The TREE of plant science education

Aurora Levesley is the Project Officer for the Gatsby Plant Science TREE. The TREE grew out of the Gatsby Plant Science Summer Schools as a means of sharing the valuable resources produced for and during the Schools. Here she discusses the value of the TREE’s online lectures, which are the subject of a current New Phytologist paper. 

David Beerling at the Gatsby Plant Science Summer School
David Beerling gives a lecture at the Gatsby Plant Science Summer School. This is one of many lectures that have been edited for interactive online delivery and shared on the Plant Science TREE.

The Plant Science TREE is a free online central repository of plant science educational resources. More than 90 research academics and publishers have contributed over 2000 resources, including online research lectures, research-led lecture slides, practicals, video clips and other resources on topical plant science. It was developed by the University of Leeds with funding from the Gatsby Charitable Foundation, and is currently used by scientists, educators and students from over 320 institutes worldwide.

Many students enter biological sciences courses with little interest in or knowledge of plants, and engaging students with plant science early in their studies is arguably an important step in reversing the decline in uptake of this vulnerable yet strategically important subject linked to food security and other globally important issues. Prof Alison Baker of the Centre for Plant Sciences at the University of Leeds, says of the TREE: “The aim is to put a tool in the hands of educators that will engage students in plant science and research, especially where expertise is becoming limited.”

Our recent study, published in New Phytologist, showed the online research lectures that form a large part of the TREE successfully engage undergraduates with plant science (Levesley et al 2014, New Phytologist Early View).

In this study, undergraduates from four UK universities were provided with links to online research lectures as part of their course. The lectures, filmed at the Gatsby Plant Science summer schools, were given by research leaders but pitched at a level to engage undergraduates and provided a first-hand insight into how discoveries are made and science is carried out.

Not only were the online lectures successful in engaging students with plant science and research in general, but students were unanimous in the opinion that they were a good way to learn about a subject. Interestingly the study also showed that the online viewing experience was comparable to watching the research lectures live.

These online undergraduate research lectures are freely available through the Plant Science TREE. Our study shows they represent a valuable plant science education tool to help lecturers and teachers introduce cutting-edge research examples that address globally relevant applied initiatives – as well as curiosity-driven research – to their students. As such they have the potential to change student attitudes to plant science, engage students in research and are able to reach a large and wide global student audience.

The full reference for the Plant Science TREE paper is: Levesley A, Paxton S, Collins R, Baker A and Knight CD. “Engaging students with plant science: the Plant Science TREE”, New Phytologist http://dx.doi.org/10.1111/nph.12905, published online ahead of print in June 2014.

 

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!

Effector-triggered defence: A new concept in plant pathogen defence

In June, a team of Brassica researchers from the University of Hertfordshire proposed a new classification for a type of plant defence mechanism: effector-triggered defence (ETD).

Henrik Stotz is first author of the paper describing ETD, currently In Press in Trends in Plant Science. He explains, “In the same way that humans have developed immune responses against human disease pathogens, crops can be bred for resistance against disease pathogens, but we need to improve our understanding of effective resistance mechanisms within plants. Our research enhances the traditional understanding of the plant defence system and describes a new concept, which is how plants protect themselves against the pathogens that grow in the space outside plant cells (the apoplast) – a new concept called effector-triggered defence or ETD.”

Traditionally, plant pathogen defence is broken into two broad forms: pathogen-triggered immunity (PTI) and effector-triggered immunity (ETI). PTI is the first action the plant takes against a pathogen and is triggered when the pathogen lands on the plant. The pathogen releases molecules called effectors into the plant cells, which the plant recognises and reacts against. If the effectors are not recognised, the pathogen can spread with little resistance.

The team from Hertfordshire, led by Bruce Fitt, argue that one line of defence, R gene-mediated host resistance against fungal pathogens that grow in the space between cells, is not adequately explained by either mechanism.

Effector-triggered defence (ETD) is mediated by R genes encoding cell surface-bound receptor-like proteins that engage the receptor-like kinase SOBIR1 – an extracellular recognition. The response is host cell death after an extended period of endophytic pathogen growth. This is in contrast to ETI, in which detection of the pathogen occurs within cells and usually triggers fast host cell death.

ETD is described in Stotz et al. (In Press) Trends in Plant Science DOI: http://dx.doi.org/10.1016/j.tplants.2014.04.009

The quotes used in this article are from this BBSRC Press Release. This story was originally posted on the UK Brassica Research Community website.

 

Funding round-up: Summer 2014

Categories: funding
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Published on: July 16, 2014

Here’s your irregular round-up of funding opportunities. Some of these deadlines will already be burned into your brains, but hopefully there a few useful new ones for you to think about!

Many of the options below are only available if you are a member of a society. Funding is one of many benefits to joining a learned society (blog post on this from Sarah Blackford), and if you’re a student your institution might even pay for the membership fee for you.

 

Travel – conferences

British Mycological Society Small Grants: Deadlines 20 July, 20 September, 20 December, 20 March every year. Not pure plant science, but worth a look if you work on plant-fungi interactions or soil. Grants available for fieldwork, travel to meetings, to buy books or scientific equipment.

The Genetics Society Conference Grants: Deadlines 1 August, 1 November, 1 February, 1 May. Two types of grants are available depending on whether the event is linked to the Genetics Society or not.

(more…)

SEB 2014: The future is bright in the Plant Section

Categories: conferences
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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.

ADAS Boxworth Open Day

Categories: guest blogger
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Published on: June 26, 2014

Charlotte White, crop physiologist at environmental and agricultural consultancy ADAS, reports from the ADAS Boxworth Open Day where science from ADAS is showcased alongside work funded by Defra and HGCA as well as private enterprises. It is a great opportunity for scientists, agronomists, farmers and seed/agrochemical representatives to network and discuss their needs and current work.

adas boxworth

On the 3rd of June ADAS Boxworth in Cambridgeshire opened its fields to welcome around 200 visitors. The rather wet morning, which made the behind the scenes setup soggy, dissipated in time for the mid-day opening and the afternoon was lovely and sunny. Visitors included farmers, agronomists, members of the seed and agrochemical industry, students and the farming press.

On arrival visitors were welcomed with a complementary hog roast and could register for BASIS and NRoSO points. At reception there was a demonstration of electrical weeding, which had a lot of interest, along with updates on the SCEPTRE project, the fertiliser value of anaerobic digestate and the HGCA stand. There were then two routes: wheat followed by oilseed rape or oilseed rape followed by wheat. The majority took the latter.

The oilseed rape field had a number of Defra, HGCA and commercially funded project demonstration plots. These included optimising seed rates/row widths, and the project I was demonstrating, which looks at precision applications of late foliar nitrogen fertiliser to increase yield and feed value of the rape-meal (CC: described in this UKBRC factsheet). Dr Steve Ellis spoke about pollen beetle thresholds and neonicotinoids, while Dr Faye Richie was on hand to answer questions on oilseed rape diseases relevant to this season and give updates on the latest findings from the pathology group. The industry variety and product demo plots appeared to have a high yield potential and formed the perfect environment to catch up with sponsors and collaborators. As you turned the corner in the field it was a surprise to find Ken Smith stood in a soil pit promoting good soil management on behalf of HGCA, a topic which always generates a lot of interest and gets people talking!

The wheat field was across the farm road and had a similar mix of government, levy and industry funded project demonstration plots, industry stands and variety and product plots. Prof Roger Sylvester-Bradley explained the yield enhancement network (YEN), an innovation competition to help growers break existing cereal yield records. The demonstration plots, testing ‘innovative ideas’ to maximise grain filling, included irrigation, reflective soil strips and plot cooling (if you are interested in entering the YEN competition, visit the website). The triticale demo plots also received a lot of attention and Dr Sarah Clarke and Dr Daniel Kindred were on hand to discuss the benefits of triticale – it out-yields wheat as a second cereal – and to promote the LearN project, which is using a novel on-farm approach to investigate nitrogen monitoring and management. Jonathan Blake was there to discuss the HGCA Fungicide Performance work, and had some interesting demonstration plots to show yellow rust and septoria tritici control. In addition to these and other interesting research demonstration plots, national ADAS experts in weed, pest and disease management were around to answer all manner of questions. Visitors were kept lingering long after the 4pm close.

For me, it was a long and invigorating day and great to talk to farmers and agronomists about their experiences with late application of foliar nitrogen and to provide an update on the latest project findings, as well as seeing what everyone else in ADAS has been working on. Don’t worry if you missed it, keep your eye out for flyers for future open days!

Image credit: Charlotte White

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

Summer at GARNet

Categories: Arabidopsis, GARNet
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Published on: June 13, 2014
Cosmos Flower by Alfred Borchard, via Free Images
Cosmos Flower by Alfred Borchard, via Free Images

A summer of conferences

We’re gearing up to go to a few major conferences before our own in September, so watch out for Ruth, Lisa, Jim or me at EPSO, SEB, ASPB, SynBio SEED and ICAR.

There are loads of UK meetings for plant scientists coming up: Early career events New Phytologist Next Generation ScientistsSCI Young Researchers in Agrisciences and Frontiers in Plant ResearchBreeding Plants to Cope with Future Climate Change; the CPIB Summer School in Mathematical Modelling; and the HvCP workshops.

If you’re attending these or any other event this summer and want to try your hand at writing a meeting report or blog post, please get in touch – we’re always looking for guest bloggers!

 

GARNet2014 logo 200

GARNet 2014: The Ongoing Green Revolution

For us, the biggest event of the summer is the finale – GARNet 2014 in September. Our conference is the biggest Arabidopsis event in Europe this year and we have a fantastic line-up, so it’s an unmissable opportunity to catch up with collaborators and colleagues past, present and future. We’re taking early bird registrations and abstract submissions for short talks and posters until 30 June. If you’re a post-doc or PhD student, you could win a bursary to cover the cost of your trip! For more information, go to: http://garnet2014.org/

 

BIS Capital Consultation

Before all the inspiring talks and networking, we’re working on a response to this BIS consultation about capital investment until 2020. Capital investment in science infrastructure will total over £5 billion between 2015 and 2020, and BIS are asking the whole STEM community for input on how this investment will be managed. GARNet is putting together a response and if you have anything to input, please do email me. If you want to know more, the 110 page consultation document is here. For a bitesize overview, I suggest you take a look at these two excellent Guardian Science Blogs by Stephen Curry and Claire Viney. Also, the Guardian is hosting a live online Q&A session with a panel, to include David Willetts, on Monday lunchtime.

 

GARNish … coming next week

It can’t really be summer at GARNet without the June edition of GARNish – don’t worry, it will be with you next week!

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