique des Particules (ex SPP) ( DPP ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay, School of Physics and Astronomy, University of Birmingham [Birmingham], European Southern Observatory ( ESO ), Département de Physique Nucléaire (ex SPhN) ( DPHN ), Univers, Transport, Interfaces, Nanostructures, Atmosphère et environnement, Molécules ( UTINAM ), Institut national des sciences de l'Univers ( INSU - CNRS ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ), Max-Planck-Institut für Astronomie ( MPIA ), STScI, University of California [Irvine] ( UCI ), ISO Data Centre ( ESA - Espagne ), European Space Agency ( ESA ), Laboratoire d'études spatiales et d'instrumentation en astrophysique ( LESIA ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Observatoire de Paris-Université Paris Diderot - Paris 7 ( UPD7 ) -Centre National de la Recherche Scientifique ( CNRS ), Institut Lagrange de Paris, Sorbonne Universités, Research Institute of Forest Resource Information Techniques, Chinese Academy of Forestry, Laboratoire de Physique Nucléaire et de Hautes Énergies ( LPNHE ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut National de Physique Nucléaire et de Physique des Particules du CNRS ( IN2P3 ) -Université Paris Diderot - Paris 7 ( UPD7 ) -Centre National de la Recherche Scientifique ( CNRS ), Korea Institute for Advanced Study ( KIAS ), Department of Astronomy ( Ohio State University ), Ohio State University [Columbus] ( OSU ), Institute of Infection, Immunity & Inflammation, University of Glasgow, Sainsbury Laboratory Cambridge, University of Cambridge [UK] ( CAM ), Equipe de Recherche sur l’Utilisation des Données Individuelles en lien avec la Théorie Economique ( ERUDITE ), Université Paris-Est Créteil Val-de-Marne - Paris 12 ( UPEC UP12 ) -Université Paris-Est Marne-la-Vallée ( UPEM ), Institute of Physics, Universidade de Brasilia [Brasília] ( UnB ), Department of Chemical and Biomolecular Engineering, University of California [Berkeley], Max-Planck-Institut für Astrophysik ( MPA ), Bioinformatics and Functional Genomics Research Group, Cancer Research Center (IBMCC-CIC, CSIC-USAL), University of Wisconsin-Madison [Madison], Texas Tech University Health Sciences Center, Texas Tech University [Lubbock] ( TTU ), Institute for Astronomy ( IfA ), University of Hawaii, Research Institute of Organic Agriculture ( FiBL ), Dept. of Physics, Princess Margaret Hospital, University of Toronto-Princess Margaret Hospital, J. A. Baker Institute, Cornell University, The Observatories of the Carnegie Institution for Science, Economics, Bangor, Physics Department, Carnegie Mellon University [Pittsburgh] ( CMU ), Institut d'Astrophysique de Paris ( IAP ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire Inflammation, Tissus épithéliaux et Cytokines ( LITEC ), School of Physics, Korea Institute for Advanced Study, Korea Institute for Advanced Study-Korea Institute for Advanced Study, Recherches Epistémologiques et Historiques sur les Sciences Exactes et les Institutions Scientifiques ( REHSEIS ), Université Paris Diderot - Paris 7 ( UPD7 ) -Centre National de la Recherche Scientifique ( CNRS ), Galaxies, Etoiles, Physique, Instrumentation ( GEPI ), Institut national des sciences de l'Univers ( INSU - CNRS ) -Observatoire de Paris-Université Paris Diderot - Paris 7 ( UPD7 ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire d'astrophysique de l'observatoire de Besançon ( LAOB ), Universidad Politécnica de Madrid ( UPM ), Universidad de Jaén ( UJA ), Institute of Space Sciences [Barcelona] ( ICE-CSIC ), Spanish National Research Council [Madrid] ( CSIC ), Department of Physics and Astronomy - Stellar Astrophysics Centre, Department of Physics, The Leverhulme Trust, University of St Andrews. School of Physics and Astronomy, University of St Andrews. Centre for Contemporary Art, Astrophysique Interprétation Modélisation (AIM (UMR_7158 / UMR_E_9005 / UM_112)), Département de Physique des Particules (ex SPP) (DPP), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Observatoire de Paris, PSL Research University (PSL)-PSL Research University (PSL)-Université Paris Diderot - Paris 7 (UPD7), Institut d'astrophysique spatiale (IAS), Université Paris-Sud - Paris 11 (UP11)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Aix Marseille Université (AMU)-Centre National d'Études Spatiales [Toulouse] (CNES), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7), Universidad Autonoma de Madrid (UAM), Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Aix Marseille Université (AMU), Université de Franche-Comté (UFC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS), University of California [Irvine] (UCI), University of California-University of California, ISO Data Centre (ESA - Espagne), European Space Agency (ESA), PSL Research University (PSL)-PSL Research University (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique Nucléaire et de Hautes Énergies (LPNHE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Department of Astronomy (Ohio State University), Ohio State University [Columbus] (OSU), Universidade de Brasilia [Brasília] (UnB), University of Wisconsin-Madison, Texas Tech University [Lubbock] (TTU), Institute for Astronomy [Honolulu] (IfA), University of Hawai'i [Honolulu] (UH), Research Institute of Organic Agriculture (FiBL), University of Toronto, Bangor University, Carnegie Mellon University [Pittsburgh] (CMU), Recherches Epistémologiques et Historiques sur les Sciences Exactes et les Institutions Scientifiques (REHSEIS), PSL Research University (PSL)-PSL Research University (PSL)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'astrophysique de l'observatoire de Besançon (LAOB), Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3), Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS), Sorbonne Université (SU), Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université Pierre et Marie Curie - Paris 6 (UPMC), Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Université Paris-Est Marne-la-Vallée (UPEM), Research Institute of Organic Agriculture - Forschungsinstitut für biologischen Landbau (FiBL), Cornell University [New York], Carnegie Observatories, Carnegie Institution for Science [Washington], 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)-Université Paris Diderot - Paris 7 (UPD7), PSL Research University (PSL)-PSL Research University (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Observatoire de Paris, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)
Subjects: Astrophysics, E-SCIENCE, 01 natural sciences, HISTORIES, TARGET SELECTION, Observatory, QB Astronomy, 010303 astronomy & astrophysics, R2C, QC, media_common, QB, Physics, CATALOGS, Point (typography), ~DC~, Astrophysics::Instrumentation and Methods for Astrophysics, 520 Astronomie und zugeordnete Wissenschaften, atlases, GALAXIES, X-RAY SURVEYS, BDC, Astrophysics - Instrumentation and Methods for Astrophysics, METALLICITY, [PHYS.ASTR.IM]Physics [physics]/Astrophysics [astro-ph]/Instrumentation and Methods for Astrophysic [astro-ph.IM], TELESCOPE, media_common.quotation_subject, astro-ph.GA, Phase (waves), FOS: Physical sciences, Astrophysics::Cosmology and Extragalactic Astrophysics, MASS, [ PHYS.ASTR.CO ] Physics [physics]/Astrophysics [astro-ph]/Cosmology and Extra-Galactic Astrophysics [astro-ph.CO], Data-driven, Data cube, [PHYS.ASTR.CO]Physics [physics]/Astrophysics [astro-ph]/Cosmology and Extra-Galactic Astrophysics [astro-ph.CO], surveys, 0103 physical sciences, ddc:530, Instrumentation and Methods for Astrophysics (astro-ph.IM), Astrophysics::Galaxy Astrophysics, 010308 nuclear & particles physics, Astronomy and Astrophysics, DAS, 115 Astronomy, Space science, Catalogues, 530 Physik, Astrophysics - Astrophysics of Galaxies, Galaxy, Baryon, QC Physics, [PHYS.ASTR.GA]Physics [physics]/Astrophysics [astro-ph]/Galactic Astrophysics [astro-ph.GA], Space and Planetary Science, Sky, Astrophysics of Galaxies (astro-ph.GA), ddc:520, catalogs, astro-ph.IM, SDSS-IV MANGA
Abstract: Open Access. Original content from this work may be used under the terms of the Creative Commons Attribution 3.0 licence. Any further distribution of this work must maintain attribution to the author(s) and the title of the work, journal citation and DOI., The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in operation since 2014 July. This paper describes the second data release from this phase, and the 14th from SDSS overall (making this Data Release Fourteen or DR14). This release makes the data taken by SDSS-IV in its first two years of operation (2014-2016 July) public. Like all previous SDSS releases, DR14 is cumulative, including the most recent reductions and calibrations of all data taken by SDSS since the first phase began operations in 2000. New in DR14 is the first public release of data from the extended Baryon Oscillation Spectroscopic Survey; the first data from the second phase of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2), including stellar parameter estimates from an innovative data-driven machine-learning algorithm known as ¿The Cannon¿ and almost twice as many data cubes from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous release (N = 2812 in total). This paper describes the location and format of the publicly available data from the SDSS-IV surveys. We provide references to the important technical papers describing how these data have been taken (both targeting and observation details) and processed for scientific use. The SDSS web site (www.sdss.org) has been updated for this release and provides links to data downloads, as well as tutorials and examples of data use. SDSS-IV is planning to continue to collect astronomical data until 2020 and will be followed by SDSS-V. © 2018. The American Astronomical Society.., Funding for the Sloan Digital Sky Survey IV has been provided by the Alfred P. Sloan Foundation, the U.S. Department of Energy Office of Science, and the Participating Institutions. SDSS-IV acknowledges support and resources from the Center for High-Performance Computing at the University of Utah. The SDSS web site is www.sdss.org.
Published: 2018

7. The FERONIA receptor kinase maintains cell-wall integrity during salt stress through Ca2+ signaling

Author: Ming-Che Liu, Alexis Peaucelle, Heather N. Cartwright, Qiaohong Duan, José R. Dinneny, Ina Schmitz-Thom, Wei Feng, Leonie Steinhorst, Jörg Kudla, Daniel Kita, Robert Yvon, Vinh Doan, Jacob Maman, Alice Y. Cheung, Hen-Ming Wu, Department of Plant Biology, Carnegie Institution for Science [Washington], University of Massachusetts System (UMASS), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), Institut für biologie und biotechnologie der pflanzen, Westfälische Wilhelms-Universität Münster (WWU), Department of Biology, Stanford University, Sainsbury Laboratory, Cambridge University, National Science Foundation (NSF) Plant Genome Research Program [IOS 1238202], NIH NIGMS [R01 GM123259-01], Carnegie Institution for Science Endowment, NSF [IOS-1146941, IOS-1147165, IOS-1645854], German Research Foundation [Ku 931/14-1], Howard Hughes Medical Institute, Simons Foundation, and Dinneny, José R.
Subjects: 0106 biological sciences, 0301 basic medicine, Mutant, Arabidopsis, chemistry.chemical_element, Calcium, 01 natural sciences, Salt Stress, General Biochemistry, Genetics and Molecular Biology, Article, Cell wall, 03 medical and health sciences, Cell Wall, Extracellular, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Calcium Signaling, Receptor, Plant Physiological Phenomena, Vegetal Biology, biology, Arabidopsis Proteins, Kinase, Endoplasmic reticulum, Phosphotransferases, biology.organism_classification, Cell biology, Corrosion, 030104 developmental biology, chemistry, Pectins, General Agricultural and Biological Sciences, Biologie végétale, 010606 plant biology & botany
Abstract: SUMMARY Cells maintain integrity despite changes in their mechanical properties elicited during growth and environmental stress. How cells sense their physical state and compensate for cell-wall damage is poorly understood, particularly in plants. Here we report that FERONIA (FER), a plasma-membrane-localized receptor kinase from Arabidopsis, is necessary for the recovery of root growth after exposure to high salinity, a widespread soil stress. The extracellular domain of FER displays tandem regions of homology with malectin, an animal protein known to bind diglucose in vitro and important for protein quality control in the endoplasmic reticulum. The presence of malectin-like domains in FER and related receptor kinases has led to widespread speculation that they interact with cell-wall polysaccharides and can potentially serve a wall-sensing function. Results reported here show that salinity causes softening of the cell wall and that FER is necessary to sense these defects. When this function is disrupted in the fer mutant, root cells explode dramatically during growth recovery. Similar defects are observed in the mur1 mutant, which disrupts pectin cross-linking. Furthermore, fer cell-wall integrity defects can be rescued by treatment with calcium and borate, which also facilitate pectin cross-linking. Sensing of these salinity-induced wall defects might therefore be a direct consequence of physical interaction between the extracellular domain of FER and pectin. FER-dependent signaling elicits cell-specific calcium transients that maintain cell-wall integrity during salt stress. These results reveal a novel extracellular toxicity of salinity, and identify FER as a sensor of damage to the pectin-associated wall., In Brief For plant cells, growth requires maintenance of cell-wall integrity. Feng et al. show that salinity weakens the cell wall, which triggers FER-mediated calcium signaling to prevent root cells from bursting during growth under salt stress. The extracellular domain of FER physically interacts with pectin, indicating a potential sensing mechanism.
Published: 2018

8. The Second APOKASC Catalog: The Empirical Approach

Author: Christian Nitschelm, Daniel Huber, Thomas Kallinger, D. A. García-Hernández, Verne V. Smith, Matthew Shetrone, Sarbani Basu, Szabolcs Mészáros, Olga Zamora, Jennifer A. Johnson, Joel C. Zinn, Saskia Hekker, José G. Fernández-Trincado, Timothy C. Beers, Katia Cunha, Henrik Jönsson, Jennifer Sobeck, Benoit Mosser, Victor Silva Aguirre, Rafael A. García, Dennis Stello, Yvonne Elsworth, Jamie Tayar, Enrico Corsaro, William J. Chaplin, Léo Girardi, Fred Hearty, Jon A. Holtzman, Savita Mathur, Peter M. Frinchaboy, Guy S. Stringfellow, Keivan G. Stassun, Aldo Serenelli, Marc H. Pinsonneault, Thaíse S. Rodrigues, Deokkeun An, Department of Astronomy (Ohio State University), Ohio State University [Columbus] (OSU), School of Physics and Astronomy, University of Birmingham [Birmingham], Institute of Space Sciences [Barcelona] (ICE-CSIC), Spanish National Research Council [Madrid] (CSIC), Stellar Astrophysics Centre [Aarhus] (SAC), Aarhus University [Aarhus], Astrophysique Interprétation Modélisation (AIM (UMR7158 / UMR_E_9005 / UM_112)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Visio per computador i robotica (VICOROB), Universitat de Girona (UdG), J. A. Baker Institute, Cornell University [New York], Sydney Institute for Astronomy (SIfA), The University of Sydney, Instituut voor Sterrenkunde [Leuven], Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Laboratoire d'études spatiales et d'instrumentation en astrophysique (LESIA (UMR_8109)), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Department of Physics and Astronomy [Aarhus], National University of Singapore (NUS), Department of Psychology, St John's University, Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CR CHUM), Centre Hospitalier de l'Université de Montréal (CHUM), Université de Montréal (UdeM)-Université de Montréal (UdeM), Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), Univers, Transport, Interfaces, Nanostructures, Atmosphère et environnement, Molécules (UMR 6213) (UTINAM), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Astrophysique Interprétation Modélisation (AIM (UMR_7158 / UMR_E_9005 / UM_112)), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7), Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS), Cornell University, PSL Research University (PSL)-PSL Research University (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Centre de recherche du Chum [Montréal] (CRCHUM), and Sainsbury Laboratory Cambridge
Subjects: Stellar population, oscillations (including pulsations) [stars], fundamental parameters [stars], KEPLER, FOS: Physical sciences, Astrophysics, Astrophysics::Cosmology and Extragalactic Astrophysics, 01 natural sciences, 0103 physical sciences, OSCILLATIONS, Astrophysics::Solar and Stellar Astrophysics, Statistical dispersion, stars abundances, FIELD, 010303 astronomy & astrophysics, Red clump, Scaling, ComputingMilieux_MISCELLANEOUS, Astrophysics::Galaxy Astrophysics, Solar and Stellar Astrophysics (astro-ph.SR), Physics, MIXING-LENGTH, 010308 nuclear & particles physics, Astronomy and Astrophysics, Radius, Surface gravity, AGES, RED GIANTS, Stars, Star cluster, Astrophysics - Solar and Stellar Astrophysics, Space and Planetary Science, OPEN CLUSTERS, Astrophysics::Earth and Planetary Astrophysics, BOLOMETRIC CORRECTIONS, [PHYS.ASTR]Physics [physics]/Astrophysics [astro-ph], STARS, ASTEROSEISMIC MASS
Abstract: We present a catalog of stellar properties for a large sample of 6676 evolved stars with APOGEE spectroscopic parameters and \textit{Kepler} asteroseismic data analyzed using five independent techniques. Our data includes evolutionary state, surface gravity, mean density, mass, radius, age, and the spectroscopic and asteroseismic measurements used to derive them. We employ a new empirical approach for combining asteroseismic measurements from different methods, calibrating the inferred stellar parameters, and estimating uncertainties. With high statistical significance, we find that asteroseismic parameters inferred from the different pipelines have systematic offsets that are not removed by accounting for differences in their solar reference values. We include theoretically motivated corrections to the large frequency spacing ($\Delta \nu$) scaling relation, and we calibrate the zero point of the frequency of maximum power ($\nu_{\rm max}$) relation to be consistent with masses and radii for members of star clusters. For most targets, the parameters returned by different pipelines are in much better agreement than would be expected from the pipeline-predicted random errors, but 22\% of them had at least one method not return a result and a much larger measurement dispersion. This supports the usage of multiple analysis techniques for asteroseismic stellar population studies. The measured dispersion in mass estimates for fundamental calibrators is consistent with our error model, which yields median random and systematic mass uncertainties for RGB stars of order 4\%. Median random and systematic mass uncertainties are at the 9\% and 8\% level respectively for RC stars., Comment: 29 pages, 26 figures. Submitted ApJSupp. Comments welcome. For access to the main data table (Table 5) use https://www.dropbox.com/s/k33td8ukefwy5tv/APOKASC2_Table5.txt?dl=0; for access to the individual pipeline values (Table 6) use https://www.dropbox.com/s/vl9s2p3obftrv8m/APOKASC2_Table6.txt?dl=0
Published: 2018
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9. The ash dieback invasion of Europe was founded by two genetically divergent individuals

Author: Adam Vivian-Smith, Kentaro Yoshida, Halvor Solheim, Christine Fosker, Ari M. Hietala, Bernardo J. Clavijo, David Swarbreck, Gemy Kaithakottil, Lawrence Percival-Alwyn, Mark McMullan, Philip Jennings, James K. M. Brown, Diane G. O. Saunders, Matthew D. Clark, Walter Verweij, Louisa Williamson, Jonathan M. Wright, Lorelei Bilham, J. Allan Downie, Elizabeth S. Orton, Renaud Ioos, Dan MacLean, Maryam Rafiqi, Mark Blaxter, Georgios Koutsovoulos, Gonzalo Garcia Accinelli, Tsuyoshi Hosoya, Ben J. Ward, Anne Edwards, Neil Hall, Claude Husson, McMullan, Mark, Earlham Institute [Norwich], Kew Botanical Garden, John Innes Centre [Norwich], Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, The Sainsbury Laboratory, Department of Agrobioscience - Graduate School of Agricultural Science, Kobe University, National Museum of Nature and Science, Fera Science Limited, Laboratoire de la Santé des Végétaux, Unité de Mycologie (LSV Nancy), Laboratoire de la Santé des Végétaux, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Norwegian Institute of Bioeconomy Research (NIBIO), Edinburgh Genomics, The Natural History Museum [London] (NHM), Biotechnology and Biological Sciences Research Council (BBSRC) BB/L024055/1, CyVerse UK of the Earlham Institute National Capability in e-Infrastructure, BBSRC BBS/E/J/000CA523, Department of Environment Food and Rural Affairs (Defra) BBS/E/J/000CA523, Economic and Social Research Council, Forestry Commission, Natural Environment Research Council (NERC), Scottish Government under Tree Health and Plant Biosecurity Initiative BB/L01291X/1, French National Research Agency (ANR) of the Investissements d'Avenir programme ANR-11-LABX-0002-01, BBSRC National Capability in Genomics grant BB/J010375/1, BBSRC Institute Strategic Programme Grant for Bioinformatics BB/ J004669/1, The Sainsbury Laboratory [Norwich] (TSL), Konan University [Kobe, Japan], Unité de Mycologie, and Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL)
Subjects: 0301 basic medicine, safety, Population genetics, [SDV]Life Sciences [q-bio], DIVERSITY, sécurité, Introgression, Biology, Fraxinus, Article, cinder, 03 medical and health sciences, Ascomycota, DNA POLYMORPHISM, medicine, PATHOGEN HYMENOSCYPHUS PSEUDOALBIDUS, REVEALS INSIGHTS, POPULATION-STRUCTURE, cendre, Ecology, Evolution, Behavior and Systematics, Plant Diseases, FUNGAL, Genetic diversity, GENOME EVOLUTION, PLANT-PATHOGENS, Ecology, Host (biology), Haplotype, Hymenoscyphus fraxineus, Ecological genetics, biology.organism_classification, frêne, medicine.drug_formulation_ingredient, FRAXINUS-EXCELSIOR, RESISTANCE, haploïde, 030104 developmental biology, Haplotypes, 13. Climate action, Evolutionary biology, Genome, Fungal, europe
Abstract: Accelerating international trade and climate change make pathogen spread an increasing concern. Hymenoscyphus fraxineus, the causal agent of ash dieback, is a fungal pathogen that has been moving across continents and hosts from Asian to European ash. Most European common ash trees (Fraxinus excelsior) are highly susceptible to H. fraxineus, although a minority (~5%) have partial resistance to dieback. Here, we assemble and annotate a H. fraxineus draft genome, which approaches chromosome scale. Pathogen genetic diversity across Europe and in Japan, reveals a strong bottleneck in Europe, though a signal of adaptive diversity remains in key host interaction genes. We find that the European population was founded by two divergent haploid individuals. Divergence between these haplotypes represents the ancestral polymorphism within a large source population. Subsequent introduction from this source would greatly increase adaptive potential of the pathogen. Thus, further introgression of H. fraxineus into Europe represents a potential threat and Europe-wide biological security measures are needed to manage this disease.
Published: 2018

10. SUPERMAN prevents class B gene expression and promotes stem cell termination in the fourth whorl of Arabidopsis thaliana flowers

Author: Thomas Jack, Pradeep Das, Elliot M. Meyerowitz, Nathanaël Prunet, Weibing Yang, Department of Biological Sciences, Dartmouth College, Division of Biology and Biological Engineering, Howard Hughes Medical Institute, California Institute of Technology (CALTECH), Sainsbury Laboratory, University of Cambridge, Reproduction et développement des plantes (RDP), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), National Science Foundation [IOS-0926347], National Institutes of Health [R01 GM104244], Gordon and Betty Moore Foundation [GBMF3406], Prunet, Nathanaël, Meyerowitz, Elliot M., Dartmouth College [Hanover], Howard Hughes Medical Institute (HHMI), Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon)
Subjects: 0301 basic medicine, Gynoecium, [SDV]Life Sciences [q-bio], microscopie confocale, Mutant, Stamen, Biology, confocal microscopy, verticille, 03 medical and health sciences, SUPERMAN, stem cells, boundary formation, flower development, cellule souche, Arabidopsis thaliana, Superman, Gene, Whorl (botany), Genetics, floral organ identity, Multidisciplinary, développement de la fleur, arabidopsis thaliana, fungi, food and beverages, Biological Sciences, formation de bourgeon, organe floral, biology.organism_classification, stem cell, body regions, identité génique, 030104 developmental biology, Stem cell
Abstract: Significance The Arabidopsis thaliana flower is a complex structure that consists of discrete floral organs (sepals, petals, stamens, and carpels) that are separated by regions lacking organ growth called boundaries. The SUPERMAN ( SUP ) gene functions to define the boundary between the male organs (stamens) and female organs (carpels) in the flower. Previous work on boundary formation in plants has focused on growth repression, rather than on identity separation. Using live confocal imaging, we demonstrate that SUP functions by keeping the male and female developmental programs spatially and temporally separate, which is critical for the fertility of the flower. In addition, we show a second role of SUP in the timely termination of floral stem cells.
Published: 2017

11. Frontiers In Plant Science

Author: Alexander Bucksch, Acheampong Atta-Boateng, Akomian F. Azihou, Dorjsuren Battogtokh, Aly Baumgartner, Brad M. Binder, Siobhan A. Braybrook, Cynthia Chang, Viktoirya Coneva, Thomas J. DeWitt, Alexander G. Fletcher, Malia A. Gehan, Diego Hernan Diaz-Martinez, Lilan Hong, Anjali S. Iyer-Pascuzzi, Laura L. Klein, Samuel Leiboff, Mao Li, Jonathan P. Lynch, Alexis Maizel, Julin N. Maloof, R. J. Cody Markelz, Ciera C. Martinez, Laura A. Miller, Washington Mio, Wojtek Palubicki, Hendrik Poorter, Christophe Pradal, Charles A. Price, Eetu Puttonen, John B. Reese, Rubén Rellán-Álvarez, Edgar P. Spalding, Erin E. Sparks, Christopher N. Topp, Joseph H. Williams, Daniel H. Chitwood, Biological Sciences, University of Georgia [USA], Yale University [New Haven], Laboratory of Applied Ecology, University of Abomey-Calavi, University of Abomey Calavi (UAC), Virginia Tech [Blacksburg], Baylor University, The University of Tennessee [Knoxville], Sainsbury Laboratory Cambridge, University of Cambridge [UK] (CAM), Division of Biology, University of Washington, Bothell, University of Washington-Bothell, Donald Danforth Plant Science Center, Department of Wildlife & Fisheries Sciences, Department of Plant Pathology & Microbiology, Texas A&M University [College Station], University College of London [London] (UCL), Florida State University [Tallahassee] (FSU), Cornell University, Department of Botany and Plant Pathology, Purdue University [West Lafayette], Department of Medicine [San Francisco], University of California [San Francisco] (UCSF), University of California-University of California, Department of Biology, Saint Louis University, Department of Plant Science, Pennsylvania State University (Penn State), Penn State System-Penn State System, Center for Organismal Studies, Universität Heidelberg [Heidelberg], University of California Davis - Department of Plant Biology, University of California, Department of Molecular & Cell Biology [Berkeley], University of California [Berkeley], Program in Bioinformatics and Computational Biology, University of North Carolina [Chapel Hill] (UNC), University of North Carolina System (UNC)-University of North Carolina System (UNC), Forschungszentrum Juelich, Modeling plant morphogenesis at different scales, from genes to phenotype (VIRTUAL PLANTS), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), National Institute for Mathematical and Biological Synthesis, Finnish Geospatial Research Institute (FGI), Centro de Investigacion y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), University of Wisconsin-Madison, Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware [Newark], NimBIOS, ANR-11-BINF-0002,IBC,Institut de Biologie Computationnelle de Montpellier(2011), Université d’Abomey-Calavi = University of Abomey Calavi (UAC), Sainsbury Laboratory Cambridge University (SLCU), Cornell University [New York], University of California [San Francisco] (UC San Francisco), University of California (UC)-University of California (UC), Universität Heidelberg [Heidelberg] = Heidelberg University, University of California (UC), University of California [Berkeley] (UC Berkeley), Forschungszentrum Jülich GmbH, Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de la Recherche Agronomique (INRA)-Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), 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)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-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)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), ANR-11-BINF-0002,IBC,Institut de biologie Computationnelle(2011), 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)-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)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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, 0301 basic medicine, topology, Bioengineering, Morphology (biology), F62 - Physiologie végétale - Croissance et développement, Review, lcsh:Plant culture, Topology, 01 natural sciences, F50 - Anatomie et morphologie des plantes, 03 medical and health sciences, Plant science, ddc:570, Botany, morphology, lcsh:SB1-1110, Topology (chemistry), 2. Zero hunger, plant biology, Port de la plante, Morphologie végétale, U10 - Informatique, mathématiques et statistiques, mathematics, Modeling, Modèle de simulation, modeling, 15. Life on land, Plant biology, Natural resource, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, 030104 developmental biology, plant science, Plant morphology, Anatomie végétale, Biologie, Modèle mathématique, 010606 plant biology & botany
Abstract: The geometries and topologies of leaves, flowers, roots, shoots, and their arrangements have fascinated plant biologists and mathematicians alike. As such, plant morphology is inherently mathematical in that it describes plant form and architecture with geometrical and topological techniques. Gaining an understanding of how to modify plant morphology, through molecular biology and breeding, aided by a mathematical perspective, is critical to improving agriculture, and the monitoring of ecosystems is vital to modeling a future with fewer natural resources. In this white paper, we begin with an overview in quantifying the form of plants and mathematical models of patterning in plants. We then explore the fundamental challenges that remain unanswered concerning plant morphology, from the barriers preventing the prediction of phenotype from genotype to modeling the movement of leaves in air streams. We end with a discussion concerning the education of plant morphology synthesizing biological and mathematical approaches and ways to facilitate research advances through outreach, cross-disciplinary training, and open science. Unleashing the potential of geometric and topological approaches in the plant sciences promises to transform our understanding of both plants and mathematics. National Science Foundation through NSF [DBI-1300426] University of Tennessee, Knoxville, Knoxville, TN, United States This work was assisted through participation in the Morphological Plant Modeling: Unleashing geometric and topological potential within the plant sciences Investigative Workshop at the National Institute for Mathematical and Biological Synthesis, sponsored by the National Science Foundation through NSF Award #DBI-1300426, with additional support from The University of Tennessee, Knoxville, Knoxville, TN, United States.
Published: 2017

12. Remorin: a membrane raft plasmodesmal protein involved in potyvirus propagation?

Author: Simon, Vincent, Perraki, A., Gronnier, Julien, Germain, V., Mongrand, Sebastien, German-Retana, Sylvie, Biologie du fruit et pathologie (BFP), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, The Sainsbury Laboratory (TSL), Laboratoire de biogenèse membranaire (LBM), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), The Sainsbury Laboratory [Norwich] (TSL), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD). FRA., and ProdInra, Archive Ouverte
Subjects: [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, virus phytopathogène, Potyvirus, Plasmodesmata, Remorin, TuMV, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, phytopathogenic virus, santé des plantes, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, virologie végétale, plant health, pathologie végétale, [SDV.BV.PEP] Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy
Abstract: UMR BFP - Equipe Virologie; Remorin: a membrane raft plasmodesmal protein involved in potyvirus propagation?. 16. Rencontres de Virologie Végétale (RVV 2017)
Published: 2017

13. Epigenome and Transcriptome Studies during Dormancy in Sweet Cherry Flower Buds

Author: Vimont, Noémie, Arkoun, Mustapha, Yvin, Jean-Claude, Wigge, Philip A., Dirlewanger, Elisabeth, Cortijo, Sandra, Wenden, Bénédicte, ProdInra, Archive Ouverte, Biologie du fruit et pathologie (BFP), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, Agro Innovation International-Centre Mondial d'Innovation - Groupe Roulier, The Sainsbury Laboratory (TSL), Université Sciences et Technologies - Bordeaux 1-Institut National de la Recherche Agronomique (INRA)-Université Bordeaux Segalen - Bordeaux 2, Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), and The Sainsbury Laboratory [Norwich] (TSL)
Subjects: flower bud, changement climatique, dormancy, digestive, oral, and skin physiology, fungi, food and beverages, fruit tree, cerisier doux, fruit, épigénome, dormance, stomatognathic system, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, bourgeon floral, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, transcriptome, global change, arbre fruitier
Abstract: Epigenome and Transcriptome Studies during Dormancy in Sweet Cherry Flower Buds. Plant and Animal Genome XXV
Published: 2017

14. Fluctuations of the transcription factor ATML1 generate the pattern of giant cells in the Arabidopsis sepal

Author: Pau Formosa-Jordan, Adrienne H. K. Roeder, José Teles, Heather M Meyer, Yassin Refahi, Gwyneth C. Ingram, Henrik Jönsson, Rita San-Bento, James C. W. Locke, Graduate Field of Genetics, Genomics and Development, Cornell University, Weill Institute for Cell and Molecular Biology, Sainsbury Laboratry, University of Cambridge, Reproduction et développement des plantes (RDP), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Sainsbury Laboratory, University of Cambridge [UK] (CAM), Computational Biology and Biological Physics, Lund University, Department of Applied Mathematics and Theoretical Physics, Queen's University [Belfast] (QUB), Microsoft Research, Department of Biochemistry, Hôpital Lapeyronie, Section of Plant Biology, School of Integrated Plant Science, National Science Foundation, 10S-1553030 10S-1256733, Gatsby Charitable Foundation GAT3272/GLC GAT3395/PR4, Vetenskapsradet VR2013:4632, Herchel Smith Foundation, Cornell University [New York], Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Sainsbury Laboratory Cambridge University (SLCU), The Sainsbury Laboratory [Norwich] (TSL), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), and Lund University [Lund]
Subjects: 0301 basic medicine, Cell type, QH301-705.5, Science, [SDV]Life Sciences [q-bio], Cell fate determination, Biology, General Biochemistry, Genetics and Molecular Biology, endoreduplication, modelling, 03 medical and health sciences, sepal, pattern formation, Live cell imaging, Arabidopsis, transcription factors, Botany, Endoreduplication, giant cell, Biology (General), Transcription factor, cell fate specification, ATML1, modélisation, General Immunology and Microbiology, cellule epidermique, fluctuation, General Neuroscience, arabidopsis thaliana, General Medicine, Cell cycle, biology.organism_classification, Cell biology, 030104 developmental biology, Giant cell, Medicine, facteur de transcription
Abstract: Multicellular development produces patterns of specialized cell types. Yet, it is often unclear how individual cells within a field of identical cells initiate the patterning process. Using live imaging, quantitative image analyses and modeling, we show that during Arabidopsis thaliana sepal development, fluctuations in the concentration of the transcription factor ATML1 pattern a field of identical epidermal cells to differentiate into giant cells interspersed between smaller cells. We find that ATML1 is expressed in all epidermal cells. However, its level fluctuates in each of these cells. If ATML1 levels surpass a threshold during the G2 phase of the cell cycle, the cell will likely enter a state of endoreduplication and become giant. Otherwise, the cell divides. Our results demonstrate a fluctuation-driven patterning mechanism for how cell fate decisions can be initiated through a random yet tightly regulated process.
Published: 2017

15. Morphological plant modeling: Unleashing geometric and topologic potential within the plant sciences

Author: Joseph H. Williams, Daniel H. Chitwood, Lilan Hong, Mao Li, Anjali S. Iyer-Pascuzzi, Erin E. Sparks, Thomas J. DeWitt, Cynthia C. Chang, Edgar P. Spalding, Dorjsuren Battogtokh, Jonathan P. Lynch, Samuel Leiboff, Diego Hernán Díaz Martínez, R. J. Cody Markelz, Eetu Puttonen, John B. Reese, Laura L. Klein, Alexis Maizel, Malia A. Gehan, Mathilde Balduzzi, Washington Mio, Christopher N. Topp, Ciera C. Martinez, Alexander Bucksch, Christophe Pradal, Julin N. Maloof, Alexander G. Fletcher, Viktoiriya Coneva, Laura Miller, Hendrik Poorter, Siobhan A. Braybrook, Wojtek Palubicki, Acheampong Atta-Boateng, Rubén Rellán-Álvarez, Akomian Fortuné Azihou, Charles A. Price, Brad M. Binder, Aly Baumgartner, University of Georgia [USA], Yale University [New Haven], Laboratory of Applied Ecology, University of Abomey-Calavi, University of Abomey Calavi (UAC), Modeling plant morphogenesis at different scales, from genes to phenotype (VIRTUAL PLANTS), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de la Recherche Agronomique (INRA)-Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), 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)-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)-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)-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), Virginia Tech [Blacksburg], Baylor University, The University of Tennessee [Knoxville], Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), University of Washington-Bothell, Donald Danforth Plant Science Center, Department of Wildlife & Fisheries Sciences, Department of Plant Pathology & Microbiology, Texas A&M University [College Station], School of Mathematics and Statistics [Sheffield] (SoMaS), University of Sheffield [Sheffield], Florida State University [Tallahassee] (FSU), Cornell University [New York], Department of Botany and Plant Pathology, Purdue University [West Lafayette], Saint Louis University, Pennsylvania State University (Penn State), Penn State System, Center for Organismal Studies, Universität Heidelberg [Heidelberg], University of California Davis - Department of Plant Biology, University of California, Department of Molecular & Cell Biology [Berkeley], University of California [Berkeley], University of California-University of California, University of North Carolina [Chapel Hill] (UNC), University of North Carolina System (UNC), Forschungszentrum Juelich, National Institute for Mathematical and Biological Synthesis, Finnish Geospatial Research Institute (FGI), Centro de Investigacion y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), University of Wisconsin-Madison, Duke University [Durham], Université d’Abomey-Calavi = University of Abomey Calavi (UAC), 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)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-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)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Universität Heidelberg [Heidelberg] = Heidelberg University, University of California (UC), University of California [Berkeley] (UC Berkeley), University of California (UC)-University of California (UC), Forschungszentrum Jülich GmbH, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Sainsbury Laboratory Cambridge, and Cornell University
Subjects: 0106 biological sciences, topology, Population, Biology, Topology, 01 natural sciences, 03 medical and health sciences, White paper, Botany, morphology, education, 030304 developmental biology, 2. Zero hunger, Plant biology, 0303 health sciences, education.field_of_study, mathematics, modeling, Vegetation, 15. Life on land, Natural resource, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Outreach, plant science, 13. Climate action, Plant morphology, 010606 plant biology & botany
Abstract: Plant morphology is inherently mathematical in that morphology describes plant form and architecture with geometrical and topological descriptors. The geometries and topologies of leaves, flowers, roots, shoots and their spatial arrangements have fascinated plant biologists and mathematicians alike. Beyond providing aesthetic inspiration, quantifying plant morphology has become pressing in an era of climate change and a growing human population. Modifying plant morphology, through molecular biology and breeding, aided by a mathematical perspective, is critical to improving agriculture, and the monitoring of ecosystems with fewer natural resources. In this white paper, we begin with an overview of the mathematical models applied to quantify patterning in plants. We then explore fundamental challenges that remain unanswered concerning plant morphology, from the barriers preventing the prediction of phenotype from genotype to modeling the movement of leafs in air streams. We end with a discussion concerning the incorporation of plant morphology into educational programs. This strategy focuses on synthesizing biological and mathematical approaches and ways to facilitate research advances through outreach, cross-disciplinary training, and open science. This white paper arose from bringing mathematicians and biologists together at the National Institute for Mathematical and Biological Synthesis (NIMBioS) workshop titled “Morphological Plant Modeling: Unleashing Geometric and Topological Potential within the Plant Sciences” held at the University of Tennessee, Knoxville in September, 2015. Never has the need to quantify plant morphology been more imperative. Unleashing the potential of geometric and topological approaches in the plant sciences promises to transform our understanding of both plants and mathematics.
Published: 2016

16. Rust fungal effectors mimic host transit peptides to translocate into chloroplasts

Author: Petre, Benjamin, Lorrain, Cécile, Saunders, Diane G.O., Win, Joe, Sklenar, Jan, Duplessis, Sébastien, Kamoun, Sophien, Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), The Sainsbury Laboratory (TSL), The Genome Analysis Centre (TGAC), John Innes Center (JIC), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), The Sainsbury Laboratory [Norwich] (TSL), INRA Contrat Jeune Scientifique (CJS), European Union, AgreenSkills' fellowship [267196], Laboratory of Excellence (Labex) ARBRE [12RW53], Leverhulme early career fellowship, computational biology at TGAC, BBSRC, INRA CJS, Labex ARBRE, French National Research Agency through the Labex ARBRE [ANR-12-LABXARBRE-01], Young Scientist Grant POPRUST [ANR-2010-JCJC-1709-01], Gatsby Charitable Foundation, and European Project: 267196,EC:FP7:PEOPLE,FP7-PEOPLE-2010-COFUND,AGREENSKILLS(2012)
Subjects: Fungal Proteins, Protein Transport, Chloroplasts, Populus, Virulence Factors, Basidiomycota, [SDV]Life Sciences [q-bio], Molecular Mimicry, food and beverages, Plant Diseases
Abstract: International audience; Parasite effector proteins target various host cell compartments to alter host processes and promote infection. How effectors cross membrane‐rich interfaces to reach these compartments is a major question in effector biology. Growing evidence suggests that effectors use molecular mimicry to subvert host cell machinery for protein sorting. We recently identified chloroplast‐targeted protein 1 (CTP1), a candidate effector from the poplar leaf rust fungus Melampsora larici‐populina that carries a predicted transit peptide and accumulates in chloroplasts and mitochondria. Here, we show that the CTP1 transit peptide is necessary and sufficient for accumulation in the stroma of chloroplasts. CTP1 is part of a Melampsora‐specific family of polymorphic secreted proteins. Two members of that family, CTP2 and CTP3, also translocate in chloroplasts in an N‐terminal signal‐dependent manner. CTP1, CTP2 and CTP3 are cleaved when they accumulate in chloroplasts, while they remain intact when they do not translocate into chloroplasts. Our findings reveal that fungi have evolved effector proteins that mimic plant‐specific sorting signals to traffic within plant cells.
Published: 2016

17. A pigeonpea gene confers resistance to Asian soybean rust in soybean

Author: Gustavo Tristão, Geeta Iyer, Karen Bacot, Burkhard Steuernagel, Brande B. H. Wulff, Sérgio Hermínio Brommonschenkel, Sônia Regina Nogueira, Gregory J. Rairdan, H. Peter van Esse, Gilda Rauscher, Jamile Camargos de Oliveira, Jong-Min Baek, Lisa Panichelli, Doug R. Cook, Bernardo do V A Melo, Eric R. Ward, Gustavo Augusto Guimarães, Dan MacLean, Shipra Mittal, Girma M. Tabor, Gusui Wu, Cintia G. Kawashima, Ebony Johnson, Costas Bouyioukos, Jonathan D. G. Jones, Karen E Broglie, Cintia G Kawashima, The Sainsbury Laboratory, Norwich, U.K., Gustavo Augusto Guimarães, Dep. de Fitopatologia, Universidade Federal de Viçosa, SONIA REGINA NOGUEIRA, CPAF-Acre, Dan MacLean, The Sainsbury Laboratory, Norwich, U.K., Doug R. Cook, Department of Plant Pathology, University of California Davis, Davis, California, USA., Burkhard Steuernagel, The John Innes Centre, Norwich, U.K., Jongmin Baek, Department of Plant Pathology, University of California Davis, Davis, California, USA., Costas Bouyioukos, The John Innes Centre, Norwich, U.K., Bernardo do V. A. Melo, Dep. de Fitopatologia, Universidade Federal de Viçosa, Gustavo Tristão, Dep. de Fitopatologia, Universidade Federal de Viçosa, Jamile Camargos de Oliveira, Dep. de Fitopatologia, Universidade Federal de Viçosa, Gilda Rauscher, Agricultural Biotechnology, DuPont-Pioneer, Wilmington, Delaware, USA., Shipra Mittal, Agricultural Biotechnology, DuPont-Pioneer, Wilmington, Delaware, USA., Lisa Panichelli, Agricultural Biotechnology, DuPont-Pioneer, Wilmington, Delaware, USA., Karen Bacot, Agricultural Biotechnology, DuPont-Pioneer, Wilmington, Delaware, USA., Ebony Johnson, Agricultural Biotechnology, DuPont-Pioneer, Wilmington, Delaware, USA., Geeta Iyer, Agricultural Biotechnology, DuPont-Pioneer, Wilmington, Delaware, USA., Girma Tabor, Agricultural Biotechnology, DuPont-Pioneer, Wilmington, Delaware, USA., Brande B H Wulff, The John Innes Centre, Norwich, U.K., Eric Ward, The John Innes Centre, Norwich, U.K., Gregory J Rairdan, Agricultural Biotechnology, DuPont-Pioneer, Wilmington, Delaware, USA., Karen E Broglie, Agricultural Biotechnology, DuPont-Pioneer, Wilmington, Delaware, USA., Gusui Wu, Agricultural Biotechnology, DuPont-Pioneer, Wilmington, Delaware, USA., H Peter van Esse, The Sainsbury Laboratory, Norwich, U.K., Jonathan D G Jones, The Sainsbury Laboratory, Norwich, U.K., and Sérgio H Brommonschenkel, Dep. de Fitopatologia, Universidade Federal de Viçosa.
Subjects: Fitomejoramiento, 0106 biological sciences, 0301 basic medicine, Glycine max, Soja, Genótipo, Guandu, 01 natural sciences, Applied Microbiology and Biotechnology, Plant breeding, Molecular clonación, Cajanus, Molecular cloning, Doença de planta, Plant diseases and disorders, Cultivar, Roya de la soja, Legume, biology, Pigeon peas, food and beverages, Guandul, Fungicide, Phakopsora pachyrhizi, Molecular Medicine, Soybean rust, Biotechnology, Beans, Enfermedades y desórdenes de las plantas, Melhoramento genético vegetal, Variedade resistente, Biomedical Engineering, Bioengineering, Fungus, Plant disease resistance, Ferrugem asiática, Crop, 03 medical and health sciences, Clonagem, Semillas de soja, Frijoles, Fungo, Asian soybean, fungi, Fungi, Leguminosa com grão, biology.organism_classification, Pigeonpea gene, 030104 developmental biology, Agronomy, Phakpsora pachyrhizi, Soybeans, Feijão, Cajanus cajan, 010606 plant biology & botany
Abstract: Asian soybean rust (ASR), caused by the fungus Phakopsora pachyrhizi, is one of the most economically important crop diseases, but is only treatable with fungicides, which are becoming less effective owing to the emergence of fungicide resistance. There are no commercial soybean cultivars with durable resistance to P. pachyrhizi, and although soybean resistance loci have been mapped, no resistance genes have been cloned. We report the cloning of a P. pachyrhizi resistance gene CcRpp1 (Cajanus cajan Resistance against Phakopsora pachyrhizi 1) from pigeonpea (Cajanus cajan) and show that CcRpp1 confers full resistance to P. pachyrhizi in soybean. Our findings show that legume species related to soybean such as pigeonpea, cowpea, common bean and others could provide a valuable and diverse pool of resistance traits for crop improvement.
Published: 2016

18. Spatio-temporal registration of 3D microscopy image sequences of Arabidopsis floral meristems

Author: Michelin, Gaël, Refahi, Yassin, Wightman, Raymond, Jönsson, Henrik, Traas, Jan, Godin, Christophe, Malandain, Grégoire, Morphologie et Images (MORPHEME), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut de Biologie Valrose (IBV), Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Signal, Images et Systèmes (Laboratoire I3S - SIS), Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis (I3S), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis (I3S), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Reproduction et développement des plantes (RDP), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Sainsbury Laboratory Cambridge, University of Cambridge [UK] (CAM), Modeling plant morphogenesis at different scales, from genes to phenotype (VIRTUAL PLANTS), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Signal, Images et Systèmes (Laboratoire I3S - SIS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis (I3S), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Sainsbury Laboratory Cambridge University (SLCU), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de la Recherche Agronomique (INRA)-Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), 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)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-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)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), 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)-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)-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)-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 Recherche en Informatique et en Automatique (Inria) - Institut National de Recherche en Informatique et en Automatique (Inria) - Institut de Biologie Valrose (IBV), Centre National de la Recherche Scientifique (CNRS) - Institut National de la Santé et de la Recherche Médicale (INSERM) - Université Nice Sophia Antipolis (UNS) - Centre National de la Recherche Scientifique (CNRS) - Institut National de la Santé et de la Recherche Médicale (INSERM) - Université Nice Sophia Antipolis (UNS) - Signal, Images et Systèmes (SIS), Université Nice Sophia Antipolis (UNS) - Centre National de la Recherche Scientifique (CNRS) - Université Nice Sophia Antipolis (UNS) - Centre National de la Recherche Scientifique (CNRS) - Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis (I3S), Université Nice Sophia Antipolis (UNS) - Centre National de la Recherche Scientifique (CNRS) - Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Lyon (ENS Lyon) - Institut National de la Recherche Agronomique (INRA) - Université Claude Bernard Lyon 1 (UCBL) - Centre National de la Recherche Scientifique (CNRS), University of Cambridge, and Institut National de Recherche en Informatique et en Automatique (Inria) - Institut National de Recherche en Informatique et en Automatique (Inria) - Institut National de la Recherche Agronomique (INRA) - Centre de coopération internationale en recherche agronomique pour le développement [CIRAD] : UMR51
Subjects: Confocal microscopy, developmental biology, Arabidopsis thaliana, [INFO.INFO-TI] Computer Science [cs]/Image Processing, [INFO.INFO-TI]Computer Science [cs]/Image Processing [eess.IV], fungi, food and beverages, [SDV.BDD.MOR]Life Sciences [q-bio]/Development Biology/Morphogenesis, floral meristem, [SDV.BDD.MOR] Life Sciences [q-bio]/Development Biology/Morphogenesis
Abstract: International audience; The shoot apical meristem (SAM) is at the origin of all the plant above-ground organs (including stems, leaves and flowers) and is a biological object of interest for the understanding of plant morphogenesis. The quantification of tissue growth at a cellular level requires the analysis of 3D microscopic image sequences of developing meristems. To address inter-individual variability, it is also required to compare individuals. This obviously implies the ability to process inter-individual registration, i.e. to compute spatial and temporal correspondences between sequences from different meristems.In the present work, we propose a spatial registration method dedicated to microscopy floral meristem (FM) images, and the identification, for a given still image of a meristem, of its best corresponding time-point in a sequence of an other individual (temporal registration).
Published: 2016

19. The Poplar Rust-Induced Secreted Protein (RISP) Inhibits the Growth of the Leaf Rust Pathogen Melampsora larici-populina and Triggers Cell Culture Alkalinisation

Author: Benjamin ePetre, Arnaud eHECKER, Hugo eGermain, Pascale eTsan, Jan eSklenar, Gervais ePelletier, Armand eSéguin, Sébastien eDuplessis, Nicolas eRouhier, Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), The Sainsbury Laboratory (TSL), Université du Québec à Trois-Rivières (UQTR), Cristallographie, Résonance Magnétique et Modélisations (CRM2), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Canadian Forest Service, Laurentian Forestry Centre, Natural Resources Canada (NRCan), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), The Sainsbury Laboratory, John Innes Centre [Norwich], Groupement de Recherche en Biologie Végétale & Centre de Recherche sur les Interactions Bassins Versants-Ecosystèmes Aquatiques, Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), The Sainsbury Laboratory [Norwich] (TSL), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL), Laurentian Forestry Centre, ANR (ANR-11-LABX-0002-01), Region Lorraine, INRA, Gatsby Charitable Foundation, European Research Council, Biotechnology and Biological Sciences Research Council (BBSRC), and European Project: 267196,EC:FP7:PEOPLE,FP7-PEOPLE-2010-COFUND,AGREENSKILLS(2012)
Subjects: 0106 biological sciences, 0301 basic medicine, Populus trichocarpa, propriété antifongique, [SDV]Life Sciences [q-bio], Rust (fungus), Nicotiana benthamiana, Plant Science, champignon pathogène, Biology, lcsh:Plant culture, 01 natural sciences, Microbiology, 03 medical and health sciences, protéine sécrétée, obligate biotroph, Extracellular, lcsh:SB1-1110, Pathogen, ComputingMilieux_MISCELLANEOUS, Original Research, arbre, peptide elicitor, fungi, antifungal activity, plant immunity, rust fungus, food and beverages, Melampsora, biology.organism_classification, Apoplast, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], 030104 developmental biology, melampsora larici populina, Cell culture, 010606 plant biology & botany
Abstract: International audience; Plant cells secrete a wide range of proteins in extracellular spaces in response to pathogen attack. The poplar rust-induced secreted protein (RISP) is a small cationic protein of unknown function that was identified as the most induced gene in poplar leaves during immune responses to the leaf rust pathogen Melampsora larici-populina, an obligate biotrophic parasite. Here, we combined in planta and in vitro molecular biology approaches to tackle the function of RISP. Using a RISP-mCherry fusion transiently expressed in Nicotiana benthamiana leaves, we demonstrated that RISP is secreted into the apoplast. A recombinant RISP specifically binds to M. larici-populina urediniospores and inhibits their germination. It also arrests the growth of the fungus in vitro and on poplar leaves. Interestingly, RISP also triggers poplar cell culture alkalinisation and is cleaved at the C-terminus by a plant-encoded mechanism. Altogether our results indicate that RISP is an antifungal protein that has the ability to trigger cellular responses.
Published: 2016

20. Regulation of Meristem Morphogenesis by Cell Wall Synthases in Arabidopsis

Author: Monika S. Doblin, Christoph Schuster, Varodom Charoensawan, Cherie T. Beahan, Antony Bacic, Weibing Yang, Raymond Wightman, Elliot M. Meyerowitz, Alexis Peaucelle, Sainsbury Laboratory, University of Cambridge, ARC Centre of Excellence in Plant Cell Walls, University of Adelaide-University of Queensland [Brisbane]-School of BioSciences [Melbourne], Faculty of Science [Melbourne], University of Melbourne-University of Melbourne-Faculty of Science [Melbourne], University of Melbourne-University of Melbourne, Department of Biochemistry, Faculty of Science, Mahidol University [Bangkok]-Ramathibodi Hospital, Integrative Computational BioScience Center, Mahidol University [Bangkok], Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Howard Hughes Medical Institute and Division of Biology and Biological Engineering, California Institute of Technology (CALTECH), Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), University of Queensland [Brisbane]-School of BioSciences [Melbourne], University of Melbourne-University of Melbourne-University of Adelaide, European Project: 267196,EC:FP7:PEOPLE,FP7-PEOPLE-2010-COFUND,AGREENSKILLS(2012), Yang, Weibing [0000-0002-2379-5729], Schuster, Christoph [0000-0002-1948-2367], Wightman, Raymond [0000-0003-1295-4875], and Apollo - University of Cambridge Repository
Subjects: 0301 basic medicine, XYLAN, [SDV]Life Sciences [q-bio], education, Meristem, Morphogenesis, Arabidopsis, Biology, General Biochemistry, Genetics and Molecular Biology, Article, Cell wall, 03 medical and health sciences, PECTIN, Cell Wall, Gene Expression Regulation, Plant, BIOSYNTHETIC HOMOGALACTURONAN GALACTURONOSYLTRANSFERASE, Gene expression, Botany, MUTANTS REVEALS, Primordium, RNA, Messenger, health care economics and organizations, GENE-EXPRESSION, Regulation of gene expression, Agricultural and Biological Sciences(all), THALIANA, Biochemistry, Genetics and Molecular Biology(all), Arabidopsis Proteins, Sequence Analysis, RNA, Glycosyltransferases, food and beverages, Meristem maintenance, biology.organism_classification, Cell biology, 030104 developmental biology, CELLULOSE, GROWTH, ARABINOGALACTAN, SHOOT APICAL MERISTEM, General Agricultural and Biological Sciences
Abstract: The cell walls of the shoot apical meristem (SAM), containing the stem cell niche that gives rise to the above-ground tissues, are crucially involved in regulating differentiation. It is currently unknown how these walls are built and refined or their role, if any, in influencing meristem developmental dynamics. We have combined polysaccharide linkage analysis, immuno-labelling and transcriptome profiling of the SAM to provide a spatio-temporal plan of the walls of this dynamic structure. We find that meristematic cells express only a core subset of 152 genes encoding cell wall glycosyltransferases (GTs). Systemic localization of all these GT mRNAs by in situ hybridization reveals members with either enrichment in or specificity to apical subdomains such as emerging flower primordia, and a large class with high expression in dividing cells. The highly localized and coordinated expression of GTs in the SAM suggests distinct wall properties of meristematic cells, and specific differences between newly forming walls and their mature descendants. Functional analysis demonstrates that a subset of CSLD genes is essential for proper meristem maintenance, confirming the key role of walls in developmental pathways.
Published: 2016

21. Recurrent evolution of heat-responsiveness in Brassicaceae COPIA elements

Author: Pietzenuk B, Markus C, Gaubert H, Bagwan N, Merotto A, Etienne Bucher, Pecinka A, Department of Plant Breeding and Genetics, Cornell University [New York], Department of Plant Physiology, Umeå University, Department of Plant Breeding and Genetics [Cologne], Max Planck Institute for Plant Breeding Research (MPIPZ), Department of Crop Science, North Carolina State University [Raleigh] (NC State), University of North Carolina System (UNC)-University of North Carolina System (UNC), Department of Plant Biology, Royal Veterinary and Agricultural University = Kongelige Veterinær- og Landbohøjskole (KVL ), The Sainsbury Laboratory [Norwich] (TSL), Cardiovascular Proteomics, Centro Nacional de Investigaciones Cardiovasculares, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), German Research Foundation (DFG) [AP1859-2], Science Priority Program Adaptomics [1529], Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES) fellowship [BEX 10896/14-7], Cornell University, The Royal Veterinary and Agricultural University, The Sainsbury Laboratory, John Innes Centre [Norwich], and AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA)
Subjects: Hot Temperature, Retroelements, Evolution, Research, [SDV]Life Sciences [q-bio], copia, Arabidopsis, Terminal Repeat Sequences, Brassicaceae, Heat stress, food and beverages, Evolution, Molecular, Gene Expression Regulation, Plant, ONSEN, Genome, Plant, Heat-Shock Response, Phylogeny
Abstract: Background The mobilization of transposable elements (TEs) is suppressed by host genome defense mechanisms. Recent studies showed that the cis-regulatory region of Arabidopsis thaliana COPIA78/ONSEN retrotransposons contains heat-responsive elements (HREs), which cause their activation during heat stress. However, it remains unknown whether this is a common and potentially conserved trait and how it has evolved. Results We show that ONSEN, COPIA37, TERESTRA, and ROMANIAT5 are the major families of heat-responsive TEs in A. lyrata and A. thaliana. Heat-responsiveness of COPIA families is correlated with the presence of putative high affinity heat shock factor binding HREs within their long terminal repeats in seven Brassicaceae species. The strong HRE of ONSEN is conserved over millions of years and has evolved by duplication of a proto-HRE sequence, which was already present early in the evolution of the Brassicaceae. However, HREs of most families are species-specific, and in Boechera stricta, the ONSEN HRE accumulated mutations and lost heat-responsiveness. Conclusions Gain of HREs does not always provide an ultimate selective advantage for TEs, but may increase the probability of their long-term survival during the co-evolution of hosts and genomic parasites. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1072-3) contains supplementary material, which is available to authorized users.
Published: 2016

22. Heterologous Expression Screens in Nicotiana benthamiana Identify a Candidate Effector of the Wheat Yellow Rust Pathogen that Associates with Processing Bodies

Author: Jan Sklenar, Sophien Kamoun, Cécile Lorrain, Joe Win, Ksenia V. Krasileva, Sébastien Duplessis, Diane G. O. Saunders, Benjamin Petre, Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), The Sainsbury Laboratory (TSL), ANR (ANR-12-LABXARBRE-01, ANR-2010-JCJC-1709-01), European Project: 267196, Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), The Sainsbury Laboratory [Norwich] (TSL), Gijzen, Mark, The Sainsbury Laboratory, John Innes Centre [Norwich], and The Genome Analysis Centre (TGAC)
Subjects: Cell Membranes, Nicotiana benthamiana, Plant Science, Pathogenesis, champignon phytopathogène, Pathology and Laboratory Medicine, Biochemistry, Tandem Mass Spectrometry, Protein Interaction Mapping, Aetiology, lcsh:Science, Liquid, Fungal protein, Microscopy, Confocal, Vegetal Biology, Effector, Plant Biochemistry, Microbiology and Parasitology, food and beverages, Plants, Microbiologie et Parasitologie, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Cellular Structures and Organelles, Infection, Cell Physiology, Imaging Techniques, In silico, Virulence, 03 medical and health sciences, Open Reading Frames, Botany, Genetics, Computer Simulation, RNA, Messenger, Grasses, Plant Diseases, lcsh:R, fungi, Organisms, Biology and Life Sciences, Plant, Plant Pathology, 030104 developmental biology, lcsh:Q, Biologie végétale, Cereal Crops, 0301 basic medicine, Leaves, [SDV]Life Sciences [q-bio], Messenger, lcsh:Medicine, Cell Fusion, Gene Expression Regulation, Plant, Medicine and Health Sciences, 2.1 Biological and endogenous factors, plante modèle, Pathogen, Triticum, 2. Zero hunger, Microscopy, Chromatography, Multidisciplinary, biology, Plant Anatomy, pipeline, Agriculture, Infectious Diseases, In Vivo Imaging, protéine, Confocal, Wheat, Host-Pathogen Interactions, Research Article, General Science & Technology, Green Fluorescent Proteins, Plant Pathogens, Crops, Research and Analysis Methods, Fungal Proteins, nicotiana benthamiana, Tobacco, effecteur moléculaire, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Enhancer, Basidiomycota, Gene Expression Profiling, Membrane Proteins, Cell Biology, biology.organism_classification, Plant Leaves, Gene Expression Regulation, puccinia striiformis f sp tritici, RNA, Heterologous expression, Chromatography, Liquid, Crop Science
Abstract: International audience; Rust fungal pathogens of wheat (Triticum spp.) affect crop yields worldwide. The molecular mechanisms underlying the virulence of these pathogens remain elusive, due to the limited availability of suitable molecular genetic research tools. Notably, the inability to perform high-throughput analyses of candidate virulence proteins (also known as effectors) impairs progress. We previously established a pipeline for the fast-forward screens of rust fungal candidate effectors in the model plant Nicotiana benthamiana. This pipeline involves selecting candidate effectors in silico and performing cell biology and protein-protein interaction assays in planta to gain insight into the putative functions of candidate effectors. In this study, we used this pipeline to identify and characterize sixteen candidate effectors from the wheat yellow rust fungal pathogen Puccinia striiformis f sp tritici. Nine candidate effectors targeted a specific plant subcellular compartment or protein complex, providing valuable information on their putative functions in plant cells. One candidate effector, PST02549, accumulated in processing bodies (P-bodies), protein complexes involved in mRNA decapping, degradation, and storage. PST02549 also associates with the P-body-resident ENHANCER OF mRNA DECAPPING PROTEIN 4 (EDC4) from N. benthamiana and wheat. We propose that P-bodies are a novel plant cell compartment targeted by pathogen effectors.
Published: 2016

23. A stochastic multicellular model identifies biological watermarks from disorders in self-organized patterns of phyllotaxis

Author: Christophe Godin, Teva Vernoux, Etienne Farcot, Géraldine Brunoud, Yassin Refahi, Alain Jean-Marie, Minna Pulkkinen, Reproduction et développement des plantes (RDP), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Sainsbury Laboratory, University of Cambridge [UK] (CAM), University of Nottingham, UK (UON), Institut National de Recherche en Informatique et en Automatique (Inria), Laboratoire d'Etudes des Ressources Forêt-Bois (LERFoB), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), 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)-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), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Sainsbury Laboratory Cambridge University (SLCU), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Models for the performance analysis and the control of networks (MAESTRO), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), AgroParisTech, Modeling plant morphogenesis at different scales, from genes to phenotype (VIRTUAL PLANTS), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de la Recherche Agronomique (INRA)-Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), 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)-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)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), HFSP grant RGP0054-2013 BioSensors (Human Frontier Science Program) to TV and CG, Inria Project Lab Morphogenetics and ANR-funded Institute of Computational Biology (IBC) to CG, Jan Traas’s ERC Morphodynamics & INRA CJS to YR, École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), 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)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-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)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Sainsbury Laboratory Cambridge, and Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Inria Sophia Antipolis - Méditerranée (CRISAM)
Subjects: 0301 basic medicine, noise, croissance végétale, Stochastic modelling, QH301-705.5, permutations, Science, [SDV]Life Sciences [q-bio], Arabidopsis, Plant Biology, Plant Development, Model system, multi-scale modeling, Biology, Models, Biological, modèle de croissance, General Biochemistry, Genetics and Molecular Biology, modèle stochastique, 03 medical and health sciences, phyllotaxis, Gene Expression Regulation, Plant, emergence, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Biology (General), phyllotaxie, General Immunology and Microbiology, Ecology, General Neuroscience, Locality, General Medicine, Phyllotaxis, Biological noise, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Multicellular organism, Shoot apex, Plant development, 030104 developmental biology, Developmental Biology and Stem Cells, A. thaliana, inhibitory fields, Medicine, organogénèse, Biological system, Plant Shoots, Research Article
Abstract: Exploration of developmental mechanisms classically relies on analysis of pattern regularities. Whether disorders induced by biological noise may carry information on building principles of developmental systems is an important debated question. Here, we addressed theoretically this question using phyllotaxis, the geometric arrangement of plant aerial organs, as a model system. Phyllotaxis arises from reiterative organogenesis driven by lateral inhibitions at the shoot apex. Motivated by recurrent observations of disorders in phyllotaxis patterns, we revisited in depth the classical deterministic view of phyllotaxis. We developed a stochastic model of primordia initiation at the shoot apex, integrating locality and stochasticity in the patterning system. This stochastic model recapitulates phyllotactic patterns, both regular and irregular, and makes quantitative predictions on the nature of disorders arising from noise. We further show that disorders in phyllotaxis instruct us on the parameters governing phyllotaxis dynamics, thus that disorders can reveal biological watermarks of developmental systems. DOI: http://dx.doi.org/10.7554/eLife.14093.001, eLife digest Plants grow throughout their lifetime, forming new flowers and leaves at the tips of their stems through a patterning process called phyllotaxis, which occurs in spirals for a vast number of plant species. The classical view suggests that the positioning of each new leaf or flower bud at the tip of a growing stem is based on a small set of principles. This includes the idea that buds produce inhibitory signals that prevent other buds from forming too close to each other. When computational models of phyllotaxis follow these ‘deterministic’ principles, they are able to recreate the spiral pattern the buds form on a growing stem. In real plants, however, the spiral pattern is not always perfect. The observed disturbances in the pattern are believed to reflect the presence of random fluctuations – regarded as noise – in phyllotaxis. Here, using numerical simulations, Refahi et al. noticed that the patterns of inhibitory signals in a shoot tip pre-determine the locations of several competing sites where buds could form in a robust manner. However, random fluctuations in the way cells perceive these inhibitory signals could greatly disturb the timing of organ formation and affect phyllotaxis patterns. Building on this, Refahi et al. created a new computational model of bud patterning that takes into account some randomness in how cells perceive the inhibitory signals released by existing buds. The model can accurately recreate the classical spiral patterns of buds and also produces occasional disrupted patterns that are similar to those seen in real plants. Unexpectedly, Refahi et al. show that these ‘errors’ reveal key information about how the signals that control phyllotaxis might work. These findings open up new avenues of research into the role of noise in phyllotaxis. The model can be used to predict how altering the activities of genes or varying plant growth conditions might disturb this patterning process. Furthermore, the work highlights how the structure of disturbances in a biological system can shed new light on how the system works. DOI: http://dx.doi.org/10.7554/eLife.14093.002
Published: 2016

24. Analyses of pig genomes provide insight to porcine demography and evolution

Author: Ronan Kapetanovic, Patrice Dehais, Zhi-Qiang Du, Loretta Auvil, Ricardo H. Ramirez-Gonzalez, Kyung-Tai Lee, Patrick Chardon, Hiroyuki Kanamori, Gary A. Rohrer, Jianguo Zhang, Celine Chen, Simon D. M. White, Guojie Zhang, Jian Wang, Hyeonju Ahn, Ole Madsen, Miguel Pérez-Enciso, Richard Clark, Bruce R. Southey, Yasuhiro Takeuchi, Bronwen Aken, Bo Thomsen, Frank Panitz, Katie E. Fowler, Peter F. Stadler, Jennifer Harrow, Takeya Morozumi, Ryan Cheng, Christian Bendixen, Laurent A. F. Frantz, Yogesh Paudel, Sara Botti, Kellye Eversole, Jaebum Kim, Jian Ma, Matthew Jones, Jan Gorodkin, Zhi-Liang Hu, John C. Schwartz, Suneel Kumar Onteru, Tae-Hun Kim, Fioravante De Sapio, Nizar Drou, Stephen M. J. Searle, Wan Sheng Liu, Yingrui Li, Yao Lu, Thomas Faraut, Richard P. M. A. Crooijmans, Joan K. Lunney, Göran O. Sperber, Bert Dibbits, Denis Milan, Richard M. Leggett, Boris Capitanu, Xun Xu, Bertrand Servin, Megan Bystrom, Carol Scott, Kyle M. Schachtschneider, Bouabid Badaoui, Harris A. Lewin, Mirte Bosse, Sang-Haeng Choi, Yongming Sang, Jane Rogers, Patric Jern, Kerstin Howe, Sean Humphray, Henrik Hornshøj, Martien A. M. Groenen, Jerzy Jurka, James M. Reecy, Frank Blecha, Darren K. Griffin, Susan Fairley, Jonas Blomberg, Claire Rogel-Gaillard, Eung-Woo Park, Jonathan V. Sweedler, Hong-Seog Park, Stuart McLaren, Denise Carvalho-Silva, Christopher K. Tuggle, Géraldine Pascal, Rashmi Wali, Mario Caccamo, Katherine M. Mann, Lawrence B. Schook, C M Clee, James G. R. Gilbert, Christian Anthon, Merete Fredholm, Chankyu Park, Harry D. Dawson, Craig W. Beattie, Elisabetta Giuffra, Zhan Bujie, Kyu-Won Kim, Toby Hunt, Jae-Hwan Kim, Daniel Berman, Shuhong Zhao, Hakim Tafer, Jin-Tae Jeon, Sandra L. Rodriguez-Zas, Hendrik-Jan Megens, Linda Scobie, Jie Zhang, Alan Archibald, Joshua G. Schraiber, Jitendra Narayan, Alexander Hayward, Lucy Matthews, Lauretta A. Rund, Jane E. Loveland, Peixiang Ni, Denis M. Larkin, Song-Jung Oh, Dinh Truong Nguyen, Kyooyeol Lee, Lars Bolund, João Fadista, William Chow, Jun Wang, Hirohide Uenishi, Shengting Li, Eric Fritz, Heebal Kim, Geoffrey J. Faulkner, Martine Yerle, Michael P. Murtaugh, Max F. Rothschild, Carol Churcher, Greger Larson, Anna Anselmo, Laboratoire de radiobiologie et d'étude du génome (LREG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-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)-Université de Toulouse (UT), The Genome Analysis Centre (TGAC), Parco Tecnologico Padano, CERSA, Department of Clinical Genetics, Odense University Hospital, The Wellcome Trust Sanger Institute [Cambridge], Système d'Information des GENomes des Animaux d'Elevage (SIGENAE), Institut National de la Recherche Agronomique (INRA), Faculty of Life Sciences, Division of Genetics and Bioinformatics, Faculty of Life Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory [Hong Kong], The University of Hong Kong (HKU), Beijing Genomics Institute [Shenzhen] (BGI), Department of Biochemistry, University of Nijmegen, The Netherlands, University of Nijmegen, Molecular Carcinogenesis [Sutton], Institute of cancer research, Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur] (IFCE)-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Université de Tours (UT), Canadian Light Source Inc., University of Saskatchewan [Saskatoon] (U of S), Department of Mechanical Engineering, University of Auckland, University of Auckland [Auckland], ANR-07-GANI-0001,DELISUS,An integrated study of the haplotypic variability at the whole genome level on animals finely phenotyped from French porcine populations(2007), European Project: LSHB-CT-2006-037377, European Project: 249894,EC:FP7:ERC,ERC-2009-AdG,SELSWEEP(2010), European Project: 38710,SABRE, European Project: 222664,EC:FP7:KBBE,FP7-KBBE-2007-2A,QUANTOMICS(2009), European Commission, European Research Council, Biotechnology and Biological Sciences Research Council (UK), Wellcome Trust, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS), Université de Tours, Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Sainsbury Laboratory Cambridge, Centre National de la Recherche Scientifique (CNRS)-Université de Tours-Institut Français du Cheval et de l'Equitation [Saumur]-Institut National de la Recherche Agronomique (INRA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Recherche Agronomique (INRA), and Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: pig, Evolution, receptor, Molecular Sequence Data, Population Dynamics, Sus scrofa, sus-scrofa, Locus (genetics), Genomics, Biology, Animal Breeding and Genomics, Genome, Article, genomic, taste, 03 medical and health sciences, Phylogenetics, evolution, Genetics, Animals, animal, Fokkerij en Genomica, Domestication, gene, Gene, Phylogeny, Demography, 030304 developmental biology, 0303 health sciences, locus, variants, Multidisciplinary, Phylogenetic tree, [SDV.BA]Life Sciences [q-bio]/Animal biology, 0402 animal and dairy science, 04 agricultural and veterinary sciences, sequence, 040201 dairy & animal science, Models, Animal, WIAS, genetic, Selective sweep, complex
Abstract: For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ∼1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model., The research leading to these results has received funding from the European Research Council under the European Community’s Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no. 249894 (SelSweep)
Published: 2012

25. MASCP Gator: An Aggregation Portal for the Visualization of Arabidopsis Proteomics Data

Author: Ian Castleden, Stefanie Wienkoop, Matthias Hirsch-Hoffmann, Hirofumi Nakagami, Klaas J. van Wijk, Sandra K. Tanz, Christophe Bruley, Norbert Rolland, Joshua L. Heazlewood, Sacha Baginsky, Steven P. Briggs, Wilhelm Gruissem, A. Harvey Millar, R R Schmidt, Katja Baerenfaller, Alexandra M. E. Jones, Hiren J. Joshi, Waltraud X. Schulze, Volker Egelhofer, Tetsuro Toyoda, Wolfram Weckwerth, Qi Sun, Joint BioEnergy Institute, Department of Biology, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Max Planck Institute of Molecular Plant Physiology (MPI-MP), Max-Planck-Gesellschaft, Department of plant Biology, Cornell University, Molecular Systems Biology, universite de Vienne, Laboratoire d'Etude de la Dynamique des Proteomes, Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Biosciences et de Biotechnologies de Grenoble (ex-IRTSV) (BIG), Institut National de la Santé et de la Recherche Médicale (INSERM)-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)-Université Grenoble Alpes (UGA), 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), RIKEN Plant Science Center and RIKEN Bioinformatics and Systems Engineering Division, The Sainsbury Laboratory, Sainsbury Laboratory, Division of Biology, University of California [San Diego] (UC San Diego), University of California-University of California, Centre of Excellence for Computational Systems Biology, The University of Western Australia (UWA), Australian Research Council Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis of Biomolecular Networks, Cornell University [New York], Laboratoire d'étude de la dynamique des protéomes (LEDyP), Université Joseph Fourier - Grenoble 1 (UJF)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), 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), The Sainsbury Laboratory [Norwich] (TSL), University of California (UC)-University of California (UC), U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research [DE-AC02-05CH11231], AGRON-OMICS [LSHG-CT-2006-037704], Australian Research Council, Australian Research Council Centre of Excellence in Plant Energy Biology, Ministry of Education, Culture, Sports, Science and Technology [21770059], Institut National de la Santé et de la Recherche Médicale (INSERM)-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)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), and 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)
Subjects: 0106 biological sciences, Bioinformatics, Physiology, Research areas, Arabidopsis, plant, Plant Science, Proteomics, 01 natural sciences, World Wide Web, User-Computer Interface, 03 medical and health sciences, proteomics, Resource (project management), online resources, Genetics, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Phosphorylation, Databases, Protein, database, 030304 developmental biology, Internet, 0303 health sciences, biology, Arabidopsis Proteins, business.industry, data mining, Hyperlink, biology.organism_classification, Visualization, Identification (information), information networks, aggregator, The Internet, business, Protein Kinases, 010606 plant biology & botany
Abstract: Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (H.J.J., J.L.H.); Department of Biology, Eidgenossisch Technische Hochschule Zurich, CH-8092 Zurich, Switzerland (M. H.-H., K. B., W. G.); Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany (S. B.); Max-Planck Institute for Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (R. S., W. X. S.); Department of Plant Biology, Cornell University, Ithaca, New York 14853 (Q. S., K.J.v.W.); Molecular Systems Biology, University of Vienna, 1090 Vienna, Austria (V. E., S. W., W. W.); Institut National de la Sante et de la Recherche Medicale, Laboratoire d'Etude de la Dynamique des Proteomes, U880, F-38000 Grenoble, France (C. B.); Commissariat a l'Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Institut de Recherches en Technologies et Sciences pour le Vivant, F-38000 Grenoble, France (C.B., N.R.); Universite Joseph Fourier, F-38000 Grenoble, France (C. B., N.R.); CNRS, Laboratoire de Physiologie Cellulaire Vegetale, UMR5168, F-38000 Grenoble, France (N.R.); INRA, UMR1200, F-38000 Grenoble, France (N.R.); RIKEN Plant Science Center and RIKEN Bioinformatics and Systems Engineering Division, Tsurumi-ku, Yokohama 230-0045, Japan (T.T., H.N.); The Sainsbury Laboratory, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom (A.M.J.); Division of Biology, University of California San Diego, La Jolla, California 92093 (S.P.B.); and Centre of Excellence for Computational Systems Biology (I.C.) and Australian Research Council Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis of Biomolecular Networks (I.C., S.K.T., A.H.M.), University of Western Australia, Crawley 6009, Western Australia, Australia
Published: 2010

26. The receptor kinase FERONIA regulates phosphatidylserine localization at the cell surface to modulate ROP signaling

Author: Smokvarska, Marija, Bayle, Vincent, Maneta-Peyret, Lilly, Fouillen, Laetitia, Poitout, Arthur, Dongois, Armelle, Fiche, Jean-Bernard, Gronnier, Julien, Garcia, José, Höfte, Herman, Nolmann, Marcelo, Zipfel, Cyril, Maurel, Christophe, Moreau, Patrick, Jaillais, Yvon, Martiniere, Alexandre, Institut des Sciences des Plantes de Montpellier (IPSIM), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, 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 de Montpellier (UM), Reproduction et développement des plantes (RDP), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de biogenèse membranaire (LBM), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Plateforme Bordeaux Metabolome, Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-MetaboHUB-Bordeaux, MetaboHUB-MetaboHUB, Centre de Biologie Structurale [Montpellier] (CBS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Department of Plant and Microbial Biology [Zurich, Suisse], Universität Zürich [Zürich] = University of Zurich (UZH), Zentrum für Molekularbiologie der Pflanzen (ZMBP), Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Zurich Basel Plant Science Center, Universität Zürich [Zürich] = University of Zurich (UZH)-University of Basel (Unibas), The Sainsbury Laboratory [Norwich] (TSL), ANR-11-INBS-0010,METABOHUB,Développement d'une infrastructure française distribuée pour la métabolomique dédiée à l'innovation(2011), University of Zurich, and Martiniere, Alexandre
Subjects: 1000 Multidisciplinary, phosphatidylserine, Multidisciplinary, 10126 Department of Plant and Microbial Biology, [SDV]Life Sciences [q-bio], Arabidopsis, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, 580 Plants (Botany), 10211 Zurich-Basel Plant Science Center, FERONIA, Fer
Abstract: International audience; Cells maintain a constant dialog between the extracellular matrix and their plasma membrane to fine tune signal transduction processes. We found that the receptor kinase FERONIA (FER), which is a proposed cell wall sensor, modulates phosphatidylserine plasma membrane accumulation and nano-organization, a key regulator of Rho GTPase signaling in Arabidopsis. We demonstrate that FER is required for both Rho-of-Plant 6 (ROP6) nano-partitioning at the membrane and downstream production of reactive oxygen species upon hyperosmotic stimulus. Genetic and pharmacological rescue experiments indicate that phosphatidylserine is required for a subset of, but not all, FER functions. Furthermore, application of FER ligand shows that its signaling controls both phosphatidylserine membrane localization and nanodomains formation, which, in turn, tunes ROP6 signaling. Together, we propose that a cell wall–sensing pathway controls via the regulation of membrane phospholipid content, the nano-organization of the plasma membrane, which is an essential cell acclimation to environmental perturbations.
Published: 2023

27. Plants, fungi and oomycetes: a 400-million year affair that shapes the biosphere

Author: Sophien Kamoun, Paul Kenrick, Francis Martin, Christine Strullu-Derrien, Marc-André Selosse, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Department of Earth Sciences [NHM London] (DES-NHM), The Natural History Museum [London] (NHM), Interactions Arbres-Microorganismes (IAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Norwich Research Park, The Sainsbury Laboratory [Norwich] (TSL), Laboratoire d'Excellence ARBRE, ANR-11-LABX-0002-01 Laboratoire d'Excellence BCDiv., European Project: 298735, Biologie Intégrative des Populations, École pratique des hautes études (EPHE)-Centre National de la Recherche Scientifique (CNRS), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), The Sainsbury Laboratory (TSL), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Physiology, DIVERSITY, EFFECTOR, Plant Science, Biology, co-evolution, RHYNIE CHERT, 01 natural sciences, 10(th) New Phytologist Workshop, 03 medical and health sciences, ATMOSPHERIC OXYGEN, Mycorrhizal fungi, Botany, Oomycota, LAND PLANTS, terrestrialization, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, 030304 developmental biology, 0303 health sciences, GENOME EVOLUTION, Atmospheric oxygen, Ecology, plants, Biosphere, biogeochemical cycles, LINEAGE, POTATO FAMINE PATHOGEN, Eumycota, plant-fungal interactions, MYCORRHIZAL FUNGI, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, CARBON-CYCLE, 010606 plant biology & botany, Rhynie chert
Abstract: absent
Published: 2015

28. A snapshot of molecular plant-microbe interaction research

Author: Artemis Giannakopoulou, Clément Pellegrin, Rainer Boni, Sebastian Wittulsky, Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), The Sainsbury Laboratory (TSL), Molecular Plant Biology and Phytopathology Department, Institute of Plant Biology, University of Zurich, Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), and The Sainsbury Laboratory [Norwich] (TSL)
Subjects: Physiology, Ecology, diagnosis, plant-pathogen interaction, receptor, [SDV]Life Sciences [q-bio], Arms race, Plant microbe, Environmental ethics, Translational research, Plant Science, Biology, symbiosis, mycorrhizal fungi, resistance, effector, translational research, Mycorrhizal fungi, International congress, Snapshot (computer storage)
Abstract: Plants and microbes are in a continuous arms race to maintain their predominance within their particular niche. Understanding the complexity of these plant–microbe interactions is of utmost importance as it can provide new insights into the mechanisms mediating disease processes and in turn inspire new plant breeding strategies. The International Society for Molecular Plant–Microbe Interactions (IS-MPMI) invited scientists from around the world to share their findings during the XVI International Congress on Molecular Plant–Microbe Interactions, which was held on the beautiful island of Rhodes in Greece (Fig. 1). The congress was organized by the Agricultural University of Athens, the Hellenic Phytopathology Society, and the Hellenic Society of Phytiatry and provided over 1100 participants from 55 countries with the opportunity to present and discuss their current and future research. A great number of talks and posters were presented, however our aim within this report is to provide a snapshot of the discipline by focusing on just some of the exciting research and discussions which took place. The key topics discussed were virulence factors, epigenetic regulation, hormones, symbiosis factors, toxins, signaling pathways, microbe recognition, immunity, and pathogen diagnostics. Effector biology was also a recurrent theme in many plenary and concurrent sessions, indicating the importance of a topic that was also highlighted recently by a Virtual Special Issue in New Phytologist (see Kuhn & Panstruga, 2014). In addition to this, throughout the meeting next generation sequencing (NGS) techniques were described and shown to be shedding new light on long-standing issues in microbial ecology.
Published: 2015

29. Three BUB1 and BUBR1/MAD3-related spindle assembly checkpoint proteins are required for accurate mitosis in Arabidopsis

Author: Paganelli, Laetitia, Caillaud, Marie-Cécile, Quentin, Michael, Damiani, Isabelle, govetto, Benjamin, Lecomte, Philippe, Karpov, Pavel A, Abad, Pierre, Chabouté, Marie Edith, Favery, Bruno, Institut Sophia Agrobiotech (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), UMR 7254, Centre National de la Recherche Scientifique (CNRS), The Sainsbury Laboratory [Norwich] (TSL), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine (NASU), UR 2357 conventionné avec l'Université de Strasbourg, INRA, French Government (National Research Agency, ANR) ANR-08-GENM-014 ANR-11-LABX-0028-01, Ministere de la Recherche et l'Enseignement Superieure, Institut Sophia Agrobiotech [Sophia Antipolis] (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), The Sainsbury Laboratory, John Innes Centre [Norwich], Institut de Biologie Moléculaire des Plantes (IBMP)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie moléculaire des plantes (IBMP), Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA)
Subjects: mitosis, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, checkpoint, nematode, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, cell cycle, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, giant cell, ComputingMilieux_MISCELLANEOUS, kinetochore
Abstract: The above article, first published online on Wiley Online Library (wileyonlinelibrary.com), and in New Phytologist 205: 202–215, has been retracted by agreement between the authors, the journal Editor-in-Chief, Alistair Hetherington, and John Wiley & Sons Ltd. Since publication of the above article, it has been brought to our attention that errors occurred in the construction of Figs 1 and 2(a); some components were inappropriately edited and duplicated, including the duplication and editing of images that first appeared in Caillaud et al. (2009), which were used by the authors as a basic template. Consequently, the integrity of the yeast two-hybrid experiments reported in the article is undermined, and, with agreement of all parties, the decision has been made to retract this article. We apologize for any inconvenience the publication of this work may have caused our readers. See : https://doi.org/10.1111/nph.14225; The spindle assembly checkpoint (SAC) is a refined surveillance mechanism which ensures that chromosomes undergoing mitosis do not segregate until they are properly attached to the spindle microtubules (MT). The SAC has been extensively studied in metazoans and yeast, but little is known about its role in plants. We identified proteins interacting with a MT-associated protein MAP65-3, which plays a critical role in organising mitotic MT arrays, and carried out a functional analysis of previously and newly identified SAC components. We show that Arabidopsis SAC proteins BUB3.1, MAD2, BUBR1/MAD3s and BRK1 interact with each other and with MAP65-3. We found that two BUBR1/MAD3s interacted specifically at centromeres. When stably expressed in Arabidopsis, BRK1 localised to the kinetochores during all stages of the mitotic cell cycle. Early in mitosis, BUB3.1 and BUBR1/MAD3.1 localise to the mitotic spindle, where MAP65-3 organises spindle MTs. A double-knockout mad3.1 mad3.2 mutant presented spindle MT abnormalities, chromosome misalignments on the metaphase plate and the production of lagging chromosomes and micronuclei during mitosis. We conclude that BRK1 and BUBR1/MAD3-related proteins play a key role in ensuring faithful chromosome segregation during mitosis and that their interaction with MAP65-3 may be important for the regulation of MT-chromosome attachment.
Published: 2015

30. Natural variation for anthocyanin accumulation under high-light and low-temperature stress is attributable to the ENHANCER OF AG-4 2 (HUA2) locus in combination with PRODUCTION OF ANTHOCYANIN PIGMENT1 (PAP1) and PAP2

Author: Ilk, Nadine, Ding, Jia, Ihnatowicz, Anna, Koornneef, Maarten, Reymond, Matthieu, Max Planck Institute for Plant Breeding Research (MPIPZ), The Sainsbury Laboratory (TSL), Lab Plant Protect & Biotechnol, Intercollegiate Faculty of Biotechnoloy UG & MUG, Genet Lab, Wageningen University and Research Centre [Wageningen] (WUR), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, The Sainsbury Laboratory [Norwich] (TSL), and Wageningen University and Research [Wageningen] (WUR)
Subjects: Anthocyanin, epistasis, Quantitative trait loci, Flowering time, Arabidopsis thaliana, [SDV]Life Sciences [q-bio], fungi, food and beverages, flowering time, PAP2, Pap2, PAP1, Pap1, anthocyanin, carbohydrates (lipids), HUA2, Hua2, quantitative trait loci, Epistasis, Groep Koornneef, EPS
Abstract: Growing conditions combining high light intensities and low temperatures lead to anthocyanin accumulation in plants. This response was contrasted between two Arabidopsis thaliana accessions, which were used to decipher the genetic and molecular bases underlying the variation of this response. Quantitative trait loci (QTLs) for flowering time (FT) and anthocyanin accumulation under a high-light and low-temperature scenario versus a control environment were mapped. Major QTLs were confirmed using near-isogenic lines. Candidate genes were examined using mutants and gene expression studies as well as transgenic complementation. Several QTLs were found for FT and for anthocyanin content, of which one QTL co-located at the ENHANCER OF AG-4 2 (HUA2) locus. That HUA2 is a regulator of both pathways was confirmed by the analysis of loss-of-function mutants. For a strong expression of anthocyanin, additional allelic variation was detected for the PRODUCTION OF ANTHOCYANIN PIGMENT1 (PAP1) and PAP2 genes which control the anthocyanin pathway. The genetic control of variation for anthocyanin content was dissected in A. thaliana and shown to be affected by a common regulator of flowering and anthocyanin biosynthesis together with anthocyanin-specific regulators.
Published: 2015

31. The Control of Growth Symmetry Breaking in the Arabidopsis Hypocotyl

Author: Herman Höfte, Alexis Peaucelle, Raymond Wightman, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), European Project: 267196,EC:FP7:PEOPLE,FP7-PEOPLE-2010-COFUND,AGREENSKILLS(2012), and Sainsbury Laboratory
Subjects: media_common.quotation_subject, [SDV]Life Sciences [q-bio], Arabidopsis, Biology, Microscopy, Atomic Force, Asymmetry, Microtubules, Models, Biological, General Biochemistry, Genetics and Molecular Biology, Cell wall, 03 medical and health sciences, 0302 clinical medicine, Cell Wall, Botany, Tip growth, Symmetry breaking, Anisotropy, media_common, 030304 developmental biology, 0303 health sciences, Esterification, Agricultural and Biological Sciences(all), Biochemistry, Genetics and Molecular Biology(all), Isotropy, Hypocotyl, Biomechanical Phenomena, Anisotropic cell growth, Biophysics, Pectins, General Agricultural and Biological Sciences, Cortical microtubule, 030217 neurology & neurosurgery
Abstract: in press; Complex shapes in biology depend on the ability of cells to shift from isotropic to anisotropic growth during development. In plants, this growth symmetry breaking reflects changes in the extensibility of the cell walls. The textbook view is that the direction of turgor-driven cell expansion depends on the cortical microtubule (CMT)-mediated orientation of cellulose microfibrils [1, 2]. Here, we show that this view is incomplete at best. We used atomic force microscopy (AFM) to study changes in cell-wall mechanics associated with growth symmetry breaking within the hypocotyl epidermis. We show that, first, growth symmetry breaking is preceded by an asymmetric loosening of longitudinal, as compared to transverse, anticlinal walls, in the absence of a change in CMT orientation. Second, this wall loosening is triggered by the selective de-methylesterification of cell-wall pectin in longitudinal walls, and, third, the resultant mechanical asymmetry is required for the growth symmetry breaking. Indeed, preventing or promoting pectin de-methylesterification, respectively, increased or decreased the stiffness of all the cell walls, but in both cases reduced the growth anisotropy. Finally, we show that the subsequent CMT reorientation contributes to the consolidation of the growth axis but is not required for the growth symmetry breaking. We conclude that growth symmetry breaking is controlled at a cellular scale by bipolar pectin de-methylesterification, rather than by the cellulose-dependent mechanical anisotropy of the cell walls themselves. Such a cell asymmetry-driven mechanism is comparable to that underlying tip growth in plants [3] but also anisotropic cell growth in animal cells [4].
Published: 2015

32. Quantifying gene expression domains in plant shoot apical meristems

Author: Pau Formosa-Jordan, Benoit Landrein, Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), Max Planck Institute for Plant Breeding Research (MPIPZ), Reproduction et développement des plantes (RDP), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Formosa-Jordan, Pau
Subjects: [SDV] Life Sciences [q-bio], quantitative image analysis, stem cells, [SDV]Life Sciences [q-bio], inflorescence meristem, Arabidopsis, expression domain, confocal microscopy, floral meristem
Abstract: Accepted version of the manuscript for publication in the Book "Flower Development: Methods and Protocols, Second Edition. Jose Luis Riechmann and Cristina Ferrandiz, eds. Methods in Molecular Biology. Springer. "; The shoot apical meristem is the plant tissue that produces the plant aerial organs such as flowers and leaves. To better understand how does the shoot apical meristem develop and adapt to the environment, imaging developing shoot meristems expressing fluorescence reporters through laser confocal microscopy is becoming increasingly important. Yet, there are not many computational pipelines enabling a systematic and high-throughput characterisation of the produced microscopy images. This chapter provides a simple method to analyse 3D images obtained through laser scanning microscopy and quantitatively characterise radially or axially symmetric 3D fluorescence domains expressed in a tissue or organ by a reporter. Then, it presents different computational pipelines aiming at performing high-throughput quantitative image analysis of gene expression in plant inflorescence and floral meristems. This methodology has notably enabled to characterise quantitatively how stem cells responded to environmental perturbations in the Arabidopsis inflorescence meristem and will open new avenues in the use of quantitative analysis of gene expression in shoot apical meristems. Overall, the presented methodology provides a simple framework to analyse quantitatively gene expression domains from 3D confocal images at the tissue and organ level, which can be applied to shoot meristems and other organs and tissues.
Published: 2022

33. Effector proteins of rust fungi

Author: S. Duplessis, Benjamin Petre, David L. Joly, Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), The Sainsbury Laboratory, Université de Moncton, Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), and Sainsbury Laboratory Cambridge
Subjects: MESH: Epitopes, [SDV]Life Sciences [q-bio], Rust (fungus), Virulence, Genomics, Plant Science, Biology, lcsh:Plant culture, Pucciniales, Mini Review Article, transcriptomics, MESH: Electrophoresis, Paper, Botany, MESH: Antibodies, Bacterial, genomics, MESH: Glycolipids, MESH: Species Specificity, lcsh:SB1-1110, MESH: Polysaccharides, Bacterial, MESH: Salmonella, Genetics, Obligate, Effector, Host (biology), MESH: Hexosamines, MESH: Molecular Weight, effectoromics, MESH: Chromatography, Gas, MESH: Hemagglutination, food and beverages, MESH: Salmonella typhimurium, biology.organism_classification, MESH: Fatty Acids, carbohydrates (lipids), rust fungi, MESH: Chromatography, Thin Layer, Pucciniaceae, lipids (amino acids, peptides, and proteins), Function (biology), MESH: Immunodiffusion
Abstract: International audience; It has been assumed in the past that the lipid moieties of endotoxic lipopolysaccharides are quite similar if not identical. This has been tested in the reported work here, where the chemical composition and biological activities of the glycolipids of two heptoseless Re mutants, Salmonella minnesota R595 and Salmonella typhimurium SL1102, have been studied and compared. The two glycolipids, extracted with chloroform-methanol (4:1), showed identical thin-layer chromatographic patterns. The molar ratios for hexosamine, fatty acids, phosphorus, 2-keto-3-deoxyoctonate, total amines, and total nitrogen of the purified glycolipids were in the same range, but small differences could be established. Both glycolipids contained the same major fatty acids, i.e., lauric, myristic, palmitic, and 3-hydroxymyristic acids, in similar but not identical ratios. On paper electrophoresis, the acid hydrolysates of the two glycolipids showed analogous components. In the determination of molecular weight, whereas S. minnesota R595 glycolipid did not show concentration dependence, the molecular weight measured for S. typhimurium SL1102 increased with its concentration. The molecular weight of the fully endotoxic R595 glycolipid has been found to be 17,000 +/- 1,500. Both glycolipids showed similar activities in the Shwartzman skin reaction, Limulus-lysate clotting assay, mouse lethality, and enhancement of nonspecific resistance, but the R595 preparation appeared to be more active on a weight basis in some parameters than SL1102. Using passive hemagglutination, we observed cross-reactivity between the glycolipids. In the gel-diffusion test, they revealed clear identity. The antiserum against S. minnesota R595 neutralized the Shwartzman skin reactivity not only of R595 but also of SL1102 glycolipid. These results confirm that there are identical immunodeterminant group(s) in the two glycolipids. On the other hand, chemical analytical data for two glycolipids showed only similarities, indicating that although both glycolipids are of comparable chemical nature, differences between them exist.
Published: 2014

34. Subcellular and supracellular mechanical stress prescribes cytoskeleton behavior in Arabidopsis cotyledon pavement cells

Author: Henrik Jönsson, Elliot M. Meyerowitz, Pawel Krupinski, Olivier Hamant, Pascale Milani, Alexandre Berquand, Raymond Wightman, Arun Sampathkumar, Arezki Boudaoud, Division of Biology and Biological Engineering, Howard Hughes Medical Institute (HHMI), Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), Lund University [Lund], Reproduction et développement des plantes (RDP), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Bruker Nano GmbH, Bruker AXS, Partenaires INRAE, Sainsbury Lab, Norwich Research Park, California Institute of Technology (CALTECH), Howard Hughes Medical Institute, Gordon and Betty Moore Foundation [GBMF3406], Gatsby Charitable Foundation, US Department of Energy [DE-FG02-88ER13873], Agence Nationale de la Recherche [ANR-10-BLAN-1516], European Research Council [307387], Swedish Research Council, Crafoord Foundation, École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), The Sainsbury Laboratory [Norwich] (TSL), Wightman, Raymond [0000-0003-1295-4875], Jonsson, Henrik [0000-0003-2340-588X], and Apollo - University of Cambridge Repository
Subjects: computational modeling, Time Factors, [SDV]Life Sciences [q-bio], Cell, Turgor pressure, GROWTH ANISOTROPY, Arabidopsis, Plant Biology, Microscopy, Atomic Force, Mechanotransduction, Cellular, Microtubules, Biology (General), Cytoskeleton, Feedback, Physiological, Pavement cells, Microscopy, Video, ORGANOGENESIS, CORTICAL MICROTUBULES, General Neuroscience, cytoskeleton, General Medicine, POSITIONAL INFORMATION, medicine.anatomical_structure, Medicine, biomechanic, SHOOT APICAL MERISTEM, Cotyledon, CELLULOSE SYNTHASE, Research Article, microtubule, QH301-705.5, Science, FUNCTIONAL ASSOCIATION, KATANIN, Biology, Models, Biological, General Biochemistry, Genetics and Molecular Biology, biomechanics, FORCE, Stress (mechanics), Cell wall, Microtubule, Botany, medicine, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Computer Simulation, Cell Shape, General Immunology and Microbiology, ORIENTATION, Cell Biology, Plant cell, Biophysics, cell wall, Stress, Mechanical
Abstract: Although it is a central question in biology, how cell shape controls intracellular dynamics largely remains an open question. Here, we show that the shape of Arabidopsis pavement cells creates a stress pattern that controls microtubule orientation, which then guides cell wall reinforcement. Live-imaging, combined with modeling of cell mechanics, shows that microtubules align along the maximal tensile stress direction within the cells, and atomic force microscopy demonstrates that this leads to reinforcement of the cell wall parallel to the microtubules. This feedback loop is regulated: cell-shape derived stresses could be overridden by imposed tissue level stresses, showing how competition between subcellular and supracellular cues control microtubule behavior. Furthermore, at the microtubule level, we identified an amplification mechanism in which mechanical stress promotes the microtubule response to stress by increasing severing activity. These multiscale feedbacks likely contribute to the robustness of microtubule behavior in plant epidermis. DOI: http://dx.doi.org/10.7554/eLife.01967.001, eLife digest The surfaces of plants are covered in epithelial cells that come in many different shapes, suggesting that individual cells must have some control over their own shape. An unusually shaped epithelial cell is the pavement cell, which looks like a jigsaw puzzle piece and is found in the leaves of many flowering plants. Relatively little was known about the exact contribution of mechanical properties of the wall to this shape. Furthermore, although it was known that parts of pavement cells are rich in microtubules—tubes of protein that act as a scaffold inside the cell— the possibility that shape impacts the behavior of microtubules was not fully addressed. Now, using a combination of computer modelling and experiments, Sampathkumar et al. reveal that the shape of the pavement cells relies in part on the response of the microtubules to stress. In an individual cell, microtubules align along the direction of the largest stress, with a protein severing those microtubules that are not aligned in this direction. As the stress inside a cell is determined in part by the cell’s shape, this sets up a feedback loop: the stress resulting from the cell shape aligns the microtubules that reinforce the cell wall, thus maintaining the shape of the cell. An external stress applied to the epithelium can override this internal stress. Because all of the plant cells are under turgor pressure from the inside, pressure from the outside, like squeezing a balloon, changes the stress pattern, causing the realignment of the microtubules so as to resist the new stress. This shows that the microtubules respond to local stresses within a cell, and are continually responsive to stress changes. DOI: http://dx.doi.org/10.7554/eLife.01967.002
Published: 2014

35. EXPRSS: an Illumina based high-throughput expression-profiling method to reveal transcriptional dynamics

Author: Eric Kemen, Jonathan D. G. Jones, Ghanasyam Rallapalli, Kee Hoon Sohn, Cécile Segonzac, Graham J Etherington, Dan MacLean, Alexandre Robert-Seilaniantz, The Sainsbury Laboratory (TSL), Max Planck Institute for Plant Breeding Research (MPIPZ), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institute of Agriculture and Environment, Gatsby Charitable foundation, Dorothy Hodgkin Postgraduate award, The Sainsbury Laboratory [Norwich] (TSL), Jones, Jonathan D. G., AGROCAMPUS OUEST-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA)
Subjects: DNA, Complementary, [SDV]Life Sciences [q-bio], Tag-seq, Arabidopsis, Down-Regulation, RNA-Seq, Biology, EXPRSS, DNA sequencing, 03 medical and health sciences, Complementary DNA, Next generation sequencing, Genetics, High throughput expression profiling, Genomic library, RNA, Messenger, 3' Untranslated Regions, RNA-seq, Gene Library, Oligonucleotide Array Sequence Analysis, 030304 developmental biology, 0303 health sciences, Sequence Analysis, RNA, Three prime untranslated region, Gene Expression Profiling, Methodology Article, 030302 biochemistry & molecular biology, Computational Biology, High-Throughput Nucleotide Sequencing, Up-Regulation, Gene expression profiling, Restriction enzyme, DNA microarray, Biotechnology
Abstract: Background Next Generation Sequencing technologies have facilitated differential gene expression analysis through RNA-seq and Tag-seq methods. RNA-seq has biases associated with transcript lengths, lacks uniform coverage of regions in mRNA and requires 10–20 times more reads than a typical Tag-seq. Most existing Tag-seq methods either have biases or not high throughput due to use of restriction enzymes or enzymatic manipulation of 5’ ends of mRNA or use of RNA ligations. Results We have developed EXpression Profiling through Randomly Sheared cDNA tag Sequencing (EXPRSS) that employs acoustic waves to randomly shear cDNA and generate sequence tags at a relatively defined position (~150-200 bp) from the 3′ end of each mRNA. Implementation of the method was verified through comparative analysis of expression data generated from EXPRSS, NlaIII-DGE and Affymetrix microarray and through qPCR quantification of selected genes. EXPRSS is a strand specific and restriction enzyme independent tag sequencing method that does not require cDNA length-based data transformations. EXPRSS is highly reproducible, is high-throughput and it also reveals alternative polyadenylation and polyadenylated antisense transcripts. It is cost-effective using barcoded multiplexing, avoids the biases of existing SAGE and derivative methods and can reveal polyadenylation position from paired-end sequencing. Conclusions EXPRSS Tag-seq provides sensitive and reliable gene expression data and enables high-throughput expression profiling with relatively simple downstream analysis. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-341) contains supplementary material, which is available to authorized users.
Published: 2014

36. Natural variation in seed very long chain fatty acid content is controlled by a new isoform of KCS18 in [i]Arabidopsis thaliana[/i]

Author: Olivier Loudet, Sylvain Raffaele, Marine Froissard, Alain Lécureuil, Sophie Jasinski, Martine Miquel, Philippe Guerche, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, The Sainsbury Laboratory (TSL), 'Genetique et Amelioration des Plantes' department of INRA, 'Biologie Vegetale' department of INRA, and The Sainsbury Laboratory [Norwich] (TSL)
Subjects: 0106 biological sciences, Candidate gene, Heredity, [SDV]Life Sciences [q-bio], Mutant, Arabidopsis, lcsh:Medicine, Plant Science, Plant Genetics, Biochemistry, 01 natural sciences, chemistry.chemical_compound, Plant Genomics, Protein Isoforms, lcsh:Science, 2. Zero hunger, Genetics, chemistry.chemical_classification, 0303 health sciences, education.field_of_study, Multidisciplinary, biology, Fatty Acids, Chromosome Mapping, food and beverages, Plants, Lipids, Phenotypes, Phenotype, Seeds, Fatty acid elongation, Research Article, Arabidopsis Thaliana, Genotypes, Quantitative Trait Loci, Very long chain fatty acid, Population, Quantitative trait locus, Chromosomes, Plant, 03 medical and health sciences, Model Organisms, Plant and Algal Models, 3-Oxoacyl-(Acyl-Carrier-Protein) Synthase, Point Mutation, education, Biology, Crosses, Genetic, Genetic Association Studies, 030304 developmental biology, Quantitative Traits, Complex Traits, Arabidopsis Proteins, lcsh:R, Fatty acid, Lipid Metabolism, biology.organism_classification, Protein Structure, Tertiary, Amino Acid Substitution, chemistry, lcsh:Q, Oils, 010606 plant biology & botany
Abstract: Oil from oleaginous seeds is mainly composed of triacylglycerols. Very long chain fatty acids (VLCFAs) are major constituents of triacylglycerols in many seed oils and represent valuable feedstock for industrial purposes. To identify genetic factors governing natural variability in VLCFA biosynthesis, a quantitative trait loci (QTL) analysis using a recombinant inbred line population derived from a cross between accessions Bay-0 and Shahdara was performed in Arabidopsis thaliana. Two fatty acid chain length ratio (CLR) QTL were identified, with one major locus, CLR. 2, accounting for 77% of the observed phenotypic variation. A fine mapping and candidate gene approach showed that a key enzyme of the fatty acid elongation pathway, the beta-ketoacyl-CoA synthase 18 (KCS18), was responsible for the CLR. 2 QTL detected between Bay-0 and Shahdara. Association genetics and heterologous expression in yeast cells identified a single point mutation associated with an alteration of KCS18 activity, uncovering the molecular bases for the modulation of VLCFA content in these two natural populations of Arabidopsis. Identification of this kcs18 mutant with altered activity opens new perspectives for the modulation of oil composition in crop plants. Citation: Jasinski S, Lecureuil A, Miquel M, Loudet O, Raffaele S, et al. (2012) Natural Variation in Seed Very Long Chain Fatty Acid Content Is Controlled by a New Isoform of KCS18 in Arabidopsis thaliana. PLoS ONE 7(11): e49261. doi:10.1371/journal.pone.0049261
Published: 2012

37. Genome evolution in filamentous plant pathogens: why bigger can be better

Author: Sophien Kamoun, Sylvain Raffaele, Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), The Sainsbury Laboratory, John Innes Centre [Norwich], Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), and The Sainsbury Laboratory [Norwich] (TSL)
Subjects: 0106 biological sciences, Genome evolution, Virulence Factors, Virulence, Bacterial genome size, Biology, 01 natural sciences, Microbiology, Genome, Evolution, Molecular, 03 medical and health sciences, plante pathogène, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Genome size, Gene, 030304 developmental biology, Plant Diseases, 2. Zero hunger, Genetics, 0303 health sciences, General Immunology and Microbiology, Host (biology), Fungi, Infectious Diseases, Host-Pathogen Interactions, évolution du génome, Genome, Fungal, 010606 plant biology & botany
Abstract: Many species of fungi and oomycetes are plant pathogens of great economic importance. Over the past 7 years, the genomes of more than 30 of these filamentous plant pathogens have been sequenced, revealing remarkable diversity in genome size and architecture. Whereas the genomes of many parasites and bacterial symbionts have been reduced over time, the genomes of several lineages of filamentous plant pathogens have been shaped by repeat-driven expansions. In these lineages, the genes encoding proteins involved in host interactions are frequently polymorphic and reside within repeat-rich regions of the genome. Here, we review the properties of these adaptable genome regions and the mechanisms underlying their plasticity, and we illustrate cases in which genome plasticity has contributed to the emergence of new virulence traits. We also discuss how genome expansions may have had an impact on the co-evolutionary conflict between these filamentous plant pathogens and their hosts.
Published: 2012

38. Towards a quantitative assessment of architectures for FSPM

Author: Palubicki, Wojciech, Godin, Christophe, Prusinkiewicz, Premyslaw, Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), Modeling plant morphogenesis at different scales, from genes to phenotype (VIRTUAL PLANTS), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de la Recherche Agronomique (INRA)-Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), 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)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-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)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Développement et amélioration des plantes (UMR DAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Department of Computer Science [Calgary] (CPSC), University of Calgary, DeJong, Theodore and Da Silva, David, Sainsbury Laboratory Cambridge, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), 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)-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)-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)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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: [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, ComputingMilieux_MISCELLANEOUS
Abstract: International audience; no abstract
Published: 2010

39. Putative pectate lyase PLL12 and callose deposition through polar CALS7 are necessary for long-distance phloem transport in Arabidopsis

Author: Lothar Kalmbach, Matthieu Bourdon, Ilya Belevich, Josip Safran, Adrien Lemaire, Jung-ok Heo, Sofia Otero, Bernhard Blob, Jérôme Pelloux, Eija Jokitalo, Ykä Helariutta, Department of Plant Molecular Biology, Université de Lausanne = University of Lausanne (UNIL), Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), Biologie du Fruit, Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1 (UB), Helsinki Institute of Life Science (HiLIFE), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Transfrontalière BioEcoAgro - UMR 1158 (BioEcoAgro), Université d'Artois (UA)-Université de Liège-Université de Picardie Jules Verne (UPJV)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-JUNIA (JUNIA), Université catholique de Lille (UCL)-Université catholique de Lille (UCL), Biologie des Plantes et Innovation - UR UPJV 3900 (BIOPI), Université de Picardie Jules Verne (UPJV)-Transfrontalière BioEcoAgro - UMR 1158 (BioEcoAgro), Université catholique de Lille (UCL)-Université catholique de Lille (UCL)-Université d'Artois (UA)-Université de Liège-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-JUNIA (JUNIA), HiLIFE - Institute of Biotechnology [Helsinki] (BI), Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, and Apollo - University of Cambridge Repository
Subjects: pectin, cell wall, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, symplastic transport, General Agricultural and Biological Sciences, phloem, General Biochemistry, Genetics and Molecular Biology, callose, plant vascular development
Abstract: In plants, the phloem distributes photosynthetic products for metabolism and storage over long distances. It relies on specialized cells, the sieve elements, which are enucleated and interconnected through large so-called sieve pores in their adjoining cell walls. Reverse genetics identified PECTATE LYASE LIKE 12 (PLL12) as critical for plant growth and development. Using genetic complementations, we established that PLL12 is required exclusively late during sieve element differentiation. Structural homology modeling, enzyme inactivation, and overexpression suggest a vital role for PLL12 in sieve element specific pectin remodeling. While short distance symplastic diffusion is unaffected, the pll12 mutant is unable to accommodate sustained plant development due to an incapacity to accommodate increasing hydraulic demands on phloem long distance transport as the plant grows – a defect that is aggravated when combined with another sieve element specific mutant callose synthase 7 (cals7). Establishing CALS7 as a specific sieve pore marker, we investigated the sub36 cellular dynamics of callose deposition in the developing sieve plate. Using fluorescent CALS7 then allowed identifying structural defects in pll12 sieve pores that are moderate at the cellular level but become physiologically relevant due to the serial arrangement of sieve elements in the sieve tube. Overall, pectin degradation through PLL12 appears subtle in quantitative terms. We therefore speculate that PLL12 may act as a regulator to locally remove homogalacturonan thus potentially enabling further extracellular enzymes to access and modify the cell wall during sieve pore maturation.
Published: 2023

40. Direct inhibition of phosphate transport by immune signaling in Arabidopsis

Author: Dindas, Julian, DeFalco, Thomas A, Yu, Gang, Zhang, Lu, David, Pascale, Bjornson, Marta, Thibaud, Marie-Christine, Custódio, Valéria, Castrillo, Gabriel, Nussaume, Laurent, Macho, Alberto P, Zipfel, Cyril, University of Zurich, Zipfel, Cyril, Zurich Basel Plant Science Center, Universität Zürich [Zürich] = University of Zurich (UZH)-University of Basel (Unibas), The Sainsbury Laboratory [Norwich] (TSL), National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences [Changchun Branch] (CAS), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-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), Plant Environmental Physiology and Stress Signaling (PEPSS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), University of Nottingham, UK (UON), European Project: 309858,EC:FP7:ERC,ERC-2012-StG_20111109,PHOSPHINNATE(2012), European Project: 773153,IMMUNO-PEPTALK, 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)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Signalisation de l'Adaptation des Végétaux à l'Environnement (SAVE), and Biologie végétale et microbiologie environnementale - UMR7265 (BVME)
Subjects: 0106 biological sciences, kinase, [SDV]Life Sciences [q-bio], Arabidopsis, Genetics and Molecular Biology, 1100 General Agricultural and Biological Sciences, 580 Plants (Botany), 01 natural sciences, Plant Roots, General Biochemistry, Genetics and Molecular Biology, Phosphates, 03 medical and health sciences, 10126 Department of Plant and Microbial Biology, Gene Expression Regulation, Plant, 1300 General Biochemistry, Genetics and Molecular Biology, Report, root microbiome, Phosphate Transport Proteins, Gene Regulatory Networks, 10211 Zurich-Basel Plant Science Center, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, phosphate, 2. Zero hunger, 0303 health sciences, Arabidopsis Proteins, 2800 General Neuroscience, PHT1, 15. Life on land, electrophysiology, General Biochemistry, plant immunity, General Agricultural and Biological Sciences, 010606 plant biology & botany
Abstract: Summary Soil availability of inorganic ortho-phosphate (PO43−, Pi) is a key determinant of plant growth and fitness.1 Plants regulate the capacity of their roots to take up inorganic phosphate by adapting the abundance of H+-coupled phosphate transporters of the PHOSPHATE TRANSPORTER 1 (PHT1) family2 at the plasma membrane (PM) through transcriptional and post-translational changes driven by the genetic network of the phosphate starvation response (PSR).3, 4, 5, 6, 7, 8 Increasing evidence also shows that plants integrate immune responses to alleviate phosphate starvation stress through the association with beneficial microbes.9, 10, 11 Whether and how such phosphate transport is regulated upon activation of immune responses is yet uncharacterized. To address this question, we first developed quantitative assays based on changes in the electrical PM potential to measure active Pi transport in roots in real time. By inserting micro-electrodes into bulging root hairs, we were able to determine key characteristics of phosphate transport in intact Arabidopsis thaliana (hereafter Arabidopsis) seedlings. The fast Pi-induced depolarization observed was dependent on the activity of the major phosphate transporter PHT1;4. Notably, we observed that this PHT1;4-mediated phosphate uptake is repressed upon activation of pattern-triggered immunity. This inhibition depended on the receptor-like cytoplasmic kinases BOTRYTIS-INDUCED KINASE 1 (BIK1) and PBS1-LIKE KINASE 1 (PBL1), which both phosphorylated PHT1;4. As a corollary to this negative regulation of phosphate transport by immune signaling, we found that PHT1;4-mediated phosphate uptake normally negatively regulates anti-bacterial immunity in roots. Collectively, our results reveal a mechanism linking plant immunity and phosphate homeostasis, with BIK1/PBL1 providing a molecular integration point between these two important pathways., Highlights • Real-time, PHT1-mediated Pi transport can be measured in roots via PM depolarization • Immune activation represses Pi transport in a BIK1/PBL1-dependent manner • PHT1s are direct substrates of BIK1 and PBL1 • Pi uptake modulates anti-bacterial immunity and the root microbiome, Phosphate (Pi) is a crucial determinant of plant growth and fitness. Dindas, DeFalco, et al. show that immune activation in roots actively represses Pi uptake. This inhibition is achieved via direct phosphorylation of key Pi transporters by the central immune kinases BIK1 and PBL1, which leads to increased anti-bacterial defense.
Published: 2022

41. A combination of chitooligosaccharide and lipochitooligosaccharide recognition promotes arbuscular mycorrhizal associations in Medicago truncatula

Author: Kira Gysel, Feng Feng, Simona Radutoiu, Zoltan Bozsoki, Giles E. D. Oldroyd, Kasper R. Andersen, Mikkel B. Thygesen, Sébastien Fort, Jongho Sun, Guru V. Radhakrishnan, Aleksander Gavrin, Jens Stougaard, Tak Lee, Feng, Feng [0000-0003-1382-305X], Radhakrishnan, Guru V [0000-0003-0381-8804], Lee, Tak [0000-0001-7008-7605], Fort, Sébastien [0000-0002-6133-9900], Gavrin, Aleksander [0000-0003-0179-8491], Gysel, Kira [0000-0003-4245-9998], Thygesen, Mikkel B [0000-0002-0158-2802], Andersen, Kasper Røjkjær [0000-0002-4415-8067], Stougaard, Jens [0000-0002-9312-2685], Oldroyd, Giles ED [0000-0002-5245-6355], Apollo - University of Cambridge Repository, Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), Aarhus University [Aarhus], Centre de Recherches sur les Macromolécules Végétales (CERMAV ), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), University of Copenhagen = Københavns Universitet (KU), and Oldroyd, Giles E D [0000-0002-5245-6355]
Subjects: 0106 biological sciences, 0301 basic medicine, Lipopolysaccharides, General Physics and Astronomy, Oligosaccharides, Chitin, 01 natural sciences, Plant Roots, Cell Wall, Gene Expression Regulation, Plant, Mycorrhizae, Plant symbiosis, Plant Immunity, Arbuscular mycorrhiza, lcsh:Science, Plant Proteins, Regulation of gene expression, Multidisciplinary, biology, Cell Death, Kinase, food and beverages, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Medicago truncatula, Cell biology, 3. Good health, Signalling, Signal Transduction, Science, Protein Serine-Threonine Kinases, Article, General Biochemistry, Genetics and Molecular Biology, Cell wall, 03 medical and health sciences, Symbiosis, Tobacco, Pattern recognition receptors in plants, Chitosan, fungi, General Chemistry, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, Plant Leaves, 030104 developmental biology, lcsh:Q, Function (biology), [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis, 010606 plant biology & botany
Abstract: Plants associate with beneficial arbuscular mycorrhizal fungi facilitating nutrient acquisition. Arbuscular mycorrhizal fungi produce chitooligosaccharides (COs) and lipo-chitooligosaccharides (LCOs), that promote symbiosis signalling with resultant oscillations in nuclear-associated calcium. The activation of symbiosis signalling must be balanced with activation of immunity signalling, which in fungal interactions is promoted by COs resulting from the chitinaceous fungal cell wall. Here we demonstrate that COs ranging from CO4-CO8 can induce symbiosis signalling in Medicago truncatula. CO perception is a function of the receptor-like kinases MtCERK1 and LYR4, that activate both immunity and symbiosis signalling. A combination of LCOs and COs act synergistically to enhance symbiosis signalling and suppress immunity signalling and receptors involved in both CO and LCO perception are necessary for mycorrhizal establishment. We conclude that LCOs, when present in a mix with COs, drive a symbiotic outcome and this mix of signals is essential for arbuscular mycorrhizal establishment., Polysaccharide molecules chitooligosaccharides (COs) and peptidoglycan not only activate plant immunity but also trigger plant symbiosis signalling. Here the authors show that a combination of COs and lipochitooligosaccharides (LCOs) act synergistically to suppress immunity and promote symbiosis to facilitate beneficial fungal associations.
Published: 2019

42. Traitement d'image 4D (espace + temps) pour caractérisation quantitative de la croissance et de la déconstruction des plantes

Author: Refahi, Yassin, Paës, Gabriel, Traas, Jan, Jönsson, Henrik, Fractionnement des AgroRessources et Environnement (FARE), Université de Reims Champagne-Ardenne (URCA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Reproduction et développement des plantes (RDP), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), ANR-19-CE43-0010,BIOMOD,Analyse Multiéchelle et Modélisation Spatio-temporelle de la Déconstruction de la Biomasse Lignocellulosique(2019), Yassin, Refahi, and Analyse Multiéchelle et Modélisation Spatio-temporelle de la Déconstruction de la Biomasse Lignocellulosique - - BIOMOD2019 - ANR-19-CE43-0010 - AAPG2019 - VALID
Subjects: [SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2021

43. Subcellular and supracellular mechanical stress prescribes cytoskeleton behavior in Arabidopsis cotyledon pavement cells

Author: Meyerowitz, Elliot [Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom, Division of Biology and Biological Engineering, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, United States]
Published: 2014
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44. Chaperone-like protein DAY plays critical roles in photomorphogenesis

Author: Sung Hee Lee, Hee-Kyung Ahn, Tak Lee, Insuk Lee, Hyun Sook Pai, Ilyeong Choi, Dong Hye Seo, Ji Woo Kim, Ho Seok Lee, Huikyong Cho, Jae Hee Kim, Julian Bünting, Young Eun Jeon, Youssef Belkhadir, D. Lee, Tae Wuk Kim, Jung Min Lee, Man Ho Oh, Ahn, Hee-Kyung [0000-0002-8884-0156], Lee, Tak [0000-0001-7008-7605], Lee, Du-Hwa [0000-0003-4106-7730], Lee, Insuk [0000-0003-3146-6180], Belkhadir, Youssef [0000-0001-7149-7139], Pai, Hyun-Sook [0000-0003-1345-5840], Apollo - University of Cambridge Repository, Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Yonsei University Seoul, Korea, University of East Anglia [Norwich] (UEA), Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-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 Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), College of Life Sciences and Biotechnology, Korea University, Chungnam National University (CNU), Hanyang University, Vienna Biocenter - VBC [Austria], and Yonsei University
Subjects: 0106 biological sciences, 0301 basic medicine, Chlorophyll, Chloroplasts, Light, [SDV]Life Sciences [q-bio], Arabidopsis, General Physics and Astronomy, 631/449/2653/1359, 01 natural sciences, chemistry.chemical_compound, 38/1, Gene Expression Regulation, Plant, Morphogenesis, Brassinosteroid, RNA-Seq, 14/19, 13/89, Multidisciplinary, biology, Chemistry, article, Plant morphogenesis, Plant physiology, food and beverages, Plants, Genetically Modified, Recombinant Proteins, Cell biology, Chloroplast, Transmembrane domain, Gene Knockdown Techniques, Photomorphogenesis, 38/39, Microtubule-Associated Proteins, Signal Transduction, Science, 38/90, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Brassinosteroids, Etiolation, Light responses, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Endomembrane system, 14/35, 631/449/2686, Arabidopsis Proteins, fungi, Membrane Proteins, General Chemistry, HSP40 Heat-Shock Proteins, 030104 developmental biology, Seedlings, Chaperone (protein), Mutation, 14/63, biology.protein, Protein Kinases, Biogenesis, 010606 plant biology & botany
Abstract: Photomorphogenesis, light-mediated development, is an essential feature of all terrestrial plants. While chloroplast development and brassinosteroid (BR) signaling are known players in photomorphogenesis, proteins that regulate both pathways have yet to be identified. Here we report that DE-ETIOLATION IN THE DARK AND YELLOWING IN THE LIGHT (DAY), a membrane protein containing DnaJ-like domain, plays a dual-role in photomorphogenesis by stabilizing the BR receptor, BRI1, as well as a key enzyme in chlorophyll biosynthesis, POR. DAY localizes to both the endomembrane and chloroplasts via its first transmembrane domain and chloroplast transit peptide, respectively, and interacts with BRI1 and POR in their respective subcellular compartments. Using genetic analysis, we show that DAY acts independently on BR signaling and chlorophyll biogenesis. Collectively, this work uncovers DAY as a factor that simultaneously regulates BR signaling and chloroplast development, revealing a key regulator of photomorphogenesis that acts across cell compartments., Chloroplast development and brassinosteroid (BR) signaling both regulate plant photomorphogenesis. Here the authors show that DAY, a DnaJ-like domain-containing membrane protein, regulates both processes by binding and stabilizing both BRI1, the BR receptor, and POR, a key enzyme in chlorophyll biosynthesis.
Published: 2021
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45. Cassava diseases caused by Xanthomonas phaseoli pv. manihotis and Xanthomonas cassavae

Author: Zárate‐Chaves, Carlos, Gómez de la Cruz, Diana, Verdier, Valérie, López, Camilo, Bernal, Adriana, Szurek, Boris, Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-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 Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), The Sainsbury Laboratory [Norwich] (TSL), Universidad Nacional de Colombia [Bogotà] (UNAL), Universidad de los Andes [Bogota] (UNIANDES), Challenge Research Program on RTB, ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, 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: quantitative resistance, Xanthomonas, fungi, cassava bacterial blight, food and beverages, cassava bacterial necrosis, cassava, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy
Abstract: International audience; Xanthomonas phaseoli pv. manihotis (Xpm) and X. cassavae (Xc) are two bacterial pathogens attacking cassava. Cassava bacterial blight (CBB) is a systemic disease caused by Xpm, which might have dramatic effects on plant growth and crop production. Cassava bacterial necrosis is a nonvascular disease caused by Xc with foliar symptoms similar to CBB, but its impacts on the plant vigour and the crop are limited. In this review, we describe the epidemiology and ecology of the two pathogens, the impacts and management of the diseases, and the main research achievements for each pathosystem. Because Xc data are sparse, our main focus is on Xpm and CBB.
Published: 2021

46. What is quantitative plant biology?

Author: Autran, Daphné, Bassel, George W., Chae, Eunyoung, Ezer, Daphne, Ferjani, Ali, Fleck, Christian, Hamant, Olivier, Hartmann, Félix P., Jiao, Yuling, Johnston, Iain G., Kwiatkowska, Dorota, Lim, Boon L., Mahönen, Ari Pekka, Morris, Richard J., Mulder, Bela M., Nakayama, Naomi, Sozzani, Ross, Strader, Lucia C., Ten Tusscher, Kirsten, Ueda, Minako, Wolf, Sebastian, Sub Theoretical Biology, Theoretical Biology and Bioinformatics, Sub Theoretical Biology, Theoretical Biology and Bioinformatics, Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), University of Birmingham [Birmingham], National University of Singapore (NUS), Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), Tokyo Gakugei University, University of Freiburg [Freiburg], Reproduction et développement des plantes (RDP), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Physique et Physiologie Intégratives de l’Arbre en environnement Fluctuant (PIAF), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), University of Chinese Academy of Sciences [Beijing] (UCAS), University of Bergen (UiB), Silesian University in Opava, The University of Hong Kong (HKU), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, John Innes Centre [Norwich], FOM Institute for Atomic and Molecular Physics (AMOLF), Imperial College London, North Carolina State University [Raleigh] (NC State), University of North Carolina System (UNC), Utrecht University [Utrecht], Tohoku University [Sendai], Universität Heidelberg [Heidelberg], Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Biotechnology and Biological Sciences Research Council (BBSRC), and Universität Heidelberg [Heidelberg] = Heidelberg University
Subjects: 0106 biological sciences, 0301 basic medicine, Computer science, biology, Ecology (disciplines), Rehabilitation, biomathematics, Physical Therapy, Sports Therapy and Rehabilitation, General Medicine, Plant, Plant biology, 01 natural sciences, Data science, Field (computer science), 03 medical and health sciences, 030104 developmental biology, Robustness (computer science), Citizen science, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Noise (video), quantitative plant biology, Topology (chemistry), 010606 plant biology & botany, Interdisciplinarity
Abstract: Quantitative plant biology is an interdisciplinary field that builds on a long history of biomathematics and biophysics. Today, thanks to high spatiotemporal resolution tools and computational modelling, it sets a new standard in plant science. Acquired data, whether molecular, geometric or mechanical, are quantified, statistically assessed and integrated at multiple scales and across fields. They feed testable predictions that, in turn, guide further experimental tests. Quantitative features such as variability, noise, robustness, delays or feedback loops are included to account for the inner dynamics of plants and their interactions with the environment. Here, we present the main features of this ongoing revolution, through new questions around signalling networks, tissue topology, shape plasticity, biomechanics, bioenergetics, ecology and engineering. In the end, quantitative plant biology allows us to question and better understand our interactions with plants. In turn, this field opens the door to transdisciplinary projects with the society, notably through citizen science.
Published: 2021

47. Host-interactor screens of Phytophthora infestans RXLR proteins reveal vesicle trafficking as a major effector-targeted process

Author: Jan Sklenar, Yasin F. Dagdas, Silke Robatzek, Sophien Kamoun, Joe Win, Rosa Lozano-Durán, Jack H. Vossen, Benjamin Petre, Mauricio P Contreras, Alexandra M. E. Jones, Ahmed Abd-El-Haliem, Sebastian Schornack, Frank L.H. Menke, Roger Castells-Graells, Tolga O. Bozkurt, Martin H. Schattat, The Sainsbury Laboratory [Norwich] (TSL), and Biotechnology and Biological Sciences Research Council (BBSRC)
Subjects: 0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], Plant Biology, Nicotiana benthamiana, Plant Science, 0601 Biochemistry and Cell Biology, 01 natural sciences, Interactome, 2.1 Biological and endogenous factors, Protein Interaction Maps, Aetiology, Pathogen, Plant Proteins, 0303 health sciences, Effector, food and beverages, Cell biology, Infectious Diseases, Host-Pathogen Interactions, Phytophthora infestans, Infection, SNARE Proteins, Endosome, Immunoprecipitation, Large-Scale Biology Articles, Plant Biology & Botany, 0607 Plant Biology, Endosomes, Biology, 03 medical and health sciences, Tobacco, Genetics, Life Science, Transport Vesicles, SB, 030304 developmental biology, Plant Diseases, 0604 Genetics, Host (biology), Cell Membrane, fungi, QK, Proteins, Cell Biology, biology.organism_classification, QR, Plant Breeding, 030104 developmental biology, Biochemistry and Cell Biology, Function (biology), 010606 plant biology & botany
Abstract: Pathogens modulate plant cell structure and function by secreting effectors into host tissues. Effectors typically function by associating with host molecules and modulating their activities. This study aimed to identify the host processes targeted by the RXLR class of host-translocated effectors of the potato blight pathogen Phytophthora infestans. To this end, we performed an in planta protein-protein interaction screen by transiently expressing P. infestans RXLR effectors in Nicotiana benthamiana leaves followed by co-immunoprecipitation (co-IP) and liquid chromatography tandem mass spectrometry (LC-MS/MS). This screen generated an effector-host protein interactome matrix of 59 P. infestans RXLR effectors x 586 N. benthamiana proteins. Classification of the host interactors into putative functional categories revealed over 35 biological processes possibly targeted by P. infestans. We further characterized the PexRD12/31 family of RXLR-WY effectors, which associate and co-localize with components of the vesicle trafficking machinery. One member of this family, PexRD31, increased the number of FYVE positive vesicles in N. benthamiana cells. FYVE positive vesicles also accumulated in leaf cells near P. infestans hyphae, indicating that the pathogen may enhance endosomal trafficking during infection. We anticipate that the interactome dataset we generated will serve as a useful community resource for functional studies of P. infestans effectors and of effector-targeted host processes.
Published: 2021

48. The molecular signatures of compatible and incompatible pollination in Arabidopsis

Author: Frédérique Rozier, Jonathan Legrand, Martine Da Rocha, Jérémy Just, Thierry Gaude, Antoine Larrieu, Isabelle Fobis-Loisy, Lucie Riglet, Chie Kodera, Fobis-Loisy, Isabelle [0000-0003-4522-2515], Apollo - University of Cambridge Repository, Reproduction et développement des plantes (RDP), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut Sophia Agrobiotech (ISA), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Côte d'Azur (UCA), Ecole normale supérieure de Lyon (Ens Lyon), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Nice Sophia Antipolis (1965 - 2019) (UNS), University of Leeds, Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), and ANR-14-CE11-0021,Invader,Réponse des épidermes végétaux aux intrusions cellulaires(2014)
Subjects: 0106 biological sciences, incompatible pollination, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Pollination, Pollen-stigma interaction, [SDV]Life Sciences [q-bio], Arabidopsis, Single-nucleotide polymorphism, QH426-470, medicine.disease_cause, 01 natural sciences, Transcriptome, 03 medical and health sciences, Pollen, medicine, Genetics, Arabidopsis thaliana, Gene, 030304 developmental biology, 0303 health sciences, PTI pathway, biology, Compatible / incompatible pollination, food and beverages, Compatible, RNA sequencing, biology.organism_classification, Male-female transcriptome, DNA microarray, TP248.13-248.65, Research Article, 010606 plant biology & botany, Biotechnology, SNPs
Abstract: Background Fertilization in flowering plants depends on the early contact and acceptance of pollen grains by the receptive papilla cells of the stigma. Deciphering the specific transcriptomic response of both pollen and stigmatic cells during their interaction constitutes an important challenge to better our understanding of this cell recognition event. Results Here we describe a transcriptomic analysis based on single nucleotide polymorphisms (SNPs) present in two Arabidopsis thaliana accessions, one used as female and the other as male. This strategy allowed us to distinguish 80% of transcripts according to their parental origins. We also developed a tool which predicts male/female specific expression for genes without SNP. We report an unanticipated transcriptional activity triggered in stigma upon incompatible pollination and show that following compatible interaction, components of the pattern-triggered immunity (PTI) pathway are induced on the female side. Conclusions Our work unveils the molecular signatures of compatible and incompatible pollinations both at the male and female side. We provide invaluable resource and tools to identify potential new molecular players involved in pollen-stigma interaction.
Published: 2021
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49. Molecular mechanism of cytokinin-activated cell division in Arabidopsis

Author: Elliot M. Meyerowitz, Henrik Jönsson, Katharina Schiessl, Weibing Yang, A. V. Gurzadyan, Raymond Wightman, Sandra Cortijo, Niklas Korsbo, Pawel Roszak, Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), Howard Hughes Medical Institute (HHMI), Wightman, Raymond [0000-0003-1295-4875], Korsbo, Niklas [0000-0001-9811-3190], Jonsson, Henrik [0000-0003-2340-588X], Schiessl, Katharina [0000-0002-7694-0619], Gurzadyan, Aram [0000-0003-0618-9361], and Apollo - University of Cambridge Repository
Subjects: 0106 biological sciences, Cytoplasm, Cytokinins, Cell division, [SDV]Life Sciences [q-bio], Meristem, Active Transport, Cell Nucleus, Arabidopsis, Mitosis, Meristem growth, Karyopherins, 01 natural sciences, 03 medical and health sciences, chemistry.chemical_compound, Plant Growth Regulators, Gene Expression Regulation, Plant, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, 030304 developmental biology, Cell Nucleus, 0303 health sciences, Multidisciplinary, Arabidopsis Proteins, Cell growth, fungi, food and beverages, Cell Cycle Checkpoints, Cell biology, chemistry, Cytokinin, Trans-Activators, Signal transduction, Cell Division, Cytokinesis, Signal Transduction, 010606 plant biology & botany
Abstract: Cell cycle regulation The hormone cytokinin regulates various aspects of plant development and physiology, largely by managing cell proliferation. Yang et al. show that cytokinin promotes nuclear localization of the transcription factor MYB3R4, which activates the expression of two importins and genes that tip the cell into the next phase of the cell cycle. The importins facilitate further MYB3R4 accumulation within the nucleus, accelerating the progression into mitosis. MYB3R4 and the importins dissipate when the nuclear membrane dissolves at prometaphase, so there is only one round of mitotic activation per cell cycle. Science , this issue p. 1350
Published: 2021

50. Plant evolution driven by symbiotic and pathogenic interactions

Author: Delaux, Pierre-Marc, Schornack, Sebastian, Evolution des Interactions Plantes-Microorganismes, Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), ANR-17-CE20-0006,EVOLSYM,Découverte de réseaux moléculaires symbiotiques chez les plantes par des approches basée sur l'évolution(2017), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), European Project: 637537,H2020,ERC-2014-STG,ACHILLES-HEEL(2015), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)
Subjects: fungi, food and beverages, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: International audience; During 450 million years of diversification on land, plants and microbes have evolved together. This is reflected in today's continuum of associations ranging from parasitism to mutualism. Through phylogenetics, cell biology and reverse genetics extending beyond flowering plants into Bryophytes, scientists have started to unravel the genetic basis and evolutionary trajectories of plant-microbe associations. Protection against pathogens and support of beneficial, symbiotic, microorganisms are sustained by a blend of conserved and clade-specific plant mechanisms evolving at different speeds. We propose that symbiosis consistently emerges from the co-option of protection mechanisms and general cell biology principles. Exploring and harnessing the diversity of molecular mechanisms employed in non-flowering plant-microbe interactions may extend the possibilities for engineering symbiosis-competent and pathogen resilient crops.
Published: 2021

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