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

Categories: funding, plant pathogens
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Published on: October 28, 2014
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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

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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.

Arabidopsis Research Round-up

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 OxfordCambridge 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

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

Session 2: Genome Biology

Session 3: Natural Variation

Session 4: Systems and Synthetic Biology

Onwards and Upwards for the Global Plant Council

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

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

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

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

Arabidopsis Research Round-up

Categories: Arabidopsis, Global, Round-up
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Published on: October 9, 2014

It’s a strong week for the institutes this week with appearances in the Round-up from Rothamsted ResearchThe Sainsbury Laboratory and the John Innes CentreThe Sainsbury Laboratory at the University of Cambridge also gets a mention, as does the University of Glasgow also gets a mention with Emily Larson’s contribution to a newPlant Method.

 

  • Hsiao A-S, Haslam RP, Michaelson LV, Liao P, Napier JA and Chye M-L. Gene expression in plant lipid metabolism in Arabidopsis seedlings. PLOS One, 29 September 2014. DOI: 10.1371/journal.pone.0107372. [Open Access]

This paper was a collaborative effort between scientists from Hong Kong, and Richard HaslamLouise Michaelson and Johnathan Napier from Rothamsted Research. Using quantitative, real-time PCR analysis, the researchers investigated whether target genes associated with acyl-lipid transfer, b-oxidation and triacylglycerol synthesis and hydrolysis were under diurnal control in early seedling growth. A number of differentially expressed genes between two and five-day old seedlings suggest that yes, lipid metabolism in Arabidopsis seedling development is under diurnal control.

 

  • Paganelli L, Caillaud M-C, Quentin M, Damiani I, Givetto B, Lecomte P, Karpov PA, Abad P, Chabouté M-E and Favery B. Three BUB1 and BUBR1/MAD3-related spindle assembly checkpoint proteins are required for accurate mitosis in Arabidopsis. New Phytologist, 29 September 2014. DOI: 10.1111/nph.13073.

Marie-Cecile Caillaud, affiliated to The Sainsbury Laboratory and the John Innes Centre, contributed to this New Phytologist paper investigating protein interactions during plant mitosis. Though the spindle assembly checkpoint (SAC) has been studied extensively in metazoans and yeast, little is known about the roles of microtubule-associated proteins in plants. This research demonstrates the key roles that the Arabidopsis SAC proteins BRK1, BUBR/MAD3 and their associates play in ensuring chromosomes do not segregate before they have properly formed kinetochore attachments.

 

  • Lee S, Lee H-J, Jung J-H and Park C-M. The Arabidopsis thaliana RNA-binding protein FCA regulates thermotolerance by modulating the detoxification of reactive oxygen species. New Phytologist, 30 September 2014. DOI: 10.1111/nph.13079.

Working with Korean colleagues, Jae-Hoon Jung from The Sainsbury Laboratory at Cambridge University contributed to this paper in which the role of the RNA-binding protein FCA is discussed in terms of heat stress. The researchers found that transgenic plants over-expressing the FCA gene were resistant to heat stress, while FCAdefective mutants were sensitive to it. It is proposed that FCA induces thermotolerance by triggering antioxidant accumulations under heat stress conditions.

 

  • Larson ER, Tierney ML, Tinaz B and Domozych DS. Using monoclonal antibodies to label living root hairs: a novel tool for studying cell wall microarchitecture and dynamics in Arabidopsis. Plant Methods, 2 October 2014. DOI: 10.1186/1746-4811-10-30. [Open Access]

Calling all root biologists! Here’s a new Plant Method for live cell labeling of roots with monoclonal antibodies that bind to specific cell wall polymers. Developed by researchers from the US and also involving Emily Larson from the University of Glasgow, the protocol allows for direct visualization of cell wall dynamics throughout development in stable transgenic plant lines.

 

  • Yang L, Zhao X, Paul M, Zhu H, Zu Y and Tang Z. Exogenous trehalose largely alleviates ionic unbalance, ROS burst and PCD occurrence induced by high salinity in Arabidopsis seedlings. Frontiers in Plant Science, 03 October 2014. DOI: 10.3389/fpls.2014.00570. [Open Access]

This Chinese-led paper also involved Matthew Paul from Rothamsted Research, who provided data analysis and helped to prepare the manuscript. Here, the scientists demonstrate the ability of trehalose to improve Arabidopsis’ resistance to salt stress by regulating the redox state of the plant, as well as programmed cell death and distribution of ions.

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Welcome , today is Friday, October 31, 2014