GARNet goes global with the Global Plant Council

If you follow me on Twitter (@GARNetweets) then you’ll know that I’ve been out of the office quite a lot recently, attending a variety of conferences.

Charis has already blogged about our trip to Manchester for the Society of Experimental Biology conference a couple of weeks ago, but I’ve also been helping out our colleague Ruth Bastow at some conferences further afield.

The Global Plant CouncilAs well as being GARNet’s part-time co-ordinator, Ruth is also Executive Director for the Global Plant Council (GPC) – a coalition of global crop and plant science societies that aims to connect the wealth of knowledge and expertise from around the world to help find solutions to global plant science challenges.

The GPC is focusing on three priority initiatives: firstly the creation of a Digital Seed Bank, which aims to capture and exploit the wealth of diversity in crop collections around the globe. The Digital Seed Bank is part of larger project; the Diversity Seek Initiative (DivSeek), whose mission is to unlock the potential of crop diversity stored in genebanks around the world and make it available to all so that it can enhance the productivity, sustainability and resilience of crops and agricultural systems.

This is an ambitious project and will need to tackle problems such as how to tag or assign a DOI to genetic resources, just as you can to a journal paper. If this can be done, scientists will be able to trace published work or data back to a single seed, accession or group, and know where they can find and access that germplasm to cross-reference and compare data. A grand aspiration, but aim high and you never know what you might achieve!

GPC is also working to join up global research and policy in the areas of biofortification and stress resilience. There are many scientists across the globe working on the improvement of crops, whether by traditional or marker assisted breeding, or using GM or synthetic biology technologies – wouldn’t it be great if we could facilitate better global collaborations on these projects?

The Convention Centre Dublin, or The Coke Can, to its friends!
The Convention Centre Dublin, or The Coke Can, to its friends!

The GPC is made up of (at present) 28 member organisations, including some big players such as the American Society of Plant Biologists (ASPB), the European Plant Science Organisation (EPSO), the Society for Experimental Biology (SEB) and our own UK Plant Sciences Federation (UKPSF).

As members of these societies, many researchers are also members of the GPC by default – whether they realise it or not! To help spread the word to these organisation’s members, I’ve been helping Ruth to man (woman?) an exhibition booth.

So first we flew off to Dublin and attended EPSO’s Plant Biology Europe 2014 conference (23–26th June). This was held at the Convention Centre Dublin in Ireland (known locally, I’m reliably informed, as the ‘Coke Can’!).

Delegates at the EPSO conference came from all over the world
Delegates at the EPSO conference came from all over the world

Our booth was well attended and generated lots of interest from not just European plant scientists as you might expect, but also the global community. Rather than just collecting email addresses in a list, we collected business cards, or got people to fill in a GPC card, and pinned them to a world map so we could see exactly how ‘global’ the GPC’s reach is – I was surprised to meet delegates in Dublin from as far afield as Africa, Australia and New Zealand!

As well as working on the booth, we also had the opportunity to hear some great talks, including a public evening lecture given by Charles Godfray from Oxford University. Charles put a population biologist’s twist on ‘The Challenge of Global Food Security”; lamenting our ‘Malthusian pessimism’ about the need to feed 10 billion people by 2050 and resistance to technologies that might allow us to do this, Godfray said that failure is not an option – “If we fail to have food security, everything will fail,” he said. A sobering thought!

Portland is known for being a bit on the "alternative" side
Portland is known for being a bit on the “alternative” side

After Dublin, and a week in Manchester at SEB, I was back on the plane again; this time heading to Portland in Oregon in the US’s pacific northwest. After a few days’ holiday exploring this very cool ‘hipster’ city and sampling the infamous Voodoo Donuts, Ruth and I set up our GPC booth, this time at the Oregon Convention Centre for the ASPB Plant Biology 2014 conference.

As you can see from the map we generated this time, it was a different demographic who visited the booth; mostly researchers from the US, Canada and western Europe, although we did speak to a few people from Asia and Latin America too. The GPC’s giveaway pens went down a treat here and I came home with only one left!

Our Global Plant Council map at the ASPB conference
Our Global Plant Council map at the ASPB conference

Again, I found some time between exhibit sessions to attend a few talks, and was particularly impressed by journalist/food writer Nathanael Johnson, winner of the ASPB award for Leadership in Science. He spoke about the challenge of communicating science to the public, arguing “facts are not enough”. The big issues in science, he said, are simply too big and too complex for people to grasp, so instead they will grasp at small pieces of information they can understand – and this is often how things like the anti-vaccination movement, or anti-GM campaigners get started. Building trust between scientists, industry and the public is of huge importance, because simply giving people piles of ‘evidence’ has no impact a) if people do not understand it, and b) if there is an assumption that it is inaccurate or they are being misled.

Ruth in the Booth
Ruth in the Booth

So now I’m back in the GARNet office (though the weather here in Coventry is just as hot as it was in Portland!) but only for a week. This weekend the whole GARNet team is off to Vancouver for the International Conference on Arabidopsis Research (ICAR), so stay tuned for more blog posts and tweets from Canada!

SEB 2014: The future is bright in the Plant Section

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Published on: July 1, 2014

Lisa and I are at the Society of Experimental Biology’s 2014 (SEB 2014) conference this week. The highlight so far was the first session, when the Plant Section gathered for talks from their President’s Medallist Cristobal Uauy and three Young Scientist Award Finalists: Beth Dyson, Caroline Upton, Stephanie Johnson.

Cristobal Uauy spoke first about his career and work on wheat genetics. He was frank about the difficulties of working with wheat, but said, “I’m not going to complain about how difficult it is to work on wheat, and blah blah blah … because actually it’s getting much better.”

This optimism was sustained throughout Cristobal’s talk. He aims to improve yield in wheat, and has found a trait that increases grain width by what looks like a tiny amount – but the difference adds up very quickly. Over 20 grains, you gain the equivalent of one whole grain. Scaled up to a field, this trait would give an extra 700 loaves of bread. This is certainly something to be proud of, yet Cristobal is excited about increasing this 5% difference to 20% or 30%. His current trait is the result of a mutation on just one copy of the gene – he hopes to find and modify its homologues on the other ancient genomes that make up the huge modern wheat genome.

Cristobal is keen to promote crop research. He pointed out that Arabidopsis dwarfs all other plant species at SEB meetings, yet the current focus on food security in the plant science community necessitates breakthroughs in crop science. At GARNet obviously we have Views on this, but as Cristobal said at the beginning of his talk, “A huge number of people all over the world eat wheat – so anything we can do to improve wheat will have a huge impact.”

Cristobal is a member of the SEB Plant Section Committee, and has started a new sub-group within the Plant Section entitled Crop Molecular Genetics. If you’re interested in getting involved, I’m sure he’d love to speak to you.

The Young Scientist Award Finalists also gave inspiring talks:

  • Beth Dyson measured metabolite, amino acid and organic acid levels in Arabidopsis plants grown in optimum and cold conditions. She has identified key mechanisms that enable photosynthesis to respond to low temperatures.
  • Caroline Upton’s research on barley roots is laying the groundwork in transparent soil methodology. She finds it far easier to analyse images from roots grown in transparent soil than the CT images she initially had to work with.
  • Stephanie Johnson outlined her PhD project on the molecular mechanisms that gives Stay-Green Sorghum its desirable trait. She spent 3 months with experts at the University of Queensland generating transgenic sorghum and is now waiting to confirm the hypothesis developed from her early models.

The President’s Medal and the Young Scientist Awards are both intended to reward and encourage early career excellence and the speakers were all worthy of this recognition. The UK plant sciences community rightly speaks out regularly about funding cuts and skills gaps, but this morning’s session was a refreshing celebration of the talent our community produces and nurtures.

June GARNish is here!

Categories: conferences, GARNet
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Published on: June 19, 2014

GARNish 21 cover 1000

The June edition of GARNish is now available to download! Open up (or scroll down) for:

  • The latest news and views from our community
  • A report from our April Software Carpentry Bootcamp
  • A guide to finding and sharing microarray data on GEO
  • A list of equipment funded by the ALERT13 bid
  • An overview of the OpenPlant synthetic biology centre
  • An introduction to the great outreach work of the British Society of Plant Pathologists
  • Spotlights on the University of Worcester and Queen’s University Belfast

Travel grants 2014

Categories: conferences
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Published on: February 18, 2014

It’s that time of year when conference registrations are open and early bird deadlines are coming up fast. If you want to go to one but are unsure about the cost, take a look at the travel grants below. They all have fairly simple application processes and several deadlines throughout the year, but get your applications in within the next few weeks for summer conferences.

Remember, if you’re a student, you can use your training grant to pay for conference fees and travel. Attending and presenting posters or talks at conferences is an important part of a PhD studentship.

  • Company of Biologists travel grants from the Society of Experimental Biology: Deadlines 31 March, 30 June, 30 September, 31 December 2014. Funding to attend a UK (£250) or international (£500) conference. You have to be a member of SEB, or to buy a multi-year membership, to apply.
  • Honor Fell travel award from the British Society for Cell Biology, sponsored by the Company of Biologists: Rolling deadline. Up to £300 for UK meetings and more for international travel is available to students and post-docs.
  • Biochemical Society travel grant: 7 deadlines throughout 2014 – submit as early as possible. Members of the Biochemical Society can apply for a travel grant of up to £750 to attend a meeting.
  • British Society of Plant Pathology travel grants: Deadlines 28 Febrary, 31 May, 31 August, 30 November 2014. Travel funds are available for BSPP members to assist with expenses for conferences, study tours and visits. The amount available varies, but will not be more than half the cost of your trip.
  • Society of Biology travel grants: Students and early career researchers can apply for £500 for overseas travel in connection with biological study, teaching, research, or attending a conference.
  • Genetics Society Conference Grants: Deadlines 1 May, 1 August, 1, November. Up to £750 is available to PhD students and post-docs within two years of their viva to cover travel, accommodation, and registration cost for conferences and meetings. Also, up to £150 is available for travel to Genetics Society meetings.

Why not try and get some funds to attend UK conferences PlantSci 2014 (£200 is up for grabs for the best student/postdoc talks!), SEB 2014 or our very own GARNet 2014?

Recently in the GARNet community…

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Published on: January 24, 2014

GARNet news

Lisa and I went to the Brassica Growers Association Conference on Tuesday. I wrote two posts on it over on the UK-BRC website, and Lisa put together a very informative Storify of tweets on the #BGAconference stream.

The UK Plant Sciences Federation has been collecting opinions, facts and data for the past year or so and is now ready to launch a report entitled UK Plant Science: Current Status and Future Challenges. Lisa and I helped out with this report so keep an eye out for it on Tuesday and let us know what you think!

I went to the SEB Synthetic Biology conference last week and have written a short report for the SEB Bulletin about it – I’ll share it when it is published. There was some excellent plant science there. Antonio Scialdone presented the plant-arithmatic work from Martin Howard’s lab – you can read his open access 2013 paper modelling starch degredation over night here (Scialdone et al., eLife 2013;2:e00669). Oliver Ebenhoeh discussed how mathematical models for photosynthesis and plant metabolism can help synthetic biology be done in plants and other photosynthetic organisms.

 

On the GARNet website

If you missed some January funding deadlines, there are plenty more opportunities to submit your proposal – take a look at the funding round-up on our website for ideas for fellowships, travel, collaborations or straightforward research grants.

Lisa is continuing to write her weekly Arabidopsis research round-up, which you can find on the GARNet news pages. It’s the best way to keep informed of what fellow UK Arabidopsis researchers are up to. This week, papers from GARNet committee members Heather Knight and Cyril Zipfel feature.

 

Your chance to present your work

PlantSci 2014 is in York on 31 March/1 April, and abstract submission is open until the end of February. There are two £200 cash prizes to be won by early career researchers giving short talks, so make sure you submit an abstract! There won’t be a traditional poster session, but delegates are invited to bring mini-posters to discuss during the networking sessions. Abstracts for the mini-posters will be included in the abstract book.

Further away in September, GARNet 2014 is your second chance to present your work at either a poster session or as a short talk. Registration and abstract submission are both open, and news about special opportunities for students will be coming very soon.

Finally, I’ve been reliably informed that the FSPB/EPSO Plant Biology Conference organisers are looking for proposals for short talks for the Big Data in Plant Science session, so if you’re planning on going and do ‘big data,’ think about submitting an abstract!

Register now for GARNet’s 2014 events

We have been busy arranging two great events for 2014! Registration for both Software Carpentry for Plant Scientists (9-10 April) and Arabidopsis: The Ongoing Green Revolution (9-10 September) is now open.

 

On 9-10 April we are hosting a Software Carpentry bootcamp for plant scientists – an Introduction to Programming for Biologists. For those of you who don’t know about Software Carpentry, it is a foundation that teaches good practice in scientific computing, with the aim of providing all scientists with basic, but reliable and transferable, programming skills. If you’ve ever run through the rain to Computing to have a large ChIP-chip dataset split so you can attempt an Excel analysis on it, you’ll know how valuable that is (based on real events – feel free to insert your own experiences there …)!

We’ve worked with the Software Sustainability Institute to develop a programme suitable for both complete beginners and scientists how know their way around the Terminal/Command Prompt but want to improve their skills and learn how to write reliable, re-usable code they can share with their colleagues and collaborators. Registration is £50 and discounted on-campus accommodation is available.

 

Later in the year, the GARNet general meeting is returning for one time only on 9-10 September at the University of Bristol. Our theme is ‘Arabidopsis: The Ongoing Green Revolution’. We have a line up of excellent speakers, including plenary talks from Alistair Hetherington (University of Bristol), Andrew Millar (University of Edinburgh), Rob Martienssen from Cold Spring Harbor Laboratories, and Paul Schulze-Lefert and Maarten Koornneef from the Max Planck Institute for Plant Breeding Research. 

The full line-up and registration details can be found by visiting www.garnet2014.org. More information will appear on there closer to the time of the conference. Registration costs £150 for two days, lunch and refreshments on both days, and a drinks reception on the afternoon of 9 September. We’d also love to see you at our conference dinner on the evening of the 9 September at the Bristol Marriott Royal Hotel (£44 per head for three courses and wine on the tables).

Plant research goes EPIC

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Published on: October 25, 2013
A DNA molecule that is methylated on both strands on the center cytosine. DNA methylation plays an important role for epigenetic gene regulation in development

Early last week I attended the EPIC (Epigenomics of Plants International Consortium) one day symposium on Mapping the Epigenomes of Plants and Animals at the John Innes Centre. Epigenomics is an exciting branch of biology, with active, cutting-edge research ongoing in plants, animals and microbes alike.

The EPIC Planning Committee aim to crack and control the ‘second code’ of biology (they overview the field and their plans in a 2012 open access Plant Cell paper). A major step toward this ambitious goal is the CoGe Epigenomics Browser, a web-based comparative genomics system that provides access to 20,000 genomes from 15,000 organisms, and users can take advantage of over 30 tools for the analysis, comparison, and visualisation of genomic data from the scale of whole genomes to individual nucleotides. The creators of CoGe, Eric Lyons and Brian Gregory, have worked with iPlant to build a secure and versatile user-data management system, and like iPlant CoGe has a Wiki with extensive tutorials and support pages.

The biggest session at the Symposium was on DNA methylation. Gavin Kelsey, Mary Gehring and Rob Martienssen, who is speaking at GARNet 2014, spoke about the mechanisms of parental imprinting and their impact, which can continue for generations – and I have to say, at this point I wondered how many lab conflicts and frustration-inducing experimental problems are caused by our current lack of understanding about epigenomic effects!

Julie Ahringer and Doris Wagner spoke about their research digging down into the physical properties of epigenomic features and the mechanisms of chromatin regulation. Oliver Stegle and Claude Becker are both working on understanding how genome, transcriptome, epigenome and environment interact to produce a phenotype. Xiaofeng Cao is applying this approach to controlling agricultural traits in rice.

There were a few non-plant science speakers, including Eric Miska who presented his research on piRNAs, which he has shown are vital for maintaining fertility over generations and are also involved in sperm production. Interestingly Blake Meyers has identified phasiRNAs in maize, small RNAs that are involved in sperm production and he suggested they may have convergently evolved to fulfil a similar role as piRNAs.

Image credit: Christoph Boch via Wikimedia Commons. “Details: The picture shows the crystal structure of a short DNA helix with sequence “accgcCGgcgcc”, which is methylated on both strands at the center cytosine.”

 

AHDB Crop Research Conference: Knowing your enemy

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Published on: October 9, 2013

GARNet Research and Engagement Officer Lisa Martin reports on the AHDB Crop Research Conference.

On 25 September, I hopped on the train down to London to attend the Agriculture and Horticulture Development Board (AHDB)’s Crop Research Conference. This event set out to bring together researchers and the agricultural industry “to take the latest research out of the laboratory and into the field”. The theme for the day was “Knowing your enemy – the future of crop protection” and speakers were divided into three categories.

In ‘Advances in Genomics’ we heard from Lin Field from Rothamsted Research, who spoke about her work in insect genomics. Paul Birch from the James Hutton Institute also provided insights into Phytophthera pathogenomics and disease resistance, while Rick Mumford from the Food and Environment Research Agency (FERA) spoke on the subject of advances in plant diagnostics.

In particular, Dr Mumford highlighted the recent development of Loop-mediated isothermal AMPlification (LAMP) technology; a rapid, field-based diagnostic method of DNA amplification that has the ability to produce conclusive test results in as little as 10–15 minutes, and provides improvements over traditional PCR methods. He also spoke about how next generation sequencing (NGS) is being used to identify new plant viruses, especially a recent breakthrough in identifying a novel virus responsible for internal carrot browning.

On to ‘Population and Evolutionary Biology’. In this section, John Lucas from Rothamsted Research gave an update on the evolution of fungicide resistance, while Paul Nicholson from the John Innes Centre spoke on the subject of wheat resistance to Fusarium head blight. Rothamsted’s Stephen Parnell also gave a very interesting talk on how mathematical modelling can help predict the spread of pests and diseases through early warning surveillance.

Also in this section was a presentation by Paul Neve from the University of Warwick’s Crop Centre, which was on the subject of herbicide resistance in weeds. Dr Neve explained that low rate herbicide application allows for the selection of hereditary resistance traits in weeds, and once that resistance is endemic, it can have devastating effects. To this end, Dr Neve’s work mostly focuses on understanding the evolutionary processes that lead to resistance, as this, he believes, is the key to combating the outcomes of resistance.

L-R: Allan Downie, Jurriaan Ton, Alison Karley and panel Chair Keith Norman from Velcourt Ltd. Photo by Lisa Martin.

Lastly, after lunch, it was time for some ‘Lessons from Ecology’ and here presentations were given by Alison Karley, an agroecologist from the James Hutton Institute who works on optimising biocontrol; Jurriaan Ton from the University of Sheffield who brought us up to speed with recent advances in understanding and manipulating plant immunity; and finally Allan Downie from the John Innes Centre and co-ordinator of the Nornex consortium of scientists working on Ash Dieback disease.

A champion of open access, Professor Downie declared that “open access data will revolutionise science” and highlighted the ways in which crowdsourcing and citizen science are being used to understand Ash Dieback. These methods include the Facebook game Fraxinus that has allowed members of the public to help increase understanding of the Hymenoscyphus pseudoalbidus (a.k.a. Chalara fraxinea) genome, and the open access website OpenAshDieback, to which scientists are being encouraged to contribute data analysis and knowledge in the hope of, ultimately, limiting the impact of Ash Dieback.

To end on a high note over wine and canapés, the Science Minister David Willetts had been invited to present awards to the winners of a PhD student poster competition. The deserving winner was Rachel Goddard from John Innes Centre whose work on finding alternative semi-dwarfing genes that confer yield benefits to crop plants without compromising plant immunity caught the judges’ eyes. Congratulations, Rachel!

I live-tweeted throughout the conference, so please check out @GARNetweets for more insights, or search Twitter for #AHDBconf. You can also find the poster and speaker abstracts, and the speaker presentations, on the HGCA website here, and photos of the event are here.

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