October 2014 - Weeding the Gems

Arabidopsis Research Round-up

Categories: Arabidopsis, Global, Open Access, 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 RRS1^SLH1-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 …

by Charis Cook

Categories: funding, plant pathogens

Tags: early career researchers, funding

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Published on: October 28, 2014

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:

(more…)

Plant synthetic biology takes centre stage

by Charis Cook

Categories: conferences, synthetic biology, teaching resources

Tags: conference, synthetic biology

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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

by Guest Blogger

Categories: Arabidopsis, Global, Round-up

Tags: Arabidopsis, arabidopsis thaliana, GARNet committee, genetics, genome research, John Innes Centre, Jonathan Jones, Nicholas Harberd, Paula Kover, PLOS Pathogens, The Sainsbury Laboratory, university of bath, University of Oxford

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Published on: October 23, 2014

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

by Charis Cook

Categories: GARNet

Tags: GARNet, GARNet workshop, iPlant, Journal of Experimental Botany

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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.

Arabidopsis Research Round-up

by Guest Blogger

Categories: Arabidopsis, Global, Round-up

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Published on: October 16, 2014

Two new UK Arabidopsis papers for your reading pleasure this week: a Plant, Cell & Environment paper involving researchers from Hull and York, and a New Phytologistpaper proposing a new model of flowering time in annual plants, which involved Oxbridge scientists.

Atkinson LJ, Sherlock DJ and Atkin OK. Source of nitrogen associated with recovery of relative growth rate in Arabidopsis thaliana acclimated to sustained cold treatment. Plant, Cell & Environment, 8 October 2014. DOI: 10.1111/pce.12460.

Lindsay Atkinson from the University of Hull’s Geography Department worked with York biology research technician David Sherlock and an Australian plant scientist on this paper in Plant, Cell & Environment. The team looked at whether plants acclimated to the cold were able to recover their previous relative growth rate, and if so, whether soil N status played a part in the plant’s efficiency of doing this. It was found that both increased N use efficiency and increase in nitrogen content per se play a role in the recovery of carbon metabolism in the cold.

Guilbaud CSE, Dalchau N, Purves DW and Turnbull LA. Is ‘peak N’ key to understanding the timing of flowering is annual plants? New Phytologist, 8 October 2014. DOI: 10.1111/nph.13095. [Open Access]

A previously prevailing theory suggests that flowering time in annual plants has evolved over evolutionary time to maximize fitness over a particular season length. However, in this paper a team from Oxford, Cambridge and Zurich propose a new model whereby flowering time is instead underpinned by peak uptake of nitrogen. Using mathematical models, and comparing against data collected from Arabidopsis thaliana, the researchers predict that flowers will never emerge after ‘peak N time’, and suggest further correlations between flowering time, vegetative growth rates and response to increased N availability.

Also spotted: acknowledgements for behind-the-scenes contributions from GARNet committee members Antony Dodd (Bristol) and Nick Harberd (Oxford).

GARNet 2014 presentations available online

by Guest Blogger

Categories: Arabidopsis, conferences, GARNet

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Published on: October 15, 2014

As you’ll already know, we held our GARNet 2014 conference, Arabidopsis: The Ongoing Green Revolution, at the University of Bristol on the 9th and 10th September. If you didn’t know, you can read Charis’ report on it by clicking here to go to the main GARNet website, or here to see some photos!

Some of the researchers who spoke at our conference have kindly agreed to share their GARNet 2014 presentations with you online – please click the links in the programme below to view or download a PDF copy of the speaker’s slides.

Programme

Session 1: Physiology & Productivity

Alistair Hetherington, University of Bristol: The response of stomata to environmental signals
Miriam Gifford, University of Warwick: Understanding plant root developmental plasticity using cell-specific genomes
Steve Penfield, University of Exeter: A cryptic switch formed by external temperature coincidence generates a life history strategy for Arabidopsis
Beatriz Lagunas, University of Warwick: The AtSCL26 transcription factor controls cross-talk between GA- and Nitrogen- control of root architecture in Arabidopsis thaliana roots

Session 2: Genome Biology

Siobhan Brady, University of California, Davis, USA: Getting to the root of things: spatiotemporal gene regulatory networks in plant roots
Ian Henderson, University of Cambridge: Unravelling interactions between genetic diversity and recombination in Arabidopsis
Antony Dodd, University of Bristol: Circadian signalling between subcellular genomes
Emily Hawkes, John Innes Centre: Evolutionary conservation of an Arabidopsis long non-coding RNA, COOLAIR, supports a regulatory function

Session 3: Natural Variation

Maarten Kournneef, Max Planck Institute for Plant Breeding Research, Germany: Exploring Arabidopsis natural variation
Adrian Brennan, University of Durham: Population genetic strcuture and natural variation of the model plant Arabidopsis thaliana in its native southern range extremes
Javier Agusti, University of Oxford: Using natural variation to identify new cambium regulators
Monika Mierzwinska, University of Aberdeen: Natural variation in endodermal development and plant mineral nutrient homeostasis

Session 4: Systems and Synthetic Biology

Session 5: Plant Interactions with their Environment

Paul Schulze-Lefert, Max Planck Institute for Plant Breeding Research, Germany: Functions of the Arabidopsis bacterial root microbiota in plant health
Cyril Zipfel, The Sainsbury Laboratory, Norwich: Regulation of early receptor kinase-mediated immune signalling
Kerry Franklin, University of Bristol: Sunlight, photoreceptors and plant development
Sophie Berckhan, University of Nottingham: Why do plants sense oxygen?

Onwards and Upwards for the Global Plant Council

by Charis Cook

Categories: biofortified foods, Global, UKPSF

Tags: global plant council, news, UKPSF

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Published on: October 14, 2014

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…)

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