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.

Investment in plant science training

Categories: funding
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Published on: October 7, 2014

The planet needs more plant scientists.

As a headline in The Scientist last week, this statement was unambiguously qualified by its ‘Opinion’ prefix. But for the UK plant sciences community it is a dangerous fact: the skills gaps in plant and agricultural sciences expertise and very limited plant science content on undergraduate courses were highlighted in the UKPSF report on the status of UK plant science.

The news that some 375 students will receive PhD training in agriculture and food security over the next five years is therefore very welcome. On Friday, Vince Cable announced the locations of 12 new Doctoral Training Partnerships, funded by a £125 million investment from BBSRC. 1250 PhD students will be trained, of which 30% (375) will be trained specifically in agricultural and food security science, 20% (250) will focus on industrial biotechnology and bioenergy, and 40% (500) on world-class ‘frontier’ bioscience – all areas in which plant science plays a key role. The remaining 10% (125) of students will work within BBSRC’s ‘Bioscience for Health’ theme.

We at GARNet are looking forward to seeing the impacts on plant science, from food security and bioenergy to the as yet unknown, that will come from the hundreds of plant scientists starting their training and careers in the next few years. As every student in the centres will have to do a funded three-month internship working in a different area from their PhD project, it will also be interesting to see how this impact spreads into areas like policy, funding and government over time.

Congratulations to all the organisations involved in the new Centres, lead by Imperial College London, the John Innes Centre, Newcastle University, University College London (not plant science), the University of Bristol, the University of Cambridge, the University of Edinburgh, the University of Leeds, the University of Manchester, the University of Nottingham, the University of Oxford and the University of Warwick.

Arabidopsis Research Round-up

Apologies there hasn’t been an Arabidopsis Research Round-up for a few weeks, I’ve been on annual leave getting married! Here’s a catch up of the newest Arabidopsis research papers from the UK community over the last month, including one from a GARNet committee member, and one from a former GARNet PI.

 

  • Schatlowski N, Wolff P, Santos-González J, Schoft V, Siretskiy A, Scott R, Tamaru H and Köhler C. Hypomethylated pollen bypasses the interploidy hybridization barrier in Arabidopsis. The Plant Cell, 1 September 2014. DOI: 10.1105/tpc.114.130120.

Rod Scott from the University of Bath was involved on this Plant Cell paper. With Swedish, Austrian and Swiss colleagues, it was identified that, through the suppression of expressed imprinted genes, hypomethylation can occur in pollen that alters the epigenetic control of the ‘interploidy hybridization barrier’. Based on these findings, the researchers here present a novel method for the generation of viable triploid Arabidopsis plants, which could have significant impact for plant breeding.

 

  • Chew YH, Wenden B, Flis A, et alMultiscale digital Arabidopsis predicts individual organ and whole-organism growth. Proceedings of the National Academy of Sciences of the United States of America, 2 September 2014. DOI: 10.1073/pnas.1410238111. [Open Access]

You can tell former GARNet PI Andrew Millar from the University of Edinburgh led this paper – it’s all about linking the Arabidopsis research community! Quantitative modeling is undeniably an important tool in modern predictive biology, but understanding plants at a molecular level doesn’t necessarily help us to ‘bridge the genotype to phenotype gap’ and predict how molecular changes affect the whole organism, or vice versa. Linking together several models across multiple scales, Millar and colleagues here present a validated multiscale model of Arabidopsis rosette growth, enabling prediction of how genetic regulation and biochemical dynamics may affect organ and whole-plant growth.

 

  • Chao D-Y, Baraniecka P, Danku J, Koprivova A, Lahner B, Luo H, Yakubova E, Dilkes BP, Kopriva S and Salt DE. Variation in sulfur and selenium accumulation is controlled by naturally occurring isoforms of the key sulfur assimilation enzyme APR2 across the Arabidopsis thaliana species range. Plant Physiology, 18 September 2014. DOI: 10.1104/pp.114.247825. [Open Access]

GARNet committee member and ‘Mr Ionomics’ David Salt, from the University of Aberdeen, was the lead on this new paper in Plant Physiology, working with colleagues from the John Innes Centre, Purdue, Cologne and Shanghai. This study used linkage mapping in synthetic F2 populations to investigate the natural variation in total leaf sulphur and selenium levels across a wide range of Arabidopsis thaliana accessions. Though the significance is not yet understood, it was found that the catalytic capacity of APR2, an enzyme important in allowing the accumulation of sulphur and selenium in leaves, varied by four orders of magnitude.

 

  • Fujikura U, Elsaesser L, Breuninger H, Sanchez-Rodriguez C, Ivakov A, Laux T, Findlay K, Persson S and Lenhard M. Atkinesin-13A modulates cell wall synthesis and cell expansion in Arabidopsis thaliana via the THESEUS1 pathway. PLOS Genetics, 18 September 2014. DOI: 10.1104/pp.114.247825. [Open Access]

For plants to grow they need to not only proliferate their cells, but expand the size of the cells too. Since plant cells are encased in a rigid cell wall, the cell wall structure must be temporarily loosened to allow expansion and the deposition of additional cell wall materials. Working with a German-led team and colleagues in Australia, Kim Findlay from the John Innes Centre contributed to this paper, which discusses the roles of AtKINESIN-13-A and its homologue AtKINESIN-13B in limiting cell expansion and size in Arabidopsis thaliana.

 

  • Johansson H, Jones HJ, Foreman J, Hemsted JR, Stewart K, Grima R and Halliday KJ. Arabidopsis cell expansion is controlled by a photothermal switch.Nature Communications, 26 September 2014. DOI: 10.1038/ncomms5848. [Open Access]

A second appearance in today’s Round-up for the University of Edinburgh’s Karen Halliday, and another paper discussing cell expansion. This time, this Nature Communications paper explores the finding that phytochrome B-controlled growth in the Arabidopsis hypocotyl is strictly regulated by temperature: a shift in temperature induces a dramatic reversal of response from inhibition to promotion of hypocotyl elongation by light.

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Welcome , today is Sunday, October 26, 2014