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October 9th 2020

    There are more than 35 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.

Selected Publications

Arico D, Legris M, Castro L, et al. Neighbour signals perceived by phytochrome B increase thermotolerance in Arabidopsis. Plant Cell Environ. 2019;42(9):2554-2566. doi:10.1111/pce.13575

Cabello JV, Chan RL. Arabidopsis and sunflower plants with increased xylem area show enhanced seed yield. Plant J. 2019;99(4):717-732. doi:10.1111/tpj.14356

Godoy Herz MA, Kubaczka MG, Brzyzek G, et al. Light Regulates Plant Alternative Splicing through the Control of Transcriptional Elongation. Mol Cell. 2019;73(5):1066-1074.e3. doi:10.1016/j.molcel.2018.12.005

Gómez MS, Falcone Ferreyra ML, Sheridan ML, Casati P. Arabidopsis E2Fc is required for the DNA damage response under UV-B radiation epistatically over the microRNA396 and independently of E2Fe. Plant J. 2019;97(4):749-764. doi:10.1111/tpj.14158

Lescano I, Bogino MF, Martini C, et al. Ureide Permease 5 (AtUPS5) Connects Cell Compartments Involved in Ureide Metabolism. Plant Physiol. 2020;182(3):1310-1325. doi:10.1104/pp.19.01136

Lorenzo CD, Alonso Iserte J, Sanchez Lamas M, et al. Shade delays flowering in Medicago sativa. Plant J. 2019;99(1):7-22. doi:10.1111/tpj.14333

Luccioni L, Krzymuski M, Sánchez-Lamas M, Karayekov E, Cerdán PD, Casal JJ. CONSTANS delays Arabidopsis flowering under short days. Plant J. 2019;97(5):923-932. doi:10.1111/tpj.14171

Perotti MF, Ribone PA, Cabello JV, Ariel FD, Chan RL. AtHB23 participates in the gene regulatory network controlling root branching, and reveals differences between secondary and tertiary roots. Plant J. 2019;100(6):1224-1236. doi:10.1111/tpj.14511

Ré DA, Cambiagno DA, Arce AL, et al. CURLY LEAF Regulates MicroRNA Activity by Controlling ARGONAUTE 1 Degradation in Plants. Mol Plant. 2020;13(1):72-87. doi:10.1016/j.molp.2019.10.003

Righini S, Rodriguez EJ, Berosich C, Grotewold E, Casati P, Falcone Ferreyra ML. Apigenin produced by maize flavone synthase I and II protects plants against UV-B-induced damage. Plant Cell Environ. 2019;42(2):495-508. doi:10.1111/pce.13428

Major Funding Sources

- Argentinean National Reseasrch Council (CONICET)

- Agencia Nacional de Pomoción Científica y Tecnológica (ANPCyT).

October 9th 2020

Arabidopsis research in Austria 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.maxperutzlabs.ac.at/research/research-groups#c369), the Institute of Science and Technology, Austria (IST Austria) (https://ist.ac.at/en/research/), the Austrian Institute of Technology (AIT) (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=209112&L=1&MP=208727-210133), the University of Vienna (www.univie.ac.at/mosys) and the University of Graz (https://botanik.uni-graz.at/de/forschung/molecular-plant-physiology/).

    More than 20 research groups focus on molecular genetics (including population, epi-, and developmental genetics), RNA-, chromosome-, cell-, and glycobiology as well as stress and hormone signaling. There are vivid collaboration activities between the research groups sharing experimental tools provided by sequencing, proteomic, genome editing, phenotyping, imaging and computational facilities (https://www.viennabiocenter.org/facilities/, https://ist.ac.at/en/research/scientific-service-units/ and https://boku.ac.at/wissenschaftliche-initiativen/vibt/das-vibt-imaging-center). Furthermore, the recent establishment of the Austrian plant phenotyping network (APPN) aims to support phenotyping for fundamental and applied plant research, from Arabidopsis to trees and from subcellular to the level of whole plant architecture (https://appn.at/expertise/).

    While most Arabidopsis groups are strong in fundamental research the AIT has recently started a translational European wide project to uncover and promote tolerance to temperature and water stress in the native European oilseed Brassicaceae, Camelina sativa (UNTWIST).

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

Major update to AraPheno
https://arapheno.1001genomes.org)

Major update to AraGWAS
https://aragwas.1001genomes.org

APPN (Austrian Plant Phenotyping Network)
https://appn.at/

Conferences, Workshops and Outreach events

Participation of the Childrens’s University in Vienna, Lower and Upper Austria and the Austrian Radio channel Ö1 (https://boku.ac.at/en/lehrentwicklung/kinderboku/themen/aktivitaeten-fuer-kinder)

Open Campus at the IST Austria including stands on Arabidopsis (https://ist.ac.at/en/education/ist-for-kids/)

Participation at the Fascination of Plants Day on the 17th of May, 2019 from the Gregor Mendel Institute of Molecular Plant Biology (GMI) of the Austrian Academy of Sciences

Selected Publications

Dünser K, Gupta S, Herger A, Feraru MI, Ringli C, Kleine-Vehn J. Extracellular matrix sensing by FERONIA and Leucine-Rich Repeat Extensins controls vacuolar expansion during cellular elongation in Arabidopsis thaliana. EMBO J. 2019;38(7):e100353. doi:10.15252/embj.2018100353

Feraru E, Feraru MI, Barbez E, et al. PILS6 is a temperature-sensitive regulator of nuclear auxin input and organ growth in Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2019;116(9):3893-3898. doi:10.1073/pnas.1814015116

Plotnikova A, Kellner MJ, Schon MA, Mosiolek M, Nodine MD. MicroRNA Dynamics and Functions During Arabidopsis Embryogenesis. Plant Cell. 2019;31(12):2929-2946. doi:10.1105/tpc.19.00395

Marhava P, Hoermayer L, Yoshida S, Marhavý P, Benková E, Friml J. Re-activation of Stem Cell Pathways for Pattern Restoration in Plant Wound Healing. Cell. 2019;177(4):957-969.e13. doi:10.1016/j.cell.2019.04.015

Retzer K, Akhmanova M, Konstantinova N, et al. Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter. Nat Commun. 2019;10(1):5516.
doi:10.1038/s41467-019-13543-1.

Sasaki E, Kawakatsu T, Ecker JR, Nordborg M. Common alleles of CMT2 and NRPE1 are major determinants of CHH methylation variation in Arabidopsis thaliana. PLoS Genet. 2019;15(12):e1008492. Published 2019 Dec 30. doi:10.1371/journal.pgen.1008492.

Schoberer J, König J, Veit C, et al. A signal motif retains Arabidopsis ER-a-mannosidase I in the cis-Golgi and prevents enhanced glycoprotein ERAD. Nat Commun. 2019;10(1):3701. doi:10.1038/s41467-019-11686-9

Sims J, Copenhaver GP, Schlögelhofer P. Meiotic DNA Repair in the Nucleolus Employs a Nonhomologous End-Joining Mechanism. Plant Cell. 2019;31(9):2259-2275. doi:10.1105/tpc.19.00367

Waidmann S, Ruiz Rosquete M, Schöller M, et al. Cytokinin functions as an asymmetric and anti-gravitropic signal in lateral roots. Nat Commun. 2019;10(1):3540. doi:10.1038/s41467-019-11483-4

Zhu Q, Gallemí M, Pospíšil J, Žádníková P, Strnad M, Benková E. Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis. Development. 2019;146(17):dev175919. doi:10.1242/dev.175919
Major 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)

FEBS Fellowships  (https://www.febs.org/our-activities/fellowships/)

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

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October 9th 2020

Research on Arabidopsis thaliana remains a pillar for fundamental plant science in Belgium. This is also illustrated by the challenge to reduce the list of Arabidopsis publications in this report to a maximum number of 10.

    Nevertheless, also in Belgium plant scientists feel an increasing pressure from funding agencies, universities, and research institutes to focus on more applied research aspects. This entails for instance research on crop plants, or projects addressing topics that are relevant for climate change.

    FWO and ERC are the two main funding bodies that still promote basic research, while a number of funding initiatives by FWO and other organizations are aimed at applied research. Succeeding in these calls often means submitting projects that do not focus on Arabidopsis as a model plant. This being said, it is likely that Arabidopsis will remain a major tool to generate and test hypothesis even in applied research projects.

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

• New version of PLAZA
https://bioinformatics.psb.ugent.be/plaza/

• Belgian Galaxy launched last year (Flemish funding) https://usegalaxy.be

Conferences, Workshops and Outreach events

    Conferences for 2019 have been covered in the 2019 report. As far as I’m aware, conferences for 2020 have been postponed to 2021 due to the ongoing COVID-19 crisis.

Selected Publications

Decaestecker W, Buono RA, Pfeiffer ML, Vangheluwe N, Jourquin J, Karimi M, Van Isterdael G, Beeckman T, Nowack MK, Jacobs TB. CRISPR-TSKO: A Technique for Efficient Mutagenesis in Specific Cell Types, Tissues, or Organs in Arabidopsis. Plant Cell. 2019 Dec;31(12):2868-2887. doi: 10.1105/tpc.19.00454.

Dejonghe W, Sharma I, Denoo B, De Munck S, Lu Q, Mishev K, Bulut H, Mylle E, De Rycke R, Vasileva M, Savatin DV, Nerinckx W, Staes A, Drozdzecki A, Audenaert D, Yperman K, Madder A, Friml J, Van Damme D, Gevaert K, Haucke V, Savvides SN, Winne J, Russinova E. Disruption of endocytosis through chemical inhibition of clathrin heavy chain function. Nat Chem Biol. 2019 Jun;15(6):641-649. doi: 10.1038/s41589-019-0262-1. Epub 2019 Apr 22. PMID: 31011214

Hander T, Fernández-Fernández ÁD, Kumpf RP, Willems P, Schatowitz H, Rombaut D, Staes A, Nolf J, Pottie R, Yao P, Gonçalves A, Pavie B, Boller T, Gevaert K, Van Breusegem F, Bartels S, Stael S. Damage on plants activates Ca2+-dependent metacaspases for release of immunomodulatory peptides. Science. 2019 Mar 22;363(6433). pii: eaar7486. doi: 10.1126/science.aar7486. PMID: 30898901

Huang J, Willems P, Wei B, Tian C, Ferreira RB, Bodra N, Martínez Gache SA, Wahni K, Liu K, Vertommen D, Gevaert K, Carroll KS, Van Montagu M, Yang J, Van Breusegem F, Messens J. Mining for protein S-sulfenylation in Arabidopsis uncovers redox-sensitive sites. Proc Natl Acad Sci U S A. 2019 Oct 15;116(42):21256-21261. doi: 10.1073/pnas.1906768116. Epub 2019 Oct 2. PMID: 31578252

Li T, Natran A, Chen Y, Vercruysse J, Wang K, Gonzalez N, Dubois M, Inzé D. A genetics screen highlights emerging roles for CPL3, RST1 and URT1 in RNA metabolism and silencing. Nat Plants. 2019 May;5(5):539-550. doi: 10.1038/s41477-019-0419-7. Epub 2019 May 10. PMID: 31076735

Lu KJ, van ‘t Wout Hofland N, Mor E, Mutte S, Abrahams P, Kato H, Vandepoele K, Weijers D, De Rybel B. Evolution of vascular plants through redeployment of ancient developmental regulators. Proc Natl Acad Sci U S A. 2020 Jan 7;117(1):733-740. doi: 10.1073/pnas.1912470117. Epub 2019 Dec 24. PMID: 31874927

Ramakrishna P, Ruiz Duarte P, Rance GA, Schubert M, Vordermaier V, Vu LD, Murphy E, Vilches Barro A, Swarup K, Moirangthem K, Jørgensen B, van de Cotte B, Goh T, Lin Z, Vos U, Beeckman T, Bennett MJ, Gevaert K, Maizel A, De Smet I. EXPANSIN A1-mediated radial swelling of pericycle cells positions anticlinal cell divisions during lateral root initiation. Proc Natl Acad Sci U S A. 2019 Apr 23;116(17):8597-8602. doi: 10.1073/pnas.1820882116. Epub 2019 Apr 3. PMID: 30944225

Ramon M, Dang TVT, Broeckx T, Hulsmans S, Crepin N, Sheen J, Rolland F. Default Activation and Nuclear Translocation of the Plant Cellular Energy Sensor SnRK1 Regulate Metabolic Stress Responses and Development. Plant Cell. 2019 Jul;31(7):1614-1632. doi: 10.1105/tpc.18.00500. Epub 2019 May 13. PMID: 31123051

Vanholme R, Sundin L, Seetso KC, Kim H, Liu X, Li J, De Meester B, Hoengenaert L, Goeminne G, Morreel K, Haustraete J, Tsai HH, Schmidt W, Vanholme B, Ralph J, Boerjan W. COSY catalyses trans-cis isomerization and lactonization in the biosynthesis of coumarins. Nat Plants. 2019 Oct;5(10):1066-1075. doi: 10.1038/s41477-019-0510-0. Epub 2019 Sep 9. PMID: 31501530

Vanhaelewyn L, Viczián A, Prinsen E, Bernula P, Serrano AM, Arana MV, Ballaré CL, Nagy F, Van Der Straeten D, Vandenbussche F. Differential UVR8 Signal across the Stem Controls UV-B-Induced Inflorescence Phototropism. Plant Cell. 2019 Sep;31(9):2070-2088. doi: 10.1105/tpc.18.00929. Epub 2019 Jul 9. PMID: 31289115

Major Funding Sources

• Flanders Institute for Biotechnology (VIB; www.vib.be)

• European Union Framework (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.aspx)

• Fonds de la Recherche Scientifique (FNRS; http://www.frs-fnrs.be)

• European Research Council (http://erc.europa.eu/)

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.

October 9th 2020

In Brazil the number of institutions using Arabidopsis in their research is growing each year. At the moment, at least fifteen different institutions are using it as a model plant. We are seeing 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 investigate gene functions.

    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.

Conferences, Workshops and Outreach events

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, Cuiabá, Mato Grosso Brazil, from June 9 to 12, 2019.
Nature Conference: Advances in Metabolic Communication

October 15–18, 2019
Belmond Copacabana Palace, Rio de Janeiro, Brazil

Selected Publications

Batista-Silva W, Heinemann B, Rugen N, Nunes-Nesi A, Araújo WL, Braun HP, Hildebrandt TM. (2019) The role of amino acid metabolism during abiotic stress release. Plant Cell. Environ.  42:1630–1644. doi: 10.1111/pce.13518.

da Fonseca-Pereira P, Souza  PVL, Hou  LY, Schwab  S, Geigenberger  P, Nunes-Nesi  A, Timm  S, Fernie  AR, Thormählen  I, Araújo  WL, Daloso  DM
 (2019) Thioredoxin h2 contributes to the redox regulation of mitochondrial photorespiratory metabolism. Plant Cell Environ 43(1):188-208 doi:10.1111/pce.13640

Dantas LLB, Calixto CPG, Dourado MM, Carneiro MS, Brown JWS and Hotta CT (2019) Alternative Splicing of Circadian Clock Genes Correlates With Temperature in Field-Grown Sugarcane. Front. Plant Sci. 10:1614. doi: 10.3389/fpls.2019.01614

de Souza Chaves I, Feitosa-Araújo E, Florian A, Medeiros DB, da Fonseca-Pereira P, Charton L, Heyneke E, Apfata JAC, Pires MV, Mettler-Altmann T, Araújo WL, Neuhaus HE, Palmieri F, Obata T, Weber APM, Linka N, Fernie AR, Nunes-Nesi A (2019) The mitochondrial NAD+ transporter (NDT1) plays important roles in cellular NAD+ homeostasis in Arabidopsis thaliana. Plant J. 100(3):487-504. doi: 10.1111/tpj.14452.

Li, B., Ferreira, M.A., Huang, M. et al. The receptor-like kinase NIK1 targets FLS2/BAK1 immune complex and inversely modulates antiviral and antibacterial immunity. Nat Commun 10, 4996 (2019). https://doi.org/10.1038/s41467-019-12847-6

Lima, V.F., Medeiros, D.B., Souza, L.P., Gago, J., Fernie, A.R. and Daloso, D.M. (2019) The sucrose-to-malate ratio correlates with the faster CO 2 and light stomatal responses of angiosperms compared to ferns. New Phytol. 223(4), 1873–1887. Doi: 10.1111/nph.15927

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.

Oliveira, R.A.d.C., de Andrade, A.S., Imparato, D.O. et al. Analysis of Arabidopsis thaliana Redox Gene Network Indicates Evolutionary Expansion of Class III Peroxidase in Plants. Sci Rep 9, 15741 (2019). https://doi.org/10.1038/s41598-019-52299-y

Roca Paixão JF, Gillet FX, Ribeiro TP, Bournaud C, Lourenço-Tessutti IT, Noriega DD, Melo BP, de Almeida-Engler J, Grossi-de-Sa MF. (2019) Improved drought stress tolerance in Arabidopsis by CRISPR/dCas9 fusion with a Histone AcetylTransferase. Sci Rep 9: 8080 doi: 10.1038/s41598-019-44571-y.

Yoshida T, dos Anjos L, Medeiros DB, Araújo WL, Fernie AR, Daloso DM. 2018. Insights into ABA-mediated regulation of guard cell primary metabolism revealed by systems biology approaches. Progress in Biophysics and Molecular Biology. 146: 37-49 doi: 10.1016/j.pbiomolbio.2018.11.006.

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)

Download 2020-21 Report

October 9th 2020

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

Pollak B, Cerda A, Delmans M, Álamos S, Moyano T, West A, Gutiérrez RA, Patron NJ, Federici F, Haseloff J. Loop assembly: a simple and open system for recursive fabrication of DNA circuits. New Phytol. 2019 Apr;222(1):628-640. doi: 10.1111/nph.15625.

This method provides a simple generalized solution for DNA construction with standardized parts. The cloning system is provided under an OpenMTA license for unrestricted sharing and open access.

Conferences, Workshops and Outreach events

January 9th, 2019
Seminar: Orange on top: Is there a mutual exclusion between anthocyanin and carotenoids biosynthesis in petunia flowers?
This seminar was held on campus Las Palmeras – Universidad de Chile. Santiago Chile.
It was presented by Dr. Julian Verdonk, Wageningen University. Netherlands.
Organizers: Universidad de Chile.

March, 27th – 29th, 2019.
Symposium: First International Symposium of Food, Nutrition, Physical Fitness and Health
The symposium was held at INTA, Universidad de Chile. Santiago – Chile.
The meeting committee included several fieds associated to nutrition and health: Healty and sustainable food, nutritional genomics, Nutrition and physical activity, influence of socio-economic factors on nutrition, and urban planification, physical activity and nutrition.
The key note speakers were Dr. Alejandra Chavez-Santoscoy (Mexico), Eduardo Guerra Hernandez (Spain), Jesús Rodríguez Huertas (Spain), Dr. Bruno Gualaro (Brazil), Dr. Leandro Pereira (Brazil), Dra. Diana Parra (USA), Stefan Martens (Italy).
Organizers: Centro de investigación en Alimentos para el Bienestar en el Ciclo Vital and the Proyecto de Consolidación de la Internacionalización de la Investigación y Postgrado de la Universidad de Chile,

April 22th – 25th, 2019
EMBO Workshop: Integrative biology: From molecules to ecosystems in extreme environments (w19-107)
EMBO Workshops are meetings that cover different and evolving aspects of life-science-related subject areas and bring scientists together to present and discuss their latest findings.

Organizers: Eric Schimer, University of Edinburg, UK., Rodrigo Gutierrez, Pontificia Universidad Católica de Chile, CL, Francisca Blanco, Universidad Andres Bello, CL, Stephan Pollman, Universidad Politecnica de Madrid, ES, Laurence Lejay, INRA, Montpelier, FR
 
July 22th – 23th, 2019
3rd SCIENTIFIC MEETING ON VEGETAL BIOLOGY AND BIOTECHNOLOGY DIGV-UTAL
The meeting was held in Salón Bicentenario de la U. de Talca, Campus Lircay, Talca –
Chile.
The meeting included four thematical areas: Biotic and abiotic stress, phytogenetics resources, Vegetal development, and Ecology and molecular evolution.
Organizer: Ph.D. program on Sciences, mention plant genetics on Instituto de Ciencias
Biológicas of Universidad de Talca – Chile.

June 12th, 2019
Conference: “Sorting of Small RNAs into exosomes secreted by human cells”
The conference was held at Las Palmeras, Universidad de Chile. Santiago – Chile.
Seminar presented by Randy Schekman, Ph.D., Nobel price of Physiology/medicine 2013.
Organizers: Universidad de Chile.

October 16-18th, 2019
Conference: 2nd Energy, Efficiency and Environmental Sustainability 2019
This coneference was held at Universidad de La Serena. La Serena – Chile.
Key Note Speakers:
Gianluca Li Puma, PhD.    Loughborough University, UK
Mohamed El-Roz, PhD. Caen University, France
María Bernechea, PhD. University of Zaragoza, Spain.
Organizers: Universidad de La Serena and Centro de Estudios Avanzandos en Zonas Áridas.

September 13th, 2019
Seminar: Domestication of a Y chromosome in papaya
The seminar was held at Facultad de Ciencias Agronómicas of Universidad de Chile. Santiago – Chile.
The seminar was presented by Ray Ming, PhD. Its research is based on the genomic analysis of Papaya and the determination of sex. Dr Ming participated in the sequencing of the papaya genome.
Organizers: Departamento de Producción Agrícola, Facultad de Ciencias Agronómicas, Universidad de Chile and Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile

December 4th, 2019
Seminar: “Vegetable improvement of the cherry tree: current status and perspectives”
This seminar was held at the research building of Universidad Andres Bello. Santiago – Chile.
Seminar presented by José Quero-García PhD., from INRA (Bordeaux, France) an international expert on genetic improvement of cherry trees. The presentation was based on their findings on the generation of QTLs linked to agronomical characteristics and their usage in programs of assisted selection.
Organizer: Laboratorio de Genómica Funcional & Bioinformática, Departamento de Producción Agrícola. Universidad de Chile.

Selected Publications

Alvarez JM, Moyano TC, Zhang T, Gras DE, Herrera FJ, Araus V, O’Brien JA, Carrillo L, Medina J, Vicente-Carbajosa J, Jiang J, Gutiérrez RA. Local Changes in Chromatin Accessibility and Transcriptional Networks Underlying the Nitrate Response in Arabidopsis Roots. Mol Plant. 2019 Dec 2;12(12):1545-1560. doi: 10.1016/j.molp.2019.09.002. Epub 2019 Sep 14.

García Bossi J, Kumar K, Barberini ML, Domínguez GD, Rondón Guerrero YDC, Marino-Buslje C, Obertello M, Muschietti JP, Estevez JM. The role of P-type IIA and P-type IIB Ca2+-ATPases in plant development and growth.
J Exp Bot. 2020 Feb 19;71(4):1239-1248. doi: 10.1093/jxb/erz521.

Garrido-Bigotes A, Valenzuela-Riffo F, Figueroa CR. Evolutionary Analysis of JAZ Proteins in Plants: An Approach in Search of the Ancestral Sequence.
Int J Mol Sci. 2019 Oct 12;20(20):5060. doi: 10.3390/ijms20205060.

Rubilar-Hernández C, Osorio-Navarro C, Cabello F, Norambuena L. PI4KIIIβ Activity Regulates Lateral Root Formation Driven by Endocytic Trafficking to the Vacuole.
Plant Physiol. 2019 Sep;181(1):112-126. doi: 10.1104/pp.19.00695. Epub 2019 Jul 8.

Parra-Rojas JP, Largo-Gosens A, Carrasco T, Celiz-Balboa J, Arenas-Morales V, Sepúlveda-Orellana P, Temple H, Sanhueza D, Reyes FC, Meneses C, Saez-Aguayo S, Orellana A. New steps in mucilage biosynthesis revealed by analysis of the transcriptome of the UDP-rhamnose/UDP-galactose transporter 2 mutant. J Exp Bot. 2019 Oct 15;70(19):5071-5088. doi: 10.1093/jxb/erz262.

Silva-Sanzana C, Celiz-Balboa J, Garzo E, Marcus SE, Parra-Rojas JP, Rojas B, Olmedo P, Rubilar MA, Rios I, Chorbadjian RA, Fereres A, Knox P, Saez-Aguayo S, Blanco-Herrera F. Pectin Methylesterases Modulate Plant Homogalacturonan Status in Defenses against the Aphid Myzus persicae. Plant Cell. 2019 Aug;31(8):1913-1929. doi: 10.1105/tpc.19.00136. Epub 2019 May 24.

Sunitha S, Loyola R, Alcalde JA, Arce-Johnson P, Matus JT, Rock CD. The Role of UV-B light on Small RNA Activity During Grapevine Berry Development.
G3 (Bethesda). 2019 Mar 7;9(3):769-787. doi: 10.1534/g3.118.200805.

Timmermann T, Poupin MJ, Vega A, Urrutia C, Ruz GA, González B. Gene networks underlying the early regulation of Paraburkholderia phytofirmans PsJN induced systemic resistance in Arabidopsis PLoS One. 2019 Aug 22;14(8):e0221358. doi: 10.1371/journal.pone.0221358. eCollection 2019.

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
(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)

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

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October 9th 2020

There are a large number of Chinese research institutions that conduct Arabidopsis research. Because of the large size of the country, it is difficult to precisely estimate the exact number of research labs using Arabidopsis, although the number must be over 500. This can in part be reflected by the large number of Arabidopsis related research papers published by Chinese researchers.

    According to the 2019 MASC Report, about one-third of all Arabidopsis papers published in 2018 were from China. Not surprisingly, research topics range from developmental and hormone biology to abiotic and biotic stress, and to evolution. Hence, Arabidopsis is the model plant of choice to many groups. However, only a small portion of these labs is solely dedicated to Arabidopsis research or using Arabidopsis as the main model plant, which may be very different from many other countries.

    A major reason behind would be the current funding priority. Whereas there are dedicated grants to basic and applied research in maize, rice, wheat, and virtually each minor crop, there are no such funding programs towards Arabidopsis research. As a result, Arabidopsis is often used as an easily manipulated model system to test crop gene functions. Nevertheless, the number of Arabidopsis papers published in 2018 by Chinese researchers ranks only after rice papers, and more than those of maize or wheat.

    Most Arabidopsis research occurs in research universities, Chinese Academy of Sciences (CAS) institutes, and Chinese Academy of Agricultural Sciences institutes. In addition, most provinces have one or more agricultural universities, where you can find at least some Arabidopsis research.

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

- AraShare: A community biological resource center
http://www.arashare.cn/

- Plant Transcriptional Regulatory Map (includes updated PlantTFDB and additional resources)
http://plantregmap.cbi.pku.edu.cn/

- AHD2.0: Arabidopsis hormone database 2.0
https://bigd.big.ac.cn/ahd/

- LSD3.0: Arabidopsis leaf senescence database 3.0
https://bigd.big.ac.cn/lsd/

- PlantGSEA: a gene set enrichment analysis toolkit for plant community
http://structuralbiology.cau.edu.cn/PlantGSEA/

- 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

Conferences, Workshops and Outreach events

Major conferences held in 2019
- 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 (ICNF2019), October 10-15, 2019 Wuhan, Hubei

- 2019 National Congress of Plant Biology, October 11-14, 2019 Chengdu, Sichuan (http://www.ncpb.net/2019/)

Selected Publications

Li W, Song T, Wallrad L, Kudla J, Wang X, Zhang W. (2019) Tissue-specific accumulation of pH-sensing phosphatidic acid determines plant stress tolerance. Nat Plants. 2019 Sep;5(9):1012-1021.
Cui Y, Cao W, He Y, Zhao Q, Wakazaki M, Zhuang X, Gao J, Zeng Y, Gao C, Ding Y, Wong HY, Wong WS, Lam HK, Wang P, Ueda T, Rojas-Pierce M, Toyooka K, Kang B-H, Jiang L. (2019) A whole-cell electron tomography model of vacuole biogenesis in Arabidopsis root cells. Nat. Plants 5(1):95-105.

He J, Chen Q, Xin P, Yuan J, Ma Y, Wang X, Xu M, Chu J, Peters RJ, Wang G. (2019) CYP72A enzymes catalyse 13-hydrolyzation of gibberellins. Nat. Plants 5(10): 1057-1065.

Li H, Cai Z, Wang X, Li M, Cui Y, Cui N, Yang F, Zhu M, Zhao J, Du W, He K, Yi J, Tax FE, Hou S, Li J, Gou X. (2019) SERK receptor-like kinases control division patterns of vascular precursors and ground tissue stem cells during embryo development in Arabidopsis. Mol. Plant 12(7): 984-1002.

Qiu Q, Mei H, Deng X, He K, Wu B, Yao Q, Zhang J, Lu F, Ma J, Cao X. (2019) DNA methylation repels targeting of Arabidopsis REF6. Nat. Commun. 10(1): 2063.

Tian C, Wang Y, Yu H, He J, Wang J, Shi B, Du Q, Provart NJ, Meyerowitz EM, Jiao Y. (2019) A gene expression map of shoot domains reveals regulatory mechanisms. Nat. Commun. 10(1): 141.

Wang J, Hu M, Wang J, Qi J, Han Z, Wang G, Qi Y, Wang H-W, Zhou J-M, Chai J. (2019) Reconstitution and structure of a plant NLR resistosome conferring immunity. Science 364(6435): eaav5870.

Wang J, Wang J, Hu M, Wu S, Qi J, Wang G, Han Z, Qi Y, Gao N, Wang H-W, Zhou J-M, Chai J. (2019) Ligand-triggered allosteric ADP release primes a plant NLR complex. Science 364(6435): eaav5868.

Wang X, Ding Y, Li Z, Shi Y, Wang J, Hua J, Gong Z, Zhou JM, Yang S. (2019) PUB25 and PUB26 promote plant freezing tolerance by degrading the cold signaling negative regulator MYB15. Dev. Cell 51(2): 222-235.

You Y, Zhai Q, An C, Li C. (2019) LEUNIG_HOMOLOG mediates MYC2-dependent transcriptional activation in cooperation with the coactivators HAC1 and MED25. Plant Cell 31(9): 2187-2205.

Zhong S, Liu M, Wang Z, Huang Q, Hou S, Xu YC, Ge Z, Song Z, Huang J, Qiu X, Shi Y, Xiao J, Liu P, Guo YL, Dong J, Dresselhaus T, Gu H, Qu L-J. (2019) Cysteine-rich peptides promote interspecific genetic isolation in Arabidopsis. Science 364(6443): eaau9564.

Major Funding Sources
National Natural Science Foundation (NSFC)
http://www.nsfc.gov.cn/publish/portal1
Ministry of Science and Technology (MOST)
http://www.most.gov.cn/eng/programmes1/index.htm

October 9th 2020

Arabidopsis driven research in Czech Republic is qualitatively but also quantitatively expanding over the last decade. An important aspect of that is that for medium/small country as Czech republic is, Arabidopsis driven basic plant research is not centralized only in the capital. In fact historically first steps in Czech plant molecular biology were done already in 80ies – before the political regime change – at the Institute of Biophysics, Czech Academy of Sciences (CAS) in Brno, which is still very active, currently especially in the fields of plant molecular epigenetics and plant developmental biology.

    Over the last decade supply of EU structural funds supported expansion of not only plant science in Brno, but also in Olomouc – in these two cities existing university and Academy departments grew in quality of plant research and new joint institutes focused on the plant science were established and are stabilized over the last years. CEITEC (https://www.ceitec.eu/ - also with the participation of Masaryk university and Mendel agricultural university in respect to plant sciences) in Brno is a multidisciplinary center which includes “Genomics and Proteomics of Plant Systems” division encompassing 8 research groups with topics focused on understanding the evolutionary-based strategies of plants. The knowledge acquired by –omic approaches, combined with research experience in the areas of developmental and stress biology of plants, is subsequently used to develop new agricultural, biotechnology and biomedical applications.

    In Olomouc “The Center of the Region Haná for Biotechnological and Agricultural Research” (CRH – includes Palacký university and Inst. of Exp. Botany, CAS in respect to plant sciences) is a scientific workplace focused on plant research and plant biotechnology development. Local scientists belong to world´s top experts in reading genetic information of barley, wheat and other plants important for nutrition of the ever-growing human population. Another important focus is plant cell biology. Based on the results of basic research, they suggest procedures that enable breeders to obtain varieties of new generation with the desired properties, especially higher yield and resistance to drought, temperature fluctuations and other stress factors.

    In the capital Prague and south Bohemian city Ceské Budejovice no new EU funded big infrastructures supporting plant research were developed, but traditionally at the Charles university in Prague plant biology research at Departments of experimental plant biology and at the Department of botany is well developing with a great focus on cell and developmental biology of Arabidopsis (ERC grant to Matyáš Fendrych from the Department of exp. Plant Bilogy) and plant ecological genomics of Brassicaceae (ERC grant to Filip Kolár from the Department of Botany).

    At the Department of experimental plant biology of the University of South Bohemia partially Arabidopsis driven research is focused on the photosynthesis and regulation of gas exchange (stomata development and regulation also under the stress). The Institute of Experimental Botany in Prague (belongs to Czech Academy of Sciences) serves since the middle of the last century as a crystallization point of basic laboratory plant biology research focused on plant genetics, physiology, phytopathology and biotechnology. However, IEB is also active in applied research – esp. in apple breeding. Most of the work in this institute is based on and driven by the Arabidopsis research. The Institute of Plant Molecular Biology (IPMB of the Czech Academy of Sciences) was founded in 1990 when several genetically oriented teams split from the Institute of Experimental Botany in Prague and moved to Ceské Budejovice. This Institute contributes significantly to Czech national programs of plant biotechnology and plant protection against biotic stresses, and provides expertise on the diagnosis of quarantined plant viruses to the Ministry of Agriculture and the State Phytosanitary Administration, and on genetically modified crops to the Ministry of the Environment.

     Applied plant crop production research in Czech republic is not only done in several crop specialized institutes and breeding stations, but is partially centralized and coordinated by the Crop Research Institute in Prague which uses also Arabidopsis driven wisdom to be applied for crops.  

    PSI (Photon Systems Instruments - https://psi.cz/) company located close to Brno is contributing worldwide to the development of spectral methods to monitor plant physiology in the lab and field, but also development internationally very successful cultivation and phenotyping platforms. Currently, PSI’s main product lines include: (1) devices for chlorophyll fluorescence measurement and advanced imaging; (2) high-tech photobioreactors and other algal cultivators; (3) intelligent growth chambers and cultivation rooms; (4) customized PlantScreenTM Phenotyping Systems; (5) a range of novel LED light sources for plant cultivation and research; and (6) hand-held devices for monitoring chlorophyll fluorescence kinetics, plant reflective indices and spectral characteristics of natural and artificial light.
Overall it is obvious that in Czech republic both basic as well as applied plant research  based on Arabidopis model is flourishing over the last years and that the country also contributes to the methodology-instrumental advancement in plant biology studies.

Conferences, Workshops and Outreach events

- Plant Biology CS 2019
    Every three years, the Czech Society of Experimental Plant Biology and Plant Physiology section of the Slovak Botanical Society jointly organize meetings, which are hosted by alternating Czech and Slovak university cities. The conference titled “Plant Biology CS, 2019” took place in Ceské Budejovice (at the joint campus of the University of South Bohemia and Biology Centre of the Czech Academy of Sciences) from 25th to 30th August 2019. It was an international meeting of high quality (most plenary and key note speakers were experts in the fields from abroad) and lot of contributions were based on Arabidopsis research.

- Plant Development and Production Biology under Global Climate Change
    This was an advanced international meeting with plenary and key note speakers being prominent experts in respective fields and lot of contributions were driven by Arabidopsis research. Meeting was held in Brno, September 9th-11th 2019, and was also organized to commemorate 100 years anniversary of Mendel Agricultural University in Brno establishment.
Selected Publications

Adamusová K, Khosravi S, Fujimoto S, Houben A, Matsunaga S, Fajkus J, Fojtová M. Two combinatorial patterns of telomere histone marks in plants with canonical and non-canonical telomere repeats. Plant J. Dec 13. doi: 10.1111/tpj.14653. 2019

Janková Drdová E, Klejchová M, Janko K, Hála M, Soukupová H, Cvrcková F, Žárský V. Developmental plasticity of Arabidopsis hypocotyl is dependent on exocyst complex function. J Exp Bot. 70(4):1255-1265. doi: 10.1093/jxb/erz005. 2019

Küpper H, Benedikty Z, Morina F, Andresen E, Mishra A, Trtílek M. Analysis of OJIP Chlorophyll Fluorescence Kinetics and QA Reoxidation Kinetics by Direct Fast Imaging. Plant Physiol. 179(2):369-381. doi: 10.1104/pp.18.00953. Epub 2018 Dec 18. 2019

Leontovycová H, Kalachova T, Trdá L, Pospíchalová R, Lamparová L, Dobrev PI, Malínská K, Burketová L, Valentová O, Janda M. Actin depolymerization is able to increase plant resistance against pathogens via activation of salicylic acid signalling pathway. Sci Rep. 2019 Jul 18;9(1):10397. doi: 10.1038/s41598-019-46465-5.

Mandáková T, Pouch M, Brock JR, Al-Shehbaz IA, Lysak MA. Origin and Evolution of Diploid and Allopolyploid Camelina Genomes Were Accompanied by Chromosome Shattering. Plant Cell. 2019 Nov;31(11):2596-2612. doi: 10.1105/tpc.19.00366. Epub 2019 Aug 26.

Nowicka A, Tokarz B, Zwyrtková J, Dvorák Tomaštíková E, Procházková K, Ercan U, Finke A, Rozhon W, Poppenberger B, Otmar M, Niezgodzki I, Krecmerová M, Schubert I, Pecinka A. Comparative analysis of epigenetic inhibitors reveals different degrees of interference with transcriptional gene silencing and induction of DNA damage. Plant J. doi: 10.1111/tpj.14612. 2019

Oulehlová D, Kollárová E, Cifrová P, Pejchar P, Žárský V, Cvrcková F. Arabidopsis Class I Formin FH1 Relocates between Membrane Compartments during Root Cell Ontogeny and Associates with Plasmodesmata. Plant Cell Physiol. 2019 Aug 1;60(8):1855-1870. doi: 10.1093/pcp/pcz102.

Schorová Š, Fajkus J, Záveská Drábková L, Honys D, Schrumpfová PP. The plant Pontin and Reptin homologues, RuvBL1 and RuvBL2a, colocalize with TERT and TRB proteins in vivo, and participate in telomerase biogenesis. Plant J. Apr;98(2):195-212. doi: 10.1111/tpj.14306. 2019

Skalák J, Vercruyssen L, Claeys H, Hradilová J, Cerný M, Novák O, Placková L, Saiz-Fernández I, Skaláková P, Coppens F, Dhondt S, Koukalová Š, Zouhar J, Inzé D, Brzobohatý B. Multifaceted activity of cytokinin in leaf development shapes its size and structure in Arabidopsis. Plant J. 2019 Mar;97(5):805-824. doi: 10.1111/tpj.14285.

Zdarska M, Cuyacot AR, Tarr PT, Yamoune A, Szmitkowska A, Hrdinová V, Gelová Z, Meyerowitz EM, Hejátko J. ETR1 Integrates Response to Ethylene and Cytokinins into a Single Multistep Phosphorelay Pathway to Control Root Growth. Mol Plant. 2019 Oct 7;12(10):1338-1352. doi: 10.1016/j.molp.2019.05.012. Epub 2019 Jun 7.

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 http://eagri.cz/public/web/mze/poradenstvi-a-vyzkum/vyzkum-a-vyvoj/narodni-agentura-pro-zemedelsky-vyzkum/

October 9th 2020

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) at the Department of Plant and Environmental Sciences, University of Copenhagen, includes up-to-date facilities for Arabidopsis research.

Selected Publications

Hoffmann RD, Olsen LI, Ezike CV, Pedersen JT, Manstretta R, López-Marqués RL, Palmgren M (2019) Roles of plasma membrane proton ATPases AHA2 and AHA7 in normal growth of roots and root hairs in Arabidopsis thaliana. Physiol Plant. 166: 848-861.

Hunziker P, Halkier BA, Schulz A (2019) Arabidopsis glucosinolate storage cells transform into phloem fibres at late stages of development. J Exp Bot. 70: 4305-4317.

Millard PS, Weber K, Kragelund BB, Burow M (2019) Specificity of MYB interactions relies on motifs in ordered and disordered contexts. Nucleic Acids Res. 47: 9592-9608.

Nielsen M, Ard R, Leng X, Ivanov M, Kindgren P, Pelechano V, Marquardt S (2019) Transcription-driven chromatin repression of Intragenic transcription start sites. PLoS Genet. 15: e1007969.

Nintemann SJ, Palmgren M, López-Marqués RL (2019) Catch You on the Flip Side: A Critical Review of Flippase Mutant Phenotypes. Trends Plant Sci. 24: 468-478

Paulsen PA, Custódio TF, Pedersen BP (2019) Crystal structure of the plant symporter STP10 illuminates sugar uptake mechanism in monosaccharide transporter superfamily. Nat Commun. 10: 407

Theorin L, Faxén K, Sørensen DM, Migotti R, Dittmar G, Schiller J, Daleke DL, Palmgren M, López-Marqués RL, Günther Pomorski T (2019) The lipid head group is the key element for substrate recognition by the P4 ATPase ALA2: a phosphatidylserine flippase. Biochem J. 476: 783-794

Xu D, Hunziker P, Koroleva O, Blennow A, Crocoll C, Schulz A, Nour-Eldin HH, Halkier BA (2019) GTR-Mediated Radial Import Directs Accumulation of Defensive Glucosinolates to Sulfur-Rich Cells in the Phloem Cap of Arabidopsis Inflorescence Stem. Mol Plant. 12: 1474-1484.

Major Funding Sources

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.

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

Hanna Hõrak
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Estonian University of Life Sciences

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October 9th 2020

Arabidopsis research is mostly carried out in TalTech and University of Tartu in Estonia. Researchers in TalTech study the role of the ABCE1 protein and its homologs in RNA silencing and the function of Arabidopsis myosins. In the Institute of Technology at the University of Tartu, researchers focus on the signalling pathways that mediate stomatal responses to environmental cues. Custom-built devices that enable parallel recording of stomatal conductance in multiple intact Arabidopsis plants are used to characterise plant stomatal behaviour.

    Several independent research directions are pursued in the institute, including identification and detailed characterisation of the role of genes that control stomatal movements in response to changes in CO2 concentration and relative air humidity; and assessing potential interactions between signalling pathways that control stomatal development and movements. In the Department of Botany at the University of Tartu, Arabidopsis is used as a model to study the effects of cultivation density on individual and group performance.

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

    We continually update and improve the custom-built gas-exchange systems designed for measuring stomatal conductance, transpiration and photosynthesis in whole Arabidopsis rosettes and in leaves in controlled and adjustable conditions. Air temperature, air composition (humidity, CO2, O3 etc) and light conditions can be manipulated throughout the experiment and several plants can be recorded in parallel.

Conferences, Workshops and Outreach events

• The New Phytologist Next Generation Scientists 2020 meeting that was supposed to take place from 3-6 August in Tartu, Estonia has been postponed to 2021 due to COVID-19
https://www.newphytologist.org/nextgenevents/2020

Selected Publications

In 2019, there were no publications with leading authors from Estonia, but Estonian Arabidopsis researchers contributed to several collaboration papers.

Dittrich M, Mueller HM, Bauer H, Peirats-Llobet M, Rodriguez PL, Geilfus C-M, Carpentier SC, Rasheid KASA, Kollist H, Merilo E, et al (2019) The role of Arabidopsis ABA receptors from the PYR/PYL/RCAR family in stomatal acclimation and closure signal integration. Nat Plants 5: 1002–1011

Huang S, Waadt R, Nuhkat M, Kollist H, Hedrich R, Roelfsema MRG (2019) Calcium signals in guard cells enhance the efficiency by which abscisic acid triggers stomatal closure. New Phytol 224: 177–187

Julian J, Coego A, Lozano-Juste J, Lechner E, Wu Q, Zhang X, Merilo E, Belda-Palazon B, Park S-Y, Cutler SR, et al (2019) The MATH-BTB BPM3 and BPM5 subunits of Cullin3-RING E3 ubiquitin ligases target PP2CA and other clade A PP2Cs for degradation. Proc Natl Acad Sci 116: 15725–15734

Sun Y, Harpazi B, Wijerathna-Yapa A, Merilo E, Vries J de, Michaeli D, Gal M, Cuming AC, Kollist H, Mosquna A (2019) A ligand-independent origin of abscisic acid perception. Proc Natl Acad Sci 116: 24892–24899

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

October 9th 2020

The largest users of Arabidopsis in research: University of Helsinki, University of Turku, University of Oulu. Despite many groups focusing on plants with agricultural relevance Arabidopsis continues to be the major tool and model for basic research. Arabidopsis also continues to serve as a reference species and is used to establish conceptual models prior to testing in crop species.

    Research concentrating on strategies using Arabidopsis continues to be funded in Finland with major funding coming from the Academy of Finland, thus basic research continues to thrive in Finland in particular in the fields plant development, plant-environment interactions and photosynthesis.

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

    The National Plant Phenotyping facility (NaPPI; https://www.helsinki.fi/en/infrastructures/national-plant-phenotyping) is a shared phenotyping facility with University of Helsinki part concentrating on Arabidopsis. NaPPi is part of the European Plant Phenotyping Network (EPPN).

Conferences, Workshops and Outreach events

    The Academy of Finland-funded Centre of Excellence in the Molecular Biology of Primary Producers organized the conference “Plants in a Changing World” in Helsinki, November 6-8, 2019.

Selected Publications

Abou-Saleh RH, Hernandez-Gomez MC, Amsbury S, Miyashima S, Roszak P, Sevilem I, Toyokura K, Blob B, Heo JO, Mellor N, et al  2019. Mobile PEAR transcription factors integrate positional cues to prime cambial growth. Nature 565(7740): 490-494

Durian G, Jeschke V, Rahikainen M, Vuorinen K, Gollan PJ, Brosché M, Salojärvi J, Glawischnig E, Winter Z, Li S, Noctor G, Aro EM, Kangasjärvi J, Overmyer K, Burow M, Kangasjärvi S. 2020. PROTEIN PHOSPHATASE 2A-B’γ Controls Botrytis cinerea Resistance and Developmental Leaf Senescence. Plant Physiol 182(2):1161-1181

Gerotto C, Trotta A, Bajwa AA, Mancini I, Morosinotto T, Aro EM. 2019. Thylakoid Protein Phosphorylation Dynamics in a Moss Mutant Lacking SERINE/THREONINE PROTEIN KINASE STN8. Plant Physiol 180(3):1582-1597

Hunter K, Kimura S, Rokka A, Tran HC, Toyota M, Kukkonen JP, Wrzaczek M. 2019. CRK2 enhances salt tolerance by regulating callose deposition in connection with PLDα1. Plant Physiology 180(4): 2004-2021.

Kimura S, Hunter K, Vaahtera L, Tran HC, Vaattovaara A, Rokka A, Stolze SC, Harzen A, Citterico M, Meißner L, Wilkens MMT, Hamann T, Toyota M, Nakagami H, Wrzaczek M. 2020. CRK2-mediated control of ROS production by phosphorylation of the RBOHD C-terminus in Arabidopsis. Plant Cell. https://doi.org/10.1105/tpc.19.00525

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(7740): 485-489

Yan D, Yadav SR, Paterlini A, Nicolas WJ, Petit JD, Brocard L, Belevich I, Grison MS, Vaten A, Karami L, El-Showk S, Lee JY, Murawska GM, Mortimer J, Knoblauch M, Jokitalo E, Markham JE, Bayer EM, Helariutta Y. 2019. Sphingolipid biosynthesis modulates plasmodesmal ultrastructure and phloem unloading. Nat Plants 5(6): 604-615

Major Funding Sources

• The major funding source for plant research in Finland is the Academy of Finland (http://www.aka.fi).
• Additional funding sources are the Finnish Cultural Foundation (http://www.skr.fi) and Kone Foundation (https://koneensaatio.fi/en/).
• TEKES funds applied and translational research (https://www.businessfinland.fi/en/).

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

- Arabidopsis stock center,
http://publiclines.versailles.inra.fr

- PHENOSCOPE (http:// www.ijpb.versailles.inra.fr/en/plateformes/ppa/index. html) and PHENOPSIS (www1.montpellier.inra.fr/ibip/lepse/english/ressources/ phenopsis.htm) are high-throughput automated phenotyping platforms at Versailles and Montpellier.
- SPS tools for Functional Genomics https://www6.inra.fr/saclay-plant-sciences_eng/Infrastructures).  

- Plant Genomic center, https://cnrgv.toulouse.inra.fr/Library/Arabidopsis

- PHENOPSIS DB is an information system (http://bioweb.supagro.inra.fr/phenopsis/ Accueil.php?lang=En)

- IPS2: FlagDB++ v6.3 : Plant genomes DB, http://tools.ips2.u-psud.fr/projects/FLAGdb++/ HTML/index.shtml

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

- ChloroKb decoding the chloroplast, LPCV, Grenoble, http://chlorokb.fr/

Conferences, Workshops and Outreach events

- 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/

- The TULIP summer school 2019 “Biological interactions : from genes to ecosystems “2019 (6 to 12 July in the French Pyrenees) Pic du Midi de Bigorre, https://www.labex-tulip.fr/labex-tulip_eng/Training-and-higher-education/Summer-School/Summer-School-2019

- 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

- Molecular Basis of a Sustainable Agriculture: Focus for Montpellier-2020, Plant Nutrition and Development, 5-6 May 2020, Montpellier, https://sites.google.com/view/mbsagro/home

- 20th International Symposium on Iron Nutrition and Interactions, juin 29 - juillet 3, Reims, https://www.isinip2020.fr

- XII INTERNATIONAL SYMPOSIUM ON THE PLANT HORMONE ETHYLENE (ETHYLENE2020) - 29 JUNE TO 3 JULY 2020, Toulouse, http://ethylene2020.inp-toulouse.fr/en/index.html

-  The TULIP summer school 2020 “Biological interactions : from genes to ecosystems 11 to 17 July in the French Pyrenees) https://www.labex-tulip.fr/labex-tulip_eng/Training-and-higher-education/Summer-School/Summer-School-2020

- SPS Summer School 2020, “Plant cell walls in development, plant-microbe interactions and for the bioeconomy”, July 5-11, 2020 – Versailles (France), https://www6.inrae.fr/saclay-plant-sciences/Formation/Ecoles-d-ete/Ecole-d-ete-2020

 Selected Publications

Ariel, Federico; Lucero, Leandro; Christ, Aurelie; Mammarella, Maria Florencia; Jegu, Teddy; Veluchamy, Alaguraj; Mariappan, Kiruthiga; Latrasse, David; Blein, Thomas; Liu, Chang; Benhamed, Moussa; Crespi, Martin (2019) R-Loop Mediated trans Action of the APOLO Long Noncoding RNA. Molecular cell, DOI:10.1016/j.molcel.2019.12.015

Chantreau M, Poux C, Lensink MF, Brysbaert G, Vekemans X, Castric V. (2019) Asymmetrical diversification of the receptor-ligand interaction controlling self-incompatibility in Arabidopsis Elife. 2019 Nov 25;8. pii: e50253. doi: 10.7554/eLife.50253.

Francoz, E; Ranocha, P; Le Ru, A; Martinez, Y; Fourquaux, I; Jauneau, A; Dunand, C; Burlat, V (2019) Pectin Demethylesterification Generates Platforms that Anchor Peroxidases to Remodel Plant Cell Wall Domains DEVELOPMENTAL CELL Volume: 48 Issue: 2 Pages: 261-+ DOI: 10.1016/j.devcel.2018.11.016

Gao, Fei; Robe, Kevin; Bettembourg, Mathilde; Navarro, Nathalia; Rofidal, Valerie; Santoni, Veronique; Gaymard, Frederic; Vignols, Florence; Roschzttardtz, Hannetz; Izquierdo, Esther; Dubos, Christian The Transcription Factor bHLH121 Interacts with bHLH105 (ILR3) and Its Closest Homologs to Regulate Iron Homeostasis in Arabidopsis (2019) The Plant cell, Volume:32Issue:2 Pages:508-524, DOI:10.1105/tpc.19.00541

Khanday, I; Skinner, D; Yang, B ; Mercier, R; Sundaresan, V (2019) A male-expressed rice embryogenic trigger redirected for asexual propagation through seeds NATURE Volume: 565 Issue: 7737 Pages: 91-+ DOI: 10.1038/s41586-018-0785-8

Medici, A; Szponarski, W; Dangeville, P; Safi, A; Dissanayake, IM; Saenchai, C; Emanuel, A; Rubio, V; Lacombe, B ; Ruffel, S ; Tanurdzic, M; Rouached, H; Krouk, G (2019) Identification of Molecular Integrators Shows that Nitrogen Actively Controls the Phosphate Starvation Response in Plants PLANT CELL Volume: 31, Issue: 5, Pages: 1171-1184 DOI: 10.1105/tpc.18.00656

Michaeli, S; Clavel, M; Lechner, E; Viotti, C; Wu, J ; Dubois, M ; Hacquard, T; Derrien, B  ; Izquierdo, E; Lecorbeiller, M (2019) The viral F-box protein P0 induces an ER-derived autophagy degradation pathway for the clearance of membrane-bound AGO1 PNAS, Volume: 116, Issue: 45, Pages: 22872-22883, DOI: 10.1073/pnas.1912222116

Morel, P ; Chambrier, P; Boltz, V; Chamot, S  ; Rozier, F; Bento, SR  ; Trehin, C ; Monniaux, M; Zethof, J ; Vandenbussche, M (2019) Divergent Functional Diversification Patterns in the SEP/AGL6/AP1 MADS-Box Transcription Factor Superclade The PLANT CELL, Volume: 31, Issue: 12, Pages: 3033-3056, DOI: 10.1105/tpc.19.00162

Platre, MP ; Bayle, V ; Armengot, L ; Bareille, J; Marques-Bueno, MD; Creff, A; Maneta-Peyret, L ; Fiche, JB; Nollmann, M ; Miege, C ; Moreau, P; Martiniere, A; Jaillais, Y (2019) Developmental control of plant Rho GTPase nano-organization by the lipid phosphatidylserine SCIENCE, Volume: 364 Issue: 6435 Pages: 57-+DOI: 10.1126/science.aav9959

Voxeur, A ; Habrylo, O; Guenin, S; Miart, F ; Soulie, MC ; Rihouey, C ; Pau-Roblot, C ; Domon, JM ; Gutierrez, L ; Pelloux, J ; Mouille, G; Fagard, M; Hofte, H ; Vernhettes, S. (2019) Oligogalacturonide production upon Arabidopsis thaliana-Botrytis cinerea interaction PNAS; Volume: 116, Issue: 39, Pages: 19743-19752 DOI: 10.1073/pnas.1900317116

Major Funding Sources

• Research organizations such as CNRS, INRA, CEA or Universities provide recurrent funding to their laboratories in addition to payment of salaries of permanent researchers and technicians. Thematic calls can also be opened by these research organizations for their research laboratories to support emerging or risky projects or to facilitate the development of interdisciplinary projects.

• The French national research agency, ANR (http://www. agence-nationale-recherche.fr/en/about-anr/about-the- french-national-research-agency/), provides funding for project-based research. In 2019, the overall score of funding was around 15% of the submitted ANR projects.

• European funding:

http://erc.europa.eu/funding- and-grants Marie-Curie research programmes

http:// ec.europa.eu/research/mariecurieactions/ EMBO
http://www.embo.org/funding-awards

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.

Although the Arabidopsis research community in Greece is small, it remains active producing fascinating results and managing still to acquire funding support.

    Despite the impact on basic research, Arabidopsis is the primary model plant species opening new horizons regarding the applied research related to agronomically important species including trees and cultivated plants.

Conferences, Workshops and Outreach events

41st Conference of the Hellenic Society of Biological Sciences, 9 – 11 May 2019, Katerini

70th Conference of the Hellenic Society of Biochemistry and Molecular Biology, 29 November - 1 December 2019, Eugenides Foundation, Athens

Selected Publications

Daras G, Alatzas A, Tsitsekian D, Templalexis D, Rigas S, Hatzopoulos P. (2019) Detection of RNA-protein interactions using a highly sensitive non-radioactive electrophoretic mobility shift assay. Electrophoresis 40:1365-1371

Daras G, Rigas S, Alatzas A, Samiotaki M, Chatzopoulos D, Tsitsekian D, Papadaki V, Templalexis D, Banilas G, Athanasiadou AM, Kostourou V, Panayotou G, Hatzopoulos P. (2019) LEFKOTHEA Regulates Nuclear and Chloroplast mRNA Splicing in Plants. Dev Cell. 50: 767-779.

Valassakis C, Dervisi I, Agalou A, Papandreou N, Kapetsis G, Podia V, Haralampidis K, Ιconomidou VA, Spaink HP, Roussis A. (2019) Novel interactions of Selenium Binding Protein family with the PICOT containing 2 proteins AtGRXS14 and AtGRXS16 in Arabidopsis thaliana. Plant Science 281: 102-112.

Major Funding Sources

• State Scholarships Foundation (IKY) www.iky.gr/en/

• General Secretariat for Research and Technology (GSRT) www.gsrt.gr/central.

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

Download 2020-21 Report

October 9th 2020

In India, although there is no dedicated financial support for Arabidopsis research from the Government funding agencies, scientists can compete for grants dedicated for basic science and many projects are regularly funded on Arabidopsis exclusively; many more projects use Arabidopsis as a system to validate genes from crop plants. Consequently, the overall quality of publications on Arabidopsis research done in India has improved considerably; it is quite visible from the articles published from India in 2019. In fact many interesting articles in high impact journals have already appeared in the first few months of 2020 that we wish to include in next year’s report.”

    The Dr. Jiten Thakur’s group at NIPGR, New Delhi, has been involved in understanding of the functioning of Mediator, a huge multiprotein complex required for transcriptional regulation by studying the interaction map of Arabidopsis Mediator complex and expounded its structural topology.
 
    Dr. Sudip Chattopadhyay has nucleated a group at NIT, Durgapur, on light signalling in Arabidopsis. In the past year, his group has demonstrated the antagonistic role of a bHLH (MYC2) transcription factor and HY5 in light regulated Arabidopsis seedling development. Their study has revealed that expression of HY5 is negatively regulated by MYC2 primarily in blue light, wheeras HY5 negatively regulates MYC2 expression under multiple wavelengths of light.

    Dr. Sourav Datta’s group, at IISER, Bhopal, is mainly focusing on the role of BBX family of zinc finger transcription factors in postgerminative seedling growth, UV-B tolerance and flowering. They have recently shown that HY5 transcript levels are enhanced by over-expression of BBX31  in UV light, in a UVR8-dependent manner, suggesting that BBX31 might regulate HY5 transcription.
    
    Dr. Kishore Panigrahi and co-workers, at NISER, Bhubaneswar, using microarray analysis, have shown that expression of genes encoding components involved in light, hormone and clock pathways (including  PIF4, COL9, EPR1, CIP1, ARF18, ARR6, SAUR9 and TOC1) changes in Arabidopsis root under various light intensities, indicating their putative role in light intensity mediated root development.
    Dr. Utpal Nath’s group at IISc, Bangalore has done commendable work on the role of TCP proteins in leaf development in Arabidopsis. Employing biochemical and genetic tools, they have demonstrated that TCP4 not only stimulates auxin response but also directly activates HAT2 gene, encoding a HD-ZIP II transcription factor, imparting differentiation competence.

    
    Dr. Kalika Prasad at IISER, Thiruvanathapuram, has been exploring the role of PLETHORA (PLT) genes in organ regeneration. As part of this broader objective, recently, his group has addressed the question how multicellular organisms regenerate their tissues or organs once they are damaged. They have elucidated the molecular mechanism of organ regeneration potential using root tip as a model system and shown that the dosage of gradient-expressed PLT2 transcription factor determines the regeneration potential and organ size.

    Dr. A.K. Sarkar at NIPGR, New Delhi, has analysed the evolutionary relationship and functional sugnificance of Gibberellic Acid Stimulated Transcript (GAST)-like genes that encode small polypeptides and play diverse roles in regulating plant growth and development.

    Dr. Ashverya Laxmi’s recent work at NIPGR, New Delhi, revealed how glucose signaling helps plants develop memory against heat stress signal to respond better to subsequent heat stress treatments. This work has provided novel information about seedling adaptation and survival under heat stress conditions and fetched novel insights in to the mechanistic basis of plant plasticity.

    The focus of Dr. Ashis Nandi’s group at JNU, New Delhi, is to understand the immune machinery of plants. Previously, they reported the identification of FLD/RSI1 as an essential component of infection memory development. In an attempt to reveal the broader roles of FLD,  they have identified the role of FLD in modulating ET/JA signaling and defense against necrotrophic pathogens.

    Dr. Jyothi Vadassery, at NIPGR, New Delhi, is working on the identification of calcium channels in plant-insect interaction. Her group has identified a CYCLIC NUCLEOTIDE GATED CHANNEL19 (CNGC19) that activates herbivory-induced Ca2+ flux and consequently plant defense; loss in CNGC19 function causes decrease in defense against herbivory.

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

Dr. A.K. Sarkar’s group at NIPGR, New Delhi, has devised an improved and cost-effective protocol to isolate sufficient quantity of high-quality mRNA and miRNAs from plant tissues derived by Laser Capture Microdisection (LCM); Gautam et al. (2019) Methods Mol. Biol. 1933: 89-98. doi: 10.1007/978-1-4939-9045-0_5.

Conferences, Workshops and Outreach events

National Arabidopsis meeting (NAM) is an annual feature now and it was held from October 29-31, 2019 at NISER, Bhubaneswar, where most people working on Arabidopsis in India participated.

Selected Publications

Chakraborty M, Gangappa SN, Maurya JP, Sethi V, Srivastava AK, Singh A, Dutta S, Ojha M, Gupta N, Sengupta M, Ram H, Chattopadhyay S (2019) Functional interrelation of MYC2 and HY5 plays an important role in Arabidopsis seedling development. Plant J. 99: 1080-1097.

Challa KR, Rath M, Nath U (2019) The CIN-TCP transcription factors promote commitment to differentiation in Arabidopsis leaf pavement cells via both auxin-dependent and independent pathways. PLoS Genet. 15: e1007988.

Durgaprasad K, Roy MV, Venugopal M A, Kareem A, Raj K, et al. (2019) Gradient expression of transcription factor imposes a boundary on organ regeneration potential in plants. Cell Rep. 29: 453-463.e3.
Kumar A, Singh A, Kumar P, Sarkar AK (2019) Giberellic acid-stimulated transcript proteins evolved through successive conjugation of novel motifs and their subfunctionalization. Plant Physiol. 180: 998-1012.

Kumari S, Yadav S, Patra D, Singh S, Sarkar AK, Panigrahi KCS (2019) Uncovering the molecular signature underlying the light intensity-dependent root development in Arabidopsis thaliana. BMC Genomics. 20(1): 596.

Maji S, Dahiya P, Waseem M, Dwivedy N, Bhat DS, Dar T, Thakur JK (2019) Interaction map of Arabidopsis Mediator complex expounding its topology. Nucleic Acids Res. 47: 3904-3920.

Meena MK, Prajapati R, Krishna D, Divakaran K, Pandey Y, Reichelt M, Mathew MK, Boland W, Mithöfer A, Vadassery J (2019) The Ca2+ channel CNGC19 regulates Arabidopsis defense against Spodoptera herbivory. Plant Cell 31: 1539-1562.

Sharma M, Banday Z, Shukla BN, Laxmi A (2019) Glucose regulated Arabidopsis HLP1 acts as a key molecule in governing thermomemory. Plant Physiol. 180: 1-20.

Vadde BVL, Challa KR, Sunkara P, Hegde AS, Nath U (2019) The TCP4 transcription factor directly activates TRICHOMELESS1 and 2 and suppresses trichome initiation. Plant Physiol. 181: 1587-1599.

Yadav A, Bakshi S, Yadukrishnan P, Lingwan M, Dolde U, Wenkel S, Masakapalli SK, Datta S (2019) The B-box containing microprotein miP1a/BBX31 regulates photomorphogenesis and UV-B protection in Arabidopsis. Plant Physiol. 179: 1876-1892.

Major Funding Sources

• Department of Biotechnology (DBT), Government of India http://dbtindia.nic.in/index.asp
• Department of Science &Technology (DST), Government of India
http://www.dst.gov.in/scientific-programme/serindex.htm
• Science and Engineering Research Board (SERB), Government of India
http://www.serb.gov.in/home.php
• 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/

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

October 9th 2020

Most research funding agencies in Ireland are focused on near-term applied research. However, research on model organisms such as Arabidopsis thaliana has been funded by Science Foundation Ireland (SFI) if it is considered either oriented basic or applied research, while fellowship funding is available from the Irish Research Council  (IRC) for basic research, including on Arabidopsis.

    There is strong pressure from funding agencies via funding calls in Ireland for the research community to focus on applied research. There is a need to grow the Arabidopsis research community in Ireland to a larger scale, which can best be achieved through international partnerships combined with the recruitment priorities of the universities in Ireland. We look forward to welcoming ICAR2022 to Belfast and hope that this event can raise the profile of Arabidopsis and plant science in Ireland.
http://icar2022.arabidopsisresearch.org/
Conferences, Workshops and Outreach events

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

Selected Publications

Łangowski  L, Goñi O, Quille  P, Stephenson  S, Carmody  N, Feeney E, Barton  D, Østergaard  L and SO’Connell S (2019) A Plant Biostimulant From the Seaweed Ascophyllum nodosum (Sealicit) Reduces Podshatter and Yield Loss in Oilseed Rape Through Modulation of IND Expression. Sci Rep 9(1):16644

Zuniga-Soto E, Fitzpatrick DA, Doohan FM and Mullins E (2019) Insights into the transcriptomic response of the plant engineering bacterium Ensifer adhaerens OV14 during transformation. Scientific reports. Jul 17;9(1):1-7.

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
doi:10.1093/molbev/msz063  

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
doi:10.1105/tpc.18.00663

Duszynska, D., Vilhjalmsson, B., Bravo, R.C., Swamidatta, S., Juenger, T.E., Donoghue, M.T., Comte, A., Nordborg, M., Sharbel, T.F., Brychkova, G., McKeown, P.C. and Spillane 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. doi:10.1007/s00497-019-00369-6

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
doi:10.1016/j.plaphy.2018.06.016

Major Funding Sources
    
• Foundation Ireland (SFI); Department of Agriculture, Fisheries and Food; Irish Research Council for Science, Engineering and Technology; and the European Union.

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 Johnathan Dalzell, School of Biological Sciences, Queens University Belfast, Northern Ireland.

14. Dr. Emmanualle Graciet, School of Biology, National University of Ireland Maynooth, Ireland.

Study of Arabidopsis and of additional plant models and crops is conducted in various labs located in major research centers and universities across the country: The Hebrew University of Jerusalem, Tel Aviv University, the Weizmann Institute of Science, Ben Gurion University of the Negev, Bar Ilan University and the Technion - Israel Institute of Technology. Applied research is primarily conducted at the Agriculture Research Organization/Volcani Center. Areas of Arabidopsis research include plant physiology, biochemistry, metabolomics, cell biology, development and functional genomics. Current Arabidopsis research projects are supported by grants from the ISF, ERC, BSF and GIF.
    Conferences organized by the Israeli Society of Plant Sciences aim to promote scientific interactions and collaborations between students across the country. International conferences in these disciplines are also organized and hosted by Israeli scientists.  .

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

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

- Protocols and automation scripts for measuring circadian rhythms of fluorescence:
http://www.rachelgreenlab.com/resources.html

Conferences, Workshops and Outreach events

• The Israeli Society of Plant Sciences Conference, February 13th, 2019, Sde-Boker
• ICPMB 2019: Mitochondria - The Energy Hubs of Living Organisms, 10-15.3.2019, Ein-Gedi.

• Plant Genomics, March 18-19, 2019, The Israel Academy of Sciences and Humanities, Jerusalem

• 9th ILANIT/FISEB Conference, 17-20 February 2020, Eilat

• The Batsheva de Rothschild Seminar on Physics & Biology of Plant Growth March 30 - April 2,  2020, Ein Gedi, Israel - POSTPONED

Selected Publications

Cohen A, Hacham Y, Welfe Y, Khatib S, Avice JC, Amir R: Evidence of a significant role of glutathione reductase in the sulfur assimilation pathway. Plant J 2019.

Dakhiya Y, Green RM: Thermal imaging as a noninvasive technique for analyzing circadian rhythms in plants. New Phytol 2019, 224:1685-1696.

Hazak O, Mamon E, Lavy M, Sternberg H, Behera S, Schmitz-Thom I, Bloch D, Dementiev O, Gutman I, Danziger T, et al.: A novel Ca2+-binding protein that can rapidly transduce auxin responses during root growth. PLoS Biol 2019, 17:e3000085.

Lieberman-Lazarovich M, Yahav C, Israeli A, Efroni I: Deep Conservation of cis-Element Variants Regulating Plant Hormonal Responses. Plant Cell 2019, 31:2559-2572.

Luria G, Rutley N, Lazar I, Harper JF, Miller G: Direct analysis of pollen fitness by flow cytometry: implications for pollen response to stress. Plant J 2019, 98:942-952.

Majhi BB, Sreeramulu S, Sessa G: BRASSINOSTEROID-SIGNALING KINASE5 Associates with Immune Receptors and Is Required for Immune Responses. Plant Physiol 2019, 180:1166-1184.

Murik O, Chandran SA, Nevo-Dinur K, Sultan LD, Best C, Stein Y, Hazan C, Ostersetzer-Biran O: Topologies of N(6) -adenosine methylation (m(6) A) in land plant mitochondria and their putative effects on organellar gene expression. Plant J 2020, 101:1269-1286.

Soltabayeva A, Srivastava S, Kurmanbayeva A, Bekturova A, Fluhr R, Sagi M: Early Senescence in Older Leaves of Low Nitrate-Grown Atxdh1 Uncovers a Role for Purine Catabolism in N Supply. Plant Physiol 2018, 178:1027-1044.

Sun Y, Harpazi B, Wijerathna-Yapa A, Merilo E, de Vries J, Michaeli D, Gal M, Cuming AC, Kollist H, Mosquna A: A ligand-independent origin of abscisic acid perception. Proc Natl Acad Sci U S A 2019, 116:24892-24899.

Vela-Corcia D, Aditya Srivastava D, Dafa-Berger A, Rotem N, Barda O, Levy M: MFS transporter from Botrytis cinerea provides tolerance to glucosinolate-breakdown products and is required for pathogenicity. Nat Commun 2019, 10:2886.

11. Yaari R, Katz A, Domb K, Harris KD, Zemach A, Ohad N: RdDM-independent de novo and heterochromatin DNA methylation by plant CMT and DNMT3 orthologs. Nat Commun 2019, 10:1613.

Major Funding Sources

• ISF:  https://www.isf.org.il

• BSF and NSF-BSF: https://www.bsf.org.il/

• ERC: https://erc.europa.eu/

• GIF: http://www.gif.org.il/Pages/default.aspx

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

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October 9th 2020

There are just over 20 groups, large and small, currently working on Arabidopsis in Italy. They work mainly in Universities and the Institutes of the National Research Council (CNR) distributed throughout the country, in cities such as Rome, Milan, Naples, Bologna, Padova, Pisa, Verona, Bari, Cosenza, l’Aquila, Lecce, Perugia, Ancona, Potenza, Sassari, and Palermo.

    Authors from these laboratories conducting diversified research on Arabidopsis published more than 80 papers in 2019 with Italian scientists as lead or co-authors. Research is mainly focused on plant responses to environment and abiotic stress, oxygen sensing and signalling, plant root and reproductive development, seed germination, plant metabolism and defense responses.

    Research on Arabidopsis is funded almost exclusively by small Italian grants awarded to individual research groups by the Universities, such as in Rome and Milan, or local regional grants. Unfortunately, as in previous years, the Italian Ministry of Education, University and Research, has continued to decrease funding for basic research thus causing a reduction in the amount of work produced on Arabidopsis.

    International funding, such as European grants or Human frontiers grants (one recently attributed to L. Conti from the University of Milan) are exceptions. Despite all of this, research activities cover most topics related of Arabidopsis and the results obtained are published in high impact journals.

Conferences, Workshops and Outreach events

04-06/09/2019 - Jointed SIBV-SBI Congress. Conference. Padua, Italy.  http://www.sibv.eu/congressi-ed-eventi/congresso-congiunto-sbi-sibv

-Meet Me Tonight - 27-28th September 2019. Outreach activity. Giardini Indro Montanelli. Milan, Italy.
http://www.meetmetonight.it/il-programma/

-International Workshop in Posttranscriptional modifications September 2019, Biosciences Dept. Milano University, Italy Organizing committee, 50 participants,

Selected Publications

Alfieri A, Doccula FG, Pederzoli R, Grenzi Matteo, Bonza MC, Luoni L, Candeo A, Romano Armada N, Barbiroli A, Valentini G, Schneider TR, Bassi A, Bolognesi M, Nardini M, Costa A. The structural bases for agonist diversity in an Arabidopsis thaliana glutamate receptor-like channel. Proc Natl Acad Sci U S A. 2019; 117: 752-760.

Caselli F, Beretta VM, Mantegazza O, Petrella R, Leo G, Guazzotti A, Herrera-Ubaldo H, de Folter S, Mendes MA, Kater MM, Gregis V. REM34 and REM35 Control Female and Male Gametophyte Development in Arabidopsis thaliana Front Plant Sci. 2019 Oct 24;10:1351.

Di Mambro R, Svolacchia N, Dello Ioio R, Pierdonati E, Salvi E, Pedrazzini E, Vitale A, Perilli S, Sozzani R, Benfey PN, Busch W, Costantino P, Sabatini S. The Lateral Root Cap Acts as an Auxin Sink that Controls Meristem Size.
Current Biology. 2019;29(7):1199-1205.

Locci F, Benedetti M, Pontiggia D, Citterico M, Caprari C, Mattei B, Cervone F, De Lorenzo G “An Arabidopsis Berberine Bridge Enzyme-Like Protein Specifically Oxidizes Cellulose Oligomers And Plays A Role In Immunity”. Plant Journal. 2019; 98: 540-554.

Martignago D, Bernardini B, Polticelli F, Salvi D, Cona A, Angelini R, Tavladoraki P. The Four FAD-Dependent Histone Demethylases of Arabidopsis Are Differently Involved in the Control of Flowering Time.  Front Plant Sci. 2019; 10, 669.

Mattioli R, Francioso A, d’Erme M, Trovato M, Mancini P, Piacentini L, Casale AM, Wessjohann L, Gazzino R, Costantino P, Mosca L. Anti-inflammatory activity of polyphenolic extract from Arabidopsis thaliana in Alzheimer’s disease models. Int. J. Mol. Sci. 2019 20:708

Teardo E, Carraretto L, Moscatiello R, Cortese E, Vicario M, Festa M, Maso L, De Bortoli S, Calì T, Vothknecht UC, Formentin E, Cendron L, Navazio L, Szabo I. A chloroplast-localized mitochondrial calcium uniporter transduces osmotic stress in Arabidopsis. Nature Plants. 2019 Jun;5(6):581-588.

Termolino P, Falque M, Aiese Cigliano R, Cremona G, Paparo R, Ederveen A, Martin OC, Consiglio FM, Conicella C. Recombination suppression in heterozygotes for a pericentric inversion induces the interchromosomal effect on crossovers in Arabidopsis. Plant Journal. 2019;100(6):1163-1175.

Weits DA, Kunkowska AB, Kamps NCW, Portz KMS, Packbier NK, Nemec Venza Z, Gaillochet C, Lohmann JU, Pedersen O, van Dongen JT, Licausi F. An apical hypoxic niche sets the pace of shoot meristem activity.
Nature. 2019 May;569(7758):714-717

Zaffagnini M, Marchand CH, Malferrari M, Murail S, Bonacchi S, Genovese D, Montalti M, Venturoli G, Falini G, Baaden M, Lemaire SD, Fermani S, Trost P. Glutathionylation primes soluble glyceraldehyde-3-phosphate dehydrogenase for late collapse into insoluble aggregates. Proc Natl Acad Sci U S A. 2019;116(51):26057-26065.

 Major Funding Sources

-Local funding from:

• Sapienza University of Rome :
https://www.uniroma1.it/sites/default/files/field_file_allegati/progetti_piccoli_medi_e_grandi_0.pdf
- Progetto di Ateneo Ricerche Universitarie 2019 “Priming of defense responses in the trade-off between plant immunity and growth.” Coordinator: Simone Ferrari.

• Progetto di Ateneo Ricerche Universitarie 2019 “Molecular dynamics underlying PME activity in plant immunity. Coordinator:Vincenzo Lionetti.

• Progetto di Ateneo Ricercehe Universitarie 2019 “Interplay between proline and ROS in the fine tuning of root-meristem size in Arabidopsis. Coordinator Maurizio Trovato

• Progetto di Ateneo Ricerche Universitarie 2018/2019  “Molecular Mechanisms in developmental boundary formation. Coordinator: Sabrina Sabatini
-Roma Tre University of Rome Research-Grant to Department of Science, University ‘Roma Tre’-‘Dipartimenti di Eccellenza’

• University of Milan:
http://eng.dbs.unimi.it/ecm/home/research/funded-research-projects
Study of the physiological role played by the aminoacid-binding domain of the Arabidopsis Glutamate Receptor-like channel GLR3.3 in long-distance communication”. Coordinator: Alex Costa.
 
The Italian Ministry of Education, University and Research funded:

• PRIN2017(2019-2022) Regulatory signals and redox systems in plant growth-defence trade off. Code: 2017ZBBYNC Coordinator: Giulia De Lorenzo
https://www.miur.gov.it/documents/20182/424391/DD+n.1063+del+31-05-2019+-+ALLEGATO+A+-+LS9.pdf/8ba4cf5b-4a28-bebd-3f1b-f535de5f79c4?version=1.0&t=1559563731935

• PRIN 2017 (2019-2022) MIUR PRIN 2017 “SOUP: Signaling the Organelle Unfolded Protein response”. Code: PRIN 2017FBS8YN. P.I. Coordinator: Paolo Pesaresi.
https://expertise.unimi.it/individual?uri=http%3A%2F%2Firises.unimi.it%2Fresource%2Fproject%2F43234

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

• MSCA RISE (2016-2020) SEXSEED project - “Sexual Plant Reproduction – Seed formation” - Horizon2020- MSCA RISE 2016 - European Union (EU)- project n. 690946 - Project P.I Lucia Colombo
https://cordis.europa.eu/project/id/690946/it

• Human Frontier Science Program Organization - RGP0011/2019 - An integrative approach to decipher flowering time dynamics under drought stress. Coordinator Lucio Conti
https://www.hfsp.org/awardees/awards?field_award_type_target_id=All&field_countries_target_id&field_nationalities_target_id&page=3

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

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October 9th 2020

Arabidopsis has been used by many plant researchers as a model higher plant to understand the life phenomena of higher plants and to identify key factors and regulatory networks in environmental response and development. Because various useful resources such as multiple mutants have been developed and are available from stock centers. In addition, translational research to apply the knowledge obtained from Arabidopsis to various crops and trees has been increasing.

New Resources and Software tools available for Arabidopsis Researchers that have been initiated or funded in 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:
• Widely-targeted metabolomics (in Drop Met  http://bit.ly/2HU2ACI )
• AtMetExpress Arabidopsis metabolome expression database (http://bit.ly/1P2YByw)
• LC-MCS Branch (http://bit.ly/1P2Zhnt)
PRIMe Web Applications
• MeKO Metabolite Profiling Database for Knock-Out Mutants in Arabidopsis (MeKO)   (http://bit.ly/1QQBWYl)
• PRIMeLink integrates 3 above databases (AtMetExpress, MS2T and ReSpect) for bi-directional search from gene or metabolite (http://bit.ly/1RCX4Bc)
• ReSpect RIKEN MSn Spectral database for phytochemicals (http://bit.ly/1P2ZaIv)
• HiFi Heteroatom-containing Ion Finder (http://bit.ly/1nBxjJ6)
• PlaSMA Plant Specialized Metabolome Annotation
(http://plasma.riken.jp/)
Distribution and Redistribution
• Drop Met mass-spec based metabolome analyses (http://bit.ly/1LVEfwq)

Other RIKEN CSRS developed tools and resources:
• AtGenExpress Arabidopsis Gene Expression profile database (http://bit.ly/1P2YT8v)
 • KNApSacK Comprehensive species-metabolite relationship database (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://www.massbank.jp/en/about.html)
• Plant-PrAS (Plant-Protein Annotation Suite) (http://plant-pras.riken.jp/)
• RIPPS (RIKEN Plant Phenotyping System)
(https://academic.oup.com/pcp/article/59/10/2030/5043525)
• The Chloroplast Function Database III (https://plant.rtc.riken.jp/color/c/index.html)
• Arabidopsis nuclear-encoded chloroplast protein mutant seeds
(https://epd.brc.riken.jp/en/archives/4909)
• Arabidopsis sORF Database HanaDB-At (http://hanadb01.bio.kyutech.ac.jp/hanadb-at/)
• Hormone-like peptides in Arabidopsis (http://hanadb01.bio.kyutech.ac.jp/peptide/)
• Hormonome platform and RIKEN Plant Hormone Research Network　(http://hormones.psc.riken.jp/)
RIKEN National Science Institute - BioResource Research Center (BRC) (https://epd.brc.riken.jp/en/)
• Arabidopsis seeds, cDNA, and plant cultured cells: Exp-Plant catalog (https://plant.rtc.riken.jp/resource/index.html)
• Resource information (https://epd.brc.riken.jp/en/)
• National BioResource Project (http://nbrp.jp/index.jsp)
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)
• Plant GARDEN Plant Genome And Resource Database ENtry (https://plantgarden.jp)
• 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/)
• CoP: a database for plant co-expressed gene network (http://webs2.kazusa.or.jp/kagiana/cop0911/)
• RnR: a database for regulatory network in T87 cultured cells of Arabidopsis thaliana
 (http://webs2.kazusa.or.jp/kagiana/rnr0912/indexff.html)
National Institute for Basic Biology (http://www.nibb.ac.jp)
• nekko: a portal site for Rhizophagus irregularis genome (http://nekko.nibb.ac.jp)
•  Japanese Morning Glory Genome Database: (http://ipomoeanil.nibb.ac.jp)
• The Plant Organelles Database 3: (http://podb.nibb.ac.jp/Organellome/)
• PHYSCObase: (http://moss.nibb.ac.jp/physco.html)

Conferences, Workshops and Outreach events

-May 11-14, 2019: “Principles of pluripotent stem cells underlying plant vitality”, Tohoku Univ. (http://www.tfc.tohoku.ac.jp/event/4226.html)
- May 21-30, 2019: EMBO Practical Course “Functional live imaging of plants”, Nagoya Univ. (https://meetings.embo.org/event/19-plant-live-imaging)
- Mar. 19-21, 2020: 61st Annual Meeting of Japanese
Society of Plant Physiologists. Osaka Univ.
(https://jspp.org/annualmeeting/61/e_greeting.php)
- May 21-30, 2020: EMBO practical course “Functional Imaging of Plants”. Nagoya Univ.
- Dec. 7-10, 2020: Cold Spring Harbor Asia Conference “Integrative Epigenetics in Plants”, Awaji Yumebutai Conference Center (http://www.csh-asia.org/2020meetings/epiplant.html)
-  May/June 2021: International Symposium on Sustainable Resource Science, Yokohama, Japan
- ICAR2023 will be held in Japan for the first time in 13 years since ICAR2010.

Selected Publications

Fujii, S., Tsuchimatsu, T., Kimura, Y., Ishida, S., Tangpranomkorn, S., Shimosato-Asano, H., Iwano, M., Furukawa, S., Itoyama, W., Wada, Y., Shimizu, K.K., Takayama, S. (2019) A stigmatic gene confers interspecies incompatibility in the Brassicaceae. Nature Plants 5: 731–741

Hoshino, R., Yoshida, Y., Tsukaya, H. (2019)  Multiple steps of leaf thickening during sun-leaf formation in Arabidopsis. Plant J. 100:738-753.

Ishihara, H., Sugimoto, K., Tarr, P.T., Temman, H., Kadokura, S., Inui, Y., Sakamoto, T., Sasaki, T., Aida, M., Suzuki, T., Inagaki, S., Morohashi, K., Seki, M., Kakutani, T., Meyerowitz, E.M., Matsunaga, S. (2019) Primed histone demethylation regulates shoot regenerative competency. Nature Commun. 10: 1786.

Ishikawa, M., Morishita, M., Higuchi, Y., Ichikawa, S., Ishikawa, T., Nishiyama, T., Kabeya, Y., Hiwatashi, Y., Kurata, T., Kubo, M., Shigenobu, S., Tamada, Y., Sato, Y., Hasebe, M. (2019) Physcomitrella STEMIN transcription factor induces stem cell formation with epigenetic reprogramming. Nature Plants. 5:681-690.

Kidokoro, S., Kim, J.S., Ishikawa, T., Suzuki, T., Shinozaki, K., Yamaguchi-Shinozaki, K. (2020) DREB1A/CBF3 is repressed by transgene-induced DNA methylation in the Arabidopsis ice1-1 mutant. Plant Cell. (in press) doi: 10.1105/tpc.19.00532.

Ota, R., Ohkubo, Y., Yamashita, Y., Ogawa-Ohnishi, M., Matsubayashi, Y. (2020) Shoot-to-root mobile CEPD-like 2 integrates shoot nitrogen status to systemically regulate nitrate uptake in Arabidopsis. Nature Commun. 11: 641.

Soyano, T., Shimoda, Y., Kawaguchi, M, Hayashi, M. (2019) A shared gene drives lateral root development and root nodule symbiosis pathways in Lotus. Science 366:1021-1023.

Seto, Y., Yasui, R., Kameoka, H., Tamiru, M., Cao, M., Terauchi, R., Sakurada, A., Hirano, R., Kisugi, T., Hanada, A., Umehara, M., Seo, E., Akiyama, K., Burke, J., Takeda-Kamiya, N., Li, W., Hirano, Y., Hakoshima, T., Mashiguchi, K., Noel, J.P., Kyozuka, J., Yamaguchi, S. (2019) Strigolactone perception and deactivation by a hydrolase receptor DWARF14. Nature Commun. 10:191.

Toriba, T., Tokunaga, H., Shiga, T., Nie, F., Naramoto, S., Honda, E., Tanaka, K., Taji, T., Itoh, J.I., Kyozuka, J. (2019) BLADE-ON-PETIOLE genes temporally and developmentally regulate the sheath to blade ratio of rice leaves. Nature Commun. 10:619.

Tsugawa, H, Nakabayashi, R., Mori, T., Yamada, Y., Takahashi, M., Rai, A., Sugiyama, R., Yamamoto, H., Nakaya, T., Yamazaki, M., Kooke, R., Bac-Molenaar, J.A., Oztolan-Erol, N., Keurentjes, J.J.B., Arita, M., Saito, K. (2019) A cheminformatics approach to characterize metabolomes in stable-isotope-labeled organisms. Nature Methods. 16: 295–298.

Major Funding Sources

• RIKEN is supported by MEXT.

• Kazusa projects are supported by Chiba-Prefecture.
Grants-in-Aid for Science from MEXT, (http://www.jsps.go.jp/english/e-grants/)

• CREST of Japan Science and Technology Corporation (http://bit.ly/22I8avZ)

• ERATO of Japan Science and Technology Corporation (https://www.jst.go.jp/erato/en/index.html)

• MIRAI Program of Japan Science and Technology Corporation (http://www.jst.go.jp/mirai/jp/about/index.html)

• Strategic International Cooperative Program (SICORP), JST-NSF Joint Research Project. (http://www.jst.go.jp/inter/english/sicorp/index.html)

• “Impulsing Paradigm Change through Disruptive Technologies” (ImPACT) (http://www.jst.go.jp/impact/en/outline. html)

• MEXT “Cross-ministerial Strategic Innovation Promotion Program” (SIP) in 2014. (http://www.mext.go.jp/english/ topics/1345957.htm)

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).
• 15^th 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

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

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October 9th 2020

Agriculture and horticulture play major roles in the New Zealand economy, with major crops including ryegrass, clover and other forage crops for dairy cattle and fruits such as apple and kiwifruit. In this context, Arabidopsis is largely used as an easily manipulated model for the identification and testing of gene function, with information translated into other species.

    However, within New Zealand universities, Arabidopsis is also used for basic research into plant growth and development.

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

    Genome sequence from Pachycladon cheesemanii, a New Zealand member of the Brassicaceae that originated 1-3.5 million years ago. Useful for evolutionary studies with A. thaliana. Sequence data are available from the NCBI Bioproject database (www.ncbi.nlm.nih.gov/bioproject) under ID: PRJNA475190.

Conferences, Workshops and Outreach events

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

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

Queenstown Molecular Biology Week-Plant Satellite, Queenstown, New Zealand, 3-4 September 2020 (but likely to be cancelled due to Corona Virus)

Selected Publications

Soffe R, Bernach M, Remus-Emsermann MNP and Nock V (2019). Replicating Arabidopsis model leaf surfaces for phyllosphere microbiology. Sci Rep 9, 14420

Dong Y, Gupta S, Sievers R, Wargent J J, Wheeler D, Putterill J, Macknight R, Gecgev T, Mueller-Roeber B and Dijkwel PP (2019). Genome draft of the Arabidopsis relative Pachycladon cheesemanii reveals novel strategies to tolerate New Zealand’s high ultraviolet B radiation environment. BMC Genomics, 20:838

Sun X, Malhis N, Zhao B, Gsponer J, Rikkerink EHA. 2020. Computational disordered analysis in ethylene response factors uncovers binding motifs critical to their diverse functions. International Journal of Molecular Sciences, 21: 74  

Cyril Hamiaux, Lesley Larsen, Hui Wen Lee, Zhiwei Luo, Prachi Sharma, Bill C. Hawkins, Nigel B. Perry, Kimberley C. Snowden; Chemical synthesis and characterization of a new quinazolinedione competitive antagonist for strigolactone receptors with an unexpected binding mode. Biochem J  476: 1843–1856.

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

• 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/)

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

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October 9th 2020

The Arabidopsis community in Norway consists of groups based in Bergen, Hamar, Oslo, Stavanger, Ås, Tromsø and Trondheim. Main focus areas of research are developmental processes, response to biotic and abiotic stress as well as photosynthesis. Topics of particular interest include peptide-based and cell wall signaling processes, epigenetics and gametophytic development, jasmonic acid-based defense responses and adaptation to cold stress. Of particular interest is the translation of relevant research findings to tree species of commercial interest due to the sizeable commercial interest in forestry in Norway.

    Despite the small overall size of the community the members continue to generate high quality outputs (exemplified by the publications listed), that attract significant interest.

Selected Publications

Blagojevic D, Lee Y, Brede DA, Lind OC, Yakovlev I, Solhaug KA, Fossdal CG, Salbu B, Olsen JE (2019) Comparative sensitivity to gamma radiation at the organismal, cell and DNA level in young plants of Norway spruce, Scots pine and Arabidopsis thaliana. Planta. 2019; 250(5): 1567-1590. doi: 10.1007/s00425-019-03250-y.

Engelsdorf T, Kjaer L, Gigli-Bisceglia N, Vaahtera L, Bauer S, Miedes E, Wormit A, James L, Chairam I, Molina A, Hamann T (2019) Functional characterization of genes mediating cell wall metabolism and responses to plant cell wall integrity impairment. BMC Plant Biol. 2019; 19(1): 320. doi: 10.1186/s12870-019-1934-4.

Grytten I, Rand KD, Nederbragt AJ, Storvik GO, Glad IK, Sandve GK (2019) Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes. PLoS Comput Biol. 2019; 15(2): e1006731. doi: 10.1371/journal.pcbi.1006731.

Hornslien KS, Miller JR, Grini PE (2019) Regulation of Parent-of-Origin Allelic Expression in the Endosperm. Plant Physiol. 2019; 180(3): 1498-1519. doi: 10.1104/pp.19.00320.

Olsson V, Joos L, Zhu S, Gevaert K, Butenko MA, De Smet I (2019) Look Closely, the Beautiful May Be Small: Precursor-Derived Peptides in Plants. Annu Rev Plant Biol. 2019; 70: 153-186. doi: 10.1146/annurev-arplant-042817-040413.

Zakhartsev M (2019) Using a Multi-compartmental Metabolic Model to Predict Carbon Allocation in Arabidopsis thaliana. Methods Mol Biol. 2019; 2014: 345-369. doi: 10.1007/978-1-4939-9562-2_27.

Major Funding Sources

• Norwegian Research Council

https://www.forskningsradet.no/en/Home_page/1177315753906

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.

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October 9th 2020

Arabidopsis is undoubtedly an important object of scientific research in Poland. The total value of signed contracts for projects on this model plant by the National Science Center Poland in 2019 was 2,973,265 EUR. The net value of other ongoing NCN-funded Arabidopsis projects that have started in previous years was 9,471,097 EUR.

    Similarly to other countries, in Poland Arabidopsis has dual use as a model to study basic processes in plants and a very practical system facilitating functional studies for crop species. Due to the multidisciplinary character of plant research and complexity of studied subjects our scientists cooperate internationally. Such example could be the work of Lopez et al. published in 2019, that results from Polish-American co-operation.

Lopez VA, Park BC, Nowak D, Sreelatha A, Zembek P, Fernandez J, Servage KA, Gradowski M, Hennig J, Tomchick DR, Pawłowski K, Krzymowska M, Tagliabracci VS (2019) A Bacterial Effector Mimics a Host HSP90 Client to Undermine Immunity. Cell 179: 205-218.e221

    The authors report the discovery of bacterial effector kinase HopBF1, which has the ability to modulate plant host immunity by phosphorylation of the HSP90 protein. The work describes a new, previously unknown phenomenon in the interaction between the plant and the pathogen.
 
    In 2019, two important scientific conferences were held in Poland. The first is the 44th Federation of European Biochemical Societies Conference, during which plant-related subjects (including Arabidopsis)were widely discussed. The second conference was the 9th Polish Society of Experimental Plant Biology Conference. Here, works on Arabidopsis were very strongly represented by both Polish scientists and international leaders. In particular flowering, seed formation, epigenetics, interactions of plants with biotic and abiotic factors were discussed.

    The subject of plant responses to stress is very actively explored in Poland. This is also reflected by increasing number of papers in this field published every year.

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

Web application AFproject - a joint effort to benchmark, improve and simplify alignment-free sequence analysis. [http://afproject.org/app/]
Zielezinski et al. Benchmarking of alignment-free sequence comparison methods. Genome Biology, 2019, 20, p144. doi: 10.1186/s13059-019-1755-7

Conferences, Workshops and Outreach events

- 44th Federation of European Biochemical Societies Conference – Krakow, Poland, July 6-11, 2019

- 9th Polish Society of Experimental Plant Biology Conference - Torus, Poland, September 9–12, 2019

Selected Publications

Research conducted on Arabidopsis:

Kwasniak-Owczarek M, Kazmierczak U, Tomal A, Mackiewicz P, Janska H. 2019. Deficiency of mitoribosomal S10 protein affects translation and splicing in Arabidopsis mitochondria. Nucleic Acids Research 47(22): 11790-11806.

Kwasnik A, Wang VY-F, Krzyszton M, Gozdek A, Zakrzewska-Placzek M, Stepniak K, Poznanski J, Tong L, Kufel J. 2019. Arabidopsis DXO1 links RNA turnover and chloroplast function independently of its enzymatic activity. Nucleic Acids Research 47(9): 4751-4764.

Maszkowska J, Dębski J, Kulik A, Kistowski M, Bucholc M, Lichocka M, Klimecka M, Sztatelman O, Szymańska KP, Dadlez M, et al. 2019. Phosphoproteomic analysis reveals that dehydrins ERD10 and ERD14 are phosphorylated by SNF1-related protein kinase 2.10 in response to osmotic stress. Plant, Cell & Environment 42(3): 931-946.

Mazur R, Mostowska A, Szach J, Gieczewska K, Wójtowicz J, Bednarska K, Garstka M, Kowalewska Ł. 2019. Galactolipid deficiency disturbs spatial arrangement of the thylakoid network in Arabidopsis thaliana plants. Journal of Experimental Botany 70(18): 4689-4704.

Olszak M, Truman W, Stefanowicz K, Sliwinska E, Ito M, Walerowski P, Rolfe S, Malinowski R. 2019. Transcriptional profiling identifies critical steps of cell cycle reprogramming necessary for Plasmodiophora brassicae-driven gall formation in Arabidopsis. Plant J 97(4): 715-729.

Rozpądek P, Nosek M, Domka A, Ważny R, Jędrzejczyk R, Tokarz K, Pilarska M, Niewiadomska E, Turnau K. 2019. Acclimation of the photosynthetic apparatus and alterations in sugar metabolism in response to inoculation with endophytic fungi. Plant, Cell & Environment 42(4): 1408-1423.

You Y, Sawikowska A, Lee JE, Benstein RM, Neumann M, Krajewski P, Schmid M. 2019. Phloem Companion Cell-Specific Transcriptomic and Epigenomic Analyses Identify MRF1, a Regulator of Flowering. The Plant Cell 31(2): 325-345.

Research conducted on other plant species:

Lopez VA, Park BC, Nowak D, Sreelatha A, Zembek P, Fernandez J, Servage KA, et al. 2019. A Bacterial Effector Mimics a Host HSP90 Client to Undermine Immunity. Cell 179(1): 205-218.e221.
Pawela A, Banasiak J, Biała W, Martinoia E, Jasiński M. 2019. MtABCG20 is an ABA exporter influencing root morphology and seed germination of Medicago truncatula. The Plant journal : for cell and molecular biology 98(3): 511-523.

Major Funding Sources

• National Science Centre Poland
https://www.ncn.gov.pl/

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

• The National Centre for Research and Development https://www.ncbr.gov.pl

Yunhe Jiang, 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., King Abdullah University of Science and Technology (KAUST)

October 9th 2020

King Abdullah University of Science and Technology (KAUST) conduct most of the Arabidopsis research in Saudi Arabia. KAUST established a center (Center for Desert Agriculture, CDA) to encourage the seven plant science groups working together. The CDA researchers use model plant Arabidopsis to study the basic biological questions and also translate these knowledges to crops, aim to resolve the significant challenges in the Kingdom and the world.

    The research mainly focuses on plant-microbe interaction (Professor Heribert Hirt), root development and growth/defense trade-offs (Professor Ikram Blilou), genome editing (Professor Magdy Mahfouz) and carotenoid-related metabolic pathways (Professor Salim Al-Babili).

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/

Selected Publications

Abuauf, H., Haider, I., Jia, K.-P., Ablazov, A., Mi, J., Blilou, IHan B, Jiang Y, Cui G, et al., (2020). CATION-CHLORIDE CO-TRANSPORTER 1 (CCC1) mediates plant resistance against Pseudomonas syringae. Plant Physiology, pp.01279.2019.

Ali Z, Mahfouz MM, Mansoor S, (2020). CRISPR-TSKO: A Tool for Tissue-Specific Genome Editing in Plants. Trends in Plant Science 25, 123-6.

Eida AA, Alzubaidy HS, De Zélicourt A, et al., (2019). Phylogenetically diverse endophytic bacteria from desert plants induce transcriptional changes of tissue-specific ion transporters and salinity stress in Arabidopsis thaliana. Plant Science 280, 228-40.

Jarad M, Mariappan K, Almeida-Trapp M, et al., (2020). The Lamin-Like LITTLE NUCLEI 1 (LINC1) Regulates Pattern-Triggered Immunity and Jasmonic Acid Signaling. Frontiers in Plant Science 10.

Jia K-P, Dickinson AJ, Mi J, et al., (2019). Anchorene is a carotenoid-derived regulatory metabolite required for anchor root formation in Arabidopsis. Science Advances 5, eaaw6787.

Jiang Y, Han B, Zhang H, et al., (2019). MAP4K4 associates with BIK1 to regulate plant innate immunity. EMBO reports 20, e47965.

Julkowska MM, Saade S, Agarwal G, et al., (2019). MVApp—Multivariate Analysis Application for Streamlined Data Analysis and Curation. Plant Physiology 180, 1261-76.

Long Y, Stahl Y, Weidtkamp-Peters S, Blilou I, (2020) Visualizing Protein Associations in Living Arabidopsis Embryo. In: Bayer M, ed. Plant Embryogenesis: Methods and Protocols. New York, NY: Springer US, 167-88.

Major Funding Sources

• King Abdullah University of Science and Technology.

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

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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/

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

October 9th 2020

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

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

Conferences, Workshops and Outreach events

In 2019
- Cold spring harbor Asia conference on plant cell and development
https://www.csh-asia.org/2019meetings/plant.html
- Annual Conference of the Korean Society of Plant Biologists
- KSPB Winter conference
http://www.kspb.kr/bbs/board.php?bo_table=05_01&wr_id=90&sst=wr_hit&sod=asc&sop=and&page=1

Selected Publications

Do THT, Choi H, Palmgren M, Martinoia E, Hwang JU, Lee Y. (2019) Arabidopsis ABCG28 is required for the apical accumulation of reactive oxygen species in growing pollen tubes. Proc Natl Acad Sci U S A. 116(25):12540-12549.

Hwang K, Susila H, Nasim Z, Jung JY, Ahn JH. (2019) Arabidopsis ABF3 and ABF4 Transcription Factors Act with the NF-YC Complex to Regulate SOC1 Expression and Mediate Drought-Accelerated Flowering. Mol Plant. 12(4):489-505.

Lee HG, Seo PJ. (2019) MYB96 recruits the HDA15 protein to suppress negative regulators of ABA signaling in Arabidopsis. Nat Commun. 10(1):1713.

Lee DW, Lee S, Lee J, Woo S, Razzak MA, Vitale A, Hwang I. (2019) Molecular Mechanism of the Specificity of Protein Import into Chloroplasts and Mitochondria in Plant Cells. Mol Plant. 12(7):951-966.

Kim MH, Jeon J, Lee S, Lee JH, Gao L, Lee BH, Park JM, Kim YJ, Kwak JM. (2019) Proteasome subunit RPT2a promotes PTGS through repressing RNA quality control in Arabidopsis. Nat Plants. 2019 Dec;5(12):1273-1282.

Kim H, Yu SI, Jung SH, Lee BH, Suh MC. (2019) The F-Box Protein SAGL1 and ECERIFERUM3 Regulate Cuticular Wax Biosynthesis in Response to Changes in Humidity in Arabidopsis. Plant Cell. 31(9):2223-2240.
 Lee MH, Jeon HS, Kim SH, Chung JH, Roppolo D, Lee HJ, Cho HJ, Tobimatsu Y, Ralph J, Park OK. (2019) Lignin-based barrier restricts pathogens to the infection site and confers resistance in plants. EMBO J. 38(23):e101948.

Kim EJ, Lee SH, Park CH, Kim SH, Hsu CC, Xu S, Wang ZY, Kim SK, Kim TW. (2019) Plant U-Box40 Mediates Degradation of the Brassinosteroid-Responsive Transcription Factor BZR1 in Arabidopsis Roots. Plant Cell. 31(4):791-808.

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(1):37-51.

Song JH, Kwak SH, Nam KH, Schiefelbein J, Lee MM. (2019) QUIRKY regulates root epidermal cell patterning through stabilizing SCRAMBLED to control CAPRICE movement in Arabidopsis. Nat Commun. 10(1):1744. doi: 10.1038/s41467-019-09715-8.

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

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October 9th 2020

Authors from laboratories studying Arabidopsis in Spain published about 350 papers in the last year, which is similar to that seen in recent years. However, the proportion of papers that use previous knowledge initially obtained in Arabidopsis but use other plant species as a central object of study is growing. Indeed, since 2008, funded plant science has changed in Spain towards more applied approaches; however, Arabidopsis still is predominant among the financed lines of plant science research.
    
New Resources and Software tools available for Arabidopsis Researchers that have been initiated or funded in 2019.

    A reproducible epigenomic analysis pipeline using Galaxy and Jupyter, packaged into Docker images to facilitate transparency and reuse was developed for different Brassicaceae species, as described in
Payá-Milans M, Poza-Viejo L, San Martín-Uriz P, Lara-Astiaso D, Wilkinson MD and Crevillén P (2019) Genome-wide analysis of the H3K27me3 epigenome and transcriptome in Brassica rapa. Gigascience 8: 1-13.
 

Conferences, Workshops and Outreach events

- The “International Symposium on Plant Photobiology” was organized in Barcelona by members of the Centre for Research in Agricultural Genomics, including Profs Jaume Martínez-García and Elena Monte, and Dr Jordi Moreno-Romero (June 3-8, 2019).

- The “Small Molecules in Plant Research: Chemistry and Biology Come Together” symposium was organized by plant biologists lead by Prof. Antonio Granell in Valencia (December 10-11, 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

Abbas Crevillén P, Gómez-Zambrano A, López JA, Vázquez J, Piñeiro M and Jarillo JA (2019) Arabidopsis YAF9 histone readers modulate flowering time through NuA4-complex-dependent H4 and H2A.Z histone acetylation at FLC chromatin. New Phytologist 222: 1893-1908.

García-León M, Cuyas L, El-Moneim DA, Rodríguez L, Belda-Palazón B, Sánchez-Quant E, Fernández Y, Roux B, Zamarreño AM, García-Mina JM, Nussaume L, Rodriguez PL, Paz-Ares J, Leonhardt N and Rubio V (2019) Arabidopsis ALIX regulates stomatal aperture and turnover of abscisic acid receptors. Plant Cell 31: 2411-2429.

Gómez-Zambrano A, Merini W and Calonje M (2019) The repressive role of Arabidopsis H2A.Z in transcriptional regulation depends on AtBMI1 activity. Nature Communications 10: 2828.

González B and Vera P (2019) Folate metabolism interferes with plant immunity through 1C methionine synthase-directed genome-wide DNA methylation enhancement. Molecular Plant 12: 1227-1242.

Guzmán-Benito I, Donaire L, Amorim-Silva V, Vallarino JG, Esteban A, Wierzbicki AT, Ruiz-Ferrer V and Llave C (2019) The immune repressor BIR1 contributes to antiviral defense and undergoes transcriptional and post-transcriptional regulation during viral infections. New Phytologist 224: 421-438.

Hernández-García J, Briones-Moreno A, Dumas R and Blázquez MA (2019) Origin of gibberellin-dependent transcriptional regulation by molecular exploitation of a transactivation domain in DELLA proteins. Molecular Biology and Evolution 36: 908-918.

Julian J, Coego A, Lozano-Juste J, Lechner E, Wu Q, Zhang X, Merilo E, Belda-Palazon B, Park SY, Cutler SR, An C, Genschik P and Rodriguez PL (2019) The MATH-BTB BPM3 and BPM5 subunits of Cullin3-RING E3 ubiquitin ligases target PP2CA and other clade A PP2Cs for degradation. Proceedings of the National Academy of Sciences USA 116: 15725-15734.

Molina-Contreras MJ, Paulisic S, Then C, Moreno-Romero J, Pastor-Andreu P, Morelli L, Roig-Villanova I, Jenkins H, Hallab A, Gan X, Gomez-Cadenas A, Tsiantis M, Rodríguez-Concepción M and Martínez-García JF (2019) Photoreceptor activity contributes to contrasting responses to shade in Cardamine and Arabidopsis seedlings. Plant Cell 31: 2649-2663.

Sequeira-Mendes J, Vergara Z, Peiro R, Morata J, Araguez I, Costas C, Mendez-Giraldez R, Casacuberta JM, Bastolla U and Gutierrez C (2019) Differences in firing efficiency, chromatin, and transcription underlie the developmental plasticity of the Arabidopsis DNA replication origins. Genome Research 29: 784-797.

Wilson-Sánchez D, Lup SD, Sarmiento-Mañús R, Ponce MR and Micol JL (2019) Next-generation forward genetic screens: using simulated data to improve the design of mapping-by-sequencing experiments in Arabidopsis. Nucleic Acids Research 47: e140.

Major Funding Sources

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

    In recent time several larger individual competitive grants have been awarded to Arabidopsis researcher. In 2019 both Prof. Markus Schmid, UPSC, Department of Plant Physiology, Umeå University and Prof. Claudia Köhler, LCPU, Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala - both were appointed Wallenberg Scholars and received a grant of SEK 18 million each from the Wallenberg Foundations as a five-year grant for free research.
Earlier years, for instance Prof. Ove Nilsson, UPSC, Swedish University of Agricultural Sciences, Umeå (Wallenberg Scholar 2012) and Dr. Charles Melnyk, LCPU, Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala (Wallenberg Academy Fellow 2016) was awarded larger grants for their research from the private Knut and Alice Wallenberg Foundation.

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

• 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”

• New Phenotyping Platform for Trees Biology has just been inaugurated at Umeå Plant Science Centre
shorturl.at/fjsKU

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

• Important resources may also be listed on these plant centers’ sites:

• Plant Research and Higher Education in Southern Sweden
https://www.plantlink.se/

• The Linnean Centre for Plant Biology in Uppsala
https://lcpu.se/

Conferences, Workshops and Outreach events

18 May 2019, Fascination of Plants Day with events taking place across Swedish Plant Science hubs https://plantday18may.org/category/europe/sweden/

28 - 30 August 2019, the Scandinavian Plant Physiology Society (SPPS) conference was held in Umeå, Sweden

Selected Publications

Batista, R.A.; Moreno-Romero, J.; Qiu, Y.; et al. (2019)The MADS-box transcription factor PHERES1 controls imprinting in the endosperm by binding to domesticated transposons ELIFE e50541:8

Dukic, E.; Herdean, A.; Cheregi, O.; et al. (2019) K+ and Cl- channels/transporters independently fine-tune photosynthesis in plants Sci Rep 9:8639

Johnsson, C.; Jin, X.; Xue, W.; et al. (2019) The plant hormone auxin directs timing of xylem development by inhibition of secondary cell wall deposition through repression of secondary wall NAC-domain transcription factors Physiol Plant 165:673-689

Kloth, K.J.; Abreu, I.N.; Delhomme, N.; et al.(2019) PECTIN ACETYLESTERASE9 Affects the Transcriptome and Metabolome and Delays Aphid Feeding Plant Physiol 181:1704-1720

Lakehal, A.; Chaabouni, S.; Cavel, E.; et al. (2019) A Molecular Framework for the Control of Adventitious Rooting by TIR1/AFB2-Aux/IAA-Dependent Auxin Signaling in Arabidopsis Mol Plant 12:1499-1514

Vain, T.; Raggi, S.; Ferro, N.; et al. (2019) Selective auxin agonists induce specific AUX/IAA protein degradation to modulate plant development Proc Natl Acad Sci U S A 116:6463-6472

Van Moerkercke, A.; Duncan, O.; Zander, M.; et al. (2019) A MYC2/MYC3/MYC4-dependent transcription factor network regulates water spray-responsive gene expression and jasmonate levels Proc Natl Acad Sci U S A 116:23345-23356

You, Y.; Sawikowska, A.; Lee, J.E.; et al. (2019) Phloem Companion Cell-Specific Transcriptomic and Epigenomic Analyses Identify MRF1, a Regulator of Flowering Plant Cell 31:325-345

 Zan, Y. and Carlborg, Ö. (2019) A Polygenic Genetic Architecture of Flowering Time in the Worldwide Arabidopsis thaliana Population Mol Biol Evol 36:141-154
A more applied (maize) paper, already well cited:

Markovic, D.; Colzi, I.; Taiti, C.; et al. (2019) Airborne signals synchronize the defenses of neighboring plants in response to touch J Exp Bot. 70:691-700

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

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.

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October 9th 2020

Switzerland hosted the 11th Tri-National Arabidopsis Meeting in April 2019. Sessions on “From Arabidopsis to Crops” and “Technology Development” highlighted the progress on the MASC roadmap “From Bench to Bountiful Harvests”. The conference had world-wide attendants, which originally started by three countries Austria, Germany and Switzerland. Publications in high-impact journals are regularly produced from Switzerland, such as on plant defense and root development in 2019-2020.

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

• Kakui H, Yamazaki M, Hamaya NB, Shimizu KK,
Pollen Grain Counting Using a Cell Counter (2020) In: Pollen and Pollen Tube Biology: Methods and Protocols, Anja Geitmann (editor), MIMB, Humana Press, IN PRESS

Conferences, Workshops and Outreach events

- 11th TNAM (Tri-National Arabidopsis Meeting), 10-12 Apr 2019, Zurich
https://www.tnam2019.ethz.ch/

- 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/

- Summer schools
https://swissplantscienceweb.unibas.ch/en/education/summer-schools/
• Microbiomes in soil, plant, animal and human health (for PhDs and postdoc fellows): 11-16 July 2019    (Bern University, One Health - Interfaculty Research Cooperation)
• Improving health at the interfaces between environment, plants, animals and humans (for Bachelor and Master students): 26-30 August 2019 (Bern University, One Health - Interfaculty Research Cooperation)

- PSC Symposium 2019, Plant Response to Environment across Scales,
11 Dec 2019, Zurich
https://www.plantsciences.uzh.ch/en/outreach/conferences/plantresponseacrossscales.html

- SwissPLANT symposium 2020, 29 – 31 Jan 2020, Ovronnaz
https://swissplantscienceweb.unibas.ch/en/events/swissplant/

- Lausanne Genomics Days 2020, 10 – 11 Feb 2019, Lausanne https://biologie.cuso.ch/index.php?id=1741&L=0&tx_displaycontroller[showUid]=5156

Workshops

- OrgN2020: International workshop on organic nitrogen and plant nutrition, 2-6 Feb 2020, Monte Verità
http://www.botany.unibe.ch/orgn2020/

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

Berhin A, de Bellis D, Franke RB, Buono RA, Nowack MK, Nawrath C (2019) The Root Cap Cuticle: A Cell Wall Structure for Seedling Establishment and Lateral Root Formation. Cell. 2019 Mar 7;176(6):1367-1378.e8.

Fernández I, Cosme M, Stringlis IA, Yu K, de Jonge R, van Wees SM, Pozo MJ, Pieterse CMJ, van der Heijden MGA (2019) Molecular dialogue between arbuscular mycorrhizal fungi and the nonhost plant Arabidopsis thaliana switches from initial detection to antagonism New Phytol. 2019 Jul;223(2):867-881.

Grob S, Grossniklaus U (2019) Invasive DNA elements modify the nuclear architecture of their insertion site by KNOT-linked silencing in Arabidopsis thaliana Genome Biol. 2019 Jun 11;20(1):120.

Kesten C, Gámez-Arjona FM, Menna A, Scholl S, Dora S, Huerta AI, Huang HY, Tintor N, Kinoshita T, Rep M, Krebs M, Schumacher K, Sánchez-Rodríguez C (2019) Pathogen-induced pH changes regulate the growth-defense balance in plants. EMBO J. 2019 Dec 16;38(24):e101822.

Kurenda A, Nguyen CT, Chételat A, Stolz S, Farmer EE (2019) Insect-damaged Arabidopsis moves like wounded Mimosa pudica Proc Natl Acad Sci U S A. 2019 Dec 17;116(51):26066-26071.

Lorenzo-Orts L, Witthoeft J, Deforges J, Martinez J, Loubéry S, Placzek A, Poirier Y, Hothorn LA, Jaillais Y, Hothorn M (2019) Concerted expression of a cell cycle regulator and a metabolic enzyme from a bicistronic transcript in plants Nat Plants. 2019 Feb;5(2):184-193.

Schreier TB, Umhang M, Lee SK, Lue WL, Shen Z, Silver D, Graf A, Müller A, Eicke S, Stadler-Waibel M, Seung D, Bischof S, Briggs SP, Kötting O, Moorhead GBG, Chen J4, Zeeman SC (2019) LIKE SEX4 1 Acts as a Amylase-Binding Scaffold on Starch Granules during Starch Degradation Plant Cell. 2019 Sep;31(9):2169-2186.

Xiao Y, Stegmann M, Han Z, DeFalco TA, Parys K, Xu L, Belkhadir Y, Zipfel C, Chai J (2019) Mechanisms of RALF peptide perception by a heterotypic receptor complex. Nature. 2019 Aug;572(7768):270-274.

Yasuhiro Sato, Rie Shimizu-Inatsugi, Misako Yamazaki, Kentaro K. Shimizu & Atsushi J. Nagano (2019) Plant trichomes and a single gene GLABRA1 contribute to insect community composition on field-grown Arabidopsis thaliana BMC Plant Biology volume 19, Article number: 163 (2019)

Zhou F, Emonet A, Dénervaud Tendon V, Marhavy P, Wu D, Lahaye T, Geldner N (2020) Co-incidence of Damage and Microbial Patterns Controls Localized Immune Responses in Roots Cell. 2020 Feb 6;180(3):440-453.e18. doi: 10.1016/j.cell.2020.01.013

Major Funding Sources

• Swiss National Science Foundation (SNSF)
http://www.snf.ch/en/Pages/default.aspx

• European Research Council (ERC), https://erc.europa.eu/

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

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

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

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

• 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

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

Cheng-Hsun Ho, 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., Agriculture Biotechnology Research Center, Academia Sinica

Download 2020-2021 Report

October 9th 2020

In recent years plant/agricultural researchers in Taiwan have focused several important global challenges, such as intensifying climate change, depletion of natural resources. These problems make it urgent to undertake the agricultural transformation and industrial upgrading. Thus, advancing agricultural modernization and innovation are important. In 2018, weather was better than earlier years in Taiwan, making it a bumper harvest year for agriculture. The invested money for basic research and advancing agricultural translation research in Taiwan are several billions of US dollars, which was a new high over the last 20 years.

    Currently, scientific researchers in Taiwan more than 70% using Arabidopsis as a model plant to first test ideas and theories, and then translating to agriculture research. The main mission for all plant researchers is 1) to discover important mechanisms and to solve biological critical questions, and 2) to create edge-cutting and innovative technologies and to translate it into an industry. For example, we solve a long-standing question of plant biology on protein import machinery into chloroplasts, where photosynthesis is taking place. A key part identified to link the outer and inner membrane translocons of chloroplast. Evolutionary analyses further suggest that this chloroplast protein import machinery in a plant is from a bacterial protein secretion system.

    We have already completed many foundational works, seen many historic changes, and achieved a number of successes in 2019 and believe that we can continue and stay strong and successes in 2020.

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

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/)

7. Forestry and Resource Conservation, National Taiwan University (http://ntuf.cc.ntu.edu.tw)

8. Taiwan Rice Insertional Mutants Database

Conferences, Workshops and Outreach events

1. NPAS Seminar: 2019 Asia-Pacific drosophila neurobiology conference

2. Stem cells & developmental biology mini-symposium -division of life sciences

3. AS-NIH-TMU Joint Neuroscience Symposium
4. IBC Biophysics mini-symposium - From Physics to Diseases

5. Mini-symposium on protein structure and function

6. Joint Meetings: Abcam Epigenetics Conference and 14th Asia Epigenome Meeting (AEM) / 3rd Taipei Epigenetics and Chromatin Meeting (TECM)

7. The 17th international symposium on rice functional genomics (ISRFG 2019)

8. Radiocaesium in Agricultural Environment and Internal Radiation dose from Foods in Fukushima after the Nuclear Accident of 2011

9. Application of Organic or Inorganic Materials to Soils for Development of Sustainable Agriculture

10. 2019 IMB Symposium

11. 2020 UW Madison-Academia Sinica Stem Cell & Regenerative Medicine Symposium: Biology, Technology & Regulation

12. The 12th Shang-Fa Yang memorial lecture

13. The 13th Shang-Fa Yang memorial lecture

Selected Publications

Angkawijaya, A.E., Nguyen, V.C., and Nakamura, Y. (2019). LYSOPHOSPHATIDIC ACID ACYLTRANSFERASES 4 and 5 are involved in glycerolipid metabolism and nitrogen starvation response in Arabidopsis. New Phytol 224, 336-351.

Cho, H.Y., Lu, M.J., and Shih, M.C. (2019). The SnRK1-eIFiso4G1 signaling relay regulates the translation of specific mRNAs in Arabidopsis under submergence. New Phytol 222, 366-381.

Hsu, C.W., Lo, C.Y., and Lee, C.R. (2019). On the postglacial spread of human commensal Arabidopsis thaliana: journey to the East. New Phytol 222, 1447-1457.

Jang, G.J., Yang, J.Y., Hsieh, H.L., and Wu, S.H. (2019). Processing bodies control the selective translation for optimal development of Arabidopsis young seedlings. Proc Natl Acad Sci U S A 116, 6451-6456.

Li, Y., Xu, X., Lee, M.H., Chu, M.W., and Chien, C.L. (2019). Observation of half-quantum flux in the unconventional superconductor beta-Bi2Pd. Science 366, 238-241.

Michniewicz, M., Ho, C.H., Enders, T.A., Floro, E., Damodaran, S., Gunther, L.K., Powers, S.K., Frick, E.M., Topp, C.N., Frommer, W.B., et al. (2019). TRANSPORTER OF IBA1 Links Auxin and Cytokinin to Influence Root Architecture. Dev Cell 50, 599-609 e594.

Pecher, P., Moro, G., Canale, M.C., Capdevielle, S., Singh, A., MacLean, A., Sugio, A., Kuo, C.H., Lopes, J.R.S., and Hogenhout, S.A. (2019). Phytoplasma SAP11 effector destabilization of TCP transcription factors differentially impact development and defence of Arabidopsis versus maize. PLoS Pathog 15, e1008035.

Wang, T., Schreiber, C., Elbaz, D., Yoshimura, Y., Kohno, K., Shu, X., Yamaguchi, Y., Pannella, M., Franco, M., Huang, J., et al. (2019). A dominant population of optically invisible massive galaxies in the early Universe. Nature 572, 211-214.

Wong, M.M., Bhaskara, G.B., Wen, T.N., Lin, W.D., Nguyen, T.T., Chong, G.L., and Verslues, P.E. (2019). Phosphoproteomics of Arabidopsis Highly ABA-Induced1 identifies AT-Hook-Like10 phosphorylation required for stress growth regulation. Proc Natl Acad Sci U S A 116, 2354-2363.

Zhang, W., Wang, G., Xu, Z.G., Tu, H., Hu, F., Dai, J., Chang, Y., Chen, Y., Lu, Y., Zeng, H., et al. (2019). Lactate Is a Natural Suppressor of RLR Signaling by Targeting MAVS. Cell 178, 176-189 e115.

Major Funding Sources

• Ministry of Science and Technology, Taiwan
https://www.most.gov.tw/?l=en

• Academia Sinica
https://www.sinica.edu.tw/en)

Baris Uzilday, Ege University, Faculty of Science, This email address is being protected from spambots. You need JavaScript enabled to view it.

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October 9th 2020

Majority of the plant science in Turkey focus on crop plants such as wheat, barley or other economically important legumes. 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 (Costa et al. 2019). 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.

    When one checks the seed banks (NASC or ABRC) for ecotypes from Turkey, the results are very limited (2 different localities) (TAIR database as 28.03.2020), although Turkey is roughly 3 times larger than UK. Hence, natural variation in Turkey is highly under-represented in seed banks and inevitably in studies that investigate natural variation of Arabidopsis. Distribution map of NASC natural ecotypes stock given in Figure 45 clearly shows lack of ecotypes from Turkey in seeds banks, while Germany, UK, Spain, Sweden and France take the lead in the land area normalized list (seed bank entries per 100.000 km2).

    Since Turkey is very rich in plant biodiversity (ex: Turkey has equal or more number of plant species when compared to EU28 combined) and habitat diversity it can be reckoned that Arabidopsis natural variation in Turkey should also have the potential to be high. By considering this potential recently there is an initiative to create a collection of Arabidopsis from different geographical regions of Turkey.

    There are only few laboratories that utilize Arabidopsis as a model for physiological or molecular studies. 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) (Uzilday et al., 2015, Yalcinkaya et al. 2019) or Arabis alpina, which is an artic-alpine species.

    Moreover, it is believed that Arabis alpina originates from Anatolian mountains (Ansell et al. 2011). The number of these examples can be increased, but, overall, it can be concluded that 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

4th National Plant Physiology Symposium (UBFS2020) - https://ubfs2020.aku.edu.tr/

Selected Publications

Akkaya, Ö., & Arslan, E. (2019). Biotransformation of 2, 4-dinitrotoluene by the beneficial association of engineered Pseudomonas putida with Arabidopsis thaliana. 3 Biotech, 9(11), 408.

Arslan, E., & Akkaya, Ö. (2020). Biotization of Arabidopsis thaliana with Pseudomonas putida and assessment of its positive effect on in vitro growth. In Vitro Cellular & Developmental Biology-Plant, 1-9.

Demircan, N., Cucun, G., & Uzilday, B. (2020). Mitochondrial alternative oxidase (AOX1a) is required for the mitigation of arsenic-induced oxidative stress in Arabidopsis thaliana. Plant Biotechnology Reports, 1-11.

Eroglu, S., Karaca, N., Vogel-Mikus, K., Kavcic, A., Filiz, E., & Tanyolac, B. (2019). The conservation of VIT1-dependent iron distribution in seeds. Frontiers in plant science, 10, 907.

Gören-Saglam, N., Harrison, E., Breeze, E., Öz, G., & Buchanan-Wollaston, V. (2020). Analysis of the impact of indole-3-acetic acid (IAA) on gene expression during leaf senescence in Arabidopsis thaliana. Physiology and Molecular Biology of Plants, 1-13.

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.

Niron, H., & Türet, M. (2019). A Putative Common Bean Chalcone O-Methyltransferase Improves Salt Tolerance in Transgenic Arabidopsis thaliana. Journal of Plant Growth Regulation, 1-13.

Pandey, A., Khan, M. K., Hakki, E. E., Gezgin, S., & Hamurcu, M. (2019). Combined Boron Toxicity and Salinity Stress—An Insight into Its Interaction in Plants. Plants, 8(10), 364.

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.

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

The UK is a world leader in the quality of plant science research papers as judged by citation rate. This excellence is supported by over 600 research groups who conduct some aspect of research using Arabidopsis. However one challenge for these researchers are the limited funding opportunities to obtain support for discovery-led plant science research. Outside of individual fellowships, UKRI-BBSRC responsive mode is the only scheme that will support postdoctoral research of this nature. In total this supports around 15 grants/year that total ~£8M. This has significantly reduced since 2014 when there are a clear switch to support for more applied research in plant science. Currently UK excellence is being maintained but this is in danger as the proportion of available funding for discovery-led research declines. GARNet have explored this issue with UKRI-BBSRC and produced a document with recommendations, the primary of which is to engage researchers to engage with BBSRC as they are ‘open-for-business’ for discovery-led plant science applications.
https://www.garnetcommunity.org.uk/sites/default/files/GARNish_BBSRC_Piece.pdf

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

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

- 3D RNA-Seq Analysis Tool: Researchers at the James Hutton Institute, University of Dundee have developed the 3D RNA-Seq Analysis Tool for the comprehensive differential expression, alternative splicing analysis and visualisation of RNASeq Data.
http://ics.hutton.ac.uk/3drnaseq/

- BBSRC-funded Wheat and Rice Transformation facility at NIAB. They have capacity to transfer 100 genes inthese important crops and invite Arabidopsis researchers to submit their genes of interest.
https://www.niab.com/research/agricultural-crop-research/plant-biotechnology

Conferences, Workshops and Outreach events

- CellWall2019: University of Cambridge. July 7th-12th 2019. http://cellwall2019.org/

- IS-MPMI University of Glasgow: July 14th-18th 2019. https://www.ismpmi.org/Congress/2019/Pages/default.aspx

- 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

- Our Plants, Our Future. BSPP IYPH Conference: April 20th-21st 2020 COVID19 postponement
https://www.bspp.org.uk/conferences/our-plants-our-future/

- Genetics Society Arabidopsis Meeting: Durham University. April 21st-22nd 2020 COVID19 postponement
https://www.dur.ac.uk/conference.booking/details/?id=1403

- Sainsbury Lab Symposium: Pluripotency in plant development. SLCU September 23rd-25th 2020
https://www.slcu.cam.ac.uk/SLS20

- BSPP20: Protecting Plants, Protecting Life: December 7th-9th 2020
https://www.bspp.org.uk/conferences/bspp2020-protecting-plants-protecting-life/

- ICAR2022 will return to the UK for the first time since 2009. The meeting will take place at the ICC Belfast in Northern Ireland between June 20th-24th 2022.
http://icar2022.Arabidopsisresearch.org

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/

Fang X, Wang L, Ishikawa R, Li Y, Fiedler M, Liu F, Calder G, Rowan B, Weigel  D, Li P, Dean C (2019) Arabidopsis FLL2 promotes liquid-liquid phase separation of polyadenylation complexes. Nature. doi: 10.1038/s41586-019-1165-8

Greenwood M, Domijan M, Gould PD, Hall AJW, Locke JCW (2019) Coordinated circadian timing through the integration of local inputs in Arabidopsis thaliana. PLoS Biol. doi: 10.1371/journal.pbio.3000407

He S, Vickers M, Zhang J, Feng X. Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation (2019) Elife. doi: 10.7554/eLife.42530

Isner JC, Olteanu VA, Hetherington AJ, Coupel-Ledru A, Sun P, Pridgeon AJ, Jones GS, Oates M, Williams TA, Maathuis FJM, Kift R, Webb AR, Gough J, Franklin  KA, Hetherington AM (2019) Short- and Long-Term Effects of UVA on Arabidopsis Are Mediated by a Novel cGMP Phosphodiesterase. Curr Biol. doi: 10.1016/j.cub.2019.06.071

Kirchhelle C, Garcia-Gonzalez D, Irani NG, Jérusalem A, Moore I (2019) Two mechanisms regulate directional cell growth in Arabidopsis lateral roots. Elife doi: 10.7554/eLife.47988

Lawrence EJ, Gao H, Tock AJ, Lambing C, Blackwell AR, Feng X, Henderson IR (2019) Natural Variation in TBP-ASSOCIATED FACTOR 4b Controls Meiotic Crossover and Germline Transcription in Arabidopsis. Curr Biol. doi: 10.1016/j.cub.2019.06.084

Papanatsiou M, Petersen J, Henderson L, Wang Y, Christie JM, Blatt MR (2019) Optogenetic manipulation of stomatal kinetics improves carbon assimilation, water use, and growth. Science. doi: 10.1126/science.aaw0046

Smit ME, McGregor SR, Sun H, Gough C, Bågman AM, Soyars CL, Kroon JT, Gaudinier A, Williams CJ, Yang X, Nimchuk ZL, Weijers D, Turner SR, Brady SM, Etchells JP (2019) A PXY-Mediated Transcriptional Network Integrates Signaling Mechanisms to Control Vascular Development in Arabidopsis. Plant Cell. doi: 10.1105/tpc.19.00562

Yang W, Schuster C, Prunet N, Dong Q, Landrein B, Wightman R, Meyerowitz EM (2019) Visualization of Protein Coding, Long Noncoding, and Nuclear RNAs by Fluorescence in Situ Hybridization in Sections of Shoot Apical Meristems and Developing Flowers. Plant Physiol. doi: 10.1104/pp.19.00980

Yasrab R, Atkinson JA, Wells DM, French AP, Pridmore TP, Pound MP (2019) RootNav 2.0: Deep learning for automatic navigation of complex plant root architectures.  Gigascience. doi: 10.1093/gigascience/giz123

Major Funding Sources

• Biotechnology and Biological Sciences Research Council (BBSRC) https://bbsrc.ukri.org/

• 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/

• The Newton Fund
https://www.newtonfund.ac.uk/

Joanna Friesner, 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., Danforth Centre, St Louis

Download 2020-2021 Report

October 9th 2020

With additoonal input from the North American Arabidopsis Steering Committee (NAASC)
https://www.araport.org/community/group/naasc
1. Jose Dinneny, Stanford University (2015 - 2020) NAASC Treasurer
2. Elizabeth Haswell, Washington University- St. Louis (2015 - 2020) Representative to MASC
3. Roger Innes, Indiana University (2016 - 2021) NAASC President
4. Peter McCourt, University of Toronto (2016 - 2021)
5. Sean Cutler, University of California, Riverside (2017 - 2022)
6. Jennifer Nemhauser, University of Washington, Seattle (2017 - 2022) NAASC Vice-President
7. Federica Brandizzi, Michigan State University (2018 - 2023)
8. Anna Stepanova, NC State University (2018 - 2023) NAASC Secretary
9. Siobhan Braybrook, UCLA (2019 - 2024)
10. Keith Slotkin, Donald Danforth Plant Science Center & Univ. of Missouri-Columbia (2019 - 2024)
11. Joanna Friesner, (2006- current) NAASC Executive Director

http://arabidopsisresearch.org/index.php/en/naasc

    Due to the COVID-19 pandemic, in the spring of 2020, Arabidopsis biology (Research and Education, see below) across the United States underwent an unprecedented pause. To promote social distancing and reduce the pressure on our healthcare system, nearly all research and education using live Arabidopsis plants was halted in mid-March. The dual mission of Arabidopsis biology  has continued from home. Laboratories have refocused their efforts on training, analyzing data and writing manuscripts. NAASC, the ICAR 2020/2021 planning committee, thanks all of the dedicated researchers and educators for sacrificing the efficiency of their programs for the health of their communities.

    Due to the need to practice social distancing, we have postponed ICAR 2020 to 2021. ICAR 2021 will be held on June 21-25, 2021 in Seattle, Washington State, USA. We have retained the existing URL (http://icar2020.arabidopsisresearch.org) to avoid confusion in accessing conference information and updates. NAASC is working hard to transfer as much of the exciting schedule of ICAR 2020 as possible to the 2021 meeting. The theme of ICAR 2021 will continue to emphasize ‘Arabidopsis as a nexus for Discovery, Innovation, Application and Impact’. Due to the Seattle ICAR’s postponement, the subsequent schedule of future ICAR meetings has been shifted (see below). The organizers of ICAR 2020/2021 sincerely thank Geraint Parry, GARNet Coordinator, Motoaki Seki, MASC Japanese Country Representative, and their respective organizing committees for their willingness to shift dates.

ICAR 2021 - June 21-25th in Seattle, USA,
ICAR 2022 – June 20-24th in Belfast, Northern Ireland
ICAR 2023 – Dates to be announced later, Japan

    Arabidopsis is used in the United States for both research and education, and the line between these two often blurs. The primary funder of Arabidopsis research continues to be the U.S. National Science Foundation (NSF), with the Divisions of Integrative and Organismal Systems and Molecular & Cellular Biosciences providing the majority of funding.

    Arabidopsis research is now also being supported under the new ‘Understanding the Rules of Life’ initiative, which sits within NSF’s 10 Big Ideas and seeks to predict an organism’s phenotype by crossing different scales of research. One shift within the community, which has been happening over several years, is the movement away from laboratory groups that exclusively study Arabidopsis, and towards research groups that study multiple plants, including Arabidopsis, to leverage the available genetic and genomic resources. Highlights of recent research accomplishments are listed below. In addition, we recommend the following White Paper which discusses the future of Arabidopsis bioinformatics:

    Arabidopsis bioinformatics resources: The current state, challenges, and priorities for the future, International Arabidopsis Informatics Consortium, Plant Direct, Volume 3 / Issue 1, e00109, doi: 10.1002/pld3.109
 
    The use of Arabidopsis in Education & Outreach has quickly grown, in part due to the NSF’s Broader Impact mission, the availability and low cost of educational kits from the Arabidopsis Biological Resource Center (ABRC), and community support for education and outreach from the American Society of Plant Biologists (ASPB). There are more diverse opportunities for funding Education & Outreach in plant biology than ever before, including ASPB’s BLOOME grants and NSF’s new initiative ‘Reintegrating Biology’. In addition to Education & Outreach, ASPB supports the whole plant biology community through their education of lawmakers, annual awards and community interaction portal called Plantae.

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

- Mass-spectrometry-based draft of the Arabidopsis proteome
https://www.nature.com/articles/s41586-020-2094-2

- Improved ‘transcript-based’ annotation of Arabidopsis transposable elements
https://www.biorxiv.org/content/10.1101/2020.02.20.956714v1

- An Improved Recombineering Toolset for Plants
http://www.plantcell.org/content/32/1/100    

Conferences, Workshops and Outreach events

1(1) ICAR 2020 (6-10 July) Postponed to ICAR 2021 (June 21-25): The 31st International Conference on Arabidopsis Research (ICAR 2020, http://icar2020.arabidopsisresearch.org) was being organized by NAASC to be held this summer, 2020 at the University of Washington, Seattle, USA. However, it became clear by spring that, due to the global COVID-19 pandemic, holding the ICAR this year would not be feasible. NAASC worked with local University partners and with the organizers for ICAR 2021-Belfast and ICAR 2022-Japan to collaboratively develop a plan to postpone each of the three ICARs by one year.

    On March 23, 2020, we made this joint statement:
Due to the current global COVID-19 situation we have collaboratively decided to postpone the upcoming International Conferences on Arabidopsis Research (ICAR) by one year such that ICAR 2020 becomes ICAR 2021-Seattle, followed by ICAR 2022-Belfast and ICAR 2023-Japan.

    Therefore we hope you will be excited to sign up for ICAR 2021-Seattle (June 21-25, 2021), as well as ICAR 2022-Belfast (June 20-24, 2022), and ICAR 2023-Japan (date TBA).

    Our rationale is this: as the gravity of this global pandemic is becoming clearer, we have come to realize that it would be inadvisable to convene ICAR 2020 this July. Because the safety and health of our community are more important than convening this summer, we believe it would be irresponsible to host a large international conference where there is a substantial risk to our participants (and by extension, our friends, colleagues, and families back at home).

    Members of the worldwide Arabidopsis and plant science research communities have watched the tragic global spread of the COVID-19 disease that has affected many aspects of our daily and scientific lives. With respect to this year’s International Conference on Arabidopsis Research (ICAR 2020), the North American Arabidopsis Steering Committee (NAASC) started planning a set of options in February, in case it became clear that this year’s conference, scheduled for July, in Seattle, USA, should not be held.

    The organizers of ICAR 2020-Seattle, ICAR 2021- Belfast, UK, and ICAR 2022- Japan, convened to discuss how best to collaboratively support the global Arabidopsis community in these unprecedented and challenging times. We know that ICAR is our community’s primary annual convening, where cutting-edge research is shared and collaborations are established and strengthened. We don’t take lightly the amount of effort that has already been extended for ICAR 2020, including a diverse program consisting of 32 community-organized sessions that were chosen as part of a community competition, and 24 platform speakers invited from the international community. We also considered the planning undertaken by the UK and Japanese Arabidopsis communities for ICARs 2021 and 2022. Ultimately, we agreed we must prioritize our community’s health and safety by postponing ICAR 2020.

    The Arabidopsis community is tightly linked and interdependent. Our multinational cooperation began solidly in the early 1990’s via the joint efforts by researchers in many nations to sequence the Arabidopsis genome and continued in the 2000’s and beyond. Our collaborative partnerships remain vital today, even as regional research and educational objectives may shift to reflect evolving priorities, advances in technologies, and local funding realities, among other considerations.  
 
    Thank you for understanding the difficult position we are in with respect to this unexpected crisis.  We hope that you, and those closest to you, remain healthy, and that as a community, we can continue to support each other as much as possible.
Signed by:
•    Joanna Friesner, NAASC Executive Director, Lead ICAR 2020/2021 Organizer; on behalf of the North American Arabidopsis Steering Committee (NAASC)
•    Geraint Parry, GARNet Coordinator and Lead Organiser of ICAR2022; on behalf of the GARNet leadership group
•    Motoaki Seki, MASC Japanese Country Representative and a lead organizer of ICAR 2023; on behalf of the ICAR 2023 Organizing Committee in Japan

    Support for ICAR 2020/2021 organization is, in part, provided by the U.S. National Science Foundation under Grant No. #1518280. Any opinions, findings, & conclusions or recommendations expressed in this event, or in resulting work, are those of the participants & do not necessarily reflect the views of the NSF.

(2) Addtional US meetings/workshops in 2019:
Phenome: Tucson, Arizona; Crops in Silico- Symposium and Hackathon; Modeling across species, including Arabidopsis; Urbana, Illinois; Gordon Research Conference on Epigenetics; Holderness, New Hampshire; FASEB The Mechanisms in Plant Development: Olean, New York; ASPB Plant Synthetic Biology: San Jose, California

Selected Publications

Patricia Baldrich, Brian D. Rutter, Hana Zand Karimi, Ram Podicheti, Blake C. Meyers, Roger W. Innes (2019) Plant Extracellular Vesicles Contain Diverse Small RNA Species and Are Enriched in 10- to 17-Nucleotide “Tiny” RNAs.  The Plant Cell. doi: 10.1105/tpc.18.00872

Ken Jean-Baptiste, José L. McFaline-Figueroa, Cristina M. Alexandre, Michael W. Dorrity, Lauren Saunders, Kerry L. Bubb, Cole Trapnell, Stanley Fields, Christine Queitsch, Josh T. Cuperus (2019) Dynamics of Gene Expression in Single Root Cells of Arabidopsis thaliana. The Plant Cell. doi:10.1105/tpc.18.00785

Cao P, Kim SJ, Xing A, Schenck CA, Liu L, Jiang N, Wang J, Last RL, Brandizzi F (2019) Homeostasis of branched-chain amino acids is critical for the activity of TOR signaling in Arabidopsis. Elife. doi: 10.7554/eLife.50747

Gallego-Bartolomé, Javier, Wanlu Liu, Peggy Hsuanyu Kuo, Suhua Feng, Basudev Ghoshal, Jason Gardiner, Jenny Miao-Chi Zhao, Soo Young Park, Joanne Chory, and Steven E. Jacobsen (2019) Co-Targeting RNA Polymerases IV and V Promotes Efficient De Novo DNA Methylation in Arabidopsis. Cell. doi: 10.1016/j.cell.2019.01.029.

International Arabidopsis Informatics Consortium (2019) Arabidopsis Bioinformatics Resources: The Current State, Challenges, and Priorities for the Future. Plant Direct. doi: 10.1002/pld3.109
T F. Jupe, A.C. Rivkin, T.P. Michael, M. Zander, S.T. Motley, J.P. Sandoval, R.K. Slotkin, H. Chen, R. Castanon, J.R. Nery, J.R. Ecker. (2019) The complex architecture and epigenomic impact of plant T-DNA insertions.PLoS Genetics. doi:10.1371/journal.pgen.1007819

Mair A, Xu SL, Branon TC, Ting AY, Bergmann DC (2019) Proximity labeling of protein complexes and cell-type-specific organellar proteomes in Arabidopsis enabled by TurboID.  Elife. doi: 10.7554/eLife.47864.001

Powers SK, Holehouse AS, Korasick DA, Schreiber KH, Clark NM, Jing H, Emenecker R, Han S, Tycksen E, Hwang I, et al (2019) Nucleo-cytoplasmic Partitioning of ARF Proteins Controls Auxin Responses in Arabidopsis thaliana. Mol Cell. doi: 10.1016/j.molcel.2019.06.044

Vaidya AS, Helander JDM, Peterson FC, Elzinga D, Dejonghe W, Kaundal A, Park SY, Xing Z, Mega R, Takeuchi J et al (2019) Dynamic control of plant water use using designed ABA receptor agonists. Science. doi: 10.1126/science.aaw8848

Feihua Wu, Yuan Chi, Zhonghao Jiang, Yuanyuan Xu, Ling Xie, Feifei Huang, Di Wan, Jun Ni, Fang Yuan, Xiaomei Wu et al, (2019) Hydrogen peroxide sensor HPCA1 is an LRR receptor kinase in Arabidopsis. Nature. doi: 10.1038/s41586-020-2032-3

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 (current or past NAASC Scholars: Siobhan Brady, Jose Dinneny, Elizabeth Haswell, and Jennifer Nemhauser): http://www.hhmi.org/programs/biomedical-research/faculty-scholars
(2) HHMI Investigators (past NAASC Investigators: Dominique Bergmann, Philip Benfey, Joanne Chory, Jeff Dangl, Xinnian Dong, Joe Ecker, Elliot M. Meyerowitz, and Keiko Torii) http://www.hhmi.org/programs/biomedical-research/investigator-program
(3) HHMI Professors (past NAASC Professors: Richard M. Amasino and Bonnie Bartel) https://www.hhmi.org/developing-scientists/hhmi-professors