NIAB Wheat-Rice Transformation Resource: Open for Applications

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Published on: April 30, 2019

THE COMMUNITY RESOURCE FOR WHEAT AND RICE TRANSFORMATION is a resource for UK plant scientists to apply for their genes to be transformed into wheat or rice free of charge, funded by the BBSRC’s Biological and Bioinformatic Resources fund (BBR).

THE CURRENT ROUND OF THE APPLICATION PROCESS IS OPEN UNTIL 24TH JUNE 2019, for transformation slots in the autumn. There is an online application form via the following link:

Further details are available on the website, and enquiries should be directed to in the first instance.

One hundred novel genes will be tested during the course of this five year project, selected with help from an external project advisory group comprised of researchers, industry members and stakeholders.

We anticipate that half of the project capacity will be used by scientists working with model species such as Arabidopsis thaliana or
Brachypodium distachyon, in order to find new sources of genes and to encourage and support the scientists to test them in wheat and rice.

The project also provides capacity to characterise 50 regulatory elements in wheat and rice. Promoter and terminator sequences will be included for their expression in a wide range of tissue types.

Researchers can either nominate promoters to be included in this project. Further details are again available on the website.


Tel (direct) +44 (0)1223 345001


John Christie talks to GARNet

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Published on: April 29, 2019

John Christie discusses a recent paper just published in Plant Physiology entitled ‘De-etiolation Enhances Phototropism by Modulating NON-PHOTOTROPIC HYPOCOTYL 3 Phosphorylation Status‘.

GARNet Research Roundup: April 29th 2019

This edition of the GARNet research roundup features fundamental plant science research conducted in a range of experimental organisms. Firstly Liam Dolan’s lab in Oxford looks at the function of bHLHs proteins in cell differentiation across land plant evolution. Secondly Anthony Hall’s group at the Earlham Institute have identified a novel RecQ helicase involved in work exclusively conducted in wheat. Thirdly researchers from Nottingham work with Arabidopsis to characterise an EXPANSIN protein essential for lateral root development.

The fourth paper is the first of two that look at germination and uses a new model, Aethionema arabicum, to study the role of light in seed dormancy. This work includes research from Royal Holloway. The second ‘dormancy’ paper is from Peter Eastmond’s lab at Rothamsted and further characterises the DOG1 gene in Arabidopsis. The penultimate paper includes co-authors from Warwick and Leeds and introduces a novel chemical inhibitor of auxin transport. The final paper from researchers in Birmingham introduces the 3DCellAtlas Meristem, a powerful tool for cellular annotation of the shoot apical meristem.

Bonnot C, Hetherington AJ, Champion C, Breuninger H, Kelly S, Dolan L (2019) Neofunctionalisation of basic helix loop helix proteins occurred when embryophytes colonised the land. New Phytol. doi: 10.1111/nph.15829

Clemence Bonnot is lead author on this study from Liam Dolan’s lab at the University of Oxford in which the authors assess the role of ROOT HAIR DEFECTIVE SIX-LIKE (RSL) genes during evolution of plant development. They look at the function of a member of this bHLH transcription factor family called CbbHLHVIII identified in the charophyceaen alga Chara braunii. This gene is expressed at specific morphologically important regions in the algae and cannot rescue the function of related RSL genes in Marchantia or Arabidopsis. This suggests that the function of RSL proteins in cell differentiation has evolved by neofunctionalisation through land plant lineages.

Gardiner LJ, Wingen LU, Bailey P, Joynson R, Brabbs T, Wright J, Higgins JD, Hall N, Griffiths S, Clavijo BJ, Hall A (2019) Analysis of the recombination landscape of hexaploid bread wheat reveals genes controlling recombination and gene conversion frequency. Genome Biol. 20(1):69. doi: 10.1186/s13059-019-1675-6

Open Access

Laura Gardiner and Anthony Hall lead this work that was conducted at the Earlham Institute and uses a bespoke set of bioinformatic tools that allow fundamental questions to be asked in hexaploid wheat. They looked at crossover and gene conversion frequencies in 13 recombinant inbred mapping populations and were able to identity an important QTL and confirm functionality for a novel RecQ helicase gene. This gene does not exist in Arabidopsis and therefore this discovery-motivated research needed to be conducted in wheat. They hope that this identification will provide future opportunities to tackle the challenge of linkage drag when attempting to develop new crops varieties.

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, Voβ U, Beeckman T, Bennett MJ, Gevaert K, Maizel A, De Smet I (2019) 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 3. pii: 201820882. doi: 10.1073/pnas.1820882116

Open Access

This pan-European study is led by Priya Ramakrishna at the University of Nottingham and includes co-authors from the UK, Belgium, Germany and Denmark. The authors look at the lateral root development and characterise the function of the EXPANSIN A1 protein. This protein influences the physical changes in the cell wall that are needed to enable the asymmetry cell divisions that define the location of a new lateral root. Plants lacking EXPA1 function do not properly form lateral roots and are unable to correctly respond to an inductive auxin signal. This clearly demonstrates an important requirement for the activity of genes that transmit cell signals into the physical relationships that exist between cells.

Mérai Z, Graeber K, Wilhelmsson P, Ullrich KK, Arshad W, Grosche C, Tarkowská D, Turečková V, Strnad M, Rensing SA, Leubner-Metzger G, Scheid OM (2019) Aethionema arabicum: a novel model plant to study the light control of seed germination. J Exp Bot. pii: erz146. doi: 10.1093/jxb/erz146

Open Access

This paper includes authors from the UK, Germany, Austria and the Czech Republic including Kai Graeber and Gerhard Leubner-Metzger at Royal Holloway. They introduce the Brassica Aethionema arabicum as a new model to investigate the mechanism of germination inhibition by light as they have identified accessions that are either light-sensitive or light-neutral. In contrast germination in Arabidopsis is stimulated by light. Transcriptome analysis of Aethionema arabicum accessions reveal expression changes in key hormone-regulated genes. Overall they show that largely the same module of molecular components are involved in control of of seed dormancy irrespective of the effect of light on germination. Therefore any phenotypic changes likely result from changes in the activity organisms-specific of these genes.

Bryant FM, Hughes D, Hassani-Pak K, Eastmond PJ (2019) Basic LEUCINE ZIPPER TRANSCRIPTION FACTOR 67 transactivates DELAY OF GERMINATION 1 to establish primary seed dormancy in Arabidopsis. Plant Cell. pii: tpc.00892.2018. doi: 10.1105/tpc.18.00892

Open Access

Fiona Bryant is lead author on this research from Rothamsted Research that investigates the factors that control expression of the DOG1 gene, which is a key regulator of seed dormancy. They show that LEUCINE ZIPPER TRANSCRIPTION FACTOR67 (bZIP67) regulates DOG1 expression and have uncovered a mechanism that describes the temperature-dependent regulation of DOG1 expression. Finally they identity a molecular change that explains known allelic difference in DOG1 function, which informs different levels of dormancy in different accessions.

Oochi A, Hajny J, Fukui K, Nakao Y, Gallei M, Quareshy M, Takahashi K, Kinoshita T, Harborough SR, Kepinski S, Kasahara H, Napier RM, Friml J, Hayashi KI (2019) Pinstatic acid promotes auxin transport by inhibiting PIN internalization. Plant Physiol. 2019 Apr 1. pii: pp.00201.2019. doi: 10.1104/pp.19.00201

Open Access

This Japanese-led study includes co-authors from the Universities of Warwick and Leeds and describes the identification of a novel positive chemical modulator of auxin cellular efflux. This aptly named PInStatic Acid (PISA) prevents PIN protein internalization yet does not impact the SCFTIR1/AFB signaling cascade. Therefore the authors hope that PISA will be a useful tool for unpicking the cellular mechanisms that control auxin transport.

Montenegro-Johnson T, Strauss S, Jackson MDB, Walker L, Smith RS, Bassel GW. (2019) 3D Cell Atlas Meristem: a tool for the global cellular annotation of shoot apical meristems. Plant Methods. 15:33. doi: 10.1186/s13007-019-0413-0

Open Access

Thomas Montenegro-Johnson, Soeren Strauss, Matthew Jackson and Liam Walker lead this methods paper that was prepared following research that took place at the University of Birmingham and the Max Planck Institute for Plant Breeding Research in Cologne. They describe the 3DCellAtlas Meristem, a tool allows the complete cellular annotation of cells within a shoot apical meristem (SAM), which they have successfully tested in both Arabidopsis and tomato. The authors state that ‘this provides a rapid and robust means to perform comprehensive cellular annotation of SAMs and digital single cell analyses, including cell geometry and gene expression’.

GARNet Workshop on ‘Advances in Plant Imaging’

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Published on: April 24, 2019

GARNet are delighted to present a workshop on ‘Advance in Plant Imaging’ at the University of Warwick on September 9th-10th 2019.

This focussed 2-day workshop aims to introduce some of the outstanding imaging techniques that are enhancing plant science research.

Registration is now open and is ONLY £38 for students/postdoc/technicians to attend.

In order to stimulate discussion we provide opportunities for delegates to give a short talk as well as including an extended poster session.

The workshops sessions are:

  • High Resolution Microscopy for Plant Cell Biology
  • Imaging across scales from Molecules to Organism
  • Imaging with Novel Genetically encoded Reporters

Please circulate the poster below to your colleagues and around your department.

Thanks for the Society of Experimental Biology for providing support the meeting.

Please contact Geraint Parry with any questions:


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Published on: April 18, 2019

The North American Arabidopsis Steering Committee (NAASC) is committed to promoting a global plant sciences community that reflects the true diversity of all its members. To further this mission, the NAASC Diversity and Inclusion Task Force has created the DiversifyPlantSci online resource, a list of plant biologists from under-represented groups to reference for speakers, reviewers, and participants for career or mentorship opportunities.

This list is intended to highlight the diversity within the global plant science community.

We hope to increase diversity and inclusion by making it easy to expand invitations past one’s personal networks.

To Add yourself fill out this google form:        

  1. Nominate yourself if you are a plant scientist who: identifies as a woman; identifies as LGBTQIA+; has a disability; and/or is a member of an under-represented ethnic or racial group***.        
  2. Please do not nominate others, we allow self-registration only. However we strongly encourage you to forward this form’s URL to others that you know and invite them to consider signing up for inclusion.

GUIDELINES FOR LIST USAGE                               

*we’ve used some language from the DiversityEEB list, and here’s their reference:                                                                       

You may view the entries to identify diverse plant scientists for conferences, hiring, awards, etc.                                                                 

You may self-nominate by filling in the google form:         

Please do not nominate others, we allow self-registration only. However we strongly encourage you to forward this form’s URL to others that you know and invite them to consider signing up for inclusion.                                                                                                                 

We welcome the use of information provided for distributing relevant announcements, however, please use the list judiciously and do not simply spam members.

Moreover, a personal email is much more effective than a mass mailing. If you do send an email to more than one person, please use the ‘bcc’ option to reduce the likelihood of an annoying ‘reply-all’ chain.”                                                                                                                 

Filters for several categories are listed in the DiversifyPlantSci list under Data–> Filter Views: Selecting a Filter view will show only names in that category. To reset, select “None”                                                             

While we are aware that there are other categories of under- representation or disadvantage within plant sciences, we are focusing on the categories of gender/racial/ethnicity/sexual orientation/disability                                                                                                                 

All my best,

Joanna Friesner, PhD
Pronouns she/her
National Network Coordinator
Inter-institutional Network for Food, Agriculture and Sustainability (INFAS)
Agricultural Sustainability Institute (ASI)
University of California, Davis
Phone: 530-752-7556Pronouns she/herNational Network CoordinatorInter-institutional Network for Food, Agriculture and Sustainability (INFAS)
Agricultural Sustainability Institute (ASI)

GARNet Research Roundup: April 11th 2019

This edition of the GARNet Research Roundup is led by two papers from John Christie’s lab at the University of Glasgow. First is a study that looks at the function of the NPH3 protein during phototropism whilst the second paper is a collaboration with Mike Blatt’s group and has used an synthetic biology approach to increase plant biomass by altering stomatal conductance.

Third is a paper from the University Dundee and James Hutton Institute that looks at the extent of alternative splicing of long non-coding RNAs in response to cold stress.

The fourth paper is from Royal Holloway and defines the role of a MAP kinase module during meristem development. The fifth paper is led by Charles Spillane in Galway and includes Mary O’Connell at the University of Nottingham as a co-author and investigates the selective pressures that are applied to parentally imprinted genes.

The penultimate paper is from Aberystwyth and uses microCT imaging to determine grain parameters in wheat and barley whilst the final paper is from Queens Mary University of London looks at nonphotochemical quenching in Berteroa incana.

Sullivan S, Kharshiing E, Laird J, Sakai T, Christie J (2019) De-etiolation Enhances Phototropism by Modulating NON-PHOTOTROPIC HYPOCOTYL 3 Phosphorylation Status. Plant Physiol. doi: 10.1104/pp.19.00206

Open Access

Stuart Sullivan is first author on this work from John Christie’s lab at the University of Glasgow in which they investigate the functional significance of dephosphorylation of the NON-PHOTOTROPIC HYPOCOTYL 3 (NPH3) protein that occurs following activation of Phototropin receptor kinases. They show that plant greening (de-etiolation) enhances phototropic responses that are coincident with reduced NPH3 dephosphorylation and increased plasma membrane retention of the protein. They further investigate other genetic and environmental factors that impact NPH3 dephosphorylation, which allows young seedlings to maximise their establishment under changing light conditions.

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

Maria Papanatsiou is lead author on this work from the University of Glasgow that occured in the labs of Mike Blatt and John Christie. They aimed to address a phenomonen that occurs during changing environmental conditions in which stomatal dynamics lag behind biochemical photosynthetic changes. This prevents plants from maximising their outputs due to inefficiencies in gas and water exchange. In this work they express a synthetic blue light-gated K+ channel BLINK1 in guard cells. This introduced a K+ conductance to these cells resulting in accelerated stomatal opening under light exposure and closing after irradiation. Ultimately they show that this significantly increases biomass without incurring a water use cost. This approach has clear potential for improving plant productivity under changing environmental conditions.

Calixto CPG, Tzioutziou NA, James AB, Hornyik C, Guo W, Zhang R, Nimmo HG, Brown JWS (2019) Cold-Dependent Expression and Alternative Splicing of Arabidopsis Long Non-coding RNAs. Front Plant Sci. doi: 10.3389/fpls.2019.00235

Open Access

Cristiane Calixto and John Brown from the University of Dundee and the James Hutton Institute lead this study into alternative splicing of lncRNAs in response to cold. This is a follow-up to their large scale scale study on the extent of alternative splicing in Arabidopsis.  The authors identified 135 lncRNA genes with cold-dependent differential expression (DE) and/or differential alternative splicing (DAS), some of which were highly sensitive to small temperature changes. This system identified a set of lncRNAs that could be targets for future research aimed at understanding how plants respond to cold and freezing stresses.

Dóczi R, Hatzimasoura E, Farahi Bilooei S, Ahmad Z, Ditengou FA, López-Juez E, Palme K, Bögre L (2019) The MKK7-MPK6 MAP Kinase Module Is a Regulator of Meristem Quiescence or Active Growth in Arabidopsis. Front Plant Sci. doi: 10.3389/fpls.2019.00202

Open Access

Robert Doczi is the first author on this UK, Hungarian and German collaboration that is led from Royal Holloway University of London. They use genetic approaches to show that the MKK7-MPK6 MAP kinase module is a suppressor of meristem activity. They use mkk7 and mpk6 mutants as well as overexpression lines to demonstrate that perturbation of the MAPK signaling pathway alters both shoot and root meristem development and plays important roles in the control of plant developmental plasticity.

Tuteja R, McKeown PC, Ryan P, Morgan CC, Donoghue MTA, Downing T, O’Connell MJ, Spillane C (2019) Paternally expressed imprinted genes under positive Darwinian selection in Arabidopsis thaliana. Mol Biol Evol. doi: 10.1093/molbev/msz063

Open Access

Reetu Tuteja from the National University of Ireland at Galway is first author on this paper that includes Mary O’Connell from the University of Nottingham. The authors used Arabidopsis to look at 140 endosperm-expressed genes that are regulated by genomic imprinting and found that they were evolving more rapidly than expected. This investigation was extended across 34 other plant species and they found that paternally, but not maternally imprinted genes were under positive selection, indicating that imprinted genes of different parental origin were subject to different selective pressures. This data supports a model wherein positive selection effects paternally-expressed genes that are under continued conflict with maternal sporophyte tissues.

Hughes N, Oliveira HR, Fradgley N, Corke FMK, Cockram J, Doonan JH, Nibau C (2019) μCT trait analysis reveals morphometric differences between domesticated temperate small grain cereals and their wild relatives. Plant J doi: 10.1111/tpj.14312

Open Access

Nathan Hughes and Candida Nibau at the Aberystwyth University lead this work that uses microCT imaging alongside novel image analysis techniques and mathematical modeling to assess grain size and shape across accessions of wheat and barley. They find that grain depth is a major driver of shape change and that it is also an excellent predictor of ploidy levels. In addition they have developed a model that enables the prediction of the origin of a grain sample from measurements of its length, width and depth.

Wilson S, Ruban AV (2019) Enhanced NPQ affects long-term acclimation in the spring ephemeral Berteroa incana. Biochim Biophys Acta Bioenerg. doi: 10.1016/j.bbabio.2019.03.005

This study is led by Sam Wilson and Alexander Ruban at QMUL and investigates nonphotochemical quenching in the Arabidopsis-relative Berteroa incana. They show that light tolerance and ability to recover from light stress is greatly enhanced in Berteroa compared to Arabidopsis. This is due to faster synthesis of zeaxanthin and a larger xanthophyll cycle (XC) pool available for deepoxidation. This result gives B.incana a greater capacity for protective NPQ allowing enhanced light-harvesting capability when acclimated to a range of light conditions. The authors suggest this short-term protection prevents the need for the metabolic toll of making long-term acclimations.

Opportunities at ICAR2020: Seattle

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Published on: April 8, 2019

Hi all,

I want to let you know that the ICAR 2020 conference webpage is up and that we (NAASC) are doing new and exciting things for ICAR 2020 – Seattle!

In response to community feedback we’ve gathered an External Advisory Board to discuss approaches to better meet the needs of plant science researchers and educators interested in a moderate sized conference such as ICAR, and that focuses on the resources, techniques, and fundamental research taking place in Arabidopsis labs and in other labs that depend on Arabidopsis knowledge and resources.

We consistently heard that attendees prioritize the chance to present their work, especially in a talk; that most want greater diversity in the invited speakers list and in conference session topics. In response we’ve dramatically changed our and we anticipate a highly engaging and more diverse program in Seattle next summer.

Some FIRSTS for ICAR 2020- Seattle:

  • Please share this call with your students and postdocs as we’ve reserved a number of sessions to be organized by early-career researchers
    • 31 July 2019: Deadline to apply to organize and invite speakers for a community-proposed ICAR 2020 symposium.
    • Selected symposia organizers will be provided budgets to enable them to recruit speakers for their sessions. Proposers may be at any career stage and are not limited to faculty submitters.
  • We are seeking community input on invited speakers for the non-community organized part of the program, and on the new themes we’ve developed with significant discussion with our international External Advisory Board.
  • Finally- we are putting significant emphasis on building, engaging, and supporting the diversity of our community, be it new parents, under-represented minorities, LGBTQ scientists, students, and others. We’re engaging in various approaches to enable fuller participation and inter-personal connections and are soliciting input via our survey/proposal submission mechanism, where we’ll invite folks to join and/or lead various groups at ICAR 2020.
  • As part of our diversity and inclusion endeavor, a NAASC subcommittee launched the DiversifyPlantSci list in February and there are nearly 250 plant scientists that have signed up.
  • Beyond ICAR, our DiversifyPlantSci list could be value to you– e.g. as you and colleagues consider inviting visiting speakers for local seminars. Please see the description below; I encourage you to join (if applicable) and please share with your labs and colleagues.
    • We’ve even gotten some press in Science Magazine! “Just last week, a group of plant scientists started a new database for women, members of underrepresented racial and ethnic minority groups, people who identify as LGBTQ, and people with disabilities; as of today, 124 plant scientists are already on the list.” (now up to nearly 250)
  • Twitter: #ICAR2020 @ICAR_2020  
  • DiversifyPlantSci Twitter: @DiversifyPlants

Reintroducing the UK Plant Science Federation

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Published on: April 4, 2019

Over the past few weeks the GARNet coordinator, Geraint Parry, has been voted as Chairman of the UK Plant Science Federation (UKPSF), where he will represent the ideas of the GARNet community on this national committee.

So what’s the difference?

During anedotal conversations there is some confusion in the community regarding the difference between GARNet and UKPSF. To clarify:

GARNet is a BBSRC-funded community network that is focused on supporting researchers that are involved in fundamental plant science. These activities include knowledge exchange through online (website and blog) and social media platforms, organisation of meetings and workshops as well as representing the needs of fundamental plant scientists in discussions with the BBSRC or in government consultations on relevant topics, such as gene editing, big data or immigration policy.

GARNet is a member of UKPSF, which has a much broader remit that is currently primarily focused on education and policy. The UKPSF was founded in 2011 with the ambitious aim of bringing together plant scientists across all disciplines, from Arabidopsis to Ecology, in order to provide a unified voice for UK plant science.

Over the subsequent years the management of UKPSF has moved within the Royal Society of Biology (RSB) as a Special Advisory Committee. Therefore any organisation that is a member of RSB has the option of interacting with the UKPSF. Currently there are 21 member organisations that, as originally planned, cross the spectrum of UK plant science and include participants from academia, education, industry, learned societies and publishers. Each member organisation provides input into the advisory board that meets twice yearly whilst more immediate decisions are made by the UKPSF Executive Committee, which meets four times annually. The members of the Executive Commitee are listed here so please contact any of them if you have an issue that you feel needs to be raised. The Chairpersons email is yet contact information for all other members can be easily found online and they will be happy to receive your correspondence.

What is the role of UKPSF?

In its early years UKPSF organised an annual broad-based conference that brought together people with an interest in different areas of plant science who might not ordinarily communicate. However this conference has not taken place over the past few years, due in part to the challenges of finding a place for a very general meeting in an already packed conference and workshop schedule.

With over 18000 members the RSB is the largest society that focuses on all areas of the biological sciences. Therefore the primary role of the UKPSF is to ensure that plant science is represented throughout RSB activities and more generally within the wider public and scientific communities.

Growing the Future

Over the past few years members of UKPSF have interacted with the community to produce the ‘Growing the Future’ report. This important document outlines the exciting potential for UK plant science to tackle many societal challenges over the coming decades through ‘Improving crops and agricultural systems, ‘Plant health and biosecurity’, ‘Plant biotechnology’ and ‘Biodiversity and ecosystems’. This document was introduced at a breakfast reception at the House of Commons on January 29th in an event that included contributions from Stephen Metcalfe MP, Lord Matt Ridley, UKPSF Chair Rick Mumford, Professor Dale Sanders from the John Innes Centre and Professor Belinda Clarke from AgriTech East.

Where now for UKPSF?

Following publication of ‘Growing the Future’ the challenge for UKPSF is to now follow up on the recommendations outlined the document in order to support plant-focused activities at RSB.

Initially the executive are working with RSB to promote plant science in their career-facing activities during Biology Week 2019. Secondly members of the committee are involved in policy discussions on the future of genetic technologies in the UK. This primarily will occur during a ‘Workshop on Genetic Technologies’ on May 10th and the recommendations from this forum will be disseminated through usual Royal Society of Biology channels. In addition UKPSF are working with Celia Knight to promote the undergraduate RSB Plant Health Studentships that are funded through DEFRA, the BSPP, N8 Agrifood and the David Colegrave Foundation.

The UKPSF Chairman is also acting as the National Coordinator for upcoming Fascination of Plants day (FoPD19) on May 18th. If you are organising an event then please communicate it to the National Coordinator.

Future UKPSF activities will primarily rely on funding from RSB so there is limited scope to what can be achieved individually through direct activities of the committee ‘on the ground’. However the significant reach of RSB is extremely useful in promoting the outstanding resources developed by member organisations that aim to develop an educational and public interest in plant science.

Please get in contact with UKPSF if you would like the executive group to suggest any specific activities with which they could be involved.

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