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 wider Arabidopsis and plant community supports MASC by appointing individual country representatives, who are nationally and internationally well connected Arabidopsis researchers. To date 34 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 2018, International Convention Centre, Sydney 23-26th September 2018. Annual national conference that includes several symposia dedicated to plant research. This conference incorporated the annual Australian Society of Plant Biologists meeting for 2018 (www.asps.org.au).

    Upcoming Events:

    Translational Photosynthesis Conference 2019: Innovations in agriculture for food security, Brisbane Convention Centre, Queensland, 30th June 2019

    14th International Conference on Tetrapyrrole Photoreceptors in Photosynthetic Organisms, Sydney, July 21 -24 2019

    The Australian Society of Plant Scientists conference, ASPS 2019, and Grains Satellite meeting, LaTrobe University, Melbourne, 26 - 29th Nov 2019.

    Herbicide Discovery & Development 2020 (HDD2020). The University of Western Australia, Perth, Jan 15th 2020.

    The International Congress on Plant Molecular Biology (IPMB), Cairns Convention Centre, Queensland, 24th Oct 2021.

    6. Selected Publications

    Bhatia N, Åhl H, Jönsson H, Heisler MG (2019) Quantitative analysis of auxin sensing in leaf primordia argues against proposed role in regulating leaf dorsoventrality. Elife. 22;8. pii: e39298

    Eimer H, Sureshkumar S, Singh Yadav A, Kraupner-Taylor C, Bandaranayake C,Seleznev A, Thomason T, Fletcher SJ, Gordon SF, Carroll BJ, Balasubramanian S. (2018) RNA-Dependent Epigenetic Silencing Directs Transcriptional Downregulation Caused by Intronic Repeat Expansions. Cell. 23;174(5):1095-1105

    Colas des Francs-Small C, Vincis Pereira Sanglard L, Small I (2018) Targeted cleavage of nad6 mRNA induced by a modified pentatricopeptide repeat protein in plant mitochondria. Commun Biol. 11;1:166

    Ebert B, Rautengarten C, McFarlane HE, Rupasinghe T, Zeng W, Ford K, Scheller HV, Bacic A, Roessner U, Persson S, Heazlewood JL (2018) A Golgi UDP-GlcNAc transporter delivers substrates for N-linked glycans and sphingolipids. Nat Plants. 4(10):792-801

    Sánchez-Rodríguez C, Shi Y, Kesten C, Zhang D, Sancho-Andrés G, Ivakov A,Lampugnani ER, Sklodowski K, Fujimoto M, Nakano A, Bacic A, Wallace IS, Ueda T,Van Damme D, Zhou Y, Persson S (2018) The Cellulose Synthases Are Cargo of the TPLATE Adaptor Complex. Mol Plant. 5;11(2):346-349

    Crisp PA, Smith AB, Ganguly DR, Murray KD, Eichten SR, Millar AA, Pogson BJ (2018)RNA Polymerase II Read-Through Promotes Expression of Neighboring Genes inSAL1-PAP-XRN Retrograde Signaling. Plant Physiol. 178(4):1614-1630

    Kerbler SM, Taylor NL, Millar AH (2019) Cold sensitivity of mitochondrial ATP synthase restricts oxidative phosphorylation in Arabidopsis thaliana. New Phytol. 221(4):1776-1788

    Belt K, Van Aken O, Murcha M, Millar AH, Huang S (2018) An Assembly Factor Promotes Assembly of Flavinated SDH1 into the Succinate Dehydrogenase Complex. Plant Physiol. 177(4):1439-1452

    Wang L, Waters MT, Smith SM (2018) Karrikin-KAI2 signalling provides Arabidopsisseeds with tolerance to abiotic stress and inhibits germination under conditions unfavourable to seedling establishment. New Phytol. 219(2):605-618

    Chen W, Salari H, Taylor MC, Jost R, Berkowitz O, Barrow R, Qiu D, Branco R,Masle J (2018) NMT1 and NMT3 N-Methyltransferase Activity Is Critical to LipidHomeostasis, Morphogenesis, and Reproduction. Plant Physiol. 177(4):1605-1628.

    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

    Although Austria is a small European country with around 8.8 mio inhabitants Arabidopsis research is highly active at seven institutions, the University of Natural Resources & Life Science Vienna (BOKU) (www.dagz.boku.ac.at/en/), the Gregor Mendel Institute of Molecular Plant Biology (GMI) (www.gmi.oeaw.ac.at/), the Max F. Perutz Laboratories (MFPL) (https://www.mfpl.ac.at/), the Institute of Science and Technology, Austria (IST Austria) (ist.ac.at/en/), the AIT Austrian Institute of Technology (https://www.ait.ac.at/themen/improvement-of-plant-quality-vigor/), the University of Salzburg, Division of Plant Physiology (https://www.uni-salzburg.at/index.php?id=32790&L=1&MP=205208-207110), the University of Vienna (www.univie.ac.at/mosys) and the University of Graz (https://botanik.uni-graz.at/de/forschung/molecular-plant-physiology/). The 23 research groups focus on molecular genetics (including population, epi-, and developmental genetics), RNA-, chromosome-, cell-, and glyco-biology as well as stress and hormone signaling. There is a vivid collaboration activity between the research groups sharing experimental tools provided by sequencing, proteomic, genome editing, phenotyping, imaging and computational facilities (https://www.viennabiocenter.org/facilities/).

    3. New Resources and Software tools available for Arabidopsis Researchers that have been initiated or funded in 2018/ early 2019.

    Vertical microscope with Airyscan resolution

    von Wangenheim D, Hauschild R, Fendrych M, Barone V, Benková E, Friml J. (2017) Live tracking of moving samples in confocal microscopy for vertically grown roots. Elife. 6. pii: e26792. doi: 10.7554/eLife.26792.

    Root chip allowing for immediate treatments and simultaneous confocal live imaging

    Fendrych M, Akhmanova M, Merrin J, Glanc M, Hagihara S, Takahashi K, Uchida N, Torii KU, Friml J (2018) Rapid and reversible root growth inhibition by TIR1 auxin signalling. Nat Plants. 4:453-459. doi: 10.1038/s41477-018-0190-1.

    Nanopore

    Schon MA, Kellner MJ, Plotnikova A, Hofmann F, Nodine MD (2018) NanoPARE: parallel analysis of RNA 5' ends from low-input RNA. Genome Res 28:1931-42.doi: 10.1101/gr.239202

    Arabidopsis Embryo Transcriptome

    Hofmann F, Schon MA, Nodine MD (2018) The embryonic transcriptome of Arabidopsis thaliana. Plant Reprod. [epub] preprint: bioRxiv:479584.doi: 10.1007/s00497-018-00357-2

    Root Development Methods and Protocols Part of the Methods in Molecular Biology book series

    DOI https://doi.org/10.1007/978-1-4939-7747-5

    Conferences and Workshops

    21st European Network on Plant Endomembrane Research, ENPR 2018; 4.-7. September 2018 (Main organisers Yasin Dagdas and Jürgen Kleine-Vehn)

    Selected Publications

    Adamowski M, Narasimhan M, Kania U, Glanc M, De Jaeger G, Friml J (2018) A Functional Study of AUXILIN-LIKE1 and 2, Two Putative Clathrin Uncoating Factors in Arabidopsis. Plant Cell. 30:700-716.doi: 10.1105/tpc.17.00785

    Glanc M, Fendrych M, Friml J. (2018) Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division. Nat Plants 4:1082-1088 doi: 10.1038/s41477-018-0318-3

    Herrmann A, Livanos P, Lipka E, Gadeyne A, Hauser MT, Van Damme D, Müller S (2018) Dual localized kinesin-12 POK2 plays multiple roles during cell division and interacts with MAP65-3. EMBO Rep. 19: pii: e46085. doi: 10.15252/embr.201846085.

    Higo A, Kawashima T, Borg M, Zhao M, López-Vidriero I, Sakayama H, Montgomery SA, Sekimoto H, Hackenberg D, Shimamura M, Nishiyama T, Sakakibara K, Tomita Y, Togawa T, Kunimoto K, Osakabe A, Suzuki Y, Yamato KT, Ishizaki K, Nishihama R, Kohchi T, Franco-Zorrilla JM, Twell D, Berger F, Araki T. (2018) Transcription factor DUO1 generated by neo-functionalization is associated with evolution of sperm differentiation in plants. Nat Commun 9:5283.doi: 10.1038/s41467-018-07728-3

    Kania U, Nodzynski T, Lu Q, Hicks GR, Nerinckx W, Mishev K, Peurois F, Cherfils J, De Rycke RM, Grones P, Robert S, Russinova E, Friml J (2018) Endosidin 4 inhibitor targets the SEC7 domain-type ARF-GEFs and interferes with subcellular trafficking in eukaryotes. Plant Cell. 30:2553-2572. doi: 10.1105/tpc.18.00127

    Kurzbauer MT, Pradillo M, Kerzendorfer C, Sims J, Ladurner R, Oliver C, Janisiw MP, Mosiolek M, Schweizer D, Copenhaver GP, Schlögelhofer P (2018). Arabidopsis thaliana FANCD2 Promotes Meiotic Crossover Formation. Plant Cell. 30:415-428. doi: 10.1105/tpc.17.00745

    Pedrotti L, Weiste C, Nägele T, Wolf E, Lorenzin F, Dietrich K, Mair A, Weckwerth W, Teige M, Baena-González E, Dröge-Laser W (2018) Snf1-RELATED KINASE1-Controlled C/S1-bZIP Signaling Activates Alternative Mitochondrial Metabolic Pathways to Ensure Plant Survival in Extended Darkness. Plant Cell. 30:495-509. doi: 10.1105/tpc.17.00414.

    Salanenka Y, Verstraeten I, Löfke C, Tabata K, Naramoto S, Glanc M, Friml J (2018) Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane. Proc Natl Acad Sci U S A 115:3716-3721. doi: 10.1073/pnas.1721760115

    Shin YJ, Vavra U, Veit C, Strasser R (2018) The glycan-dependent ERAD machinery degrades topologically diverse misfolded proteins. Plant J. 94:246-259. doi: 10.1111/tpj.13851.

    Smakowska-Luzan E, Mott GA, Parys K, Stegmann M, Howton TC, Layeghifard M, Neuhold J, Lehner A, Kong J, Grünwald K, Weinberger N, Satbhai SB, Mayer D, Busch W, Madalinski M, Stolt-Bergner P, Provart NJ, Mukhtar MS, Zipfel C, Desveaux D, Guttman DS, Belkhadir Y (2018) An extracellular network of Arabidopsis leucine-rich repeat receptor kinases. Nature 553:342-6. doi: 10.1038/nature25184

    Wang H, Jiang D, Axelsson E, Lorković ZJ, Montgomery S, Holec S, Pieters BJGE, Al Temimi AHK, Mecinović J, Berger F (2018) LHP1 Interacts with ATRX through Plant-Specific Domains at Specific Loci Targeted by PRC2. Mol Plant.11:1038-1052. doi: 10.1016/j.molp.2018.05.004

    Wurzinger B, Nukarinen E, Nägele T, Weckwerth W, Teige M (2918) The SnRK1 Kinase as Central Mediator of Energy Signaling between Different Organelles. Plant Physiol. 176:1085-1094. doi: 10.1104/pp.17.01404.

    Major Funding Sources

    European Research Council (ERC) Advanced grant

    EPICLINES “Elucidating the causes and consequences of the global pattern of epigenetic variation in Arabidopsis thaliana” Magnus Nordborg, Gregor Mendel Institute of Molecular Plant Biology

    ETAP “Tracing Evolution of Auxin Transport and Polarity in Plants” Jiri Friml, Institute of Science and Technology Austria

    European Research Council (ERC) Starting grant

    AuxinER “Project Mechanisms of Auxin-dependent Signaling in the Endoplasmic Reticulum” to Jürgen Kleine-Vehn, University of Natural Resources and Life Sciences, Vienna

    FEAR-SAP “Project Function and Evolution of Attack and Response Strategies during Allelopathy in Plants” Claude Becker, Gregor Mendel Institute of Molecular Plant Biology

    sRNA-EMB “Small RNA regulation of the body plan and epigenome in Arabidopsis embryos” Michael Nodine, Gregor Mendel Institute of Molecular Plant Biology

    Further funding Sources

    FWF https://www.fwf.ac.at/

    OeAD (https://oead.at/en/to-austria/grants-and-scholarships/)

    Austrian Academy of Sciences (ÖAW) (www.oeaw.ac.at/stipendien-foerderungen/stipendien-preise/nachwuchsfoerderung/)

    Vienna Science and Technology Fund (WWTF) (wwtf.at/index.php?lang=EN)

    Austrian Research Promotion Agency (FFG) (www.ffg.at/en)

    Further funding sources at the European level

    ERA-CAPS http://www.eracaps.org/

    ITN-EU MEICOM https://cordis.europa.eu/project/rcn/211682/factsheet/en

    ITN-EU EPIDIVERSE https://cordis.europa.eu/project/rcn/211879/factsheet/en

    Marie Skłodowska-Curie actions (http://ec.europa.eu/research/mariecurieactions/)

    EMBO Long-Term Fellowships (www.embo.org/funding-awards/fellowships)

  • 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

    Research Facilities
    Arabidopsis Research Centers in Belgium:

    VIB-UGent Center for Plant Systems Biology, https://www.psb.ugent.be/
    University of Ghent https://www.ugent.be/en
    University of Leuven https://www.kuleuven.be/english
    University of Antwerpen https://www.uantwerpen.be/en/
    University of Hasselt http://www.uhasselt.be/en
    Universite catholique de Louvain https://uclouvain.be/fr/index.html
    University of Liege https://www.ulg.ac.be/cms/c_5000/en/home

    Arabidopsis research topics in Belgium include cell cycle regulation (D. Inzé, L. De Veylder), root and leaf growth and development (D. Inzé, T. Beeckman, M. Nowack, G. Beemster, M. Van Lijsebettens, K. Vissenberg, B. De Rybel), oxidative stress and cell death (F. Van Breusegem, M. Nowack, P. Motte, H. Asard), genome annotation and evolution (S. Maere, Y. Van de Peer, K. Vandepoele), proteomics (G. De Jaeger, 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

    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/).

    Other developed resources include:
    • Platform for semi-automated kinematic analysis of growth in Arabidopsis root tips and leaves
    • Phenotyping platforms
    • Metabolomics and Enzyme activity assays for antioxidant system.
    • Leaf 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

    TF2Network, a tool for predicting transcription factor regulators and gene regulatory networks in Arabidopsis using publicly available binding site information (https://www.ncbi.nlm.nih.gov/pubmed/29272447 )

    Curse, an online curation tool for building expression atlases and co-expression networks from public RNA-Seq data (https://www.ncbi.nlm.nih.gov/pubmed/30590391)

    Conferences and Workshops

    Regulatory Oxylipins | VIB Conference series

    https://vibconferences.be/event/regulatory-oxylipins

    International Conference on Polyploidy | VIB Conference series

    https://vibconferences.be/event/international-conference-on-polyploidy

    ABPP 2019 Target discovery and visualization using chemical probes

    https://agenda.kuleuven.be/en/content/abpp-2019-target-discovery-and-visualization-using-chemical-probes

    Selected Publications

    Bhosale R, Boudolf V, Cuevas F, Lu R, Eekhout T, Hu Z, Van Isterdael G, Lambert GM, Xu F, Nowack MK, Smith RS, Vercauteren I, De Rycke R, Storme V, Beeckman T, Larkin JC, Kremer A, Höfte H, Galbraith DW, Kumpf RP, Maere S, De Veylder L.: A Spatiotemporal DNA Endoploidy Map of the Arabidopsis Root Reveals Roles for the Endocycle in Root Development and Stress Adaptation. Plant Cell. 2018 Oct;30(10):2330-2351. doi: 10.1105/tpc.17.00983. Epub 2018 Aug 16. PMID: 30115738

    Corso M, Doccula FG, de Melo JRF, Costa A, Verbruggen N (2018) Endoplasmic reticulum-localized CCX2 is required for osmotolerance by regulating ER and cytosolic Ca2+ dynamics in Arabidopsis. Proc Natl Acad Sci U S A. 2018 Apr 10;115(15):3966-3971. doi: 10.1073/pnas.1720422115. PMID: 29581277

    Gao Z, Daneva A, Salanenka Y, Van Durme M, Huysmans M, Lin Z, De Winter F, Vanneste S, Karimi M, Van de Velde J, Vandepoele K, Van de Walle D, Dewettinck K, Lambrecht BN, Nowack MK (2018) KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. Nat Plants. 2018 Jun;4(6):365-375. doi: 10.1038/s41477-018-0160-7 PMID: 29808023

    Houbaert A, Zhang C, Tiwari M, Wang K, de Marcos Serrano A, Savatin DV, Urs MJ, Zhiponova MK, Gudesblat GE, Vanhoutte I, Eeckhout D, Boeren S, Karimi M, Betti C, Jacobs T, Fenoll C, Mena M, de Vries S, De Jaeger G, Russinova E (2018) POLAR-guided signalling complex assembly and localization drive asymmetric cell division. Nature. 2018 Nov;563(7732):574-578. doi: 10.1038/s41586-018-0714-x. PMID: 30429609

    Miyashima S, Roszak P, Sevilem I, Toyokura K, Blob B, Heo JO, Mellor N, Help-Rinta-Rahko H, Otero S, Smet W, Boekschoten M, Hooiveld G, Hashimoto K, Smetana O, Siligato R, Wallner ES, Mähönen AP, Kondo Y, Melnyk CW, Greb T, Nakajima K, Sozzani R, Bishopp A, De Rybel B, Helariutta Y (2019) Mobile PEAR transcription factors integrate positional cues to prime cambial growth. Nature. 2019 Jan;565(7740):490-494. doi: 10.1038/s41586-018-0839-y. PMID: 30626969

    Orman-Ligeza B, Morris EC, Parizot B, Lavigne T, Babé A, Ligeza A, Klein S, Sturrock C, Xuan W, Novák O, Ljung K, Fernandez MA, Rodriguez PL, Dodd IC, De Smet I, Chaumont F, Batoko H, Périlleux C, Lynch JP, Bennett MJ, Beeckman T, Draye X (2018) The Xerobranching Response Represses Lateral Root Formation When Roots Are Not in Contact with Water. Curr Biol.28(19):3165-3173.e5. doi: 10.1016/j.cub.2018.07.074. PMID: 30270188

    Oyarce P, De Meester B, Fonseca F, de Vries L, Goeminne G, Pallidis A, De Rycke R, Tsuji Y, Li Y, Van den Bosch S, Sels B, Ralph J, Vanholme R, Boerjan W (2019) Introducing curcumin biosynthesis in Arabidopsis enhances lignocellulosic biomass processing. Nat Plants. 2019 Feb;5(2):225-237. doi: 10.1038/s41477-018-0350-3. PMID: 30692678

    Van Leene J, Han C, Gadeyne A, Eeckhout D, Matthijs C, Cannoot B, De Winne N, Persiau G, Van De Slijke E, Van de Cotte B, Stes E, Van Bel M, Storme V, Impens F, Gevaert K, Vandepoele K, De Smet I, De Jaeger G (2019) Capturing the phosphorylation and protein interaction landscape of the plant TOR kinase. Nat Plants. 2019 Mar;5(3):316-327. doi: 10.1038/s41477-019-0378-z. PMID: 30833711

    Vaseva II, Qudeimat E, Potuschak T, Du Y, Genschik P, Vandenbussche F, Van Der Straeten D (2018) The plant hormone ethylene restricts Arabidopsis growth via the epidermis. Proc Natl Acad Sci U S A. 2018 Apr 24;115(17):E4130-E4139. doi: 10.1073/pnas.1717649115. PMID: 29643073

    Zhang Z, Coenen H, Ruelens P, Hazarika RR, Al Hindi T, Oguis GK, Vandeperre A, van Noort V, Geuten K (2018) Resurrected Protein Interaction Networks Reveal the Innovation Potential of Ancient Whole-Genome Duplication. Plant Cell. 2018 Nov;30(11):2741-2760. doi: 10.1105/tpc.18.00409. PMID: 30333148

    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 L. Araújo
    Departamento de Biologia Vegetal
    Universidade Federal de Viçosa
    36570-900 Viçosa, MG, Brazil
    This email address is being protected from spambots. You need JavaScript enabled to view it.

    Adriano Nunes Nesi
    Departamento de Biologia Vegetal
    Universidade Federal de Viçosa
    36570-900 Viçosa, MG, Brazil
    This email address is being protected from spambots. You need JavaScript enabled to view it.

    Use of Arabidopsis

    In Brazil the number of institutions using Arabidopsis in their research is growing each year. At the moment, at least ten different institutions are using it as a model plant.
    Although research with Arabidopsis in Brazil range from developmental and hormone biology to abiotic and biotic stress, only a relatively small number of these labs is solely dedicated to Arabidopsis research or using Arabidopsis as the main model plant.

    Hence, other species are usually employed, particularly crop species, given that dedicated grants programs are usually able to fund research projects in sugarcane, tomato, maize, rice, coffee, but virtually there is no such funding programs towards Arabidopsis.

    It is important to mention that research in Brazil is only starting to use Arabidopsis and there is a gradual increase in the usage of Arabidopis as a model plant to molecular and genetic studies due to its power as an easily manipulated model system to test crop gene functions.

    Conferences, Workshops and Outreach events

    XXII International Congress of Genetics, Foz de Iguaçu, Rio Grande do Sul, Brazil. The Congress occured from September 10 to 14, 2018 and it had the overarching theme of “Genetics for a World in Evolution”.

    47th Annual Meeting of the Brazilian Society for Biochemistry and Molecular Biology (SBBq), Joinville, Santa Catarina, Brazil, May 26th to 29th, 2018
    VI Simpósio Brasileiro de Genética Molecular de Plantas, Campos do Jordao, Sao Paulo Brazil, from April 29 to May 03, 2019.

    XVII Brazilian Congress of Plant Physiology, which will be held in Cuiabá, Mato Grosso Brazil, from June 9 to 12, 2019.

    65th Brazilian Congress of Genetics, Águas de Lindóia, SP, from September 17th  to 20th. The central theme of this event will be “Edition of Genes and Genome”

    Selected Publications

    Antunes D, Jorge NAN, Garcia de Souza Costa M, Passetti F, Caffarena ER (2019) Unraveling RNA dynamical behavior of TPP riboswitches: a comparison between Escherichia coli and Arabidopsis thaliana. Sci Rep. 12;9(1):4197. doi: 10.1038/s41598-019-40875-1.

    Calil IP, Quadros IPS, Araújo TC, Duarte CEM, Gouveia-Mageste BC, Silva JCF Brustolini OJB, Teixeira RM, Oliveira CN, Milagres RWMM, Martins GS, Chory J, Reis PAB, Machado JPB, Fontes EPB (2018) A WW domain-containing protein forms immune nuclear bodies against begomoviruses. Mol. Plant 11, 1449–1465. doi: 10.1016/j.molp.2018.09.009

    Campos WF, Dressano K, Ceciliato PHO, Guerrero-Abad JC, Silva AL,Fiori CS, Morato do Canto A, Bergonci T, Claus LAN, Silva-Filho MC, Moura DS (2018) Arabidopsis thaliana rapid alkalinization factor 1-mediated root growth inhibition is dependent on calmodulin-like protein 38. J Biol Chem. 293(6):2159-2171. doi: 10.1074/jbc.M117.808881.

    Cavalcanti JHF, Kirma M, Barros JAS, Quinhones CGS, Pereira-Lima ÍA, Obata T, Nunes-Nesi A, Galili G, Fernie AR, Avin-Wittenberg T, Araújo WL (2018)  An L,L-diaminopimelate aminotransferase mutation leads to metabolic shifts and growth inhibition in Arabidopsis. J Exp Bot. 69(22):5489-5506. doi: 10.1093/jxb/ery325.

    da Fonseca-Pereira P, Daloso DM, Gago J, de Oliveira Silva FM, Condori-Apfata JA, Florez-Sarasa I, Tohge T, Reichheld JP, Nunes-Nesi A, Fernie AR, Araújo WL (2019) The Mitochondrial Thioredoxin System Contributes to the Metabolic Responses Under Drought Episodes in Arabidopsis. Plant Cell Physiol. 60(1):213-229. doi: 10.1093/pcp/pcy194.

    Lima-Melo Y, Gollan PJ, Tikkanen M, Silveira JAG, Aro EM (2019) Consequences of photosystem-I damage and repair on photosynthesis and carbon use in Arabidopsis thaliana. Plant J. 97(6):1061-1072. doi: 10.1111/tpj.14177.

    Lopes KL, Rodrigues RAO, Silva MC, Braga WGS, Silva-Filho MC (2019) The Zinc-Finger Thylakoid-Membrane Protein FIP Is Involved With Abiotic Stress Response in Arabidopsis thaliana. Front Plant Sci. 18;9:504. doi: 10.3389/fpls.2018.00504.

    Martí Ruiz MC, Hubbard KE, Gardner MJ, Aubry S, Hotta CT, Mohd-Noh NI, Lan H, Robertson FC, Hearn TJ, Jung HJ, Tsai Y-C, Dodd AN, Hannah M, Carré IA, Braam J and Webb AAR (2018) Circadian oscillations of cytosolic free calcium regulate the Arabidopsis circadian clock. Nature Plants 4(9):690-698. doi: 10.1038/s41477-018-0224-8.

    Pereira WEL, Ferreira CB, Caserta R, Melotto M, de Souza AA (2019) Xylella fastidiosa subsp. pauca and fastidiosa Colonize Arabidopsis Systemically and Induce Anthocyanin Accumulation in Infected Leaves. Phytopathology.109(2):225-232. doi: 10.1094/PHYTO-05-18-0155-FI.

    Silva, G. F., Silva, E. M., Correa, J. P., Vicente, M. H., Jiang, N. , Notini, M. M., Junior, A. C., De Jesus, F. A., Castilho, P. , Carrera, E. , López‐Díaz, I. , Grotewold, E. , Peres, L. E. and Nogueira, F. T. (2019), Tomato floral induction and flower development are orchestrated by the interplay between gibberellin and two unrelated microRNA‐controlled modules. New Phytol, 221: 1328-1344. doi:10.1111/nph.15492

    Thiers KLL, da Silva JHM, Sartori GR, Dos Santos CP, Saraiva KDDC, Roque ALM, Arnholdt-Schmitt B, Costa JH (2019) Polymorphisms in plastoquinol oxidase (PTOX) from Arabidopsis accessions indicate SNP-induced structural variants associated with altitude and rainfall. J Bioenerg Biomembr. 51(2):151-164. doi: 10.1007/s10863-018-9784-6

    van Es SW, Silveira SR, Rocha DI, Bimbo A, Martinelli AP, Dornelas MC, Angenent GC, Immink RGH (2018) Novel functions of the Arabidopsis transcription factor TCP5 in petal development and ethylene biosynthesis. Plant J. 94(5):867-879. doi: 10.1111/tpj.13904.

    Major Funding Sources

    • National Council for Scientific and Technological Devel- opment (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)

    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.

  • 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

    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

    GENIUS is a user-friendly web server that uses a novel machine learning algorithm to infer functional gene networks focused on specific genes and experimental conditions that are relevant to biological functions of interest. These functions may have different levels of complexity, from specific biological processes to complex traits that involve several interacting processes. GENIUS also enriches the network with new genes related to the biological function of interest, with accuracies comparable to highly discriminative Support Vector Machine methods.
    Availability and Implementation: GENIUS currently supports eight model organisms and is freely available for public use at http://networks.bio.puc.cl/genius.
    Contact: This email address is being protected from spambots. You need JavaScript enabled to view it.

    GENIUS: web server to predict local gene networks and key genes for biological functions.
    Puelma T, Araus V, Canales J, Vidal EA, Cabello JM, Soto A, Gutiérrez RA. Bioinformatics. 2017 Mar 1;33(5):760-761. doi: 10.1093/bioinformatics/btw702.

    Contreras-López O, Moyano TC, Soto DC, Gutiérrez RA.
    Step-by-Step Construction of Gene Co-expression Networks from High-Throughput Arabidopsis RNA Sequencing Data. Methods Mol Biol. 2018;1761:275-301. doi: 10.1007/978-1-4939-7747-5_21.

    Contreras-López O, Moyano TC, Soto DC, Gutiérrez RA (2018)

    Step-by-Step Construction of Gene Co-expression Networks from High-Throughput Arabidopsis RNA Sequencing Data. Methods Mol Biol.  1761:275-301. doi: 10.1007/978-1-4939-7747-5_21.

    The authors provide step-by-step instructions using published RNA-seq experimental data obtained from a public database. This guide includes basic instructions for the operation of widely used open source platforms such as Bio-Linux, R, and Cytoscape. Even though the data we used in this example was obtained from Arabidopsis thaliana, the workflow developed in this guide can be easily adapted to work with RNA-seq data from any organism.

    Conferences and Workshops

    January 9th - 18th, 2018

    COURSE: “GENETICAL IMPROVEMENT IN PSEUDOCEREALS AND THE SOCIO-CULTURAL IMPLICANCES.”

    This course was held at Universidad de Chile, Santiago - Chile.

    The Ph.D. program “Ciencias Silvoagropecuarias y Veterinarias” offered the course entitled “Genetical improvement in Pseudocereals and the socio-cultural implications” to students.

    Organizer: Escuela de Postgrado, Facultad de Ciencias Agronomicas, Universidad de Chile.

    July 23th - 24th, 2018

    2ND SCIENTIFIC MEETING ON VEGETAL BIOLOGY AND BIOTECHNOLOGY

    The meeting was held in Salón Bicentenario de la U. de Talca, Campus Lircay, Talca – Chile.

    The meeting was organized including three thematical areas: Biotic and abiotic stress, phytogenetics resources, and molecular and functional ecology.

    Organizer: Ph.D. program on Sciences, mention plant genetics on Instituto de Ciencias Biológicas of Universidad de Talca – Chile.

    August 21th, 2018.

    SEMINAR WAYNE PARROTT. PLANT BREEDING AND CRISPR

    Seminar presented by Wayne Parrot Ph.D., an international expert on the research of new techniques of genetical improvement of agronomical species from the University of Georgia.

    Organizer: American Academy of Science and Technology, UCDavis Chile, Universidad Andrés Bello and Universidad de Talca.

    October 2nd – 3rd, 2018

    WORKSHOP ON PLANT CELL WALL

    This workshop was held at Plant Biotechnology Center at Universidad Andres Bello, Santiago – Chile.

    Organizers: Plant Biotechnology Center, Universidad Andrés Bello and Chilean Society of Plant Biologists.

    Guests:

    Marie-Christine Ralet, INRA, PVPP, Nantes

    Jerome Pelloux, Universite de Picardie, BIOPI

    Susana Sáez-Aguayo, UNAB       

    María Alejandra Moya, Universidad de Talca

    Carlos Gaete, Universidad de Talca

    Reinaldo Campos, UNAB

    Jaime Eyzaguirre, UNAB

    Raúl Herrera, Universidad de Talca

    Francisca Blanco, UNAB

    November 29th, 2018

    WORKSHOP “APPLIED PLANT BIOLOGY III”

    This workshop was held at Auditorio Instituto de Ciencias Biológicas, Talca – Chile.

    Organized by The Functional Genomics, Biochemistry & plant physiology group, ICB – Universidad de Talca.

    December 3rd – 6th, 2018

    XIII CHILEAN PLANT BIOLOGY MEETING

    The last meeting was held at Enjoy Hotel in Puerto Varas – Chile. It included several symposiums for instance Plant Biotic Interactions, Natural Variation & Plant Breeding, Ecophysiology and Plant-Water Relationship, Iron Homeostasis and Plant Nutrition, Plant Biotechnology for Agriculture Development, Postharvest. Nearly 250 abstracts were submitted, including works from national and international research centers, presented by undergrad and graduated students, young scientist, and faculty from the major plant research centers in the country.

    Organizer: Chilean Society of Plant Biologists

    Guests:

    Paul Dupree (University of Cambridge, United Kingdom)

    Santiago Elena (CSIC Valencia, Spain)

    Li Li (Cornell University, USA)

    Ross Atkinson (PFR, New Zealand)

    Jorge Paiva (Portugal, Poland)

    François Chaumont (LIBST, Belgium)

    Claudio Pastenes (Universidad de Chile)

    Guillermo Toro (CEAF)

    Italo Cuneo (PUCV)

    Romina Pedreschi (PUCV)

    Raúl Herrera (Universidad de Talca)

    Miguel Angel Sánchez (ChileBio)

    January 14th - 20th, 2019

    INTERNATIONAL GRADUATE COURSE ON ECOPHYSIOLOGY OF THE RHIZOSPHERE

    This workshop was held at Parque Katalapi, Región de Los Lagos, Chile

    Main topics of the course: Soil properties, Plant nutrition, Rhizosphere components, Mycorrhizae diversity, Nitrogen fixation, Salt tolerance, Cluster roots functioning, Rhizodeposition, organic matter and soil microorganisms, Plant growth promoting rhizobacteria (PGPR), Endophyte, Phytoremediation, Molecular plant microbe-interaction.

    Organizers: Luisa Bascuñán, Universidad de Concepción; Alex Valentine, Stellenboch University; Alejandra Zúñiga Feest, Universidad Austral de Chile.

    Guests:

    Ricardo Aroca (CSIC),

    Eduardo Blumwald (U. California-Davis),

    Hans Lambers (U. Western Australia),

    Bruce Osborn (U. College Dublin),

    Alex Valentine (U. Stellenboch),

    Teodoro de la Coba (CEAZA),

    Julieta Orlando (UChile),

    Nestor Fernandez del Saz (UdeC).

    January 9th, 2019

    SEMINAR: ORANGE ON TOP: IS THERE MUTUAL EXCLUSION BETWEEN ANTHOCYANIN AND CAROTENOIDS BIOSYNTHESIS IN PETUNIA FLOWERS?

    This seminar was held at Facultad de Ciencias of Universidad de Chile (Santiago – Chile)

    Organizers: Universidad de Chile – Santiago, Chile.

    Guest:

    Dr. Julian Verdonk, Wageningen University. The Netherlands

    Selected Publications

    Arraño-Salinas P, Domínguez-Figueroa J, Herrera-Vásquez A, Zavala D, Medina J, Vicente-Carbajosa J, Meneses C, Canessa P, Moreno AA, Blanco-Herrera F (2018) WRKY7, -11 and -17 transcription factors are modulators of the bZIP28 branch of the unfolded protein response during PAMP-triggered immunity in Arabidopsis thaliana. Plant Sci. 277:242-250. doi: 10.1016/j.plantsci.2018.09.019.

    Duran C, Arce-Johnson P, Aquea F (2018) Methylboronic acid fertilization alleviates boron deficiency symptoms in Arabidopsis thaliana. Planta. 248(1):221-229. doi: 10.1007/s00425-018-2903-0.

    Fredes I, Moreno S, Díaz FP, Gutiérrez RA (2018) Nitrate signaling and the control of Arabidopsis growth and development. Curr Opin Plant Biol.47:112-118. doi: 10.1016/j.pbi.2018.10.004. Review.

    Gras DE, Vidal EA, Undurraga SF, Riveras E, Moreno S, Dominguez-Figueroa J, Alabadi D, Blázquez MA, Medina J, Gutiérrez RA (2018) SMZ/SNZ and gibberellin signaling are required for nitrate-elicited delay of flowering time in Arabidopsis thaliana. J Exp Bot.  23;69(3):619-631. doi: 10.1093/jxb/erx423.

    Henríquez-Valencia C, Arenas-M A, Medina J, Canales J (2018) Integrative Transcriptomic Analysis Uncovers Novel Gene Modules That Underlie the Sulfate Response in Arabidopsis thaliana. Front Plant Sci. 2018 Apr 10;9:470. doi: 10.3389/fpls.2018.00470.

    Ibeas MA, Grant-Grant S, Coronas MF, Vargas-Pérez JI, Navarro N, Abreu I, Castillo-Michel H, Avalos-Cembrano N, Paez Valencia J, Perez F, González-Guerrero M, Roschzttardtz H (2019) The Diverse Iron Distribution in Eudicotyledoneae Seeds: From Arabidopsis to Quinoa. Front Plant Sci. 2019 Jan 15;9:1985. doi: 10.3389/fpls.2018.01985.

    Salinas-Grenet H, Herrera-Vásquez A, Parra S, Cortez A, Gutiérrez L, Pollmann S, León G, Blanco-Herrera F (2018) Modulation of Auxin Levels in Pollen Grains Affects Stamen Development and Anther Dehiscence in Arabidopsis. Int J Mol Sci. 19(9). pii: E2480. doi: 10.3390/ijms19092480.

    Rodriguez-Furlán C, Rubilar-Hernández C, Norambuena L (2018) Chemical Genomics Translatability from Unicellular to Multicellular Models.
    Methods Mol Biol. 1795:189-201. doi: 10.1007/978-1-4939-7874-8_16.

    Romero-Romero JL, Inostroza-Blancheteau C, Orellana D, Aquea F, Reyes-Díaz M, Gil PM, Matte JP, Arce-Johnson P (2018) Stomata regulation by tissue-specific expression of the Citrus sinensis MYB61 transcription factor improves water-use efficiency in Arabidopsis. Plant Physiol Biochem. 130:54-60. doi: 10.1016/j.plaphy.2018.06.034.

    Zúñiga A, Fuente F, Federici F, Lionne C, Bônnet J, de Lorenzo V, González B (2018) An Engineered Device for Indoleacetic Acid Production under Quorum Sensing Signals Enables Cupriavidus pinatubonensis JMP134 To Stimulate Plant Growth. ACS Synth Biol. 15;7(6):1519-1527. doi: 10.1021/acssynbio.8b00002.

    Major Funding Sources

    FONDECYT- Fondo Nacional de Desarrollo Científico y Tecnológico (http://www.conicyt.cl/fondecyt/)

    FONDAP- Fondo de Financiamiento de Centros de Investigación en Áreas Prioritarias

    (http://www.conicyt.cl/fondap/)

    PIA- Programa de Investigación Asociativa

    https://www.conicyt.cl/pia/sobre-pia/lineas-accion/centros-cientificos-y-tecnologicos-de-excelencia-programa-de-financiamiento-basal/

    (http://www.conicyt.cl/pia/)

    Iniciativa Científica Milenio

    (http://www.iniciativamilenio.cl/)

    FONDEF (Fondo de Fomento al Desarrollo Científico y Tecnológico)

    (http://www.conicyt.cl/fondef/)

    CORFO- Corporación de Fomento de la Producción

    (https://www.corfo.cl/sites/cpp/home)

  • China Open or Close

    2. Prepared by (Name, Email, Institution)

    Yuling Jiao, This email address is being protected from spambots. You need JavaScript enabled to view it., Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

    3. New Resources and Software tools available for Arabidopsis Researchers that have been initiated or funded in 2018/ early 2019.

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

    - AHD2.0: Arabidopsis hormone database 2.0

    http://ahd.cbi.pku.edu.cn/

    - PlantGSEA: a gene set enrichment analysis toolkit for

    plant community

    http://structuralbiology.cau.edu.cn/PlantGSEA/

    - PlantTFDB: Plant transcription factor database

    http://planttfdb.cbi.pku.edu.cn/link.php

    - PsRobot: Plant small RNA analysis toolbox

    http://omicslab.genetics.ac.cn/psRobot/

    - Shoot cell type-specific expression ebrowser

    http://jiaolab.genetics.ac.cn/shootapex.html

    4. Conferences, Workshops and Outreach events

    Please provide a list of conferences, workshops and outreach events that your country hosted in 2018 or plan to host over the coming year(s).

    Major conferences held in 2018

    - 2nd International Conference on Plant Meristem Biology (Meristem 2018), June 9-10, 2018, Hefei, Anhui (www.meristem2018.com)

    - 3rd Molecular Plant International Symposium: Plant-Environment Interactions, June 12-15, 2018, Xi’an, Shaanxi (http://www.mplant.org/2018symposium/)

    - Agricultural Bioscience International Conference 2018 (ABIC 2018), September 15-18, 2018, Weifang, Shandong

    - 2018 National Congress of Plant Biology, October 18-22, 2018 Tai’an, Shandong (http://www.ncpb.net/2018/)

    Highlights on upcoming international events

    - 30th International Conference on Arabidopsis Research (ICAR2019), June 16-21, 2019, Wuhan, Hubei

    - International Symposium on Plant Receptor Kinases and Cell Signaling, June 21-23, 2019, Beijing

    - 21st International Conference on Nitrogen Fixation (ICNF 2019), October 10-15, 2019 Wuhan, Hubei

    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.

    Ding Y, Jia Y, Shi Y, Zhang X, Song C, Gong Z, Yang S. (2018) OST1-mediated BTF3L phosphorylation positively regulates CBFs during plant cold responses. EMBO J. 37(8): e98228.

    Liang T, Mei S, Shi C, Yang Y, Peng Y, Ma L, Wang F, Li X, Huang X, Yin Y, Liu H. (2018) UVR8 interacts with BES1 and BIM1 to regulate transcription and photomorphogenesis in Arabidopsis. Dev. Cell 44(4): 512-523.

    Peng Y, Chen L, Li S, Zhang Y, Xu R, Liu Z, Liu W, Kong J, Huang X, Wang Y, Cheng B, Zheng L, Li Y. (2018) BRI1 and BAK1 interact with G proteins and regulate sugar-responsive growth and development in Arabidopsis. Nat. Commun. 9(1):1522.

    Shi B, Guo X, Wang Y, Xiong Y, Wang J, Hayashi KI, Lei J, Zhang L, Jiao Y. (2018) Feedback from lateral organs controls shoot apical meristem growth by modulating auxin transport. Dev Cell 44(2): 204-216.

    Wang G, Wang C, Liu W, Ma Y, Dong L, Tian J, Yu Y, Kong Z. (2018) Augmin antagonizes katanin at microtubule crossovers to control the dynamic organization of plant cortical arrays. Curr. Biol. 28(8): 1311-1317.

    Wang J, Grubb LE, Wang J, Liang X, Li L, Gao C, Ma M, Feng F, Li M, Li L, Zhang X, Yu F, Xie Q, Chen S, Zipfel C, Monaghan J, Zhou J-M. (2018) A regulatory module controlling homeostasis of a plant immune kinase. Mol. Cell 69(3): 493-504.

    Xing L, Liu Y, Xu S, Xiao J, Wang B, Deng H, Lu Z, Xu Y, Chong K. (2018) Arabidopsis O-GlcNAc transferase SEC activates histone methyltransferase ATX1 to regulate flowering. EMBO J. 37(19): e98115

    Yang L, Wang H-N, Hou X-H, Zou Y-P, Han T-S, Niu X-M, Zhang J, Zhao Z, Todesco M, Balasubramanian S, Guo Y-L. (2018) Parallel evolution of common allelic variants confers flowering diversity in Capsella rubella. Plant Cell 30(6): 1322-1336.

    Yang Y, Liang T, Zhang L, Shao K, Gu X, Shang R, Shi N, Li X, Zhang P, Liu H. (2018) UVR8 interacts with WRKY36 to regulate HY5 transcription and hypocotyl elongation in Arabidopsis. Nat. Plants 4(2): 98-107.

    Zhan N, Wang C, Chen L, Yang H, Feng J, Gong X, Ren B, Wu R, Mu J, Li Y, Liu Z, Zhou Y, Peng J, Wang K, Huang X, Xiao S, Zuo J. (2018) S-nitrosylation targets GSNO reductase for selective autophagy during hypoxia responses in plants. Mol. Cell 71(1):142-154.

  • 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

     

    New Resources and Software tools available for Arabidopsis Researchers that have been initiated or funded in 2018 or early 2019

    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.


    Conferences, Workshops and Outreach events

    - 43rd FEBS Congress 7.-12. July, 2018 Prague, Czech Republic
    - ACPD2018  - “Auxins and Cytokinins in Plant Development”, July 1–5, 2018, Prague
    - Plant Biology CS 2019, University of South Bohemia and Biology Centre CAS, Ceske Budejovice, Czech Republic 25th-30th 2019  www.plantbiologycs.cz

    Selected Publications

    >Aleš Pencík, Rubén Casanova-Sáez, Veronika Pilarová, Asta Žukauskaite, Rui Pinto, José Luis Micol, Karin Ljung, Ondrej Novák (2018) Ultra-rapid auxin metabolite profiling for high-throughput mutant screening in Arabidopsis, Journal of Experimental Botany,69: 2569–2579, https://doi.org/10.1093/jxb/ery084
    >Ferretti, U., Ciura, J. , Ksas, B. , Rác, M. , Sedlárová, M. , Kruk, J. , Havaux, M. and Pospíšil, P. (2018), Chemical quenching of singlet oxygen by plastoquinols and their oxidation products in Arabidopsis. Plant J, 95: 848-861. doi:10.1111/tpj.13993
    > Ivan Kulich, Zdenka Vojtíková, Peter Sabol, Jitka Ortmannová, Vilém Nedela, Eva Tihlaríková, Viktor Žárský (2018) Exocyst Subunit EXO70H4 Has a Specific Role in Callose Synthase Secretion and Silica Accumulation. Plant Physiology 176 (3) 2040-2051; DOI: 10.1104/pp.17.01693
    > Janecková, H, Husicková, A, Ferretti, U, et al (2018) The interplay between cytokinins and light during senescence in detached Arabidopsis leaves. Plant Cell Environ. 41: 1870– 1885. https://doi.org/10.1111/pce.13329
    > Ilík, P.,  Špundová, M. , Šicner, M. , Melkovicová, H. , Kucerová, Z. , Krchnák, P. , Fürst, T. , Vecerová, K. , Panzarová, K. , Benediktyová, Z. and Trtílek, M. (2018), Estimating heat tolerance of plants by ion leakage: a new method based on gradual heating. New Phytol, 218: 1278-1287. doi:10.1111/nph.15097
    > Miroslav Ovecka, Daniel von Wangenheim, Pavel Tomancák, Olga Šamajová, George Komis & Jozef Šamaj (2018) Multiscale imaging of plant development by light-sheet fluorescence microscopy. Nature Plants, vol. 4, pages639–650

    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.

    1. Czech Science Foundation/GACR, Prague
    http://www.gacr.cz
    2. Ministry of Education, Youth and Sports of Czech Republic, Prague
    http://www.msmt.cz/research-and-development-1
    Both institutions support also bilateral projects with selected countries. Targeted or applied research is since recently supported also by the Technology Agency of the Czech Republic (TACR) and Arabidopsis model is accepted as a driver for applications.
    3. Technology Agency of the Czech Republic
    http://www.tacr.cz/english/
    4.Ministry of Agriculture, National Agency for Agricultural Research (NAZV) might support projects using Arabidopsis as a driver for the applied research
    https://goo.gl/JPGv1O

     

  • 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
  • Estonia Open or Close

    Liina Jakobson
    This email address is being protected from spambots. You need JavaScript enabled to view it.
    Tallinn University of Technology

    Hanna Hõrak
    This email address is being protected from spambots. You need JavaScript enabled to view it.
    Estonian University of Life Sciences

    The research of Estonian Arabidopsis community is mainly focused on stomatal regulation in response to abiotic stressors, myosin functions in plant development and plant-pathogen interactions.

    New Resources and Software tools available for Arabidopsis Researchers that have been initiated or funded in 2018/ early 2019.

    Gas exchange analysis equipment, new improved and much faster version #3, which enables real-time gas exchange measurements such as stomatal conductance, transpiration, photosynthesis etc of single intact Arabidopsis plants in a controlled and adjustable conditions. Air temperature, air composition (humidity, CO2, O3 etc) and light conditions can be manipulated throughout the experiment.

    Selected Publications

    Hannes Kollist, Sara I.Zandalinas, Soham Sengupta, Maris Nuhkat, Jaakko Kangasjärvi, Ron Mittler (2019). Rapid Responses to Abiotic Stress: Priming the Landscape for the Signal Transduction Network. Trends in Plant Science, 24 (1), 25−37.10.1016/j.tplants.2018.10.003.

    Jalakas, Pirko; Tulva, Ingmar; Kangor, Tiia; Sooväli, Pille; Rasulov, Bakhtier; Tamm, Ülle; Koppel, Mati; Kollist, Hannes; Merilo, Ebe; (2018). Gas exchange-yield relationships of malting barley genotypes treated with fungicides and biostimulants. European Journal of Agronomy, 99, 129−137.10.1016/j.eja.2018.07.001.

    Merilo, Ebe; Yarmolinsky, Dmitry; Jalakas, Pirko; Parik, Helen; Tulva, Ingmar; Rasulov, Bakhtier; Kilk, Kalle; Kollist, Hannes (2018). Stomatal VPD Response: There Is More to the Story Than ABA. Plant Physiology, 176 (1), 851−864.10.1104/pp.17.00912.

    Ojangu, E.-L.; Ilau, B.; Tanner, K.; Talts, K.; Ihoma, E.; Dolja, V. V.; Paves, H.; Truve, E. (2018). Class XI Myosins Contribute to Auxin Response and Senescence-Induced Cell Death in Arabidopsis. Frontiers in Plant Science, 9.10.3389/fpls.2018.01570.

    Tõldsepp, K; Zhang, J; Takahashi, Y; Sindarovska, Y; Hõrak, H; Ceciliato, PH. O.; Koolmeister, K; Wang, YS; Vaahtera, L; Jakobson, L; Yeh, CY; Park, J; Brosche, M; Kollist, H; Schroeder, JI. (2018). Mitogen-activated protein kinases MPK4 and MPK12 are key components mediating CO2-induced stomatal movements. The Plant Journal, 96 (5), 1018−1035.10.1111/tpj.14087.

    Major Funding Sources

    Estonian Research Council
    www.etag.ee

    Centre of Excellences funded by European Regional Development Fund, coordinated in Estonia by Archimedes Foundation. www.archimedes.ee

  • 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.

    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).

    Groups at the University of Helsinki are developing PhenomatoR, an R package to integrate different phenotypic data from different souces (several phenotyping platforms as well as data from conventional approaches) with mathematical normalization of repeats and other features. A manuscript is currently in preparation and the software will be available as R package.

    National Plant Phenotyping Infrastructure https://www.helsinki.fi/en/infrastructures/national-plant-phenotyping

    PhenomatoR: An R Package for the Analysis of Large-Scale Phenomics Data https://github.com/jsalojar/PhenomatoR

    Conferences and Workshops

    International Conference on Arabidopsis Research, Turku, Finland, June 25 to 29, 2018

    Plants in a Changing Climate “Integration of Photosynthesis, Adaptation and Development”, Helsinki Finland, November 6-8, 2019

    Selected Publications

    Abou-Saleh RH, Hernandez-Gomez MC, Amsbury S, Paniaqua C, Bourdon M, Miyashima S, Helariutta Y, Fuller M, Budtova T, Connell SD, Ries ME, Benitez-Alfonso Y (2018) Interactions between callose and cellulose revealed through the analysis of biopolymer mixtures. Nature Communications 9(1):4538

    Koskela MM, Brünje A, Ivanauskaite A, Grabsztunowicz M, Lassowskat I, Neumann U, Dinh TV, Sindlinger J, Schwarzer D, Wirtz M, Tyystjarvi E, Finkemeier I, Mulo P (2018) Chloroplast acetyltransferase NSI is required for state transitions in Arabidopsis thaliana. Plant Cell 30: 1695–1709

    Nikkanen L, Toivola J, Trotta A, Guinea Diaz M, Tikkanen M, Aro EM, Rintamäki E. (2018) Regulation of cyclic electron flow by chloroplast NADPH-dependent thioredoxin system. Plant Direct 2(11):e00098

    Sierla M, Hõrak H, Overmyer K, Waszczak C, Yarmolinsky D, Maierhofer T, Vainonen JP, Salojärvi J, Denessiouk K, Laanemets K, Tõldsepp K, Vahisalu T, Gauthier A, Puukko T, Paulin L, Auvinen P, Geiger D, Hedrich R, Kollist H, Kangasjärvi J (2018) The Receptor-like Pseudokinase GHR1 Is Required for Stomatal Closure. Plant Cell 30 (11):2813-2837

    Shapiguzov A, Vainonen J, Hunter K, Tossavainen H, Tiwari A, Järvi S, Hellman M, Aarabi F, Alseekh S, Wybouw B, Van Der Kelen K, Nikkanen L, Krasensky-Wrzaczek J, Sipari N, Keinänen M, Tyystjärvi E, Rintamäki E, De Rybel B, Salojärvi J, Van Breusegem F, Fernie AR, Brosché M, Permi P, Aro EM, Wrzaczek M, Kangasjärvi J. 2019. Arabidopsis RCD1 coordinates chloroplast and mitochondrial functions through interaction with ANAC transcription factors. eLife 8: e43284

    Smetana O, Mäkilä R, Lyu M, Amiryousefi A, Sánchez Rodríguez F, Wu MF, Solé-Gil A, Leal Gavarrón M, Siligato R, Miyashima S, Roszak P, Blomster T, Reed JW, Broholm S, Mähönen AP (2019) High levels of auxin signalling define the stem-cell organizer of the vascular cambium. Nature 565: 485–489.

    Vaattovaara A, Brandt B, Sitaram R, Safronov O, Veidenberg A, Luklová M, Kangasjärvi J, Löytynoja A, Hothorn M, Salojärvi J, Wrzaczek M. 2019. Mechanistic insights into the evolution of DUF26-containing proteins in land plants. Communications Biology 2: 56.

    Wirthmueller L, Asai S, Rallapalli G, Sklenar J, Fabro G, Kim DS, Lintermann R, Jaspers P, Wrzaczek M, Kangasjärvi J, MacLean D, Menke FLH, Banfield MJ, Jones JDG (2018) Arabidopsis downy mildew effector HaRxL106 suppresses plant immunity by binding to RADICAL-INDUCED CELL DEATH1. New Phytologist 220(1):232-248

    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.

    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/).

    - IPS2: FlagDB++ v6.3 : Integrative database around plant genomes, http://tools.ips2.u-psud.fr/projects/FLAGdb++/HTML/index.shtml

    ATOMEdb: Arabidopsis thaliana ORFeome database, http://tools.ips2.u-psud.fr/ATOMEdb

    -LPCV, Grenoble:

    ChloroKb: decoding the chloroplast, http://big.cea.fr/drf/big/english/Pages/News/Scientific-results/L56_GCurien.aspx, for direct access http://chlorokb.fr/

    Conferences and Workshops

    Plant Organ Growth Symposium 2019 , Bordeaux, France, April 24 - 26, 2019, https://symposium.inra.fr/pogs2019

    23rd International Conference on Plant Growth Substances, Universite Paris-Descartes, Paris, France, June 25 - 29, 2019, https://www.ipgsa2019.com/

    SPS Summer School 2019, Specialized plant metabolites: from analysis to engineering

    June 30 – July 4, 2019 – Versailles and Orsay, France, https://www6.inra.fr/saclay-plant-sciences_eng/Teaching-and-training/Summer-schools/Summer-School-2019

    Doctoral Training: Biology at Different Scales: Interplay between Physics and Integrative Biology, from May 27, 2019 to Jun 7, 2019 – Les Houches, France, https://www.houches-school-physics.com/program/program-2019/doctoral-training-biology-at-different-scales-interplay-between-physics-and-integrative-biology-412721.kjsp?RH=1529674446765

    Selected Publications

    Castrec B, Dian C, Ciccone S, Ebert CL, Bienvenut WV, Le Caer JP, Steyaert JM, Giglione C, Meinnel T (2018) Structural and genomic decoding of human and plant myristoylomes reveals a definitive recognition pattern. Nat Chem Biol. 14(7):671-679

    Derrien B, Clavel M, Baumberger N, Iki T, Sarazin A, Hacquard T, Ponce MR, Ziegler-Graff V, Vaucheret H, Micol JL, Voinnet O, Genschik P (2018) A Suppressor Screen for AGO1 Degradation by the Viral F-Box P0 Protein Uncovers a Role for AGO DUF1785 in sRNA Duplex Unwinding. Plant Cell. 30(6):1353-1374

    Gonneau M, Desprez T, Martin M, Doblas VG, Bacete L, Miart F, Sormani R, Hématy K, Renou J, Landrein B, Murphy E, Van De Cotte B, Vernhettes S, De Smet I, Höfte H (2018) Receptor Kinase THESEUS1 Is a Rapid Alkalinization Factor 34 Receptor in Arabidopsis. Curr Biol. 28(15):2452-2458.

    Hugouvieux V, Silva CS, Jourdain A, Stigliani A, Charras Q, Conn V, Conn SJ, Carles CC, Parcy F, Zubieta C (2018) Tetramerization of MADS family transcription factors SEPALLATA3 and AGAMOUS is required for floral meristem determinacy in Arabidopsis. Nucleic Acids Res. 46(10):4966-4977

    Morel P, Heijmans K, Ament K, Chopy M, Trehin C, Chambrier P, Rodrigues Bento S, Bimbo A, Vandenbussche M (2018) The Floral C-Lineage Genes Trigger Nectary Development in Petunia and Arabidopsis. Plant Cell. 30(9):2020-2037.

    Nassrallah A, Rougée M, Bourbousse C, Drevensek S, Fonseca S, Iniesto E, Ait-Mohamed O, Deton-Cabanillas AF, Zabulon G, Ahmed I, Stroebel D, Masson V, Lombard B, Eeckhout D, Gevaert K, Loew D, Genovesio A, Breyton C, De Jaeger G, Bowler C, Rubio V, Barneche F (2018) DET1-mediated degradation of a SAGA-like deubiquitination module controls H2Bub homeostasis. Elife. 7. pii: e37892.

    Perraki A, Gronnier J, Gouguet P, Boudsocq M, Deroubaix AF, Simon V, German-Retana S, Legrand A, Habenstein B, Zipfel C, Bayer E, Mongrand S, Germain V (2018) REM1.3's phospho-status defines its plasma membrane nanodomain organization and activity in restricting PVX cell-to-cell movement. PLoS Pathog.14(11):e1007378

    Platre MP, Noack LC, Doumane M, Bayle V, Simon MLA, Maneta-Peyret L, Fouillen L, Stanislas T, Armengot L, Pejchar P, Caillaud MC, Potocký M, Čopič A, Moreau P, Jaillais Y (2018) A Combinatorial Lipid Code Shapes the Electrostatic Landscape of Plant Endomembranes. Dev Cell. 45(4):465-480

    Tang N, Shahzad Z, Lonjon F, Loudet O, Vailleau F, Maurel C (2018) Natural variation at XND1 impacts root hydraulics and trade-off for stress responses in Arabidopsis. Nat Commun. 9(1):3884

    Zervudacki J, Yu A, Amesefe D, Wang J, Drouaud J, Navarro L, Deleris A (2018) Transcriptional control and exploitation of an immune-responsive family of plant retrotransposons. EMBO J. 37(14).

    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.)

    Use of Arabidopsis

    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.

    Resources and Software tools available for Arabidopsis Researchers that have been initiated or funded in 2018 or early 2019

    - 1001 Genomes Project
    http://1001genomes.org/

    - German Plant Phenotyping Network
    http://www.dppn.de/dppn/EN/Home/home_node.html

    - The Arabidopsis Protein Phosphorylation Site Database http://phosphat.uni-hohenheim.de/index.html: in addition to the database, the PhosPhAt offers a plant-specific phosphorylation site predictor

    - GABI Primary Database
    http://www.gabipd.org/

    - Plant Genome and Systems Biology Databases
    http://pgsb.helmholtz-muenchen.de/plant/plantsdb.jsp

    - Plant Transcription Factor Database
    http://plntfdb.bio.uni-potsdam.de/v3.0/

    - The AraGWAS Catalog: a curated and standardized Arabidopsis thaliana GWAS catalog
    https://aragwas.1001genomes.org

    qPortal: A large set of software tools and portlets are accessible via the recently established web-based science portal of the Quantitative Biology Center (QBiC) of the University of Tübingen (https://portal.qbic.uni-tuebingen.de/portal/web/qbic/software).

    nQuire: a statistical framework for ploidy estimation using next generation sequencing. nQuire is implemented as a stand-alone Linux command line tool in the C programming language and is available at https://github.com/clwgg/nQuire.


    findGSE: estimating genome size variation within human and Arabidopsis using k-mer frequencies. The R package of findGSE is freely available at https://github.com/schneebergerlab/findGSE and supported on linux and Mac systems

    myTAI: evolutionary transcriptomics with R. The myTAI package is available at https://github.com/HajkD/myTAI and https://cran.r-project.org/web/packages/myTAI/index.html

    Conferences, Workshops and Outreach events

    Conferences

    - 11th Tri-National Arabidopsis Meeting, 10. – 12. April 2019, Zürich, Switzerland

    - International Plant Science Conference (Botanikertagung), 15. – 19. September 2019, Rostock, Germany

    - Conference on Climate Change-Linked Stress Tolerance in Plants,13. – 16. May 2019, Hannover, Germany (http://www.keystonesymposia.org/index.cfm?e=Web.Meeting.Program&meetingid=1655&subTab=program)

    - EMBL Conference: CO2 Fixation Summit, 03. – 04. June 2019, Heidelberg, Germany (https://www.embl.de/training/events/2019/COS19-01/index.html)

    - 15th International Rapeseed Congress, 16. – 19. June 2019, Berlin, Germany (https://www.irc2019-berlin.com/)

    - 5th Plants and People (P&P) Conference, 03. – 04.09.2019, Potsdam, Germany (https://plants-and-people.mpg.de/)

    - 16th Horizons in Molecular Biology Symposium, 09. – 12.09.2019, Göttingen, Germany (https://www.horizons-molbio.de/)

    - International Plant Science Conference (Botanikertagung), 15. – 19.09.2019, Rostock, Germany (https://www.botanikertagung2019.de/)

    - 24th EUCARPIA Maize and Sorghum Conference, 07. – 09.10.2019, Weihenstephan/Freising, Germany (https://www.events.tum.de/frontend/index.php?sub=120)

    - 9th International Conference on Functional-Structural Plant Models (FSPM2020), 05. – 09. October 2020, Hannover, Germany (https://www.fspm2020.net/).

    Workshops

    4th Summer Academy on Plant Molecular Biology, 23. – 25. September 2019, Heiligkreuztal, Germany (https://www.summer-academy-2019.info/)

    7th European Workshop on Plant Peptides & Receptors, 11. – 13. September 2019, Freudenstadt, Germany (http://www.plant-peptides-and-receptors2019.uni-tuebingen.de/)

    TUM Summer School on „Selection and Breeding“, 25. June to – 02. July 2019, Herrsching am Ammersee, Germany (http://www.plantbreeding.wzw.tum.de/index.php?id=133)

    Outreach Events

    The PLANT2030 is an initiative from the German Federal Ministry of Education and Research (BMBF) that fosters research projects within public-private partnerships (http://www.pflanzenforschung.de/de/plant-2030/uberblick).

    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.

    - Wissenschaftsscheune, “The Science Barn” (http://www.wissenschaftsscheune.de/)


    - Open House of the Tübingen MPI (http://www.eb.tuebingen.mpg.de/institute/information-for-the-public.html)
    - Frag die Erbse, “Ask the Pea” booklet series (http://www.mpimp-golm.mpg.de/22409/Frag_die_Erbse_Booklet)

    - 5th International Fascination of Plant Day, 18. May 2019, (https://www.pflanzenforschung.de/de/plant-2030/termine/2019-05-18-5th-international-fascination-plants-day-2019).

    - 5th Plants and People (P&P) Conference, 03. – 04.09.2019, Potsdam, Germany (https://plants-and-people.mpg.de/)

    Selected Publications

    Brackmann K, Qi J, Gebert M, Jouannet V, Schlamp T, Grünwald K, Wallner ES, Novikova DD, Levitsky VG, Agustí J, Sanchez P, Lohmann JU, Greb T (2018). Spatial specificity of auxin responses coordinates wood formation. Nat Commun 9:875. doi: 10.1038/s41467-018-03256-2.

    Capovilla G, Delhomme N, Collani S, Shutava I, Bezrukov I, Symeonidi E, de Francisco Amorim M, Laubinger S, Schmid M (2018).PORCUPINE regulates development in response to temperature through alternative splicing. Nat Plants, doi: 10.1038/s41477-018-0176-z.

    Damianos S. Skopelitis, Kristine Hill, Simon Klesen, Cristina F. Marco, Patrick von Born,Daniel H. Chitwood & Marja C.P. Timmermans (2018). Gating of miRNA movement at defined cell-cell interfaces governs their impact as positional signals. Nature Comm. 9:3107, doi: 10.1038/s41467-018-05571-0.

    Durán P, Thiergart T, Garrido-Oter R, Agler M, Kemen E, Schulze-Lefert P, Hacquard S (2018).Microbial Interkingdom Interactions in Roots Promote Arabidopsis Survival. Cell 175:973-983.e14. doi: 10.1016/j.cell.2018.10.020.

    Förster S, Schmidt LK, Kopic E, Anschütz U, Huang S, Schlücking K, Köster P, Waadt R, Larrieu A, Batistič O, Rodriguez PL, Grill E, Kudla J, Becker D (2019).Wounding-Induced Stomatal Closure Requires Jasmonate-Mediated Activation of GORK K+ Channels by a Ca2+ Sensor-Kinase CBL1-CIPK5 Complex. Dev Cell 48:87-99, doi: 10.1016/j.devcel.2018.11.014.

    Holzwart E, Huerta AI, Glöckner N, Garnelo Gómez B, Wanke F, Augustin S, Askani JC, Schürholz AK, Harter K, Wolf S (2018). BRI1 controls vascular cell fate in the Arabidopsis root through RLP44 and phytosulfokine signaling. Proc Natl Acad Sci USA 30: 201814434, doi: 10.1073/pnas.1814434115.

    Hoppen C, Müller L, Albrecht AC, Groth G (2019).The NOP-1 peptide derived from the central regulator of ethylene signaling EIN2 delays floral senescence in cut flowers. Sci Rep. 9:1287, doi: 10.1038/s41598-018-37571-x.

    Hyun, Y., Vincent, C., Tilmes, V., Bergonzi, S., Kiefer, C., Richter, R., Martinez-Gallegos, R., Severing, E., Coupland, G. (2019) A regulatory circuit conferring varied flowering response to cold in annual and perennial plants. Science 363: 409-412, doi: 10.1126/science.aau8197.

    Neu A, Eilbert E, Asseck LY, Slane D, Henschen A, Wang K, Bürgel P, Hildebrandt M, Musielak TJ, Kolb M, Lukowitz W, Grefen C, Bayer M (2019). Constitutive signaling activity of a receptor-associated protein links fertilization with embryonic patterning in Arabidopsis thaliana. Proc Natl Acad Sci USA 116:5795-5804, doi: 10.1073/pnas.1815866116.

    Speth C, Szabo EX, Martinho C, Collani S, Zur Oven-Krockhaus S, Richter S, Droste-Borel I, Macek B, Stierhof YD, Schmid M, Liu C, Laubinger S (2018). Arabidopsis RNA processing factor SERRATE regulates the transcription of intronless genes. Elife 7: e37078, doi: 10.7554/eLife.37078.

    Major Funding Sources

    The German Science Foundation (DFG) is the major source financing Arabidopsis research in Germany
    http://www.dfg.de/en/index.jsp

    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

    These instiutions conduct some research with Arabidopsis

    - Agricultural University of Athens, Athens, Greece
    - Aristotle University of Thessaloniki, Thessaloniki, Greece
    - National and Kapodistrian University of Athens, Athens, Greece
    - University of Crete, Crete, Greece
    - Mediterannean Agronomic Institute of Chania, Chania, Crete, Greece

    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

    Selected Publications

    Papoutsoglou P, Makris A, Burns J, Kendig AL, Sheikh M, Kuschner CE, Whitney G, Caiola H, Doonan JH, Vlachonasios KE, McCain ER, Hark AT. (2018). The Histone Acetyltransferase GCN5 and the Transcriptional Coactivator ADA2b Affect Leaf Development and Trichome Morphogenesis in Arabidopsis. Planta 248: 613-628

    Panteris E, Diannelidis BE, Adamakis ID. (2018) Cortical microtubule orientation in Arabidopsis thaliana root meristematic zone depends on cell division and requires severing by katanin. Journal of Biological Research-Thessaloniki 25: 12

    Podia V, Milioni D, Katsareli E, Valassakis C, Roussis A, Haralampidis K. (2018) Molecular and functional characterization of Arabidopsis thaliana VPNB1 gene involved in plant vascular development. Plant Science 277: 11–19

    Podia V, Milioni D, Martzikou M, Haralampidis K. (2018) The role of Arabidopsis thaliana RASD1 gene in ABA‐dependent abiotic stress response. Plant Biology 20: 307-317

    Poulios S, Vlachonasios KE. (2018) Synergistic action of GCN5 and CLAVATA1 in the regulation of gynoecium development in Arabidopsis thaliana. New Phytologist 220: 593-608

    Tsitsekian D, Daras G, Alatzas A, Templalexis D, Hatzopoulos P, Rigas S. (2018) Comprehensive analysis of Lon proteases in plants highlights independent gene duplication events. Journal of Experimental Botany doi: 10.1093/jxb/ery440

    Tornkvist A, Liu C, Moschou P. (2019) Proteolysis and Nitrogen: emerging insights. Journal of Experimental Botany doi: 10.1093/jxb/erz024

    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

    Use of Arabidopsis

    The research  activitiesin India continue to be centered around understanding molecular mechanisms involved in plant development, light, hormone and sugar signalling, plant-pathogen interaction and abiotic stress tolerance.

    Ashis Kumar Nandi’s group established that polycomb-group repressor protein MEDEA attenuates plant defense to maintain the balance between growth and development. The group identified Arabidopsis thalianaOXIDATION-RELATED ZINC FINGER 1 (AtOZF1) protein and showed that it promotes NPR1-independent SA signalling in Arabidopsis. This group has also established the role of the AP2-family protein APD1 in systemic acquired resistance.

    Girdhar Pandey’s group is working on the relationship of mineral nutrient deficiency and abiotic stress signaling pathways, especially Ca2+ mediated signaling under stress condition and the involvement of CBL-CIPK components.

    Dr Laxmi’s group has functionally characterized members of a glucose-regulated FLZ (FCS-Like Zinc Finger gene family (FLZ6 and FLZ10) and shown that the regulation is mediated through SnRK1 and TOR kinases in plants, which are ancient master regulators of energy signaling, growth and resilience.

    Majee’s group using ASK13 overexpression and knockdown lines have shown that ASK13 positively influences seed germination and seedling growth, particularly under abiotic stress.

    Dr Utpal Nath’s group has elucidated the redundnat role of two phytochrome ‘B’ (PHYB) interacting transcription factors, VOZ1 and VOZ2 (VASCULAR PLANT ONE-ZINC FINGER), in promoting flowering by modulating CONSTANS (CO) function(Figure), and that too independent of FLC (Flowering Locus C), the well worked out floral repressor.In addition, this group has also defined a role of class II TCP genes in regulating trichome differentiation, establishing a link  between organ morphogenesis and cellular differentiation.

    Sribash Roy’s group has been involved in collection of Indian populations of Arabidopsis thaliana, collected from different altitudes of Western Himalaya and have shown that these accessions genetically distinct from the other world population. Further studies are likely to provide insight into the evolution and adaptation mechanisms of the Himalayan populations of A. thaliana.

    New Resources and Software tools available for Arabidopsis Researchers that have been initiated or funded in 2018 or early 2019
     
    A database containing 636 gene entries related to 44 types of different stress factors with their related information related to Arabidopsis thaliana, has been created by Borkotoky et al. ( 2018). Details are as follows:

    Borkotoky et al. (2018) The Arabidopsis Stress Responsive Gene DatabaseInternational Journal of Plant Genomics Volume 2013, http://dx.doi.org/10.1155/2013/949564

    Conferences, Workshops and Outreach events

    Indian Society for Plant Physiology (ISPP) organized an International Conference of Plant Physiology-2018 (IPCC-2018) at NBRI Lucknow during 2-5th December, 2018, where several articles on Arabidopsis were presented and discussed.

    Selected Publications

    - Jamsheer KM, Shukla BN, Jindal S, Gopan N, Mannully CT and Laxmi A (2018) The FCS-like zinc finger scaffold of the kinase SnRK1 is formed by the coordinated actions of the FLZ domain and intrinsically disordered regions. J. Biol. Chem. 293(34):13134-13150

    - Kumar S, Choudhary P, Gupta M, Nath U (2018) VASCULAR PLANT ONE-ZINC-FINGER1 (VOZ1) and VOZ2  interact with CONSTANS and promote photoperiodic flowering transition. Plant Physiol. 176: 2917-2930

    - Rao V, Petla BP, Verma P, Salvi P, Kamble NU, Ghosh S, Kaur H, Saxena SC, Majee M (2018) Arabidopsis SKP1-like protein13 (ASK13) positively regulates seed germination and seedling growth under abiotic stress. J Exp Bot. 69:3899-3915

    - Roy S (2018) Arabidopsis natural variants and the Indian scenario. Current Science, 114, 263-265.

    - Roy S, Gupta P, Rajabhoj MP, Maruthachalam R, Nandi AK (2018) The polycomb-group repressor MEDEA attenuates pathogen defense. Plant Physiology 177:1728-1742,

    - Sarkar, S., Das, A., Khandagale, P., Maiti, IB., Chattopadhyay, S. and Dey, N. (2018). Interaction of Arabidopsis TGA3 and WRKY53 transcription factors on Cestrum yellow leaf curling virus (CmYLCV) promoter mediates salicylic acid‑dependent gene expression in planta. Planta247:181–199.

    - Singh A, Yadav AK, Kaur K, Sanyal SK, Jha SK, Fernandes JL, Sharma P, Tokas I, Pandey A, Luan S, Pandey GK (2018) Protein Phosphatase 2C, AP2C1 Interacts with and Negatively Regulates the Function of CIPK9 under Potassium Deficient Conditions in Arabidopsis. Journal of Experimental Botany. 69(16): 4003-4015.

    - Singh N, Swain S, Singh A, Nandi AK (2018) AtOZF1 positively regulates defense against bacterial pathogens and NPR1- independent salicylic acid signaling. Mol Plant Microbe Interact 2018 31:323-333

    - Vadde BVL, Challa KR, Nath U (2018) The TCP4 transcription factor regulates trichome cell differentiation by directly activating GLABROUS INFLORESCENCE STEMS in Arabidopsis thaliana. Plant J. 93: 259-269

    - Yadav AK, Jha SK, Sanyal SK, Luan S, Pandey GK. (2018) Arabidopsis Calcineurin B-like proteins differentially regulate phosphorylation activity of CBL-interacting protein kinase 9. Biochemical Journal. 475(16): 2621-2636.

    Major Funding Sources

    Department of Biotechnology (DBT), Government of India http://dbtindia.nic.in/

    Department of Science & Technology (DST), Government of India http://www.dst.gov.in/

    Science and Engineering Research Board (SERB), Government of India http://www.serbonline.in/

    Council of Scientific and Industrial Research (CSIR), New Delhi http://www.csirhrdg.res.in/

    Indian Council of Agricultural Research (ICAR), New Delhi http://www.icar.org.in/

    University Grants Commission, New Delhi
    https://www.ugc.ac.in/

  • Ireland Open or Close

    Prof. Charles Spillane

    Genetics & Biotechnology Lab, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, University Road, Galway H91 REW4, Ireland. E-mail: This email address is being protected from spambots. You need JavaScript enabled to view it. 

    Website: www.spillanelab.org

    Use of Arabidopsis

    Ireland (population > 4.6 million) has a relatively small and diverse plant research community (approx 30-40 research groups). There are currently no private sector institutions working with Arabidopsis thaliana in Ireland.
     
    The following research groups in Ireland are conducting research using the model plant Arabidopsis thaliana:
     
    1. Prof Charles Spillane, Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway (NUI Galway), Ireland.
    2. Dr. Ronan Sulpice, Plant Systems Biology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway (NUI Galway), Ireland.
    3. Dr. Sara Farrona, Plant Developmental Epigenetics Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway (NUI Galway), Ireland.
    4. Dr. Zoe Popper, Plant Cell Wall Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway (NUI Galway), Ireland.
    5. Dr. Frank Wellmer, Plant Developmental Genetics, Smurfit Institute of Genetics, Trinity College Dublin.
    6. Dr. Paul McCabe, School of Biology & Environmental Science, University College Dublin, Dublin, Ireland.
    7. Dr. Carl Ng, School of Biology & Environmental Science, University College Dublin, Dublin, Ireland.
    8. Dr. Fiona Doohan, School of Biology & Environmental Science, University College Dublin, Dublin, Ireland.
    9. Dr. Rainer Melter, School of Biology and Environmental Science, University College Dublin (UCD), Dublin, Ireland.
    10. Dr. Marcel Jansen, Zoology, Ecology & Plant Science (ZEPs), University College Cork, Ireland.
    11. Prof. Astrid Wingler, Zoology, Ecology & Plant Science (ZEPs), University College Cork, Ireland.
    12. Dr. Fuquan Liu, School of Biological Sciences, Queens University Belfast, Northern Ireland.
    13. Dr. Emmanualle Graciet, School of Biology, National University of Ireland Maynooth, Ireland.
    14. Dr. Mario Fares, Smurfit Institute of Genetics, Trinity College Dublin. RIP.

    Conferences, Workshops and Outreach events

    There is an annual Irish Arabidopsis Meeting which aims to bring together the Arabidopsis researcher community in Ireland.

    Publications

    Alvarez-Ponce, D., Ruiz-González, M., Vera-Sirera, F., Feyertag, F., Perez-Amador, M. and Fares, M (2018) Arabidopsis Heat Stress-Induced Proteins Are Enriched in Electrostatically Charged Amino Acids and Intrinsically Disordered Regions. International journal of molecular sciences, 19(8), p.2276.

    Coffey, A. and Jansen, M.A (2019) Effects of natural solar UV-B radiation on three Arabidopsis accessions are strongly affected by seasonal weather conditions. Plant physiology and biochemistry, 134, pp.64-72.

    Duszynska, D., Vilhjalmsson, B., Bravo, R.C., Swamidatta, S., Juenger, T.E., Donoghue, M.T., Comte, A., Nordborg, M., Sharbel, T.F., Brychkova, G. and McKeown, P.C (2019) Transgenerational effects of inter-ploidy cross direction on reproduction and F2 seed development of Arabidopsis thaliana F1 hybrid triploids. Plant Reproduction, pp.1-15.

    Engelhorn, J., Wellmer, F. and Carles, C.C (2018). Profiling Histone Modifications in Synchronized Floral Tissues for Quantitative Resolution of Chromatin and Transcriptome Dynamics. In Plant Chromatin Dynamics (pp. 271-296). Humana Press, New York, NY.

    Hohenstatt, M.L., Mikulski, P., Komarynets, O., Klose, C., Kycia, I., Jeltsch, A., Farrona, S. and Schubert, D., 2018. PWWP-DOMAIN INTERACTOR OF POLYCOMBS1 interacts with Polycomb-group proteins and histones and regulates Arabidopsis flowering and development. The Plant Cell, 30(1), pp.117-133

    Käppel, S., Melzer, R., Rümpler, F., Gafert, C. and Theißen, G (2018) The floral homeotic protein SEPALLATA 3 recognizes target DNA sequences by shape readout involving a conserved arginine residue in the MADS domain. The Plant Journal, 95(2), pp.341-357.

    Mermaz, B., Liu, F. and Song, J (2018) RNA Immunoprecipitation Protocol to Identify Protein–RNA Interactions in Arabidopsis thaliana. In Plant Chromatin Dynamics (pp. 331-343). Humana Press, New York, NY.

    Mikulski, P., Hohenstatt, M.L., Farrona, S., Smaczniak, C., Stahl, Y., Kalyanikrishna, K., Kaufmann, K., Angenent, G.C. and Schubert, D (2019) The chromatin-associated protein PWO1 interacts with plant nuclear lamin-like components to regulate nuclear size. The Plant Cell, Jan 1

    Ó’Maoiléidigh, D.S., Stewart, D., Zheng, B., Coupland, G. and Wellmer, F (2018) Floral homeotic proteins modulate the genetic program for leaf development to suppress trichome formation in flowers. Development, 145(3), p.dev157784.

    Rümpler, F., Theißen, G. and Melzer, R (2018). A conserved leucine zipper-like motif accounts for strong tetramerization capabilities of SEPALLATA-like MADS-domain transcription factors. Journal of experimental botany, 69(8), pp.1943-1954.

    Tuteja, R., McKeown, P.C., Ryan, P., Morgan, C.C., Donoghue, M.T., Downing, T., O’Connell, M.J. and Spillane, C (2019) Paternally expressed imprinted genes under positive Darwinian selection in Arabidopsis thaliana. Molecular Biology and Evolution  Mar 26

    Xu, Y., Prunet, N., Gan, E.S., Wang, Y., Stewart, D., Wellmer, F., Huang, J., Yamaguchi, N., Tatsumi, Y., Kojima, M. and Kiba, T (2018) SUPERMAN regulates floral whorl boundaries through control of auxin biosynthesis. The EMBO journal, 37(11), p.e97499.

    Zheng, B., Thomson, B. and Wellmer, F (2018) A Specific Knockdown of Transcription Factor Activities in Arabidopsis. In Plant Transcription Factors (pp. 81-92). Humana Press, New York, NY.

    Major Funding Sources

    Funding sources for Arabidopsis research in Ireland have to date included Science Foundation Ireland (SFI); Department of Agriculture, Fisheries and Food; Irish Research Council for Science, Engineering and Technology; and the European Union.

  • 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

    Use of Arabidopsis

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

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

    Conferences, Workshops and Outreach events

    - 10th Symposium of the International Society of Root Research (ISRR10) 8-12 July, 2018, Yearim Hotel, Israel
    - International Conference of Plant Mitochondrial Biology, 10-15.3.2019, Ein-Gedi, Israel
    - The Israeli Society of Plant Sciences Conference, February 13th, 2019, Sde-Boker, Israel

    Publications

    Abu-Abied M, Belausov E, Hagay S, Peremyslov V, Dolja V, Sadot E (2018) Myosin XI-K is involved in root organogenesis, polar auxin transport, and cell division J Exp Bot. 69(12), 2869-2881.

    Battat M, Eitan A, Rogachev I, Hanhineva K, Fernie AR, Tohge T, Beekwilder J, Aharoni A. (2019) A MYB Triad Controls Primary and Phenylpropanoid Metabolites for Pollen Coat Patterning. Plant Physiol. doi: 10.1104/pp.19.00009.

    Butenko Y, Lin A, Naveh L, Kupervaser M, Levin Y, Reich Z, Adam Z (2018) Differential Roles of the Thylakoid Lumenal Deg Protease Homologs in Chloroplast Proteostasis. Plant Physiol. 178(3), 1065-1080.

    Chen T, Fluhr R (2018) Singlet Oxygen Plays an Essential Role in the Root’s Response to Osmotic Stress Plant Physiol. 177(4),1717-1727.

    Dahan-Meir T, Filler-Hayut S, Melamed-Bessudo C, Bocobza S, Czosnek H, Aharoni A, Levy AA (2018) Efficient in planta gene targeting in tomato using geminiviral replicons and the CRISPR/Cas9 system. Plant J. 95(1), 5-16.

    Roth, O., Alvarez, J. P., Levy, M., Bowman, J. L., Ori, N., & Shani, E. (2018). The KNOXI Transcription Factor SHOOT MERISTEMLESS Regulates Floral Fate in Arabidopsis. Plant Cell, 30(6), 1309-1321.

    Shkolnik, D., Nuriel, R., Bonza, M. C., Costa, A., & Fromm, H. (2018). MIZ1 regulates ECA1 to generate a slow, long-distance phloem-transmitted Ca2+ signal essential for root water tracking in Arabidopsis. PNAS, 115(31), 8031-8036.

    Shor E, Potavskaya R, Kurtz A, Paik I, Huq E and Green R. (2018) PIF-Mediated Sucrose Regulation of the Circadian Oscillator is Light Quality and Temperature Dependent. Genes. 9(12), 628.

    Singh, A.P., Fridman, Y., Holland, N., Ackerman-Lavert, M., Zananiri, R., Jaillais, Y., Henn, A., and Savaldi-Goldstein, S. (2018). Interdependent Nutrient Availability and Steroid Hormone Signals Facilitate Root Growth Plasticity. Dev Cell 46(1), 59-72.

    Zhang Y, Nasser V1, Pisanty O, Omary M, Wulff N, Di Donato M, Tal I, Hauser F, Hao P, Roth O, Fromm H, Schroeder JI, Geisler M, Nour-Eldin HH, Shani E. (2018). A transportome-scale amiRNA-based screen identifies redundant roles of Arabidopsis ABCB6 and ABCB20 in auxin transport. Nature comm., 9(1), 4204.

    Major Funding Sources

    - ISF
    - BSF
    - NSF-BSF
    - ERC

     

  • 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

    A few groups mainly in the Universities and in the CNR (National Research Council) laboratories continue to utilize Arabidopsis as a model organism for plant biology research and their results are published in high impact journals. Research is mainly focused on root and flower development, seed germination, xylem differentiation, ion transport in plant vacuoles, plant defense responses and plant responses to environment.

    New Resources and Software tools available for Arabidopsis Researchers that have been initiated or funded in 2018/ early 2019

    Single and multiple Arabidopsis T-DNA insertion lines, as well as overexpressing lines, GUS- YFP- and GFP-tagged lines, RNA-seq data described in publications are available.

    Conferences and Workshops

    Advances in Plant Reproduction – from gametes to seeds- SEB conference Florence 30 June - 1 July 2018

     

    Selected Publications

    Benedetti M, Verrascina I, Pontiggia D, Locci F, Mattei B, De Lorenzo G, Cervone F. (2018) Four Arabidopsis berberine bridge enzyme-like proteins are specific oxidases that inactivate the elicitor-active oligogalacturonides. PLANT JOURNAL. Apr; 94(2):260-273. 

    Carabelli M, Possenti M, Sessa G, Ruzza V, Morelli G, Ruberti I. (2018)

    Arabidopsis HD-Zip II proteins regulate the exit from proliferation during leaf development in canopy shade. JOURNAL OF EXPERIMENTAL BOTANY 69: 5419-5431

    Cucinotta M, Manrique S, Cuesta C, Benkova E, Novak O, and Colombo L. (2018)

    CUP-SHAPED COTYLEDON1 (CUC1) and CUC2 regulate cytokinin homeostasis to determine ovule number in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY, 69 (21): 5169–5176

    Di Ruocco G, Bertolotti G, Pacifici E, Polverari L, Tsiantis M, Sabatini S, Costantino P, Dello Ioio R.(2018) Differential spatial distribution of miR165/6 determines variability in plant root anatomy. DEVELOPMENT Jan 9;145(1). pii: dev153858

    Ghelli R, Brunetti P, Napoli N, De Paolis A, Cecchetti V, Tsuge T, Serino G, Matsui M, Mele G, Rinaldi G, Palumbo A, Costantino P and Cardarelli M (2018) A newly identified flower-specific splice variant of AUXIN RESPONSE FACTOR 8 Regulates Stamen Elongation and Endothecium Lignification in Arabidopsis. PLANT CELL, 30: 620-637

    Lorrai R, Gandolfi F, Boccaccini A, Ruta V, Possenti M, Tramontano A, Costantino P, Lepore R, Vittorioso P. (2018)Genome-wide RNA-seq analysis indicates that the DAG1 transcription factor promotes hypocotyl elongation acting on ABA, ethylene and auxin signaling SCIENTIFIC REPORT; 8:1-13

    Mainieri D, Marrano CA, Prinsi B, Maffi D, Tschofen M, Espen L, Stöger E, Faoro F, Pedrazzini E, Vitale A. (2018) Maize 16-kD γ-zein forms very unusual disulfide-bonded polymers in the end oplasmic reticulum: implications for prolamin evolution. JOURNAL OF EXPERIMENTAL BOTANY 69:5013-5027.

    Mattioli R, Biancucci M, El Shall A, Costantino P, Mosca L, Funck D, and Trovato M. (2018). Proline synthesis in developing microspores is required for full pollen development and fertility. BMC PLANT BIOLOGY. 18:356

    Mizzotti C, Rotasperti L, Moretto M, Tadini L, Resentini F, Galliani B M., Galbiati M, Engelen K, Pesaresi P and Masiero S (2018). Arabidopsis silique transcriptome discloses essential genes in fruit development and maturation. PLANT PHYSIOLOGY, 178(3):1249-1268.

    Pacifici E, Di Mambro R, Dello Ioio R, Costantino P, Sabatini S. (2018)Acidic cell elongation drives cell differentiation in the Arabidopsis root. EMBO JOURNAL. Aug 15;37(16).

    Punzo P, Ruggiero A, Possenti M, Nurcato R, Costa A, Morelli G, Grillo S, Batelli G. (2018) The PP2A-interactor TIP41 modulates ABA responses in Arabidopsis thaliana. PLANT JOURNAL. 94 (6): 991-1009

    Major Funding Sources

    The Italian Ministry of Education, University and Research funded:

    --a Project SIR( 2015-2018) for independence of young researcher, on ‘MADS box transcription factor SHORT VEGETATIVE PHASE, understanding the molecular
    mechanism and involvement in sense and antisense transcript regulation. RBSI14BTZR. Coordinator Veronica Gregis;


    -Local funding from: Sapienza University of Rome, Roma Tre University of Rome  and University of Milan

    Other funding:

    -Project Horizon 2020 EU RISE project “EXPOSEED” Exploring the molecular control of seed yield in crops (https://ec.europa.eu/research/mariecurieactions/about/research-innovation-staff-exchange_en)


    -Project Promotion of consumer health of the National technological cluster Agrifood. Participant Ida Ruberti.

  • Japan Open or Close

    Motoaki Seki, This email address is being protected from spambots. You need JavaScript enabled to view it.">This email address is being protected from spambots. You need JavaScript enabled to view it., RIKEN CSRS

    Masatomo Kobayashi, This email address is being protected from spambots. You need JavaScript enabled to view it.">This email address is being protected from spambots. You need JavaScript enabled to view it., RIKEN BRC

    Arabidopsis Research Facilities

    The Leading Research Institutes and Universities that use Arabidopsis as a National Project:

    RIKEN CSRS(http://www.csrs.riken.jp/en/). CSRS (Director Kazuo Shinozaki), established in 2013 to conduct basic research integrating plant scientists, chemists and chemical biologists to work forsolutionstocriticalscientific,technicalandsocialissues withspecialfocusonsustainable production of natural resources and useful materials, and resilient agriculture under climate change. CSRS contributes to many goals of the United Nations Sustainable Development Goals (SDGs) and COP21 Paris Agreement goals by applied research through interdisciplinary R&D for sustainable production of energy, efficient engineering and production of useful plant biomass, renewable chemical materials and bioplastics, efficient catalysts, as well as crop production under climate change. In the next phase of CSRS, data science and chemical biology become more important for the advancement of plant science. In addition to Arabidopsis, CSRSuses other plants such as Brachypodium, cassava, rubber, sorghumand others.

    RIKEN BRC(https://epd.brc.riken.jp/en/).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 clones, ORF clones of transcription factors, TAC clones, and vectors), 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.

    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/?ln=en)integratingdatabasesrelatedtoplantomicsstudies. Manually curated literature information on DNA markersof 65plants.

    AIST, National Institute of Advanced Industrial Science and Technology - 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 (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.

    Nagoya University, WPI ITbM(http://www.itbm.nagoya-u.ac.jp/). World Premier International Research Center (WPI) Institute of TransformativeBio-Molecules(ITbM)ofNagoyaUniversity 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 andothers.

    Determining principles in the birth of new plant species: elucidation of lock-and-key molecular systems in sexual reproduction(http://bit.ly/2mrqD4T). Project goal is to clarify primary mechanism in the birth of new species by revealing a whole picture of molecule-leveled understanding of “lock-and-keys” in plant reproduction through active interdisciplinary collaborative research. Scientific Research on Innovative Areas MEXT Grant-in Aid Project FY2016-2020. Multi-organization representative: Tetsuya Higashiyama, ITbM/Nagoya University.

    Integrative system of autonomous environmental signal recognition and memorization for plant plasticity (http://www.rs.tus.ac.jp/plantmemory/en/). Project goal is 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.

    University of Tokyo.

    In The University of Tokyo, basic science studies on Arabidopsis were led by Professors Hiroo Fukuda and Hirokazu Tsukaya, focusing on mechanisms of cell fate determination, long-distance transports of peptides, vascular tissue differentiation and roles of metabolites on plant morphogenesis,, under supports Grant-in-Aid for Scientific Research from MEXT.

    NaraInstituteofScienceandTechnology.

    Principles of pluripotent stem cells underlying plant vitality (2017-2022)(http://www.plant-stem-cells.jp/en/). This project aims to answer the key questions: How do plants augment stem cell populations, and how do plants maintain them over long periods of time? The project members investigate the machinery of stem cell division and the regulatory system underlying maintenance of pluripotency and genome integrity. LedbyMasaaki Umeda, Grant-in-Aid for Scientific Research on InnovativeAreasfromMEXT.

    Elucidation of the strategies of mechanical optimization in plants toward the establishment of the bases for sustainable structure system (2018-2023) (http://bsw3.naist.jp/plant-structure-opt/). This research project aims to understand the mechanical optimization of plants on a multi-scale (molecular, cellular, tissue, and individual) level. Also, we aim to sublimate the mechanical optimization strategy of plants into new energy-saving / material-saving building designs, new material models, and to create a base for the next-generation of sustainable structural systems. Led by Taku Demura, Grant-in-Aid for Scientific Research on InnovativeAreasfromMEXT.

    National Institute for Basic Biology. (2017-2022)(http://photosynthesis.nibb.ac.jp/). Project goal is to elucidate the regulatory mechanisms of photosynthesis by incorporating a new perspective, the regulation of the proton motive force into basic photosynthesis research with the goal of improving photosynthetic efficiency. We expect to establish strategies to re-optimize the photosynthetic performance under any environment. LedbyJun Minagawa, Grant-in-Aid for Scientific Research on InnovativeAreasfromMEXT.

    Okayama University. Innovations for Light-Energy Conversion (2017-2022)(http://photoenergy-conv.net/). Project goal is to elucidate the molecular mechanisms of light-energy harvesting and their utilization reactions by various photosynthetic protein-complexes, especially the photosynthetic water-oxidation enzyme photosystem II, and their applications in the development of artificial photosynthetic systems. Led by Jian-Ren Shen, Grant-in-Aid for Scientific Research on Innovative Areas from MEXT.

     

    New Resources and Software tools available for Arabidopsis Researchers that have been initiated or funded in 2018 or early 2019

    RIKEN National Science Institute - Center for Sustainable Resource Science (CSRS)(http://www.csrs.riken.jp/en/).

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

    PRIMe Web Applications

    Distribution and Redistribution

    • Drop Met mass-spec based metabolome analyses(http://)

    Other RIKEN CSRS developed tools and resources

     

    AtGenExpressArabidopsisGeneExpressionprofile database (http://bit.ly/1P2YT8v)

    • KNApSacKComprehensivespecies-metaboliterelationshipdatabase(http://bit.ly/1LfFkyZ)(NAIST)

    • Plant-PrAS (Plant-Protein Annotation Suite) database of physicochemical and structural properties, and novel functional region in plant proteomes (http://plant-pras.riken.jp/)

    • MassBank Public repository of mass spectral data for sharing spectra among research communities (http://

    • Plant-PrAS (Plant-Protein Annotation Suite) (http://plant-pras.riken.jp/)

    RIPPS (RIKEN Plant Phenotyping System) (http://bit.ly/1sObBEE)

    Plant and Cell Physiology, Volume 59, Issue 10, 1 October 2018, Pages 2030–2038,

    https://doi.org/10.1093/pcp/pcy122

    The Chloroplast Function Database (http://rarge-v2.psc.riken.jp/chloroplast/)

    RIKEN Arabidopsis Phenome Information Database (http://rarge.psc.riken.jp/phenome/)

    •HanaDB

    RIKEN National Science Institute - BioResource Research Center (BRC)(https://epd.brc.riken.jp/en/)

    Kazusa DNA Research Institute (http://www.kazusa.or.jp/e/).

    ・KOMICS Kazusa Metabolomics Database portal (http://www.kazusa.or.jp/komics/en/)

    MassBase: a plant metabolome database (http://bit.ly/1Rlf9Dd)

    MS-MS Fragment Viewer database (http://bit.ly/1QWjPUm)

    PGDBj Plant Genome DataBase Japan(http://pgdbj.jp/?ln=en)

    KaPPA-View4 for integration of transcriptome and metabolome data on metabolic maps (http://kpv.kazusa.or.jp/)

    MFSearcher molecular formula searcher (http://bit.ly/1RN2BFp)

    Conferences and Workshops

    13-15,2019:60thAnnualMeeting of Japanese Society of Plant Physiologists. Nagoya Univ. (https://jspp.org/annualmeeting/60/E-index.html)

    Japan-Taiwan Plant Biology 2019 (JTPB2019): Nagoya Univ. (https://jspp.org/annualmeeting/JTPB2019/

    Selected Publications

    Kurihara, Y., Makita, Y., Kawashima, M., Fujita, T., Iwasaki, S. and Minami, M. (2018) Transcripts from downstream alternative transcription start sites evade uORF-mediated inhibition of gene expression in Arabidopsis. Proc Natl Acad Sci U S A. 115:7831-7836. doi: 10.1073/pnas.1804971115.

    Kuroha, T., Nagai, K., Gamuyao, R., Wang, D.R., Furuta, T., Nakamori, M., Kitaoka, T., Adachi, K., Minami, A., Mori, Y., Mashiguchi, K., Seto, Y., Yamaguchi, S., Kojima, M., Sakakibara, H., Wu, J., Ebana, K., and Ashikari, M. (2018) Ethylene-Gibberellin Signaling Underlies Adaptation of Rice to Periodic Flooding. Science, 361, 6398, 181-186. doi: 10.1126/science.aat1577.

    Nakaminami, K., Okamoto, M., Higuchi-Takeuchi, M., Yoshizumi, T., Yamaguchi, Y., Fukao, Y., Shimizu, M., Ohashi, C., Tanaka, M., Matsui, M., Shinozaki, K., Seki, M. and Hanada, K. (2018) AtPep3 is a hormone-like peptide that plays a role in the salinity stress tolerance of plants. Proc Natl Acad Sci U S A. 115:5810-5815. doi:10.1073/pnas.1719491115.

    Sakamoto, T., Tsujimoto-Inui, Y.,Sotta, N., Hirakawa, T., M. Matsunaga, T., Fukao, F., Matsunaga, S. and Fujiwara, T. (2018) Proteasomal degradation of BRAHMA promotes Boron tolerance in Arabidopsis. Nature Communications 9: 5285. doi: 10.1038/s41467-018-0739.

    Takahashi, F., Suzuki, T., Osakabe, Y., Betsuyaku, S., Kondo, Y., Dohmae, N., Fukuda, H., Yamaguchi-Shinozaki, K. and Shinozaki, K. (2018) A small peptide modulates stomatal control via abscisic acid in long-distance signalling. Nature 556:235-238. doi:10.1038/s41586-018-0009-2.

    Toyota, M., Spencer, D., Sawai-Toyota, S., Jiaqi, W., Zhang, T., Koo, A.J., Howe, G.A. and Gilroy, S. (2018) Glutamate triggers long-distance, calcium-based plant defense signaling. Science 361:1112-1115. doi:10.1126/science.aat7744.

    Uchida, N., Takahashi, K., Iwasaki, R., Yamada, R., Yoshimura, M., Endo, T.A., Kimura, S., Zhang, H., Nomoto, M., Tada, Y., Kinoshita, T., Itami, K., Hagihara, S., and Torii, K.U. (2018) Chemical hijacking of auxin signaling with an engineeredauxin-TIR1 pair. Nature Chem. Biol. 14:299-305. doi: 10.1038/nchembio.2555.

    Uraguchi, D., Kuwata, K., Hijikata, Y., Yamaguchi, R., Imaizumi, H., Sathiyanarayanan, A.M., Rakers, D., Mori, N., Akiyama, K., Irle, S., McCourt, P., Kinoshita, T., Ooi, T. and Tsuchiya, Y. (2018) A femto-molar range suicide germination stimulant for the parasitic plant Striga hermonthica. Science, 362, 1301-1305. doi: 10.1126/science.aau5445.

    Yamaguchi, N., Huang, J., Tatsumi, Y., Abe, M., Sugano, S.S., Kojima, M., Takebayashi, Y., Kiba, T. Yokoyama, R., Nishitani, K., Sakakibara, H. and Ito, T. (2018) Chromatin-mediated feed-forward auxin biosynthesis in floral meristem determinacy. Nature Commun. 9:5290. doi: 10.1038/s41467-018-07763-0.

    Yu, L.J., Suga, M., Wang-Otomo, Z.Y. and Shen, J.R. (2018) Structure of photosynthetic LH1-RC super-complex at 1.9 Å resolution. Nature 556:209-213. doi: 10.1038/s41586-018-0002-9.

    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.

    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.)

    Conferences, Workshops and Outreach events

    Queenstown Reaserch Week: Plant Biology Satellite. Queenstown, New Zealand. 30-31 August 2018

    Plant Science Central. Palmerston North, New Zealand. 2-4 July 2019

    International Congress on Photosynthesis.Rotorua, New Zealand. 2-7 August 2020

    Selected Publications

    Bulman S, Richter F, Marschollek S, Benade F, Julke S and Ludwig-Müller (2018) Arabidopsis thaliana expressing PbBSMT, a gene encoding a SABATHtype methyltransferase from the plant pathogenic protist Plasmodiophora brassicae, show leaf chlorosis and altered host susceptibility. Plant Biology 21 Suppl 1:120-130 doi: 10.1111/plb.12728

    Choi S, Jayaraman J and Sohn KH (2018) Arabidopsis thaliana SOBER1 (SUPPRESSOR OF AVRBSTELICITED RESISTANCE 1) suppresses plant immunity triggered by multiple bacterial acetyltransferase effectors. New Phytologist 219:324-335 doi: 10.1111/nph.15125

    Gould KS, Jay-Allemand C, Logan BA, Baissac Y and Bidel LPR (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 154:11-22 doi: 10.1016/j.envexpbot.2018.02.006

    Moss, SMA, Wang T, Voogd C, Brian LA, Wu R, Hellens RP, Allan AC, Putterill J and Varkonyi-Gasic E (2018) AcFT promotes kiwifruit in vitro flowering when overexpressed and Arabidopsis flowering when expressed in the vasculature under its own promoter. Plant Direct 2:e00068 doi: 10.1002/pld3.68

    Newman TE, Lee J, Williams SJ, Chio S, Halane MK, Zhou J, Solomon P, Kobe B, Jones JDG, Segonzac C and Sohn KH (2018) Autoimmunity and effector recognition in Arabidopsis thaliana can be uncoupled by mutations in the RRS1-R immune receptor. New Phytologist doi: 10.1111/nph.15617

    Raad M, Glare TR, Brochero HL, Muller C and Rostás M (2019) Transcriptional reprogramming of Arabidopsis thaliana defence pathways by the entomopathogen Beauveria bassiana correlates with resistance against a fungal pathogen but not against insects. Frontiers in Microbiology. Doi: 10.3389/fmicb.2019.00615

    Watkin, SAJ, Keown JR, Richards E, Goldstone DC, Devenish SRA and Pearce FG (2018) Plant DHDPR forms a dimer with unique secondary structure features that preclude higher-order assembly. Biochemistry Journal 475:137-150 doi: 10.1042/BCJ20170709.

    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.

    Conferences, Workshops and Outreach events

    The national plant biology conference in Bergen had a strong Arabidopsis element.
    https://norplantbio2018.w.uib.no/
    The next one will be in November 2019 in Oslo

    Selected Publications

    Engelsdorf T, Gigli-Bisceglia N, Veerabagu M, McKenna JF, Vaahtera L, Augstein F, Van der Does D, Zipfel C, Hamann T (2018) The plant cell wall integrity maintenance and immune signaling systems cooperate to control stress responses in Arabidopsis thaliana. Sci Signal. 11(536). pii: eaao3070. doi: 10.1126/scisignal.aao3070.

    Gigli-Bisceglia N, Engelsdorf T, Strnad M, Vaahtera L, Khan GA, Yamoune A, Alipanah L, Novák O, Persson S, Hejatko J, Hamann T (2018) Cell wall integrity modulates Arabidopsis thaliana cell cycle gene expression in a cytokinin- and nitrate reductase-dependent manner. Development. 145(19). pii: dev166678. doi: 10.1242/dev.166678.

    Shi CL, von Wangenheim D, Herrmann U, Wildhagen M, Kulik I, Kopf A, Ishida T, Olsson V, Anker MK, Albert M, Butenko MA, Felix G, Sawa S, Claassen M, Friml J, Aalen RB (2018) The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. Nat Plants. (8):596-604. doi: 10.1038/s41477-018-0212-z.

    Urbancsok J, Bones AM, Kissen R (2018) Benzyl Cyanide Leads to Auxin-Like Effects Through the Action of Nitrilases in Arabidopsis thaliana.Front Plant Sci. 2018 Aug 24;9:1240. doi: 10.3389/fpls.2018.01240. eCollection 2018.

    Major Funding Sources

    Norwegian Research Council
    https://www.forskningsradet.no/en/Home_page/1177315753906

     

  • Poland Open or Close

    Robert Malinowski
    Department of Integrative Plant Biology
    Institute of Plant Genetics of the Polish Academy of Sciences
    Ul. Strzeszynska 34
    60-479 Warszawa
    This email address is being protected from spambots. You need JavaScript enabled to view it.

    Use of Arabidopsis

    Arabidopsis thaliana has turned out to be a very successful model to study different aspects of Plant Sciences. At present numerous research groups in Poland use this plant as a major research object. This is reflected by growing population of research grants and publications of Polish scientists.

    The main granting institution – National Science Center Poland (https://www.ncn.gov.pl), creates positive environment for basic research in Poland. Most successful Arabidopsis research topics are related to RNA molecular biology and molecular aspects of transcriptional and posttranscriptional regulation. Recently we can also see more independent groups working on physiological aspects of plant adaptation to adverse environmental conditions as well as successful research groups whose work aims at understanding of various plant-pathogen interactions. It is also remarkable that more frequently our researchers explore genetic diversity in Arabidopsis to address fundamental biological questions or to support research on crop plants.

    Similarly to other European countries we are also facing the fact that GMO plants cannot be commercially used. This fact has downgrading impact on translational applied plant research where findings on Arabidopsis can be transferred to important crop plants. Never the less we can observe slow but significant development of initiatives where Arabidopsis brings solutions for plant breeding and other sectors of agriculture.

    It is our mission as Arabidopsis community to explain the system and its usefulness to crop researchers and industrial entities. The future work in Poland is to highlight the importance of research conducted on this plant and to prevent the situation where strict division between basic and applied research occurs. In particular we need to support further development of “proof of concept” projects since this aspect has not been properly addressed in Poland.

    New Resources and Software tools available for Arabidopsis Researchers that have been initiated or funded in 2018 or early 2019

    The mirEX  - Arabidopsis pri-miRNA Expression Atlas http://www.combio.pl/mirex1/

    tRex –Database of tRNA-derived short fragments (tRFs) and tRNAs in Arabidopsis thaliana
    http://combio.pl/trex

    Conferences, Workshops and Outreach events

    - Congres BIO2018, Gdansk 18-21 September 2018

    - IPG PAS Integrative Plant Biology Conference, Poznan 7-9 November 2018

    - The 44th FEBS Congress, Krakow 6-11 July 2019

    - 9th Conference of the Polish Society of Experimental Plant Biology, Torun 9-12 September 2019

    - 7th Central European Congress of Life Sciences EUROBIOTECH 2019, Kraków 23-25 September 2019

    Selected Publications

    Knop, K., Stepien, A., Barciszewska-Pacak, M., Taube, M., Bielewicz, D., Michalak, M., Borst, J.W., Jarmolowski, A., and Szweykowska-Kulinska, Z. (2016). Active 5’ splice sites regulate the biogenesis efficiency of Arabidopsis microRNAs derived from intron-containing genes. Nucleic Acids Research 45, 2757-2775.

    Pislewska-Bednarek, M., Nakano, R.T., Hiruma, K., Pastorczyk, M., Sanchez-Vallet, A., Singkaravanit-Ogawa, S., Ciesiołka, D., Takano, Y., Molina, A., Schulze-Lefert, P., and Bednarek, P. (2018). Glutathione Transferase U13 Functions in Pathogen-Triggered Glucosinolate Metabolism. Plant physiology 176, 538-551.

    Rozpadek, P., Nosek, M., Domka, A., Wazny, R., Jedrzejczyk, R., Tokarz, K., Pilarska, M., Niewiadomska, E., and Turnau, K. (2019). Acclimation of the photosynthetic apparatus and alterations in sugar metabolism in response to inoculation with endophytic fungi. Plant, Cell & Environment 42, 1408-1423.

    Sura, W., Kabza, M., Karlowski, W.M., Bieluszewski, T., Kus-Slowinska, M., Pawełoszek, Ł., Sadowski, J., and Ziolkowski, P.A. (2017). Dual Role of the Histone Variant H2A.Z in Transcriptional Regulation of Stress-Response Genes. The Plant Cell 29, 791.


    Szechynska-Hebda, M., Kruk, J., Górecka, M., Karpinska, B., and Karpinski, S. (2010). Evidence for Light Wavelength-Specific Photoelectrophysiological Signaling and Memory of Excess Light Episodes in Arabidopsis The Plant Cell 22, 2201

    Walerowski, P., Gündel, A., Yahaya, N., Truman, W., Sobczak, M., Olszak, M., Rolfe, S., Borisjuk, L., and Malinowski, R. (2018). Clubroot Disease Stimulates Early Steps of Phloem Differentiation and Recruits SWEET Sucrose Transporters within Developing Galls. The Plant Cell 30, 3058-3073.

    Zmienko, A., Samelak-Czajka, A., Kozlowski, P., Szymanska, M., and Figlerowicz, M. (2016). Arabidopsis thaliana population analysis reveals high plasticity of the genomic region spanning MSH2, AT3G18530 and AT3G18535 genes and provides evidence for NAHR-driven recurrent CNV events occurring in this location. BMC Genomics 17, 893.

    Major Funding Sources

    National Science Center Poland
    https://www.ncn.gov.pl

    Foundation for Polish Science
    https://www.fnp.org.pl

  • Poland Open or Close

    Robert Malinowski


    Department of Integrative Plant Biology
    Institute of Plant Genetics of the Polish Academy of Sciences
    Ul. Strzeszynska 34
    60-479 Warszawa
    This email address is being protected from spambots. You need JavaScript enabled to view it.

    Use of Arabidopsis

    Arabidopsis thaliana has turned out to be a very successful model to study different aspects of Plant Sciences. At present numerous research groups in Poland use this plant as a major research object. This is reflected by growing population of research grants and publications of Polish scientists.

    The main granting institution – National Science Center Poland (https://www.ncn.gov.pl), creates positive environment for basic research in Poland. Most successful Arabidopsis research topics are related to RNA molecular biology and molecular aspects of transcriptional and posttranscriptional regulation. Recently we can also see more independent groups working on physiological aspects of plant adaptation to adverse environmental conditions as well as successful research groups whose work aims at understanding of various plant-pathogen interactions. It is also remarkable that more frequently our researchers explore genetic diversity in Arabidopsis to address fundamental biological questions or to support research on crop plants.

    Similarly to other European countries we are also facing the fact that GMO plants cannot be commercially used. This fact has downgrading impact on translational applied plant research where findings on Arabidopsis can be transferred to important crop plants. Never the less we can observe slow but significant development of initiatives where Arabidopsis brings solutions for plant breeding and other sectors of agriculture.

    It is our mission as Arabidopsis community to explain the system and its usefulness to crop researchers and industrial entities. The future work in Poland is to highlight the importance of research conducted on this plant and to prevent the situation where strict division between basic and applied research occurs. In particular we need to support further development of “proof of concept” projects since this aspect has not been properly addressed in Poland.

    New Resources and Software tools available for Arabidopsis Researchers that have been initiated or funded in 2018 or early 2019

    The mirEX  - Arabidopsis pri-miRNA Expression Atlas http://www.combio.pl/mirex1/

    tRex –Database of tRNA-derived short fragments (tRFs) and tRNAs in Arabidopsis thaliana
    http://combio.pl/trex

    Conferences, Workshops and Outreach events

    - Congres BIO2018, Gdansk 18-21 September 2018

    - IPG PAS Integrative Plant Biology Conference, Poznan 7-9 November 2018

    - The 44th FEBS Congress, Krakow 6-11 July 2019

    - 9th Conference of the Polish Society of Experimental Plant Biology, Torun 9-12 September 2019

    - 7th Central European Congress of Life Sciences EUROBIOTECH 2019, Kraków 23-25 September 2019

    Selected Publications

    Knop, K., Stepien, A., Barciszewska-Pacak, M., Taube, M., Bielewicz, D., Michalak, M., Borst, J.W., Jarmolowski, A., and Szweykowska-Kulinska, Z. (2016). Active 5’ splice sites regulate the biogenesis efficiency of Arabidopsis microRNAs derived from intron-containing genes. Nucleic Acids Research 45, 2757-2775.

    Pislewska-Bednarek, M., Nakano, R.T., Hiruma, K., Pastorczyk, M., Sanchez-Vallet, A., Singkaravanit-Ogawa, S., Ciesiołka, D., Takano, Y., Molina, A., Schulze-Lefert, P., and Bednarek, P. (2018). Glutathione Transferase U13 Functions in Pathogen-Triggered Glucosinolate Metabolism. Plant physiology 176, 538-551.

    Rozpadek, P., Nosek, M., Domka, A., Wazny, R., Jedrzejczyk, R., Tokarz, K., Pilarska, M., Niewiadomska, E., and Turnau, K. (2019). Acclimation of the photosynthetic apparatus and alterations in sugar metabolism in response to inoculation with endophytic fungi. Plant, Cell & Environment 42, 1408-1423.

    Sura, W., Kabza, M., Karlowski, W.M., Bieluszewski, T., Kus-Slowinska, M., Pawełoszek, Ł., Sadowski, J., and Ziolkowski, P.A. (2017). Dual Role of the Histone Variant H2A.Z in Transcriptional Regulation of Stress-Response Genes. The Plant Cell 29, 791.


    Szechynska-Hebda, M., Kruk, J., Górecka, M., Karpinska, B., and Karpinski, S. (2010). Evidence for Light Wavelength-Specific Photoelectrophysiological Signaling and Memory of Excess Light Episodes in Arabidopsis The Plant Cell 22, 2201

    Walerowski, P., Gündel, A., Yahaya, N., Truman, W., Sobczak, M., Olszak, M., Rolfe, S., Borisjuk, L., and Malinowski, R. (2018). Clubroot Disease Stimulates Early Steps of Phloem Differentiation and Recruits SWEET Sucrose Transporters within Developing Galls. The Plant Cell 30, 3058-3073.

    Zmienko, A., Samelak-Czajka, A., Kozlowski, P., Szymanska, M., and Figlerowicz, M. (2016). Arabidopsis thaliana population analysis reveals high plasticity of the genomic region spanning MSH2, AT3G18530 and AT3G18535 genes and provides evidence for NAHR-driven recurrent CNV events occurring in this location. BMC Genomics 17, 893.

    Major Funding Sources

    National Science Center Poland
    https://www.ncn.gov.pl

    Foundation for Polish Science
    https://www.fnp.org.pl

  • Saudi Arabia Open or Close

    Yunhe Jiang
    This email address is being protected from spambots. You need JavaScript enabled to view it.
    King Abdullah University of Science and Technology (KAUST)

    New Resources and Software tools available for Arabidopsis Researchers that have been initiated or funded in 2018/ early 2019.

    MVApp, Multivariate analysis application for streamlined data analysis and curation
    http://mvapp.kaust.edu.sa/MVApp/

    Conferences, Workshops and Outreach events

    Plant Science workshop, Thuwal, Saudi Arabia, April 14-25, 2019
    https://psws.kaust.edu.sa/

    Selected Publications

    Abuauf, H., Haider, I., Jia, K.-P., Ablazov, A., Mi, J., Blilou, I., and Al-Babili, S. (2018). The Arabidopsis DWARF27 gene encodes an all-trans-/9-cis-β-carotene isomerase and is induced by auxin, abscisic acid and phosphate deficiency. Plant Science 277, 33-42.

    Al-Younis, I., Wong, A., Lemtiri-Chlieh, F., Schmöckel, S., Tester, M., Gehring, C., and Donaldson, L. (2018). The Arabidopsis thaliana K+-Uptake Permease 5 (AtKUP5) Contains a Functional Cytosolic Adenylate Cyclase Essential for K+ Transport. Frontiers in Plant Science 9.

    Aman, R., Mahas, A., Butt, H., Aljedaani, F., and Mahfouz, M. (2018). Engineering RNA Virus Interference via the CRISPR/Cas13 Machinery in Arabidopsis. Viruses 10.

    de Zélicourt, A., Synek, L., Saad, M.M., Alzubaidy, H., Jalal, R., Xie, Y., Andrés-Barrao, C., Rolli, E., Guerard, F., Mariappan, K.G., Daur, I., Colcombet, J., Benhamed, M., Depaepe, T., Van Der Straeten, D., and Hirt, H. (2018). Ethylene induced plant stress tolerance by Enterobacter sp. SA187 is mediated by 2‐keto‐4‐methylthiobutyric acid production. PLoS genetics 14, e1007273.

    Eida, A.A., Ziegler, M., Lafi, F.F., Michell, C.T., Voolstra, C.R., Hirt, H., and Saad, M.M. (2018). Desert plant bacteria reveal host influence and beneficial plant growth properties. PLOS ONE 13, e0208223.

    Serrano, N., Ling, Y., Mahfouz, M.M., Veluchamy, A., Gehring, C., Gao, G., Benhamed, M., Woo, Y.H., Atia, M., Mokhtar, M., Bazin, J., Crespi, M., and Reddy, A.S.N. (2018). Thermopriming triggers splicing memory in Arabidopsis. Journal of Experimental Botany 69, 2659-2675.

    Völz, R., Kim, S.-K., Mi, J., Rawat, A.A., Veluchamy, A., Mariappan, K.G., Rayapuram, N., Daviere, J.-M., Achard, P., Blilou, I., Al-Babili, S., Benhamed, M., and Hirt, H. (2019). INDETERMINATE-DOMAIN 4 (IDD4) coordinates immune responses with plant-growth in Arabidopsis thaliana. PLOS Pathogens 15, e1007499.
    Julkowska, M.M., Saade, S., Gao, G., Morton, M.J.L., Awlia, M., Tester, M.A., MVApp.pre-release_v2.0 mmjulkowska/MVApp: MVApp.pre-release_v2.0, DOI: 10.5281/zenodo.1067974


    Major Funding Sources

    King Abdullah University of Science and Technology.

  • Singapore Open or Close

    Eunyoung Chae
    This email address is being protected from spambots. You need JavaScript enabled to view it.
    National University of Singapore

    Use of Arabidopsis

    Arabidopsis research in Singapore is mainly led by PIs at the National University of Singapore (NUS), Temasek Life Sciences Laboratory (TLL) and Nanyang Technological University (NTU). Plant research community in Singapore also includes researchers working on rice and leafy vegetables to which knowledges gained in Arabidopsis research is actively being transferred and vice versa. Despite being small in an urban setting, research community in Singapore embraces big challenges in environmental sustainability and food security by advancing our basic understanding on plants using Arabidopsis as a major model system. Our areas of research is diverse with complementary strengths, ranging from developmental biology, plant immunity, stress biology, evolutionary genetics, and stem cell biology.  

    Conferences, Workshops and Outreach events


    18th International Congress of Developmental Biology (June 18-22, 2017)
    http://isdb2017.com/

    RNA Biology Symposium (September 13-14, 2018)
    https://www.csi.nus.edu.sg/ws/rna-biology-symposium

    10th Anniversary Conference, Mechanobiology Institute, National University of Singapore (November 7-10, 2018)
    https://mbi.nus.edu.sg/mbi-10th-anniversary-conference/

    Molecular mechanisms of developmental and regenerative biology (November 11-13, 2018)
    http://meetings.embo.org/event/18-devandregeneration

    Selected Publications

    Hong JH, Savina M, Du J, Devendran A, Kannivadi Ramakanth K, Tian X, Sim WS, Mironova VV, Xu J (2017) A Sacrifice-for-Survival Mechanism Protects Root Stem Cell Niche from Chilling Stress. Cell. 170(1):102-113.e14. doi: 10.1016/j.cell.2017.06.002. Epub 2017 Jun 22.

    Lau OS, Song Z, Zhou Z, Davies KA, Chang J, Yang X, Wang S, Lucyshyn D, Tay IHZ, Wigge PA, Bergmann DC (2018)
    Direct Control of SPEECHLESS by PIF4 in the High-Temperature Response of Stomatal Development. Curr Biol. Apr 23;28(8):1273-1280.e3. doi: 10.1016/j.cub.2018.02.054.

    Li C, Zhang B, Chen B, Ji L, Yu H (2018) Site-specific phosphorylation of TRANSPARENT TESTA GLABRA1 mediates carbon partitioning in Arabidopsis seeds.
    Nat Commun. 9(1):571. doi: 10.1038/s41467-018-03013-5.

    Li X, Tu H, Pan SQ (2018) Agrobacterium Delivers Anchorage Protein VirE3 for Companion VirE2 to Aggregate at Host Entry Sites for T-DNA Protection. Cell Rep. 25(2):302-311.e6. doi: 10.1016/j.celrep.2018.09.023.

    Liang Z, Shen L, Cui X, Bao S, Geng Y, Yu G, Liang F, Xie S, Lu T, Gu X, Yu H (2018) DNA N6-Adenine Methylation in Arabidopsis thaliana. Dev Cell. 45(3):406-416.e3. doi: 10.1016/j.devcel.2018.03.012. Epub 2018 Apr 12.

    Park BS, Yao T, Seo JS, Wong ECC, Mitsuda N, Huang CH, Chua NH (2018) Arabidopsis NITROGEN LIMITATION ADAPTATION regulates ORE1 homeostasis during senescence induced by nitrogen deficiency. Nat Plants. 4(11):898-903. doi: 10.1038/s41477-018-0269-8.

    Ravindran P, Kumar PP (2019) Regulation of Seed Germination: The Involvement of Multiple Forces Exerted via Gibberellic Acid Signaling. Mol Plant. 12(1):24-26. doi: 10.1016/j.molp.2018.12.013.

    Ravindran P, Verma V, Stamm P, Kumar PP (2017) A Novel RGL2-DOF6 Complex Contributes to Primary Seed Dormancy in Arabidopsis thaliana by Regulating a GATA Transcription Factor. Mol Plant. 10(10):1307-1320. doi: 10.1016/j.molp.2017.09.004.

    Seo JS, Sun HX, Park BS, Huang CH, Yeh SD, Jung C, Chua NH (2018) ELF18-INDUCED LONG-NONCODING RNA Associates with Mediator to Enhance Expression of Innate Immune Response Genes in Arabidopsis. Plant Cell. 29(5):1024-1038. doi: 10.1105/tpc.16.00886

    Sun H, Qiao Z, Chua KP, Tursic A, Liu X, Gao YG, Mu Y, Hou X, Miao Y (2018) Profilin Negatively Regulates Formin-Mediated Actin Assembly to Modulate PAMP-Triggered Plant Immunity. Curr Biol. 28(12):1882-1895.e7. doi: 10.1016/j.cub.2018.04.045.

    Tao Z, Shen L, Gu X, Wang Y, Yu H, He Y (2017) Embryonic epigenetic reprogramming by a pioneer transcription factor in plants.Nature. 2017 Nov 2;551(7678):124-128. doi: 10.1038/nature24300

    Major Funding Sources

    National Research Foundation Singapore (Prime Minister’s Office Singapore) https://www.nrf.gov.sg/
    Ministry of Education, Singapore
    https://www.moe.gov.sg/
    Agri-Food and Veterinary Authority of Singapore (AVA)
    https://www.ava.gov.sg/
    Temasek Foundation Innovates
    http://www.temasekfoundation-innovates.org.sg/

  • 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

    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

    New Resources and Software tools available for Arabidopsis Researchers that have been initiated or funded in 2018/ early 2019.

    - Next generation breeding program, will be starting in the second half of 2019 focusing on genome editing, approximately 7M USD/yr for 7 years.

    Conferences, Workshops and Outreach events
    - In year 2019, Cold Spring Harbor Asia conference on plant cell and development

    Publications

    - Han S, Cho H, Noh J, Qi J, Jung HJ, Nam H, Lee S, Hwang D, Greb T, Hwang I (2018) BIL1-mediated MP phosphorylation integrates PXY and cytokinin signaling in secondary growth. Nat Plants. 4:605-614.
    - Kang BC, Yun JY, Kim ST, Shin Y, Ryu J, Choi M, Woo JW, Kim JS. (2018) Precision genome engineering through adenine base editing in plants. Nat Plants. 4:427-431.
    - Kim H, Kim HJ, Vu QT, Jung S, McClung CR, Hong S, Nam HG. (2018) Circadian control of ORE1 by PRR9 positively regulates leaf senescence in Arabidopsis. Proc Natl Acad Sci U S A. 115:8448-8453.
    - Kim JY, Yang W, Forner J, Lohmann JU, Noh B, Noh YS. (2018) Epigenetic reprogramming by histone acetyltransferase HAG1/AtGCN5 is required for pluripotency acquisition in Arabidopsis. EMBO J. 37. pii: e98726.
    - Kim TW, Youn JH, Park TK, Kim EJ, Park CH, Wang ZY, Kim SK, Kim TW. (2018) OST1 Activation by the Brassinosteroid-Regulated Kinase CDG1-LIKE1 in Stomatal Closure. Plant Cell. 30:1848-1863.
    - Kwon Y, Shen J, Lee MH, Geem KR, Jiang L, Hwang I. (2018) AtCAP2 is crucial for lytic vacuole biogenesis during germination by positively regulating vacuolar protein trafficking. Proc Natl Acad Sci U S A. 115:E1675-E1683.
    - Lee HG, Seo PJ. (2019) MYB96 recruits the HDA15 protein to suppress negative regulators of ABA signaling in Arabidopsis. Nat Commun. 10:1713.
    - Lee Y, Yoon TH, Lee J, Jeon SY, Lee JH, Lee MK, Chen H, Yun J, Oh SY, Wen X, Cho HK, Mang H, Kwak JM. (2018) A Lignin Molecular Brace Controls Precision Processing of Cell Walls Critical for Surface Integrity in Arabidopsis. Cell. 173:1468-1480.e9.
    - Nguyen HH, Lee MH, Song K, Ahn G, Lee J, Hwang I. (2018) The A/ENTH Domain-Containing Protein AtECA4 Is an Adaptor Protein Involved in Cargo Recycling from the trans-Golgi Network/Early Endosome to the Plasma Membrane. Mol Plant. 11:568-583.
    - Park HJ, Baek D, Cha JY, Liao X, Kang SH, McClung CR, Lee SY, Yun DJ, Kim WY. (2019) HOS15 Interacts with the Histone Deacetylase HDA9 and the Evening Complex to Epigenetically Regulate the Floral Activator GIGANTEA. Plant Cell. 31:37-51.

    Major Funding Sources

    - National Research Funding (Korea) (https://www.nrf.re.kr/)
    - Rural Development Agency (Korea) (https://www.rda.go.kr/)

     

  • 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

    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.

    New Resources and Software tools available for Arabidopsis Researchers that have been initiated or funded in 2018 or early 2019

    Some software packages were made available to the community, including:

    “Easymap: a program that eases mapping-by-sequencing of large insertions and point mutations.”, developed by D. Wilson-Sánchez, S.D. Lup, S. Andreu-Sánchez and J.L. Micol. Available at http://genetics.edu.umh.es/resources/easymap/

    “MyROOT: a method and software for the semiautomatic measurement of primary root length in Arabidopsis seedlings”, developed by I. Betegón‐Putze, A. González, X. Sevillano, D. Blasco‐Escámez, A.I. Caño‐Delgado. Available at https://www.cragenomica.es/research-groups/brassinosteroid-signaling-in-plant-development

    Conferences, Workshops and Outreach events

    - The “XIV Meeting on Plant Molecular Biology” was organized by plant biologists lead by Prof. Óscar Lorenzo in Salamanca (July 4-6, 2018).

    - The “III Workshop on New Frontiers in Plant Biology” was organized by members of the Center of Plant Biotechnology and Genomics lead by Prof Antonio Molina in Madrid (May 30-June 1, 2018).

    - The “At the Forefront of Plant Research 2019” workshop was organized by members of the Centre for Research in Agricultural Genomics lead by Prof José Luis Riechmann in Barcelona (May 6-8, 2019).

    - SEB Annual Meeting: July 2nd-5th, Sevilla:
    http://www.sebiology.org/events/event/seb-seville-2019

    - SEB Plant and Cell Symposium on Impact of chromatin domains on plant phenotypes: December 9th-11th, El Escorial, near Madrid Spain.
    https://www.sebiology.org/events/event/impact-of-chromatin-domains-on-plant-phenotypes

    Selected Publications

    AAbbas M, Hernández-García J, Pollmann S, Samodelov SL, Kolb M, Friml J, Hammes UZ, Zurbriggen MD, Blázquez MA and Alabadí D (2018) Auxin methylation is required for differential growth in Arabidopsis. PNAS 115: 6864-6869.
    Fábregas N, Lozano-Elena F, Blasco-Escámez D, Tohge T, Martínez-Andújar C, Albacete A, Osorio S, Bustamante M, Riechmann JL, Nomura T, Yokota T, Conesa A, Alfocea FP, Fernie AR and Caño-Delgado AI (2018) Overexpression of the vascular brassinosteroid receptor BRL3 confers drought resistance without penalizing plant growth. Nature Communications 9: 4680.

    Gómez-Zambrano A, Crevillén P, Franco-Zorrilla JM, López JA, Moreno-Romero J, Roszak P, Santos-González J, Jurado S, Vázquez J, Kohler C, Solano R, Piñeiro M and Jarillo JA (2018) Arabidopsis SWC4 binds DNA and recruits the SWR1 Complex to modulate histone H2A.Z deposition at key regulatory genes. Molecular Plant 11: 815-832.

    Huertas R, Catalá R, Jiménez-Gómez JM, Castellano MM, Crevillén P, Piñeiro M, Jarillo JA and Salinas J (2019) Arabidopsis SME1 regulates plant development and response to abiotic stress by determining spliceosome activity specificity. Plant Cell 31: 537-554.

    Martínez C, Espinosa-Ruíz A, de Lucas M, Bernardo-García S, Franco-Zorrilla JM and Prat S (2018) PIF4-induced BR synthesis is critical to diurnal and thermomorphogenic growth. EMBO Journal 37: e99552.

    Mateo-Bonmatí E, Esteve-Bruna D, Juan-Vicente L, Nadi R, Candela H, Lozano FM, Ponce MR, Pérez-Pérez JM and Micol JL (2018) INCURVATA11 and CUPULIFORMIS2 are redundant genes that encode epigenetic machinery components in Arabidopsis. Plant Cell 30: 1596-1616.

    Ojeda V, Pérez-Ruiz JM and Cejudo FJ (2018) 2-cys peroxiredoxins participate in the oxidation of chloroplast enzymes in the dark. Molecular Plant 11: 1377-1388.

    Olate E, Jiménez-Gómez JM, Holuigue L and Salinas J (2018) NPR1 mediates a novel regulatory pathway in cold acclimation by interacting with HSFA1 factors. Nature Plants 4: 811-823.

    Ortiz-Alcaide M, Llamas E, Gómez-Cadenas A, Nagatani A, Martínez-García JF and Rodríguez-Concepción M (2019) Chloroplasts modulate elongation responses to canopy shade by retrograde pathways Involving HY5 and Abscisic Acid. Plant Cell 31: 384-398.

    Sánchez-Montesino R, Bouza-Morcillo L, Márquez J, Ghita M, Durán-Nebreda S, Gómez L, Holdsworth MJ, Bassel G and Oñate-Sánchez L (2019) A regulatory module controlling GA-mediated endosperm cell expansion is critical for seed germination in Arabidopsis. Molecular Plant 12: 71-85.

    Major Funding Sources

    About 80 grants from the State Research Agency of Spain (Ministry of Science, Innovation and Universities) fund Arabidopsis research projects at individual laboratories.

    Additional Information

    Authors from laboratories studying Arabidopsis in Spain published about 400 papers in the last year. Prof. Crisanto Gutiérrez was awarded a European Research Council Advanced Grant (“Exploiting genome replication to design improved plant growth strategies”).

    Prof. José Luis Micol was elected President of the Genetics Society of Spain.

     

  • 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

    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.

    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.

    2019 Highlights
    -    Trinational Arabidopsis meeting will be held in Zurich in April 2019.  
    Switzerland has had regularly a high-quality publications (e.g. Paape T et al., Nat Commun. 2018, Schumacher P et al., Nat Commun. 2018, Schmid MW et al., Nat Commun. 2018, Hohmann U et al., Nat Plants. 2018, Song YH et al.,Nat Plants. 2018).

    New Resources and Software tools available for Arabidopsis Researchers that have been initiated or funded in 2018 or early 2019

    - Software tools
    - Homeolog expression quantification methods for allopolyploids
    Kuo TCY, Hatakeyama M, Tameshige T, Shimizu KK, Sese J.
    Brief Bioinform. 2018 Dec 27.
    doi: 10.1093/bib/bby121.

    - Resources
    Rapid extraction of living primary veins from the leaves of Arabidopsis thaliana.
    Kurenda A, Farmer EE.
    Protocol Exchange (2018)
    doi:10.1038/protex.2018.119

    Conferences, Workshops and Outreach events

    Conferences

    -       PSC Summer school 2018, Responsible Research and Innovation in Plant Sciences, 10 – 14 Sep 2018, Einsiedeln

    https://www.plantsciences.uzh.ch/dam/jcr:e9880fdf-8519-4805-b551-29705dbbea29/Flyer_PSC_Summer_School_2018_final%5B2%5D.pdf

    -       Plant Receptor Kinases and Related Pathways, 30 Oct 2018, Zurich

    https://www.botinst.uzh.ch/dam/jcr:c8706be2-9920-45f9-a570-e8692a2cbd60/Programm_RLK-Symposium.pdf

    -       PSC Symposium 2018, Breakthroughs in Plant Sciences,

    5 Dec 2018, Zurich

    https://www.plantsciences.uzh.ch/en/outreach/conferences/breakthroughs-in-plant-sciences.html

    -       SwissPLANT symposium 2019, 30 Jan - 1 Feb 2019, Meiringen

    https://swissplantscienceweb.unibas.ch/fileadmin/user_upload/swissplantscienceweb/Event/Swissplant/swissplant2019_program_v2.pdf

    -       Lausanne Genomics Days 2019, 7 – 8 Feb 2019, Lausanne http://www.genomyx.ch/thur-feb-7-fri-feb-8-2019-lausanne-genomics-days-2019/

    -       Biology19, 7 – 8 Feb 2019, Zurich

    https://www.biology19.ch/

    -       11th TNAM (Tri-National Arabidopsis Meeting), 10-12 Apr 2019, Zurich

    https://www.tnam2019.ethz.ch/

    -       SwissPLANT symposium 2020, 29 – 31 Jan 2020, Ovronnaz

    https://swissplantscienceweb.unibas.ch/en/events/swissplant/

    Workshops

    Outreach Activities

    -       Plant Science at School

    Continuing Education Program in Plant Sciences for Secondary School Teachers

    Over the past four 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

     

    Selected Publications

    Arongaus AB, Chen S, Pireyre M, Glöckner N, Galvão VC, Albert A, Winkler JB, Fankhauser C, Harter K, Ulm R (2018) Arabidopsis RUP2 represses UVR8-mediated flowering in noninductive photoperiods Genes Dev. 2018 Oct 1;32(19-20):1332-1343. doi: 10.1101/gad.318592.118.

    de Wit M, George GM, Ince YÇ, Dankwa-Egli B, Hersch M, Zeeman SC, Fankhauser C (2018) Changes in resource partitioning between and within organs support growth adjustment to neighbor proximity in <i>Brassicaceae</i> seedlings. Proc Natl Acad Sci U S A. 115(42):E9953-E9961. doi: 10.1073/pnas.1806084115.

    Hohmann U, Nicolet J, Moretti A, Hothorn LA, Hothorn M (2018) The SERK3 elongated allele defines a role for BIR ectodomains in brassinosteroid signalling. Nat Plants 4(6):345-351. doi: 10.1038/s41477-018-0150-9.

    Nguyen CT, Kurenda A, Stolz S, Chételat A, Farmer EE (2018) Identification of cell populations necessary for leaf-to-leaf electrical signaling in a
    wounded plant Proc Natl Acad Sci U S A. 115(40):10178-10183. doi: 10.1073/pnas.1807049115.
    Paape T, Briskine RV, Halstead-Nussloch G, Lischer HEL, Shimizu-Inatsugi R, Hatakeyama M, Tanaka K, Nishiyama T, Sabirov R, Sese J, Shimizu KK (2018) - Patterns of polymorphism and selection in the subgenomes of the allopolyploid Arabidopsis kamchatica. Nat Commun. 9(1):3909.  doi: 10.1038/s41467-018-06108-1.

    Schmid MW, Heichinger C, Coman Schmid D, Guthörl D, Gagliardini V, Bruggmann R, Aluri S, Aquino C, Schmid B, Turnbull LA, Grossniklaus U (2018) Contribution of epigenetic variation to adaptation in Arabidopsis Nat Commun. 9(1):4446. doi: 10.1038/s41467-018-06932-5

    Schreier TB, Cléry A, Schläfli M, Galbier F, Stadler M, Demarsy E, Albertini D, Maier BA, Kessler F, Hörtensteiner S, Zeeman SC, Kötting O (2018) Plastidial NAD-Dependent Malate Dehydrogenase: A Moonlighting Protein Involved in Early Chloroplast Development through Its Interaction with an FtsH12-FtsHi Protease Complex Plant Cell. 2018 Aug;30(8):1745-1769. doi: 10.1105/tpc.18.00121. Epub 2018 Jun 22.

    Schumacher P, Demarsy E, Waridel P, Petrolati LA, Trevisan M, Fankhauser C (2018)
    A phosphorylation switch turns a positive regulator of phototropism into an inhibitor of the process Nat Commun. 9(1):2403.  doi: 10.1038/s41467-018-04752-1.

    Song YH, Kubota A, Kwon MS, Covington MF, Lee N, Taagen ER, Laboy Cintrón D, Hwang DY, Akiyama R, Hodge SK, Huang H, Nguyen NH, Nusinow DA, Millar AJ, Shimizu KK, Imaizumi T (2018) Molecular basis of flowering under natural long-day conditions in Arabidopsis Nat Plants. 4(10):824-835. doi: 10.1038/s41477-018-0253-3.

    Major Funding Sources

    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/

     

  • Taiwan Open or Close

    Cheng-Hsun Ho, This email address is being protected from spambots. You need JavaScript enabled to view it.
    Agriculture Biotechnology Research Center, Academia Sinica

    New Resources and Software tools available for Arabidopsis Researchers that have been initiated or funded in 2018 or early 2019

    Please provide a list of all resources based in your country that are accessible for use both by Arabidopsis researchers in your country and by the global community.
    1. Plants of Taiwan (http://tai2.ntu.edu.tw)
    2. Orchidstra 2.0 - A Transcriptomics Resource for the Orchid Family (http://orchidstra2.abrc.sinica.edu.tw/orchidstra2/index.php)
    3. Taiwan Biobank (https://www.twbiobank.org.tw/new_web/)
    4. Database of Native Plant in Taiwan (http://www.hast.biodiv.tw/Announce/projectContentE.aspx)
    5. Discover Plants of Taiwan (http://taiwanplants.ndap.org.tw)
    6. Herbarium of Taiwan Forestry Research Institute (http://taif.tfri.gov.tw/cht/) Herbarium School of 7. Forestry and Resource Conservation, National Taiwan University (http://ntuf.cc.ntu.edu.tw)
    7. Taiwan Rice Insertional Mutants Database

    Conferences, Workshops and Outreach events

    1. TAIWAN Prostate Cancer Consortium Mini-symposium.

    2. Taiwan Protein Project (TPP) Symposium

    3. EMBO Workshop- Neural Development

    4. 2018 IPMB Scientific Advisory Board Meeting

    5. 2018 NTU- CUHKPlant Biology Symposium

    6. 19th International Symposium on Iron Nutrition and Interactions in Plants (ISINIP)

    7. Global Leadership Summit Taiwan

    8. NPAS Seminar: 2019 ASIA-PACIFIC DROSOPHILA NEUROBIOLOGY CONFERENCE

    9. AS-NIH-TMU Joint Neuroscience Symposium

    10. The 17th International Symposium on Rice Functional Genomics (ISRFG2019)

    11. SFEM 2018/IUFRO 4.02.02

    12. The 6th Taiwan–Japan Ecology Workshop

    13. 7th ASIAN SYMPOSIUM OF FERNS & LYCOPHYTES

    14. Frontiers in BioAgricultural Research: The 20th Anniversary of the Agricultural Biotechnology Research Center, Academia Sinica

    15. 2019 Symposium on Biotechnology Development in Taiwan – Medical Structural Biology and Cryo-EM Technology

    16. International Membrane Conference in Taiwan (IMCT2019)

    17. International Conference on Planarization / CMP Technology (ICPT 2019)

    18. The 2nd International Conference on Nanomaterials and Advanced Composites


    Selected Publications

    - Chao, Y.C., Fleischer, J., and Yang, R.B. (2018). Guanylyl cyclase-G is an alarm pheromone receptor in mice. EMBO J 37, 39-49.

    - Chen, H.F., Hsu, C.M., and Huang, Y.S. (2018). CPEB2-dependent translation of long 3’-UTR Ucp1 mRNA promotes thermogenesis in brown adipose tissue. EMBO J 37.

    - Chen, Y.L., Chen, L.J., Chu, C.C., Huang, P.K., Wen, J.R., and Li, H.M. (2018). TIC236 links the outer and inner membrane translocons of the chloroplast. Nature 564, 125-129.

    - Grillet, L., Lan, P., Li, W., Mokkapati, G., and Schmidt, W. (2018). IRON MAN is a ubiquitous family of peptides that control iron transport in plants. Nat Plants 4, 953-963.
    5.

    - Li, F.W., Brouwer, P., Carretero-Paulet, L., Cheng, S., de Vries, J., Delaux, P.M., Eily, A., Koppers, N., Kuo, L.Y., Li, Z., et al. (2018). Fern genomes elucidate land plant evolution and cyanobacterial symbioses. Nat Plants 4, 460-472.

    - Lin, P.P., Jaeger, A.J., Wu, T.Y., Xu, S.C., Lee, A.S., Gao, F., Chen, P.W., and Liao, J.C. (2018). Construction and evolution of an Escherichia coli strain relying on nonoxidative glycolysis for sugar catabolism. Proc Natl Acad Sci U S A 115, 3538-3546.

    - Liu, C.P., Tsai, T.I., Cheng, T., Shivatare, V.S., Wu, C.Y., Wu, C.Y., and Wong, C.H. (2018). Glycoengineering of antibody (Herceptin) through yeast expression and in vitro enzymatic glycosylation. Proc Natl Acad Sci U S A 115, 720-725.

    - Liu, W., Duttke, S.H., Hetzel, J., Groth, M., Feng, S., Gallego-Bartolome, J., Zhong, Z., Kuo, H.Y., Wang, Z., Zhai, J., et al. (2018). RNA-directed DNA methylation involves co-transcriptional small-RNA-guided slicing of polymerase V transcripts in Arabidopsis. Nat Plants 4, 181-188.

    - Ren, R., Wang, H., Guo, C., Zhang, N., Zeng, L., Chen, Y., Ma, H., and Qi, J. (2018). Widespread Whole Genome Duplications Contribute to Genome Complexity and Species Diversity in Angiosperms. Mol Plant 11, 414-428

    - Xu, F., Kuo, T., Rosli, Y., Liu, M.S., Wu, L., Chen, L.O., Fletcher, J.C., Sung, Z.R., and Pu, L. (2018). Trithorax Group Proteins Act Together with a Polycomb Group Protein to Maintain Chromatin Integrity for Epigenetic Silencing during Seed Germination in Arabidopsis. Mol Plant 11, 659-677.

    Major Funding Sources

    Ministry of Science and Technology, Taiwan (https://www.most.gov.tw/?l=en)
    Academia Sinica (https://www.sinica.edu.tw/en)

  • Turkey Open or Close

    Baris Uzilday, Ege University, Faculty of Science,

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

    Additional Information about Arabidopsis research in your country

    Majority of the plant science in Turkey focus on crop plants such as wheat as plant material. This is not surprising since Turkey is among the gene centers of wheat and some other crops and has a large arable land, which is roughly 1/5 of total of EU28. Also, Turkey has rich plant diversity due to diverse habitat types and in recent years plant scientist has focused on biology of endemic plant species that reside in these habitats.

    There are only few laboratories that utilize Arabidopsis as a model for physiological or molecular studies (some of them are listed above in the publications). However, in the recent years, some laboratories also started to utilize Arabidopsis-related model species (ARMS) that are found in Turkey to elucidate differential responses between Arabidopsis and its extremophile relatives at biochemical and molecular level. Some example plant species are extreme halophyte Schrenkiella parvula (Eutrema parvulum) that is found around Salt Lake (central Anatolia, Turkey) or Arabis alpina, which is an artic-alpine species. Turkey has a biodiversity potential that can be synergistically exploited in conjugation with Arabidopsis and tools it provide to researchers.

    Conferences, Workshops and Outreach events

    3rd National Plant Physiology Symposium (UBFS2018)

    Selected Publications

    Arıkan, B., Özden, S., & Turgut-Kara, N. (2018). DNA methylation related gene expression and morphophysiological response to abiotic stresses in Arabidopsis thaliana. Environmental and Experimental Botany, 149, 17-26.

    Cevher-Keskin, B., Yıldızhan, Y., Yüksel, B., Dalyan, E., & Memon, A. R. (2019). Characterization of differentially expressed genes to Cu stress in Brassica nigra by Arabidopsis genome arrays. Environmental Science and Pollution Research, 26(1), 299-311.

    Çelik, Ö., Atak, Ç., & Suludere, Z. (2018). Comparative transcriptional profiling of soybean orthologs of arabidopsis trichome developmental genes under salt stress. Plant molecular biology reporter, 36(1), 82-93.

    Kayihan, D.S., Kayihan, C., Çiftçi, Y.Ö. (2019). Moderate level of toxic boron causes differential regulation of microRNAs related to jasmonate and ethylene metabolisms in Arabidopsis thaliana. Turkish Journal of Botany, 43(2), 167-172.

    Koç, I., Yuksel, I., & Caetano-Anollés, G. (2018). Metabolite-Centric Reporter Pathway and Tripartite Network Analysis of Arabidopsis Under Cold Stress. Frontiers in bioengineering and biotechnology, 6.

    Pehlivan, N. (2019). Stochasticity in transcriptional expression of a negative regulator of Arabidopsis ABA network. 3 Biotech, 9(1), 15.

    Surgun-Acar, Y., Zemheri-Navruz, F. (2019). 24-Epibrassinolide promotes arsenic tolerance in Arabidopsis thaliana L. by altering stress responses at biochemical and molecular level. Journal of plant physiology, 238, 12-19.

    Uzilday, B., Ozgur, R., Sekmen, A. H., & Turkan, I. (2018). Endoplasmic reticulum stress regulates glutathione metabolism and activities of glutathione related enzymes in Arabidopsis. Functional Plant Biology, 45(2), 284-296.

    Yalcinkaya, T., Uzilday, B., Ozgur, R., Turkan, I. (2019). The roles of reactive carbonyl species in induction of antioxidant defence and ROS signalling in extreme halophytic model Eutrema parvulum and glycophytic model Arabidopsis thaliana. Environmental and Experimental Botany, 160, 81-91.

    Major Funding Sources

    The Scientific and Technological Research Council of Turkey (TUBITAK)

    https://www.tubitak.gov.tr/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

    Use of Arabidopsis

    The United Kingdom has approximately 45 academic departments and research institutes that are actively conducting Arabidopsis research.

    New Resources and Software tools available for Arabidopsis Researchers that have been initiated or funded in 2018 or early 2019

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

    - The PhenomUK: The UK Plant Phenomics Network is a Technology Touching Life network grant that provides phenotyping opportunities for UK researchers to use the core facilities situated around the country. https://www.phenomuk.net/

    - Ara-BOX-cis database allows interrogation on how bHLHs and bZIPs (which are expressed in seedlings) regulate genes downstream of perfect G-boxes (CACGTG).
    http://araboxcis.org/

    - The DNA BioFoundry at the Earlham Institute. This synthetic biology hub allows facile preparation of golden gate clones for use by plant scientists. http://www.earlham.ac.uk/earlham-dna-foundry

    - Community Wheat Transformation resource allows UK Arabidopsis researchers to propose for their gene of interest to be introduced into wheat. https://www.niab.com/transgenic

    - Visit the GARNet Resources Page for a categorised list of software tools available for plant scientists. These have been curated from the pages of previous MASC Annual reports so are up to date with new resources. https://www.garnetcommunity.org.uk/resources

    - The Computer Vision Lab at the University of Nottingham is developing a range of software tools for plant phenotyping in which Arabidopsis is used as a test organism,  https://www.nottingham.ac.uk/research/groups/cvl/projects/the4dplant.aspx

    - Advice for Gene Editing in Arabidopsis from Jonathan Jones’ lab at The Sainsbury Lab, Norwich.
    Castel B, Tomlinson L, Locci F, Yang Y, Jones JDG (2019) Optimization of T-DNA architecture for Cas9-mediated mutagenesis in Arabidopsis. PLoS One https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0204778

    Conferences, Workshops and Outreach events

    - GARNet2018: University of York. September 18th-19th 2018. GARNet welcomed 80 delegates to its biennial meeting in which researchers learnt about cutting edge areas of plant biology. http://garnet2018.weebly.com/
    - GARNet-New Phytologist CRISPR Workshop: University of Bristol. March 23rd-24th 2018. Over 100 delegates learnt about the technical and regulatory issues surrounding the use of gene editing technology. https://garnet-ge-workshop.weebly.com/
    - GARNet-CyverseUK RNAseq Analysis Workshop. December 10th-12th 2018. This event held at the Earlham institute provides software tools available for the analysis of this widely used source of data. http://www.earlham.ac.uk/cyverse-uk-rnaseq-workshop-2018
    - Plant Preview 2018: Lancaster University. September 3-4th 2018 http://wp.lancs.ac.uk/plastidpreview2018/
    - BSPP Imaging Plant-Microbe Interactions. University of Warwick. December 10th-11th 2018 http://www.bspp.org.uk/meetings/bspppres2018.php
    - The Hidden Half at the University of Nottingham is an outstanding scientific and science communication project that uses X-ray computed tomography to visualise plant roots.  https://www.nottingham.ac.uk/hiddenhalf/home.aspx
    - RMS Botanical Microscopy 2019: University of Oxford. April 14th-18th 2019. https://www.rms.org.uk/discover-engage/event-calendar/botanical-microscopy-2019.html
    - European Plant Science Retreat: University of Nottingham. July 8th-10th 2019.
    https://epsr2019.wordpress.com/about/
    - IS-MPMI University of Glasgow: July 14th-18th 2019. https://www.ismpmi.org/Congress/2019/Pages/default.aspx
    - CellWall2019: University of Cambridge. July 7th-12th 2019. http://cellwall2019.org/
    - GARNet workshop on Advances in Plant Imaging. University of Warwick. September 9th-10th 2019. https://garnetimaging19.weebly.com/    
    - Plants Planet People Symposium: Kew Gardens. September 4th-5th 2019 https://www.newphytologist.org/symposia/ppp2019

    Selected Publications

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

    Calixto CPG, Guo W, James AB, Tzioutziou NA, Entizne JC, Panter PE, Knight H,  Nimmo HG, Zhang R, Brown JWS (2018) Rapid and Dynamic Alternative Splicing Impacts the  Arabidopsis Cold Response Transcriptome. Plant Cell. doi: 10.1105/tpc.18.00177

    Choi K, Zhao X, Tock AJ, Lambing C, Underwood CJ, Hardcastle TJ, Serra H, Kim  J, Cho HS, Kim J, Ziolkowski PA, Yelina NE, Hwang I, Martienssen RA, Henderson IR (2018) Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis thaliana transposons and gene regulatory regions. Genome Res. doi: 10.1101/gr.225599.117

    Frank A, Matiolli CC, Viana AJC, Hearn TJ, Kusakina J, Belbin FE, Wells Newman D, Yochikawa A, Cano-Ramirez DL, Chembath A, Cragg-Barber K, Haydon MJ, Hotta CT, Vincentz M, Webb AAR, Dodd AN (2018) Circadian Entrainment in Arabidopsis by the Sugar-Responsive Transcription Factor bZIP63. Curr Biol. doi: 10.1016/j.cub.2018.05.092

    Gould PD, Domijan M, Greenwood M, Tokuda IT, Rees H, Kozma-Bognar L, Hall AJ,  Locke JC (2018) Coordination of robust single cell rhythms in the Arabidopsis circadian clock via spatial waves of gene expression. Elife. doi: 10.7554/eLife.31700

    Li XR, Deb J, Kumar SV, Østergaard L (2018) Temperature Modulates Tissue-Specification Program to Control Fruit Dehiscence in Brassicaceae. Mol Plant. doi: 10.1016/j.molp.2018.01.003

    Srivastava AK, Orosa B, Singh P, Cummins I, Walsh C, Zhang C, Grant M, Roberts MR, Anand GS, Fitches E, Sadanandom A (2018) SUMO Suppresses the Activity of the Jasmonic Acid Receptor CORONATINE INSENSITIVE1. Plant Cell. doi: 10.1105/tpc.18.00036

    Walker J, Gao H, Zhang J, Aldridge B, Vickers M, Higgins JD, Feng X (2018) Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. Nat Genet. doi: 10.1038/s41588-017-0008-5

    Williams A, Pétriacq P, Schwarzenbacher RE, Beerling DJ, Ton J (2018) Mechanisms of  glacial-to-future atmospheric CO(2) effects on plant immunity. New Phytol. doi: 10.1111/nph.15018

    Whitewoods CD, Cammarata J, Nemec Venza Z, Sang S, Crook AD, Aoyama T, Wang XY, Waller M, Kamisugi Y, Cuming AC, Szövényi P, Nimchuk ZL, Roeder AHK, Scanlon  MJ, Harrison CJ (2018) CLAVATA Was a Genetic Novelty for the Morphological Innovation of 3D Growth in Land Plants. Curr Biol. doi: 10.1016/j.cub.2018.05.068

    Wibowo A, Becker C, Durr J, Price J, Spaepen S, Hilton S, Putra H, Papareddy R, Saintain Q, Harvey S, Bending GD, Schulze-Lefert P, Weigel D, Gutierrez-Marcos J (2018) Partial maintenance of organ-specific epigenetic marks during plant asexual reproduction leads to heritable phenotypic variation. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1805371115

    Major Funding Sources

    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/

    The Leverhulme Trust: https://www.leverhulme.ac.uk/

  • United States Open or Close

    Joanna Friesner, NAASC Executive Director (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) https://www.araport.org/community/group/naasc

    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.

    New Resources and Software tools available for Arabidopsis Researchers that have been initiated or funded in 2018 or early 2019

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

    1.    DiversifyPlantSci Resource: NAASC is committed to promoting a global plant sciences community that reflects the true diversity of all its members. To further this mission the NAASC Diversity and Inclusion Task Force have created the DiversifyPlantSci online resource, a list of plant biologists from under-represented groups* to reference for consideration when inviting speakers, reviewers, and participants for career or mentorship opportunities. This list is intended to highlight the diversity within the global plant science community. We hope to increase diversity and inclusion by making it easy to expand invitations past one’s personal networks. *List includes plant scientists who identify in 1 or more of these under-represented categories as defined by NSF: Women; persons with disabilities; and three racial and ethnic groups—blacks, Hispanics, and American Indians or Alaska Natives—are underrepresented in US STEM; we also include Filipino. www.nsf.gov/statistics/2017/nsf17310/digest/introduction/
    a.    You may add your name (or forward to others to add themselves) at this google form URL: https://goo.gl/forms/s461eDrbKzoK1JzD2
    b.    Public list: https://tinyurl.com/DiversifyPlantSci; Twitter: @DiversifyPlants
    2.    ViVa: Visualizing Variation in the Arabidopsis thaliana 1001 genomes project
    a.    tool website: plantsynbiolab.bse.vt.edu/ViVa
    b.    tool description: https://www.biorxiv.org/content/10.1101/488395v1?rss=1    

    Conferences, Workshops and Outreach events

    1.    6-10 July, 2020: ICAR 2020: Novel Approaches and Planning Underway for the 31st International Conference on Arabidopsis Research: Seattle, Washington, USA, at the University of Washington, Seattle. The next ICAR (http://icar2020.arabidopsisresearch.org) will be organized by NAASC in Seattle for the first time. Notably, NAASC is undertaking new approaches to develop an exciting and diverse program. We will achieve this in four ways:
    a.    We will invite session proposals from the community via an online interface (preliminary submission deadline: 31 July 2019*. This new approach will enable platform concurrent sessions to be proposed and organized by the community and will include funds to cover registration costs for organizers and speakers in the selected sessions. Covering registration will enable session leaders to recruit speakers and simultaneously enable new, creative topics to be put forth by the plant science community.
    b.    We will solicit new session topics and invited speaker nominations from the community via the online interface*. This approach will expand the conference’s diversity of themes and speakers.
    c.    NAASC recently developed the DiversifyPlantSci online resource to promote diversity, inclusion and equity (https://tinyurl.com/DiversifyPlantSci); “DiversifyPlantSci” is a list of self-identified plant scientists from under-represented groups to reference when inviting speakers and participants for ICAR sessions. This list is intended to highlight the diversity within the global plant science community. NAASC will strongly encourage diversity within community session proposals and invited speaker lists and will monitor submissions to ensure they reflect geographic and institutional diversity as well as diversity in career stage, gender, topic, etc. We are also setting aside several platform sessions to be organized by students and postdocs to promote career development.
    d.    An international external advisory board (EAB) was convened for ICAR 2020, an effort led by Jose Dinneny of NAASC, and chaired by past NAASC member, Blake Meyers (Danforth Center). The EAB met several times in late 2017/early 2018 and provided numerous recommendations to NAASC with respect to ICAR 2020. The ICAR 2020 EAB members are listed at the NAASC site: www.araport.org/community/group/naasc

    These new approaches will contribute to a new and creative ICAR program, enable us to get beyond the ‘usual networks’, and develop an engaging plant science conference that is inclusive and welcoming to all.
    *The online interface for submissions and input can be found via the survey linked at the ICAR 2020 homepage; the site also contains the preliminary deadline for community submissions for propsals (31 July 2019): http://icar2020.arabidopsisresearch.org

    2.    November, 2018: “Broadening the Impact of Plant Science Through Community-Based Innovation, Evaluation and Sharing of Outreach Programs” Workshop*: José Dinneny, Liz Haswell, Roger Innes and Joanna Friesner of NAASC led the workshop at UC Davis (Davis, CA, USA); the workshop’s overarching objective was to “re-envision how plant science outreach programs are funded, evaluated, acknowledged and shared within the plant science community” with specific focus on being more Innovative, Inclusive, and Integrative in how plant scientists engage with students, the broader public, and leverage the power of plants to improve our world now and in the future. A white paper generated by workshop participants is in development.

    3.    November 2018: “Seeds of Change: Using Plants to Broaden the Impact of Science in Society” Minisymposium*- Videos of talks are posted at https://www.araport.org/community/group/naasc. The symposium featured these 7 speakers with titles: “Overview on Science Outreach Approaches, J. Dinneny”, “Developing the next generation of diverse scientists: Be A Scientist program as a model for University-public school partnerships, M. Wildermuth”;  “Rapid-cycling Brassica rapa as an educational a model plant, R. Amasino”; “Let the real you shine: programs to enhance diversity and inclusion in graduate education, Y. Sun”; “Democratizing science education, A. Schnoes”; “Improving science literacy through art, R. Hangarter”; “Podcasting for community-building and community-broadening, L. Haswell”.
    a.    Videos at: https://www.araport.org/community/group/naasc

    4.    June 2018: “ Communicating Science in the Age of Fake News: Broadening Your Impact” Workshop*: Roger Innes (moderator) and Liz Haswell, of NAASC, organized this community workshop which focused on effectively communicating science with the general public, during the 2018 ICAR in Finland. Presentation slides and summary are posted at https://community.plantae.org/article/5053302916895475351/communicating-science-in-the-age-of-fake-news-broadening-your-impact. The workshop’s main objectives were to share effective public science engagement activities and to enable conversations amongst participants that can lead to future discussions and implementation of novel ideas and approaches. The presenters cover a diverse set of public engagement activities (e.g. hands-on activities at public gatherings, YouTube videos, educational modules for schools, social media, etc.) followed by Q&A and small group breakout discussions of success stories and challenges that were overcome during public engagement. Speakers presented on: “Overview/Objectives, R. Innes”; “The public engagement imperative, O. Leyser”; “Reaching out to K-12, A. N. Stepanova”, “Overcoming the language barrier with fascinating plants, K. Sims-Huopaniemi; and “The 2Blades Foundation, H. P. van Esse”.
    a.    Presentation slides and workshop findings summary at: https://community.plantae.org/article/5053302916895475351/communicating-science-in-the-age-of-fake-news-broadening-your-impact
    * These workshops were based upon work supported by the National Science Foundation under Grant No. #1518280. Any opinions, findings, and conclusions or recommendations expressed in this event, or in resulting work, are those of the participants and do not necessarily reflect the views of the NSF.

    5.    May 2018: “The Future of Arabidopsis Bioinformatics” Workshop: The International Arabidopsis Informatics Consortium (IAIC), initiated in 2010 by NAASC and led by former NAASC member Blake Meyers (Danforth Center) held this NSF-supported workshop in St. Louis, Missouri, USA, to evaluate the current status of Arabidopsis informatics and chart a course for future research and development (for more details please see the IAIC report in this MASC report’s section on Community resources). The workshop participants published a white paper outlining the current state, challenges, and priorities for the future of Arabidopsis bioinformatics resources (https://doi.org/10.1002/pld3.109). This workshop was based upon work supported by the National Science Foundation under Grant No. #11062348. Any opinions, findings, and conclusions or recommendations expressed in this event, or in resulting work, are those of the participants and do not necessarily reflect the views of the NSF.


    Selected Publications

    1.    Hadia Ahmed, T. C. Howton, Yali Sun, Natascha Weinberger, Youssef Belkhadir & M. Shahid Mukhtar (2018) Network biology discovers pathogen contact points in host protein-protein interactomes. Nature Communications; https://www.nature.com/articles/s41467-018-04632-8
    2.     Arabidopsis bioinformatics resources (2019) The current state, challenges, and priorities for the future. International Arabidopsis Informatics Consortium. Plant Direct. 3:1–7. https://doi.org/10.1002/pld3.109
    3.    Bou Daher F, Chen Y, Bozorg B, Clough J, Jönsson H, Braybrook SA (2018) Anisotropic growth is achieved through the additive mechanical effect of material anisotropy and elastic asymmetry. Elife. doi: 10.7554/eLife.38161
    4.    Javier Brumos, Linda M. Robles, Jeonga Yun, Savannah Jackson, Jose M. Alonso, Anna N. Stepanova (2018) Local Auxin Biosynthesis Is a Key Regulator of Plant Development. Developmental Cell. 2018; https://doi.org/10.1016/j.devcel.2018.09.022
    5.    de Luis Balaguer MA, Fisher AP, Clark NM, Fernandez-Espinosa MG, Möller BK, Weijers D, Lohmann JU, Williams C, Lorenzo O, Sozzani R (2017). Predicting gene regulatory networks by combining spatial and temporal gene expression data in Arabidopsis root stem cells. Proc Natl Acad Sci; doi: 10.1073/pnas.1707566114
    6.    Joanna Friesner, et. al. Siobhan M. Brady (2017) The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology. Plant Phys; https://doi.org/10.1104/pp.17.01490
    7.    Gaudinier A, Rodriguez-Medina J, Zhang L, Olson A, Liseron-Monfils C, Bågman AM, Foret J, Abbitt S, Tang M, Li B, Runcie DE, Kliebenstein DJ, Shen B, Frank MJ, Ware D, Brady SM (2018) Transcriptional regulation of nitrogen-associated metabolism and growth.  Nature; doi: 10.1038/s41586-018-0656-3
    8.    Hongqing Guo, Trevor M. Nolan, Gaoyuan Song, Sanzhen Liu, Zhouli Xie, Jiani Chen, Patrick S. Schnable, Justin W. Walley, Yanhai Yin (2018) FERONIA Receptor Kinase Contributes to Plant Immunity by Suppressing Jasmonic Acid Signaling in Arabidopsis thaliana.  Current Biology; https://doi.org/10.1016/j.cub.2018.07.078
    9.    Jakub Rajniak, Ricardo F. H. Giehl, Evelyn Chang, Irene Murgia, Nicolaus von Wirén & Elizabeth S. Sattely (2018) Biosynthesis of redox-active metabolites in response to iron deficiency in plants. Nature Chem Biology. 2018; https://www.nature.com/articles/s41589-018-0019-2
    10.    Masatsugu Toyota, Dirk Spencer, Satoe Sawai-Toyota, Wang Jiaqi, Tong Zhang, Abraham J. Koo, Gregg A. Howe, Simon Gilroy (2018) Glutamate triggers long-distance, calcium-based plant defense signaling. Science. 2018; http://science.sciencemag.org/content/361/6407/1112


    Major Funding Sources

    US Arabidopsis Research is primarily supported by funding through the Federal Government via the National Science Foundation (NSF): http://www.nsf.gov/
    Additional support has 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/
    National Aeronautics and Space Administration (NASA): http://www.nasa.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:
    (1) HHMI Faculty Scholars; e.g. Siobhan Brady, Jose Dinneny, Elizabeth Haswell, Jennifer Nemhauser, Elizabeth Sattely
    (2) HHMI Investigators; Phil Benfey, Dominique Bergmann, Xuemei Chen, Joanne Chory, Jeff Dangl, Xinnian Dong, Joe Ecker, Mark Estelle, Sheng Yang He, Steve Jacobsen, Zach Lippmann, Rob Martienssen, Elliot Meyerowitz, Craig Pikaard, Elizabeth Sattely, Keiko Torii and Ning Zheng (the next anticipated competition opens in 2020!)  

    Additional Information

    1.    In fall 2018, Federica Brandizzi (MSU-DOE Plant Research Laboratory, Michigan State University) and Anna Stepanova (North Carolina State University) were elected by the North American Arabidopsis community to serve a five-year term. They replaced Sally Assmann (Penn State University) and Erich Grotewold (Michigan State University) who had concluded their five-year term of service.

    a.    Federica and Anna join these NAASC members, in order of longest to shortest elected service on NAASC: Elizabeth Haswell (Washington University in St. Louis), José R. Dinneny (Stanford University), Peter McCourt (University of Toronto), Roger Innes (Indiana University), Sean Cutler (UC Riverside), and Jennifer Nemhauser (University of Washington- Seattle).

    b.    Current and former NAASC members, and NAASC information, can be found at: https://www.araport.org/community/group/naasc

    2.    US researchers that use Arabidopsis and were elected as fellows of the National Academy of Science in 2018 include (1) Joy M. Bergelson; Professor and Chair, Department of Ecology and Evolution, The University of Chicago, Chicago; (2) Sean Cutler; Professor (current NAASC member), Department of Botany and Plant Sciences, University of California, Riverside, and (3) Richard  D. Vierstra; George and Charmaine Mallinckrodt Professor of Biology (recent NASAC member), Department of Biology, Washington University, St. Louis.

    3.    TapRoot Podcast (https://plantae.org/podcasts/the-taproot/) by Elizabeth Haswell, NAASC member: One challenge with outreach and retention activities is reaching geographically, ideologically, or intellectually isolated individuals. Podcasting provides an alternative source of support and community for plant science trainees, with low barriers to access, production, and distribution, and a highly diverse audience. While podcasts are rapidly growing in popularity they are underutilized as a mechanism for science outreach. Of the over half a million active podcasts, less than 1000 are related to science. In 2017, Ivan Baxter and I started The Taproot Podcast (tagline: “We tell the story behind the science”) with support from ASPB and Plantae. In each episode, we discuss the publication of a plant biology paper with one of its authors, addressing the narratives that aren’t represented in a final manuscript—such as technology development, work-life balance, career gaps, gender discrimination, and student mental health. About half of our podcast guests work on Arabidopsis specifically. We also maintain an active @taprootpodcast Twitter account (>1200 followers) to foster discussion and solicit feedback, and to reach as broad an audience as possible. Ultimately, we aim to foster a sense of belonging, agency and community among plant biology trainees, thereby improving diversity and inclusion. We have released 17 episodes over two seasons with over 34,000 downloads to date. According to a survey in the summer of 2018, 46% of our listeners identify as female, over 50% are PhD students and postdocs, and 85% are in North America or Europe. Future efforts will aim to continue to seek guests with diverse ethnicity, career level, geographical location, and research area, in part by crowdsourcing suggestions via Twitter. In addition, we will engage with a more global audience and have identified several young plant biology leaders in South America and Africa to serve as ambassadors for the podcast in their countries.