Welcome to the Multinational Arabidopsis Steering Committee!

The most recent 2017/2018 Country Reports can be downloaded here. If you require separate country reports then please contact the MASC coordinator This email address is being protected from spambots. You need JavaScript enabled to view it..

The reports below are from 2016 so please download the reports from 2018 for the most up to date editions!

The wider Arabidopsis and plant community supports MASC by appointing individual country representatives, who are nationally and internationally well connected Arabidopsis researchers. To date 29 countries support MASC and the international Arabidopsis community. Researchers from all over the world working with Arabidopsis are highly encouraged to get involved with MASC in order to further strengthen the network, international collaboration and data sharing.


 

  • Argentina Open or Close
    Marcelo J. Yanovsky (This email address is being protected from spambots. You need JavaScript enabled to view it.) Instituto Leloir (FIL and CONICET)

    Arabidopsis Research Facilities

    There are more than 30 groups conducting varied research with Arabidopsis in Argentina. They work in different Institutes and Universities scattered throughout the country in cities such as Buenos Aires, Rosario, Mar del Plata, Santa Fe, Córdoba, Mendoza and Bariloche.

    Current Arabidopsis Projects

    The research topics and research groups include, among others, water transport (Gabriela Amodeo), responses to water deficit (Raquel Chan, Norberto Iusem), light signaling and photomorphogenesis (Jorge Casal, Carlos Ballaré, Javier Botto), responses to UV-B light (Paula Casati, Carlos Ballaré, Raúl Cassia), oxidative stress (Nestor Carrillo, Daniel Gonzalez, Estela Valle, Diego Gomez Casati), leaf growth and development (Javier Palatnik, Ramiro Rodriguez), circadian rhythms (Marcelo Yanovsky), flowering time (Pablo Cerdán), flower development (Jorge Muschietti, Gabriela Pagnussat, Eduardo Zabaleta, Ariel Goldraij), hormone biology (Lorenzo Lamatina, Ana Laxalt, Carlos García Mata, Santiago Mora García, Ruben Bottini), carbohydrate metabolism (Graciela Salerno, Fernando Carrari), root growth and development (José Estevez) biotic stress responses (Sebastián Azurmendi, Mariana del Vas, María Elena Alvarez), gene expression, micro RNAs and alternative splicing (Pablo Manavella, Javier Palatnik, Marcelo Yanovsky, Alberto Kornblihtt).

    Conferences and Workshops

    The 11th International Plant Molecular Biology Congress, with strong participation of Arabidopsis researchers, was held in Iguazú Falls, at the border of Argentina and Brazil, and was organized by a bi-national Argentine-Brazilian Committee.


    Selected Publications

    • MicroRNA miR396 Regulates the Switch between Stem Cells and Transit-Amplifying Cells in Arabidopsis Roots. Rodriguez RE, Ercoli MF, Debernardi JM, Breakfield NW, Mecchia MA, Sabatini M, Cools T, De Veylder L, Benfey PN, Palatnik JF (2015) Plant Cell 27(12):3354-66.
    • KH domain protein RCF3 is a tissue-biased regulator of the plant miRNA biogenesis cofactor HYL1. Karlsson P, Christie MD, Seymour DK, Wang H, Wang X, Hagmann J, Kulcheski F, Manavella PA (2015) Proc Natl Acad Sci U S A. 112(45):14096-101.
    • The spliceosome assembly factor GEMIN2 attenuates the effects of temperature on alternative splicing and circadian rhythms. Schlaen RG, Mancini E, Sanchez SE, Perez-Santángelo S, Rugnone ML, Simpson CG, Brown JW, Zhang X, Chernomoretz A, Yanovsky MJ (2015) Proc Natl Acad Sci U S A. 112(30):9382-7.
    • Induced folding in RNA recognition by Arabidopsis thaliana DCL1. Suarez IP, Burdisso P, Benoit MP, Boisbouvier J, Rasia RM (2015) Nucleic Acids Res. 43(13):6607-19.


    Major Funding Sources

    Argentinean National Research Council (CONICET) and Agencia Nacional de Pomoción Científica y Tecnológica (ANPCyT).

  • Australia Open or Close

    1. Prepared by (Name, Email, Institution)

    Monika Murcha, This email address is being protected from spambots. You need JavaScript enabled to view it., The University of Western Australia

    2. Use of Arabidopsis

    Can you approximate the number of institutions and/or labs in your country that use Arabidopsis in their research.

    There are over 60 research groups located at most Universities across the country and within Commonwealth Scientific Research Organisation (CSIRO) facilities.

    3. Open Resources for Arabidopsis Researchers

    The Plant Detectives Manual: teaching resource tool that focuses on using Arabidopsis for plant science research.

    https://press.anu.edu.au/publications/plant-detectives-manual

    4. New Software Tools

    Please provide a list of software tools recently developed in your country that are open access and available to the global community of Arabidopsis researchers.

    SUBA4: The SubCellular Proteomic Database, housing large scale proteomic, GFP localization data In sillico abundance estimations for Arabidopsis proteins.http://suba.plantenergy.uwa.edu.au/

    RICE DB: Rice DB facilitates and integrates direct comparison of rice annotations to Arabidopsis allowing parallel comparison between these two model species within one database. http://ricedb.plantenergy.uwa.edu.au/

    Plant stress and root cell methylomes. (http://listerlab.org/browsers.html)

    Arabidopsis Transposable Element browser. (http://plantenergy.uwa.edu.au/~lister/annoj/browser_te_variants.html)

    MASCP Gator: a proteomics aggregation utility that displays information from a variety of online Arabidopsis proteomic resources. http://gator.masc-proteomics.org/

    1001 Proteomes: Arabidopsis non-synonymous SNP browser created from data made available as part of the 1001 Genomes consortium. http://1001proteomes.masc-proteomics.org/

    5. Conferences, Workshops and Outreach events

    COMBIO 2017 Adelaide and COMBIO 2018 Sydney; Combined Biological Sciences Annual Conference. Annual national conference that includes several symposia dedicated to plant research. This conference incorporates the annual Australian Society of Plant Biologists meeting. https://www.asbmb.org.au

    Lorne Conferences; Annual conferences held at Lorne, Victoria dedicated to” Protein Structure and Function” and “Genome biology”.

    The Virtual Plant Cell (VPC) developed by the Centre of excellence in Plant Energy Biology allows users to become immersed in and interact with a plant cell, learn about the importance of phosphate and walk through labs and facilities such as The Plant Accelerator. Aimed at primary and senior school students. https://www.youtube.com/channel/UCEIGuXCAGkkHgAZP9LWbXgA

    6. Selected Publications

    Australian researchers have published over 170 articles involving Arabidopsis; Pubmed search using keyword searches Arabidopsis (Title/Abstract) and Australia (affiliation) since Jan 2017-Mar 2018). Selected publications indicating the breadth of outputs are listed below.

    Lonhienne T, Garcia MD, Pierens G, Mobli M, Nouwens A, Guddat LW. Structural insights into the mechanism of inhibition of AHAS by herbicides. Proc Natl Acad Sci U S A. 2018 Feb 27;115(9):E1945-E1954. doi: 10.1073/pnas.1714392115.

    Wen Z, Tyerman SD, Dechorgnat J, Ovchinnikova E, Dhugga KS, Kaiser BN. Maize NPF6 Proteins Are Homologs of Arabidopsis CHL1 That Are Selective for Both Nitrate and Chloride. Plant Cell. 2017 Oct;29(10):2581-2596. doi:10.1105/tpc.16.00724.

    David R, Burgess A, Parker B, Li J, Pulsford K, Sibbritt T, Preiss T, Searle IR. Transcriptome-Wide Mapping of RNA 5-Methylcytosine in Arabidopsis mRNAs and Noncoding RNAs. Plant Cell. 2017 Mar;29(3):445-460. doi: 10.1105/tpc.16.00751.

    Li L, Nelson CJ, Trösch J, Castleden I, Huang S, Millar AH. Protein Degradation Rate in Arabidopsis thaliana Leaf Growth and Development. Plant Cell. 2017 Feb;29(2):207-228. doi: 10.1105/tpc.16.00768.

    Pornsiriwong W, Estavillo GM, Chan KX, Tee EE, Ganguly D, Crisp PA, Phua SY, Zhao C, Qiu J, Park J, Yong MT, Nisar N, Yadav AK, Schwessinger B, Rathjen J, Cazzonelli CI, Wilson PB, Gilliham M, Chen ZH, Pogson BJ. A chloroplast retrograde signal, 3'-phosphoadenosine 5'-phosphate, acts as a secondary messenger in abscisic acid signaling in stomatal closure and germination. Elife. 2017 Mar 21;6. pii: e23361. doi: 10.7554/eLife.23361.

    Wang L, Wu LM, Greaves IK, Zhu A, Dennis ES, Peacock WJ. PIF4-controlled auxin pathway contributes to hybrid vigor in Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2017 Apr 25;114(17):E3555-E3562. doi: 10.1073/pnas.1703179114.

    Crisp PA, Ganguly DR, Smith AB, Murray KD, Estavillo GM, Searle I, Ford E, Bogdanović O, Lister R, Borevitz JO, Eichten SR, Pogson BJ. Rapid Recovery Gene Downregulation during Excess-Light Stress and Recovery in Arabidopsis. Plant Cell. 2017 Aug;29(8):1836-1863. doi: 10.1105/tpc.16.00828.

    Rautengarten C, Birdseye D, Pattathil S, McFarlane HE, Saez-Aguayo S, Orellana A, Persson S, Hahn MG, Scheller HV, Heazlewood JL, Ebert B. The elaborate route for UDP-arabinose delivery into the Golgi of plants. Proc Natl Acad Sci U S A. 2017 Apr 18;114(16):4261-4266.

    Garcia MD, Nouwens A, Lonhienne TG, Guddat LW. Comprehensive understanding of acetohydroxyacid synthase inhibition by different herbicide families. Proc Natl Acad Sci U S A. 2017 Feb 14;114(7):E1091-E1100.

    Schneider R, Tang L, Lampugnani ER, Barkwill S, Lathe R, Zhang Y, McFarlane HE, Pesquet E, Niittyla T, Mansfield SD, Zhou Y, Persson S. Two Complementary

    Mechanisms Underpin Cell Wall Patterning during Xylem Vessel Development. Plant Cell. 2017 Oct;29(10):2433-2449.

    7. Major Funding Sources

    Fundamental and translational research can be funded by the Australian Research Council (www.arc.gov.au)

    Translational research is funded by the Grains Research Development Corporation (http://grdc.com.au)

    Industry collaborations can be funded by the Australian Research Council Linkage Programs (www.arc.gov.au)


  • Austria Open or Close
    Marie-Theres Hauser (This email address is being protected from spambots. You need JavaScript enabled to view it.) University of Natural Resources and Life Sciences BOKU, Vienna

    Arabidopsis Research Facilities

    University of Natural Resources & Life Science Vienna (BOKU), Department of Applied Genetics & Cell Biology (DAGZ) (http://www.dagz.boku.ac.at/en/)
    Gregor Mendel Institute of Molecular Plant Biology (GMI) (http://www.gmi.oeaw.ac.at/)
    Max F. Perutz Laboratories (MFPL) (http://www.mfpl.ac.at/)
    Institute of Science and Technology, Austria (IST Austria)(http://www.ist.ac.at/en/)
    AIT Austrian Institute of Technology (http://www.ait.ac.at/)
    University of Salzburg, Division of Plant Physiology (http://www.uni-salzburg.at/index.php?id=32701&L=1)
    University of Vienna, Ecogenomics and Systems Biology (http://www.univie.ac.at/mosys)
    VBCF ProTech facility (http://www.vbcf.ac.at/facilities/protein-technologies/)
    VBCF PlantsS facility (http://www.vbcf.ac.at/facilities/plant-sciences/)

    Research Groups

    Population Genetics

    Magnus Nordborg (http://www.gmi.oeaw.ac.at/research-groups/magnus-nordborg): Scientific Director of the GMI.

    Molecular Biology and Signaling

    Andreas Bachmair (http://www.mfpl.ac.at/mfpl-group/group/bachmair.html): Stress response pathways, posttranslational modification by Ubiquitin and by SUMO; Claudia Jonak (http://www.ait.ac.at/): Stress signal transduction and cellular responses; Markus Teige (http://www.univie.ac.at/mosys/markus_teige_cv.html): signaling in acclimation to stress, organellar signaling; Irute Meskiene (http://www.univie.ac.at/mosys/groups.html): stress signaling and protein phosphatases

    Chromosome Biology

    Peter Schlögelhofer (http://www.mfpl.ac.at/mfpl-group/group/schloegelhofer.html): meiotic recombination

    Epigenetics

    Frederic Berger (http://www.gmi.oeaw.ac.at/research-groups/frederic-berger): Chromatin architecture and function; Ortrun Mittelsten Scheid (http://www.gmi.oeaw.ac.at/research-groups/mittelsten-scheid): Epigenetic changes in plants


    Development

    Wolfgang Busch (http://www.gmi.oeaw.ac.at/research-groups/wolfgang-busch): Regulation of root development in Arabidopsis; Michael Nodine (http://www.gmi.oeaw.ac.at/research
    -groups/michael-nodine): Small RNA functions in plant embryos; Eva Benkova (http://ist.ac.at/en/research/research-groups/benkova-group): Hormonal regulation of plant development; Jiri Friml (http://ist.ac.at/research/research-groups/friml-group): Auxin transport, cell polarity and endocytic trafficking

    Molecular Genetics & Cell Biology

    Marie-Theres Hauser (http://www.dagz.boku.ac.at/en/abteilung-fuer-
    pflanzengenetik-und-zellbiologie/ag-hauser): development, stress; Jürgen Kleine Vehn (http://www.dagz.boku.ac.at/arbeitsgruppen/team-kleine-vehn/): phytohormonal crosstalk, differential growth regulation; Barbara Korbei (http://www.dagz.boku.ac.at/pgz/korbei): Elucidating the role of TOL proteins in post-Golgi trafficking

    Glycobiology

    Richard Strasser (http://www.dagz.boku.ac.at/en/mzg/strasser/): Function of N-glycans; Doris Lucyshyn (http://www.dagz.boku.ac.at/en/abteilung-fuer-pflanzengenetik-und-zellbiologie/ag-abas/projekt-lucyshyn): O-GlcNAcylation; Raimund Tenhaken (http://www.uni-salzburg.at/index.php?id=32790&L=1): Nucleotide sugars biosynthesis and function

    RNA Metabolism

    Mariya Kalyna (http://www.dagz.boku.ac.at/en/abteilung-fuer-
    pflanzengenetik-und-zellbiologie/ag-hauser/projekt-kalyna): Alternative splicing

    Plant Pathogen Interaction

    Youssef Belkhadir (http://www.gmi.oeaw.ac.at/research-groups/youssef-belkhadir): Plant cell signalling at the interface of growth and defences; Armin Djamei (http://www.gmi.oeaw.ac.at/research-groups/armin-djamei): Effectomics - exploring the toolbox of plant pathogens

    Current Arabidopsis Projects

    Doctoral programmes financed by the FWF

     

    ITN (international training network)

    • 2013-2017 “CALIPSO - Calcium and Light Signals in Photosynthetic Organisms” (itn-calipso.univie.ac.at/)
    • 2013-2017 “COMREC: Control of Meiotic Recombination: Arabidopsis to Crops” (http://www.birmingham.ac.uk/comrec)

     

    ERC

    • 2011-2016 “MAXMAP: Developing maximum-resolution genotype-phenotype maps using whole-genome polymorphism data”
    • 2012-2017 “PSDP: Polarity and subcellular dynamics in plants”
    • 2014-2019 “EFFECTOMICS- elucidating the toolbox of biotrophic pathogens”
    • 2015-2020 “sRNA-EMB: Small RNA regulation of the body plan and epigenome in Arabidopsis embryos”
    • 2015-2020 “AuxinER: Mechanism of Auxin-dependent Signaling in the Endoplasmatic Reticulum” 

     

    ERA-CAPS projects

    • 2014-2017 “Dimorphic fruits, seed and seedlings as adaptation mechanisms to abiotic stress in unpredictable environments (SeedAdapt)”
    • 2014-2017 “EURO-PEC - European Plant Embryology Consortium”
    • 2015-2018 “Evolution of sexual reproduction in plants (EVOREPRO)”
    • 2014-2017 “The role of the N-end rule pathway in controlling plant response to the environment (N-vironment)”
    • 2014-2017 "Delineating the crossover control networks in plants (DeCOP)"

     

    WWTF projects

    • 2011-2018 “Plant Cell and Molecular Biology”
    • 2014-2018 “Quantitative Live Imaging to Determine the Regulatory Impact of Chromatin Dynamics” 

     

    FWF projects

    • 2008-2019 “Chromosome Dynamics“ SFB 34
    • 2013-2016 “SINUDYN – Stress-induced nucleosome dynamics in plants”
    • 2014-2017 “Impact of a new histone H2A variant on chromatin structure and dynamics”
    • 2014-2017 “N-vironment - The role of the N-end rule in plant response to the environment” 
    • 2014-2017 “In vivo Protein Interaction during Cell Signaling”
    • 2014-2017 “N-vironment - The role of the N-end rule in plant response to the environment” 
    • 2014-2019 “TOL Proteins in post-Golgi Trafficking in Plants”
    • 2015-2016 “Epigenetic Reprogramming of the Plant Paternal Genome”
    • 2015-2017 “Root growth Control and Epistasis”
    • 2015-2017 “Elucidating Salicylic Acid Sensing in Biotrophic Smut Fungi”
    • 2015-2017 “Hormone cross-talk drives nutrient-dependent root development”
    • 2015-2017 “Pectin signaling in responses to heavy metals and pathogens”
    • 2015-2018 “Dissecting the glycan-dependent ERAD pathway in plants”
    • 2015-2018 “Signaling Salt Stress to the chromatin”
    • 2015-2018 “Characterization of an essential virulence factor in the maize pathogen Ustilago maydis”
    • 2015-2018 “EXO70 exocyst subunits in morphogenesis and adaptation”
    • 2015-2019 “Small RNAdirected reprogramming of lineage-specific epigenomes in plant embryos”
    • 2016-2017 “The histone variant H2A.W: a novel component that structures chromatin domains”
    • 2016-2018 “Evolution of the chromatin organization in plants”
    • 2016-2018 “The role of PLD zeta1 in iron dependent root growth regulation”
    • 2016-2019 “Importance of Lewis A Epitopes for Pseudomonas syringae Infection of Arabidopsis” 

     

    DFG

    2011-2017 “Evolutionary plant solutions to ecological challenges: Molecular mechanisms underlying adaptive traits in the Brassicaceae s.l. (Adaptomics)”

     

    APART fellowship of the Austrian Academie of Sciences

    2014-2018 “O-GlcNAc Modification of Plant Proteins“

     

    Arabidopsis Tools and Resources

    Fred Berger: Several antibodies against Arabidopsis histones
    VBCF PlantsS facility: offering state of the art growth chambers and greenhouse space along with automated phenotyping
    VBCF ProTech facility: offering made-to-order CRISPR/Cas9 transgenics
    Andreas Bachmair: Mutants in ubiquitin conjugation, in vitro SUMO conjugation assay
    IST Austria: root chip tracking system, light sheet (SPIM) microscope for Arabidopsis roots, lateral roots, apical hook (not published), vertical confocal microscope allowing automatic tracking of the root growth (not published), platform for specific cell ablation combined with real-time imaging in plants

    Outreach Activities

    Fascination of plant day, May 18, 2016. (http://www.plantday12.eu/home.htm)
    European Researchers Night, Sept 25, 2016 (http://www.fit-for-future.at/calipso)
    Long night of Research, April 22, 2016 (http://www.langenachtderforschung.at/)
    Open campus day IST Austria presenting, May 31, 2015
    Open campus day IST Austria presenting, June 5, 2015

    Conferences and Workshops

    Vienna Region Plant Network Meeting, Feb 2015, Vienna, University of Natural Resources and Life Sciences
    Symposium “Pair, Share and Care: Chromosomes throughout Life”, Vienna, Sept 2015
    VBC PhD Symposium “Communication: let’s talk about it”, Nov 2015 Vienna Austria
    Vienna Region Plant Network Meeting, Nov 2015, Vienna Biocenter Campus
    “11th Microsymposium on Small RNAs” May 2016 Vienna Austria
    EMBO Workshop “New Model systems for early land plant evolution” June 2016 Vienna Austria
    “Tri-National Arabidopsis Meeting (TNAM)” Sept 2016 Vienna, Austria
    International Conference “Plant Organellar Signaling 2016” (http://www.plant-organellar-signaling.eu/)

    Selected Publications

    • DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation. Dubin MJ, Zhang P, Meng D, Remigereau MS, Osborne EJ, Paolo Casale F, Drewe P, Kahles A, Jean G, Vilhjálmsson B, Jagoda J, Irez S, Voronin V, Song Q, Long Q, Rätsch G, Stegle O, Clark RM, Nordborg M (2015) Elife 4:e05255.
    • “SnRK1-triggered switch of bZIP63 dimerization mediates the low-energy response in plants. Mair A, Pedrotti L, Wurzinger B, Anrather D, Simeunovic A, Weiste C, Valerio C, Dietrich K, Kirchler T, Nägele T, Vicente Carbajosa J, Hanson J, Baena-González E, Chaban C, Weckwerth W, Dröge-Laser W, Teige M (2015) Elife 05828.
    • How cells coordinate waste removal through their major proteolytic pathways. Martens S, Bachmair A (2015) Nat Cell Biol. 17(7):841-2.
    • Actin-dependent vacuolar occupancy of the cell determines auxin-induced growth repression. Scheuring D, Löfke C, Krüger F, Kittelmann M, Eisa A, Hughes L, Smith RS, Hawes C, Schumacher K, Kleine-Vehn J (2016) Proc Natl Acad Sci U S A. 113(2):452-7.
    • Auxin regulates SNARE-dependent vacuolar morphology restricting cell size. Löfke C, Dünser K, Scheuring D, Kleine-Vehn J (2015) Elife 4. doi: 10.7554/eLife.05868.

    Major Funding Sources

    Austrian Academy of Sciences (ÖAW)
    http://www.oeaw.ac.at/en/fellowship-funding/stipendien-preise/nachwuchsfoerderung-der-oeaw/
    Austrian Research Promotion Agency (FFG)
    http://www.ffg.at/en
    Austrian Science Fund (FWF) http://www.fwf.ac.at/en/
    European Union:
    Seventh Framework Programme (FP7) http://ec.europa.eu/research/fp7/index_en.cfm
    European Research Council (ERC) http://erc.europa.eu/
    Marie Skłodowska-Curie actions http://ec.europa.eu/research/mariecurieactions/
    Vienna Science and Technology Fund (WWTF)
    http://wwtf.at/index.php?lang=EN
    OeAD http://www.oead.at/projects_cooperations/EN/

  • Belgium Open or Close

    Moritz K. Nowack (This email address is being protected from spambots. You need JavaScript enabled to view it.) VIB-Ghent University, Plant Systems Biology

    Arabidopsis Research Facilities

    Arabidopsis research topics in Belgium include cell cycle regulation (D. Inzé, L. De Veylder), root and leaf growth and development (D. Inzé, T. Beeckman, G. Beemster, M. Van Lijsebettens, K. Vissenberg), oxidative stress and cell death (F. Van Breusegem, M. Nowack, P. Motte, H. Asard), genome annotation and evolution (S. Maere, Y. Van de Peer, P. Rouzé, K. Vandepoele), proteomics (G. De Jaegher, I. De Smet), tree biotechnology and bioenergy (W. Boerjan, B. Vanholme), cell biology (D. Geelen, D. Van Damme), hormone biology (D. Van Der Straeten , J. Russinova E., Prinsen, A. Goossens), carbohydrates (E. Van Damme, P. Van Dijck; F. Roland), membrane proteins (M. Boutry), abiotic stress (N. Verbruggen; C. Hermans, Y. Guisez; M. Hanikenne), flowering (C. Périlleux; P. Tocquin) and plant pathogen interaction (G. Angenon, B. Cammue, L. Gheysen; P. du Jardin, J. Vanderleyden, P. Delaplace, J. Dommes).

    Current Arabidopsis Projects

    Belgian Arabidopsis projects are funded by university-, regional-, federal-, or European-level grants, but not within calls specifically targeting this model plant species or plants.

    A Belgian national research project (IAP), coordinated by D. Inzé, focuses on how root and shoot influence each other and how this interaction contributes to the development of the plant. This program also involves T. Beeckman, F. Van Breusegem G. Beemster, L. De Veylder, M. Boutry, X. Draye, N. F. Chaumont, and C. Périlleux. Malcolm Bennett (Univ. Nottingham, UK) is an international partner in this project. For more information, see http://www.iuap-mars.be/.

    FWO (Research Foundation – Flanders) research grants were appointed to L. De Veylder to study DNA damage checkpoint control (in collaboration with I. De Smet), to F. Roland to study energy signalling, to F. Van Breusegem to study redox control of proteins, to E. Van Damme to study lectin-carbohydrate interactions, to Moritz Nowack to study programmed cell death in plant reproduction, and to D. Van Der Straeten to study mitochondrial editing factors.

    An F.R.S.-FNRS grant was appointed to C. Hermans to study mineral influences on root architecture.

    An ERC Starting Grant was obtained by Moritz Nowack for work on developmental programmed cell death in Arabidopsis roots (2015- 2020)

    An ERC Consolidator Grant was obtained by Daniel Van Damme for work on cell division control in Arabiodpis roots (2016- 2021)

    An Odysseus Group II grant was obtained by Bert De Rybel, to work on cellular patterning in Arabidopsis embryogenesis http://www.fwo.be/en/fellowships-funding/research-projects/odysseusprogramme/

    Outlook on Arabidopsis Research

    There is a gradual move to other model species besides Arabidopsis, particularly crop species. Arabidopsis may remain the species of choice to pioneer new molecular genetics approaches due to its strengths as a small plant with short generation time that is easily transformable. Limitation however in applicability and possibilities to use when larger sample sizes are required (e.g. metabolomics, proteomics, biochemistry approaches are pretty much limited to whole plant level).

    Arabidopsis Tools and Resources

    The Department of Plant Systems Biology (PSB) continuously develops and disseminates an exhaustive collection of destination vectors, designed for the functional analysis of genes in plant cells and compatible with the recombinational cloning Gateway technology (www.psb.ugent.be/gateway/).

    The Yield Booster website provides the scientific community with information on genes and molecular mechanisms that govern plant growth and productivity. Data on model plants (including Arabidopsis) as well as crops are presented (www.yieldbooster.org/).

    PLAZA is an access point for plant comparative genomics centralizing genomic data produced by different genome sequencing initiatives. It integrates plant sequence data and comparative genomics methods and provides an online platform to perform evolutionary analyses and data mining within the green plant lineage (http://bioinformatics.psb.ugent.be/plaza/ugent.be/plaza/).

    Other developed resources include:

    • Platform for semi-automated kinematic analysis of growth in Arabidiospsis root tips and leaves
    • Phenotyping platforms
    • Metabolomics and Enzyme activity assays for antioxidant system.
    • VLeaf modelling platform based simulation models of Arabidopsis root tip and leaf growth.
    • A collection of adventitious rooting mutants
    • Marker lines for cell cycle, DNA stress, and meiosis specific events
    • Marker lines for developmental cell death


    Conferences and Workshops

    Selected Publications

    • Cyclic programmed cell death stimulates hormone signaling and root development in Arabidopsis. Xuan W, Band LR, Kumpf RP, Van Damme D, Parizot B, De Rop G, Opdenacker D, Möller BK, Skorzinski N, Njo MF, De Rybel B, Audenaert D, Nowack MK, Vanneste S, Beeckman T (2016) Science 351(6271):384-7.
    • ROTUNDA3 function in plant development by phosphatase 2A-mediated regulation of auxin transporter recycling. Karampelias M, Neyt P, De Groeve S, Aesaert S, Coussens G, Rolčík J, Bruno L, De Winne N, Van Minnebruggen A, Van Montagu M, Ponce MR, Micol JL, Friml J, De Jaeger G, Van Lijsebettens M (2016) Proc Natl Acad Sci U S A. 113(10):2768-73.
    • The DELLA protein SLR1 integrates and amplifies salicylic acid- and jasmonic acid-dependent innate immunity in rice. de Vleesschauwer D, Seifi S, Filipe O, Haeck A, Nguyen Huu S, Demeestere K, Höfte MM (2016) Plant Physiol. pii: pp.01515.2015.
    • It’s Time for Some “Site”-Seeing: Novel Tools to Monitor the Ubiquitin Landscape in Arabidopsis thaliana. Walton A, Stes E, Cybulski N, Van Bel M, Iñigo S, Durand AN, Timmerman E, Heyman J, Pauwels L, De Veylder L, Goossens A, De Smet I, Coppens F, Goormachtig S, Gevaert K (2016) Plant Cell 28(1):6-16.
    • An improved toolbox to unravel the plant cellular machinery by tandem affinity purification of Arabidopsis protein complexes. Van Leene J, Eeckhout D, Cannoot B, De Winne N, Persiau G, Van De Slijke E, Vercruysse L, Dedecker M, Verkest A, Vandepoele K, Martens L, Witters E, Gevaert K, De Jaeger G (2015) Nat Protoc. 10(1):169-87.

    Major Funding Sources

    Flanders Institute for Biotechnology (VIB; www.vib.be)
    European Union Framework Programs (cordis.europa.eu/)
    Belgian Federal Science Policy Office (www.belspo.be)
    Institute for the Promotion of Innovation by Science and Technology in Flanders (IWT; www.iwt.be)
    Research Foundation – Flanders (FWO; http://www.fwo.be/en/index.aspxbe/en/index.aspx)
    Fonds de la Recherche Scientifique (FNRS; http://www.frs-fnrs.be)
    European Research Council (http://erc.europa.eu/)

  • Brazil Open or Close
    Wagner Araújo (This email address is being protected from spambots. You need JavaScript enabled to view it.); Adriano Nunes (This email address is being protected from spambots. You need JavaScript enabled to view it.) Universidade Federal de Viçosa, Viçosa

    Arabidopsis Research Facilities

    There is currently a growing interest in using Arabidopsis as a model plant for research in Brazil.
    The groups working with Arabidopsis are distributed throughout the country in cities such as Brasília, Campinas, Fortaleza, Porto Alegre, Piracicaba, Rio de Janeiro, São Paulo, Viçosa and Fortaleza.
    There is currently no dedicated Arabidopsis consortia or centers in Brazil, but Arabidopsis is commonly used by plant biologists as a model organism. Brazilian funding agencies funds a number of projects in which Arabidopsis is employed as a model; however, most of those projects presents also an applied version using crops of interest in Brazil.
    Research topics and research groups in Brazil include, among others: plant growth and development, biotic and abiotic stress responses, phytohormonal crosstalk and biology, cell signalling mechanisms, circadian rhythms, carbohydrate metabolism, micro RNA, plant-insect-pathogen interactions, mitochondrial metabolism and transport, plant senescence and chlorophyll catabolism, system biology, oxidative stress, plant cell wall,

    Current Arabidopsis Research Projects

    Camila Caldana, CTBE/CNPEM, Campinas: Regulation of plant growth by the target of rapamycin (TOR) pathway.
    Michel Georges Albert Vincentz, CBMEG-UNICAMP, Campinas: Define the architecture of the gene regulatory network related to AtbZIP63: an Arabidopsis thaliana bZIP type transcriptional factor invovled in the control of energetic homeostasis.
    Maria Magdalena Rossi, IB-USP, São Paulo: Manipulation of senescence and chlorophyll catabolism for yield and nutritional quality improvement.
    Márcio de Castro Silva Filho, ESALQ-USP, Piracicaba: Deciphering the molecular mechanisms involved in the localization of organelar proteins as well as the complex plant-insect-pathogen interactions.
    Daniel Scherer de Moura, ESALQ-USP, Piracicaba: AtRALF1 perception mechanisms: its receptors and the dissociation between ion fluxes and the negative regulation of celular expansion.
    Alessandra Alves de Souza, IAC, APTA, Cordeirópolis: Functional study of genes associated with plant defense to pathogens: focus on the control of Xylella fastidiosa, the causal agent of citrus variegated chlorosis
    Ivan de Godoy Maia, IB-Unesp, Botucatu: Plant uncoupling mitochondrial proteins: functional analysis employing RNA-seq and knockout mutants.
    Marcelo Mendes Brandao, CBMEG-UNICAMP, Campinas: System biology techniques applied to the agriculture: transcriptomes and interactomes analyses.
    Juan Armando Casas Mollano, IQ-USP, São Paulo: Functional characterization of the newly discovered family of MUT9 kinases in Arabidopsis thaliana and sugarcane.

    There are other researchers involved in several Arabidopsis projects that should be also mentioned:
    Paulo Mazzafera, IB-UNICAMP, Campinas
    Celso Benedetti, LNBio/CNPEM, Campinas
    Fabio Tebaldi Nogueira, ESALQ-USP, Piracicaba
    Hana Masuda, UFABC, São Bernardo
    Marcelo Menossi, IB/UNICAMP, Campinas
    Marco Aurelio Zezzi Arruda, IQ-UNICAMP, Campinas
    Marcelo Dornelas, IB- UNICAMP, Campinas
    Ione Salgado, IB- UNICAMP, Campinas
    Carlos Hotta, IQ-USP, São Paulo
    Adriano Nunes-Nesi (UFV, Viçosa)
    Elizabeth B. Fontes (UFV, Viçosa)
    Wagner L. Araújo (UFV, Viçosa)
    Thomas Willians (UnB, Brasília)
    Márcia Margis (UFRGS, Porto Alegre)
    Luis Fernando Revers (EMBRAPA, Bento Gonçalves)
    Paulo Cavalcanti Gomes Ferreira (UFRJ, Rio de Janeiro)
    Adriana Hemerly (UFRJ, Rio de Janeiro)

    Outlook on Arabidopsis Research

    It is important to mention that research in Brazil is only starting to use Arabidopsis and other species are usually employed, particularly crop species. There is a gradual increase in the usage of Arabidopis as a model plant to molecular and genetic studies due to its power.
    Although funding in Brazil is available through several calls, it is becoming increasingly difficult to obtain funding for basic research, particularly to finance Arabidopsis research, given that the general trend is a more supportive program for applied research.

    Arabidopsis Tools and Resources

    This is still an area that needs to be developed in Brazil.

    Conferences and Workshops

    The International Plant Molecular Biology Congress was held in Iguazu Falls, Brazil, in October 25th - 30th, 2015
    XV Brazilian Congress of Plant Physiology/I Brazil-Israel Plant Science Conference, was held in Iguazu Falls, Brazil in September 28th - October 2nd 2015

    Selected Publications

    AIP1 is a novel Agenet/Tudor domain protein from Arabidopsis that interacts with regulators of DNA replication, transcription and chromatin remodeling. Brasil JN, Cabral LM, Eloy NB, Primo LMF, Barroso-Neto IL, Grangeiro LPP, Gonzalez N, Inzé D, Ferreira PCG, Hemerly AS (2015) BMC Plant Biology 15: 1-21
    Overexpression of mitochondrial uncoupling protein 1 (UCP1) induces a hypoxic response in Nicotiana tabacum leaves. Barreto P, Okura V, Pena IA, Maia R, Maia IG, Arruda P (2016) Journal of Experimental Botany 67: 301-13
    Revisiting the Non-Animal Peroxidase Superfamily. Trends in Plant Science. Lazzarotto F, Turchetto-Zolet AC, Margis-Pinheiro M (2015) 20: 807-13
    The ASYMMETRIC LEAVES Complex Employs Multiple Modes of Regulation to Affect Adaxial-Abaxial Patterning and Leaf Complexity. Husbands AY, Benkovics AH, Nogueira FTS, Lodha M, Timmermans MCP (2015) The Plant Cell 27: 3321-35
    TOR Signaling and Nutrient Sensing. Dobrenel T, Caldana C, Hanson J, Robaglia C, Vincentz M, Veit B, Meyer C (2016) Annual Review of Plant Biology 67: 261-85

    Major Funding Sources

    Major fundings agencies in Brazil include:
    National Council for Scientific and Technological Development (CNPq-Brazil)
    Brazilian Federal Agency for Support and Evaluation of Graduate Education (CAPES-Brazil)
    Foundation for Research Assistance of the Sao Paulo (FAPESP-Brazil)
    Foundation for Research Assistance of the Rio de Janeiro State (FAPERJ-Brazil)
    Foundation for Research Assistance of the Rio Grande do Sul State (FAPERGS-Brazil)
    Foundation for Research Assistance of the Minas Gerais State (FAPEMIG-Brazil)

  • Canada Open or Close
    Dario Bonetta (This email address is being protected from spambots. You need JavaScript enabled to view it.) University of Ontario - Institute of Technology, Ontario

    Arabidopsis Research Facilities

    Approximately 55 groups conduct varied research with Arabidopsis in Canada.

    Outlook on Arabidopsis Research

    Funding for Arabidopsis research is largely from NSERC, one of the three federal funding agencies in Canada. Basic research in plant biology continues to be underfunded. Indeed, compared to non-plant applicants to NSERC, plant biology has seen a steady decrease in funding since 2009 (personal communication David Guttman, University of Toronto).

    Arabidopsis Tools and Resources

    Bio-Analytic Resource for Plant Biology (BAR; http://bar.utoronto.ca) hosted by the Department of Cell and Systems Biology, University of Toronto.
    Centre for the Analysis of Genome Evolution and Function (CAGEF), Department of Cell and Systems Biology, University of Toronto.

    Selected Publications

    • 50 years of Arabidopsis research: highlights and future directions. Provart NJ, Alonso J, Assmann SM, Bergmann D, Brady SM, Brkljacic J, Browse J, Chapple C, Colot V, Cutler S, Dangl J, Ehrhardt D, Friesner JD, Frommer WB, Grotewold E, Meyerowitz E, Nemhauser J, Nordborg M, Pikaard C, Shanklin J, Somerville C, Stitt M, Torii KU, Waese J, Wagner D, McCourt P (2016) New Phytol. 209(3):921-44.
    • Structure-function analysis identifies highly sensitive strigolactone receptors in Striga. Toh S, Holbrook-Smith D, Stogios PJ, Onopriyenko O, Lumba S, Tsuchiya Y, Savchenko A, McCourt P (2015) Science. 350(6257):203-7.
    • PARASITIC PLANTS. Probing strigolactone receptors in Striga hermonthica with fluorescence. Tsuchiya Y, Yoshimura M, Sato Y, Kuwata K, Toh S, Holbrook-Smith D, Zhang H, McCourt P, Itami K, Kinoshita T, Hagihara S (2015) Science. 349(6250):864-8.

    Major Funding Sources

    Natural Science and Engineering Research Council (NSERC) (http://www.nserc-crsng.gc.ca)
    Genome Canada (http://www.genomecanada.ca/en/)

  • Chile Open or Close
    Francisca Blanco-Herrera (This email address is being protected from spambots. You need JavaScript enabled to view it.) Centro de Biotecnología Vegetal, Universidad Andres Bello, Santiago; Rodrigo Gutiérrez (This email address is being protected from spambots. You need JavaScript enabled to view it.) Pontificia Universidad Católica de Chile, Santiago

    Arabidopsis Research Facilities

    • Centro de Biotecnología Vegetal, UNAB, Santiago (http://cbv.unab.cl/)
    • Centro de Biotecnología Vegetal, Universidad de Chile, Santiago
    • Centro de Ciencia y Biotecnología Vegetal PUC, P. Universidad Católica de Chile, Santiago (http://agronomia.uc.cl/centros-unidades-y-laboratorios/cecibuc)
    • Millennium Nucleus in Plant Systems and Synthetic Biology, P. Universidad Católica de Chile, Santiago (http://www.genomicavegetal.cl/ )
    • Department of Molecular Genetics and Microbiology, P. Universidad Católica de Chile, Santiago
    • Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Santiago
    • Center for Applied Ecology and Sustainability, Santiago
    • Instituto de Ciencias Biológicas, Universidad de Talca, Talca (http://biologia.utalca.cl/index.html)

     

    Patricio Arce’s lab is interested in viral spread and the effect of viral infections in plants, employing Arabidopsis and the most important fruit plant in Chile, Vitis vinifera. Using functional genetics methods they could identify genes affected by the infection, and are currently looking for the key regulators of the plant response.

    Holuigue’s lab goal is to better understand plant defense mechanisms in response to stress, particularly Salicylic Acid (SA) functions using Arabidopsis. They could identify and functionally characterize SA-induced defense genes, and study the mechanism how SA induces their expression.

    Rodrigo Gutierrez’ lab goal is to understand how nitrogen signaling intersects with other signaling networks to control plant growth and development. This is essential to improve nitrogen use efficiency in plants or the amino acid content of seeds, important issues for health, agriculture and human nutrition.

    Xavier Jordana’s lab studies mitochondrial RNA editing. Their goal is to contribute to the characterization of a large gene family encoding nuclear factors (PPR proteins) controlling the specificity of the 400 Arabidopsis editing sites, via isolation of mutant plants and analysis of editing defects.

    Josefina Poupin’s group focuses in obtaining new insights into the mechanisms underlying the enhancement of salt-stress tolerance in the salt-sensitive Arabidopsis Col-0 plants, when inoculated with the PGPR strain Burkholderia phytofirmans PsJN.

    Felipe Aquea’s lab focuses on GCN5, an important histone acetyltransferase required for gene expression involved in many developmental pathways in plants and animals. They could identify a set of potential direct target genes of AtGCN5 through a combination of ChIP-Seq and genome-wide transcriptional profiling usingRNA-seq.

    Francisca Blanco’s lab studies signaling pathways associated to endoplasmic reticulum stress during plant-pathogen interaction. They are especially focused on SA signaling pathways involved in plant responses to bacterial infection.
    Ariel Orellana’s lab studies regulation of polysaccharides biosynthesis in the Golgi Apparatus. They could identify some Arabidopsis proteins sharing molecular characteristics with Nucleotide Sugar Transporters (NSTs) from other organisms, transporting GDP sugars. They focus on determining the substrate specificity of these NSTs via transient expression in plants, stable over-expression in Arabidopsis and insertional mutant lines.

    Gabriel León’s lab studies the molecular mechanisms that regulate the development and function of pollen grain.

    Lorena Norambuena’s lab focuses on endocytosis. Using chemical biology, they have described a lateral root formation mechanism in Arabidopsis induced by endocytic trafficking via a mechanism distinctive from auxin-driven promotion of lateral root formation.

    Michael Handford’s lab is interested in the study of Arabidopsis sugar alcohol metabolism. By using reverse genetics, they identified AtSDH, which oxidizes sorbitol, and characterized atsdh- mutants to be more resistant to drought stress.

    Pablo Figueroa’s lab studies the connection between Jasmonate and abiotic stress such as high salinity, a relationship not well understood at cellular and molecular levels. They investigated JA signaling activation by NaCl and its effect on primary root growth, and found that JA-responsive JAZ genes were upregulated by salt stress in a COI1-dependent manner.

    Javier Canales’ lab focuses on the molecular mechanisms underlying plant response to nutrients, specifically on their complex interactions in metabolic pathways.

    Current Arabidopsis Projects

    Rodrigo Gutiérrez. Howard Hughes Medical Institute International Early Career Scientist. Fondecyt grant (2014-2018), funded by Conicyt. FONDAP Center for Genome Regulation (http://www.genomacrg.cl/), funded by Conicyt (2016-2020). Millennium Nucleus Center for Plant Systems and Synthetic Biology (www.genomicavegetal.cl), funded by ICM (2015-2017).

    Michael Handford. “Sorbitol synthesis and its role in abiotic stress tolerance in non-Rosaceae species”. Sponsored by Fondecyt 1140527, Anillo ACT-1110 (2014-2018).

    Francisca Blanco. “Adaptive response to salt stress, mediated by salicylic acid in Arabidopsis thaliana”. Funded by Núcleo UNAB 590 DI-590-14/N (2014-2016).

    Felipe Aquea. Sponsored by FONDECYT 11130567, CAPES FB-002-2014, Millennium Nucleus NC130030 (2014-2017).

    Gabriel León. Funded by Fondecyt 1120766 and UNAB DI-74-12/R (2013-2016).

    Loreto Holuigue. “Study of the Mechanisms that Regulate Salicylic Acid Levels and Functions in the Redox Modulation of Defense Responses Against Biotic and Abiotic Stress in Arabidopsis”. Funded by Conicyt FONDECYT 1141202, (2014-2018).

    Xavier Jordana. “Mitochondrial Biogenesis and Function in Plants: Insights into the Role of Respiratory Complex II, Sirtuins and Pentatricopeptide Repeat Proteins”. Funded by Conicyt (2014-2018).

    Pablo Figueroa. “Elucidating Molecular Links Involved in the Crosstalk Between Salt-Elicited Responses and Jasmonate Signaling Pathway in Arabidopsis thaliana Roots”. Funded by Conicyt (2012-2016).

    Ariel Orellana. “The role of the UDP-rhamnose transporters in the biosynthesis of rhamnogalacturonan -I and -II in Arabidopsis thaliana”. FONDECYT 1151335. Funded by Conicyt (2014-2018).

    Javier Canales. “Uncovering gene regulatory networks involved in the crosstalk between sulfur and nitrogen nutrition in Arabidopsis thaliana”. FONDECYT 11150070. Funded by Conicyt (2015-2019).

    Outlook on Arabidopsis Research

    Our research community is very small as can be easily deduced from the previous section. However, the few groups are very active in research and training. The main research focus is on metabolism and responses to environmental cues (abiotic and biotic). In many instances, there are close ties to the Chilean industry and research groups use Arabidopsis and some other plant model systems that are of interest to the local economy (e.g. grapes, fruit trees). We believe this will continue to be the case in coming years with not much space to grow in terms of number of independent groups or topics. The recent changes in funding higher education (plan for gratuity in most Universities) has created much uncertainty and major research Universities in the country are not investing or expanding at the moment. Chile is also suffering major changes in the way Science and Technology is conducted at the government level, which introduces uncertainties. It is difficult to foresee how research will change in the upcoming years as a result of these changes. For example, the President recently announced creation of the Ministry for Science and Technology. How this will impact science research direction and funding possibilities is unknown at this stage, but we certainly all hope it will be for the best.

    Arabidopsis Tools and Resources

    Constructing simple biological networks for understanding complex high-throughput data in plants Moyano TC, Vidal EA, Contreras-López O, Gutiérrez RA (2015) Methods Mol Biol. 1284:503-26.
    In this chapter, the authors provide detailed methods for users without prior knowledge of bioinformatics to construct gene networks and derive hypotheses that can be experimentally verified. Step-by-step instructions for acquiring, integrating, analyzing, and visualizing genome-wide data are provided for two widely used open source platforms, R and Cytoscape. The examples provided are based on Arabidopsis data, but the protocols presented should be readily applicable to any organism for which similar data can be obtained.

    Outreach Activities

    • “Lectures On the Cell Wall”. Guests: Dr. Helen North (INRA de Versailles, France), Dr Marie- Christine Ralet (INRA de Nantes, France). Organizers: Dr. Ariel Orellana, Dr. Susana Saez-Aguayo (Universidad Andres Bello), 24-26 November, 2015.
    • International Meeting “Plant Stress and Sustainable Agriculture”. Guests: Dr. Serge Delrot, Dr. Tierry Candresse, Dr. Philippe Galluschi, Dr. Dominique Rolin, Dr. Alain Blanchard (University of Bordeaux), Dr. Alan Bennett, Dr. Dario Cantú (University OF CALIFORNIA – DAVIS). Organizers: Dr. Patricio Arce (Pontificia Universidad Católica de Chile), 30 June, 2015.
    • Seminar “A systems approach to improved root traits”. Guest: Dr. Philip Benfey (DUKE University, USA).Organizer: Dr. Rodrigo Gutierrez (Pontificia Universidad Católica de Chile), 21 January, 2016.
    • Seminar “Diversity Seek (Divseek): An International Partnership to Harness the Genetic Potential of Crop Diversity”. Guest: Dr. Ruth Bastow (Director of The Global Plant Council). Organizer: Dr. Rodrigo Gutierrez (Pontificia Universidad Católica de Chile), 3 November, 2015.

    Conferences and Workshops

    "First Meeting of the Chilean Society of Plant Biologist" (X Chilean Plant Biology Meeting). Valdivia, Chile, 2-5 December, 2015.
    As it is now a tradition, the conference consists of sessions ranging across plant sciences: Systems and Synthetic Biology, Cell and Developmental Biology, Breeding and Genetics, Biotic/Abiotic Stress, Ecophysiology and Metabolism. Attendees comprise primarily students, young scientists and faculty from major Universities and research institutes in Chile. Nearly 180 M.Sc. or Ph.D. students are among the participants who with their great enthusiasm and hard work will be the future world leaders of our research field.
    Guests: Natasha Raikhel (UC Riverside, USA), Zhenbiao Yang (UC Riverside, USA), Dan Klessig (Cornell University, USA), Ian Fergusson (Plant and Food Research, New Zeland), Jose Quero Garcia (INRA, France)
    Organizers: Chilean Society of Plant Biologist

    Selected Publications

    • The Calcium Ion Is a Second Messenger in the Nitrate Signaling Pathway of Arabidopsis. Riveras E, Alvarez JM, Vidal EA, Oses C, Vega A, Gutiérrez RA (2015) Plant Physiology169(2):1397-404.
    • Transcriptional networks in the nitrate response of Arabidopsis thaliana. Vidal EA, Álvarez JM, Moyano TC, Gutiérrez RA (2015) Curr Opin Plant Biol. 27:125-32. 
    • The UDP-glucose: glycoprotein glucosyltransferase (UGGT), a key enzyme in ER quality control, plays a significant role in plant growth as well as biotic and abiotic stress in Arabidopsis thaliana. Blanco-Herrera F, Moreno AA, Tapia R, Reyes F, Araya M, D’Alessio C, Parodi A, Orellana A (2015) BMC Plant Biol. 15:127.
    • The dynamic of the splicing of bZIP60 and the proteins encoded by the spliced and unspliced mRNAs reveals some unique features during the activation of UPR in Arabidopsis thaliana. Parra-Rojas J, Moreno AA, Mitina I, Orellana A (2015) PLoS One 10(4):e0122936.
    • Male sterility in Arabidopsis induced by overexpression of a MYC5-SRDX chimeric repressor. Figueroa P, Browse J (2015) Plant J. 2015 Mar;81(6):849-60. doi: 10.1111/tpj.12776.

    Major Funding Sources

    http://www.conicyt.cl
    http://www.iniciativamilenio.cl/
    http://www.corfo.cl
    http://www.fia.cl

  • Czech Republic Open or Close
    Viktor Žárský (This email address is being protected from spambots. You need JavaScript enabled to view it.) Charles University, Department of Exp. Plant Biol. and Inst. of Exp. Bot. Acad. Sci. of the Czech Rep. Prague

    Arabidopsis Research Facilities

    In the Czech republic Arabidopsis research is focused mostly on the three major areas - cell biology, plant growth regulators biology, developmental biology and cytogenetics/genome biology. Traditional centers of experimental plant research exist at the universities and institutes of the Academy of Sciences of the Czech Republic.

    • In Brno:

    Masaryk University - https://www.muni.cz/sci/314010
    Mendel University - http://ubfr.af.mendelu.cz/en/?lang=en
    Institute of Biophysics - http://www.ibp.cz/en/
    “Central European Institute of Technology (CEITEC)” (http://www.ceitec.eu/) in Brno includes big units devoted to genomics and proteomics of plant systems used for studies in cell and developmental biology and cytogenomics.

    • In Olomouc:

    Palacky university in Olomouc - http://www.prf.upol.cz/en/menu/departments/
    Institute of Experimental Botany - http://www.ueb.cas.cz/en
    “Centre of the Region Hana for Biotechnological and Agricultural Research” (http://www.cr-hana.eu/en/index.html) in Olomouc combines researchers from Palacky University, Crop Research Institute (VURV) and Institute of Experimental Botany ASCR with many links with the commercial sphere.

    • In České Budějovice:

    Institute of Plant Molecular Biology - http://www.umbr.cas.cz/

    • In Prague:

    Institute of Experimental Botany - http://www.ueb.cas.cz/en
    Charles University in Prague - http://kfrserver.natur.cuni.cz/english/index.html

    Current Arabidopsis Projects

    Arabidopsis research in the Czech Republic is funded mostly on the individual grants basis. In 2014 the Department of Experimental Plant Biology at the Charles University was granted a “Centre of plant experimental biology, Charles University” project supported by the Ministry of Education of the Czech Republic. In 2015 twenty seven projects using Arabidopsis as a model were funded by the Czech Science Foundation (GACR). Among the biggest ones there were:

    • “Study of the phosphorylation in Katanin1 and microtubules severing in Arabidopsis”
    • “Molecular mechanisms controlling homeostasis of plant growth regulatory compound auxin”
    • “Global proteomic analysis of temperature perception in Arabidopsis and its interaction with cytokinin signalling”
    • “Role of gama-tubulin in the coordiantion of microtubuli nucleation and cytokinesis with the DNA damage in plants”
    • “Role of formins in plant cell morphogenesis”
    • “Structural and functional components of plant telomeres”
    • “Elucidating molecular mechanisms of cytokinin-ethylene crosstalk in the plant development”
    • “Impact of temperature and photosynthetically active radiation on dynamics of regulation of photosystem II function in higher plants”
    • “Deciphering of molecular mechanisms of light and hormonal signalling integration in plant development”.

    Outlook on Arabidopsis Research

    Plant research infrastructure development was funded by the EU funds over the last several years and Arabidopsis-driven research is well established and important in the Czech Republic, supported both by the CSF and the Ministry of Education. It is expected that in coming years Arabidopsis research in Czech epublic will be further stably well supported mostly on the individual projects basis.

    Arabidopsis Tools and Resources

    BRNO - CEITEC - Central European Institute of Technology
    Proteomics Core Facility (http://www.ceitec.eu/ceitec-mu/proteomics-core-facility/z8)

    The Core Facility is part of Czech National Affiliated Centre of INSTRUCT. All CEITEC core facilities are available to external users (academia and companies). Czech and international researchers from universities and research institutes interested in accessing core facilities can benefit from support of CEITEC – open access project funded by the Ministry of Education, Youth and Sports of the Czech Republic.

    Outreach Activities

    OLOMOUC - “Centre of the Region Hana for Biotechnological and Agricultural Research” using Arabidopsis as a fundamental research model, also includes The Department of Genetic Resources for Vegetables, Medicinal and Special Plants CRI and keeps a broad collection of genetic resources of vegetables (9,245 accessions), medicinal, aromatic and culinary plants (MAPs, 828 accessions) traditionally grown in Central Europe and a collection of fungi (mainly morel).
    http://www.cr-hana.eu/en/research-and-development/research-programs/genetic-resources-of-vegetables-and-special-crops/

    Selected Publications

    • Lack of Phosphatidylglycerol Inhibits Chlorophyll Biosynthesis at Multiple Sites and Limits Chlorophyllide Reutilization in Synechocystis sp Strain PCC 6803. Kopecna J, Pilny J, Krynicka V, Tomcala A, Kis M, Gombos Z, Komenda J, Sobotka R (2015) Plant Physiology 169(2): 1307-17
    • Genome Structure of the Heavy Metal Hyperaccumulator Noccaea caerulescens and Its Stability on Metalliferous and Nonmetalliferous Soils. Mandakova T, Singh V, Kramer U, Lysak MA (2015) Plant Physiology 169(1): 674-89
    • The Arabidopsis mitogen-activated protein kinase 6 is associated with -tubulin on microtubules, phosphorylates EB1c and maintains spindle orientation under nitrosative stress. Kohoutova L, Kourova H, Nagy SK, Volc J, Halada P, Meszaros T, Meskiene I, Bogre L, Binarova P (2015) New Phytologist 207(4):1061-74
    • Cell Wall Maturation of Arabidopsis Trichomes Is Dependent on Exocyst Subunit EXO70H4 and Involves Callose Deposition. Kulich I, Vojtikova, Z, Glanc M, Ortmannova J, Rasmann S, Zarsky V (2015) Plant Physiology 168(1):120-31
    • Homology-dependent repair is involved in 45S rDNA loss in plant CAF-1 mutants. Muchova V, Amiard S, Mozgova I, Dvorackova M, Gallego ME, White C, Fajkus J (2015) Plant Journal 81(2):198-209

    Major Funding Sources

    Both major funding agencies for basic research - Czech Science Foundation (GACR) and Ministry of Education of CR (MSMT CR) - support regularly projects based on the use of Arabidopsis as a model plant. Both institutions support also bilateral projects with selected countries.

  • Denmark Open or Close
    Michael Palmgren (This email address is being protected from spambots. You need JavaScript enabled to view it.) University of Copenhagen, Department of Plant and Environmental Sciences

    Arabidopsis Research Facilities

    Arabidopsis research in Denmark primarily takes place at University of Copenhagen. Arabidopsis research is also carried out at University of Aarhus. Copenhagen Plant Science Centre (CPSC) is a new initiative at University of Copenhagen scheduled to be completed in 2017. CPSC will be rooted in the Department of Plant and Environmental Sciences and will include up-to-date facilities for Arabidopsis research.

    Current Arabidopsis Projects

    There are no dedicated Arabidopsis consortia or centers in Denmark, but Arabidopsis is commonly used by plant biologists as a model organism. The Danish National Research Foundation funds a number of major Centers of Excellence. In two such centers Arabidopsis is employed as a model organism: Centre for Membrane Pumps in Cells and disease (Pumpkin; plant work directed by Prof. Michael Palmgren) and Center for Dynamic Molecular Interactions (Dynamo; directed by Prof. Barbara Ann Halkier).

    Outlook on Arabidopsis Research

    In Denmark it is becoming increasingly difficult to obtain funding for basic research on Arabidopsis as the general trend is shifting towards supporting applied research.

    Selected Publications

    • A phospholipid uptake system in the model plant Arabidopsis thaliana. Poulsen LR, López-Marqués RL, Pedas PR, McDowell SC, Brown E, Kunze R, Harper JF, Pomorski TG, Palmgren M (2015) Nat Commun. 6:7649
    • Retromer contributes to immunity-associated cell death in Arabidopsis. Munch D, Teh OK, Malinovsky FG, Liu Q, Vetukuri RR, El Kasmi F, Brodersen P, Hara-Nishimura I, Dangl JL, Petersen M, Mundy J, Hofius D (2015) Plant Cell 27(2):463-79
    • The bifurcation of the cyanogenic glucoside and glucosinolate biosynthetic pathways. Clausen M, Kannangara RM, Olsen CE, Blomstedt CK, Gleadow RM, Jørgensen K, Bak S, Motawie MS, Møller BL (2015) Plant J. 84(3):558-73
    • The glucosinolate biosynthetic gene AOP2 mediates feed-back regulation of jasmonic acid signaling in Arabidopsis. Burow M, Atwell S, Francisco M, Kerwin RE, Halkier BA, Kliebenstein DJ (2015) Mol Plant. 8(8):1201-12
    • Simple and robust determination of the activity signature of key carbohydrate metabolism enzymes for physiological phenotyping in model and crop plants. Jammer A, Gasperl A, Luschin-Ebengreuth N, Heyneke E, Chu H, Cantero-Navarro E, Großkinsky DK, Albacete AA, Stabentheiner E, Franzaring J, Fangmeier A, van der Graaff E, Roitsch T (2015) J Exp Bot. 66(18):5531-42
  • Finland Open or Close
    Michael Wrzaczek (This email address is being protected from spambots. You need JavaScript enabled to view it.) Division of Plant Biology, Department of Biosciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland

    Arabidopsis Research Facilities

    Research concentrating on Arabidopsis is carried out at several universities in Finland with two main centres at the Universities of Helsinki and Turku.

    Research at the University of Helsinki focuses on plant stress responses and plant development. Research projects address the role of reactive oxygen species (ROS) as signaling molecules in plants, the role of transcription factors in the stress response, receptor and receptor-like kinase signaling, plant stem cell maintenance, root development, plant-pathogen interactions, as well as the role of the proteasome in the regulation of flowering. Groups in Helsinki are also exploiting the natural variation of Arabidopsis thaliana to identify new regulators of stress tolerance. A saturating mutant screen is currently being carried out with the goal to identify components in early stomatal signaling downstream of apoplastic ROS. Identification of ozone-sensitive mutants is followed by analysis of their gas-exchange parameters. Causative mutations are being identified by genome resequencing. The flower-related ubiquitin proteasome system project is currently characterizing a collection of about 100 Arabidopsis T-DNA mutants using the new phenotyping facility (http://blogs.helsinki.fi/nappi-blog/). In the future the research will be extended towards plant pathogen interactions in the flower and also towards translational approaches using crop species. The receptor-ligand signaling group is aiming to integrate plant biochemistry and physiology with evolutionary analysis to facilitate translational research using Arabidopsis as a tool to provide insights into complex gene families for subsequent application in crops.
    Research at the University of Turku is centered on stress signaling and photosynthesis. Projects address the role of protein kinases and protein phosphatases as well as the regulation of photosynthesis and the integration of the chloroplastic light harvesting machinery into cell- and plant-wide signaling networks.

    The Centre of Excellence (CoE) “Molecular Biology of Primary Producers” (2014-2019) funded by the Academy of Finland brings together groups from Turku and Helsinki in order to combine expertise on plant development, stress signaling and photosynthesis. While several plant species and also cyanobacteria are being used Arabidopsis continues to be the most important model for the fundamental research carried out within the Centre of Excellence.

    Current Arabidopsis Projects

    Academy of Finland Centre of Excellence “Molecular Biology of Primary Producers” (2014-2019) directed by Prof. Eva-Mari Aro (University of Turku) as chair and Prof. Jaakko Kangasjärvi (University of Helsinki) as vice-chair.
    Dr. Ari Pekka Mähönen (University of Helsinki, Institute of Biotechnology): Stem cell dynamics in Arabidopsis root cambium (2013-2018). Funded by the Academy of Finland.
    Dr. Michael Wrzaczek (University of Helsinki, Department of Biosciences): Understanding peptide ligands and their receptors in plants (2014-2019). Funded by the Academy of Finland.

    Outlook on Arabidopsis Research

    In Helsinki, the Viikki Plant Science Centre (ViPS) has been established with 31 PIs, 208 researchers and 9.1 million € funding in 2015. While ViPS encompasses research on plants in general, Arabidopsis is one of the core tools used by most research teams to address fundamental questions and unravel molecular mechanisms. Plant Science has been named as a focus and marketing area of the new HiLife centre, with ViPS used as an example of an excellent and successful research program. A plant biology master’s degree with heavy involvement of ViPS will begin in the autumn of 2017. The vision of ViPS is to attract internationally visible top level researchers; to stimulate multidisciplinary research environments; to participate in research and infrastructure core facilities also outside the University; to take an active role in post-graduate education. Research on Arabidopsis or using Arabidopsis as a tool continues to be a major factor in Finnish plant science. Efforts include translation of knowledge from Arabidopsis towards tree research. As many research groups at ViPS use Arabidopsis as their model species there is a heavy emphasis on Arabidopsis research in the Doctoral Programme in Plant Sciences and Arabidopsis continues to be the primary model system to address fundamental research questions in all levels of education.

    Arabidopsis Tools and Resources

    A community resource based on the saturating mutant screen for novel components in early stomatal signaling downstream of apoplastic ROS will available by the end of 2016.

    The group of Ari-Pekka Mähönen has created a new multi-site gateway system for easy construction of inducible cell-type specific expression constructs for Arabidopsis (Siligato et al., 2016).

    Work on the phenotypic analysis of a mutant collection for cysteine-rich receptor-like kinases (Bourdais et al., 2015) has led to the creation of a software package for the analysis of heterogenous phenotypic data. This will be available as a package for the programming language R during 2016 from Dr. Jarkko Salojärvi (Salojärvi & Wrzaczek, in preparation).

    A phenomics facility has been built at the Viikki campus of the University of Helsinki (http://blogs.helsinki.fi/nappi-blog). This high throughput facility is part of a National Plant Phenotyping Infrastructure that also includes a high precision unit at the University of Eastern Finland. The Viikki facility will accommodate tools for morphological and physiological analysis of Arabidopsis by imaging (fluorescence and thermal).

    Outreach Activities

    Plant biology groups working with Arabidopsis at the University of Helsinki have started to introduce school classes to molecular plant biology in spring 2016.
    Outreach activities have been done towards high school students on scientific career choice and towards general public on genetically improved organisms.

    Conferences and Workshops

    • The 11th Finnish Plant Science Days (Kasvitieteen Päivät). University of Turku, Turku, Finland. May 25-26, 2016
    • The biannual Finnish-Japanese plant science meeting will be held in autumn 2016 in Finland
    • The National Plant Phenotyping Infrastructure will arrange Nordic meetings and a winter school in “Current challenges in plant phenotyping”

    Selected Publications

    Finnish researchers contributed to 36 publications referring to Arabidopsis from 2015 according to Pubmed.

    • MultiSite Gateway compatible cell type-specific gene inducible system for plants. Siligato R, Yadav SR, Ma G, Lehesranta S, Ma G, Ursache R, Sevilem I, Zhang J, Gorte M, Prasad K, Wrzaczek M, Heidstra R, Murphy A, Scheres B, Mähönen AP (2016) Plant Physiology 170(2):627-641.
    • Integration of photosynthesis, development and stress as an opportunity for plant biology. Allahverdiyeva Y, Battchikova N, Brosché M, Fujii H, Kangasjärvi S, Mulo P, Mähönen AP, Nieminen K, Overmyer K, Salojärvi J, Wrzaczek M (2015) New Phytologist 208(3):647-655.
    • Large-scale phenomics identifies primary and fine-tuning roles for CRKs in responses related to oxidative stress. Bourdais G, Burdiak P, Gauthier A, Nitsch L, Salojärvi J, Rayapuram C, Idänheimo N, Hunter K, Kimura S, Merilo E, Vaattovaara A, Oracz K, Kaufholdt D, Pallon A, Anggoro DT, Glów D, Lowe J, Zhou J, Mohammadi O, Puukko T, Albert A, Lang H, Ernst D, Kollist H, Brosché M, Durner J, Borst JW, Collinge DB, Karpinski S, Lyngkjaer M, Robatzek S, Wrzaczek M, Kangasjärvi J (2015) PLoS Genetics 7(11):e1005373.
    • Quantitative trait loci mapping and transcriptome analysis reveal candidate genes regulating the response to ozone in Arabidopsis thaliana. Xu E, Vaahtera L, Horak H, Hincha DK, Heyer AG, Brosché M (2015) Plant Cell & Environment 38(7):1418-33.
    • Light acclimation involves dynamic re-organization of the pigment-protein megacomplexes in non-appressed thylakoid domains. Suorsa M, Rantala M, Mamedov F, Lespinasse M, Trotta A, Grieco M, Vuorio E, Tikkanen M, Järvi S, Aro EM (2015) Plant Journal 84(2):360-373.

    Major Funding Sources

    Academy of Finland (http://www.aka.fi)
    University of Helsinki (http://www.helsinki.fi/university)
    Finnish Cultural Foundation (http://www.skr.fi)

  • France Open or Close
    Catherine Perrot-Rechenmann (This email address is being protected from spambots. You need JavaScript enabled to view it.), CNRS Saclay Plant Sciences Labex, Gif sur Yvette; Loïc Lepiniec (This email address is being protected from spambots. You need JavaScript enabled to view it.) Saclay Plant Sciences LaBex, Institut Jean-Pierre Bourgin, INRA, Versailles

    Current Arabidopsis Projects

    The Institute of Plant Sciences Paris-Saclay, IPS2, located in Orsay France, was created by restructuring several Plant Biology Institutes associated with 3 universities (Paris-Sud, University of Evry and Paris-Diderot), the CNRS and INRA. IPS2 aims to better understand the molecular mechanisms controlling plant growth and their responses to biotic and abiotic stresses while developing a continuum from fundamental to translational research in Plant Sciences.

    Current research focuses on the analysis of model plants using multidisciplinary approaches (from genomics, bioinformatics to biochemistry, genetics and physiology) and 3 plant-dedicated platforms with expertise in transcriptomics and RNA sequencing, metabolomics, and translational biology, including TILLING mutant collections of diverse crop species (tomato, Brachypodium distachyon, melon and cucumber). Among the projects to transfer the knowledge obtained from Arabidopsis to crop species are: improving biomass by manipulating metabolic pathways/rate-limiting enzymes, improving root architecture to improve nutrient uptake and drought resistance, improving pathogen resistance by manipulating MAPK signalling.

    We wish all the best to this newly created Plant Institute.

    Outlook on Arabidopsis Research

    Research organizations such as CNRS, INRA or CEA provide regular funding to affiliated research laboratories in addition to payment of salaries of permanent researchers and technicians.

    The French national research agency, ANR (http://www.agence-nationale-recherche.fr/en/about-anr/about-the-french-national-research-agency/), provides funding for project-based research. Main applications based on social issues are not appropriate to support fundamental research in general, including in plant biology. Funding on Arabidopsis projects is constantly decreasing, which severely affects research activities of French labs.
    Fundamental research might, however, be taken into account again for coming grants as announced by the French government.

    Arabidopsis Tools and Resources

    The Arabidopsis thaliana Stock Centre at INRA Versailles continuously makes available T-DNA insertion mutants, natural accessions, RIL populations or nearly isogenic lines to the scientific community (http://www-ijpb.versailles.inra.fr/en/plateformes/cra/index.html).

    Two high-throughput automated phenotyping platforms, PHENOSCOPE at Versailles (contact O. Loudet, http://www.ijpb.versailles.inra.fr/en/plateformes/ppa/index.html) and PHENOPSIS at Montpellier (contact C. Granier, www1.montpellier.inra.fr/ibip/lepse/english/ressources/phenopsis.htm) are available to the community to grow up to 750 or 500 Arabidopsis plants, respectively, under fully controlled environment. PHENOPSIS DB is an information system providing comprehensible resources for the analysis of genotype x environment interactions in Arabidopsis thaliana (http://bioweb.supagro.inra.fr/phenopsis/Accueil.php?lang=En). A French plant phenomic network named PHENOME is also dedicated to high throughput phenotyping for crops (https://www.phenome-fppn.fr/phenome_eng/).

    Outreach Activities

    The Scientific Group of Interest “Plant Biotechnologies” (GIS BV, http://www.gisbiotechnologiesvertes.com/en/presentation-du-gis-bv) is build on a large public-private partnership community, which gathers public research institutes (including work performed on model plants as Arabidopsis), seed companies, technical institutes, sector representatives, and competitive clusters.

    Conferences and Workshops

    The 26th edition of the International Conference on Arabidopsis Research (ICAR 2015) took place in Paris from 5th to 9th of July 2015. The meeting was organized by the French Society of Plant Biologists (SFBV, http://sfbv.snv.jussieu.fr/) with the scientific and organisational assistance of members of the Saclay Plant Sciences Laboratory network of excellence (SPS LabEx, http://www6.inra.fr/saclay-plant-sciences). ICAR 2015 was a great success with up to 1054 registrations, scientists coming from 38 distinct countries from all over the world.

    Selected Publications

    • Primary transcripts of microRNAs encode regulatory peptides. Lauressergues D, Couzigou JM, Clemente HS, Martinez Y, Dunand C, Bécard G, Combier JP (2015) Nature 520(7545):90-3. doi: 10.1038/nature14346.
    • Plants Encode a General siRNA Suppressor That Is Induced and Suppressed by Viruses. Shamandi N, Zytnicki M, Charbonnel C, Elvira-Matelot E, Bochnakian A, Comella P, Mallory AC, Lepere G, Saez-Vasquez J, and Vaucheret H (2015) PLoS Biol 13, e1002326.
    • A receptor pair with an integrated decoy converts pathogen disabling of transcription factors to immunity. Le Roux C, Huet G, Jauneau A, Camborde L, Trémousaygue D, Kraut A, Zhou B, Levaillant M, Adachi H, Yoshioka H, Raffaele S, Berthomé R, Couté Y, Parker JE, Deslandes L (2015) Cell 161(5):1074-88. doi: 10.1016/j.cell.2015.04.025.
    • A mechanically sensitive cell layer regulates the physical properties of the Arabidopsis seed coat. Creff A, Brocard L, Ingram G (2015) Nat Commun. 6:6382. doi: 10.1038/ncomms7382.
    • OCTOPUS Negatively Regulates BIN2 to Control Phloem Differentiation in Arabidopsis thaliana. Anne P, Azzopardi M, Gissot L, Beaubiat S, Hématy K, Palauqui JC. (2015) Curr Biol. 25(19):2584-90. doi: 10.1016/j.cub.2015.08.033.

    Major Funding Sources

    ANR, thematic calls organized in societal issues (http://www.agence-nationale-recherche.fr/en/funding-opportunities/)

    Investissement d’avenir (PIA 1 and 2 in progress) by Ministère de l’Education nationale, de l’enseignement supérieur et de la recherche (http://www.enseignementsup-recherche.gouv.fr/cid55892/comprendre-le-programme-investissements-d-avenir.html)

    European fundings: ERC (http://erc.europa.eu/funding-and-grants), Marie-Curie research programmes (http://ec.europa.eu/research/mariecurieactions/) and EMBO (http://www.embo.org/funding-awards)

  • Germany Open or Close
    Klaus Harter (This email address is being protected from spambots. You need JavaScript enabled to view it.); Marília K. F. de Campos (This email address is being protected from spambots. You need JavaScript enabled to view it.) University of Tübingen, Tübingen

    Arabidopsis Research Facilities

    Arabidopsis research in Germany is performed in all corners of the country and this wide distribution also reflects the high diversity of topics explored by German scientists. The major sites hosting Arabidopsis researchers are Universities, Max Planck Institutes, Helmholtz Centers and Leibniz Institutes.

    In order to maintain and enhance collaborations and communication, German Arabidopsis researchers count on the coordinating activities of the ‘Arabidopsis Functional Genomics Network’ (AFGN). Established in 2001 following the completion of the Arabidopsis genome sequencing, the AFGN was funded by the German Science Foundation (DFG) until 2010. Today the AFGN operates under the umbrella of the German Botanical Society (DBG) and its actions include the maintenance of a mailing list for advertising events, job postings, inquiries on seeds, plasmids and resources, as well as any other topic of interest for the plant community in Germany and Europe. A newly designed website has been recently launched and contains a complete description of the AFGN efforts in promoting interactions among German researchers (http://www.dbg-afgn.de/).

    Current Arabidopsis Projects

    The Arabidopsis functional genomics research is supported by German and European organizations. The DFG is the major funding body via several instruments exemplified below. In 2013 the DFG awarded Klaus Harter with a 3-year grant for the MASC/AFGN coordinator to be finalized in mid June 2016. German Arabidopsis researchers are also funded via grants awarded by the European Research Council (ERC), Marie Skłodowska-Curie actions, as well as from private initiative.

    Individual Funding

    Currently the DFG provides funding to a total of 191 individual projects concerning Arabidopsis research. Of these, 7 are funded by the Emmy Noether Programme, 2 by the Heisenberg Programme, 7 are research fellowships and 175 are individual research grants.

    Priority Programmes

    Arabidopsis researchers are involved in 3 priority programmes.

    • SPP 1710 (since 2014) Dynamics of thiol-based redox switches in cellular physiology
    • SPP 1529 (since 2011) Evolutionary plant solutions to ecological challenges: molecular mechanisms underlying adaptive traits in the Brassicaceae s.l.
    • SPP 1530 (since 2011) Flowering time control: from natural variation to crop improvement

    Collaborative Research Centers

    Arabidopsis researchers are involved in 13 collaborative research centers, out of which 3 mainly focus on Arabidopsis.

    • SFB 1101 (since 2014) Molecular encoding of specificity in plant processes
    • SFB 973 (since 2012) Priming and memory of organismic responses to stress
    • SFB 648 (since 2005) Molecular mechanisms of information processing in plants

    Research Training Groups

    • GRK 2064 (since 2015) Water use efficiency and drought stress responses: from Arabidopsis to Barley
    • GRK 1525 (since 2009) The dynamic response of plants to a changing environment

    Research Units

    • FOR 948 (since 2009) Nitrogen uptake, metabolism and remobilization in leaves during plant senescence
    • FOR 1186 (since 2009) Photorespiration: Origins and metabolic integration in interacting compartments
    • FOR 964 (since 2008) Calcium signaling via protein phosphorylation in plant model cell types during environmental stress adaption
    • FOR 1061 (since 2008) Dynamic storage functions of plant vacuoles during cold and osmotic stress
    • FOR 804 (since 2007) Retrograde signalling in plants

    European Research Council

    The ERC currently funds 11 Arabidopsis research projects in Germany, comprising of 4 Advanced Grants, 2 Consolidator Grants and 5 Starting Grants

    Arabidopsis Tools and Resources

    Outreach Activities

    The PLANT2030 initiative from the German Federal Ministry of Education and Research (BMBF) fosters research projects within public-private partnerships. Two Arabidopsis related projects are listed below.

    • PLANT-KBBE IV NESTOR (2014-2017): Nematode susceptibility targets for a durable resistance
    • PLANT-KBBE IV (2014-2017): Control of the abiotic stress response in plants by DELLA proteins and chemicals

    German institutions are very active in communicating plant science to the general public. Max Planck Institutes, for instance, offer guided tours, events and informative booklets for people of all ages. Some examples are listed below.

    Conferences and Workshops

    • Deutsche Botanikertagung, Munich, 30 August - 3 September, 2015 (http://botanikertagung2015.de/)
    • Tri-National Arabidopsis Meeting (TNAM) biannual conference, hosted by colleagues from Germany, Austria and Switzerland. 10th TNAM, Vienna, Austria, 14-16 September, 2016
    • Conference Molecular Biology of Plants, Dabringhausen (http://pflanzen-molekularbiologie.de/):

    29th Conference, 23-26 February 2016
    28th Conference, 24-27 February 2015

    Selected Publications

    German Arabidopsis researchers were involved in 494 publications since last year’s report (search at NCBI using “Arabidopsis”[All Fields] AND “Germany”[Affiliation] AND “2015/05/01”[Date - Publication] : “3000”[Date - Publication]). Highlights are listed below.

    • Endler A, Kesten C, Schneider R, Zhang Y, Ivakov A, Froehlich A, Funke N, Persson (2015) A Mechanism for Sustained Cellulose Synthesis during Salt Stress. Cell 162(6):1353-64.
    • Albert I, Böhm H, Albert M, Feiler CE, Imkampe J, Wallmeroth N, Brancato C, Raaymakers TM, Oome S, Zhang H, Krol E, Grefen C, Gust AA, Chai J, Hedrich R, Van den Ackerveken G, Nürnberger T (2015) An RLP23-SOBIR1-BAK1 complex mediates NLP-triggered immunity. Nature Plants 1(10):15140.
    • Wagner S, Behera S, De Bortoli S, Logan DC, Fuchs P, Carraretto L, Teardo E, Cendron L, Nietzel T, Füßl M, Doccula FG, Navazio L, Fricker MD, Van Aken O, Finkemeier I, Meyer AJ, Szabò I, Costa A, Schwarzländer M (2015) The EF-Hand Ca2+ Binding Protein MICU Choreographs Mitochondrial Ca2+ Dynamics in Arabidopsis. Plant Cell 27:3190-212.
    • Bai Y, Müller DB, Srinivas G, Garrido-Oter R, Potthoff E, Rott M, Dombrowski N, Münch PC, Spaepen S, Remus-Emsermann M, Hüttel B, McHardy AC, Vorholt JA, Schulze-Lefert P (2015) Functional overlap of the Arabidopsis leaf and root microbiota. Nature 528(7582):364-9
    • Kriegel A, Andrés Z, Medzihradszky A, Krüger F, Scholl S, Delang S, Patir-Nebioglu MG, Gute G, Yang H, Murphy AS, Peer WA, Pfeiffer A, Krebs M, Lohmann JU, Schumacher K (2015) Job Sharing in the Endomembrane System: Vacuolar Acidification Requires the Combined Activity of V-ATPase and V-PPase. Plant Cell 27(12):3383-96.

    Major Funding Sources

    Major funding source for Arabidopsis research is the German Science Foundation (DFG) (http://www.dfg.de/en/). Contact: Catherine Kistner (This email address is being protected from spambots. You need JavaScript enabled to view it.)

  • Greece Open or Close
    Polydefkis Hatzopoulos (This email address is being protected from spambots. You need JavaScript enabled to view it.), Agricultural University of Athens, Athens

    Arabidopsis Research Facilities

    Agricultural University of Athens, Athens, Greece

    Polydefkis Hatzopoulos (This email address is being protected from spambots. You need JavaScript enabled to view it.)
    Dimitra Milioni (This email address is being protected from spambots. You need JavaScript enabled to view it.)
    Stamatis Rigas (This email address is being protected from spambots. You need JavaScript enabled to view it.)
    Dimitris Tsitsigianis (This email address is being protected from spambots. You need JavaScript enabled to view it.)

    Aristotle University of Thessaloniki, Thessaloniki, Greece

    Angelos Kanellis (This email address is being protected from spambots. You need JavaScript enabled to view it.)
    Konstantinos Vlachonasios (This email address is being protected from spambots. You need JavaScript enabled to view it.)
    Emmanouil Panteris (This email address is being protected from spambots. You need JavaScript enabled to view it.)

    National and Kapodistrian University of Athens, Athens, Greece

    Kosmas Haralampidis (This email address is being protected from spambots. You need JavaScript enabled to view it.)
    Andreas Rousiis (This email address is being protected from spambots. You need JavaScript enabled to view it.)

    University of Crete, Crete, Greece

    Kriton Kalantidis (This email address is being protected from spambots. You need JavaScript enabled to view it.)

    Mediterannean Agronomic Institute of Chania, Chania, Crete, Greece

    Panagiotis Kalaitzis (This email address is being protected from spambots. You need JavaScript enabled to view it.)
    Technological University of Athens, Athens, Greece
    Georgios Banilas (This email address is being protected from spambots. You need JavaScript enabled to view it.)

    Current Arabidopsis Projects

    Arabidopsis still remains the model species used as reference to validate gene regulatory networks of crop species that are difficult to work with. The knowledge gained from Arabidopsis can be applied on agronomically important crops like olive trees, tomato, grapes and peaches etc.

    Arabidopsis research is mainly focused on the following topics:

    • The role of HSP90 and Pescadillo-like proteins on plant development
    • Organellar biogenesis
    • Protein trafficking and signal transduction
    • The interplay between potassium transport and auxin homeostasis
    • Molecular and functional characterization of genes encoding WD40 and Armadillo domain proteins
    • Role of selenium binding proteins in Arabidopsis development and during abiotic stress

    Outlook on Arabidopsis Research

    Funding resources for research activities are significantly reduced having a major impact on basic research grants related to Arabidopsis. However, there is a general trend to shift towards other model species apart from Arabidopsis that may attract the interest of industrial partners.

    Conferences and Workshops

    37th Hellenic Society for Biological Science (EEBE) meeting. Volos, Greece

    Selected Publications

    • Transcriptional profiling unravels potential metabolic activities of the olive leaf non glandular trichome. Koudounas K, Manioudaki ME, Kourti A, Banilas G, Hatzopoulos P (2015) Front Plant Sci. 6(633).
    • A defence-related Olea europaea β-glucosidase hydrolyses and activates oleuropein into a potent protein cross-linking agent. Koudounas K, Banilas G, Michaelidis C, Demoliou C, Rigas S, Hatzopoulos P (2015) J Exp Bot. 66(7): 2093-106.
    • RNAi-mediated silencing of the Arabidopsis thaliana ULCS1 gene, encoding a WDR protein, results in cell wall modification impairment and plant infertility. Beris D, Kapolas G, Livanos P, Roussis A, Milioni D, Haralampidis K (2016) Plant Sci. 245:71-83.
    • Potassium transporter TRH1 subunits assemble regulating root-hair elongation autonomously from the cell fate determination pathway. Daras G, Rigas S, Tsitsekian D, Iacovides TA, Hatzopoulos P (2015) Plant Sci. 231:131-7.
    • Brassinosteroid nuclear signaling recruits HSP90 activity. Samakovli D, Margaritopoulou T, Prassinos C, Milioni D, Hatzopoulos P. (2014) New Phytol. 203(3):743-57.

    Major Funding Sources

    Grants from the European Union
    State Scholarships Foundation (IKY) (www.iky.gr)
    General Secretariat for Research and Development (GSRT), HELLENIC REPUBLIC MINISTRY OF EDUCATION AND RELIGIOUS AFFAIRS (www.gsrt.gr)
    National and Kapodistrian University of Athens, Special Account for Research Grants, (http://www.elke.uoa.gr/)

  • India Open or Close
    Jitendra P. Khurana (This email address is being protected from spambots. You need JavaScript enabled to view it.) University of Delhi South Campus, New Delhi, India; Ramamurthy Srinivasan (This email address is being protected from spambots. You need JavaScript enabled to view it.) National Research Centre on Plant Biotechnology, IARI, New Delhi, India

    Arabidopsis Research Facilities

    In India, the number of groups working on Arabidopsis is steadily increasing. The major areas of research include regulation of organ development, patterning, plant pathogen interaction, abiotic stress, light, hormone and sugar signaling. Some of the important centres working on Arabidopsis are CCMB, Hyderabad; IISc, Bangalore; NIT, Durgapur; University of Delhi South Campus; NIPGR, New Delhi; NRCPB, New Delhi; JNU, New Delhi; IHBT, Palampur; IISER, Thiruvanathapuram; IISER, Mohali; IISER, Bhopal; IIT, Roorkee; NCBS, Bangalore; NISER, Bhubaneswar.
    Most of the funding for these projects comes in the form of competitive grants from Government agencies like the Department of Biotechnology, the Council for Scientific and Industrial Research, and the Department of Science and Technology, all based in New Delhi.

    Current Arabidopsis Projects

    There are several ongoing projects, most of them are sanctioned for a 3-year duration and in some cases for 5 years. Additionally, some ongoing projects are funded by the respective institutes in-house. Only the projects that have been approved in the past one year are listed below.

    • Prof. Sudip Chattopadhyay (NIT, Durgapur); Investigation of functional interrelations of bZIP transcription factors: ZBF2/GBF1, HY5 and HYH of light signaling pathways in Arabidopsis thaliana. Funded by the Department of Science and Technology, Govt. of India; Under the scheme: JC Bose National Fellowship; 2016-2021.
    • Dr. Sourav Datta (IISER, Bhopal); Molecular approach to enhance soil phosphate extraction by plants and reduce the application of fertilizers. Funded by the Department of Biotechnology, Govt. of India; Under the scheme: Innovative Young Biotechnologists Award (IYBA); 2015-2018.

    Outlook on Arabidopsis Research

    The future of Arabidopsis research in India looks bright. Looking at the influx of young faculty, availability of funds from different governmental agencies and the quality of publications in recent years, bodes well for Arabidopsis research in India.

    Arabidopsis Tools and Resources

    Ravi Maruthachalam at IISER, Thiruvanthapuram, is pursuing centromeric histone H3 (CEN H3) based haploid induction system to answer a variety of questions. He is exploiting natural variation in Arabidopsis accessions available for in vivo haploid induction. In A. thaliana, genome elimination frequently occurs in the offspring of two individuals that carry different versions of CEN H3. The genomic rearrangements observed in the Arabidopsis plants are similar to those observed in several human cancer and other genetic diseases. Ravi’s group has shown that Arabidopsis could serve as a useful model system for studying these genome rearrangements and provide useful information on these human disorders.

    Dr. Ananda Sarkar’s group at NIPGR, New Delhi, has described a method to solate both high quality RNA and miRNAs from LCM-derived embryonic root apical meristematic tissue, which is both efficient as well as cost-effective. This has been accomplished by modifying and improving the tissue fixation, processing, sectioning and RNA isolation steps that involves minimal use of kits. (Sci Rep. 2016; 6:21577. doi: 10.1038/srep21577).

    Outreach Activities

    In addition to researchers working on Arabidopsis exclusively, there are many other laboratories that use Arabidopsis as a model system for gene function validation of the heterologous genes from crop plants like rice, wheat and pea. The resources available are shared with those who wish to start the programme a fresh using Arabidopsis as a system. Some of the genes identified based on work done on Arabidopsis for agronomically important traits like flowering time and root architecture are being tested in crop plants like tomato, rice and Brassica. The financial support for such projects is received from Governmental funding agencies.

    A few of the college teachers engaged in imparting training to undergraduate students have also shown interest in using Arabidopsis mutants to explain their utility in understanding the regulation of plant development by endogenous cues like hormones and external signals like light.

    Conferences and Workshops

    One of the important conferences held in India where Arabidopsis research was discussed in many presentations was the “3rd International Plant Physiology Congress: Challenges and Strategies in Plant Biology Research” held at Jawaharlal Nehru University (JNU), New Delhi, India, during December 11-14; It was jointly organized by the Indian Society of Plant Physiologists, JNU and NIPGR, New Delhi, and also supported by the American Society of Plant Biologists, USA. A large number of foreign and Indian delegates participated; number of participants in fact exceeded 600. Another meeting exclusively focused on Arabidopsis was the “Arabidopsis Research Conference 2016” that was held during March 20–22, 2016 at the IISER, Mohali. This meeting was attended by the majority of the researchers working on Arabidopsis in India. Presentations were made by the group leaders as well as young students and post-doctoral fellows. A couple of delegates from the UK and Australia also participated in this conference.

    Selected Publications

    • Salt-Induced remodeling of spatially restricted clathrin-independent endocytic pathways in Arabidopsis root. Baral A, Irani NG, Fujimoto M, Nakano A, Mayor S, Mathew MK (2015) Plant Cell 27: 1297-315.
    • Divergence in patterns of leaf growth polarity is associated with the expression divergence of miR396. Das Gupta M, Nath U (2015) Plant Cell 27(10):2785-99.
    • Interaction of MYC2 and GBF1 results in functional antagonism in blue light mediated Arabidopsis seedling development. Maurya JP, Sethi V, Gangappa SN, Gupta N, Chattopadhyay S (2015) Plant Journal 83:439-50.
    • Multiple interactions between glucose and brassinosteroid signal transduction pathways in Arabidopsis are uncovered by whole-genome transcriptional profiling. Gupta A, Singh M, Laxmi A (2015) Plant Physiology 168(3): 1091-105.
    • Calcineurin B-like protein-interacting protein kinase CIPK21 regulates osmotic and salt stress responses in Arabidopsis. Pandey GK, Kanwar P, Singh A, Steinhorst L, Pandey A, Yadav AK, Tokas I, Sanyal SK, Kim BG, Lee SC, Cheong YH, Kudla J, Luan S (2015) Plant Physiology 169(1):780-92.

    Major Funding Sources

    Additional Information

    In addition to the information previously provided, below some of other work is highlighted.

    Ashis Nandi’s lab at JNU, New Delhi works on salicylic acid (SA) signaling and systemic acquired resistance (SAR). Using transcriptome profile of a constitutive SA signaling mutant, his group has identified a zinc finger protein that promotes SA signaling in both NPR1-dependent and –independent pathways.

    Ashverya Laxmi’s lab at NIPGR, New Delhi, has contributed towards understanding the role of sugars as a signaling molecule in regulating plant growth and development. In the past year, they have shown interaction between glucose and brassinosteroid in regulation of lateral root development in Arabidopsis.

  • Israel Open or Close
    Sigal Savaldi-Goldstein (This email address is being protected from spambots. You need JavaScript enabled to view it.) Technion - Israel Institute of Technology, Haifa, Israel

    Arabidopsis Research Facilities

    Arabidopsis research is conducted in different labs located in six major research centers and universities: The Hebrew University of Jerusalem, Tel Aviv University, the Weizmann Institute of Science, Ben Gurion University of the Negev, Agriculture Research Organization/Volcani Center and the Technion.

    Areas of research include plant physiology, biochemistry, development and genomics.

    Three new Arabidopsis research labs were established by young PIs:

    • Dr. Yariv Brotman, Ben-Gurion University (project leader, Max Planck Institute, Golm, Germany)
    • Dr. Idan Efroni, The Hebrew University of Jerusalem (postdoctoral training: the lab of Kenneth Birnbaum, NYU, US)
    • Dr. Roy Weinstain, Tel Aviv University (postdoctoral training: the lab of Roger Tsien, UCSD, US)
    • Dr. Assaf Zemach , Tel Aviv University (postdoctoral training: the lab of Daniel Zilberman, UC Berkeley US)

    Current Arabidopsis Projects

    The Israeli Centers of Research Excellence (I-CORE) program is aimed at fundamentally strengthening the long term positioning of Israel’s academic research, promote national and international research collaborations, and to assist in the recruitment of new excellent researchers, by the gradual establishment of “Centers of Excellence” – leading research centers specializing in innovative and groundbreaking research in a range of fields.
    The I-CORE PLANT ADAPTATION TO CHANGING ENVIRONMENT, includes Arabidopsis and crop research, brings together plant biologists and computer scientists with the following research approaches:

    • Deciphering the genetic and epigenetic factors affecting short- and long-term (trans-generational) phenotypic plasticity and adaptation to environmental changes
    • Elucidating the mechanisms underlying the interactions of the environment with intrinsic developmental programs, and the role of phytohormones in stress responses
    • Elucidating the key factors regulating plant metabolism and catabolism under stress with focus on the switch-points driving cell death versus cell vitality
    • Dynamics of cell structures (cell wall, membranes, organelles, and protein complexes) and their role in stress responses
    • Laying a foundation for a computational perspective of plant behavior under a changing environment, and predictions of selected genetic and environmental perturbations that will bring the plant to a desired metabolic or functional state

    (http://www.icore-plants.tau.ac.il/); Effective funding, until 2021.

    Outlook on Arabidopsis Research

    Tel Aviv University will establish a school for Plant Sciences and Food security, demonstrating the university commitment to the promotion of plant sciences research at the university.

    Outreach Activities

    Summer Course 2015: Plant Signaling in Changing Environment

    Conferences and Workshops

    Canada-Israel Workshop on Plant Biology and Agriculture in the 21st Century, Ottawa, 2-4 November, 2015
    Plant Stress: Student Organised Conference at the Weizmann Institute, 17 February, 2016

    Selected Publications

    About 60 research articles employing Arabidopsis were published since the beginning of 2015 and until March 2016.

    Major Funding Sources

    The Israel Science Foundation (ISF). (http://www.isf.org.il/english/)
    Chief Scientist. Israel Ministry of Agriculture.

  • Italy Open or Close
    Maura Cardarelli (This email address is being protected from spambots. You need JavaScript enabled to view it.),IBPM-National Research Council (CNR), c/o Sapienza University of Rome, Department of Biology and Biotecnology, Rome

    Arabidopsis Research Facilities

    Several Italian groups continue to utilize Arabidopsis as a model organism for plant biology research and their results are published in high impact journals. Work is mainly performed in individual laboratories; however networks and collaborations are common. Facilities for growth, handling and analysis of Arabidopsis are often shared among groups.Research is mainly focused on root, flower and hypocotyl development, seed germination, characterization of the signalling pathways involved in oligogalacturonides-mediated resistance, ion homeostasis mechanisms and plant response to environment.

    Current Arabidopsis Projects

    The Italian Ministry of Education, University and Research has funded several Arabidopsis projects (2013-2016), including a large network project entitled “The control of plant root growth: a systems biology approach”, whose partners are I. Ruberti (IBPM-CNR, Rome), C. Tonelli (University of Milan), Emanuele De Paoli (University of Udine), Luisa Di Paola (Università Campus Biomedico, Roma), Eugenia Schininà (Sapienza University, Rome), S. Sabatini/P. Costantino (Sapienza University, Rome). This project is coordinated by Paolo Costantino.

    The Italian Ministry has funded a project (PRIN 2014-2017) on “Genetic and epigenetic control of ovule number and fertility in Arabidopsis”. Coordinator: Lucia Colombo.
    A collaboration funded by the Italian Ministry of Foreign Affairs is continuing between the Italian laboratories of M. Cardarelli/G. Serino/P. Costantino (CNR/Sapienza University) and the Japanese laboratories of T. Tsuge/M. Matsui (Kyoto Univ./Riken). The goal is to find common regulatory networks controlling stamen and hypocotyl growth in Arabidopsis.

    A research project entitled: “Cross-talks between reactive Oxygen Species, jasmonates and lipid peroxidation during root formation in response to heavy metals and metalloids and fungus infection” is currently funded by Sapienza University of Rome.

    Additional funding comes from the EU: ERC grants have been awarded to S. Sabatini/P. Costantino and F. Cervone/G. deLorenzo, and from MC-IRSES - International research staff exchange scheme (IRSES), “The physiology and genetics of fruit formation: from genes to networks” (FRUIT-look) FP7-PEOPLE-2013-IRSES, Coordinator: UNIMI Italy. Participants: Sweden (SVERIGES LANTBRUKSUNIVERSITET) and Spain (AGENCIA ESTATAL CONSEJO SUPERIOR DE INVESTIGACIONES CIENTIFICAS). Period: 2014-2017.

    Outlook on Arabidopsis Research

    Several groups have participated in the call from the Italian Ministry of Education, University and Research (PRIN 2015) and are applying for international and national grants.However, Arabidopsis research in Italy is getting very limited support, as compared to research on crops. Future work will focus on the continuation of the main research projects while many groups are seeking fundings for applied research on species other than Arabidopsis.

    Arabidopsis Tools and Resources

    S. Sabatini/P. Costantino group has developed a mathematical model simulating the role of the hormone cytokinin on the position of the transition zone, the boundary were root cell lose their capacity to divide and start differentiating.

    M. Kater/L. Colombo group have developed a protocol for laser micro-dissection of reproductive meristems coupled to RNA sequencing and for ChIP-sequencing of transcription factors related to flower development.

    M. Galbiati has developed synthetic promoters for the spatio-temporal control of gene expression in guard cells.

    Outreach Activities

    Several Arabidopsis researchers from Milan and Rome were involved in planning and organizing the ‘Fascination of Plants’ day under the umbrella of EPSO (European Plant Science Organisation) in May 18, 2015.

    The group of Ida Ruberti participates in the project Promotion of consumer health of the National technological cluster Agrifood.
    M. Kater/L. Colombo have a strong outreach program related to flower, fruit and seed development in the frame European Researcher’s night (Meet me Tonight).

    Conferences and Workshops

    • 59th Annual Congress of the Italian Society of Agricultural Genetics “Feeding the planet: plant science and breeding for the future of agriculture”. Milano, September 8-11, 2015, (included a session at World Expo 2015)
    • 109th Conference of the Italian Society of Botany-International Plant Science Conference (IPSC) - with the patronage of World Expo 2015, Pavia, September 14-18, 2015
    • C. Tonelli was the organizer of the International Conference “Water and Food Security. The role of Science in Food Security and Environmental Sustainability” held in Venice, May 6-7, 2015

    Selected Publications

    • Plant immunity triggered by engineered in vivo release of oligogalacturonides, damage-associated molecular patterns. Benedetti M, Pontiggia D, Raggi S, Cheng Z, Scaloni F, Ferrari S, Ausubel FM, Cervone F, De Lorenzo G (2015) PNAS (USA) 112 (17) 5533-8.
    • The COP9 SIGNALOSOME is required for postembryonic meristem maintenance in Arabidopsis thaliana. Franciosini A, Moubayidin L, Du K, Matari NH, Boccaccini A, Butera S, Vittorioso P, Sabatini S, Jenik PD, Costantino P, Serino G (2015) Mol Plant 8:1623-34.
    • Cadmium-inducible expression of the ABC-type transporter AtABCC3 increases phytochelatin-mediated Cd tolerance in Arabidopsis. Brunetti P, Zanella L, De Paolis A, Di Litta D, Cecchetti V, Falasca G, Barbieri M, Altamura MM, Costantino P, and Cardarelli M (2015) J Exp Bot 66(13):3815-29.
    • Changing the spatial pattern of TFL1 expression reveals its key role in the shoot meristem in controlling Arabidopsis flowering architecture. Baumann K, Venail J, Berbel A, Domenech MJ, Money T, Conti L, Hanzawa Y, Madueno F, Bradley D (2015) J Exp Bot. 66(15):4769-80.
    • The Arabidopsis RNA-binding protein AtRGGA regulates tolerance to salt and drought stress. Ambrosone A, Batelli G, Nurcato R, Aurilia V, Punzo P, Bangarusamy DK, Ruberti I, Sassi M, Leone A, Costa A, Grillo S (2015)Plant Physiol. 168(1):292-306.

    Major Funding Sources

  • Japan Open or Close
    Minami Matsui (This email address is being protected from spambots. You need JavaScript enabled to view it.) and Keiko Sugimoto (This email address is being protected from spambots. You need JavaScript enabled to view it.) RIKEN Center for Sustainable Resource Science

    Arabidopsis Research Facilities

    Coordinated projects continuing in 2015/2016:

    Kazusa DNA Research Institute (http://www.kazusa.or.jp/e/) Laboratory of Plant Genomics and Genetics, Plant DNA Analysis Group, Metabolomics Team, Bioresources team, Biomass Team. Genome Informatics Group developed the portal site Plant Genome DataBase Japan PGDBj (http://pgdbj.jp) integrating databases related to plant omics studies. Manually curated literature information on DNA markers of 55 plants.

    RIKEN National Science Institute - Center for Sustainable Resource Science (CSRS) (http://www.csrs.riken.jp/en/)CSRS (Director Kazuo Shinozaki), established in 2013 to conduct basic research and also seek out, identify, and work for solutions for critical scientific, technical and social issues with special focus on Green Innovation, as well as sustainable production of energy and resources. CSRS integrates plant scientists, chemists and chemical biologists. Chemists and plant biologists from its Biomass Engineering Research Division (BMEP) (http://www.csrs.riken.jp/en/labs/bepcd/) focus on applied research through interdisciplinary innovation for plant biomass production and renewable chemical materials and bioplastics. Besides Arabidopsis, the program uses Brachypodium as a model of grass biomass.

    RIKEN National Science Institute - BioResource Center (BRC) (http://epd.brc.riken.jp/en/), (This email address is being protected from spambots. You need JavaScript enabled to view it.)The Experimental Plant Division (Masatomo Kobayashi) collects, preserves and distributes plant resources developed in Japan. The project is funded by the Japanese government through the National BioResource Project (NBRP, http://www.nbrp.jp/index.jsp). The Arabidopsis resources in RIKEN BRC include seeds (mutants, transgenic lines, and natural accessions), DNA materials (full-length cDNA and TAC clones), and cultured cells (T87 and At wt cell lines). The center also distributes full-length cDNA clones and cultured cells of model plants such as rice, Brachypodium distachyon and tobacco to the international research community.

    AIST Advanced Industrial Science and Technology National Institute - BioProduction Research Institute (https://unit.aist.go.jp/bpri/) Plant research includes studies of plant gene regulation, plant molecular biology, plant biotechnology, biomaterial production, and genetic resources. Plant Gene Regulation Research Group (Nobutaka Mitsuda, Sumire Fujiwara, and Masaru Ohme-Takagi) (http://bit.ly/1QIwEjP) focuses on study of plant transcription factors and related molecules and techniques. Group developed CRES-T gene-silencing and other technologies for functional analysis and engineering of important traits in model and economic plants.

    WPI ITbM (http://www.itbm.nagoya-u.ac.jp/) World Premier International Research Center (WPI) Institute of Transformative Bio-Molecules (ITbM) of Nagoya University is the first MEXT WPI institute to study plant science. Ambitious full-scale collaboration between synthetic chemists, plant and animal biologists, and theoreticians led by Director Kenichiro Itami, Vice-director Tetsuya Higashiyama and others.

    Integrative system of autonomous environmental signal recognition and memorization for plant plasticity (http://www.rs.tus.ac.jp/plantmemory/en/) Project goal to clarify distributed response of cells and tissues of plants and determine how plants control such information through plant unique whole-organism dynamic signal transduction system in response to environmental stimuli. Scientific Research on Innovative Areas MEXT Grant-in Aid Project FY2015-2019. Multi-organization representative: Toshinori Kinoshita, ITbM/Nagoya University.

    Multidimensional Exploration of Logics of Plant Development (MEXT) (2013-2017) (http://bit.ly/1TyA7Fg) Project to delineate systems coordinating intercellular and intracellular signals, functions of key differentiation genes, and control of metabolism, under combined efforts of 9 core research groups, 4 supporting facilities/teams, and 18 research groups (2013-2015) using multiple model species. Four facilities/teams assist in metabolomics, use of an Arabidopsis thaliana transcription factor library, development of a new model system, Marchantia polymorpha, and mathematical modeling. Multidisciplinary collaborative approach will explore unprecedented research directions. Led by Hirokazu Tsukaya.

    The Plant Cell Wall as Information Processing System (2012-2017) (https://www.plantcellwall.jp/en/) Program goal to elucidate molecular processes for information processing and self-regulation capabilities of the cell wall by understanding molecular mechanisms by which land plants sense and interact with environment via information processing systems in cell walls. Led by Kazuhiko Nishitani, Tohoku University. Grant-in-Aid for Scientific Research on Innovative Areas from MEXT.

    Creation of fundamental technologies contribute to the elucidation and application for the robustness in plants against environmental changes” Started 2015, Core Research for Evolutional Science and Technology (JST-CREST) (http://bit.ly/1TyzoDT) coordinated with PRESTO (Sakigake). Goal to establish environmentally-adaptive-plant design systems for stable food supply in age of climate change via highly precise quantitative analysis of environmental response mechanisms of plants, modeling of plant environmental response mechanisms, and evaluation of plant characters modified by sophisticated reconstruction of genes or genotype. Led by Satoshi Tabata (Kasuza DNA Research Inst.)

    Creation of essential technologies to utilize carbon dioxide as a resource through the enhancement of plant productivity and the exploitation of plant products. Started in 2011, Core Research for Evolutional Science and Technology (JST-CREST) (http://bit.ly/1pbVdMH). Goal to create basic technologies to use plant photosynthetic functions and biomass that will enable efficient carbon dioxide utilization. Led by Akira Isogai (Nara Institute of Science and Technology)

    JST-ALCA Japan Science and Technology Agency - Advanced Low Carbon Technology Research and Development Program (http://www.jst.go.jp/alca/en/index) provides competitive funding for research up to ten year period in biotechnology, chemical and energy processes and systems, materials.

    JST-NSF “Metabolomics: Advancing the Scientific Promise to Better Understand Plant Specialized Metabolism for a Low-Carbon Society” (http://1.usa.gov/1LVBpaI), research led by Lloyd W. Sumner (The Samuel Roberts Nobel Foundation) and K. Saito (RIKEN), Oliver Fiehn (Univ. of California at Davis) and M. Arita (NIG).

    ERATO Higashiyama Live-Holonics Project (2010-2016) (http://www.liveholonics.com/en/) headed by T. Higashiyama, Nagoya University. Project studies intercellular signaling in multicellular organisms with complete control of cells and molecules under microscope by developing new live-cell analysis technologies.

    Japan Advanced Plant Science Research Network (http://www.psr-net.riken.jp/) started in 2011-2017. Program’s nine centers of excellence in universities and research institutes support plant research for green innovation.

    NC-CARP Network of Centers of Carbon Dioxide Resource Studies in Plants (http://nc-carp.org/index) Program in GRENE; Green Network of Excellence. Organizer: Hiroo Fukuda. Started in 2011, ending in 2016. Aims at innovation of plant biomass technology by collaboration among Plant Science, Agriculture, Engineering and Chemistry, and education of this new area.

    DREB project: Application of Arabidopsis stress-related genes to molecular breeding of drought tolerant rice and wheat supported by MAFF and JIRCAS; (http://bit.ly/227H1Tp) (Kazuko Yamaguchi-Shinozaki U. Tokyo, Kazuo Shinozaki RIKEN, others of IRRI, CIAT, CIMMYT, Embrapa) After identifying and applying DREB genes in Arabidopsis, DREB gene function in stress tolerance were recognized as well conserved in any important crops. Project develops stress-tolerant soybean, rice and wheat.

    East Asia Science and Innovation Area Joint Research Program (e-ASIA) (http://bit.ly/1P30g72) JST-NSTDA (Thailand)-MOST (Vietnam) on “Biomass and Plant Science”. Research led by Motoaki Seki (RIKEN CSRS). Ham Huy Le (Institute of Agricultural Genetics) and Jarunya Narangajavana (Mahidol University).

    Current Arabidopsis Projects

    Kazusa DNA Research Institute

    Kazusa Metabolomics Database (KOMICS) web portal to databases, tools and other information was developed through plant metabolomics studies of Daisuke Shibata, including integration of transcriptome and metabolome data on metabolic maps, a plant metabolome database, co-expressed gene search tools and regulatory network research. (http://www.kazusa.or.jp/komics/en/)

    AIST Bioproduction Research Institute, Gene Regulation Research Group

    CRES-T was applied to more than 1,600 Arabidopsis transcription factors and most T2 seeds were harvested individually. For transcriptional repressors, the group produced more than 300 VP16-fused constructs and harvested individual T2 seeds. The group also prepared Gateway entry clones of ca. 2,000 transcription factors (without stop codon) in collaboration with M. Matsui group in RIKEN. The group developed yeast one-/two-hybrid library using the entry clones and established high-throughput screening system. (http://bit.ly/1QIwEjP)

    RIKEN National Science Institute - BioResource Center (BRC)

    SABRE2: database connecting plant EST/Full-Length cDNA Clones with Arabidopsis information. Plant resources with homologous genes are searched, together with related TAIR gene models and annotations, by specifying a Resource ID, a TAIR AGI code or a keyword. All SABRE resources available from core facilities of Japan NBRP (National BioResource Project) (http://bit.ly/1RYOkI3)

    RIKEN National Science Institute - Center for Sustainable Resource Science (CSRS)

    • Metabolome platform using GC-MS, LC-MS, CE-MS and NMR (Kazuki Saito, Masami Hirai, Jun Kikuchi, Tetsuya Sakurai). CSRS established the Arabidopsis metabolomics platform (http://prime.psc.riken.jp/), consisting of mass spectrometry-based untargeted metabolomics, mass spectrometry-based widely-targeted metabolomics, and NMR-based metabolomics.
    • Hormonome platform and RIKEN Plant Hormone Research Network: (Hitoshi Sakakibara, Mitsunori Seo)CSRS established highly sensitive high-throughput phytohormone quantification platform consisting of mass spectrometry-based technology. Platform is conducting a wide range of collaborative research in plant hormone biology (http://hormones.psc.riken.jp/)
    • Transcriptome platform using next generation sequencers. RIKEN ACCC and IMS (Motoaki Seki, Keiichi Mochida, Minami Matsui, Takaho Endo, Piero Carninci, Kazuo Shinozaki)
    • Proteome platform: Plant Phosphoproteome Database (RIPP-DB) CSRS (Hirofumi Nakagami, Ken Shirasu) and Keio University (Yasushi Ishihama, Naoyuki Sugiyama) High-throughput shotgun phosphoproteomics tool for plants and phosphorylation site databases (http://bit.ly/224sjjk) (http://pepbase.iab.keio.ac.jp)
    • Phenome platform RIKEN Activation tagging lines Database and Full-length-cDNA- overexpressing (FOX)Arabidopsis lines (M. Matsui) (http://bit.ly/1WdrX2Z), Rice FOX Arabidopsis line Database (http://ricefox.psc.riken.jp/), RIKEN Arabidopsis Genome Encyclopedia II (RARGE II) integrated phenotype database of Arabidopsis mutant traits using controlled vocabulary (Takashi Kuromori, T. Sakurai, K. Shinozaki) (http://rarge-v2.psc.riken.jp/)
    • The Chloroplast Function Database II (Fumiyoshi Myouga, K. Shinozaki) Comprehensive database analyzed by combining genotypic and phenotypic multiparametic analysis of Arabidopsis tagged-lines for nuclear-encoded chloroplast proteins. (http://rarge.psc.riken.jp/chloroplast/)
    • Analysis of small Open Reading Frame (Kousuke Hanada, M. Matsui, M. Seki) They identified ~8,000 sORFs with high coding potential in intergenic regions of the Arabidopsis genome (http://bit.ly/1P2YUt6)
    • MassBank (Masanori Arita, Takaaki Nishioka, K. Saito) Public repository of mass spectral data for sharing spectra among research communities. The data is useful for chemical identification and structure elucidation of metabolites detected by mass spectrometers. (http://www.massbank.jp/en/about.html)
    • PosMed Positional Medline (Y. Makita, N. Kobayashi, T. Toyoda) Semantic web association study (SWAS) search engine ranks resources including Arabidopsis genes and metabolites, using associations between user-specified phenotypic keywords and resources connected directly or inferentially via a semantic web of biological databases such as MEDLINE, OMIM, pathways, co-expressions, molecular interactions and ontology terms (http://omicspace.riken.jp/)
    • High-throughput genome-wide biochemical analysis using wheat germ cell-free-based protein array technology. The method developed by Proteo-Science Center of Ehime University (Keiichirou Nemoto and Tatsuya Sawasaki)(http://bit.ly/21ssVcQ) and RIKEN CSRS (M. Seki and K. Shinozaki) is useful for in vitro screening of substrate protein, interacting protein or chemical compound.
    • RIPPS (RIKEN Plant Phenotyping System) (K. Shinozaki, Miki Fujita, Kaoru Urano) Automated system for evaluating plant growth under environmental stress conditions developed by the Gene Discovery Research Group of CSRS. RIPPS provides high-throughput and accurate measurements of plant traits, facilitating understanding of gene function in a wide range of environmental conditions (http://bit.ly/24U4Ujx)
    • PASMet - Prediction, Analysis and Simulation of Metabolic Reaction Networks (Kansuporn Sriyudthsak, Masami Hirai) PASMet is a web-based platform for predicting, modelling and analyzing metabolic systems. Non-commercial and user-friendly tool to assist non-experts in mathematical modelling, in silico computing or programming to work on computational biology (http://pasmet.riken.jp/)
    • Plant-PrAS (Plant-Protein Annotation Suite) (A. Kurotani, Y. Yamada, AA. Tokmakov, Y. Kuroda, Y. Fukami, K. Shinozaki, T. Sakurai) Analyzed predicted multiple physicochemical and secondary structural parameters using over 20 analysis tools with whole amino acid sequences from genomes of representative plant species (Arabidopsis thaliana, Glycine max, Populus trichocarpa, Oryza sativa, Physcomitrella patens, and Cyanidioschyzon merolae) for which genome sequencing was achieved, and organized those results as Plant-PrAS. (http://plant-pras.riken.jp/)
    • “Development of Synthetic Promoters for Acceleration of Biomass Production” JST-ALCA project (http://bit.ly/1SRr7de) led by Yoshiharu Yamamoto (Gifu Univ.).
    • Plant Promoter Database, ppdb (http://ppdb.agr.gifu-u.ac.jp) (Yoshiharu Yamamoto, Gifu Univ.) http://bit.ly/1LVwnep was updated to ver. 3.0. Large TSS data of a NGS incorporated into the database.

    Arabidopsis Tools and Resources

    Kazusa DNA Research Institute

    RIKEN BRC

    RIKEN CSRS

    PRIMe Platform for RIKEN Metabolomics (http://prime.psc.riken.jp/). Arabidopsis metabolomics platform publicly available platform resources:

    PRIMe Web Applications

    Distribution and Redistribution

    Other RIKEN CSRS developed tools and resources:

    Conferences and Workshops

    • Nov. 29-Dec. 2, 2016: Cold Spring Harbor Asia Conference in Japan, “Latest Advances in Plant Development and Environmental Response” Awaji Island, Kobe (http://bit.ly/1TKqqDK) Mar. 18-10, 2016: 57th Annual Meeting of Japanese Society of Plant Physiologists (http://bit.ly/1RNsULu)
    • Nov. 30-Dec. 4, 2015: 8th Plant Biomechanics International Conference, Nagoya (http://bit.ly/1TKsATT)
    • Nov. 24-25, 2015: International Symposium “Towards Increased Plant Productivity through Understanding of Environmental Responses and Epigenetic Regulation” RIKEN, Yokohama Campus. Sponsorship: RIKEN CSRS; Bioscience and Biotechnology Center, Nagoya Univ.; JST CREST (http://bit.ly/1TKqm6O)
    • Oct. 8-9, 2015: ICPES 2015: 17th International Conference on Plant and Environment Sciences, Osaka (http://bit.ly/1TKrtU9)

    Selected Publications

    • Tip-localized receptors control pollen tube growth and LURE sensing in Arabidopsis. Takeuchi H, Higashiyama T (2016) Nature 531:245-8.
    • Rapid Elimination of the Persistent Synergid through a Cell Fusion Mechanism. Maruyama et al. (2015) Cell 161(4):907-18.
    • PARASITIC PLANTS. Probing strigolactone receptors in Striga hermonthica with fluorescence. Tsuchiya Y et al. (2015) Science. 349(6250):864-8.
    • Decentralized circadian clocks process thermal and photoperiodic cues in specific tissues. Hanako et al. (2015) Nature Plants 1, Article number: 15163 doi:10.1038/nplants.2015.163
    • PRC2 represses dedifferentiation of mature somatic cells in Arabidopsis. Ikeuchi et al. (2015) Nature Plants 1, Article number: 15089 doi:10.1038/nplants.2015.89

    Major Funding Sources

  • Netherlands Open or Close
    Ben Scheres (This email address is being protected from spambots. You need JavaScript enabled to view it.) Wageningen UR, Plant Developmental Biology, Wageningen; Sacco de Vries (This email address is being protected from spambots. You need JavaScript enabled to view it.) Wageningen UR, Laboratory of Biochemistry, Wageningen Edit

    Arabidopsis Research Facilities

    Leiden University: Auxin and pattern formation (Offringa), DNA repair and recombination (Hooykaas). Metabolomics facility for plant defence compounds (Klinkhamer).
    Utrecht University: Sugar sensing networks and phase transitions (Smeekens), Flooding stress and light avoidance (Pierik/Voesenek), Plant-Microbe interactions (Pieterse), Multi-scale modelling (ten Tusscher).
    Wageningen University: Floral transcription factor networks (Angenent), Strigolactone signalling (Bouwmeester), Root development and stem cells (Scheres), Receptor kinase biology and Embryogenesis (De Vries/Weijers).
    University of Amsterdam/VU: Abiotic stress response, lipid signalling, volatile signaling (Testerink/Haring), Chromatin structure (Koes).

    Current Arabidopsis Projects

    • EU-ITN-MERIT: Metabolic Reprogramming by Induction of Transcription (2012-2015 Smeekens).
    • ERA-CAPS: Plasticity of flowering time in response to environmental signals in Arabidopsis thaliana (FLOWPLAST) (2014-2017 Angenent)
    • ERA-CAPS: European Plant Embryology Consortium (2014-2017, Weijers, Scheres)
    • Dose-dependent BBM action (2015-2019-Boutilier)
    • Role of TCP transcription factors in growth (2013-2017, Immink)
    • NWO-VENI: Evolutionary aspects of the MADS domain transcription factor FUL (2014-2017, Bemer)
    • NWO-GSU (2015-2020) Ronald Pierik. Moving from tip to base: how local far-red signalling regulates distant growth.
    • NWO-ALW (2014-2017) Ronald Pierik. Unravelling molecular mechanisms of plant competition: the interplay between above- and belowground competitive responses in Arabidopsis thaliana.
    • EMBO Long term fellowship (Oct2015-Oct2017) Scott Hayes, with Ronald Pierik. Mechanism and functional significance of salt-mediated inhibition of plant shade avoidance.
    • NWO-VIDI (2013-2018) Ronald Pierik. When growing tall is not an option: down-regulation of shoot elongation in the shade.
    • NWO-VIDI (2015-2019) Kirsten ten Tusscher. Lateral root patterning in plants: multi-scale modelling of complex feedbacks.
    • NWO-ALW (Mar2013-Jan2016) Flooding stress tolerance: an ecomolecular approach using Arabidopsis and wild relatives.
    • NWO-Veni (Jan2013-Jan2016) After the rains: unravelling the molecular mechanisms driving post flooding recovery in plants
    • NWO-ALW (Sep2015-Sep2019) A novel role for ethylene in conferring anoxia tolerance: mechanism and significance
    • NWO-GSU (Sep2015-Sep2019) NO problem: ethylene-induced regulation of nitric oxide confers flooding tolerance in plants
    • NWO-DBT (Jan2016-Jan2020) Understanding responses to simultaneously and sequentially occurring abiotic stresses typical of climate change in rice and Arabidopsis
    • ERC-StG (consolidator) Dolf Weijers - CELLPATTERN (2011-2016)
    • NWO-VIDI Bert De Rybel - The molecular and cellular basis of vascular tissue formation (2014-2019)
    • NWO-VENI Colette ten Hove - Dissecting the origin of an ancient tissue (2013-2016)
    • NWO-VICI Dolf Weijers - The evolutionary and structural basis for specificity in plant hormone response (2015-2020)

    Outlook on Arabidopsis Research

    Funding possibilities increasingly rely on comparative and evolutionary research among Arabidopsis accessions, relatives of Arabidopsis or non-relative wild plants and crops.

    Arabidopsis Tools and Resources

    • Phenovator: Flood e.a. Plant Methods 2016 12:14 (http://plantmethods.biomedcentral.com/articles/10.1186/s13007-016-0113-y). Facility for high-throughput phenotyping of Arabidopsis growth and photosynthesis.
    • Angenent laboratory: ChIP-seq (both TFs and histon modifications), SELEX-seq, Immunoprecipitation-Mass Spectrometry. Pac-Bio for RNA-seq of splicing variants.
    • Scheres laboratory: collaboration with physics (prof. Bela Mulder) for simulation of microtubule dynamics on realistic cell surface shapes.

    Outreach Activities

    The Top Sector policy of the Ministry of Economic Affairs allows funding of various collaborative projects between breeding companies and Academia. In these projects we translate knowledge and tools obtained from our Arabidopsis research to crops, e.g. brassica, lettuce and tomato. An example is a project funded by the Ministry of Economic affairs and 3 Dutch breeding companies aiming at a translation of our knowledge about ambient temperature regulation of flowering time in Arabidopsis to cauliflower. (2012-2016; 2016-2020).

    Conferences and Workshops

    • Experimental Plant Science Annual Meeting Lunteren
    • Bi-yearly international summerschool Environmental Signaling in Plants (8th version held in 2015).
    • 15th New Phytologist Workshop (Ravenstein, The Netherlands) Flooding stress: signaling through perturbations in oxygen, ethylene, nitric oxide and light

    Selected Publications

    • Transcriptional control of tissue formation throughout root development. Moreno-Risueno MA, Sozzani R, Yardimci GG, Petricka JJ, Vernoux T, Blilou I, Alonso J, Winter CM, Ohler U, Scheres B, Benfey PN (2015) Science 350:426-430.
    • Evolution of DNA-binding sites of a floral master regulatory transcription factor. Muiño JM, de Bruijn S, Pajoro A, Geuten K, Vingron M, Angenent GC, Kaufmann K (2015) Mol Biol Evol 33(1):185-20.
    • Arabidopsis BIRD zinc finger proteins jointly stabilize tissue boundaries by confining the cell fate regulator SHORT-ROOT and contributing to fate specification. Long Y, Smet W, Cruz-Ramirez A, Castelijns B, de Jonge W, Mahonen AP, Bouchet B, Sanchez-Perez G, Akhmanova A, Scheres B, Blilou I (2015) The Plant Cell 27:1185-99.
    • A bHLH-based feedback loop restricts vascular cell proliferation in plants. Vera-Sirera F, De Rybel B, Úrbez C, Kouklas E, Pesquera M, Álvarez-Mahecha JC, Minguet EG, Tuominen H, Carbonell J, Borst JW, Weijers D, Blázquez MA (2015) Dev Cell. 23:432-43.
    • Origin of SERKs: Bioinformatics Analysis of the Somatic Embryogenesis Receptor Kinases. Aan den Toorn M, Albrecht C, de Vries SC (2015) Mol Plant 8:762-82
  • New Zealand Open or Close

    Lynette Brownfield, This email address is being protected from spambots. You need JavaScript enabled to view it., University of Otago, Department of Biochemistry, Dunedin.

    3. Use of Arabidopsis

    Arabidopsis is used as a research tool in approximately eight institutions in New Zealand (University of Auckland, University of Otago, Massey University, University of Canterbury, Lincoln University and Victoria University, AgResearch Ltd, Plant and Food Research Ltd.)

    6. Conferences, Workshops and Outreach events

    Please provide a list of conferences, workshops and outreach events that your country hosted in the past year or will host in coming years.

    AustralAsia Genetics Society Meeting, July 3-6, 2017, Dunedin, New Zealand.

    Plant Science Central, 4-6 July, 2017, Palmerston North, New Zealand.

    Queenstown Molecular Biology Meeting (including a Plant Satellite) August 28-31, Queenstown, New Zealand.

    7. Selected Publications

    Please highlight up to 10 publications from the past year led by a researchers from your country that reflect the breadth of outputs. Please consider including a mix of fundamental and applied research.

    Brendolise C, Espley RV, Lin-Wang K, Laing W, Peng Y, McGhie T, Dejnoprat S, Tomes S, Hellens RP and Allan AC (2017) Multiple copies of a simple MYB-binding site confers trans-regulation by specific flavonoid-related R2R3 MYBs in diverse species. Frontiers in Plant Science 8:1864.

    Cabout, S, Leask, MP, Varghese S, Yi J, Peters B, Conze LL, Köhler C and BrownfieldL (2017). The meiotic regulator JASON utilizes alternative translation initiation sites to produce differentially localized forms. Journal of Experimental Botany, 68: 4205-4217.

    Gould KS, Jay-Allemand C, Logan BA, Baissac Y and Bidel LP (2018). When are foliar anthocyanins useful to plants? Re-evaluation of the photoprotection hypothesis using Arabidopsis thaliana mutants that differ in anthocyanin accumulation. Environmental and Experimental Botany.DOI: 10.1016/j.envexpbot.2018.02.006

    Jibran R, Hunter DA, Cooney J, Tahir J and Dijkwel P (2017). Arabidopsis AGAMOUS regulates sepal senescence by driving jasmonate production. Frontiers in Plant Science 8: 2101.

    Pathirana R, West P, Hedderley D and Eason J. (2017). Cell death patterns in Arabidopsis cells subjected to four physiological stressors indicate multiple signalling pathways and cell cycle phase specificity. Protoplasma254: 635-647.

    Ridge S, Deokar A, Lee R, Daba K, Macknight RC, Weller J L and Tar’an, B (2017). The chickpea Early Flowering 1 (Efl1) locus is an ortholog of Arabidopsis ELF3. Plant Physiology, 175: 802-815.

    8. Major Funding Sources

    Please provide name and link to the funding sources that are responsible for supporting the Arabidopsis research in your country.

    The Marsden Fund administered by the Royal Society of New Zealand (http://www.royalsociety.org.nz/programmes/funds/marsden/)

    Ministry for Business, Innovation and Employment (MBIE; http://www.mbie.govt.nz/) through:

    -       Core funding to Crown Research Institutes

    -       The Endeavour fund (http://www.mbie.govt.nz/info-services/science-innovation/investment-funding/current-funding/2018-endeavour-round)

    The Catalyst Fund (http://www.mbie.govt.nz/info-services/science-innovation/investment-funding/current-funding/catalyst-fund)
    The Agricultural and Marketing Research and Development Trust (AGMARDT: http://agmardt.org.nz/).

     

  • Norway Open or Close

    Prepared by: Thorsten Hamann This email address is being protected from spambots. You need JavaScript enabled to view it.

    Norwegian University of Science and Technology

    Use of Arabidopsis

    In 2017 the Norwegian plant biology community held their national conference in Hamar in central Norway with around 60 attendees from all Norwegian universities and research institutes as well as invited speakers from eight different countries. The scientific program during the two-day event covered a diverse range of topics in lectures as well as workshops and public panels where questions like “how to inspire the next generation of plant scientists?” or “Public and political acceptance for genome editing in plant based food production” were discussed. In parallel Karin Metzlaff from the European Plant Science Organization (EPSO) gave a presentation introducing the organization, its aims and activities. The scientific program was quite diverse illustrated by the examples like: heritable phenotypic changes induced by epigenetic reprogramming; gene and genome dosage on hybrididzation barriers in Arabidopsis lyrata and arenosa; PP2A as a regulator of methionine metabolism in plant immunity and linking CALPAIN-controlled development to gene expression networks through trascriptomics. It was also interesting to see how often Arabidopsis had originally acted as foundation for targeted follow up research projects in crop species like strawberry, wheat and Norway spruce. The scientific activities of the well-organized conference were complemented by the social program involving a conference dinner aboard the historic side-wheel paddle steam boat “Skibladner” while exploring Lake Mjøsa.

    Selected Publications

    With respect to publication activities, 2017 was a very good year with more than 30 articles having been published that contain contributions from members of the Norwegian Arabidopsis community. Here attention is being drawn to just a few representative publications in journals like PNAS, J. Ex. Bot. and Plant, Cell and Environment, which illustrate nicely the breadth of Arabidopsis research in Norway. The articles cover topics like endosperm-based hybridization barriers explaining gene flow (Lafon-Placette et al., 2017); peptide-based signaling processes during stress response and abscission (Vie et al., 2017) and the impact of protein phosphatase 2A methylation on environmental stress responses (Creighton et al., 2017).

    Creighton, M. T., Kolton, A., Kataya, A. R. A., Maple-Grødem, J., Averkina, I. O., Heidari, B. and Lillo, C. (2017). Methylation of protein phosphatase 2A-Influence of regulators and environmental stress factors. Plant. Cell Environ. 40, 2347–2358.

    Lafon-Placette, C., Johannessen, I. M., Hornslien, K. S., Ali, M. F., Bjerkan, K. N., Bramsiepe, J., Glöckle, B. M., Rebernig, C. A., Brysting, A. K., Grini, P. E., et al. (2017). Endosperm-based hybridization barriers explain the pattern of gene flow between Arabidopsis lyrata and Arabidopsis arenosa in Central Europe. Proc. Natl. Acad. Sci. 114, E1027–E1035.

    Vie, A. K., Najafi, J., Winge, P., Cattan, E., Wrzaczek, M., Kangasjärvi, J., Miller, G., Brembu, T. and Bones, A. M. (2017). The IDA-LIKE peptides IDL6 and IDL7 are negative modulators of stress responses in Arabidopsis thaliana. J. Exp. Bot. 68, 3557–3571.

    Major Funding Sources

    Research Council of Norway

    www.rcn.no

    The annual plant biology
conference was also financially supported through grants by the Norwegian research council and the Scandinavian Plant Physiology Society www.spps.se

  • South Korea Open or Close

    Inhwan Hwang, This email address is being protected from spambots. You need JavaScript enabled to view it., Pohang University of Science and Technology

    3. Use of Arabidopsis

    Can you approximate the number of institutions and/or labs in your country that use Arabidopsis in their research.

    100 Institutions and 500 labs

    6. Conferences, Workshops and Outreach events

    Please provide a list of conferences, workshops and outreach events that your country hosted in the past year or will host in coming years.

    - Plant Winter Conference of Korean Society of Plant Biologists

    - Annual meeting of Korean Society of Plant Biologists

    -Annual meeting of Korean Society of Molecular and Cell Biologists

    - The first Asian conference on Plant-based Pharmaceuticals.

    7. Selected Publications

    Please highlight up to 10 publications from the past year led by a researchers from your country that reflect the breadth of outputs. Please consider including a mix of fundamental and applied research.

    -       Kim JH, Cho SK, Oh TR, Ryu MY, Yang SW, Kim WT. (2017) MPSR1 is a cytoplasmic PQC E3 ligase for eliminating emergent misfolded proteins in Arabidopsis thaliana. Proc Natl Acad Sci U S A. 114:E10009-E10017.

    -       Lee DH, Park SJ, Ahn CS, Pai HS. (2017) MRF Family Genes Are Involved in Translation Control, Especially under Energy-Deficient Conditions, and Their Expression and Functions Are Modulated by the TOR Signaling Pathway. Plant Cell. 29:2895-2920.

    -       Lee JH, Jung JH, Park CM. (2017) Light Inhibits COP1-Mediated Degradation of ICE Transcription Factors to Induce Stomatal Development in Arabidopsis. Plant Cell. 29:2817-2830.

    -       Khare D, Choi H, Huh SU, Bassin B, Kim J, Martinoia E, Sohn KH, Paek KH, Lee Y. (2017) Arabidopsis ABCG34 contributes to defense against necrotrophic pathogens by mediating the secretion of camalexin. Proc Natl Acad Sci U S A. 114:E5712-E5720.

    -       Ahn G, Kim H, Kim DH, Hanh H, Yoon Y, Singaram I, Wijesinghe KJ, Johnson KA, Zhuang X, Liang Z, Stahelin RV, Jiang L, Cho W, Kang BH, Hwang I. (2017) SH3 Domain-Containing Protein 2 Plays a Crucial Role at the Step of Membrane Tubulation during Cell Plate Formation. Plant Cell. 29:1388-1405.

    -       Ha JH, Lee HJ, Jung JH, Park CM. (2017) Thermo-Induced Maintenance of Photo-oxidoreductases Underlies Plant Autotrophic Development. Dev Cell. 41:170-179.e4.

    -       Arnaud D, Lee S, Takebayashi Y, Choi D, Choi J, Sakakibara H, Hwang I. (2017) Cytokinin-Mediated Regulation of Reactive Oxygen Species Homeostasis Modulates Stomatal Immunity in Arabidopsis. Plant Cell. 29:543-559.

    -       Cha JY, Kim J, Kim TS, Zeng Q, Wang L, Lee SY, Kim WY, Somers DE. (2017) GIGANTEA is a co-chaperone which facilitates maturation of ZEITLUPE in the Arabidopsis circadian clock. Nat Commun. 8:3.

    -       Nawkar GM, Kang CH, Maibam P, Park JH, Jung YJ, Chae HB, Chi YH, Jung IJ, Kim WY, Yun DJ, Lee SY. (2017) HY5, a positive regulator of light signaling, negatively controls the unfolded protein response in Arabidopsis. Proc Natl Acad Sci U S A. 114:2084-2089.

    -       Hwang Y, Choi HS, Cho HM, Cho HT. (2017) Tracheophytes Contain Conserved Orthologs of a Basic Helix-Loop-Helix Transcription Factor That Modulate ROOT HAIR SPECIFIC Genes. Plant Cell. 29:39-53

    -       Park JS, Frost JM, Park K, Ohr H, Park GT, Kim S, Eom H, Lee I, Brooks JS, Fischer RL, Choi Y. (2017) Control of DEMETER DNA demethylase gene transcription in male and female gamete companion cells in Arabidopsis thaliana. Proc Natl Acad Sci U S A. 114:2078-2083. 

    8. Major Funding Sources

    Please provide name and link to the funding sources that are responsible for supporting the Arabidopsis research in your country.

    - Systems & Synthetic Agrobiotech Center (~ 10 M USD/yr by Rural Development Administration, Korea).

    - Agricultural Life Science Center (~ 10 M USD/yr by Rural Development Administration, Korea).

    - Systems understanding of plant senescence and life history (~9 M USD/yr for 10 years by Institute of Basic Research)

    - Woojangchoon Project focusing on carbon metabolism reengineering (0.9 M USD/yr for 5 years) supported by Rural Developmental Agency, Kore

     

  • Spain Open or Close

    José Luis Micol, This email address is being protected from spambots. You need JavaScript enabled to view it., Universidad Miguel Hernández, Elche, Spain

    3. Use of Arabidopsis

    Can you approximate the number of institutions and/or labs in your country that use Arabidopsis in their research.

    About 100 laboratories.

    4. Open Resources for Arabidopsis Researchers

    Please provide a list of experimental resources based in your country that are accessible for use both by Arabidopsis researchers in your country and by the global community.

    5. New Software Tools

    Please provide a list of software tools recently developed in your country that are open access and available to the global community of Arabidopsis researchers.

    6. Conferences, Workshops and Outreach events

    Please provide a list of conferences, workshops and outreach events that your country hosted in the past year or will host in coming years.

    The “XV Spanish - Portuguese Congress on Plant Physiology” was organized by plant biologists lead by Prof. Teresa Altabella in Barcelona (June 26-30, 2017).

    7. Selected Publications

    Please highlight up to 10 publications from the past year led by a researchers from your country that reflect the breadth of outputs. Please consider including a mix of fundamental and applied research.

    Balanzà V, Martínez-Fernández I, Sato S, Yanofsky MF, Kaufmann K, Angenent GC, Bemer M and Ferrandiz C (2018) Genetic control of meristem arrest and life span in Arabidopsis by a FRUITFULL-APETALA2 pathway. Nature Communications 9: 565.

    Barbado C, Córdoba-Canero D, Arizaa RR and Roldán-Arjona T (2018) Nonenzymatic release of N7-methylguanine channels repair of abasic sites into an AP endonuclease-independent pathway in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America 115: E916-E924.

    Carrasco-López C, Hernández-Verdeja T, Perea-Resa C, Abia D, Catalá R and Salinas J (2017) Environment-dependent regulation of spliceosome activity by the LSM2-8 complex in Arabidopsis. Nucleic Acids Research 45: 7416-7431.

    Castaño-Miquel L, Mas A, Teixeira I, Seguí J, Perearnau A, Thampi BN, Schapire AL, Rodrigo N, La Verde G, Manrique S, Coca M and Lois LM (2017) SUMOylation inhibition mediated by disruption of SUMO E1-E2 interactions confers plant susceptibility to necrotrophic fungal pathogens. Molecular Plant 10: 709-720.

    Chini A, Monte I, Zamarreno AM, Hamberg M, Lassueur S, Reymond P, Weiss S, Stintzi A, Schaller A, Porzel A, García-Mina JM and Solano R (2018) An OPR3-independent pathway uses 4,5-didehydrojasmonate for jasmonate synthesis. Nature Chemical Biology 14: 171-178.

    González-Arzola K, Díaz-Quintana A, Rivero-Rodríguez F, Velázquez-Campoy A, De la Rosa MA and Díaz-Moreno I (2017) Histone chaperone activity of Arabidopsis thaliana NRP1 is blocked by cytochrome c. Nucleic Acids Research 45: 2150-2165.

    Martín G, Rovira A, Veciana N, Soy J, Toledo-Ortiz G, Gommers CMM, Boix M, Henriques R, Minguet EG, Alabadí D, Halliday KJ, Leivar P and Monte E (2018) Circadian waves of transcriptional repression shape PIF-regulated photoperiod-responsive growth in Arabidopsis. Current Biology 28: 311-318.

    Martínez-Pérez M, Aparicio F, López-Gresa MP, Bellés JM, Sánchez-Navarro JA and Pallás V (2017) Arabidopsis m(6)A demethylase activity modulates viral infection of a plant virus and the m(6)A abundance in its genomic RNAs. Proceedings of the National Academy of Sciences of the United States of America 114: 10755-10760.

    Pérez-Ruiz JM, Naranjo B, Ojeda V, Guinea M and Cejudo FJ (2017) NTRC-dependent redox balance of 2-Cys peroxiredoxins is needed for optimal function of the photosynthetic apparatus. Proceedings of the National Academy of Sciences of the United States of America 114: 12069-12074.

    Vergara Z, Sequeira-Mendes J, Morata J, Peiró R, Hénaff E, Costas C, Casacuberta JM and Gutierrez C (2017) Retrotransposons are specified as DNA replication origins in the gene-poor regions of Arabidopsis heterochromatin. Nucleic Acids Research 45: 8358-8368.

    Zhou Y, Romero-Campero FJ, Gómez-Zambrano A, Turck F and Calonje M (2017) H2A monoubiquitination in Arabidopsis thaliana is generally independent of LHP1 and PRC2 activity. Genome Biology 18: 69.

    8. Major Funding Sources

    Please provide name and link to the funding sources that are responsible for supporting the Arabidopsis research in your country.

    About 80 grants from the Ministry of Economy, Industry and Competitiveness of Spain fund Arabidopsis research projects at individual laboratories.

     

  • Sweden Open or Close
    Maria E. Eriksson (This email address is being protected from spambots. You need JavaScript enabled to view it.) Umeå University, Umeå Plant Science Centre, Umeå

    3. Use of Arabidopsis

    At least ten institutions use Arabidopsis as one of their major plant model species.

    4. Open Resources for Arabidopsis Researchers

    National resources available to the Arabidopsis community

    • Max Lab hosted by Lund University; https://www.maxiv.lu.se/

    Dedictated to high-throughput, nanovolume characterization and crystallization of biological macromolecules

    • Science for Life Laboratory (SciLifeLab) is a national resource center dedicated to large scale research in molecular biosciences and medicine with two sites; in Stockholm and Uppsala. The major funding for SciLifeLab comes from strategic grants from the Swedish government, http://www.scilifelab.se

    • Umeå Plant Science Centre has developed and maintains platforms of genomics, proteomics, metabolomics, quantification of plant growth regulators and wood analysis http://www.upsc.se, found under “resources”

    • The Swedish Metabolomics Centre in Umeå is a national resource, http://www.swedishmetabolomicscentre.se/

    5. New Software Tools

    The PlantGenIE platform; web portals for enabling in-depth exploration of poplar, Norway spruce, and Arabidopsis http://plantgenie.org/

    Computational Genetics Division Uppsala University, Carlborg Lab

    http://www.computationalgenetics.se/

    6. Conferences, Workshops and Outreach events

    Meetings in 2018:

    The European Congress on Photosynthesis Research, organized by the International Society for Photosynthesis Research, June 25 – 28, Uppsala, Sweden

    The 13th European Nitrogen Fixation Conference 2018, August 18 – 21, Stockholm, Sweden

    'Fascination of Plants Day' is celebrated at most major plant science centres across Sweden, which also regularly host outreach activities to highlight research on plants.

    7. Selected Publications

    1.         Hafrén A, et al. (2017) Selective autophagy limits cauliflower mosaic virus infection by NBR1-mediated targeting of viral capsid protein and particles. Proceedings of the National Academy of Sciences of the U. S. A. 114(10): E2026-E2035

    2.         Lafon-Placette C, et al. (2017) Endosperm-based hybridization barriers explain the pattern of gene flow between Arabidopsis lyrata and Arabidopsis arenosa in Central Europe. Proceedings of the National Academy of Sciences of the U. S. A. 114(6):E1027-E1035

    3.         Ganeteg U, et al. (2017) Amino acid transporter mutants of Arabidopsis provides evidence that a nonmycorrhizal plant acquires organic nitrogen from agricultural soil. Plant, Cell & Environment 40(3):413-423

    4.         MatíasHernández L, et al. (2017) AaMYB1 and its orthologue AtMYB61 affect terpene metabolism and trichome development in Artemisia annua and Arabidopsis thaliana. The Plant Journal 90(3):520-534

    5.         Meyer HM, et al. (2017) Fluctuations of the transcription factor ATML1 generate the pattern of giant cells in the Arabidopsis sepal. eLife 6:e19131

    6.         Jonsson K, Boutté Y, Singh RK, Gendre D, & Bhalerao RP (2017) Ethylene Regulates Differential Growth via BIG ARF-GEF-Dependent Post-Golgi Secretory Trafficking in Arabidopsis. The Plant Cell 29(5):1039

    7.         Teixeira PF, et al. (2017) A multi-step peptidolytic cascade for amino acid recovery in chloroplasts. Nature Chemical Biology 13:15

    8.         Majda M, et al. (2017) Mechanochemical Polarization of Contiguous Cell Walls Shapes Plant Pavement Cells. Developmental Cell 43(3):290-304.e294

    9.         Zhang B, et al. (2017) BLADE-ON-PETIOLE proteins act in an E3 ubiquitin ligase complex to regulate PHYTOCHROME INTERACTING FACTOR 4 abundance. eLife 6:e26759

    8. Major Funding Sources

    • The Swedish Research Council (VR); http://www.vr.se

    VR supports researcher-initiated, basic research

    • The Swedish Foundation for Strategic Research; http://www.stratresearch.se

    Supports strategic research in natural science, engineering and medicine

    • The Swedish Agency for Innovation Systems (VINNOVA); http://www.vinnova.se

    Promotes sustainable growth by funding needs-driven research and the development of effective innovation systems

    • The Swedish Research Council Formas; http://www.formas.se

    Supports research (rather applied) and need-driven research in the areas Environment, Agricultural Sciences and Spatial Planning

    • The Wallenberg Foundations; http://www.wallenberg.org/en

    Private foundations supporting researcher initiated basic research as well as larger centers of excellence devoted to functional genomics and other strategic areas

    • Carl Trygger’s Foundation for Scientific Research; http://www.carltryggersstiftelse.se/

    A private foundation supporting research within the areas of agriculture, forestry, biology, chemistry and physics

    • The Kempe Foundations; http://www.kempe.com

    Private foundations devoted to support scientific research in Northern Sweden

    • Stiftelsen Olle Engkvist Byggmästare; http://engkviststiftelserna.se/

    A private foundation supporting basic science

    • Sven and Lily Lawski’s foundation for research in Natural Sciences (Biochemistry and Genetics); http://www.lawskistiftelsen.se/

    A private foundation supporting basic science

     

  • Switzerland Open or Close

    2. Prepared by (Name, Email, Institution)

    Kentaro K. Shimizu This email address is being protected from spambots. You need JavaScript enabled to view it.

    Misako Yamazaki This email address is being protected from spambots. You need JavaScript enabled to view it.

    University of Zurich

    Swiss Plant Science Web This email address is being protected from spambots. You need JavaScript enabled to view it.

    3. Use of Arabidopsis

    Can you approximate the number of institutions and/or labs in your country that use Arabidopsis in their research.

    c.a. 12 institutions and c.a 100 labs.

    4. Open Resources for Arabidopsis Researchers

    Please provide a list of experimental resources based in your country that are accessible for use both by Arabidopsis researchers in your country and by the global community.

    -       Swiss-Prot database contributes to TAIR database

    -       Genevestigator (https://genevestigator.com/gv/)

    As a facility or database, we have these resources below.

    -       Functional Genomics Center Zurich

    -       The Neuchâtel Platform of Analytical Chemistry (the Mass Spectrometry and Metabolomics Unit and the Nuclear Magnetic Resonance Unit, http://www.unine.ch/npac)

    -       Bio-molecular Analysis Platform (collaborative basis, http://biveg.unige.ch/en/services/bma/)

    -       Genetic Diversity Center (e.g. genome-wide polymorphisms of Arabidopsis halleri)

    6. Conferences, Workshops and Outreach events

    Please provide a list of conferences, workshops and outreach events that your country hosted in the past year or will host in coming years.

    Conferences

    -       PSC Summer school 2017, Understanding Risks and Resilience in Plant Systems, 29 May – 2 June 2017, Einsiedeln

    https://www.plantsciences.uzh.ch/dam/jcr:a5bb24c5-840b-419c-9232-32ceddea37bf/Flyer_PSC_Summer_School_2017.pdf

    -       PSC Symposium 2017, Dynamics of Plant Development & Evolution

    30 November - 1 December 2017, Zurich

    http://www.plantsciences.uzh.ch/en/outreach/conferences/Dynamics-of-Plant-Development-and-Evolution.html

    -       SwissPLANT 2018 Symposium, 31 January - 2 February 2018, Meiringen

    https://swissplantscienceweb.ch/de/swissplant-2018-symposium/

    -       Lausanne Genomics Days 2018, 5 – 6 February 2018, Lausanne

    http://www.genomyx.ch/mon-feb-5-tues-feb-6-2018-lausanne-genomics-days-2018/

    -       PSC Summer School 2018, Responsible Research and Innovation in Plant Sciences 10-14 September 2018, Einsiedeln, Switzerland

    https://www.plantsciences.uzh.ch/en/teaching/summerschool.html

    -       PSC Symposium 2018, Working Title: 20th Anniversary Symposium Zurich-Basel Plant Science Center – Breakthroughs in Plant Sciences – From the laboratory to the world, 5 December 2018, Zurich

    Workshops

    Molecular studies in natura - How plants sense and react in the nature, 19 February 2018, Zurich

    Plant Development and Evolution from molecules to ecosystems, 20-22 February 2018, Zurich

    Outreach Activities

    -       Plant Science at School

    Continuing Education Program in Plant Sciences for Secondary School Teachers

    Over the past seven years, this program has become a national example of successful collaboration between researchers, teachers and regional learning centers.

    http://www.plantsciences.uzh.ch/outreach/atschool.html

    -       PSC Discovery Program for Youth – new Agora project

    In collaboration with educators of the ETH MINT Lernzentrum, the Zurich-Basel Plant Science Center (PSC) offers workshops for school classes at the secondary school level.

    http://www.plantsciences.uzh.ch/de/outreach/discovery.html

    http://www.snf.ch/en/funding/science-communication/agora/Pages/default.aspx

    7. Selected Publications

    Please highlight up to 10 publications from the past year led by researchers from your country that reflect the breadth of outputs. Please consider including a mix of fundamental and applied research.

    -       Diffusible repression of cytokinin signalling produces endodermal symmetry and passage cells.

    Andersen TG, Naseer S, Ursache R, Wybouw B, Smet W, De Rybel B, Vermeer JEM, Geldner N.

    doi: 10.1038/nature25976.

    -       Local auxin production underlies a spatially restricted neighbor-detection response in Arabidopsis.

    Michaud O, Fiorucci AS, Xenarios I, Fankhauser C.

    Proc Natl Acad Sci U S A. 2017 Jul 11;114(28):7444-7449doi: 10.1073/pnas.1702276114.

    -       Local adaptation (mostly) remains local: reassessing environmental associations of climate-related candidate SNPs in Arabidopsis halleri.

    Rellstab C, Fischer MC, Zoller S, Graf R, Tedder A, Shimizu KK, Widmer A, Holderegger R, Gugerli F.

    Heredity (Edinb). 2017 Feb;118(2):193-201.

    doi: 10.1038/hdy.2016.82.

    -       Agrobacterium-mediated floral dip transformation of the model polyploid species Arabidopsis kamchatica.

    Yew CL, Kakui H, Shimizu KK.

    J Plant Res. 2018 Mar;131(2):349-358.

    doi: 10.1007/s10265-017-0982-9.

    -       RALF4/19 peptides interact with LRX proteins to control pollen tube growth in Arabidopsis.

    Mecchia MA, Santos-Fernandez G, Duss NN, Somoza SC, Boisson-Dernier A, Gagliardini V, Martínez-Bernardini A, Fabrice TN, Ringli C, Muschietti JP, Grossniklaus U.

    doi: 10.1126/science.aao5467.

    -       Brassinosteroid signaling directs formative cell divisions and protophloem differentiation in Arabidopsis root meristems.

    Kang YH, Breda A, Hardtke CS.

    doi: 10.1242/dev.145623.

    -       Mechanistic basis for the activation of plant membrane receptor kinases by SERK-family coreceptors.

    Hohmann U, Santiago J, Nicolet J, Olsson V, Spiga FM, Hothorn LA, Butenko MA, Hothorn M.

    Proc Natl Acad Sci U S A. 2018 Mar 12. pii: 201714972.

    doi: 10.1073/pnas.1714972115.

    8. Major Funding Sources

    Please provide name and link to the funding sources that are responsible for supporting the Arabidopsis research in your country.

    1. Swiss National Science Foundation (SNSF) http://www.snf.ch/en/Pages/default.aspx 2. European Research Council (ERC), https://erc.europa.eu/

    3. SystemsX.ch, http://www.systemsx.ch/

    4. Syngenta (Plant Science Center - Syngenta Fellowship), https://www.plantsciences.uzh.ch/en/research/fellowships/ syngenta.html

    5. Research and Innovation Staff Exchange (RISE) of European Commission http://ec.europa.eu/research/mariecurieactions/about/ research-innovation-staff-exchange_en

    6. State Secretariat for Education, Research, and Innovation (SERI), https://www.sbfi.admin.ch/sbfi/en/home. html

    7. University Research Priority Program of Evolution in Action: From Genomes to Ecosystems (directors: Beat Keller, Ueli Grossniklaus, University of Zurich) http://www.evolution.uzh.ch/en.html

    8. Japan Science and Technology Agency (JST), Core Research for Evolutional Science and Technology (CREST), https://www.jst.go.jp/kisoken/crest/en/

  • United Kingdom Open or Close
    Geraint Parry (This email address is being protected from spambots. You need JavaScript enabled to view it.), Cardiff University, UK

    1. Use of Arabidopsis

    The United Kingdom has approximately 45 academic departments and research institutes that are actively conducting Arabidopsis research. The BBSRC is the major funder of Arabidopsis research, which includes institutional support for the John Innes Centre and Rothamsted ResearcH.

    2. Open Resources for Arabidopsis Researchers

    Please provide a list of experimental resources based in your country that are accessible for use both by Arabidopsis researchers in your country and by the global community.

    - The Eurasian Arabidopsis Stock Centre (uNASC) is based at the University of Nottingham. http://arabidopsis.info/

    3. New Software Tools

    Please provide a list of software tools recently developed in your country that are open access and available to the global community of Arabidopsis researchers.

    - The Centre for Integrative Biology based at the University of Nottingham has developed a range of open source software, hardware and other resources.

    https://www.cpib.ac.uk/tools-resources/

    - The Bassal Lab at the University of Birmingham have developed tools for analysis of gene expression and interaction networks in Arabidopsis seeds.

    http://www.georgebassellab.com/online-tools/

    In addition they have developed 3DCellAtlas that describes a computational approach to perform digital single cell analyses in 3D plant organs.

    http://www.georgebassellab.com/3d-cell-atlas/

    - The Millar lab at the University of Edinburgh has developed BioDare2 as a repository for circadian, biological data, providing a platform for data sharing and period analysis.

    https://biodare2.ed.ac.uk/welcome

    - Research at the John Innes Centre have developed Leaf-GP (Growth Phenotypes) an open and automated software application for measuring growth phenotypes for arabidopsis and wheat

    https://github.com/Crop-Phenomics-Group/Leaf-GP/releases

    - The Tsaftaris lab at he University of Edinburgh have developed Phenotiki is an affordable, easy-to-use, maintain and deploy image-based plant phenotyping platform.

    http://phenotiki.com/

    - Plant Methods published in the UK have collated a set of resources entitled ‘Plants in Computer Vision’: https://www.biomedcentral.com/collections/PCV

    - The Cell Architect program has been developed by researchers at the John Innes Centre and is designed to recognise microtubule (MT) and measure MT pattern changes induced by different chemicals https://github.com/TeamMacLean/CellArchitect

    4. Conferences, Workshops and Outreach events

    Please provide a list of conferences, workshops and outreach events that your country hosted in the past year or will host in coming years.

    In 2017 and 2018 GARNet have and will organise conferences and workshops attended by Arabidopsis researchers:

    - CyVerseUK Workshop: Bioinformatic Tools for Biologists, University of York March 21-22nd 2017

    https://www.eventbrite.co.uk/e/cyverseuk-workshop-tickets-29982258743#

    - SEB-GARNet meeting on From Proteome to Phenotype: role of post-translational modifications: University of Edinburgh December 11th-13th 2017

    http://www.sebiology.org/events/event/from-proteome-to-phenotype

    - GARNet Gene Editing Workshop: University of Bristol March 26-27th 2018

    http://garnet-ge-workshop.weebly.com/

    - GARNet2018: a Plant Science Showcase: September 18-19th 2018

    http://www.garnet2018.weebly.com/

    - New Phytologist Next Generation Scientists: Norwich 24th-26th 2017

    https://www.newphytologist.org/news/view/124

    5. Selected Publications

    Please highlight up to 10 publications from the past year led by a researchers from your country that reflect the breadth of outputs. Please consider including a mix of fundamental and applied research.

    The majority set of UK publications that feature Arabidopsis are documented on the GARNet blog: http://blog.garnetcommunity.org.uk/arabidopsis-research-roundups/

    Di Mambro R, De Ruvo M,,, Pacifici E, Salvi E, Sozzani R, Benfey PN,, Busch W, Novak O, Ljung K, Di Paola L, Marée AFM, Costantino P, Grieneisen VA, Sabatini S (2017) Auxin minimum triggers the developmental switch from cell division to cell differentiation in the Arabidopsis root. Proc Natl Acad Sci U S A 10.1073/pnas.1705833114

    Elena López-Calcagno P, Omar Abuzaid A, Lawson T, Anne Raines C (2017) Arabidopsis CP12 mutants have reduced levels of phosphoribulokinase and impaired function of the Calvin-Benson cycle. J Exp Bot http:/​/​dx.​doi.​org/10.1093/jxb/erx084

    Harumain ZA, Parker HL, Muñoz García A, Austin MJ, McElroy CR, Hunt AJ, Clark JH, Meech JA, Anderson CW, Ciacci L, Graedel TE, Bruce NC, Rylott EL (2017) Towards financially viable phytoextraction and production of plant-based palladium catalysts. Environ Sci Technol. http://dx.doi.org/ 10.1021/acs.est.6b04821

    Jackson MD, Xu H, Duran-Nebreda S, Stamm P, Bassel GW (2017) Topological analysis of multicellular complexity in the plant hypocotyl. Elife http:/​/​dx.​doi.​org/10.7554/eLife.26023

    O’Connor DL, Elton S, Ticchiarelli F, Hsia MM, Vogel JP, Leyser O (2017) Cross-species functional diversity within the PIN auxin efflux protein family. Elife. doi: 10.7554/eLife.31804

    Pass DA, Sornay E, Marchbank A, Crawford MR, Paszkiewicz K, Kent NA, Murray JAH (2017) Genome-wide chromatin mapping with size resolution reveals a dynamic sub-nucleosomal landscape in Arabidopsis. PLoS Genet. doi: 10.1371/journal.pgen.1006988

    Rizza A, Walia A, Lanquar V, Frommer WB, Jones AM (2017) In vivo gibberellin gradients visualized in rapidly elongating tissues. Nat Plants. doi: 10.1038/s41477-017-0021-9

    Zhang H, Gannon L, Hassall KL, Deery MJ, Gibbs DJ, Holdsworth MJ, van der Hoorn RAL, Lilley KS, Theodoulou FL (2017) N-terminomics reveals control of Arabidopsis seed storage proteins and proteases by the Arg/N-end rule pathway. New Phytol. doi: 10.1111/nph.14909

    6. Major Funding Sources

    Please provide name and link to the funding sources that are responsible for supporting the Arabidopsis research in your country.

    Biotechnology and Biological Sciences Research Council (BBSRC) http://www.bbsrc.ac.uk/

    The Gatsby Charitable Foundation http://www.gatsby.org.uk/

    European Research Council http://ec.europa.eu/research/era/index_en.htm

    Natural Environment Research Council http://www.nerc.ac.uk

    The Gates Foundation http://www.gatesfoundation.org/

     

  • United States Open or Close
    2. Prepared by

    Joanna Friesner, NAASC Coordinator (This email address is being protected from spambots. You need JavaScript enabled to view it.), University of California, Davis, with input from the North American Arabidopsis Steering Committee (NAASC): Doris Wagner, NAASC President (University of Pennsylvania); Rick Vierstra (Washington University in St. Louis); Sarah Assmann (Penn State University); Erich Grotewold (Michigan State University); Elizabeth Haswell (Washington University in St. Louis); Jose Dinneny, NAASC Treasurer (Stanford University), Roger Innes (Indiana University), Peter McCourt (University of Toronto- Canada); Sean Cutler (University of California, Riverside); and Jennifer Nemhauser (University of Washington, Seattle);

    3. Use of Arabidopsis

    It's not straightforward to get accurate numbers of Arabidopsis users in the United States. However, according to two major resources, The Arabidopsis Information Resource (TAIR) and the Arabidopsis Biological Resource Center (ABRC), estimates are that there are approximately 4,700 labs that use Arabidopsis resources registered in the US, and 12,500 people.

    4. Open Resources for Arabidopsis Researchers

    Please provide a list of experimental resources based in your country that are accessible for use both by Arabidopsis researchers in your country and by the global community.

    There are a large number of US institutions, companies, and facilities that conduct Arabidopsis research and it would be impossible to list them all. Therefore, we list the primary resource entity, ABRC (https://abrc.osu.edu/seed-handling), the US stock center which, in partnership with the European Stock Centre (NASC, UK) and RIKEN BioResourceCenter (Japan), provide valuable Arabidopsis seed and other resources to the global community. The Arabidopsis Biological Resource Center collects, preserves, reproduces and distributes diverse seed and other stocks of Arabidopsis thaliana and related species. Resources are donated by researchers from around the world. ABRC has been providing Arabidopsis and related species seed and other resources for research and education since 1991. At present ABRC has about 4,000 characterized mutant and 2,000 transgenic lines. Overall the seed collection is approaching half a million (~490,000) counting all the characterized and uncharacterized T-DNA lines, as well as the natural accessions. More than 100,000 samples are shipped annually to researchers and educators from 60 countries. ABRC holdings include: Arabidopsis seed stocks and clones, Arabidopsis cell lines and protein chips, seed and clone resources from related species, Cloning vectors and host strain, Education kits.

    5. New Software Tools

    Please provide a list of software tools recently developed in your country that are open access and available to the global community of Arabidopsis researchers.

    1. A new discrete dynamic model of ABA-induced stomatal closure predicts key feedback loops. Albert R, Acharya BR, Jeon BW, Zañudo JGT, Zhu M, Osman K, Assmann SM. PLoS Biol. 2017 Sep 22;15(9):e2003451. http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2003451  
    2. GRACE (Gene Regulatory network inference ACcuracy Enhancement); Enhancing gene regulatory network inference through data integration with markov random fields. Michael Banfa,1 and Seung Y. Rhee. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5286517/
    3. GENIST is an algorithm to infer gene regulatory networks from spatial and temporal datasets. https://github.com/madeluis/GENIST
    4. eGenPub, a text mining system for extending computationally mapped bibliography for UniProt Knowledgebase by capturing centrality. https://academic.oup.com/database/article/doi/10.1093/database/bax081/4627699
    5. Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
    6. UpSetR: an R package for the visualization of intersecting sets and their properties. https://academic.oup.com/bioinformatics/article/33/18/2938/3884387
    7. Workflow and web application for annotating NCBI BioProject transcriptome data. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5467576/
    8. http://araport.org/ The Arabidopsis Information Portal, started through work by the International Arabidopsis Informatics Consortium in 2012. The new portal has been online since April 2014. While not a new tool, this is a key contribution by the US Arabidopsis community.
    9. https://www.arabidopsis.org: TAIR have successfully moved to a subscription-based model, and their non-profit organization, Phoenix Bioinformatics, continues TAIR’s annotation work. Open access is available after one year, and TAIR continues to provide free access for students using TAIR in their coursework upon request from the course organizer. While not a new tool, this is a key contribution by the US Arabidopsis community.

    6. Conferences, Workshops and Outreach events

    Please provide a list of conferences, workshops and outreach events that your country hosted in the past year or will host in coming years.

    The North American Arabidopsis Steering Committee (NAASC) hosted the 28th International Conference on Arabidopsis Research (ICAR): "Arabidopsis Research in 2017 and Beyond", June 2017 in St. Louis, Missouri, USA. 470 attendees from 20 countries participated in 29 sessions including 4 Keynote lectures, 18 plenary and concurrent sessions, and 7 workshops. The program focused especially on female and early career speakers; of 46 invited speakers, 46% were female (including 3 of 4 Keynotes), and 41% were ‘early-career’ speakers at the level of assistant professor or earlier. Of 10 concurrent session chairs, 5 were female and 6 were early-career invited speakers, providing exposure and a diverse program since chairs selected the 50 talks from submitted abstracts. Platform sessions featured nearly 100 oral presentations and there were nearly 350 poster presentations. NAASC encouraged session chairs to prioritize early-career researchers and diversity in submitter gender and location. NAASC developed for ICAR 2017 new career-building and enhancing activities that proved to be successful. Three pre-ICAR skills-based workshops were developed in collaboration with the Danforth Plant Sciences Center and funded by an award from the US National Science Foundation (NSF). Two additional early career-focused workshops were held during ICAR 2017. The skills-based workshops included (1) "Data Carpentry": an example-driven workshop on basic concepts, skills and tools for working more effectively with data via short tutorials alternate with hands-on practical exercises. (2) "ATAC-seq Hands-on Workshop on mapping chromatin accessibility and TF footprints": a wet-lab and computational introduction to the ATAC-seq process. (3) "Hackathon for High-throughput Phenotyping": an activity that expanded on the introduction to genomics data and data management and analysis for genomics research. The career-exploration panel workshops were, firstly, "Careers Beyond the Academy" including Working in Science Communication; Career Development for Success in Industry and Elsewhere; Working at USDA and Other Government Jobs; Working at a PUI (Primarily Undergraduate Institution); Advocating for Plant Science and Careers in Science Policy; Careers for Scientists in Intellectual Property (IP) Law; and Industry Job Search in US and France; and secondly, "Careers in Industry" featuring panelists from NewLeaf Symbiotics, BioGenerator, CONVIRON, and Monsanto. In the workshops, four of seven, and three of four panelists, respectively, were female. Several community-organized workshops at ICAR 2017 addressed impacts on scientists including "Communicating Your Science to Peers and Beyond", and "Overcoming the Imposter Phenomenon in Academic Science – an Interactive Workshop to Combat Imposter Thoughts." As a bit of extra fun, science and networking, the ICAR 2017 party was hosted by the Danforth Center which generously opened its doors with an open house, including site tours, for conference attendees. NAASC and Danforth staff collaborated to develop a scientific and social program that enabled science exchange in an informal setting. The activities concluded with a party featuring VO5, a live 9-piece disco band, and lots of great local food and dancing.

    Planning for ICAR 2020- US- is underway. NAASC members assembled an international External Advisory Board (EAB) for ICAR 2020 which is scheduled to return to the US after rotations in Europe and Asia. The EAB began discussions and meetings in winter 2017 to envision new approaches, sessions, and activities for the US-located ICAR to ensure the meeting stays relevant and valuable to the international Arabidopsis community. The discussion by the EAB has primarily involved considering new and exciting scientific plant biology topics, an invigorated focus on bringing in new voices from the community, and novel activities and approaches to enhance collaboration, participation, and information sharing. NAASC members are expected to announce the selected date and location for ICAR 2020 during ICAR 2018 in Finland.

    7. Selected Publications

    Please highlight up to 10 publications from the past year led by researchers from your country that reflect the breadth of outputs. Please consider including a mix of fundamental and applied research.

    The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology.

    Friesner J, Assmann SM, Bastow R, Bailey-Serres J, Beynon J, Brendel V, Buell CR, Bucksch A, Busch W, Demura T, Dinneny JR, Doherty CJ, Eveland AL, Falter-Braun P, Gehan MA, Gonzales M, Grotewold E, Gutierrez R, Kramer U, Krouk G, Ma S, Markelz RJC, Megraw M, Meyers BC, Murray JAH, Provart NJ, Rhee S, Smith R, Spalding EP, Taylor C, Teal TK, Torii KU, Town C, Vaughn M, Vierstra R, Ware D, Wilkins O, Williams C, Brady SM.

    Plant Physiol. 2017 Dec;175(4):1499-1509. doi: 10.1104/pp.17.01490.

    PMID:29208732 

    Chemical hijacking of auxin signaling with an engineered auxin-TIR1 pair.

    Uchida N, Takahashi K, Iwasaki R, Yamada R, Yoshimura M, Endo TA, Kimura S, Zhang H, Nomoto M, Tada Y, Kinoshita T, Itami K, Hagihara S, Torii KU.

    Nat Chem Biol. 2018 Mar;14(3):299-305. doi: 10.1038/nchembio.2555. Epub 2018 Jan 22.

    PMID: 29355850 

    The MBD7 complex promotes expression of methylated transgenes without significantly altering their methylation status.

    Li D, Palanca AMS, Won SY, Gao L, Feng Y, Vashisht AA, Liu L, Zhao Y, Liu X, Wu X, Li S, Le B, Kim YJ, Yang G, Li S, Liu J, Wohlschlegel JA, Guo H, Mo B, Chen X, Law JA.

    Elife. 2017 Apr 28;6. pii: e19893. doi: 10.7554/eLife.19893.

    PMID: 28452714 

    Mechanism of Dual Targeting of the Phytochrome Signaling Component HEMERA/pTAC12 to Plastids and the Nucleus.

    Nevarez PA, Qiu Y, Inoue H, Yoo CY, Benfey PN, Schnell DJ, Chen M.

    Plant Physiol. 2017 Apr;173(4):1953-1966. doi: 10.1104/pp.16.00116. Epub 2017 Feb 23.

    PMID:28232584 

    A Multipurpose Toolkit to Enable Advanced Genome Engineering in Plants.

    Čermák T, Curtin SJ, Gil-Humanes J, Čegan R, Kono TJY, Konečná E, Belanto JJ, Starker CG, Mathre JW, Greenstein RL, Voytas DF.

    Plant Cell. 2017 Jun;29(6):1196-1217. doi: 10.1105/tpc.16.00922. Epub 2017 May 18.

    PMID: 28522548

    8. Major Funding Sources

    Please provide name and link to the funding sources that are responsible for supporting the Arabidopsis research in your country.

    US Arabidopsis Research is primarily supported by funding through the Federal Government via the National Science Foundation (NSF): http://www.nsf.gov/;

    Additional support may come from these sources:

    US Department of Agriculture (USDA): http://www.usda.gov/

    US Department of Energy (DOE): http://energy.gov/

    National Institutes of Health (NIH): http://www.nih.gov/

    Private Sources:

    Howard Hughes Medical Institute HHMI)- alone and partnered with several other organizations, support a number of prominent US Arabidopsis researchers and educators:

    HHMI Faculty Scholars (1); e.g. Siobhan Brady, Jose Dinneny, Elizabeth Haswell, Jennifer Nemhauser, Elizabeth Sattely

    HHMI Investigators (2); e.g. Phil Benfey, Dominique Bergmann, Xuemei Chen, Joanne Chory, Jeff Dangl, Xinnian Dong, Joe Ecker, Mark Estelle, Sheng Yang He, Steve Jacobsen, Rob Martienssen, Elliot Meyerowitz, Keiko Torii and Ning Zheng

    HHMI Professors (1); e.g. Rick Amasino, Bonnie Bartel, and Bob Goldberg

    (1) http://www.hhmi.org/programs/biomedical-research/faculty-scholars

    (2) http://www.hhmi.org/programs/biomedical-research/investigator-program

    (3) https://www.hhmi.org/developing-scientists/hhmi-professors