Great British Success in ERA-CAPS

The ERA-CAPS funding call was a major EU initiative that was focused on plant sciences. Recently the second set of successfully funded projects were announced, even though the funding levels have not been confirmed. Amongst these twelve successful bids, eight feature UK plant scientists (including four from the JIC). These successful projects are highlighted below:
Project Name: DesignStarch, Designing starch: harnessing carbohydrate polymer synthesis in plants

The UK representative Rob Field is a biochemist based at the John Innes Centre. The objective of this project is to ‘gain a profound understanding of the regulation and control of the biophysical and biochemical processes involved in the formation of the complex polymeric structure that is the starch granule’, which will involve in vitro analysis of the enzymology of starch formation with the ultimate aim of transferring their findings back into plants.

EfectaWheat: An Effector- and Genomics-Assisted Pipeline for Necrotrophic Pathogen Resistance Breeding in Wheat

James Cockram (NIAB) is the project leader on this grant that proposes to investigate the economically important wheat leaf spot group (LSG) of necrotrophic pathogens. The project will use a range of techniques such as high-density genotyping, pathogen re-sequencing and advanced virulence diagnosis to deliver a genomics- and effector-based pipeline for the genetic dissection of LSG host-pathogen interactions across Europe.

EVOREPRO: Evolution of Sexual Reproduction in Plants

Both David Twell (Leicester) and Jose Gutierrez-Marcos (Warwick) are included in this seven-group consortium that aims to investigate the origin of the mechanisms that predate double fertilization in plants. The project will take a comparative gene expression-based approach to investigate gametogenesis across Marchantia, Physcomitrella, Amborella, Arabidopsis and a range of crop species. The expected findings will allow the identification of specific mechanisms that are targeted by environmental stresses during sexual reproduction in crops and will assist in the selection of stress-resistant cultivars.

INTREPID: Investigating Triticeae Epigenomes for Domestication

GARNet advisory board member Anthony Hall (Liverpool) leads this group which includes long time collaborator Mike Bevan (JIC). This project will look at variations in the epigenome across eight diverse wheat lines with the aim of determined how epigenetic marks are re-set and stabilized during the formation of new wheat hybrids and how they might influence gene expression.

MAQBAT: Mechanistic Analysis of Quantitative Disease Resistance in Brassicas by Associative Transcriptomics

John Innes Centre scientist Chris Ridout leads this six PI consortium that will look at pathogen resistance in Brassica napus, where diseases are a major limiting factor in growth success. Almost 200 lines of B.napus will be screened against a range of specific and general pathogens in the aim of discovering important disease resistance loci. One proposed aspect of the work will look at the role of glucosinolates in both disease resistace and seed quality. The project also includes UK B.napus expert Bruce Fitt (Hertfordshore).

PHYTOCAL: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae crops

Karen Halliday (Edinburgh) leads this three-PI group that will investigate the link between phytochrome signaling and resource allocation in both Arabidopsis and B.rapa. One aim of the project will be to build models that predict the dual action of phytochrome and photosynthesis on resource management and biomass production.

RegulaTomE: Regulating Tomato quality through Expression

Cathie Martin (JIB) leads this largest successful consortium of 8 labs that aim to link transcriptional regulation of metabolic pathways with tomato quality. Loci contributing to abiotic stress tolerance will also be identified toward the combined goals of obtaining more nutritious, stable and sustainable crops. The project will lead to regulatory gene identification (an important advance in terms of fundamental understanding), and provide new tools for metabolic engineering of fruit quality.

SOURSI: Simultaneous manipulation of source and sink metabolism for improved crop yield

Lee Sweetlove (Oxford) leads this group that aims to understand the linkages between source and sink tissues in the assimilation of carbon and nitrogen. The project claims to implement a metabolic engineering strategy of unprecedented scale in plants exploiting the new technique of biolistic combinatorial co-transformation.

Arabidopsis Research Roundup

Categories: Arabidopsis, GARNet, Global, UKPSF
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Published on: May 14, 2015

Your UK Arabidopsis Research Round-up this week contains studies that aim to define a network of lateral root formation, elucidate modes of calcium signaling, determine mechanisms of epigenetic memory and also the influence of exon-edge evolution in determining the extent of selective pressure.

Liu J, Whalley HJ, Knight MR. Combining modelling and experimental approaches to explain how calcium signatures are decoded by calmodulin-binding transcription activators (CAMTAs) to produce specific gene expression responses. New Phytologist. 2015 Apr 27. doi: 10.1111/nph.13428.

Marc Knight’s group at the University of Durham have attempted to decode the complex mechanism by which calcium controls changes in gene expression. They have developed an experimentally parameterized model that reveals calcium signals are amplified by the binding of calmodulin and calmodulin-binding transcription activators (CAMTAs). Interestingly, the model suggests that gene expression change in response to a calcium signature is defined by the previous history of that signal.

Lavenus J, Goh T, Guyomarc’h S, Hill K, Lucas M, Voß U, Kenobi K, Wilson MH, Farcot E, Hagen G, Guilfoyle TJ, Fukaki H, Laplaze L, Bennett MJ. Inference of the Arabidopsis Lateral Root Gene Regulatory Network Suggests a Bifurcation Mechanism That Defines Primordia Flanking and Central Zones. Plant Cell. 2015 May 5. pii: tpc.114.132993.

The biology of lateral root (LR) formation has been well researched over the past decade although a full robust regulatory network that controls this process has remained elusive. CPIB at the University of Nottingham, together with European collaborators have used a series of transcriptomic datasets to develop a time-delay correlation algorithm (TDCor) to infer the gene expression network (GRN) controlling LR initiation. The GRNs associated with AUXIN RESPONSE FACTOR7 and ARF5 predict a mutual inhibition and a patterning mechanism that controls flanking and central zone specification of LR primordia.

Berry S, Hartley M, Olsson TS, Dean C, Howard M Local chromatin environment of a Polycomb target gene instructs its own epigenetic inheritance. Elife. 2015 May 8;4. doi: 10.7554/eLife.07205.

Epigenetic ‘memory’ allows plant cells to retain a memory of past environmental or development events. One key regulator of this process is the Polycomb Repressive Complex2 (PRC2). Histone proteins that are modified by the PRC2 can be inherited through cell division. The groups of Mark Howard and Caroline Dean at the JIC investigated whether this inheritance directs long term memory in a cis or trans manner. Two copies of the Arabidopsis FLC gene, which is a target for PRC2, were monitored in the same plant. Interestingly they reveal that one FLC copy could be silenced but the other remained active, providing evidence that epigenetic memory, at least of FLC, is stored in trans but not in cis.

Bush SJ, Kover PX, Urrutia AO. Lineage-specific sequence evolution and exon edge conservation partially explain the relationship of evolutionary rate and expression level in A. thaliana. Mol Ecol. 2015 Apr 30. doi: 10.1111/mec.13221.

Alongside genetic changes in response to phenotypic adaptation, the elements of a genes DNA structure can also affect evolutionary rates. In Arabidopsis the ‘edge’ of exons, which flank introns and contain splice enhancers are known to have a higher degree of evolutionary conservation compared to coding regions. Dr Arazi Urrutia and collaborators from the University of Bath assessed selective pressure (measured by dN/dS) and showed that exon edge conservation partially explains the relationship between rates of protein evolution and expression level. Without any consideration of exon-edge conservation can potentially increase the number of genes designated as being under adaptive selection. Therefore the authors conclude that exon-edge conversation should be an important consideration when assessing overall dN/dS ratios.

The GM debate and the UK General Election

He hasn’t officially started in his role yet, but here’s a blog post from GARNet’s new Coordinator! In light of the upcoming General Election, Geraint Parry talks politics and highlights what the different parties’ manifestos have to say about the genetic modification of crops.

Please note these are the personal opinions of the author and do not necessarily represent the views of GARNet or its committee.  

Photo ‘hugovk’, used under a CC BY-NC-SA 2.0 license.

Unless you have been living under a very large rock you’ll be aware that the UK will be going to the polls on Thursday (7th May) for the 2015 General Election. Recently there have been many excellent articles about the Science and Technology policies of the different political parties, including a repository of information supplied by the Society of Biology and a voting recommendation by The Guardian.

Aside from the obvious and real concerns about the levels of future funding, another important issue to consider is the debate surrounding genetic modification (GM). Most people will be aware that EU regulations have recently changed so that, simply put, individual member states will be allowed to set their own policies on the growth of GM crops, albeit with a significant and important number of safeguards to ensure environmental protections. One of GARNet’s roles over the coming years is to encourage the translation of fundamental research, so the political environment surrounding the uptake of GM technology is of great importance for the future direction and efficacy of Arabidopsis research.

Photo by European Parliament, used under a CC BY-NC-ND 2.0 license.
Photo by European Parliament, used under a CC BY-NC-ND 2.0 license.

Although members of the European Parliament (MEPs) voted in favour for a change in regulations surrounding GM crops, the major UK political parties have significant differences in their policies toward this technology. Although GARNet isn’t suggesting that you decide your vote on this single issue, the GM debate might indeed be suggestive for a political party’s willingness to embrace new technologies in other areas.

Amongst the 2015 election manifestos published by the mainland UK political parties, only three of them include the word ‘genetic’ in the context of GM crops. On one hand, both the Green Party and Plaid Cymru explicitly state that they will support a ban on the cultivation of GMOs, whilst the UK Independence Party (UKIP) states that they ‘support research into GM foods, including research on the benefits and risks involved to the public’. The stance of the Green Party is particularly interesting as in my anecdotal experiences, many party members are disappointed with this policy given the wealth of scientific evidence supporting the safety and potential of GM crops.

status report coverAlthough the three major national UK political parties do not mention GMOs in their manifestos we can look back over their past histories in this area and use this as a basis for determining future policy directions. Over the past few years the Conservative government has embraced the idea of GM technology. The Environment Secretary, Owen Patterson, has given a number of high profile speeches, stating that the development of GM technology should be a priority for UK science. This opinion fits well with the recent policy document (PDF) published by the UK Plant Sciences Federation, which stated that ‘UK policymakers and regulatory bodies….remove unnecessarily burdensome regulation and ensure that science-based evidence is paramount’.

Whilst this indicates that the Conservative party is a full supporter of GM technology perhaps, as ever, the story is not as simple as it might seem. Currently the vast majority of GM crops are grown by large agri-businesses such as BASF or Monsanto. The proposed loosening of regulations will provide these companies with a foothold in the UK to grow for-profit crops. This embracing of big business is consistent with a right-wing ideology and therefore the Conservative party’s interest in GM crops could be described as much as a business opportunity as it is the chance to develop new varieties that might sustain crop protection through changing environmental conditions.

When the EU vote was taken earlier this year, Liberal Democrats were supportive of the change in policy with MEP Catherine Bearder being quoted as “welcoming the news”. Similarly, correspondences with my local Lib Dem parliamentary election candidate suggested that the party will adopt the ‘precautionary principle’ when it comes to this issue, meaning they will take an open view as scientific evidence develops in the area. Interestingly, a well-established online polling site reveals that a strong majority of people who identify as themselves Liberal Democrats support the uptake of GM-technology. Therefore, the consensus appears to be that the Liberal Democrats will support any legislation to allow the controlled growth of GM crops in the UK.

Arguably, the UK Labour party has the most interesting stance on the issue of GM crops. Although their 2015 election manifesto does not directly address this issue, their recent policy document entitled ‘Feeding the Nation’ (PDF), states that they ‘view biotechnology as a way to strengthen the UK’s food chain and reduce environmental damage….if it has public support’.

However, there appears to be some significant nuance to their policies. David Martin, a Scottish Labour MEP, supports the change in EU legislation, stating: ‘Labour MEPs have voted to give national governments the power to limit or ban the cultivation of genetically modified organisms’. Therefore, this indicates that by supporting the legislation, the Scottish MEPs would push to prevent cultivation of GMOs, at least in Scotland. It remains to be seen whether the national Labour party would use the change in legislation to support the development of GM technology or use it as a mechanism to ban the cultivation of GM crops. Reading between the lines, the Labour party may side with the weight of public opinion when it comes to this issue. Therefore it is imperative for plant scientists to continue their recent good work explaining the technology and allaying any safety concerns that members of the public might have.

The debate surrounding GM technology is fascinating in many ways, not least because it does not simply fall along standard political lines. Whatever the result of the upcoming election, it remains important for scientific advisors to impress upon policy makers the robust scientific support that exists for GM technology and the many and varied benefits that it could bring.

Onwards and Upwards for the Global Plant Council

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Published on: October 14, 2014
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Attendees at the Global Plant Council AGM (see end of post for details)

The 2014 Global Plant Council (GPC) annual general meeting (AGM) was held 2-3 October and hosted by the Society of Experimental Biology in London. GPC Individuals representing 22 member organisations from 5 continents gathered at Charles Darwin House to share updates and plan for the future.

Officially, the Global Plant Council is a coalition of plant and crop science societies from across the globe. It aims to provide a global voice for these societies, which individually represent scientists from specific countries, continents or sub-sets of plant science. During the AGM however, it became clear that in reality the GPC is a central hub, acting to instigate change in plant science research and application worldwide. This is a critical role; coordinated global action and a unified voice are essential for plant scientists to be able to effectively play a part in meeting the world challenges of hunger, energy, climate change, health and well-being, sustainability and environmental protection, which affect all of us.

The first day of the AGM was dedicated to sharing news and updates. Two working groups, who deal with Advocacy and Finance issues, praised the progress made by Ruth Bastow, the GPC’s first dedicated member of staff, since May 2013. (more…)

Training and skills in the UK plant sciences community: Have your say

Categories: UKPSF
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Published on: September 4, 2014

The UK Plant Sciences Federation have set up working groups to follow up the recommendations made in their report, which was launched in January. The Training and Skills Working group is tackling school, university, post-graduate and early career issues in the plant science – definitely a broad scope. The Chair Simon Leather is trying out ‘crowd-sourcing’ with his working group, asking anyone who wants to contribute for their opinions and suggestions about the way forward.

In a post on his personal website, Simon Leather has given a lot of information about the current status of training and skills in the UK plant science community, the main problems highlighted in the report, comments from the first Working Group meeting and some ideas to help solve the problem.

Leather argues that action is imperative: Without a well-trained cadre of plant scientists that are able to recognise whole organisms and are able to interact with industry we will see more problems arising with invasive species, our crop production industry will be severely compromised and biodiversity loss will accelerate. 

Some of the ideas to improve training and skills in plant science discussed at the Working Group are:

  • Working with teachers to encourage children and young people to take an interest in plant science
  • Raising awareness in schools and universities of the opportunities provided by a background in plant sciences
  • Working with the Society of Biology degree accreditation scheme to make sure plant science is a part of accredited courses
  • Building stronger training links between academia and industry to ensure HE courses are fit for purpose

What do you think? Do you think these are the right areas to focus on? The Working Group has come up with reasonable actions to begin making progress. I strongly encourage you to read the whole article, and to have your say on the action plan and challenges by commenting on the article.

Along with the Working Groups on Funding, Regulation and Translation, the Training and Skills group will report at the UKPSF AGM on 20 November.

Go here to read the article and comment:

PlantSci 2014 and Plant Science Careers

Categories: resource, UKPSF
Comments: 1 Comment
Published on: April 8, 2014

The GARNet team travelled up to York last week for the PlantSci 2014 conference. It was a fantastic event and I highly recommend it for future years. The variation between talks, which were all perfectly pitched for a general plant science audience, made the sessions exciting and maintained everyone’s interest.

A highlight of the conference was the Panel Discussion on the Future of UK Plant Science. The Panelists – Mike Bushell, Mark Chase, Sarah Gurr, Sandy Knapp and Dale Sanders – responded to the Status Report (download the PDF here) and spoke briefly about what they felt were the most important challenges for the UK plant science community to deal with.

To me, the most significant issues were put forward by early career researchers from the floor. The Panel and the report, which drew data from a community-wide survey, emphasised skills shortages and a lack of young talent entering the field; but several young researchers present spoke out about lack of support for those young scientists that are working in the field.

One person on a PhD program with funding for a short internship in industry or policy found it difficult to find a placement related to plant science. Two final year PhD students from very different research backgrounds spoke of their frustration in not knowing where to look for post-doctoral jobs. Despite being highly trained in areas within the ‘skills gap’ often referred to in reports, including the UKPSF report, they felt that academic post-doc positions (and the uncertain future that comes with them) were the only options they had.

If you feel passionately about education, training and/or plant science careers and career paths, see UKPSF working group call document (PDF) on information on what the UKPSF is doing to tackle these challenges. There will be UKPSF working groups on Training & Skills, Funding, Portfolio Balance, Regulation, and Translation.

Looking for a plant science job? (more…)

Recently in the GARNet community … (3)

Categories: GARNet, UKPSF
Comments: No Comments
Published on: February 21, 2014

It’s quietened down in the GARNet office this week and we’ve been catching up on things and preparing for the busy conference season. I’m looking forward to learning how to code with the delegates at our Software Carpentry workshop, and we’re going to Monogram and PlantSci 2014 at Easter too.

We’ve added a new Imaging Resources and Services page to our website. It lists five UK imaging facilities and two suggested resources for new users or students to find out more about biological imaging. The facilities provide a number of services including electron microscopy, in vivo single molecule fluorescence imaging and two-photon microscopy. There are also. Several of the listed facilities have recieved ALERT13 funding for new state-of-the-art equipment which will be available to users through a number of routes.

Nicola Patron, one of the Co-Is on the recently funded OpenPlant Multidisciplinary Synthetic Biology Research Centre, has published a Golden Gate Modular Cloning Toolbox for Plants with Sylvestre Marillonnet, who presented the Golden Gate method at last year’s GARNet conference on plant synthetic biology. The paper (Engler et al., ACS SynBio DOI:10.1021/sb4001504) is free to access, although annoyingly there are hoops to jump through, and the toolbox will be available through Addgene shortly. (edit 14/5/2014: the paper is not free to access)

If you’re a keen writer or interested in science communication, check out this database of science writing competitions. It’s not for plant scientists but it has very useful categories that make it clear whether your country of residence, career, career stage or field of expertise would prevent you entering.

Finally, if you’re a young plant scientist planning on attending PlantSci 2014, don’t forget to submit your abstract to have a chance of being selected to speak – cash prizes are available for the best talks.

In Photos: UK Plant Sciences Report Launch

Categories: UKPSF
Comments: No Comments
Published on: February 3, 2014

Thanks to Society of Biology Regional Coordinator David Urry for wielding the Society camera throughout the launch of the UKPSF report ‘UK Plant Science: Current Status and Future Challenges’, and letting me use some photos!

The GARNet website has a news piece on the launch, and tweets about the report are collected here

Not put off by the long, damp queue for the Faraday Lecture, the plant sciences community gathered in the Marble Hall at the Royal Society.

crowd 900


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