Arts and crafts with Arabidopsis

Categories: something fun
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Published on: November 14, 2014

These past couple of weeks, we at GARNet have noticed a number of amazing Arabidopsis artistic creations cropping up on our Arabidopsis twitter search tool (yes, we monitor Arabidopsis tweets – we’re cool like that). I thought I’d round them up for you – happy Friday!

 

Arabidopsis cake
Arabidopsis cake, made by Liam Walker and Mairi Walker.

I can personally confirm that this pot of flowering Arabidopsis plants is all edible (the tiny exception being the stems, which are made of wire). It was incredibly life-like, down to green sugar-dust algae clinging to the icing pot and oreo-crumb soil. The plants even had roots! It was created for a Gifford group lab meeting by Warwick undergraduate Liam Walker and his sister Mairi, who posted this photo on Twitter and kindly let me share it here.

 

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Jackie Hunter, BBSRC: “Breakthroughs will happen where disciplines coalesce”

Categories: funding, synthetic biology
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Published on: November 12, 2014

Jackie Hunter, Chief Executive of BBSRC, delivered a lunchtime presentation at the University of Warwick’s School of Life Sciences on Monday this week. She gave an overview of BBSRC investments and strategy, and spent the final twenty minutes in discussion with the gathered researchers, who posed questions from the floor.

Supporting bioscience in the UK

BBSRC is the biggest source of plant science funding in the UK. Its charter is to fund research and training in world-class bioscience, deliver social and economic impact, and to promote public dialogue.

Hunter explained that BBSRC responsive mode funding (around £150m per year) aims “to ensure excellence in science, wherever it comes from.” It must be functioning well as the UK is top of citation impact index, and the UKPSF found that UK plant science, mainly funded by BBSRC, is second only to the US in terms of publication impact. Strategic funding, capital and campus capital funding to institutes (£6m, £73m and £30m respectively) is used to maintain skills and output in economically important areas of research at the institutes; though Hunter made it clear that ‘blue sky’ research, funded via responsive mode, is important for impact as it generates both top REF scores and top impact metrics. BBSRC also invests £29M per year in specific initiatives.

When asked for advice about increasing BBSRC funding to the department, Hunter emphasised that funding allocation is based on excellence, so departments should provide an environment where excellence can flourish. She also said, “Interdisciplinarity is important: breakthroughs will happen where disciplines coalesce.”

Training and skills

There are around 2000 PhD students at any one time in the Doctoral Training Partnerships that make up part of the £71M BBSRC investment in Knowledge Exchange, Training and Skills. During the discussion session, someone asked about support later in a researcher’s career and Hunter pointed out that investment in early career fellowships must come at the expense of something else. She suggested that BBSRC may consider the value of studentships versus early career fellowships carefully, and in consultation with the community, over the next few years.

Plant science and Agriculture

Jackie Hunter is on the Agri-tech Leadership Council, which aims to increase UK agricultural exports and the value of the UK agri-tech industry by aligning public and industry funding and building skills and research output in agriculture and agri-technology. She also spoke about future directions in BBSRC’s Agriculture and Food theme: improving the nutritional qualities of plants and biopesticides regulation are both likely to become priority areas of research.

Hunter trailed two documents intended to help make two arguments, both of value to the UK plant research community. The first is an upcoming review on animal and plant health, lead by Defra and with input from BBSRC. To be launched later this month, it will be a starting point for BBSRC and Defra to develop joint strategies in tackling current animal and plant health issues, and to work together to call for more funding in this area. The second is a discussion document about synthetic biology and other new ways of working; Hunter hopes this will help make the case for trait-based, rather than methods-based, regulation of new crops.

On-going activities

Hunter also highlighted a few current initiatives our readers might be interested in.

BBSRC has invested £18m in 13 Networks in Industrial Biotechnology and Bioenergy (NIBBs). Here at GARNet, we’re in touch with the High Value Chemicals from Plants Network about a synthetic biology event next year and I recommend you join (it’s free) if you’re interested in high-value plant products or synthetic biology. The other plant science network is the Lignocellulosic Biorefinery Network.

One of Hunter’s objectives as CEO is to promote dialogue between scientists and a broad audience, and the first step towards engaging with the general public is the Great British Bioscience Festival. It is taking place this Friday, Saturday and Sunday in Bethnal Green, London, and there will be some amazing plant science among the exhibits. Lisa will be visiting the Festival to cover it for the next issue of the GARNish newsletter so stay tuned for her report!

Arabidopsis Research Round-up

Just one new paper to share with you this week!

 

  • Binkert M, Kozma-Bognar L, Terecskei K, de Veylder L, Nagy F and Ulm R. UV-B-responsive association of the Arabidopsis bZIP transcription factor ELONGATED HYPOCOTYL5 with target genes, including its own promoter. The Plant Cell, 28 October 2014. DOI: 10.1105/tpc.114.130716. [Open Access]

Though he has a joint appointment at the Hungarian Academy of Sciences, Ferenc Nagy is also SULSA Chair of Cell Biology at the University of Edinburgh. Working with Swiss, Hungarian and Belgian colleagues, this paper describes research to understand the transcription factors regulating plants’ protective responses to UV-B. It is shown that, in Arabidopsis, binding of the bZIP transcription factor ELONGATED HYPOCOTYL5 (HY5) to the promoters of UV-B-responsive genes is enhanced by UV-B independently of the UV-B photoreceptor UV RESISTANCE LOCUS8 (UVR8).

Arabidopsis Research Round-up

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Published on: October 30, 2014

It’s all about Norwich Research Park this week as Jonathan Jones, Dan MacLean (The Sainsbury Laboratory) and Caroline Dean (John Innes Centre) take the lead on this week’s papers. As a bonus, they’re all open access!

 

  • Sohn KH, Segonzac C, Rallapalli G, Sarris PF, Woo JY, Williams SJ, Newman TE, Paek KH, Kobe B and Jones JDG. The nuclear immune receptor RPS4 is required for RRS1SLH1-dependent constitutive defense activation in Arabidopsis thaliana. PLOS Genetics, 23 October 2014. DOI: 10.1371/journal.pgen.1004655. [Open Access]

While it is known that plant nucleotide-binding leucine-rich repeat (NB-LRR) disease resistance proteins recognise specific ‘avirulent’ pathogen effectors and activate immune responses, the mechanisms by which they do this are not well understood. This article challenges previous hypotheses and advances our understanding of how immune receptors activate defense in Arabidopsis.

 

  • Younsi R and MacLean D. Using 2k + 2 bubble searches to find single nucleotide polymorphisms in k-mer graphs. Bioinformatics, 24 October 2014.DOI: 10.1093/bioinformatics/btu706. [Open Access]

In this Bioinformatics paper, Younsi and MacLean from The Sainsbury Laboratory describe how they used sequence data from 16 Arabidopsis thaliana ecotypes to test and validate an algorithm capable of accurately detecting single nucleotide polymorphisms from de Bruijn graphs.

 

  • Csorba T, Questa JI, Sun Q and Dean C. Antisense COOLAIR mediates the coordinated switching of chromatin states at FLC during vernalization.Proceedings of the National Academy of Sciences of the USA, 27 October 2014. DOI: 10.1073/pnas.1419030111. [Open Access]

In previous work, Caroline Dean and colleagues from the John Innes Centre showed that expression of FLOWERING LOCUS C (FLC) is regulated epigenetically by modifications to the histones: accumulation of H3K36me6 causes FLC to be expressed, thus applying a ‘brake’ to flowering, while accumulation of H2K27me3 removes the brake. However, this is not the whole story, and now the Dean lab has identified another component of the mechanism – antisense non-coding RNA transcripts calledCOOLAIR.

You can read more about this story in this press release: Plants require COOLAIR to flower in spring.

All-expenses-paid networking in Thailand, Mexico, Brazil or Turkey …

Categories: funding, plant pathogens
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Published on: October 28, 2014
Screen Shot 2014-10-28 at 13.28.28
Plaza de Guanajuato, Mexico. By Jose Carlos Soto.

Do you fancy an all-expenses-paid trip to a meeting where you can present your work, network with senior researchers in your field, get inspired and eat good food in the sun? If you’re a UK-based early career researcher (of any nationality), it might be closer than you think.

And if the days of your ‘early career’ are past, applications are still being accepted for funding to run similar events.

There are four Researcher Links workshops open for applications at the moment:

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Plant synthetic biology takes centre stage

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Published on: October 27, 2014

On Monday and Tuesday last week I was at the Marriott Heathrow for the Global Engage Synthetic Biology Congress. Plant synthetic biology had a dedicated track, and while this meant I regretted missing some talks in the other sessions, it did enable me to be suitably impressed at the quality of plant synthetic biology research, mostly coming from the UK and Europe, and its exciting range of applications.

Plant synthetic biology at Global Engage

A highlight for me was Matias Zurbriggen’s excellent presentation on using plant signalling pathways to remotely control mammalian cells. His objective is to understand plant pathways by reconstructing them in other systems, and via research on phytochromes he has developed a tool to remotely control gene expression in mammalian cells (1) and a light-controlled switch for plant cells (2).

Birger Lindberg Møller gave an interesting and accessible talk about plant synthetic biology for high value product (HVP) synthesis. Whatever your level of expertise, if you’re interested in this area I recommend you watch this earlier version of his talk.

Continuing the HVP theme were Brian King, Vincent Martin and plenary speaker Jules Beekwilder. They all aim to make HVPs using simple chassis instead of relatively energy-intensive, and often inefficient, plants. (more…)

Arabidopsis Research Round-up

There are three new and exciting Arabidopsis papers from the UK research community this week. The University of Bath makes two appearances, once with a Genetics paper, and once in collaboration with the University of Oxford in Genome Research. Representing Norwich this week, Jonathan Jones heads up a Sainsbury Lab/John Innes Centre collaboration to investigate simultaneous changes in gene expression between Arabidopsis and a pathogen.

 

  • Gnan S, Priest A and Kover PX. The genetic basis of natural variation in seed size and seed number and their trade-off using Arabidopsis thalianaMAGIC lines. Genetics, 13 October 2014. DOI: 10.1534/genetics.114.170746.

This team from the University of Bath explored the natural variation in genes affecting seed size and seed number in Arabidopsis. Both seed size and seed number were found to be affected by non-overlapping QTLs, therefore suggesting these two traits can evolve independently of each other. Trade-off between these two traits in terms of fecundity and yield is dependent upon life history traits.

 

  • Jiang C, Mithani A, Belfield EJ, Mott R, Hurst LD and Harberd NP. Environmentally responsive genome-wide accumulation of de novo Arabidopsis thaliana mutations and epimutations. Genome Research, 14 October 2014. DOI: 10.1101/gr.177659.114. [Open Access]

GARNet committee member Nick Harberd led on this Genome Research paper, along with co-corresponding author Caifu Jiang from China, and colleagues from theUniversity of Bath and Pakistan. In animal cells, repeated or prolonged presentation of a stressor often leads to increased mutations, which can increase the risk of cancer. Being sessile, plants do not get cancer in the same way that humans do, but do they acquire more mutations? Does stress – here the example of high soil salinity is used – drive the evolution of plants through increased phenotypic diversity? Yes, it seems so.

 

  • Asai S, Rallapalli G, Piquerez SJM, Caillaud M-C, Furzer OJ, Ishaque N, Wirthmueller L, Fabro G, Shirasu K and Jones JDG. Expression profiling during Arabidopsis/downy mildew interaction reveals a highly expressed effector that attenuates responses to salicylic acid. PLOS Pathogens, 16 October 2014. DOI: 10.1371/journal.ppat.1004443. [Open Access]

Led by Jonathan Jones, scientists from The Sainsbury Laboratory in Norwich worked with Lennart Wirthmueller from the John Innes Centre, and two Japanese collaborators, to produce this PLOS Genetics paper. Though gene expression patterns have been studied independently in the pathogen Hyaloperenospora arabidopsidis, and in its host Arabidopsis thaliana, they have not been compared simultaneously. Using a high-throughput cDNA tag sequencing method, this paper describes simultaneous changes in gene expression profiles in both host and pathogen.

Data Mining with iPlant: Published

Categories: GARNet
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Published on: October 20, 2014

Data mining with iPlant

We have a new paper published! Lisa is first author on the report from last year’s Data Mining with iPlant workshop, published last week in the Journal of Experimental Botany.

As noted in the abstract, the paper ‘provides an overview of the workshop, and highlights the power of the iPlant environment for lowering barriers to using complex bioinformatics resources, furthering discoveries in plant science research and providing a platform for education and outreach programmes.’

The full reference for the paper is: Martin L, Cook C, Matasci N, Williams J and Bastow R (2014) Data Mining with iPlant: A meeting report from the 2013 GARNet workshop ‘Data Mining with iPlant’, Journal of Experimental Botany, DOI: 10.1093/jxb/eru402

You can view the paper via this toll-free link.

Don’t forget, all the tutorials from the workshop are available for anyone to use on the iPlant Wiki pages.

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