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1. Improving crop Yield potential: Underlying biological processes and future prospects

Author

Burgess, Alexandra, Masclaux-Daubresse, Céline, Strittmatter, Günter, Weber, Andreas, Taylor, Samuel Harry, Harbinson, Jeremy, Yin, Xinyou, Long, Stephen, Paul, Matthew, Westhoff, Peter, Loreto, Francesco, Ceriotti, Aldo, Saltenis, Vandasue, Pribil, Mathias, Nacry, Philippe, Scharff, Lars, Jensen, Poul Erik, Muller, Bertrand, Cohan, Jean‐pierre, Foulkes, John, Rogowsky, Peter, Debaeke, Philippe, Meyer, Christian, Nelissen, Hilde, Inzé, Dirk, Klein Lankhorst, René, Parry, Martin, Murchie, Erik, Baekelandt, Alexandra, University of Nottingham, UK (UON), Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf]-Max Planck Institute for Plant Breeding Research (MPIPZ)-Universität zu Köln = University of Cologne, Lancaster Environment Centre, Lancaster University, Wageningen University and Research [Wageningen] (WUR), University College of London [London] (UCL), University of Illinois at Urbana-Champaign [Urbana], University of Illinois System, Rothamsted Research, Biotechnology and Biological Sciences Research Council (BBSRC), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), University of Copenhagen = Københavns Universitet (UCPH), 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 de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Food Science [Copenhagen] (UCPH FOOD), Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), 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), ARVALIS - Institut du végétal [Paris], 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), AGroécologie, Innovations, teRritoires (AGIR), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics, Universiteit Gent = Ghent University (UGENT), European Commission 817690, and European Project: 817690,ERC

Subjects
food supply, photosynthesis, [SDV]Life Sciences [q-bio], [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, crop yield, nutrient remobilisation, crop improvement, organ growth
Abstract

International audience; The growing world population and global increases in the standard of living both result in an increasing demand for food, feed and other plant- derived products. In the coming years, plant- based research will be among the major drivers ensuring food security and the expansion of the bio- based economy. Crop productivity is determined by several factors, including the available physical and agricultural resources, crop management, and the resource use efficiency, quality and intrinsic yield potential of the chosen crop. This review focuses on intrinsic yield potential, since understanding its determinants and their biological basis will allow to maximize the plant's potential in food and energy production. Yield potential is determined by a variety of complex traits that integrate strictly regulated processes and their underlying gene regulatory networks. Due to this inherent complexity, numerous potential targets have been identified that could be exploited to increase crop yield. These encompass diverse metabolic and physical processes at the cellular, organ and canopy level. We present an overview of some of the distinct biological processes considered to be crucial for yield determination that could further be exploited to improve future crop productivity.

Published
2023
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2. Paving the way towards future‐proofing our crops

Author

Alexandra Baekelandt, Vandasue L. R. Saltenis, Philippe Nacry, Aleksandra Malyska, Marc Cornelissen, Amrit Kaur Nanda, Abhishek Nair, Peter Rogowsky, Laurens Pauwels, Bertrand Muller, Jonas Collén, Jonas Blomme, Mathias Pribil, Lars B. Scharff, Jessica Davies, Ralf Wilhelm, Norbert Rolland, Jeremy Harbinson, Wout Boerjan, Erik H. Murchie, Alexandra J. Burgess, Jean‐Pierre Cohan, Philippe Debaeke, Sébastien Thomine, Dirk Inzé, René Klein Lankhorst, Martin A. J. Parry, Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics, Universiteit Gent = Ghent University (UGENT), University of Copenhagen = Københavns Universitet (UCPH), 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), European Commission - DG Research and Innovation, BASF Agricultural Solutions Belgium NV, Plants for the Future European Technology Platform, Wageningen University and Research [Wageningen] (WUR), 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), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), 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), Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Department of Plant and Environmental Sciences [Copenhagen], Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Julius Kühn-Institut - Federal Research Centre for Cultivated Plants (JKI), Dynamique du protéome et biogenèse du chloroplaste (ChloroGenesis), Physiologie cellulaire et végétale (LPCV), 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), University of Nottingham, UK (UON), ARVALIS - Institut du Végétal [Ouzouer le Marché] (ARVALIS), ARVALIS - Institut du végétal [Paris], AGroécologie, Innovations, teRritoires (AGIR), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Lancaster Environment Centre, Lancaster University, and European Project: 817690,H2020 CropBooster-P

Subjects
Marketing and Consumer Behaviour, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, DIVERSITY, Biophysics, IMPROVEMENT, METABOLISM, future- proofed crops, future world scenarios, future-proofed crops, plant research, LIGNIN DEPOSITION, PLANT, crop productivity, Renewable Energy, Sustainability and the Environment, BioSolar Cells, Biology and Life Sciences, Forestry, crop yield, PE&RC, AMARANTH, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, Biofysica, DOMESTICATION, PHOSPHOLIPASE, Marktkunde en Consumentengedrag, EPS, Agronomy and Crop Science, TRAITS, RESISTANCE, Food Science
Abstract

International audience; To meet the increasing global demand for food, feed, fibre and other plant- derivedproducts, a steep increase in crop productivity is a scientifically and technicallychallenging imperative. The CropBooster- P project, a response to the H2020call ‘Future proofing our plants’, is developing a roadmap for plant research toimprove crops critical for the future of European agriculture by increasing cropyield, nutritional quality, value for non- food applications and sustainability.However, if we want to efficiently improve crop production in Europe and pri-oritize methods for crop trait improvement in the coming years, we need to takeinto account future socio- economic, technological and global developments, in-cluding numerous policy and socio- economic challenges and constraints. Basedon a wide range of possible global trends and key uncertainties, we developedfour extreme future learning scenarios that depict complementary future devel-opments. Here, we elaborate on how the scenarios could inform and direct fu-ture plant research, and we aim to highlight the crop improvement approachesthat could be the most promising or appropriate within each of these four futureworld scenarios. Moreover, we discuss some key plant technology options thatwould need to be developed further to meet the needs of multiple future learningscenarios, such as improving methods for breeding and genetic engineering. Inaddition, other diverse platforms of food production may offer unrealized poten-tial, such as underutilized terrestrial and aquatic species as alternative sources ofnutrition and biomass production. We demonstrate that although several meth-ods or traits could facilitate a more efficient crop production system in some ofthe scenarios, others may offer great potential in all four of the future learningscenarios. Altogether, this indicates that depending on which future we are head-ing toward, distinct plant research fields should be given priority if we are to meetour food, feed and non- food biomass production needs in the coming decades.

Published
2023
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3. Two chemically distinct root lignin barriers control solute and water balance

Author

Priya Ramakrishna, David E. Salt, Catherine Lapierre, Guilhem Reyt, Ashley Love, Kris Morreel, Monica Calvo-Polanco, Yann Boursiac, Paulina Flis, Satoshi Fujita, Isai Salas-González, David Tiemessen, Niko Geldner, Wout Boerjan, Gabriel Castrillo, Michael W. George, Future Food Beacon of Excellence & School of Biosciences, Curriculum in Bioinformatics and Computational Biology, University of North Carolina [Chapel Hill] (UNC), University of North Carolina System (UNC)-University of North Carolina System (UNC), Department of Plant Molecular Biology, Biophore, Université de Lausanne (UNIL), School of Chemistry [Nottingham, UK] (School of Chemistry), University of Nottingham, UK (UON), Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics, Universiteit Gent = Ghent University [Belgium] (UGENT), 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), 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], Arabidopsis, General Physics and Astronomy, STRIP DIFFUSION BARRIER, 01 natural sciences, Lignin, Plant Roots, Diffusion, chemistry.chemical_compound, CASPARIAN STRIP, RNA-Seq, DEPOSITION, Multidisciplinary, biology, Phenylpropanoid, PARTIAL RESISTANCE, Phenylpropionates, Chemistry, Cell wall, Plant physiology, food and beverages, ARABIDOPSIS, Plants, Genetically Modified, FAMILY, Casparian strip, Science, Genetics and Molecular Biology, macromolecular substances, complex mixtures, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, Xylem, LIGNIFICATION, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, BIOSYNTHESIS, TRANSCRIPTION FACTOR MYB15, Arabidopsis Proteins, Cell Membrane, fungi, technology, industry, and agriculture, Biology and Life Sciences, Water, General Chemistry, biology.organism_classification, Plant cell, MEDICAGO-TRUNCATULA, 030104 developmental biology, Microscopy, Fluorescence, Plant signalling, General Biochemistry, Mutation, Biophysics, Endodermis, Secondary metabolism, 010606 plant biology & botany, Transcription Factors
Abstract

Lignin is a complex polymer deposited in the cell wall of specialised plant cells, where it provides essential cellular functions. Plants coordinate timing, location, abundance and composition of lignin deposition in response to endogenous and exogenous cues. In roots, a fine band of lignin, the Casparian strip encircles endodermal cells. This forms an extracellular barrier to solutes and water and plays a critical role in maintaining nutrient homeostasis. A signalling pathway senses the integrity of this diffusion barrier and can induce over-lignification to compensate for barrier defects. Here, we report that activation of this endodermal sensing mechanism triggers a transcriptional reprogramming strongly inducing the phenylpropanoid pathway and immune signaling. This leads to deposition of compensatory lignin that is chemically distinct from Casparian strip lignin. We also report that a complete loss of endodermal lignification drastically impacts mineral nutrients homeostasis and plant growth., Defects in the Casparian strip, a fine band of lignin that seals root endodermal cells and plays roles in nutrient homeostasis, activate a signaling pathway leading to over-lignification. Here, the authors show that this process leads to the deposition of compensatory lignin that is chemically distinct from Casparian strip lignin.

Published
2021
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4. Constitutive Active CPK30 Interferes With Root Growth and Endomembrane Trafficking in Arabidopsis thaliana

Author

Ren Wang, Ellie Himschoot, Jian Chen, Marie Boudsocq, Danny Geelen, Jiří Friml, Tom Beeckman, Steffen Vanneste, Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics, Universiteit Gent = Ghent University (UGENT), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Institute of Science and Technology [Klosterneuburg, Austria] (IST Austria)

Subjects
Brefeldin A, EFFLUX, ENDOCYTOSIS, Biology and Life Sciences, PIN, calcium-dependent kinase, Plant Science, root, gravitropism, CPK30, CA2+, CLATHRIN, TARGETS, EFFECTORS, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, polarity, NUCLEOTIDE EXCHANGE, H+-ATPASE, DEPENDENT PROTEIN-KINASE, endosome, AUXIN TRANSPORT
Abstract

Calcium-dependent protein kinases (CPK) are key components of a wide array of signaling pathways, translating stress and nutrient signaling into the modulation of cellular processes such as ion transport and transcription. However, not much is known about CPKs in endomembrane trafficking. Here, we screened for CPKs that impact on root growth and gravitropism, by overexpressing constitutively active forms of CPKs under the control of an inducible promoter in Arabidopsis thaliana. We found that inducible overexpression of an constitutive active CPK30 (CA-CPK30) resulted in a loss of root gravitropism and ectopic auxin accumulation in the root tip. Immunolocalization revealed that CA-CPK30 roots have reduced PIN protein levels, PIN1 polarity defects and impaired Brefeldin A (BFA)-sensitive trafficking. Moreover, FM4-64 uptake was reduced, indicative of a defect in endocytosis. The effects on BFA-sensitive trafficking were not specific to PINs, as BFA could not induce aggregation of ARF1- and CHC-labeled endosomes in CA-CPK30. Interestingly, the interference with BFA-body formation, could be reverted by increasing the extracellular pH, indicating a pH-dependence of this CA-CPK30 effect. Altogether, our data reveal an important role for CPK30 in root growth regulation and endomembrane trafficking in Arabidopsis thaliana.

Published
2022
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5. Maritime Pine Genomics in Focus

Author

Lieven Sterck, Nuria de María, Rafael A. Cañas, Marina de Miguel, Pedro Perdiguero, Annie Raffin, Katharina B. Budde, Miriam López-Hinojosa, Francisco R. Cantón, Andreia S. Rodrigues, Marian Morcillo, Agathe Hurel, María Dolores Vélez, Fernando N. de la Torre, Inês Modesto, Lorenzo Federico Manjarrez, María Belén Pascual, Ana Alves, Isabel Mendoza-Poudereux, Marta Callejas Díaz, Alberto Pizarro, Jorge El-Azaz, Laura Hernández-Escribano, María Ángeles Guevara, Juan Majada, Jerome Salse, Delphine Grivet, Laurent Bouffier, Rosa Raposo, Amanda R. De La Torre, Rafael Zas, José Antonio Cabezas, Concepción Ávila, Jean-Francois Trontin, Leopoldo Sánchez, Ricardo Alía, Isabel Arrillaga, Santiago C. González-Martínez, Célia Miguel, Francisco M. Cánovas, Christophe Plomion, Carmen Díaz-Sala, María Teresa Cervera, Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics, Universiteit Gent = Ghent University (UGENT), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), Universidad Politécnica de Madrid (UPM), Universidad de Málaga [Málaga] = University of Málaga [Málaga], Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ecophysiologie et Génomique Fonctionnelle de la Vigne (UMR EGFV), Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Instituto de Biologia Experimental e Tecnológica (IBET), Centro de Investigacion en Sanidad Animal (INIA-CISA), Unité expérimentale Forêt Pierroton (UEFP), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Georg-August-University = Georg-August-Universität Göttingen, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Swammerdam Institute for Life Sciences (SILS), University of Amsterdam [Amsterdam] (UvA), Universitat de València (UV), Faculdade de Ciências [Lisboa], Universidade de Lisboa = University of Lisbon (ULISBOA), Universidad de Alcalá - University of Alcalá (UAH), Forest and Wood Technology Research Centre (CETEMAS), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Northern Arizona University [Flagstaff], Mision Biologica de Galicia (MBG), Institut Technologique Forêt Cellulose Bois-construction Ameublement (FCBA), Biologie intégrée pour la valorisation de la diversité des Arbres et de la Forêt (BioForA), Office national des forêts (ONF)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Amanda R. De La Torre

Subjects
Conifer genomics, [SDV.GEN]Life Sciences [q-bio]/Genetics, Development and adaptation, [SDE.MCG]Environmental Sciences/Global Changes, fungi, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Genome sequencing, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV.SA.SF]Life Sciences [q-bio]/Agricultural sciences/Silviculture, forestry, [STAT.ML]Statistics [stat]/Machine Learning [stat.ML], Molecular breeding, Gene expression, Mediterranean pine, [MATH]Mathematics [math], [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract

International audience; The advent of next-generation genome sequencing technologies has allowed approaching the sequencing and analysis of large and complex conifer genomes. Maritime pine (Pinus pinaster Ait.) is an economically and ecologically important conifer species widely distributed in South-West Europe, which shows a significant genetic and adaptive variability. This chapter takes on the task of reviewing the insights into the maritime pine genome sequencing breakthrough and its impact on downstream analysis. Maritime pine genome sequencing and assembly approaches are described along with the impact of related tools. A section of the state-of-the-art research on comparative, functional, structural, and translational genomics aimed at dissecting the genetic basis and the specific regulation of biological processes underlying the expression of traits of interest in maritime pine and other conifers is also described. Perspectives about the impact of these tools as well as additional research approaches are discussed.

Published
2022
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6. Evolutionary genomics of sex-related chromosomes at the base of the green lineage 2

Author

Felipe Benites, L, Bucchini, François, Sanchez-Brosseau, Sophie, Grimsley, Nigel, Vandepoele, Klaas, Piganeau, Gwenael, Biologie intégrative des organismes marins (BIOM), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Universiteit Gent = Ghent University [Belgium] (UGENT), and Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics

Subjects
mating-type loci, GC content, chlorophyta, recombination suppression, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography
Abstract

International audience; Abstract While sex is now accepted as a ubiquitous and ancestral feature of eukaryotes, direct observation of sex is still lacking in most unicellular eukaryotic lineages. Evidence of sex is frequently indirect and inferred from the identification of genes involved in meiosis from whole genome data and/or the detection of recombination signatures from genetic diversity in natural populations. In haploid unicellular eukaryotes, sex-related chromosomes are named mating-type (MTs) chromosomes and generally carry large genomic regions where recombination is suppressed. These regions have been characterized in Fungi and Chlorophyta and determine gamete compatibility and fusion. Two candidate MT+ and MT- alleles, spanning 450-650 kb, have recently been described in Ostreococcus tauri, a marine phytoplanktonic alga from the Mamiellophyceae class, an early diverging branch in the green lineage. Here, we investigate the architecture and evolution of these candidate MT+ and MT- alleles. We analysed the phylogenetic profile and GC content of MT gene families in eight different species, whose divergence has been previously estimated at up to 640 million years, and found evidence that the divergence of the two MTs alleles predates speciation in the Ostreococcus genus. Phylogenetic profiles of MT trans-specific polymorphisms in gametologs disclosed candidate MTs in two additional species, and possibly a third. These Mamiellales MT candidates are likely to be the oldest mating-type loci described to date, which makes them fascinating models to investigate the evolutionary mechanisms of haploid sex determination in eukaryotes.

Published
2021
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7. GARP transcription factors repress Arabidopsis nitrogen starvation response via ROS-dependent and -independent pathways

Author

Florence Martin, Wojciech Szponarski, Alaeddine Safi, Anne Clément-Vidal, Anna Medici, Gloria M. Coruzzi, Sandrine Ruffel, Amy Marshall-Colon, Hatem Rouached, Frédéric Gaymard, Julie Leclercq, Gabriel Krouk, Benoît Lacombe, 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), Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics, Universiteit Gent = Ghent University [Belgium] (UGENT), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), 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), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Center for Genomics and Systems Biology, Department of Biology [New York], New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU)-New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU), and ANR-14-CE19-0008,IMANA,Identification de régulations moléculaires majeures impliquées dans l'adaptation des plantes à la disponibilité en azote(2014)

Subjects
0106 biological sciences, 0301 basic medicine, GARP transcription factors, Physiology, [SDV]Life Sciences [q-bio], Plant Science, METABOLISM, 01 natural sciences, 03 medical and health sciences, HYDROGEN-PEROXIDE, TGA FACTORS, Glutaredoxin, Arabidopsis, root protoplasts, NITRATE TRANSPORTER, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Transcription factor, Gene, LONG-DISTANCE, 2. Zero hunger, THALIANA, biology, Chemistry, Biology and Life Sciences, ROS, plant growth, biology.organism_classification, GENE, NO3-UPTAKE, Cell biology, Cell sorting, PLANT-RESPONSES, 030104 developmental biology, TARGET, Nitrate transport, root nitrate uptake, Signal transduction, Starvation response, nitrogen starvation response, GLUTAREDOXINS, Functional genomics, 010606 plant biology & botany
Abstract

Plants need to cope with strong variations of nitrogen availability in the soil. Although many molecular players are being discovered concerning how plants perceive NO3− provision, it is less clear how plants recognize a lack of nitrogen. Following nitrogen removal, plants activate their nitrogen starvation response (NSR), which is characterized by the activation of very high-affinity nitrate transport systems (NRT2.4 and NRT2.5) and other sentinel genes involved in N remobilization such as GDH3. Using a combination of functional genomics via transcription factor perturbation and molecular physiology studies, we show that the transcription factors belonging to the HHO subfamily are important regulators of NSR through two potential mechanisms. First, HHOs directly repress the high-affinity nitrate transporters, NRT2.4 and NRT2.5. hho mutants display increased high-affinity nitrate transport activity, opening up promising perspectives for biotechnological applications. Second, we show that reactive oxygen species (ROS) are important to control NSR in wild-type plants and that HRS1 and HHO1 overexpressors and mutants are affected in their ROS content, defining a potential feed-forward branch of the signaling pathway. Taken together, our results define the relationships of two types of molecular players controlling the NSR, namely ROS and the HHO transcription factors. This work (i) up opens perspectives on a poorly understood nutrient-related signaling pathway and (ii) defines targets for molecular breeding of plants with enhanced NO3− uptake.

Published
2021
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8. Arabidopsis casein kinase 2 triggers stem cell exhaustion under Al toxicity and phosphate deficiency through activating the DNA damage response pathway

Author

Laurent Nussaume, Ilse Vercauteren, Geert De Jaeger, Long Nguyen, Pengliang Wei, Dominique Audenaert, Kaoru Yoshiyama, Margot Galle, Thomas Eekhout, Remy Loris, Pascale David, Dominique Eeckhout, Manon Demulder, Thierry Desnos, Paul B. Larsen, Lieven De Veylder, Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), 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), 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)), Biologie végétale et microbiologie environnementale - UMR7265 (BVME), Universiteit Gent = Ghent University (UGENT), Plant Environmental Physiology and Stress Signaling (PEPSS), 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), Tohoku University [Sendai], Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics, Vrije Universiteit Brussel (VUB), Faculty of Sciences and Bioengineering Sciences, Structural Biology Brussels, and Department of Bio-engineering Sciences

Subjects
0301 basic medicine, 0106 biological sciences, Cell cycle checkpoint, DNA damage, [SDV]Life Sciences [q-bio], Casein kinase 2, Arabidopsis, Plant Science, Ataxia Telangiectasia Mutated Proteins, 01 natural sciences, Biochemistry, Plant Roots, Phosphates, 03 medical and health sciences, Plant Cells, SOG1, structural biology, Phosphorylation, Casein Kinase II, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, biology, Chemistry, Activator (genetics), Biochemistry, Genetics and Molecular Biology(all), Arabidopsis Proteins, fungi, Cell Biology, Meristem, Cell cycle, biology.organism_classification, Plants, Genetically Modified, Cell biology, 030104 developmental biology, Intercellular Signaling Peptides and Proteins, Aluminium tolerance, Stem cell, 010606 plant biology & botany, Aluminum, Transcription Factors
Abstract

Aluminum (Al) toxicity and inorganic phosphate (Pi) limitation are widespread chronic abiotic and mutually enhancing stresses that profoundly affect crop yield. Both stresses cause a strong inhibition of root growth, resulting from a progressive exhaustion of the stem cell niche. Here, we report on a casein kinase 2 (CK2) inhibitor identified by its capability to maintain a functional root stem cell niche under Al toxic conditions. CK2 operates through phosphorylation of the cell cycle checkpoint activator SUPPRESSOR OF GAMMA RADIATION1 (SOG1), priming its activity under DNA-damaging conditions. In addition to yielding Al tolerance, CK2 and SOG1 inactivation prevents meristem exhaustion under Pi starvation, revealing the existence of a low Pi-induced cell cycle checkpoint that depends on the DNA damage activator ATAXIA-TELANGIECTASIA MUTATED. Overall, our data reveal an important physiological role for the plant DNA damage response pathway under agriculturally limiting growth conditions, opening new avenues to cope with Pi limitation. ONE-SENTENCE SUMMARY Casein kinase 2 and DNA damage response regulators play a pivotal role in the control of Arabidopsis root growth in response to Al toxicity and phosphate limitation.

Published
2021
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9. A Phelipanche ramosa KAI2 protein perceives strigolactones and isothiocyanates enzymatically

Author

Anse Jacobs, Lukas Braem, Vincent Steinmetz, Jean-Bernard Pouvreau, Guillaume Clavé, Guillaume Brun, Vincent Servajean, Sofie Goormachtig, François-Didier Boyer, Alexandre de Saint Germain, Philippe Delavault, Philippe Simier, Susann Wicke, Emmanuelle Baudu, David Cornu, Kris Gevaert, Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics, Universiteit Gent = Ghent University [Belgium] (UGENT), Laboratoire de Physiologie et Biotechnologies Végétales (LPBV), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de biologie et pathologie végétales (LBPV), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN), Humboldt-Universität zu Berlin, Institute for Integrative Biology of the Cell [Gif-sur-Yvette] (I2BC), Institut de Chimie des Substances Naturelles (ICSN), Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Department of Biomolecular Medicine, Institut Jean-Pierre Bourgin's Plant Observatory technological platforms, Paris-Sud University, AgreenSkills award from the European Union, FWO 1S15817N VS04418N, Infrastructures en Biologie Sante et Agronomie, Region Ile-de-France, Plan Cancer, Centre National de la Recherche Scientifique (CNRS) European Commission, ANR-11-LABX-0039,CHARMMMAT,CHimie des ARchitectures MoléculairesMultifonctionnelles et des MATériaux(2011), ANR-17-EURE-0007,SPS-GSR,Ecole Universitaire de Recherche de Sciences des Plantes de Paris-Saclay(2017), Universiteit Gent = Ghent University (UGENT), Humboldt University Of Berlin, Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), and Institute for Biology, Humboldt-Universitat zu Berlin, Berlin, Germany.

Subjects
0106 biological sciences, isothiocyanates, Parasitic plant, STRIGA, receptor, [SDV]Life Sciences [q-bio], Stimulation, Plant Science, strigolactones, Biology, 01 natural sciences, Biochemistry, a/b-hydrolase, Phelipanche ramosa, 03 medical and health sciences, Striga, Arabidopsis, DWARF14, KARRIKIN, α/β-hydrolase, Receptor, Molecular Biology, 030304 developmental biology, 2. Zero hunger, HORMONE-RECEPTOR, 0303 health sciences, PERCEPTION, ANALOGS, Obligate, [CHIM.ORGA]Chemical Sciences/Organic chemistry, food and beverages, Biology and Life Sciences, Cell Biology, SEED-GERMINATION, biology.organism_classification, ARABIDOPSIS, GENE, seed germination stimulant, Karrikin, PARASITIC PLANT, Weed, 010606 plant biology & botany, Biotechnology
Abstract

International audience; Phelipanche ramosa is an obligate root-parasitic weed that threatens major crops in central Europe. In order to germinate, it must perceive various structurally divergent host-exuded signals, including isothiocyanates (ITCs) and strigolactones (SLs). However, the receptors involved are still uncharacterized. Here, we identify five putative SL receptors in P. ramosa and show that PrKAI2d3 is involved in the stimulation of seed germination. We demonstrate the high plasticity of PrKAI2d3, which allows it to interact with different chemicals, including ITCs. The SL perception mechanism of PrKAI2d3 is similar to that of endogenous SLs in non-parasitic plants. We provide evidence that PrKAI2d3 enzymatic activity confers hypersensitivity to SLs. Additionally, we demonstrate that methylbutenolide-OH binds PrKAI2d3 and stimulates P. ramosa germination with bioactivity comparable to that of ITCs. This study demonstrates that P. ramosa has extended its signal perception system during evolution, a fact that should be considered for the development of specific and efficient biocontrol methods.

Published
2021
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10. Maize specialized metabolome networks reveal organ-preferential mixed glycosides

Author

Ruben Vanholme, Claudiu Niculaes, John Ralph, Hoon Kim, Atsushi Fukushima, Rebecca Dauwe, Wout Boerjan, Sandrien Desmet, Kris Morreel, Geert Goeminne, Yvan Saeys, Kevin Verstaen, Department of plant Biotechnology and Bioinformatics, Universiteit Gent = Ghent University (UGENT), Flanders Institute for Biotechnology, VIB-UGent Center for Inflammation Research [Gand, Belgique] (IRC), VIB [Belgium], Biologie des Plantes et Innovation - UR UPJV 3900 (BIOPI), Université de Picardie Jules Verne (UPJV)-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)-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), Université catholique de Lille (UCL)-Université catholique de Lille (UCL), Department of Pharmacy, and Research Institute of Life Pharmaceutical Sciences, Sunchon National University, Suncheon 57922, Republic of Korea, John Innes Centre [Norwich], Biotechnology and Biological Sciences Research Council (BBSRC), RIKEN Center for Sustainable Resource Science [Yokohama] (RIKEN CSRS), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), University of Wisconsin-Madison, and Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics

Subjects
Agriculture and Food Sciences, PREDICTION, Systems biology, [SDV]Life Sciences [q-bio], Biophysics, DIVERSITY, Spectral metadata analysis, Computational biology, Biochemistry, Zea mays, ANNOTATION, Specialized metabolism, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Structural Biology, Arabidopsis, Genetics, Metabolome, Glycosyl, AUXIN BIOSYNTHESIS, ComputingMethodologies_COMPUTERGRAPHICS, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, Phenylpropanoid, biology, Mass spectrometry, IDENTIFICATION, ELUCIDATION, Glycoside, Biology and Life Sciences, MASS-SPECTROMETRY, biology.organism_classification, ARABIDOPSIS, Computer Science Applications, ddc, Metabolic pathway, chemistry, 030220 oncology & carcinogenesis, Acyltransferase, FRAGMENTATION, PHENYLACETIC ACID, TP248.13-248.65, Research Article, Biotechnology
Abstract

Graphical abstract, Despite the scientific and economic importance of maize, little is known about its specialized metabolism. Here, five maize organs were profiled using different reversed-phase liquid chromatography-mass spectrometry methods. The resulting spectral metadata, combined with candidate substrate-product pair (CSPP) networks, allowed the structural characterization of 427 of the 5,420 profiled compounds, including phenylpropanoids, flavonoids, benzoxazinoids, and auxin-related compounds, among others. Only 75 of the 427 compounds were already described in maize. Analysis of the CSPP networks showed that phenylpropanoids are present in all organs, whereas other metabolic classes are rather organ-enriched. Frequently occurring CSPP mass differences often corresponded with glycosyl- and acyltransferase reactions. The interplay of glycosylations and acylations yields a wide variety of mixed glycosides, bearing substructures corresponding to the different biochemical classes. For example, in the tassel, many phenylpropanoid and flavonoid-bearing glycosides also contain auxin-derived moieties. The characterized compounds and mass differences are an important step forward in metabolic pathway discovery and systems biology research. The spectral metadata of the 5,420 compounds is publicly available (DynLib spectral database, https://bioit3.irc.ugent.be/dynlib/).

Published
2020
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11. Origin and Function of Structural Diversity in the Plant Specialized Metabolome

Author

Kris Morreel, Sandrien Desmet, Rebecca Dauwe, Department of plant Biotechnology and Bioinformatics, Universiteit Gent = Ghent University (UGENT), Flanders Institute for Biotechnology, Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics, Biologie des Plantes et Innovation - UR UPJV 3900 (BIOPI), Université de Picardie Jules Verne (UPJV)-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)-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), and Université catholique de Lille (UCL)-Université catholique de Lille (UCL)

Subjects
Plant growth, biosynthesis pathways, Ecology, Primary metabolism, Chemistry, [SDV]Life Sciences [q-bio], Botany, Carbon skeleton, Structural diversity, Review, Plant Science, metabolite modification, structure-function relationship, Order (biology), structural diversity, Biochemistry, QK1-989, Metabolome, Fatty acid derivatives, plant specialized metabolome, Ecology, Evolution, Behavior and Systematics, Function (biology)
Abstract

International audience; The plant specialized metabolome consists of a multitude of structurally and functionally diverse metabolites, variable from species to species. The specialized metabolites play roles in the response to environmental changes and abiotic or biotic stresses, as well as in plant growth and development. At its basis, the specialized metabolism is built of four major pathways, each starting from a few distinct primary metabolism precursors, and leading to distinct basic carbon skeleton core structures: polyketides and fatty acid derivatives, terpenoids, alkaloids, and phenolics. Structural diversity in specialized metabolism, however, expands exponentially with each subsequent modification. We review here the major sources of structural variety and question if a specific role can be attributed to each distinct structure. We focus on the influences that various core structures and modifications have on flavonoid antioxidant activity and on the diversity generated by oxidative coupling reactions. We suggest that many oxidative coupling products, triggered by initial radical scavenging, may not have a function in se, but could potentially be enzymatically recycled to effective antioxidants. We further discuss the wide structural variety created by multiple decorations (glycosylations, acylations, prenylations), the formation of high-molecular weight conjugates and polyesters, and the plasticity of the specialized metabolism. We draw attention to the need for untargeted methods to identify the complex, multiply decorated and conjugated compounds, in order to study the functioning of the plant specialized metabolome.

Published
2021
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12. Molecular networks regulating cell division during Arabidopsis leaf growth

Author

Jasmien Vercruysse, Alexandra Baekelandt, Nathalie Gonzalez, Dirk Inzé, Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics, Universiteit Gent = Ghent University [Belgium] (UGENT), Biologie du fruit et pathologie (BFP), and Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
DEPENDENT KINASE INHIBITORS, 0106 biological sciences, 0301 basic medicine, Cell division, Arabidopsis thaliana, Physiology, [SDV]Life Sciences [q-bio], Arabidopsis, GENE FAMILY, Plant Science, Biology, 01 natural sciences, organ growth, LIGASE BIG BROTHER, 03 medical and health sciences, Gene Expression Regulation, Plant, PLAY DISTINCT ROLES, Gene family, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Transcription factor, Review Papers, ORGAN SIZE, Cell growth, Arabidopsis Proteins, AcademicSubjects/SCI01210, ANAPHASE-PROMOTING COMPLEX/CYCLOSOME, fungi, Biology and Life Sciences, food and beverages, Cell cycle, biology.organism_classification, Cell biology, DNA-Binding Proteins, Plant Leaves, TRANSCRIPTION FACTORS, 030104 developmental biology, cell proliferation, CHROMATIN-REMODELING COMPLEXES, leaf size, UBIQUITIN RECEPTOR DA1, Gibberellin, cell cycle, SMALL AUXIN, Cell Division, leaf development, 010606 plant biology & botany
Abstract

Numerous genes have been identified that regulate leaf growth, which can be grouped into regulatory modules. Here, we review six important gene modules that affect cell proliferation during leaf development., Leaves are the primary organs for photosynthesis, and as such have a pivotal role for plant growth and development. Leaf development is a multifactorial and dynamic process involving many genes that regulate size, shape, and differentiation. The processes that mainly drive leaf development are cell proliferation and cell expansion, and numerous genes have been identified that, when ectopically expressed or down-regulated, increase cell number and/or cell size during leaf growth. Many of the genes regulating cell proliferation are functionally interconnected and can be grouped into regulatory modules. Here, we review our current understanding of six important gene regulatory modules affecting cell proliferation during Arabidopsis leaf growth: ubiquitin receptor DA1–ENHANCER OF DA1 (EOD1), GROWTH REGULATING FACTOR (GRF)–GRF-INTERACTING FACTOR (GIF), SWITCH/SUCROSE NON-FERMENTING (SWI/SNF), gibberellin (GA)–DELLA, KLU, and PEAPOD (PPD). Furthermore, we discuss how post-mitotic cell expansion and these six modules regulating cell proliferation make up the final leaf size.

Published
2020
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13. Ten steps to get started in Genome Assembly and Annotation

Author

Lieven Sterck, Brane Leskošek, Lucile Soler, Cederic Notredame, Erik Hjerde, Stéphanie Bocs, Mahesh Binzer-Panchal, Laurent Bouri, Henrik Lantz, Joelle Amselem, Christophe Klopp, Jean-François Gibrat, Olga Vinnere Pettersson, Salvadors Capella-Gutierrez, Anna Vlasova, Victoria Dominguez Del Angel, Institut Français de Bioinformatique, Université Paris-Saclay, Department of Chemistry, RIDER UNIVERSITY, Department of Plant Biotechnology and Bioinformatics, Ghent University [Belgium] (UGENT), Department of Plant Systems Biology, VIB, Spanish National Bioinformatics Institute (INB), Centro Nacional de Supercomputación, BSC Electronics, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra [Barcelona], Uppsala Genome Center, NGI/SciLifeLab - Department of Immunology, Genetics and Pathology, Uppsala University, Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Université de Tunis [Tunis], Laboratory of Technologies of Information and Communication and Electrical Engineering, National Superior School of Engineers of Tunis, 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), South Green Bioinformatics Platform, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Faculty of Medicine, Institute for Biostatistics and Medical Informatics, University of Ljubljana, IMBIM/NBIS/SciLifeLab, Institut Français de Bioinformatique - UMS CNRS 3601 (IFB-CORE), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Universiteit Gent = Ghent University [Belgium] (UGENT), Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Barcelona Supercomputing Center - Centro Nacional de Supercomputacion (BSC - CNS), Universitat Pompeu Fabra [Barcelona] (UPF), Université de Tunis, 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), Barcelona Supercomputing Center, Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-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), Universiteit Gent = Ghent University (UGENT), South Green Bioinformatics Platform [Montpellier], and Hjerde, Erik

Subjects
0301 basic medicine, Computer science, General assembly, Data management, [SDV]Life Sciences [q-bio], Annotation, Interoperability, Assembly, Sequence assembly, Bioinformatik och systembiologi, Genome, General Biochemistry, Genetics and Molecular Biology, F30 - Génétique et amélioration des plantes, Workflows, World Wide Web, 03 medical and health sciences, DNA--Analysis, Genomes, General Pharmacology, Toxicology and Pharmaceutics, ADN--Anàlisi, FAIR, Genome assembly, Bioinformatics and Systems Biology, General Immunology and Microbiology, business.industry, Biology and Life Sciences, General Medicine, Genome project, Articles, DNA, Opinion Article, L10 - Génétique et amélioration des animaux, ELIXIR-EXCELERATE, 030104 developmental biology, Workflow, NGS, business, Ciències de la salut [Àrees temàtiques de la UPC], Genome annotation
Abstract

As a part of the ELIXIR-EXCELERATE efforts in capacity building, we present here 10 steps to facilitate researchers getting started in genome assembly and genome annotation. The guidelines given are broadly applicable, intended to be stable over time, and cover all aspects from start to finish of a general assembly and annotation project. Intrinsic properties of genomes are discussed, as is the importance of using high quality DNA. Different sequencing technologies and generally applicable workflows for genome assembly are also detailed. We cover structural and functional annotation and encourage readers to also annotate transposable elements, something that is often omitted from annotation workflows. The importance of data management is stressed, and we give advice on where to submit data and how to make your results Findable, Accessible, Interoperable, and Reusable (FAIR). ELIXIR-EXCELERATE is funded by the European Commission within the Research Infrastructures Programme of Horizon 2020 [676559].

Published
2018
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14. JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

Author

Oriol Fornes, Anthony Mathelier, Benoit Ballester, Jeanne Chèneby, Marius Gheorghe, Arnaud Stigliani, Ge Tan, François Parcy, Aziz Khan, David J. Arenillas, Robin van der Lee, Wyeth W. Wasserman, Klaas Vandepoele, Jaime A. Castro-Mondragon, Damir Baranasic, Albin Sandelin, Shubhada Rajabhau Kulkarni, Boris Lenhard, Adrien Bessy, Centre for Molecular Medicine Norway (NCMM), Faculty of Medicine [Oslo], University of Oslo (UiO)-University of Oslo (UiO)-Rigshospitalet [Copenhagen], Department of Medical Genetics, Faculty of Medicine-Child and Family Research Institute-Centre for Molecular Medicine and Therapeutics-University of British Columbia (UBC), Physiologie cellulaire et végétale (LPCV), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Theories and Approaches of Genomic Complexity (TAGC), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics, Ghent University [Belgium] (UGENT), Computational Regulatory Genomics, Imperial College London, Institute of Clinical Sciences, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Bioinformatics Centre, Department of Biology [Copenhagen], Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Sars International Centre for Marine Molecular Biology, University of Bergen (UIB), Oslo University Hospital Radiumhospitalet, Genome Canada and Canadian Institutes of Health Research (On-Target Grants) [255ONT and BOP-149430], Natural Sciences and Engineering Research Council of Canada (Discovery Grant) [RGPIN-2017–06824], Independent Research Fund Denmark, Innovation Fund Denmark, Elixir Denmark, Wellcome Trust [106954], Biotechnology and Biological Sciences Research Council [BB/N023358/1], Medical Research Council UK [MC UP 1102/1], Weston Brain Institute: [20R74681], Research Foundation Flanders Grant [G001015N], Lundbeck Foundation, ANR-10- LABX-49-01,Labex GRAL,Labex GRAL, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute and Department of Medical Genetics, University of British Columbia (UBC), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Copenhagen University Hospital-Copenhagen University Hospital, Radboud University Medical Center [Nijmegen], Universiteit Gent = Ghent University [Belgium] (UGENT), Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute-University of British Columbia (UBC), Biotech Research and Innovation Centre (BRIC), University of Copenhagen = Københavns Universitet (KU), Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Centre for Molecular Medicine and Therapeutics-University of British Columbia (UBC), 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), VIB Department of Plant Systems Biology, University of Bergen (UiB), ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Universiteit Gent = Ghent University (UGENT), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), University of Copenhagen = Københavns Universitet (UCPH), Biotechnology and Biological Sciences Research Council (BBSRC), and Wellcome Trust

Subjects
0301 basic medicine, REPRESENTATION, Nematodes, [SDV]Life Sciences [q-bio], 05 Environmental Sciences, SPECIFICITIES, DIVERSITY, Genome browser, computer.software_genre, Genome, Bioconductor, User-Computer Interface, 0302 clinical medicine, Databases, Genetic, Database Issue, Taxonomic rank, base de données, 0303 health sciences, Database, Web application framework, BIOINFORMATICS, Genomics, Plants, ARABIDOPSIS, Multiple species, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], GENOME, Insects, 030220 oncology & carcinogenesis, Vertebrates, Erratum, Life Sciences & Biomedicine, Protein Binding, EXPRESSION, Biochemistry & Molecular Biology, libre accès, Biology, 03 medical and health sciences, Open Access, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], JASPAR, Journal Article, Genetics, Animals, Humans, Position-Specific Scoring Matrices, 030304 developmental biology, Internet, Science & Technology, Binding Sites, LANDSCAPE, Fungi, Biology and Life Sciences, 06 Biological Sciences, Binding, SITE PREDICTIONS, 030104 developmental biology, DISCOVERY, profil, 08 Information and Computing Sciences, actualisation, Transcription factor, computer, facteur de transcription, Developmental Biology, Transcription Factors
Abstract

International audience; JASPAR (http://jaspar.genereg.net) is an open-access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position frequency matrices (PFMs) and TF flexible models (TFFMs) for TFs across multiple species in six tax-onomic groups. In the 2018 release of JASPAR, the CORE collection has been expanded with 322 new PFMs (60 for vertebrates and 262 for plants) and 33 PFMs were updated (24 for vertebrates, 8 for plants and 1 for insects). These new profiles represent a 30% expansion compared to the 2016 release. In addition , we have introduced 316 TFFMs (95 for vertebrates , 218 for plants and 3 for insects). This release incorporates clusters of similar PFMs in each taxon and each TF class per taxon. The JASPAR 2018 CORE vertebrate collection of PFMs was used to predict TF-binding sites in the human genome. The predictions are made available to the scientific community through a UCSC Genome Browser track data hub. Finally , this update comes with a new web framework with an interactive and responsive user-interface, along with new features. All the underlying data can be retrieved programmatically using a RESTful API and through the JASPAR 2018 R/Bioconductor package .

Published
2017
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15. Climate change, CO2, and defense: The Metabolic, redox, and signaling perspectives

Author

Graham Noctor, Amna Mhamdi, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics, Universiteit Gent = Ghent University (UGENT), and Universiteit Gent = Ghent University [Belgium] (UGENT)

Subjects
0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], Transcriptomic Analysis, Gene-Expression, Plant Science, Plant disease resistance, Biology, 01 natural sciences, Plant Physiological Phenomena, Plant-Pathogen Interactions, 03 medical and health sciences, chemistry.chemical_compound, Intracellular Oxidative Stress, Plant defense against herbivory, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Elevated Co2, chemistry.chemical_classification, Reactive oxygen species, Arabidopsis Guard-Cells, fungi, food and beverages, Nadp-Malate Dehydrogenase, Hyaloperonospora-Arabidopsidis, Biotic stress, Pseudomonas-Syringae, 030104 developmental biology, chemistry, Biochemistry, 13. Climate action, Photorespiration, Salicylic-Acid, Signal transduction, Salicylic acid, 010606 plant biology & botany
Abstract

International audience; Ongoing human-induced changes in the composition of the atmosphere continue to stimulate interest in the effects of high CO2 on plants, but its potential impact on inducible plant defense pathways remains poorly defined. Recently, several studies have reported that growth at elevated CO2 is sufficient to induce defenses such as the salicylic acid pathway, thereby increasing plant resistance to pathogens. These reports contrast with evidence that defense pathways can be promoted by photorespiration, which is inhibited at high CO2. Here, we review signaling, metabolic, and redox processes modulated by CO2 levels and discuss issues to be resolved in elucidating the relationships between primary metabolism, inducible defense, and biotic stress resistance.

Published
2017
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16. Arabidopsis thaliana RNase H2 Deficiency Counteracts the Needs for the WEE1 Checkpoint Kinase but Triggers Genome Instability[C][W]

Author

Pooneh Kalhorzadeh, Charles I. White, Korbinian Schneeberger, Simon Amiard, Eva-Maria Willing, Toon Cools, Nancy De Winne, Lieven De Veylder, Geert De Jaeger, Zhubing Hu, Kris Gevaert, Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics, Universiteit Gent = Ghent University [Belgium] (UGENT), Génétique, Reproduction et Développement (GReD), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Santé et de la Recherche Médicale (INSERM), Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research (MPIPZ), Department of Medical Protein Research, VIB-Gent University, Department of Plant Biotechnology and Bioinformatics, Universiteit Gent = Ghent University (UGENT), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Universiteit Gent = Ghent University (UGENT)-VIB, and White, Charles

Subjects
Cell cycle checkpoint, RNase P, Molecular Sequence Data, Ribonuclease H, Arabidopsis, Eukaryotic DNA replication, [SDV.GEN] Life Sciences [q-bio]/Genetics, Plant Science, Protein Serine-Threonine Kinases, Genes, Plant, Genomic Instability, Mutation Rate, Catalytic Domain, Hydroxyurea, Amino Acid Sequence, RNase H, Base Pairing, ComputingMilieux_MISCELLANEOUS, Research Articles, Genetics, Recombination, Genetic, [SDV.GEN]Life Sciences [q-bio]/Genetics, biology, Base Sequence, Arabidopsis Proteins, Cell Biology, Cell Cycle Checkpoints, G2-M DNA damage checkpoint, Ribonucleotides, RNase MRP, Mutation, biology.protein, Origin recognition complex, Homologous recombination
Abstract

The WEE1 kinase is an essential cell cycle checkpoint regulator in Arabidopsis thaliana plants experiencing replication defects. Whereas under non-stress conditions WEE1-deficient plants develop normally, they fail to adapt to replication inhibitory conditions, resulting in the accumulation of DNA damage and loss of cell division competence. We identified mutant alleles of the genes encoding subunits of the ribonuclease H2 (RNase H2) complex, known for its role in removing ribonucleotides from DNA-RNA duplexes, as suppressor mutants of WEE1 knockout plants. RNase H2 deficiency triggered an increase in homologous recombination (HR), correlated with the accumulation of γ-H2AX foci. However, as HR negatively impacts the growth of WEE1-deficient plants under replication stress, it cannot account for the rescue of the replication defects of the WEE1 knockout plants. Rather, the observed increase in ribonucleotide incorporation in DNA indicates that the substitution of deoxynucleotide with ribonucleotide abolishes the need for WEE1 under replication stress. Strikingly, increased ribonucleotide incorporation in DNA correlated with the occurrence of small base pair deletions, identifying the RNase H2 complex as an important suppressor of genome instability.

Published
2014
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17. Structural and Functional Partitioning of Bread Wheat Chromosome 3B

Author

Catherine Feuillet, Patrick Wincker, Hélène Bergès, Sébastien Theil, Nicolas Guilhot, François Balfourier, Jacques Le Gouis, Arnaud Bellec, Josquin Daron, Julie Poulain, Natasha Glover, Philippe Leroy, Pierre Sourdille, Véronique Jamilloux, Valérie Barbe, Hadi Quesneville, Frédéric Choulet, Christine Gaspin, Lise Pingault, Klaas Vandepoele, Klaus F. X. Mayer, Arnaud Couloux, Michael Alaux, Jean-Marc Aury, Etienne Paux, Adriana Alberti, Jaroslav Dolezel, Jan Safar, Céline Durand, Jane Rogers, Sophie Mangenot, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Biologie du fruit et pathologie (BFP), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1 (UB), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Centre National de Ressources Génomiques Végétales (CNRGV), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS), Genome Analysis Centre, Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics, Universiteit Gent = Ghent University (UGENT), Munich Information Center for Protein Sequences, Partenaires INRAE, Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, and Universiteit Gent = Ghent University [Belgium] (UGENT)

Subjects
Genome evolution, Pseudogene, [SDV]Life Sciences [q-bio], Biology, Genome, Chromosomes, Plant, Polyploidy, Chromosome Segregation, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [INFO]Computer Science [cs], [MATH]Mathematics [math], Triticum, Plant Proteins, 2. Zero hunger, Whole genome sequencing, Genetics, Recombination, Genetic, Bacterial artificial chromosome, Multidisciplinary, Chromosome, food and beverages, Genome project, Bread, Meiosis, [SDE]Environmental Sciences, DNA Transposable Elements, Pseudogenes, Reference genome
Abstract

International audience; We produced a reference sequence of the 1-gigabase chromosome 3B of hexaploid bread wheat. By sequencing 8452 bacterial artificial chromosomes in pools, we assembled a sequence of 774 megabases carrying 5326 protein-coding genes, 1938 pseudogenes, and 85% of transposable elements. The distribution of structural and functional features along the chromosome revealed partitioning correlated with meiotic recombination. Comparative analyses indicated high wheat-specific inter- and intrachromosomal gene duplication activities that are potential sources of variability for adaption. In addition to providing a better understanding of the organization, function, and evolution of a large and polyploid genome, the availability of a high-quality sequence anchored to genetic maps will accelerate the identification of genes underlying important agronomic traits.

Published
2014
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18. Plastid gene expression and plant development require a plastidic protein of the mitochondrial transcription termination factor family

Author

Riet De Rycke, Jérôme Joubès, Marc Van Montagu, Hana Akbari, Margrit Frentzen, Josef Wissing, Sergei Kushnir, Miguel Garcia-Diaz, Lothar Jänsch, Klaas Vandepoele, Elena Babiychuk, Tom Beeckman, and Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium.

Subjects
Genetics, Regulation of gene expression, Multidisciplinary, biology, Arabidopsis Proteins, Mutant, fungi, Arabidopsis, food and beverages, Biological Sciences, biology.organism_classification, Zea mays, Plastid translation, Plant Leaves, Basic-Leucine Zipper Transcription Factors, Gene Expression Regulation, Plant, Protein Biosynthesis, Gene expression, Tobacco, Arabidopsis thaliana, Plastids, Plastid, Gene
Abstract

Plastids are DNA-containing organelles unique to plant cells. In Arabidopsis , one-third of the genes required for embryo development encode plastid-localized proteins. To help understand the role of plastids in embryogenesis and postembryonic development, we characterized proteins of the mitochondrial transcription termination factor (mTERF) family, which in animal models, comprises DNA-binding regulators of mitochondrial transcription. Of 35 Arabidopsis mTERF proteins, 11 are plastid-localized. Genetic complementation shows that at least one plastidic mTERF, BELAYA SMERT' (BSM), is required for embryogenesis. The main postembryonic phenotypes of genetic mosaics with the bsm mutation are severe abnormalities in leaf development. Mutant bsm cells are albino, are compromised in growth, and suffer defects in global plastidic gene expression. The bsm phenotype could be phenocopied by inhibition of plastid translation with spectinomycin. Plastid translation is essential for cell viability in dicotyledonous species such as tobacco but not in monocotyledonous maize. Here, genetic interactions between BSM and the gene encoding plastid homomeric acetyl-CoA carboxylase ACC2 suggest that there is a functional redundancy in malonyl-CoA biosynthesis that permits bsm cell survival in Arabidopsis . Overall, our results indicate that biosynthesis of malonyl-CoA and plastid-derived systemic growth-promoting compounds are the processes that link plant development and plastid gene expression.

Published
2011

19. Candidate gene variation along an altitudinal gradient in Fagus sylvatica

Author

Lalagüe, Hadrien, Fady, Bruno, Garnier‐géré, Pauline, González-Martínez, S.C., Lin, Yao-Cheng, Oddou-Muratorio, Sylvie, Sebastiani, Federico, Vendramin, Giovanni Giuseppe, Ecologie des Forêts Méditerranéennes (URFM), Institut National de la Recherche Agronomique (INRA), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics, Universiteit Gent = Ghent University [Belgium] (UGENT), Consiglio Nazionale delle Ricerche (CNR), and ProdInra, Migration

Subjects
[SDE.BE] Environmental Sciences/Biodiversity and Ecology, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, fungi, candidate gene, variation along an altitudinal gradient, fagus sylvatica, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SDV.BIO] Life Sciences [q-bio]/Biotechnology
Abstract

National audience; Beech forests (Fagus sylvatica L.) cover about 12 million hectares in Europe. Beech wood is much appreciated worldwide so that many beech forests are regularly harvested for timber production. Apart of its economical importance, European beech has also a major role in soil preservation and water cycles, which makes this species a target of ecologically-minded conservation. In order to confront the observed and predicted climatic trends, beech populations will have to adapt in situ and/or to migrate to higher latitudes/altitudes. Except in the southern part of Europe where beech seems to suffer of drought, beech groves are expending their distribution range. Then, understanding how adaptive traits and the underlying molecular variation in candidate genes evolve is a relevant subject of research. Here we present our strategy for the identification and selection of putative candidate genes involved in the response to abiotic stress in beech. About 40.000 ESTs, sequenced within the European Network of Excellence “Evoltree”, have been processed. Different criteria were adopted to select the genes. Some hundreds primer pairs were designed and tested for amplification and polymorphism. Polymorphisms at the selected genes will then be genotyped to estimate level and distribution of diversity within a population sampled along an altitudinal gradient and to dissect the role of selective pressures and demographic dynamics in European beech.

Published
2010

20. On adaptive self-organization in artificial robot organisms

Author

Ronald Thenius, Jürgen Stradner, Andy M. Tyrrell, A.C. van Rossum, Serge Kernbach, Agoston E. Eiben, Maizura Mohktar, Thomas Schmickl, Michèle Sebag, Yao Yao, Alan F. T. Winfield, Nicolas Bredeche, S.P. McKibbin, Wenguo Liu, Guy Baele, Heiko Hamann, Karl Crailsheim, Yves Van de Peer, Jon Timmis, Institute of Parallel and Distributed Systems [Stuttgart] (IPVS), Artificial Life Lab, Karl-Franzens-Universität Graz, Almende, Machine Learning and Optimisation (TAO), Laboratoire de Recherche en Informatique (LRI), Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Algorithmic number theory for cryptology (TANC), Laboratoire d'informatique de l'École polytechnique [Palaiseau] (LIX), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS)-Inria Saclay - Ile de France, Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics, Universiteit Gent = Ghent University (UGENT), University of York [York, UK], Free University of Amsterdam, Materials and Engineering Research Institute [Sheffield] (MERI), Sheffield Hallam University, Bristol Robotics Laboratory (BRL), University of the West of England [Bristol] (UWE Bristol), The 'SYMBRION' project is funded by the European Commission within the work programme 'Future and Emergent Technologies Proactive' under the grant agreement n° 216342. The 'REPLICATOR' project is funded within the work programme 'Cognitive Systems, Interaction, Robotics' under the grant agreement n° 216240., European Project: 216342,EC:FP7:ICT,FP7-ICT-2007-1,SYMBRION(2008), European Project: 216240,EC:FP7:ICT,FP7-ICT-2007-1,REPLICATOR(2008), Centre National de la Recherche Scientifique (CNRS)-Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université Paris-Sud - Paris 11 (UP11)-Laboratoire de Recherche en Informatique (LRI), Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-CentraleSupélec, Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire d'informatique de l'École polytechnique [Palaiseau] (LIX), Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X), and Universiteit Gent = Ghent University [Belgium] (UGENT)

Subjects
0209 industrial biotechnology, Collective behavior, Adaptive control, artificial organisms, Computer science, 02 engineering and technology, adaptive self-organization, [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI], 020901 industrial engineering & automation, [INFO.INFO-LG]Computer Science [cs]/Machine Learning [cs.LG], Human–computer interaction, Adaptive system, Artificial life, self-adaptation, 0202 electrical engineering, electronic engineering, information engineering, [INFO.INFO-RB]Computer Science [cs]/Robotics [cs.RO], collective robotics, Self-organization, business.industry, Biology and Life Sciences, adaptive system, Self adaptation, [INFO.INFO-MA]Computer Science [cs]/Multiagent Systems [cs.MA], Scalability, Robot, 020201 artificial intelligence & image processing, Artificial intelligence, business
Abstract

Self-organization in natural systems demonstrates very reliable and scalable collective behavior without using any central elements. When providing collective robotic systems with self-organizing principles, we are facing new problems of making self-organization purposeful, self-adapting to changing environments and faster, in order to meet requirements from a technical perspective. This paper describes on-going work of creating such an artificial self-organization within artificial robot organisms, performed in the framework of several European projects.

Published
2009
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21. The KnownLeaf literature curation system captures knowledge about Arabidopsis leaf growth and development and facilitates integrated data mining

Author

Stefanie De Bodt, Yves Van de Peer, Sara Jover-Gil, José Luis Micol, Jesper T. Gronlund, Richard G. H. Immink, Katja Baerenfaller, Sofie Van Landeghem, Gerco C. Angenent, Rubén Casanova-Sáez, Wilhelm Gruissem, Vicky Buchanan-Wollaston, Dóra Szakonyi, Pierre Hilson, Lieven Baeyens, Aalt D. J. van Dijk, Jonas Blomme, David Wilson-Sánchez, Fabio Fiorani, Asuka Kuwabara, Sean Walsh, David Esteve-Bruna, Nathalie Gonzalez, Tamara Muñoz-Nortes, Dirk Inzé, Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics, Ghent University [Belgium] (UGENT), Department of Biology, Swiss Federal Institute of Technology, Instituto de Bioingeniería, Universidad Miguel Hernández [Elche] (UMH), Warwick Systems Biology Centre, and School of Life Sciences, University of Warwick, Plant Research International, Bioscience, Wageningen University and Research Center (WUR), Genomics Research Institute (GRI), University of Pretoria (UPSpace), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Universiteit Gent = Ghent University [Belgium] (UGENT), and Wageningen University and Research [Wageningen] (WUR)

Subjects
EXPRESSION, Leaf growth, INFORMATION, Relational database, Computer science, [SDV]Life Sciences [q-bio], Arabidopsis, Context (language use), Plant Science, Scientific literature, computer.software_genre, Biochemistry, Wiskundige en Statistische Methoden - Biometris, TEXT, Open Biomedical Ontologies, Consistency (database systems), BIOS Applied Bioinformatics, lcsh:Botany, Genetics, Laboratorium voor Moleculaire Biologie, TOOL, BIOS Plant Development Systems, Mathematical and Statistical Methods - Biometris, Literature curation, Data integration, Data curation, PLANT ONTOLOGY, Biology and Life Sciences, Cell Biology, 15. Life on land, Data science, GENE, lcsh:QK1-989, PROTEIN INTERACTIONS, Data sharing, DIFFERENTIATION, MAINTENANCE, Data mining, Laboratory of Molecular Biology, computer, Developmental Biology, GENERATION
Abstract

The information that connects genotypes and phenotypes is essentially embedded in research articles written in natural language. To facilitate access to this knowledge, we constructed a framework for the curation of the scientific literature studying the molecular mechanisms that control leaf growth and development in Arabidopsis thaliana (Arabidopsis). Standard structured statements, called relations, were designed to capture diverse data types, including phenotypes and gene expression linked to genotype description, growth conditions, genetic and molecular interactions, and details about molecular entities. Relations were then annotated from the literature, defining the relevant terms according to standard biomedical ontologies. This curation process was supported by a dedicated graphical user interface, called Leaf Knowtator. A total of 283 primary research articles were curated by a community of annotators, yielding 9947 relations monitored for consistency and over 12,500 references to Arabidopsis genes. This information was converted into a relational database (KnownLeaf) and merged with other public Arabidopsis resources relative to transcriptional networks, protein–protein interaction, gene co-expression, and additional molecular annotations. Within KnownLeaf, leaf phenotype data can be searched together with molecular data originating either from this curation initiative or from external public resources. Finally, we built a network (LeafNet) with a portion of the KnownLeaf database content to graphically represent the leaf phenotype relations in a molecular context, offering an intuitive starting point for knowledge mining. Literature curation efforts such as ours provide high quality structured information accessible to computational analysis, and thereby to a wide range of applications., Current Plant Biology, 2, ISSN:2214-6628

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22. Break-induced replication is the primary recombination pathway in plant somatic hybrid mitochondria: a model for mitochondrial horizontal gene transfer.

Author

Gandini CL, Garcia LE, Abbona CC, Ceriotti LF, Kushnir S, Geelen D, and Sanchez-Puerta MV

Subjects
Nicotiana genetics, DNA Repair, Homologous Recombination, Gene Transfer, Horizontal, Mitochondria genetics
Abstract

Somatic hybrids between distant species offer a remarkable model to study genomic recombination events after mitochondrial fusion. Recently, we described highly chimeric mitogenomes in two somatic hybrids between the Solanaceae Nicotiana tabacum and Hyoscyamus niger resulting from interparental homologous recombination. To better examine the recombination map in somatic hybrid mitochondria, we developed a more sensitive bioinformatic strategy to detect recombination activity based on high-throughput sequencing without assembling the hybrid mitogenome. We generated a new intergeneric somatic hybrid between N. tabacum and Physochlaina orientalis, and re-analyzed the somatic hybrids that we previously generated. We inferred 213 homologous recombination events across repeats of 2.1 kb on average. Most of them (~80%) were asymmetrical, consistent with the break-induced replication pathway. Only rare (2.74%) non-homologous events were detected. Interestingly, independent events frequently occurred in the same regions within and across somatic hybrids, suggesting the existence of recombination hotspots in plant mitogenomes. Break-induced replication is the main pathway of interparental recombination in somatic hybrid mitochondria. Findings of this study are relevant to mitogenome editing assays and to mechanistic aspects of DNA integration following mitochondrial DNA horizontal transfer events., (© The Author(s) 2023. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Published
2023
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23. Local regulation of auxin transport in root-apex transition zone mediates aluminium-induced Arabidopsis root-growth inhibition.

Author

Li C, Liu G, Geng X, He C, Quan T, Hayashi KI, De Smet I, Robert HS, Ding Z, and Yang ZB

Subjects
Arabidopsis drug effects, Arabidopsis genetics, Arabidopsis growth & development, Arabidopsis Proteins genetics, Biological Transport, Calmodulin-Binding Proteins genetics, Calmodulin-Binding Proteins metabolism, Gene Expression Regulation, Plant, Membrane Transport Proteins genetics, Plant Roots drug effects, Plant Roots genetics, Plant Roots growth & development, Plant Roots metabolism, Stress, Physiological, Up-Regulation, Aluminum toxicity, Arabidopsis physiology, Arabidopsis Proteins metabolism, Ethylenes metabolism, Indoleacetic Acids metabolism, Membrane Transport Proteins metabolism, Plant Growth Regulators metabolism
Abstract

Aluminium (Al) stress is a major limiting factor for worldwide crop production in acid soils. In Arabidopsis thaliana, the TAA1-dependent local auxin biosynthesis in the root-apex transition zone (TZ), the major perception site for Al toxicity, is crucial for the Al-induced root-growth inhibition, while the mechanism underlying Al-regulated auxin accumulation in the TZ is not fully understood. In the present study, the role of auxin transport in Al-induced local auxin accumulation in the TZ and root-growth inhibition was investigated. Our results showed that PIN-FORMED (PIN) proteins such as PIN1, PIN3, PIN4 and PIN7 and AUX1/LAX proteins such as AUX1, LAX1 and LAX2 were all ectopically up-regulated in the root-apex TZ in response to Al stress and coordinately regulated local auxin accumulation in the TZ and root-growth inhibition. The ectopic up-regulation of PIN1 in the TZ under Al stress was regulated by both ethylene and auxin, with auxin signalling acting downstream of ethylene. Al-induced PIN1 up-regulation and auxin accumulation in the root-apex TZ was also regulated by the calossin-like protein BIG. Together, our results provide insight into how Al stress induces local auxin accumulation in the TZ and root-growth inhibition through the local regulation of auxin transport., (© 2021 Society for Experimental Biology and John Wiley & Sons Ltd.)

Published
2021
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24. TRAPID 2.0: a web application for taxonomic and functional analysis of de novo transcriptomes.

Author

Bucchini F, Del Cortona A, Kreft Ł, Botzki A, Van Bel M, and Vandepoele K

Subjects
Amino Acid Sequence, Animals, Evolution, Molecular, Gene Ontology, Humans, Molecular Sequence Annotation methods, Phylogeny, Reproducibility of Results, Sequence Homology, Amino Acid, Species Specificity, Classification methods, Computational Biology methods, Gene Expression Profiling methods, RNA-Seq methods, Web Browser
Abstract

Advances in high-throughput sequencing have resulted in a massive increase of RNA-Seq transcriptome data. However, the promise of rapid gene expression profiling in a specific tissue, condition, unicellular organism or microbial community comes with new computational challenges. Owing to the limited availability of well-resolved reference genomes, de novo assembled (meta)transcriptomes have emerged as popular tools for investigating the gene repertoire of previously uncharacterized organisms. Yet, despite their potential, these datasets often contain fragmented or contaminant sequences, and their analysis remains difficult. To alleviate some of these challenges, we developed TRAPID 2.0, a web application for the fast and efficient processing of assembled transcriptome data. The initial processing phase performs a global characterization of the input data, providing each transcript with several layers of annotation, comprising structural, functional, and taxonomic information. The exploratory phase enables downstream analyses from the web application. Available analyses include the assessment of gene space completeness, the functional analysis and comparison of transcript subsets, and the study of transcripts in an evolutionary context. A comparison with similar tools highlights TRAPID's unique features. Finally, analyses performed within TRAPID 2.0 are complemented by interactive data visualizations, facilitating the extraction of new biological insights, as demonstrated with diatom community metatranscriptomes., (© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2021
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25. The genome of the extremophile Artemia provides insight into strategies to cope with extreme environments.

Author

De Vos S, Rombauts S, Coussement L, Dermauw W, Vuylsteke M, Sorgeloos P, Clegg JS, Nambu Z, Van Nieuwerburgh F, Norouzitallab P, Van Leeuwen T, De Meyer T, Van Stappen G, Van de Peer Y, and Bossier P

Subjects
Animals, Extreme Environments, Heat-Shock Proteins, Salinity, Artemia genetics, Extremophiles
Abstract

Background: Brine shrimp Artemia have an unequalled ability to endure extreme salinity and complete anoxia. This study aims to elucidate its strategies to cope with these stressors., Results and Discussion: Here, we present the genome of an inbred A. franciscana Kellogg, 1906. We identified 21,828 genes of which, under high salinity, 674 genes and under anoxia, 900 genes were differentially expressed (42%, respectively 30% were annotated). Under high salinity, relevant stress genes and pathways included several Heat Shock Protein and Leaf Embryogenesis Abundant genes, as well as the trehalose metabolism. In addition, based on differential gene expression analysis, it can be hypothesized that a high oxidative stress response and endocytosis/exocytosis are potential salt management strategies, in addition to the expression of major facilitator superfamily genes responsible for transmembrane ion transport. Under anoxia, genes involved in mitochondrial function, mTOR signalling and autophagy were differentially expressed. Both high salt and anoxia enhanced degradation of erroneous proteins and protein chaperoning. Compared with other branchiopod genomes, Artemia had 0.03% contracted and 6% expanded orthogroups, in which 14% of the genes were differentially expressed under high salinity or anoxia. One phospholipase D gene family, shown to be important in plant stress response, was uniquely present in both extremophiles Artemia and the tardigrade Hypsibius dujardini, yet not differentially expressed under the described experimental conditions., Conclusions: A relatively complete genome of Artemia was assembled, annotated and analysed, facilitating research on its extremophile features, and providing a reference sequence for crustacean research., (© 2021. The Author(s).)

Published
2021
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27. Transcriptome Signatures in Pseudomonas simiae WCS417 Shed Light on Role of Root-Secreted Coumarins in Arabidopsis -Mutualist Communication.

Author

Yu K, Stringlis IA, van Bentum S, de Jonge R, Snoek BL, Pieterse CMJ, Bakker PAHM, and Berendsen RL

Abstract

Pseudomonas simiae WCS417 is a root-colonizing bacterium with well-established plant-beneficial effects. Upon colonization of Arabidopsis roots, WCS417 evades local root immune responses while triggering an induced systemic resistance (ISR) in the leaves. The early onset of ISR in roots shows similarities with the iron deficiency response, as both responses are associated with the production and secretion of coumarins. Coumarins can mobilize iron from the soil environment and have a selective antimicrobial activity that impacts microbiome assembly in the rhizosphere. Being highly coumarin-tolerant, WCS417 induces the secretion of these phenolic compounds, likely to improve its own niche establishment, while providing growth and immunity benefits for the host in return. To investigate the possible signaling function of coumarins in the mutualistic Arabidopsis -WCS417 interaction, we analyzed the transcriptome of WCS417 growing in root exudates of coumarin-producing Arabidopsis Col-0 and the coumarin-biosynthesis mutant f6'h1 . We found that coumarins in F6'H1-dependent root exudates significantly affected the expression of 439 bacterial genes (8% of the bacterial genome). Of those, genes with functions related to transport and metabolism of carbohydrates, amino acids, and nucleotides were induced, whereas genes with functions related to cell motility, the bacterial mobilome, and energy production and conversion were repressed. Strikingly, most genes related to flagellar biosynthesis were down-regulated by F6'H1-dependent root exudates and we found that application of selected coumarins reduces bacterial motility. These findings suggest that coumarins' function in the rhizosphere as semiochemicals in the communication between the roots and WCS417. Collectively, our results provide important novel leads for future functional analysis of molecular processes in the establishment of plant-mutualist interactions.

Published
2021
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28. Identification and characterization of Cercospora beticola necrosis-inducing effector CbNip1.

Author

Ebert MK, Rangel LI, Spanner RE, Taliadoros D, Wang X, Friesen TL, de Jonge R, Neubauer JD, Secor GA, Thomma BPHJ, Stukenbrock EH, and Bolton MD

Subjects
Cercospora growth & development, Cercospora pathogenicity, Fungal Proteins genetics, Host-Pathogen Interactions, Necrosis, Perylene metabolism, Phenotype, Phylogeny, Plant Leaves microbiology, Virulence, Virulence Factors, Beta vulgaris microbiology, Cercospora genetics, Fungal Proteins metabolism, Genome, Fungal genetics, Perylene analogs & derivatives, Plant Diseases microbiology
Abstract

Cercospora beticola is a hemibiotrophic fungus that causes cercospora leaf spot disease of sugar beet (Beta vulgaris). After an initial symptomless biotrophic phase of colonization, necrotic lesions appear on host leaves as the fungus switches to a necrotrophic lifestyle. The phytotoxic secondary metabolite cercosporin has been shown to facilitate fungal virulence for several Cercospora spp. However, because cercosporin production and subsequent cercosporin-initiated formation of reactive oxygen species is light-dependent, cell death evocation by this toxin is only fully ensured during a period of light. Here, we report the discovery of the effector protein CbNip1 secreted by C. beticola that causes enhanced necrosis in the absence of light and, therefore, may complement light-dependent necrosis formation by cercosporin. Infiltration of CbNip1 protein into sugar beet leaves revealed that darkness is essential for full CbNip1-triggered necrosis, as light exposure delayed CbNip1-triggered host cell death. Gene expression analysis during host infection shows that CbNip1 expression is correlated with symptom development in planta. Targeted gene replacement of CbNip1 leads to a significant reduction in virulence, indicating the importance of CbNip1 during colonization. Analysis of 89 C. beticola genomes revealed that CbNip1 resides in a region that recently underwent a selective sweep, suggesting selection pressure exists to maintain a beneficial variant of the gene. Taken together, CbNip1 is a crucial effector during the C. beticola-sugar beet disease process., (© 2020 This article is a U.S. Government work and is in the public domain in the USA. Molecular Plant Pathology published by John Wiley & Sons Ltd.)

Published
2021
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29. Gene expression during bacterivorous growth of a widespread marine heterotrophic flagellate.

Author

Massana R, Labarre A, López-Escardó D, Obiol A, Bucchini F, Hackl T, Fischer MG, Vandepoele K, Tikhonenkov DV, Husnik F, and Keeling PJ

Subjects
Gene Expression, Heterotrophic Processes, Oceans and Seas, Ecosystem, Stramenopiles genetics
Abstract

Phagocytosis is a fundamental process in marine ecosystems by which prey organisms are consumed and their biomass incorporated in food webs or remineralized. However, studies searching for the genes underlying this key ecological process in free-living phagocytizing protists are still scarce, in part due to the lack of appropriate ecological models. Our reanalysis of recent molecular datasets revealed that the cultured heterotrophic flagellate Cafeteria burkhardae is widespread in the global oceans, which prompted us to design a transcriptomics study with this species, grown with the cultured flavobacterium Dokdonia sp. We compared the gene expression between exponential and stationary phases, which were complemented with three starvation by dilution phases that appeared as intermediate states. We found distinct expression profiles in each condition and identified 2056 differentially expressed genes between exponential and stationary samples. Upregulated genes at the exponential phase were related to DNA duplication, transcription and translational machinery, protein remodeling, respiration and phagocytosis, whereas upregulated genes in the stationary phase were involved in signal transduction, cell adhesion, and lipid metabolism. We identified a few highly expressed phagocytosis genes, like peptidases and proton pumps, which could be used to target this ecologically relevant process in marine ecosystems.

Published
2021
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30. Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana.

Author

Li H, von Wangenheim D, Zhang X, Tan S, Darwish-Miranda N, Naramoto S, Wabnik K, De Rycke R, Kaufmann WA, Gütl D, Tejos R, Grones P, Ke M, Chen X, Dettmer J, and Friml J

Subjects
Cell Polarity, Cluster Analysis, Indoleacetic Acids, Membrane Transport Proteins, Arabidopsis genetics, Arabidopsis metabolism, Arabidopsis Proteins genetics, Arabidopsis Proteins metabolism
Abstract

Cell and tissue polarization is fundamental for plant growth and morphogenesis. The polar, cellular localization of Arabidopsis PIN-FORMED (PIN) proteins is crucial for their function in directional auxin transport. The clustering of PIN polar cargoes within the plasma membrane has been proposed to be important for the maintenance of their polar distribution. However, the more detailed features of PIN clusters and the cellular requirements of cargo clustering remain unclear. Here, we characterized PIN clusters in detail by means of multiple advanced microscopy and quantification methods, such as 3D quantitative imaging or freeze-fracture replica labeling. The size and aggregation types of PIN clusters were determined by electron microscopy at the nanometer level at different polar domains and at different developmental stages, revealing a strong preference for clustering at the polar domains. Pharmacological and genetic studies revealed that PIN clusters depend on phosphoinositol pathways, cytoskeletal structures and specific cell-wall components as well as connections between the cell wall and the plasma membrane. This study identifies the role of different cellular processes and structures in polar cargo clustering and provides initial mechanistic insight into the maintenance of polarity in plants and other systems., (© 2020 The Authors New Phytologist © 2020 New Phytologist Trust.)

Published
2021
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31. The medium-size noncoding RNA transcriptome of Ostreococcus tauri , the smallest living eukaryote, reveals a large family of small nucleolar RNAs displaying multiple genomic expression strategies.

Author

Bousquet L, Hemon C, Malburet P, Bucchini F, Vandepoele K, Grimsley N, Moreau H, and Echeverria M

Abstract

The small nucleolar RNAs (snoRNAs), essential for ribosome biogenesis, constitute a major family of medium-size noncoding RNAs (mncRNAs) in all eukaryotes. We present here, for the first time in a marine unicellular alga, the characterization of the snoRNAs family in Ostreococcus tauri , the smallest photosynthetic eukaryote. Using a transcriptomic approach, we identified 131 O. tauri snoRNAs (Ot-snoRNA) distributed in three classes: the C/D snoRNAs, the H/ACA snoRNAs and the MRP RNA. Their genomic organization revealed a unique combination of both the intronic organization of animals and the polycistronic organization of plants. Remarkably, clustered genes produced Ot-snoRNAs with unusual structures never previously described in plants. Their abundances, based on quantification of reads and northern blots, showed extreme differences in Ot-snoRNA accumulation, mainly determined by their differential stability. Most of these Ot-snoRNAs were predicted to target rRNAs or snRNAs. Seventeen others were orphan Ot-snoRNAs that would not target rRNA. These were specific to O. tauri or Mamiellophyceae and could have functions unrelated to ribosome biogenesis. Overall, these data reveal an 'evolutionary response' adapted to the extreme compactness of the O. tauri genome that accommodates the essential Ot-snoRNAs, developing multiple strategies to optimize their coordinated expression with a minimal cost on regulatory circuits., (© The Author(s) 2019. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics.)

Published
2020
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33. Identification and evolution of gene regulatory networks: insights from comparative studies in plants.

Author

Jones DM and Vandepoele K

Subjects
Gene Expression Regulation, Plants genetics, Transcription Factors, Evolution, Molecular, Gene Regulatory Networks
Abstract

The availability of genome sequences, genome-wide assays of transcription factor binding, and accessible chromatin maps have unveiled gene regulatory landscapes in plants. This understanding has ushered in comparative gene regulatory network studies that assess network rewiring between species, across time, and between biological tissues. Comparisons of cis-regulatory elements across the plant kingdom have uncovered examples of conserved sequences, but also of divergence, indicating that selective pressures can vary in different plant families. Transcription factor duplication, followed by spatiotemporal expression divergence of the duplicates, also appears to be a key mechanism of network evolution. Here, we review recent literature describing the regulation of gene expression in plants, and how comparative studies provide insights into how these regulatory interactions change and lead to gene regulatory network rewiring., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Published
2020
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34. De novo Assembly of Transcriptomes From a B73 Maize Line Introgressed With a QTL for Resistance to Gray Leaf Spot Disease Reveals a Candidate Allele of a Lectin Receptor-Like Kinase.

Author

Welgemoed T, Pierneef R, Sterck L, Van de Peer Y, Swart V, Scheepers KD, and Berger DK

Abstract

Gray leaf spot (GLS) disease in maize, caused by the fungus Cercospora zeina , is a threat to maize production globally. Understanding the molecular basis for quantitative resistance to GLS is therefore important for food security. We developed a de novo assembly pipeline to identify candidate maize resistance genes. Near-isogenic maize lines with and without a QTL for GLS resistance on chromosome 10 from inbred CML444 were produced in the inbred B73 background. The B73-QTL line showed a 20% reduction in GLS disease symptoms compared to B73 in the field ( p = 0.01). B73-QTL leaf samples from this field experiment conducted under GLS disease pressure were RNA sequenced. The reads that did not map to the B73 or C. zeina genomes were expected to contain novel defense genes and were de novo assembled. A total of 141 protein-coding sequences with B73-like or plant annotations were identified from the B73-QTL plants exposed to C. zeina . To determine whether candidate gene expression was induced by C. zeina , the RNAseq reads from C. zeina -challenged and control leaves were mapped to a master assembly of all of the B73-QTL reads, and differential gene expression analysis was conducted. Combining results from both bioinformatics approaches led to the identification of a likely candidate gene, which was a novel allele of a lectin receptor-like kinase named L-RLK-CML that (i) was induced by C. zeina , (ii) was positioned in the QTL region, and (iii) had functional domains for pathogen perception and defense signal transduction. The 817AA L-RLK-CML protein had 53 amino acid differences from its 818AA counterpart in B73. A second "B73-like" allele of L-RLK was expressed at a low level in B73-QTL. Gene copy-specific RT-qPCR confirmed that the l-rlk-cml transcript was the major product induced four-fold by C. zeina . Several other expressed defense-related candidates were identified, including a wall-associated kinase, two glutathione s-transferases, a chitinase, a glucan beta-glucosidase, a plasmodesmata callose-binding protein, several other receptor-like kinases, and components of calcium signaling, vesicular trafficking, and ethylene biosynthesis. This work presents a bioinformatics protocol for gene discovery from de novo assembled transcriptomes and identifies candidate quantitative resistance genes., (Copyright © 2020 Welgemoed, Pierneef, Sterck, Van de Peer, Swart, Scheepers and Berger.)

Published
2020
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35. PIN-driven auxin transport emerged early in streptophyte evolution.

Author

Skokan R, Medvecká E, Viaene T, Vosolsobě S, Zwiewka M, Müller K, Skůpa P, Karady M, Zhang Y, Janacek DP, Hammes UZ, Ljung K, Nodzyński T, Petrášek J, and Friml J

Subjects
Arabidopsis genetics, Arabidopsis metabolism, Arabidopsis Proteins genetics, Arabidopsis Proteins metabolism, Biological Transport, Chlorophyta genetics, Membrane Transport Proteins genetics, Plants genetics, Plants metabolism, Chlorophyta metabolism, Evolution, Molecular, Indoleacetic Acids metabolism, Membrane Transport Proteins metabolism
Abstract

PIN-FORMED (PIN) transporters mediate directional, intercellular movement of the phytohormone auxin in land plants. To elucidate the evolutionary origins of this developmentally crucial mechanism, we analysed the single PIN homologue of a simple green alga Klebsormidium flaccidum. KfPIN functions as a plasma membrane-localized auxin exporter in land plants and heterologous models. While its role in algae remains unclear, PIN-driven auxin export is probably an ancient and conserved trait within streptophytes.

Published
2019
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36. Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis .

Author

Zhu Q, Gallemí M, Pospíšil J, Žádníková P, Strnad M, and Benková E

Subjects
Abscisic Acid metabolism, Arabidopsis, Arabidopsis Proteins metabolism, Gene Expression Regulation, Developmental, Gene Expression Regulation, Plant, Gibberellins metabolism, Indoleacetic Acids metabolism, Meristem growth & development, Plant Growth Regulators metabolism, Plants, Genetically Modified, Seedlings growth & development, Germination physiology, Gravity Sensing physiology, Hypocotyl growth & development, Plant Roots growth & development
Abstract

The apical hook is a transiently formed structure that plays a protective role when the germinating seedling penetrates through the soil towards the surface. Crucial for proper bending is the local auxin maxima, which defines the concave (inner) side of the hook curvature. As no sign of asymmetric auxin distribution has been reported in embryonic hypocotyls prior to hook formation, the question of how auxin asymmetry is established in the early phases of seedling germination remains largely unanswered. Here, we analyzed the auxin distribution and expression of PIN auxin efflux carriers from early phases of germination, and show that bending of the root in response to gravity is the crucial initial cue that governs the hypocotyl bending required for apical hook formation. Importantly, polar auxin transport machinery is established gradually after germination starts as a result of tight root-hypocotyl interaction and a proper balance between abscisic acid and gibberellins.This article has an associated 'The people behind the papers' interview., Competing Interests: Competing interestsThe authors declare no competing or financial interests., (© 2019. Published by The Company of Biologists Ltd.)

Published
2019
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37. Gene space completeness in complex plant genomes.

Author

Van Bel M, Bucchini F, and Vandepoele K

Subjects
Genes, Plant, Genome, Plant, Plants genetics
Abstract

Genome annotations offer ample opportunities to study gene functions, biochemical and regulatory pathways, or quantitative trait loci in plants. Determining the quality and completeness of a genome annotation, and maintaining the balance between them, are major challenges, even for genomes of well-studied model organisms. In this review, we present a historical overview of the complexity in different plant genomes and discuss the hurdles and possible solutions in obtaining a complete and high-quality genome annotation. We illustrate there is no clear-cut answer to solve these challenges for different gene types, but provide tips on guiding the iterative process of generating a superior genome annotation, which is a moving target as our knowledge about plant genomics increases and additional data sources become available., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Published
2019
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38. Optimising orbit counting of arbitrary order by equation selection.

Author

Melckenbeeck I, Audenaert P, Van Parys T, Van De Peer Y, Colle D, and Pickavet M

Subjects
Computer Simulation, Humans, Models, Biological, Algorithms, Computational Biology methods, Computer Graphics, Data Interpretation, Statistical, Diabetes Mellitus metabolism, Protein Interaction Mapping methods, Proteins metabolism
Abstract

Background: Graphlets are useful for bioinformatics network analysis. Based on the structure of Hočevar and Demšar's ORCA algorithm, we have created an orbit counting algorithm, named Jesse. This algorithm, like ORCA, uses equations to count the orbits, but unlike ORCA it can count graphlets of any order. To do so, it generates the required internal structures and equations automatically. Many more redundant equations are generated, however, and Jesse's running time is highly dependent on which of these equations are used. Therefore, this paper aims to investigate which equations are most efficient, and which factors have an effect on this efficiency., Results: With appropriate equation selection, Jesse's running time may be reduced by a factor of up to 2 in the best case, compared to using randomly selected equations. Which equations are most efficient depends on the density of the graph, but barely on the graph type. At low graph density, equations with terms in their right-hand side with few arguments are more efficient, whereas at high density, equations with terms with many arguments in the right-hand side are most efficient. At a density between 0.6 and 0.7, both types of equations are about equally efficient., Conclusions: Our Jesse algorithm became up to a factor 2 more efficient, by automatically selecting the best equations based on graph density. It was adapted into a Cytoscape App that is freely available from the Cytoscape App Store to ease application by bioinformaticians.

Published
2019
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39. Reducing phenolic off-flavors through CRISPR-based gene editing of the FDC1 gene in Saccharomyces cerevisiae x Saccharomyces eubayanus hybrid lager beer yeasts.

Author

Mertens S, Gallone B, Steensels J, Herrera-Malaver B, Cortebeek J, Nolmans R, Saels V, Vyas VK, and Verstrepen KJ

Subjects
Beer microbiology, Biodiversity, Gene Editing, Saccharomyces classification, Saccharomyces cerevisiae classification, Clustered Regularly Interspaced Short Palindromic Repeats genetics, Saccharomyces genetics, Saccharomyces cerevisiae genetics
Abstract

Today's beer market is challenged by a decreasing consumption of traditional beer styles and an increasing consumption of specialty beers. In particular, lager-type beers (pilsner), characterized by their refreshing and unique aroma and taste, yet very uniform, struggle with their sales. The development of novel variants of the common lager yeast, the interspecific hybrid Saccharomyces pastorianus, has been proposed as a possible solution to address the need of product diversification in lager beers. Previous efforts to generate new lager yeasts through hybridization of the ancestral parental species (S. cerevisiae and S. eubayanus) yielded strains with an aromatic profile distinct from the natural biodiversity. Unfortunately, next to the desired properties, these novel yeasts also inherited unwanted characteristics. Most notably is their phenolic off-flavor (POF) production, which hampers their direct application in the industrial production processes. Here, we describe a CRISPR-based gene editing strategy that allows the systematic and meticulous introduction of a natural occurring mutation in the FDC1 gene of genetically complex industrial S. cerevisiae strains, S. eubayanus yeasts and interspecific hybrids. The resulting cisgenic POF- variants show great potential for industrial application and diversifying the current lager beer portfolio., Competing Interests: The authors have declared that no competing interests exist.

Published
2019
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40. Publisher Correction: Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza.

Author

Stein JC, Yu Y, Copetti D, Zwickl DJ, Zhang L, Zhang C, Chougule K, Gao D, Iwata A, Goicoechea JL, Wei S, Wang J, Liao Y, Wang M, Jacquemin J, Becker C, Kudrna D, Zhang J, Londono CEM, Song X, Lee S, Sanchez P, Zuccolo A, Ammiraju JSS, Talag J, Danowitz A, Rivera LF, Gschwend AR, Noutsos C, Wu CC, Kao SM, Zeng JW, Wei FJ, Zhao Q, Feng Q, El Baidouri M, Carpentier MC, Lasserre E, Cooke R, da Rosa Farias D, da Maia LC, Dos Santos RS, Nyberg KG, McNally KL, Mauleon R, Alexandrov N, Schmutz J, Flowers D, Fan C, Weigel D, Jena KK, Wicker T, Chen M, Han B, Henry R, Hsing YC, Kurata N, de Oliveira AC, Panaud O, Jackson SA, Machado CA, Sanderson MJ, Long M, Ware D, and Wing RA

Abstract

This article was not made open access when initially published online, which was corrected before print publication. In addition, ORCID links were missing for 12 authors and have been added to the HTML and PDF versions of the article.

Published
2018
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41. The Xerobranching Response Represses Lateral Root Formation When Roots Are Not in Contact with Water.

Author

Orman-Ligeza B, Morris EC, Parizot B, Lavigne T, Babé A, Ligeza A, Klein S, Sturrock C, Xuan W, Novák O, Ljung K, Fernandez MA, Rodriguez PL, Dodd IC, De Smet I, Chaumont F, Batoko H, Périlleux C, Lynch JP, Bennett MJ, Beeckman T, and Draye X

Subjects
Adaptation, Psychological physiology, Arabidopsis genetics, Arabidopsis Proteins genetics, Arabidopsis Proteins metabolism, Edible Grain growth & development, Gene Expression Regulation, Plant genetics, Meristem metabolism, Organogenesis, Plant, Plant Growth Regulators metabolism, Plants, Genetically Modified, Signal Transduction, Transcription Factors metabolism, Water metabolism, Abscisic Acid metabolism, Edible Grain metabolism, Plant Roots metabolism
Abstract

Efficient soil exploration by roots represents an important target for crop improvement and food security [1, 2]. Lateral root (LR) formation is a key trait for optimizing soil foraging for crucial resources such as water and nutrients. Here, we report an adaptive response termed xerobranching, exhibited by cereal roots, that represses branching when root tips are not in contact with wet soil. Non-invasive X-ray microCT imaging revealed that cereal roots rapidly repress LR formation as they enter an air space within a soil profile and are no longer in contact with water. Transcript profiling of cereal root tips revealed that transient water deficit triggers the abscisic acid (ABA) response pathway. In agreement with this, exogenous ABA treatment can mimic repression of LR formation under transient water deficit. Genetic analysis in Arabidopsis revealed that ABA repression of LR formation requires the PYR/PYL/RCAR-dependent signaling pathway. Our findings suggest that ABA acts as the key signal regulating xerobranching. We conclude that this new ABA-dependent adaptive mechanism allows roots to rapidly respond to changes in water availability in their local micro-environment and to use internal resources efficiently., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

Published
2018
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42. Dual localized kinesin-12 POK2 plays multiple roles during cell division and interacts with MAP65-3.

Author

Herrmann A, Livanos P, Lipka E, Gadeyne A, Hauser MT, Van Damme D, and Müller S

Subjects
Adenosine Triphosphate metabolism, Arabidopsis Proteins chemistry, Arabidopsis Proteins genetics, Binding Sites physiology, Cell Cycle physiology, Cytokinesis, Hydrolysis, Kinesins chemistry, Kinesins genetics, Membrane Fusion Proteins metabolism, Microtubules ultrastructure, Mitosis physiology, Nicotiana chemistry, Arabidopsis cytology, Arabidopsis metabolism, Arabidopsis Proteins metabolism, Cell Division, Kinesins metabolism, Microtubule-Associated Proteins metabolism
Abstract

Kinesins are versatile nano-machines that utilize variable non-motor domains to tune specific motor microtubule encounters. During plant cytokinesis, the kinesin-12 orthologs, PHRAGMOPLAST ORIENTING KINESIN (POK)1 and POK2, are essential for rapid centrifugal expansion of the cytokinetic apparatus, the phragmoplast, toward a pre-selected cell plate fusion site at the cell cortex. Here, we report on the spatio-temporal localization pattern of POK2, mediated by distinct protein domains. Functional dissection of POK2 domains revealed the association of POK2 with the site of the future cell division plane and with the phragmoplast during cytokinesis. Accumulation of POK2 at the phragmoplast midzone depends on its functional POK2 motor domain and is fine-tuned by its carboxy-terminal region that also directs POK2 to the division site. Furthermore, POK2 likely stabilizes the phragmoplast midzone via interaction with the conserved microtubule-associated protein MAP65-3/PLEIADE, a well-established microtubule cross-linker. Collectively, our results suggest that dual localized POK2 plays multiple roles during plant cell division., (© 2018 The Authors.)

Published
2018
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43. Network Modeling Unravels Mechanisms of Crosstalk between Ethylene and Salicylate Signaling in Potato.

Author

Ramšak Ž, Coll A, Stare T, Tzfadia O, Baebler Š, Van de Peer Y, and Gruden K

Subjects
Arabidopsis genetics, Arabidopsis metabolism, Crops, Agricultural genetics, Crops, Agricultural metabolism, Gene Expression Profiling methods, Gene Expression Regulation, Plant, Plant Breeding methods, Plant Immunity genetics, Solanum tuberosum metabolism, Ethylenes metabolism, Gene Regulatory Networks, Models, Genetic, Salicylic Acid metabolism, Signal Transduction genetics, Solanum tuberosum genetics
Abstract

To develop novel crop breeding strategies, it is crucial to understand the mechanisms underlying the interaction between plants and their pathogens. Network modeling represents a powerful tool that can unravel properties of complex biological systems. In this study, we aimed to use network modeling to better understand immune signaling in potato ( Solanum tuberosum ). For this, we first built on a reliable Arabidopsis ( Arabidopsis thaliana ) immune signaling model, extending it with the information from diverse publicly available resources. Next, we translated the resulting prior knowledge network (20,012 nodes and 70,091 connections) to potato and superimposed it with an ensemble network inferred from time-resolved transcriptomics data for potato. We used different network modeling approaches to generate specific hypotheses of potato immune signaling mechanisms. An interesting finding was the identification of a string of molecular events illuminating the ethylene pathway modulation of the salicylic acid pathway through Nonexpressor of PR Genes1 gene expression. Functional validations confirmed this modulation, thus supporting the potential of our integrative network modeling approach for unraveling molecular mechanisms in complex systems. In addition, this approach can ultimately result in improved breeding strategies for potato and other sensitive crops., (© 2018 American Society of Plant Biologists. All rights reserved.)

Published
2018
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44. Elucidating Tricin-Lignin Structures: Assigning Correlations in HSQC Spectra of Monocot Lignins.

Author

Lan W, Yue F, Rencoret J, Del Río JC, Boerjan W, Lu F, and Ralph J

Abstract

Tricin [5,7-dihydroxy-2-(4-hydroxy-3,5-dimethoxyphenyl)-4H-chromen-4-one] is a flavone that has been found to be incorporated in grass lignin polymers via 4'⁻O⁻β coupling. Herein, we investigated the tricin-lignin structure using nuclear magnetic resonance (NMR) methods by comparing the 1H⁻13C heteronuclear correlation (HSQC) NMR spectra of the isolated lignin with a series of dimeric and trimeric tricin-4'⁻O⁻β-ether model compounds. Results showed that the tricin moiety significantly affects the chemical shift of the Cβ/Hβ of 4'⁻O⁻β unit, producing peaks at around δC/δH 82.5⁻83.5/4.15⁻4.45, that differ from the Cβ/Hβ correlations from normal 4⁻O⁻β units formed solely by monolignols, and that have to date been unassigned.

Published
2018
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45. Methodologies for in vitro and in vivo evaluation of efficacy of antifungal and antibiofilm agents and surface coatings against fungal biofilms.

Author

Van Dijck P, Sjollema J, Cammue BP, Lagrou K, Berman J, d'Enfert C, Andes DR, Arendrup MC, Brakhage AA, Calderone R, Cantón E, Coenye T, Cos P, Cowen LE, Edgerton M, Espinel-Ingroff A, Filler SG, Ghannoum M, Gow NAR, Haas H, Jabra-Rizk MA, Johnson EM, Lockhart SR, Lopez-Ribot JL, Maertens J, Munro CA, Nett JE, Nobile CJ, Pfaller MA, Ramage G, Sanglard D, Sanguinetti M, Spriet I, Verweij PE, Warris A, Wauters J, Yeaman MR, Zaat SAJ, and Thevissen K

Abstract

Unlike superficial fungal infections of the skin and nails, which are the most common fungal diseases in humans, invasive fungal infections carry high morbidity and mortality, particularly those associated with biofilm formation on indwelling medical devices. Therapeutic management of these complex diseases is often complicated by the rise in resistance to the commonly used antifungal agents. Therefore, the availability of accurate susceptibility testing methods for determining antifungal resistance, as well as discovery of novel antifungal and antibiofilm agents, are key priorities in medical mycology research. To direct advancements in this field, here we present an overview of the methods currently available for determining (i) the susceptibility or resistance of fungal isolates or biofilms to antifungal or antibiofilm compounds and compound combinations; (ii) the in vivo efficacy of antifungal and antibiofilm compounds and compound combinations; and (iii) the in vitro and in vivo performance of anti-infective coatings and materials to prevent fungal biofilm-based infections., Competing Interests: Conflict of interest: The authors declare no conflict of interest.

Published
2018
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46. AtSERPIN1 is an inhibitor of the metacaspase AtMC1-mediated cell death and autocatalytic processing in planta.

Author

Lema Asqui S, Vercammen D, Serrano I, Valls M, Rivas S, Van Breusegem F, Conlon FL, Dangl JL, and Coll NS

Subjects
Arabidopsis Proteins chemistry, Biocatalysis, Caspases chemistry, Immunoprecipitation, Proteasome Endopeptidase Complex metabolism, Protein Binding, Protein Domains, Apoptosis, Arabidopsis cytology, Arabidopsis enzymology, Arabidopsis Proteins metabolism, Caspases metabolism, Serpins metabolism
Abstract

The hypersensitive response (HR) is a localized programmed cell death phenomenon that occurs in response to pathogen recognition at the site of attempted invasion. Despite more than a century of research on HR, little is known about how it is so tightly regulated and how it can be contained spatially to a few cells. AtMC1 is an Arabidopsis thaliana plant metacaspase that positively regulates the HR. Here, we used an unbiased approach to identify new AtMC1 regulators. Immunoaffinity purification of AtMC1-containing complexes led us to the identification of the protease inhibitor AtSerpin1. Our data clearly showed that coimmunoprecipitation between AtMC1 and AtSerpin1 and formation of a complex between them was lost upon mutation of the AtMC1 catalytic site, and that the AtMC1 prodomain was not required for the interaction. AtSerpin1 blocked AtMC1 self-processing and inhibited AtMC1-mediated cell death. Our results constitute an in vivo example of a Serpin acting as a suicide inhibitor in plants, reminiscent of the activity of animal or viral serpins on immune/cell death regulators, including caspase-1. These results indicate a conserved function of a protease inhibitor on cell death regulators from different kingdoms with unrelated modes of action (i.e. caspases vs metacaspases)., (© 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.)

Published
2018
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47. The impact of the injection mold temperature upon polymer crystallization and resulting drug release from immediate and sustained release tablets.

Author

Van Renterghem J, Dhondt H, Verstraete G, De Bruyne M, Vervaet C, and De Beer T

Subjects
Chemistry, Pharmaceutical, Crystallization, Delayed-Action Preparations chemistry, Drug Liberation, Excipients chemistry, Hydrophobic and Hydrophilic Interactions, Ketoprofen administration & dosage, Ketoprofen pharmacokinetics, Metoprolol administration & dosage, Metoprolol pharmacokinetics, Models, Chemical, Solubility, Tablets, Temperature, Delayed-Action Preparations pharmacokinetics, Drug Compounding methods, Polymers chemistry
Abstract

It was the aim of this study to elucidate the impact of the injection mold temperature upon the polymer crystallinity, its microstructure and the resulting drug release from immediate and sustained release tablets containing semi-crystalline polymers. The immediate release formulation contained 20% (w/w) ketoprofen (KETO) in poly (ethylene oxide) (PEO) and the sustained release formulation contained 20-40% (w/w) metoprolol tartrate (MPT) in polycaprolactone (PCL). Physical mixtures of drug-polymer were characterized via isothermal crystallization experiments using DSC and rheological measurements to elucidate the impact of the drug solid-state upon the crystallization kinetics. Tablets were prepared using various thermal histories (extrusion barrel temperature and injection mold temperatures). Polymer crystallinity and microstructure in the tablets was characterized via DSC and polarized optical microscopy. The polymer microstructure was altered by the various applied thermal histories. The differences in PEO crystallinity induced by the various mold temperatures did not affect the KETO dissolution from the tablets. On the other hand, MPT (20-40% w/w) dissolution from the PCL matrix when extruded at 80 °C and injection molded at 25 and 35 °C was significantly different due to the changes in the polymer microstructure. More perfect polymer crystals are obtained with higher mold temperatures, decreasing the drug diffusion rate through the PCL matrix. The results presented in this study imply that the injection mold temperature should be carefully controlled for sustained release formulations containing hydrophobic semi-crystalline polymers., (Copyright © 2018 Elsevier B.V. All rights reserved.)

Published
2018
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48. Enhanced larvicidal, antibacterial, and photocatalytic efficacy of TiO 2 nanohybrids green synthesized using the aqueous leaf extract of Parthenium hysterophorus.

Author

Thandapani K, Kathiravan M, Namasivayam E, Padiksan IA, Natesan G, Tiwari M, Giovanni B, and Perumal V

Subjects
Aedes, Animals, Anti-Bacterial Agents chemistry, Anti-Infective Agents chemistry, Asteraceae, Culex, Mosquito Vectors, Parthenogenesis, X-Ray Diffraction, Anti-Bacterial Agents pharmacology, Anti-Infective Agents pharmacology, Azo Compounds chemistry, Insecticides chemistry, Larva drug effects, Plant Extracts chemistry, Silver chemistry, Titanium chemistry
Abstract

Titanium dioxide nanoparticles are emerging as a biocompatible nanomaterial with multipurpose bioactivities. In this study, titanium dioxide (TiO 2 ) nanoparticles were effectively synthesized using the aqueous leaf extracts of Parthenium hysterophorus prepared by microwave irradiation. TiO 2 nanoparticles were fabricated by treating the P. hysterophorus leaf extracts with the TiO 4 solution. Biologically active compounds such as alcohols, phenols, alkanes, and fluoroalkanes were involved in bioreduction of TiO 4 into TiO 2 . The formation of green-engineered TiO 2 nanoparticles was confirmed by UV-vis spectroscopy, Fourier transform infrared spectroscopy (FTIR), field emission scanning electron microscopy (FESEM), and energy-dispersive X-ray (EDX) spectroscopy and further characterized by X-ray diffraction (XRD) studies. UV-vis spectroscopy analysis showed maximum absorbance at 420 nm due to surface plasmon resonance of synthesized TiO 2 NPs. FTIR spectrum of the engineered TiO 2 NPs showed the presence of bioactive compounds in the leaf extract, which acted as capping and reducing agents. FESEM exhibited an average size of 20-50 nm and a spherical shape of TiO 2 NPs. EDX analysis indicated the presence of TiO 2 NPs by observing the peaks of titanium ions. XRD results pointed out the crystalline nature of engineered TiO 2 NPs. The larvicidal activity of TiO 2 NPs was studied on fourth instar larvae of dengue, Zika virus, and filariasis mosquito vectors Aedes aegypti and Culex quinquefasciatus. Antimicrobial efficacy of TiO 2 NPs was assessed on clinically isolated pathogens Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, Klebsiella pneumoniae, Proteus vulgaris, and Staphylococcus epidermidis. Besides, we found that TiO 2 NPs are able to quickly degrade the industrially harmful pigments methylene blue, methyl orange, crystal violet, and alizarin red dyes under sunlight illumination. Overall, this novel, simple, and eco-friendly approach can be of interest for the control of vector-borne diseases, as well as to formulate new bactericidal agents and to efficiently degrade dye solutions in the polluted areas.

Published
2018
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49. Corrigendum to "European contribution to the study of ROS: A summary of the findings and prospects for the future from the COST action BM1203 (EU-ROS)" [Redox Biol. 13 (2017) 94-162].

Author

Egea J, Fabregat I, Frapart YM, Ghezzi P, Görlach A, Kietzmann T, Kubaichuk K, Knaus UG, Lopez MG, Olaso-Gonzalez G, Petry A, Schulz R, Vina J, Winyard P, Abbas K, Ademowo OS, Afonso CB, Andreadou I, Antelmann H, Antunes F, Aslan M, Bachschmid MM, Barbosa RM, Belousov V, Berndt C, Bernlohr D, Bertrán E, Bindoli A, Bottari SP, Brito PM, Carrara G, Casas AI, Chatzi A, Chondrogianni N, Conrad M, Cooke MS, Costa JG, Cuadrado A, My-Chan Dang P, De Smet B, Debelec-Butuner B, Dias IHK, Dunn JD, Edson AJ, El Assar M, El-Benna J, Ferdinandy P, Fernandes AS, Fladmark KE, Förstermann U, Giniatullin R, Giricz Z, Görbe A, Griffiths H, Hampl V, Hanf A, Herget J, Hernansanz-Agustín P, Hillion M, Huang J, Ilikay S, Jansen-Dürr P, Jaquet V, Joles JA, Kalyanaraman B, Kaminskyy D, Karbaschi M, Kleanthous M, Klotz LO, Korac B, Korkmaz KS, Koziel R, Kračun D, Krause KH, Křen V, Krieg T, Laranjinha J, Lazou A, Li H, Martínez-Ruiz A, Matsui R, McBean GJ, Meredith SP, Messens J, Miguel V, Mikhed Y, Milisav I, Milković L, Miranda-Vizuete A, Mojović M, Monsalve M, Mouthuy PA, Mulvey J, Münzel T, Muzykantov V, Nguyen ITN, Oelze M, Oliveira NG, Palmeira CM, Papaevgeniou N, Pavićević A, Pedre B, Peyrot F, Phylactides M, Pircalabioru GG, Pitt AR, Poulsen HE, Prieto I, Rigobello MP, Robledinos-Antón N, Rodríguez-Mañas L, Rolo AP, Rousset F, Ruskovska T, Saraiva N, Sasson S, Schröder K, Semen K, Seredenina T, Shakirzyanova A, Smith GL, Soldati T, Sousa BC, Spickett CM, Stancic A, Stasia MJ, Steinbrenner H, Stepanić V, Steven S, Tokatlidis K, Tuncay E, Turan B, Ursini F, Vacek J, Vajnerova O, Valentová K, Van Breusegem F, Varisli L, Veal EA, Yalçın AS, Yelisyeyeva O, Žarković N, Zatloukalová M, Zielonka J, Touyz RM, Papapetropoulos A, Grune T, Lamas S, Schmidt HHHW, Di Lisa F, and Daiber A

Published
2018
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50. The Soil-Borne Legacy.

Author

Bakker PAHM, Pieterse CMJ, de Jonge R, and Berendsen RL

Subjects
Models, Biological, Plant Roots metabolism, Plants metabolism, Plants microbiology, Rhizosphere, Soil chemistry, Host Microbial Interactions, Microbiota physiology, Plant Roots microbiology, Soil Microbiology
Abstract

Plants greatly rely on their root microbiome for uptake of nutrients and protection against stresses. Recent studies have uncovered the involvement of plant stress responses in the assembly of plant-beneficial microbiomes. To facilitate durable crop production, deciphering the driving forces that shape the microbiome is crucial., (Copyright © 2018 Elsevier Inc. All rights reserved.)

Published
2018
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