Guest Blogger, Author at Weeding the Gems

Categories: funding

Tags: award, BBSRC, fellowship, food standards agency, FSA, funding, future leaders, grants, lectureship, plant science, prize, Rank Prize, research, royal society

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Published on: May 6, 2015

Here are the details of a few funding opportunities we have recently came across for early career and more established researchers – some of the deadlines are quite soon so if you’re interested, be quick!

Royal Society Research Grants

The Royal Society invites applications for its research grants. These provide seed-corn funding for early-career UK scientists for research within the society’s remit in the natural sciences, including the history of science. The aim is to increase the availability of specialised equipment and consumables for high quality research, and to enable scientists to further develop their new projects by obtaining funding from other sources.

Applicants should have a PhD or equivalent status, be working as independent researchers within five years of their first academic position and be resident in the UK. Non-tenured researchers and retired scientists may apply if the application is related to the history of science and the applicant works in association with an eligible institution. Eligible organisations are UK universities and non-profit research organisations, including institutes funded by the UK Research Councils.

Two types of grants are available for a maximum period of 12 months: grants of up to £15,000 for specialised equipment, essential consumable materials and services, and travel and subsistence for essential field research; and grants of up to £5,000 for the publication of scholarly works on the history of science.

Deadline: 26th May 2015

BBSRC Future Leader Fellowship

The Biotechnology and Biological Sciences Research Council and the Food Standards Agency invite applications for their future leader fellowship. This enables early-career researchers to undertake independent research on any area within biotechnology and biological sciences, and to gain leadership skills.

Applications that align with the following strategic priorities are particularly welcome:

animal health;
bioenergy – generating new replacement fuels for a greener, sustainable future;
combating antimicrobial resistance;
data driven biology;
food, nutrition and health;
healthy ageing across the lifecourse;
new strategic approaches to industrial biotechnology;
reducing waste in the food chain;
replacement, refinement and reduction in research using animals;
sustainably enhancing agricultural production;
synthetic biology;
systems approaches to the biosciences;
technology development for the biosciences;
welfare of managed animals.

In addition, the FSA will co-fund proposals that have the potential to impact on issues highlighted in its emerging strategy 2015–2020 and underpinning science, evidence and information strategy. A particular interest is for proposals that aim to realise the potential of utilising big data approaches to address complex issues that will ultimately lead to benefits for consumers. Fellows whose proposals are co-funded by the FSA may undertake a short term placement with the agency.

Applicants should have a PhD, or be expecting to have passed their viva prior to 30 November 2015. They should have no more than five years’ postdoctoral research employment by this point.

Approximately 12 fellowships are available. Each fellowship is worth up to £250,000 over a period of three years. Awards include personal salary as well as support for travel and subsistence, training activities and research consumables.

Deadline: 4th June 2015

Rank Prize Nutrition Fund New Lecturer Award

The Rank Prize Funds’ nutrition committee invites applications for its new lecturer awards. These support scientists who are conducting research in an area of human nutrition or crop science in order to further their careers.

Newly-appointed lecturers, researchers of equivalent status who are based in research institutes, or fellows with their own independent support who are working in a UK institution, may apply. The post must have been started at the earliest in 2013, and applicants should normally be three to nine years from their PhD. Postdoctoral scientists supported on a senior investigator’s funding are not eligible.

Awards are worth up to £20,000 each for a period of up to two years. Funding may be used for consumables, equipment or a contribution towards a salary or student support.

Deadline: 28 August 2015

The GM debate and the UK General Election

by Guest Blogger

Categories: GARNet, UKPSF

Tags: Conservatives, crop, crop science, European Parliament, general election, genetic modification, GM, GMO, Green Party, Labour, Liberal Democrats, manifesto, Plaid Cymru, plant science, politics, technology, UKIP

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Published on: May 5, 2015

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.

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.

Although 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.

Arabidopsis Research Round-up

by Guest Blogger

Categories: Arabidopsis, Global, Round-up

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Published on: April 7, 2015

Your UK Arabidopsis Research Round-up this week includes a mixed bag of research, including a basic study that could help improve biofuel production, work on differential metabolism of sphingolipids in pollen, analysis of leaf movements of Arabidopsis plants grown in space, and more!

Lunn D, Ibbett R, Tucker GA and Lycett GW. Impact of altered cell wall composition on saccharification efficiency in stem tissue of Arabidopsis RABA GTPase-deficient knockout mutants. BioEnergy Research, 13 March 2015. DOI: 10.1007/s12155-015-9599-9. [Open Access]

In an effort to understand how plants can be manipulated for increased biofuel production, this team from the University of Nottingham is exploring a clade of Rab GTPase proteins called RABA. These proteins are involved in the control of trafficking to the cell wall, and their manipulation may help to overcome the cell wall’s inherent recalcitrance to digestion. The group first developed a saccharification process for Arabidopsis, then used this to demonstrate that rab4 mutant lines released more sugar, with or without pre-treatment, on saccharification.

Luttgeharm KD, Kimberlin AN, Cahoon RE, Cerny RL, Napier JA, Marckham JE and Cahoon EB. Sphingolipid metabolism is strikingly different between pollen and leaf in Arabidopsis as revealed by compositional and gene expression profiling. Phytochemistry, 17 March 2015. DOI: 10.1016/j.phytochem.2015.02.019.

It has been known for some time that sphingolipids are essential for make gametophytic development in Arabidopsis thaliana, but their composition and gene expression patterns have not been studied in pollen. This study, involving the work of Rothamsted’s Johnathan Napier, investigated pollen from wild type Col-0 and a long-chain base Δ4 desaturase mutant. Though we are as yet unsure why, the findings reveal that sphingolipid metabolism is very much different in Arabidopsis pollen compared to leaves.

Fisahn J, Klingele E and Barlow P. Lunar gravity affects leaf movement of Arabidopsis thaliana in the International Space Station. Planta, 21 March 2015. DOI: 10.1007/s00425-015-2280-x.

Peter Barlow from the University of Bristol is the last author on this study, which takes an interesting look at Arabidopsis plants in space! Using data collected on the International Space Station, Barlow – together with Joachim Fisahn from Germany and Emile Kingele from Switzerland – explored the relationship between oscillations of leaf movements and the lunisolar tide.

Grison MS, Brocard L, Fouillen L, et al. Specific membrane lipid composition is important for plasmodesmata function in Arabidopsis. The Plant Cell, 27 March 2015. DOI: 10.1105/tpc.114.135731.

Working with French and German collaborators, this paper involves the work of Yoselin Benitez-Alfonso from the University of Leeds. In order to understand more about the roles of the major constituents of the plasma membranes (PMs) of plasmodesmata (PD), the group isolated “native” PD membrane fractions and carried out comparative mass spectrometry analysis. They determined that lipids are laterally segregated along the PM at the PD cell-to-cell junction in Arabidopsis thaliana and that, compared to the bulk of the PM, PD membranes are enriched with sterols and sphingolipids with very long chain saturated fatty acids.

Massalski C, Bloch J, Zebisch M and Steinebrunner I. The biochemical properties of the Arabidopsis ecto-nucleoside triphosphate diphosphohydrolase AtAPY1 contradict a direct role in purinergic signalling. PLOS ONE, 30 March 2015. DOI: 10.1371/journal.pone.0115832. [Open Access]

Matthias Zebisch from the University of Oxford worked with German colleagues on this PLOS ONE paper, in which the previously assumed role of AtAPY1 is questioned. Previous work proposed that AtAPY1 was involved in growth and development, pollen germination and stress responses through a mechanism involving regulation of extracellular ATP signals. This work shows that ATP is not a substrate of AtAPY1, which is in fact more likely to function as a GDPase.

Work for GARNet!

by Guest Blogger

Categories: GARNet

Tags: GARNet, jobs, science job

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Published on: March 5, 2015

As we have mentioned on our main website, we are searching for a new GARNet Coordinator. Until now, the job has been advertised for internal Cardiff University applications only, but as of today, anyone is eligible to apply. Would you like to work for GARNet? You can find the job advertisement here: Research Associate, GARNet Coordinator.

What does a GARNet Coordinator do?

Lots of things! The GARNet Coordinator is responsible for managing the day-to-day running of the network – you can find a full job specification on the Cardiff website, but practically, the job includes things like:

Maintaining the GARNet website, mailing list, Twitter account and blog;
Organising regular meetings with our Committee, including meeting room bookings, catering and logistics, taking minutes and ensuring actions from the last meeting are completed;
Identifying opportunities for workshops and events that will benefit the plant science community, and then organising those events – recent past examples include the GARNet Conference, Software Carpentry workshops at Liverpool and Warwick, and an iPlant workshop. You’ll need to find sponsorship, book event space and hotel rooms, organise transport and catering, prepare delegate information packs, and so on;
Staying abreast of what’s currently happening in Arabidopsis and basic plant science research, and networking and liaising with members of the plant science community by attending national and international conferences such as ICAR, SEB or UKPSF;
Writing – we have written a number of papers published in peer reviewed journals, as well as meeting reports, contributions to consultations, guest blog posts and articles, our Arabidopsis Research Round-up, and the twice-yearly GARNish newsletter;
Planning and developing grant applications for resources or projects identified by the plant science community as being of value – we recently secured renewed funding for GARNet itself, and we were heavily involved with putting together the application for iPlant UK.

The GARNet Coordinator needs to be a plant scientist who is well organised, a good writer, communicator and networker. You will, on occasion, need to travel nationally and internationally, and good computer skills are a must – experience with website management, blog platforms and creative publishing software such as Adobe InDesign and Photoshop are ideal.

If you’d like any more information about the GARNet Coordinator vacancy, please feel free to submit informal enquiries to Ruth Bastow.

The closing date for applications is 19 March 2015.

iPlant is coming to the UK

by Guest Blogger

Categories: funding, GARNet

Tags: BBSRC, big data, computer programming, computer science, data analysis, engineering, iPlant, iplant UK, jobs, liverpool, nottingham, software, TGAC, TGAC< warwick, the genome analysis centre

Comments: 1 Comment

Published on: March 2, 2015

Back in 2013, the GARNet team brought the iPlant Collaborative over to the UK to run a four-day workshop. Now, we’ve secured funding to bring iPlant to the UK again – but this time, it’s here to stay!

During 2014, the GARNet team and committee – together with iPlant collaborators in the US – were busy preparing a grant application for an invited BBSRC capital funding call. Our proposal was to work with iPlant to develop a ‘node’ of iPlant here in the UK. Our application was sucessful and the award was announced at the end of January at the AAAS 2015 meeting.

What is iPlant?

Funded by the US National Science Foundation (NSF) the iPlant Collaborative provides free and open access to ‘cyberinfrastructure’, originally just for plant scientists, but now for all the life sciences. Here’s a short video clip to explain more:

Harnessing the power of some of the world’s most powerful supercomputers, iPlant users can access the cloud-based Data Store, which provides very large amounts of space for researchers to store, and quickly transfer and share ‘big data’ files.

iPlant users also have access to the Discovery Environment – a web-based, graphical interface that provides access to an ever-expanding suite of modular, integrated ‘apps’ for data analysis. Apps can be built either by the iPlant team or by more experienced users, and cover a wide range of analysis needs. They are user-friendly and very intuitive, meaning that even researchers with little or no knowledge of command line computer programming can easily run an app, or create a pipeline of apps, to analyse large and complex data files.

Why do we need iPlant UK?

iPlant, which is free for anyone around the world to use, is currently distributed across three locations in the US – the Texas Advanced Computing Center, the University of Arizona and Cold Spring Harbor Laboratory. Though the high performance computing power it utilises is currently sufficient, iPlant was designed to be extendable to spread resources between even greater numbers of ‘nodes’. iPlant UK will be the first – hopefully of many – international iPlant hubs to ensure the future sustainability of the resource on a global scale.

As we noted in our recent Journal of Experimental Botany paper, one of the drawbacks of having iPlant located solely in the US, is that technical user support is only currently available during US office hours. When we hosted our workshop at the University of Warwick in September 2013, iPlant’s US-based support engineers kindly agreed to be woken up if we needed them – and we did! Clearly that’s not an ideal solution going forwards, especially as the number of worldwide users grows and grows.

As well as having access to technical support on the GMT timezone, the project’s collaborators at the Universities of Warwick, Liverpool, Nottingham and at The Genome Analysis Centre (TGAC), aim to convert existing BBSRC-funded software tools for the iPlant environment. This will increase community access to these useful resources, and their uptake, giving the plant science community even greater opportunities for efficient, effective, collaborative research.

How will it work?

iPlant UK will run as an independent, UK-hosted iPlant node that will centralise compute power and data storage to a single site at TGAC.

The team at TGAC, managed by Dr Tim Stitt and Dr Rob Davey, will work together to install and maintain new and existing hardware infrastructure at TGAC, and once that phase is complete, they will start work to establish and launch the iPlant UK node.

Meanwhile, teams at the Universities of Warwick, Nottingham and Liverpool will convert software tools they have created from their existing formats to the iPlant environment.

University of Liverpool: Next generation sequencing workflows (led by Professor Anthony Hall). Working with the wheat community, the team at Liverpool will optimise a wheat genetic tool bench for next generation sequencing, and a pipeline for mapping-by-sequencing.
University of Warwick: Gene expression, networks and promoter motif tools and pipelines (led by Professor Jim Beynon). The Warwick team will port tools from the PRESTA project into the iPlant environment. These tools include those for identifying differential gene expressions, clustering and network inference, and promoter analysis.
University of Nottingham: Image-based phenotyping (led by Professor Tony Pridmore, Centre for Plant Integrative Biology). The team at Nottingham will convert a range of popular tools for visualising root phenotypes, so that they can be accessed and used from the iPlant environment.

If you are interested in getting involved with this project, two posts at TGAC are currently being advertised (but hurry, the closing date is tomorrow, 3rd March!)

Opportunities at Warwick and Nottingham will be announced soon so stay tuned for updates!

Arabidopsis Research Round-up

by Guest Blogger

Categories: Arabidopsis, Global, Round-up

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Published on: February 23, 2015

Some interesting and diverse papers in the Arabidopsis Research Round-up this week – check out these offerings from the University of Warwick, University College London, John Innes Centre, University of Cambridge and University of Leicester.

Szakonyi D, Van Landeghem S, Baerenfaller K, Baeyens L, Blomme J, Casanova-Saez R, De Bodt S, Esteve-Bruna D, Fiorani F, Gonzalez N, et al. The KnownLeaf literature curation system captures knowledge about Arabidopsis leaf growth and development and facilitates integrated data mining.Current Plant Biology, 7 February 2015. DOI: 10.1016/j.cpb.2014.12.002. [Open Access]

This Current Plant Biology paper was authored by a multi-national collaboration including Vicky Buchanan-Wollaston from the University of Warwick. It describes the development of KnownLeaf – a database connecting Arabidopsis leaf growth and development genotype to phenotype data mined from scientific literature. In addition, the network LeafNet has also been developed to graphically represent leaf phenotype relations in a molecular context.

Schwarte S, Wegner F, Havenstein K, Groth D, Steup M and Tiedemann R. Sequence variation, differential expression, and divergent evolution in starch-related genes among accessions of Arabidopsis thaliana. Plant Molecular Biology, 8 February 2015. DOI: 10.1007/s11103-015-0293-2.

This largely German team (though Fanny Wegner is also affiliated to University College London) is exploring genetic diversity in starch-related genes. Twenty-six different Arabidopsis accessions were sequenced, and sequence data on a further 80 accessions were accessed from public database, to determine differences in transcript levels of 25 genes. Diversity was found to vary greatly between accessions, with starch synthases and phosphorylases showing the highest levels of nucleotide diversity, and pyrophosphatases and branching enzymes being the most highly conserved.

Shimotohno A, Sotta N, Sato T, De Ruvo M, Maree AFM, Grieneisen VA and Fujiwara T. Mathematical modelling and experimental validation of spatial distribution of boron in the root of Arabidopsis thaliana identify high boron accumulation in the tip and predict a distinct root tip uptake function.Plant & Cell Physiology, 9 February 2015. DOI: 10.1093/pcp/pcv016.

Scientists from the John Innes Centre worked with Italian and Japanese colleagues to produce this offering from Plant & Cell Physiology, in which mathematical modelling is used to predict boron distribution in the Arabidopsis root tip. The model predicted that the concentration of soluble boron would be higher in a region around the quiescent centre; this was then validated experimentally by determining root boron distribution via laser ablation-inductivity-coupled plasma mass spectrometry.

Mateos JL, Madrigal P, Tsuda K, Rawat V, Richter R, Romera-Branchat M, Fornara F, Schneeberger K, Krajewski P and Coupland G. Combinatorial activities of SHORT VEGETATIVE PHASE and FLOWERING LOCUS C define distinct modes of flowering regulation in Arabidopsis. Genome Biology, 11 February 2015. DOI: 10.1186/s13059-015-0597-1. [Open Access]

Working with plant scientists from around the world, this study of the combined and individual effects of transcription factors related to the initiation of flowering in Arabidopsis also included Pedro Madrigal, who is affiliated to the Wellcome Trust Sanger Institute and the University of Cambridge. Looking at the MADS-box transcription factors FLC and SVP, which form a complex, it was found that there is substantial flexibility in the ways these proteins work together, accounting for variation and robustness in the regulation of plant flowering.

Huang Z, Ölçer-Footitt H, Footitt S and Finch-Savage WE. Seed dormancy is a dynamic state: variable responses to pre-and post-shedding environmental signals in seeds of contrasting Arabidopsis ecotypes. Seed Science Research, 12 February 2015. DOI: 10.1017/S096025851500001X.

Led by Bill Finch-Savage, this team from the University of Warwick looked at how environmental signals during seed development affected the mother plant in a winter and summer ecotype of Arabidopsis thaliana. Results presented show that environmental signals both pre- and post-shedding determine the depth of physiological dormancy and therefore the germination response to the ambient environment.

Schoft VK, Chumak N, Bindics J, Slusarz L, Twell D, Kohler C and Tamaru H. SYBR Green-activated sorting of Arabidopsis pollen nuclei based on different DNA/RNA content. Plant Reproduction, 13 February 2015. DOI: 10.1007/s00497-015-0258-2.

With colleagues from Austria, Switzerland and Sweden, David Twell from the University of Leicester was involved in the preparation of this manuscript, which describes a novel method to separate SYBR Green-stained plant sperm cells using fluorescence-activated cell sorting (FACS). This method will be of great help to anyone studying germ cell genetics and epigenetic reprogramming during sexual reproduction, and should be applicable to crop plants too.

Arabidopsis Research Round-up

by Guest Blogger

Categories: Arabidopsis, Global, Round-up

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Published on: February 9, 2015

Here’s your Arabidopsis Research Round-up for this week! Today we have plenty of Scottish delights, including papers from the University of Aberdeen, Dundee,Glasgow, Edinburgh and the James Hutton Institute. There is also new work from researchers at the University of Durham, Nottingham, Leeds and Oxford.

Pokhilko A, Bou-Torrent J, Pulido P, Rodrígues-Concepción M and Ebenhöh O. Mathematical modelling of the diurnal regulation of the MEP pathway in Arabidopsis. New Phytologist, 16 January 2015. DOI: 10.1111/nph.13258.

Alexandra Pokhilko and Oliver Ebenhöh are two members of the University of Aberdeen’s Institute for Complex Systems and Mathematical Biology. Both contributed to this New Phytologist paper, in which they describe a mathematical model of the diurnal regulation of the 2-C-methyl-d-erythritol 4-phosphate (MEP) pathway. Data show that flux through the MEP pathway is accelerated in light conditions. It is also shown that pathway products regulate the abundance and activity of DXS (the first enzyme in the pathway, 1-deoxy-d-xylulose 5-phosphate synthase), which alters flux under varying conditions.

McCormick AJ and Kruger NJ. Lack of fructose 2,6-bisphosphate compromises photosynthesis and growth in Arabidopsis in fluctuating environments. The Plant Journal, 20 January 2015. DOI: 10.1111/tpj.12765.

Here, Alistair McCormick from SynthSys at the University of Edinburgh and Nick Kruger from the University of Oxford describe their research on understanding the physiological role of the signal metabolite fructose 2,6-bisphosphate (Fru-2,6-P₂). Plants from three independent T-DNA mutant lines deficient in 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase (F2KP) grow normally in constant environments, but have reduced growth and seed yield in fluctuating light and/or temperatures. McCormick and Kruger suggest that Fru-2,6-P₂ is involved in the modulation of photoassimilate partitioning, and that this is an important determinant of growth and fitness in natural environments.

Calixto CPG, Waugh R and Brown JWS. Evolutionary relationships among barley and Arabidopsis core circadian clock and clock-associated genes.Journal of Molecular Evolution, 22 January 2015. DOI: 10.1007/s00239-015-9665-0.

Presented by scientists from the James Hutton Institute and the University of Dundee, this paper provides a comprehensive analysis of circadian clock and clock-associated genes in Arabidopsis thaliana, barley, and eight other plant species. It is proposed that the common ancestor of Arabidopsis and barley had two-thirds of the key clock components identified in Arabidopsis prior to the divergence of monocot and dicot groups.

Verma V, Sivaraman J, Srivastava AK, Sadanandom A and Kumar PP. Destabilization of interaction between cytokinin signalling intermediates AHP1 and ARR4 modulates Arabidopsis development. New Phytologist, 30 January 2015. DOI: 10.1111/nph.13297.

Working with Singaporean colleagues, this New Phytologist paper involved the work of Ari Sadanandom from the University of Durham. The group describe their research on the previously poorly understood relationship between histidine phosphotransfer proteins (e.g. AHP1) and response regulator proteins (e.g. ARR4 ).

Wilson MH, Holman TJ, Sørensen I, et al. Multi-omics analysis identifies genes mediating the extension of cell walls in the Arabidopsis thaliana root elongation zone. Frontiers in Cell & Developmental Biology, 2 February 2015. DOI: 10.3389/fcell.2015.00010. [Open Access]

Scientists from the University of Leeds and the University of Nottingham (including former GARNet committee member Malcolm Bennett) here describe a multi-omics approach to understanding the regulation of cell wall extension in Arabidopsis roots.

Preuten T, Blackwood L, Christie JM and Fankhauser C. Lipid anchoring of Arabidopsis phototropin 1 to assess the functional significance of receptor internalization: should I stay or should I go? New Phytologist, 3 February 2015. DOI: 10.1111/nph.13299.

John Christie and student Lisa Blackwood from the University of Glasgow were involved in another New Phytologist paper, led by a Swiss team from Lausanne. The group is attempting to work out why, when irradiated, a fraction of the plasma membrane-associated phototropin 1 (phot1) blue light receptor is internalized into the cytoplasm. Transgenic plants expressing a lipidated version of phot1 permanently anchored to the plasma membrane were used to assess the effect of internalisation on receptor turnover, phototropism and other phot1-mediated effects, however, data suggest that internalisation is not linked to receptor turnover or desensitisation.

Arabidopsis Research Round-up

by Guest Blogger

Categories: Arabidopsis, Global, Round-up

Tags: No Tags

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Published on: January 21, 2015

Lots of new and interesting papers to catch up on from the New Year break this week. Fans of proteomics will be happy as we have three proteomics papers fromEdinburgh, Cambridge and Birmingham! The John Innes Centre and University of Warwick also have an update for us on how histone dynamics affect transcription;Norwich and Sainsbury Lab Cambridge-based researchers tell us more about ELF3; Rothamsted scientists reveal roles for CER2-LIKE proteins; and Donna Bond andProfessor Sir David Baulcombe reveal how virus-induced gene silencing can be used to study transposable elements.

Krahmer J, Hindle MM, Martin SF, Le Bihan T and Millar AJ. Sample preparation for phosphoproteomic analysis of circadian time series in Arabidopsis thaliana. Methods in Enzymology, 26 December 2014. DOI: 10.1016/bs.mie.2014.10.022.

This useful review from former GARNet PI Andrew Millar and team discusses methods used in phosphoproteomics – the study of post-translational protein phosphorylations.

Rosa S, Ntoukakis V, Ohmido N, Pendle A, Abranches R and Shaw P. Cell differentiation and development in Arabidopsis are associated with changes in histone dynamics at the single cell level. The Plant Cell, 30 December 2014. DOI: 10.1105/tpc.114.133793. [Open Access]

In this really interesting Plant Cell paper, researchers including those from the John Innes Centre and the University of Warwick, provide evidence to suggest that stem cells have relatively mobile histones, whereas as cells differentiate, the histones become acetylated and thus more and more ‘fixed’ to the chromatin. This helps to explain how stem cells have the propensity to generate cells with different gene expression profiles, and why differentiated cells of a given type all express genes in a coordinated manner.

Box MS, Huang E, Domijan M, et al. ELF3 controls thermoresponsive growth in Arabidopsis. Current Biology, 30 December 2014. DOI: 10.1016/j.cub.2014.10.076.

Published just a little too late for Christmas (!), this paper comes from a collaboration between mostly Norwich Research Park-based scientists and those at the The Sainsbury Lab in Cambridge. The paper explores the role and function of the transcriptional regulator ELF3 (EARLY FLOWERING3). This gene encodes a protein that rapidly and reversibly binds to transcriptional targets in a temperature-dependent mechanism, thus regulating cell elongation in response to changes in ambient temperature.

Marondedze C, Wong A, Groen A, Serrano N, Jankovic B, Lilley K, Gehring C and Thomas L. Exploring the Arabidopsis proteome: influence of protein solubilization buffers on proteome coverage. International Journal of Molecular Science, 31 December 2014. DOI: 10.3390/ijms16010857. [Open Access]

Led by a Saudi Arabian team but involving the work of Arnoud Groen and Kathryn Lilley from the University of Cambridge, here’s another paper on the subject of methods in proteomics. In this work, using Arabidopsis thaliana as a model, the group assesses how variations in techniques and detergents used as the solubilisation buffer can affect the results of a proteomic study.

Roitinger E, Hofer M, Köcher T, Pichler P, Novatchkova M, Yang J, Schlögelhofer and Mechtler K. Quantitative phosphoproteomics of the ATM and ATR dependent DNA damage response in Arabidopsis thaliana. Molecular & Cellular Proteomics, 5 January 2015. DOI: 10.1074/mcp.M114.040352. [Open Access]

More proteomics! Jianhua Yang from the University of Birmingham is an author on this Austrian-led paper, in which a novel mass spec-based phosphoproteomics approach to study DNA damage repair in Arabidopsis thaliana is described. The approach allowed identification of nearly 11,000 proteins and 15,500 unique phosphopeptides, of which 134 ATM/ATR-dependent phosphopeptides were up-regulated, and 38 were down-regulated. Both known and novel targets of ATM/ATR were found.

Bond DM and Baulcombe DC. Epigenetic transitions leading to heritable, RNA-mediated de novo silencing in Arabidopsis thaliana. Proceedings of the National Academy of Sciences of the USA, 5 January 2015. DOI: 10.1073/pnas.1413053112. [Open Access]

This PNAS offering is from Donna Bond and David Baulcombe from the University of Cambridge. Investigating the mechanisms by which RNA-directed DNA methylation (RdDM) is achieved to silence transposable elements, the authors wondered whether DNA methylation can be induced de novo at naïve sites, or whether it can only re-establish epigenetic silencing of active transposable elements. Using virus-induced epigenetic silencing (VIGS)-RdDM, it is demonstrated that epigenetic silencing can be achieved in a genetic mutant plant, mediated via virus-derived small RNAs. This has great potential for use as a tool in gene silencing studies.

Haslam T, Haslam RP, Thoraval D, et al. CER2-LIKE proteins have unique biochemical and physiological functions in very-long-chain fatty acid elongation. Plant Physiology, 14 January 2015. DOI: 10.1104/pp.114.253195. [Open Access]

This article, which involved the work of Richard Haslam, Frédéric Beaudoin and Johnathan Napier from Rothamsted Research, explores the functionality of the enzyme CER2 and its homologues; required for the elongation of fatty acids with chains longer than 28 carbons. Three CER2-LIKE proteins are shown to have unique effects on the substrate specificity of the same condensing enzyme (required to catalyse the first step of the fatty acid elongation process), and furthermore are important in cuticle formation and pollen coat function.

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