Arabidopsis Research Roundup: May 27th

This weeks Arabidopsis Research Roundup sees a small number of high quality publications driven by UK-based researchers together with a couple of collaborative efforts that highlight the international aspect of research. Topics include two greatly different descriptions of how a plant responds to attack, an investigation into the intersection of vesicle and potassium transport as well as descriptions of auxin and sugar signaling.

Sarris PF, Duxbury Z, Huh SU, Ma Y, Segonzac C, Sklenar J, Derbyshire P, Cevik V, Rallapalli G, Saucet SB, Wirthmueller L, Menke FL, Sohn KH, Jones JD (2015) A Plant Immune Receptor Detects Pathogen Effectors that Target WRKY Transcription Factors. Cell 161, p1089-1100 http://dx.doi.org/10.1016/j.cell.2015.04.024

Jonathan Jones at the Sainsbury lab collaborated with his ex-PhD student Kee Hoon Sohn (now at Massey University in NZ) to produce this high profile publication in Cell. Professor Jones’s group has been in the vanguard of research into the response to bacterial pathogens and this paper adds a further layer of understanding as they show that the plant uses a bacteria’s own ‘attack mechanism’ against itself. Many bacterial effector proteins target WRKY DNA-binding protein domains in order to interfere with transcription. This work shows that the plant defence factor RRS1 also contains a WRKY domain, enabling it to ‘sense’ when the bacteria is in the cell and act as a decoy that makes the bacteria subsequently open to attack.

 

Jaouannet M, Morris JA, Hedley PE, Bos JI (2015) Characterization of Arabidopsis Transcriptional Responses to Different Aphid Species Reveals Genes that Contribute to Host Susceptibility and Non-host Resistance. PLos Pathogens 11: e1004918.

The group of Jorunn Bos at the James Hutton Institute in Dundee looked at a different aspect of the defence response whereby they investigated transcriptional responses to aphid predation on Arabidopsis. Host and non-host responses to aphids show a high degree of overlap in expression but interestingly the host response included repressive of genes involved in metabolism and oxidative response. This type of study will pave the way for the future development of aphid control strategies in crop plants and once again highlights the utility of Arabidopsis as a model system.

MyzusPersicae

Zhang B, Karnik R, Wang Y, Wallmeroth N, Blatt MR, Grefen C (2015) The Arabidopsis R-SNARE VAMP721 Interacts with KAT1 and KC1 K+ Channels to Moderate K+ Current at the Plasma Membrane Plant Cell [Epub]

Control of potassium channels is the focus of this work from Mike Blatt’s lab at the University of Glasgow. They identify a subset of SNARE proteins (that are involved in vesicle trafficing) that control K+ channels, albeit in an unconventional manner. The vesicle-associated membrane proteins 721 (VAMP721) is able to target vesicles as well as supressing the actitivty of the K+ channels KAT1 and KC. This leads to a model whereby different subsets of SNARE proteins opposingly effect K+ channel activity alongside having an effect on vesicular transport.

 

Panoli A, Martin MV, Alandete-Saez M, Simon M, Neff C, Swarup R, Bellido A, Yuan L, Pagnussat GC, Sundaresan V. (2015) Auxin Import and Local Auxin Biosynthesis Are Required for Mitotic Divisions, Cell Expansion and Cell Specification during Female Gametophyte Development in Arabidopsis thaliana. PLoS One. 10:e0126164.

The primary interest of Ranjan Swarup’s group at the University of Nottingham is in hormone signalling and root development yet he is included as a collaborator in this publication led from UC-Davies that focusses on auxin signalling during female gametophyte development. The paper shows that the YUCCA family of the auxin biosynthetic genes are asymmetrically expressed during embryo sac development and that the AUX1 and LAX1 auxin influx carriers are expressed only at both the micropylar pole of the embryo sac and in adjacent cells of the ovule. In addition aux1lax1lax2 triple mutants show numerous gametophytic developmental defects.  Given the importance of auxin in most aspects of plant development, this paper highlights the specific manner in which auxin is required for mitotic divisions, cell expansion and patterning during embryo sac development.

 

Zheng L, Shang L, Chen X, Zhang L, Xia Y, Smith C, Bevan MW, Li Y, Jing HC (2015) TANG, Encoding a Symplekin_C Domain-contained Protein, Influences Sugar Responses in Arabidopsis Plant Physiol [Epub]

Mike Bevan at the JIC is a collaborator on this Chinese driven project that investigates Arabidopsis tang1 mutants. These plants are hypersensitive to sugar amd following a classic map-based cloning approach, the TANG1 gene was found to encode a novel protein with a predicted Symplekin tight junction protein C-terminal. As TANG1 is ubquitiously expressed and has little effect on known sugar signalling pathways, the precise in vivo role of the protein remains somewhat opaque even though it is clearly an important player in the response to sugar in Arabidopsis.

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:
logo-era-caps
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
Comments: No Comments
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.

A few funding opportunities for UK plant scientists

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

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.

Arabidopsis Research Round-up

Categories: Arabidopsis, Global, Round-up
Tags: No Tags
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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!

Categories: GARNet
Comments: No Comments
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

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.

  1. 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.
  2. 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.
  3. 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!

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