Arabidopsis Research Roundup: Sept 29th

This weeks Arabidopsis Research Roundup includes papers, from Glasgow and Oxford, that look at a plants response to different abiotic stresses and uncover control mechanisms that might have potential as targets for future genetic modification or gene-editing strategies. In addition there is a study from Leeds that uncovers a novel molecular mechanism in the DNA repair pathway and finally an international group of researchers with a UK lead at Kings College use infrared microspectroscopy to investigate internal cellular structures

Ji H, Wang Y, Cloix C, Li K, Jenkins GI, Wang S, Shang Z, Shi Y, Yang S, Li X (2015) The Arabidopsis RCC1 Family Protein TCF1 Regulates Freezing Tolerance and Cold Acclimation through Modulating Lignin Biosynthesis PLoS Genetics 11(9):e1005471

Gareth Jenkins (Glasgow) is the UK lead representative on this Chinese-led study into the role of the ‘Tolerant to Chilling and Freezing 1′ (TCF1) protein. This protein is induced by the cold to move to the nucleus where it interacts with histones H3 and H4, specifically at the BLUE-COPPER-BINDING PROTEIN (BCB) locus, which is involved in lignin biosynthesis. Loss of TCF1 causes changes in the positive histone mark H3K4me2 as well as the negative mark H3K27me3, resulting in reduced lignin content and enhanced freezing tolerance. This growth phenotype was recapitulated in other mutants that have reduced level of lignin. Therefore the authors suggest that TCF controls a CBF-independent signaling pathway that reacts to cold conditions by causing cell wall remodeling. In tcf mutants this pathway does not function correctly and the plants are more tolerant to freezing conditions. This marks either TCF or the genes downstream of it as potential targets for genetic modification to develop cold-resistant plants. The associated figure is taken from PLoS Genetics.


Ling Q1, Jarvis P (2015) Regulation of Chloroplast Protein Import by the Ubiquitin E3 Ligase SP1 Is Important for Stress Tolerance in Plants Current Biology.

Paul Jarvis (Oxford) is an expert on the mechanisms that control protein import into the chloroplast and this study looks at the interaction of the TOC translocon apparatus with ubiquitin-proteasome system. The chloroplast envelope-localised E3 ubiquitin-ligase SUPPRESSOR OF PPI1 LOCUS1 (SP1) was previously known to regulate levels of TOC and so control protein import and impact the composition of the chloroplast proteome. This study is expanded to show that SP1 plays an important role in the response to abiotic stress with sp1 mutants being hypersensitive to salt, osmotic, and oxidative stresses whereas the opposite is true in SP1 OX plants. They uncover the molecular mechanism to this response by showing SP1 facilitates the depletion of the TOC apparatus, subsequently reducing the import of photosynthetic apparatus components which attenuates photosynthesis and reduced the production of potentially damaging reactive compounds in the chloroplast. The authors show that chloroplast protein import is responsive to environmental cues and this modulation of this process might open up new avenues of research for improving stress tolerance in crops.

Waterworth WM, Drury GE, Blundell-Hunter G, West CE (2015) Arabidopsis TAF1 is an MRE11-interacting protein required for resistance to genotoxic stress and viability of the male gametophyte The Plant Journal

Christopher West (Leeds) is the research lead on this investigation into the essential function of double strand breaks (DSBs) during recombination. These DSBs are repaired by the endonuclease MRE11 and this work demonstrates an interaction with the histone acetyltransferase TAF1, which is an essential gene in Arabidopsis. The remainder of the paper uses genetic and phenotypic analysis to show that TAF1 is important for gamete viability in an effect that is dosage dependent. Taf mutants are more sensitive to genotoxic stresses thus showing that the TAF1 protein has a specific role in the DNA damage response. This provides new insights into the molecular mechanisms of the DNA damage response in plants.

Warren FJ , Perston BB, Galindez-Najera SP, Edwards CH, Powell PO, Mandalari G, Campbell GM, Butterworth PJ, Ellis PR (2015) Infrared microspectroscopic imaging of plant tissues: spectral visualisation of wheat kernel and Arabidopsis leaf microstructure. Plant Journal

This international study was led by Peter Ellis (Kings College) and includes a variety of labs not usually connected with Arabidopsis work but rather are interested in the interaction between the plant cell wall and the human gut. They used Infrared microspectroscopy as a tool to investigate the microstructure of wheat kernels and Arabidopsis leaves. This technique was able to discern structures such as starch granules and protein bodies within cells. Stimulated digestion on the wheat tissues showed that digestion promotes a loss of starch as might be predicted. This article might be of interest to plant scientists who are interested in use of infrared spectroscopy.

GARNet/OpenPlant CRISPR Workshop

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Published on: September 17, 2015

GARNet and OpenPlant were delighted to invite over 140 attendees to the CRISPR-Cas workshop held at the John Innes Centre at the start of September, which was kindly sponsored by Plant Methods. This workshop was designed to introduce CRISPR technology and highlight what might be possible with his transformative technology.

Unfortunately there was a minor hiccup at the start of the day with some confusion over starting time! There was an eager group of researchers beating down the doors at 9am when registration didn’t officially begin until 10am! Hopefully the hour of lost sleep didn’t negatively affect concentration! It was very gratifying to welcome attendees from as far-a-field as Denmark, Ireland, Poland, Germany and Finland! Clearly there is a great appetite to learn about the technology, a fact that might well motivate GARNet to organise another workshop in future, watch this space!

The workshop kicked off with an introduction to OpenPlant from Professor Jim Haseloff before co-organiser Dr Nicola Patron took the attendees through a brief history of gene editing, from the discovery of restriction enzymes in 1975 through to some unpublished gene-editing results from a collaboration with the grass transformation facility at the JIC.

As the focus of the workshop was CRISPR-Cas mediated gene editing it worth reminding readers that this phenomenon was discovered in bacteria as an ‘immune’ response to viral infection. In some undoubtedly ‘Noble-prize’ worthy work it was realised that this could be repurposed for use in eukaryotes as a simple yet precise method of gene editing. In short this takes advantage of the activity of a Cas9 nuclease that is guided to a specific sequence by a 20mer complementary ‘guide-RNA’. Therefore in theory the guide RNA can be designed to target Cas9 to any sequence of interest. This results in the host DNA repair enzymes attempting to fix the error……however this process is not perfect so in many cases a mutation remains, which can abolish or alter gene/protein function.

The first keynote talk was given by Professor Holger Puchta (KIT) who described his seminal work on the use of double strand break (DSB) repair and how this can be combined with gene-editing technologies in plants. Holger described the two most Puchta_Tsunamiimportant molecular discoveries of his lifetime, namely the polymerase chain reaction and gene editing technology, which for the latter he said ‘hit him like a tsunami’ when he realised its enormous potential!

Holger gave an inspiring talk that provided attendees with the history of his work on DSB through to present day applications using CRISPR to induce DSB and homologous recombination for targeted replacement of gene-edited sequences. He ended his talk with some exciting perspectives where he believes that gene-editing technology will dramatically change the future of plant breeding.


Perspective Photo- @BioMatty

After an excellent JIC lunch, the second keynote was provided by Dr Bing Yang from Iowa State where he discussed his work using CRISPR for gene-editing in rice and maize. Bing showed that CRISPR-Cas can be successfully used with high efficiency in monocots which, given the time-consuming transformation procedures in these plants, makes it a very attractive technique for altering gene function. Importantly Bing showed that it was possible to induce bi-allelic mutations in T0 transgenic rice, thus greatly reducing the time to develop plants with altered gene function. MaizeProtocol

Arguably the most exciting part of his talk was his final slide in which Bing presented a letter from the US Department of Agriculture (USDA) that stated that his gene-edited rice lines were not considered genetically engineered (and therefore not subject to the usual regulations). If this policy is replicated for other gene edited lines and in other countries then this could be a game-changing development for our ability to use of targeted lines in many areas of plant biology and agriculture…..

The debate surrounding gene-editing will run for a while but the early signs are positive that it will more ‘acceptable’ in the court of public opinion than its related predecessor ‘genetic-modification’.

The later talks were focused on more direct uses of the technology presented by researchers at the Sainsbury Lab, JIC and University of Cambridge. Laurence Tomlinson from Jonathan Jones’s lab presented work where she used CRISPR-Cas to alter the GA signaling pathway to produce dominant dwarf tomatoes. She highlighted that it is impossible to predict the exact nature of the genetic lesion that will occur following CRISPR-Cas targeting, showing tomato plants that were either taller or shorter than wildtype plants due to either loss of function or dominant-negative versions of the protein that they targeted independently by gene editing.

Arguably the clearest talk of the day was given by Vladimir Nekrasov from Sophien Kamoun’s lab who presented a step-wise description of how he used CRISPR-Cas to produce a disease-resistant tomato. He has now selected the CRISPR-Cas transgene out of these edited plants so in theory they are now no more transgenic that any tomato with a random mutation in the gene they targeted. They are hoping to supply these tomato seeds to regions of the world where powdery mildrew is a particular problem and where they will be able to accept the seeds without the bureaucratic hurdles that might exist elsewhere.

The meeting ended with not a little corporate pizzazz from Edward Perello who is a SynBio LEAP fellow and founding member of Desktop Genetics, a company that provides a service to design bespoke CRISPR targets for a users gene of interest. Edward took the opportunity of the meeting to announce that Desktop is now supporting six new planDesktop_Pict genomes with their target design software. He is eager to collaborate with the plant community and encouraged everyone to use the software to design targets and then provide feedback as to their success rate. Importantly this is free to use for academics so if you are looking for software to use as a comparison to your own target design or as a stand alone tool for reliable target prediction then please take the website for a spin!

Overall it was a great day of talks and although there were a few minor issues that came up during feedback (thanks to the third of attendees who provided information), the majority of people found the workshop very useful. GARNet will be providing a PDF of at least some of the talks in the coming weeks so watch this space, the ArabUK newsgroup or the GARNet Facebook page for coming information!

CVPPP Meeting: Sept 10th 2015

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Published on: September 14, 2015

GARNet took on a change of pace recently with attendance to a workshop on Computer Vision Problems in Plant Phenotyping (CVPPP), which was arranged as part of the British Machine Vision conference. The majority of attendees were computer scientists who had taken on the interesting and challenging problem of measuring different aspects of plant growth.

In the workshop introduction, the co-organiser Sotirios Tsaftaris highlighted that the ability to automate phenotyping is key to the rapid selection of new crop varieties, many of which will be critical for feeding the worlds growing population. This was highlighted in recent talk at the COPO workshop where Chris Rawlings from Rothamstead introduced a phenotyping field imager that takes 1000s of images of plants grown in the field. However to get anything out of this huge production of data, the phenotypes need to be rapidly documented and analysed. When one imagines that phenotypes can be altered by both genetic variation and climatic conditions (amongst others) then it is a significant challenge to take consistent measurements and makes plain why problems with computer vision software can be a major bottleneck.

The majority of the talks at the meeting presented software programs to measure leaves in an Arabidopsis rosette and I was surprised to observe the variety of tactics that were employed for this ostensibly simple task. The main tactic employed was to use segmentation analysis to remove the complexity of a RGB image before attempting to count the leaf number. The processing of these images was conducted by a variety of different computational tactics such as ‘finger-counting’, ‘Gaussian-process-shape modeling’ or ‘fuzzy c-means’. Although I didn’t understand the detail of these programs, the researchers had had some success, although this seemed limited to plants with ~10 rosette leaves. Arguably the most complete method can be found on the PhenoTiki software, although this website still requires addition of some detailed content.

Outside of the leaf counting work there was an excellent talk by Hanno Scharr from the Julich Plant Phenotyping Centre (which havephenoSeeder a wide range of available tools) who introduced their phenoSeeder machine that aims to allow ‘3D Reconstruction of Seeds by Volume Carving’. This machine is not high throughput and is confused by raised areas on the seed but Dr Scharr demonstrated proof of principle examples that showed the method is well-suited for 3D seed phenotyping.



Overall it seemed to me that the majority of the talks described methods that were still in their infancy even though they had taken significantly computational time to generate the models. However this research area is well served with tools. The excellent describes 130+ programs that have been designed for or can be used for different aspects of plant phenotyping. Each researcher should certainly proceed with caution when using any of these programs to ensure that they are working well for their specific needs.


The UK phenotyping community is in a great position both with the ongoing UKPPN and the UK Plant Phenomics Centre in Aberystwyth, which is always looking for new collaborators. In fact there is currently a call for pilot projects with a closing date of September 25th.

Check out the GARNet Phenomics page for more details of available facilities!

Arabidopsis Research Roundup: Sept 11th

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Published on: September 11, 2015

After a slow couple of weeks the Arabidopsis Research Roundup returns with some publications in high profile journals. None more so than the widely reported study from the University of York that highlights Arabidopsis plants which are able to grow on TNT-contaminated soils. Three other broadly cell biology-based studies from the JIC, Cardiff and Nottingham look at cell wall composition, vascular patterning and polyadenylation respectively. Finally a study from the James Hutton Institute presents an improved tool for identification of DNA-binding proteins in plants.

Johnston EJ, Rylott EL, Beynon E, Lorenz A, Chechik V, Bruce NC (2015) Monodehydroascorbate reductase mediates TNT toxicity in plants Science. 349 1072-1075

The most highly reported manuscript of this week comes from Neil Bruce’s group at the University of York. This publication in Science discusses the use of plants in the removal of historic pollution from TNT-based explosions. TNT phytotoxicity results from the creation of a reactive oxygen species in the mitochondria, a reaction catalyzed by monodehydroascorbate reductase6 (MDHAR6). The authors show that an Arabidopsis mdhar6 mutant is tolerance to TNT with no significant reduction in biomass. This discovery may very well contribute toward the remediation of contaminated sites with plants. This paper has been also reported widely in the general media including at Wired or Reuters.

Seguela-Arnaud M, Smith C, Uribe MC, May S, Fischl H, McKenzie N, Bevan MW (2015) The Mediator complex subunits MED25/PFT1 and MED8 are required for transcriptional responses to changes in cell wall arabinose composition and glucose treatment in Arabidopsis thaliana. BMC Plant Biol. 5;15(1):215

Mike Bevan at the JIC leads this work, which also includes GARNet board member Sean May that investigates the control of cell wall deposition. The Arabidopsis hsr8-1 mutant has an arabinose deficiency that prevents correct hypocotyl elongation due to a cell wall defect. This mutant is rescued by mutations in the Mediator transcription complex indicating that they have some specificity for genes involved in cell wall composition. This suppression alters gene expression is several glucose-induced genes, including cell wall enzymes and those involved in flavonoid and glucosinolate biosynthetic pathways.

Randall RS, Miyashima S, Blomster T, Zhang J, Elo A, Karlberg A, Immanen J, Nieminen K, Lee JY, Kakimoto T, Blajecka K, Melnyk CW, Alcasabas A, Forzani C, Matsumoto-Kitano M, Mähönen AP, Bhalerao R, Dewitte W, Helariutta Y, Murray JA

AINTEGUMENTA and the D-type cyclin CYCD3;1 regulate root secondary growth and respond to cytokinins Biol Open. bio.013128.

The aim of this multi-national collaboration led by GARNet PI Jim Murray (Cardiff)  and Yrjo Helariutta (SLCU) was to reset some established dogma which held that the AINTEGUMENTA (ANT) was epistatic to the D-type cycling CYCD3;1 in the control of vascular patterning. However this study shows that in the vascular cambium of Arabidipsis roots both genes respond to cytokinin and are required for proper root thickening. In addition this mechanism is maintained in the roots of poplar, suggesting a common regulatory mechanism.

Kappel C, Trost G, Czesnick H, Ramming A, Kolbe B, Vi SL, Bispo C, Becker JD, de Moor C, Lenhard M (2015) Genome-Wide Analysis of PAPS1-Dependent Polyadenylation Identifies Novel Roles for Functionally Specialized Poly(A) Polymerases in Arabidopsis thaliana PLoS Genet.11(8):e1005474

Corneila De Moor is a lecturer in the RNA biology group at the University of Nottingham, School of Pharmacy. However she is involved with this German-led study that looks at nuclear poly(A) polymerase (PAPS) in Arabidopsis. The three PAPS in Arabidopsis are functional specialised and this study investigates the transcriptional profile of altered poly(A) lengths to show that the PAPS1 protein is preferentially involved in ribosome biogenesis and redox homeostasis. This suggests that expression levels are strongly linked to poly(A) tail length and that relative activities of the PAPS isoforms are used as an endogenous mechanism to co-ordinately modulate plant gene expression.

Motion GB, Howden AJ, Huitema E, Jones S (2015) DNA-binding protein prediction using plant specific support vector machines: validation and application of a new genome annotation tool Nucleic Acids Res.

Edgar Huitema is the plant science lead on this collaboration with computer scientists at the James Hutton Institute that introduces a new genome analysis tool that aims to functional annotate protein products. The focus of the study is on DNA-binding proteins and this new support vector machine model more accurately predicts this type of protein than generic versions. The model was developed in Arabidopsis but when turned to the tomato genome it annotated 36 currently uncharacterised proteins. This model is publically available and the authors hope that it will be used in combination with existing tools to increase annotation levels of DNA-binding proteins

GARNet/Egenis Meeting on Big Data.

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Published on: September 10, 2015

GARNet and the Exeter Centre for the Study of the Life Sciences (Egenis) are excited to announce a two-day workshop on ‘Integrating Large Data into Plant Science: From Big Data to Discovery’ to be held in the picturesque Dartington Hall, Totnes, Devon on April 21st-22nd 2016.

The aims of this workshop are to:
1. Introduce examples of how researchers have re-used datasets in innovative ways.
2. Examine the intrastructure that exists to support the re-use of large datasets
3. Discuss the mechanisms by which the community deals with big data.

We have an exciting program with speakers from across academia, industry and the scientific journals and includes Nick Provart (Bio-Analytic Resource, Toronto), Carole Goble CBE (Manchester), Angela Hancock (MFPL, Vienna), Gordon Simpson (JHI, Dundee), Eva Huala (Phoenix Bioinformatics) and Matt Vaughn (Texas Advanced Computing Centre). The full program will be available soon.

Due to kind support from the ERC and the BBSRC, registration for this workshop is free and there are a limited number of rooms available at Dartington Hall at a reduced rate.EgenisPoster_v2

If you are interested in attending please send email the GARNet coordinator Geraint Parry ( with a short paragraph outlining why this workshop would be useful to you. The organising committee will then let you know if you have been successfully selected so that you can plan your trip to Devon.

UK Synthetic Biology 2015

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Published on: September 6, 2015

At GARNet we have had a busy summer of synthetic biology with attendances at the HVCfP-SynBio workshop and the OpenPlant meeting. Therefore it was somewhat fitting that we extended our reach by finishing up the summer by attending the inaugural Synthetic Biology UK meeting, hosted by the Biochemical Society in London.

As one of the UK governments ‘eight great technologies’, the synthetic biology community has been growing steadily over the past three years so it was timely to bring together those who identify themselves as working in this area. However even amongst some attendees and certainly in the wider scientific community, there remains some skepticism regarding what ‘synthetic biology’ means and how it differs from conventional molecular biological approaches aimed at the generation of useful products. However it is likely that over the coming years more researchers will start to bring themselves into this community especially as in general terms it represents an attempt to standardise ‘parts’, allow easier sharing of data and best practice, development of novel technologies and production of socially and economically important products.

It was gratifying to observe that even though this was a general meeting there was an fair representation of plant scientists, even from outside of the plant OpenPlant hotbed of Cambridge and Norwich. Arguably the main benefit of the meeting was to be exposed to the innovation that is occurring in this field. This was exemplified by the presentations of Tom Ellis (Imperial College) and Patrick Cai (Edinburgh University) who are both involved in the Yeast 2.0 project. This incredibly ambitious worldwide collaboration aims to de novo synthesize chromosomes of the yeast Saccharomyces cerevisiae and then replace the endogenous genome piece by piece. Both these labs are each synthesizing an individual chromosome and are in the process of replacing the endogenous DNA with synthetic DNA, which also is often lacking introns and contains sites that allow further genetic manipulation. One related project aims to ‘SCRaMbLE’ the yeast genome to ascertain how regulatory and genic elements interact with each other. One such ‘SCRaMbLEd-line’ is able to happily grow at 37C (yeast usually grows at 30C), which appears to be a fairly significant alteration. The reason for this change is currently unknown….watch this space.

The organiser of the meeting was Vitor Pinheiro (UCL) and he also gave an outstanding talk describing the innovative work in his lab that aims to develop a new genetic code using the non-DNA nucleic acids. They have made some progress in identifying a polymerase that can read this XNA-code so the possibilities of creating an organism that uses a synthetic code are a little closer.

Modularity was one overarching theme of the meeting with Tom Ellis in particular describing a parts-kit of DNA sequences that can be easily moved around using the MoClo cloning system. This not only makes the generation of constructs easier, it also facilitates interactions between research groups, which is one of the guiding principles of synthetic biology. Nicola Patron (Sainsbury Lab, Norwich) similarly spoke about modularity in the context of plant DNA parts, a topic that has been described previously on the GARNet blog. Nicola also described using the same principles to produce a parts toolkit for the generation of clones for use with CRISPR-Cas, in an example of the marriage of synthetic biology and gene-editing, two principles that will be in the forefront of biological research over the coming decade.

Alison Smith (Cambridge) also described modularity in the design of the PhycoBricks DNA repository that was generated to facilitate the expression of novel compounds in algae. Alison expressed some frustration that the use of algae for the production of novel compounds has not yet been fully realised but the development of novel tools will make future successes easier to come by.

One exciting feature of the meeting was the opportunity for researchers who submitted posters to give flash presentations about their work. This type of presentation is a feature of most meetings these days and it takes a particular skillset to pull them off effectively: Don’t overload the slides and keep the message to one or two important points! Look out for a further wrinkle on the ‘flash’ format at the GARNet2016 meeting next September (details to follow shortly). This portion of the meeting was sponsored by Twist Bioscience, who are developing transformative DNA synthesis technology. Each of the top three performers won the delightfully dorky yet useful prize of a some Kb of synthesized DNA!

Another notably talk was from Nate Sherden, a postdoc in Sarah O’Connor’s lab at the JIC. They are interested in the biosynthetic pathways involved in the formation of secondary matabolites. Nate’s talk was an excellent candidate for the #overlyhonestmethods hashtag, as he described, with some humour and significant candour, his frustrating attempts to recapitulate the iridoid metabolic pathway. Now that the pathway has been determined by different researchers, the talk reflected his abstract which stated that it would be an ‘edifying cautionary tale revealing that the fundamental assumptions necessary for the success of combinational pathway reconstitution aren’t always true’.

Ultimately this meeting was a broad success with attendees pushing for an annual meeting, which in 2016 will be organised by Vitor Pinheiro and Susan Rosser (Edinburgh). As the ‘Refresh’ of the Synthetic Biology Roadmap will be published within the next two months it is hoped that more researchers will realise that their work lies within the broader definition of synthetic biology and will be encouraged to attend a meeting where some of the brightest minds of UK Bioscience are in attendance.

Overall this summer of Synthetic Biology has demonstrated that plant scientists are in the vanguard of this movement, whether it be in the development of standardised parts or in the production of novel compounds from a variety of experimental ‘chassis’. The funding of the OpenPlant synthetic biology centre has certainly facilitated this movement and it is hoped that the principles of ‘community and sharing’ that underpin the generation of useful molecular tools will further percolate throughout the plant science. The recent announcement that the iGEM competition will have a ‘plant-prize track’ in 2016 will hopefully stimulate interest in this competition from institutions that have a strong plant research and/or teaching focus. Much of the currently available funding relies on demonstrating the potential translation of fundamental research, which goes hand-in-glove with the principles of synthetic biology. Therefore embracing of this technology is surely an inevitable consequence of any successfully funded research program!

For a blow-by-blow account of the meeting please follow the #SBUK2015 hashtag.

(Re)-Introducing the Global Plant Council

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Published on: September 4, 2015

What is the Global Plant Council?

The Global Plant Council (GPC) is a non-profit coalition of plant, crop, agricultural and environmental science societies from across the globe. It was founded in 2009 to provide a body that can speak with a single, strong voice in the policy and decision-making arena, at the global level. By connecting plant science organizations, we are bringing together all those involved in plant and crop research, education and training, to harness the wealth of knowledge and expertise found within our membership base to strengthen and facilitate the development of plant science for global challenges.
What does the GPC do?

The GPC currently has 29 Member Organizations – of which the UK Plant Sciences Federation is one – representing over 55,000 plant and crop scientists across Europe, North and South America, Africa, Asia and Australasia. By bringing these groups together, we promote collaboration and cross-communication between scientists and societies, with a focus on key projects in priority areas. Some examples include:


– Diversity Seek (DivSeek): The GPC is working with partner organizations to bring together germplasm curators, plant and crop researchers, breeders and computational experts to unlock the potential of crop diversity stored in genebanks around the world. For more information, see Together with the American Society for Plant Biologists, the GPC is helping to develop, a forthcoming digital networking platform that will provide researchers, students, industry professionals and educators with access to plant science news, research, methods, teaching resources, funding opportunities and more from across the globe.

– Stress Resilience: Together with the Society for Experimental Biology, the GPC is hosting a Symposium on Plant Stress Resilience in Brazil in October 2015. This meeting will bring together experts in this field to showcase new approaches and technologies, share research knowledge and expertise, and facilitate cross-cultural networking and collaborations. Registration and abstract submission are open, so please consider joining us!

– Education and training: The GPC is working with volunteers and organizations to identify and share tools and resources to train and inspire the next generation of plant scientists, as well as translate these materials into many languages to expand their global reach.


As well as these activities, the GPC coordinates and manages a website, blog, and a monthly e-newsletter to help its members stay connected and up to date with global plant science research. You can also follow us on Twitter at @GlobalPlantGPC (or in Spanish at @GPC_EnEspanol), or on Facebook.



How can the GPC help me?

The GPC is directed by an Executive Board of leading figures from the world of plant and crop science research, and we also have a panel of elected representatives from each of our Member Organizations. We encourage you to communicate with the leaders of your local plant science organizations so that they can feed back to us the issues, needs and opportunities faced by plant scientists in your region.


As well as our Executive Board, which meets on a quarterly basis, the GPC has a small staff that manages the day-to-day running of the Council. Ruth Bastow is our Executive Director, and Lisa Martin is the Outreach & Communications Manager – if you have any upcoming events, funding opportunities, or exciting news to share we will be pleased to help promote these via our website, newsletter and other outreach channels. In addition, you might like to contribute an article to our blog to raise awareness of an issue, important research, an event or project in your area.


The new online plant science community platform mentioned above is still in development and will be a fantastic resource when it is finished – stay tuned! The GPC website is also a useful source of information – we have a comprehensive Events calendar to help you find meetings, conferences, workshops and symposia to attend, and our Resources area provides a range of useful documents, reports, awards, funding opportunities and other information for plant scientists. You could also sign up for our monthly e-Bulletin newsletter.



How can I help the GPC?

There are many ways you can help! Firstly, why not consider making a donation to the GPC? The GPC is not-for-profit and although our Member Organizations pay an annual membership fee, our costs are not entirely covered by this income. We therefore seek donations – however big or small – from individuals, philanthropists, funding bodies or other organizations to help us continue the important work we do.


As a global organization we know that not everyone around the world speaks or understands English, yet the majority of resources for the plant sciences are written in English. If you speak another language and would be willing to help us translate resources such as teaching tools, videos, protocols and other documents into your mother tongue, we would love to hear from you!


Another way you might like to get involved with the GPC is to help raise awareness of the work we do. If you have been invited to speak at a local, national or regional plant science event in the coming months, and would like to say a few words about the GPC, we have some PowerPoint slides and resources to help you spread the word.
We are also conducting a survey of research projects around the world that are associated with stress resilience in plants, and separately, we are also collecting information about maize research around the world. If you work in either of these areas, please tell us about your work!

Arabidopsis Research Roundup: August 27th

The Arabdopsis Research Roundup broadens its remit this week. As well as including three original research papers, which look at casparian strip formation, light and hormone signaling, we also highlight an important viewpoint article that aims to set standards for synthetic biology parts. In addition we include a meeting report from a plant synthetic biology summer school and interviews with plant scientists at the JIC, Caroline Dean and Anne Osbourn.

Kamiya T, Borghi M, Wang P, Danku JM, Kalmbach L, Hosmani PS, Naseer S, Fujiwara T, Geldner N, Salt DE (2015) The MYB36 transcription factor orchestrates Casparian strip formation Proc Natl Acad Sci USA Open Access

GARNet Advisory Board Chairman David Salt (Aberdeen) leads this international collaboration that looks at the (relatively) poorly understood Casparian strip (CS), a lignin-based filter that lies in root endodermal cells. Formation of the CS is initiated by Casparian strip domain proteins (CASPs) that recruit other proteins, which begin the process of lignin deposition. In this study the authors look upstream this process and identify the transcription factor MYB36 that directly regulates expression of CASPs and is essential for CS formation. Ectopic expression of MYB36 in root cortical tissues is sufficient to stimulate expression of CASP1-GFP and subsequent deposit a CS-like structure in the cell wall of cortex cells. These results have implications for the design of future experiments that aim to control how nutrients are taken up by the plant as even though myb36 mutants have a ‘root-defect’, they also have changes to their leaf ionome.

Sadanandom A, Ádám É, Orosa B, Viczián A, Klose C, Zhang C, Josse EM, Kozma-Bognár L, Nagy F (2015) SUMOylation of phytochrome-B negatively regulates light-induced signaling in Arabidopsis thaliana Proc Natl Acad Sci USA Open Access

Ari Sadanandom (Durham) and Ferenc Nagy (Edinburgh) are the leaders of this study that investigates the precise function of the PhyB photoreceptor protein. PhyB interacts with a wide range of downstream signaling partners including the PHYTOCHROME INTERACTING FACTOR (PIF) transcription factors. The small ubiquitin-like modifier (SUMO) peptide is conjugated to larger proteins to bring about a variety of signaling outcomes. In this case the authors find that SUMO is preferentially attached to the C-term of PhyB under red light conditions, a relationship that occurs in a diurnal pattern. SUMOylation of PhyB prevents interaction with PIF5 whilst the OVERLY TOLERANT TO SALT 1 (OTS1) protein likely de-SUMOlyates PhyB in vivo. Altered levels of PhyB SUMOylation cause distinct light-responsive phenotypes and as such this paper adds another level of regulation to the already complex known network that controls light signaling.

Schuster C, Gaillochet C, Lohmann JU (2015) Arabidopsis HECATE genes function in phytohormone control during gynoecium development Development. Open Access

Christopher Schuster who is now a postdoc based at the Sainsbury lab in Cambridge is the lead author on this investigation into the role of the HECATE (HEC) family of bHLH transcription factors on fruit development in Arabidopsis. During this process HEC proteins are involved in the response to both the phytohormones auxin and cytokinin, the authors proposing that HEC1 plays an essential role in Arabidopsis gynoecium formation.

Patron N et al (2015) Standards for plant synthetic biology: a common syntax for exchange of DNA parts New Phytologist Open Access

Carmichael RE, Boyce A, Matthewman C Patron N (2015) An introduction to synthetic biology in plant systems New Phytologist Open Access

Although not strictly based on Arabdopsis work, there are a couple of articles in New Phytologist that have broad relevance to plant scientists who are interested in plant synthetic biology. In the first of these Nicola Patron (The Sainsbury Laboratory) leads a wide consortium that aims to set parameters for the standardisation of parts in plant synthetic biology. It is hoped that as the principles of synbio are used more widley in the plant sciences that the proposals in this paper will serve as a useful guide to standidise part production. GARNet has recently written a blog post on this topic.
The associated meeting report looks at the use of plant synthetic biology in a teaching context with a synopsis of the ERASynBio summer school hosted by John Innes Centre. In this event, young researchers from a range of backgrounds were introduced to the power and potential of plant synthetic biology through a diverse course of lectures, practical session and group projects.


Vicente C (2015) An interview with Caroline Dean Development Open Access

An interview with Anne Osbourn (2015) New Phytologist Open Access

These are interviews with eminent female plant molecular biologists who both work at the John Innes Centre. Caroline Dean’s lab focuses on the epigenetic mechanisms that regulate vernalisation whilst Anne Osbourn is interested in using synthetic biology approaches to engineer metabolic pathways for the production of novel compounds.

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Welcome , today is Tuesday, October 6, 2015