October 2012 - Weeding the Gems

The genetics of broad-spectrum resistance

by Charis Cook

Categories: plant pathogens, Summary for non-specialists, teaching resources

Tags: Arabidopsis, New Phytologist, plant pathogens, summary for non-specialists, teaching resources

Comments: 1 Comment

Published on: October 30, 2012

Downy mildew infection of Arabidopsis thaliana seedlings

Highlighted article: Dmitry Lapin, Rhonda C. Meyer, Hideki Takahashi, Ulrike Bechtold, Guido Van den Ackerveken (2012) Broad-spectrum resistance of Arabidopsis C24 to downy mildew is mediated by different combinations of isolate-specific loci. New Phytologist DOI: 10.1111/j.1469-8137.2012.04344.x

It is a mark of how effective plant immune systems are that most bacteria, fungi, and viruses do not affect plants at all either because plant tissues are not suitable for them to live in, or they are fended off. Of course there are pathogens that are compatible with plants – and within species that share compatibility, there are pockets of resistance. Some sub-groups are resistant to specific pathogen isolates, and this is caused by dominant resistant genes. A much broader, more complicated, and less common form of resistance occurs when a particular accession is resistant to a whole pathogen species, or several species. This is broad-spectrum resistance, and it can be caused by a simple dominant gene or multiple genes. Natural broad-spectrum resistance is not simple to transfer from its origin to a commercial crop because it can come from a complex set of genes which are not necessarily all dominant. (more…)

Varying degrees of open access

by Charis Cook

Categories: Open Access

Tags: Friday film, publishing

Comments: No Comments

Published on: October 26, 2012

One of the things that this summer’s GARNet workshop, Making Data Accessible to All, made Ruth and I think about was the varying degrees of open access allowed by publishers. All journals accommodate open access, as some funding bodies now demand all research undertaken with their funds be published open access. This service is not free, so it will usually only be used when the funding body demands it. If open access is something you feel strongly about, PLOS have a useful ‘Open Access Spectrum,’ which can be used to judge journals on an open access grid. This may be useful in thinking about where to publish your work.

Publishing policies vary enormously. Some subscription-only journals allow open access after an embargo period of between six months and two years. Some journals allow authors to put their papers or toll-free links to the article on their personal websites or databases like PubMed Central if they chose to (sometimes immediately, sometimes after a set period of time), and others forbid any publication of their articles anywhere except the official, subscriber-only, journal website. It’s always worth a quick search for your paper if you can’t access it through the publisher – there could be an unofficial (but legal!) version or toll-free link out there somewhere!

There is information about specific plant journals below (feel free to leave a comment if I’ve missed anything out), but since it’s Friday, here is a slightly surreal and extremely one-sided video about academic publishing – thanks to aoholcombe:

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Guest post: Plantwise Knowledge Bank Map

by Guest Blogger

Categories: guest blogger, plant pathogens, resource

Tags: CABI, guest blogger, plant pathogens, resource

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Published on: October 25, 2012

Tim Holmes works for CABI, a not-for-profit international organization that improves people’s lives by providing information and applying scientific expertise to solve problems in agriculture and the environment. Plantwise is an initiative, led by CABI, to improve food security and the lives of the rural poor by reducing crop losses. It is for the Plantwise Knowledge Bank, that Tim tackles the challenge of presenting species distribution data to a diverse group of users.

Plantwise is the biggest project that the whole of CABI has ever been engaged in together. It brings together all the strands of our work, from the publishing business, through scientific research, to international development. The Knowledge Bank is my bit of the programme, and something I’m immensely proud of. We’ve been developing a suite of data and information tools over the last few years, and it’s to one of these that I’d like to introduce you now.

The Plantwise Knowledge Bank Map was the first tool concept that we presented back in 2010, and straight away it was our number one priority to make it a reality. The genesis was a crude, but cool looking, Google Earth presentation of CABI’s plant pest distribution data. The globe spun and zoomed impressively, but it wasn’t going to be the useful scientific tool that we were after. For starters you couldn’t see the whole of the Earth’s surface at once; problematic if you wanted to get a Baumgartner’s-Eye view of the worldwide range of a pest! It was problematic too if you wanted to build it into a website that would fling around large datasets AND do so for users with restricted internet bandwidth. So we trialled many different bits of mapping software and settled on something that would display a Google Maps-style projection and would let us do as much of the map production leg-work on our servers. It would be familiar and fast. (more…)

Funding round-up: Winter

by Charis Cook

Categories: funding

Tags: BBSRC, European Commission, funding

Comments: No Comments

Published on: October 23, 2012

Research awards

Gates Foundation Grand Challenges Exploration: Deadline 7 November. £100 000 is available to fund development of an idea that can help solve one of the Gates Foundation’s Grand Challenges. If you have an idea to do with agricultural development or medicinal plants, take a look at this. It is a short application, which requires no prior data – worth a try for a project too risky to pitch to a different funding body!

FP7 KBBE: Deadline 5 February. See previous blog posts (1, 2) on this call.

BBSRC Responsive Mode: Deadline 9 January. The bread and butter of plant science research. Remember to apply to Committee C if your work is to do with ‘genes or development,’ as its remit has changed. There will be a plant scientist sitting on it. Committee B remains the main route for plants and microbes.

BBSRC LINK and BBSRC Industrial Partnership Awards: Deadline 9 January. Funding available for collaboration between a research group and industrial partner, who must fund at least 50% of the total economic cost of the project for a LINK award, or 10% for an IPA.

ERC Synergy Grant: Deadline 10 January. Up to €15 000 000 is available for a project lasting up to six years. Groups of between 2 and 4 PIs and their groups can apply for this huge grant. This is part of the FP7 Ideas Work Programme and proposals must comply with their priorities. According to the Guide for Applicants, ‘The aim is to promote substantial advances in the frontiers of knowledge, and to encourage new productive lines of enquiry … methods and techniques, including unconventional approaches and investigations at the interface between established disciplines.’ (more…)

From systems biology to digital organism

by Charis Cook

Categories: synthetic biology, systems biology

Tags: BBSRC, Friday film, GARNet, survey, synthetic biology, systems biology, teaching resources

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Published on: October 19, 2012

GARNet needs your help to assess the uptake, influence and future of systems biology in the plant science community. This is the second time GARNet has conducted a survey about systems biology, as in 2006 the BBSRC commissioned GARNet to produce a report on how systems biology could best be approached in UK Arabidopsis research. We believe that report and the various activities that accompanied it helped the Arabidopsis community get its foot on the ‘System Biology Ladder’ – and to win some of the associated grants.

Now, six years later, systems biology is supporting systems biology and the digital organism efforts. We feel it is time to write a follow up report to the 2006 Systems Biology report in order to advise the BBSRC and other funders on the community’s capabilities, current needs, and readiness for future initiatives that build on Systems Biology.

Please help us collect data and information for this report by filling in a questionnaire, which will take about 20 minutes of your time. Please click here to go to the questionnaire. Please contribute your ideas before the 5th November.

Video credit: Pacific Biosciences.

Making Data Accessible to All

by Charis Cook

Categories: Workshops

Tags: data sharing, GARNet, GARNet workshop

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Published on: October 18, 2012

In July 2012, GARNet held a workshop entitled ‘Making Data Accessible to All’. Speakers included Mark Hahnel, founder of Figshare, TGAC Genome Analysis team leader David Swarbreck, senior editors and publishers from publishing groups, and a number of academics with experience in data dissemination. Together, workshop speakers and delegates discussed the current challenges in data storage, which data are ‘valuable’ and which may reasonably be left behind, and who should have the responsibility of sharing, storing, and curating data.

The report containing the summary of this workshop concludes that incentive, policing measures, and shifts in culture are needed in order for data sharing to take hold and bear fruit within biology as a whole. Funding bodies, universities, and publishers and journals can provide important ‘sticks and carrots’ by shifting priorities and attitudes to support the practice of data sharing, with all its demands. At the same time, researchers need to seriously commit to data sharing by making it part of their principal aims and outputs. In most cases, community involvement matters much more than the availability of technology. Recent initiatives to encourage data publication, such as data only journals, and data sharing, principally Dryad and Figshare, are acknowledged as important drivers of the shift toward an ethos of data sharing.

To see the resources and repositories GARNet recommends for sharing different types of data, including plant-specific ones, see this post.

Full list of speakers at the workshop: Sabina Leonelli, Andrew Millar, Nick Smirnoff, Jay Moore, Jacob Newman, Mary Traynor, Giles Jonker, Ruth Wilson, Mark Hahnel, Claire Bird, Sean May, David Swarbreck, Alan Pottage, and Paul Burlinson. Their affiliations and their presentation slides can be found on the UKPSF website.

Thinking about phytoplankton

by Charis Cook

Categories: Summary for non-specialists

Tags: algae, summary for non-specialists

Comments: No Comments

Published on: October 16, 2012

H. akashiwo on the right, with predator Favella sp.

I’m aware phytoplankton are not usual subjects for plant science research, but these small algae are quite plant-like, in general – although they don’t have organs to complicate things. Like plants, they photosynthesize and are able to respond to their environment. Importantly, unlike plants, phytoplankton are mobile, hence the name which in Greek means ‘drifting plants’. Being extremely tiny ‘plants’, phytoplankton present an excellent opportunity for plant scientists to consider synthetic biology, which seems more feasible on a cell-scale rather than an entire plant. The super-theme of the FP7 2013 funding call was ‘The Oceans of Tomorrow,’ and while that call closes in a few short months, synthetic biology, water security and bio-sensors are important research themes which are here to stay.

Highlighted article: Elizabeth L. Harvey and Susanne Menden-Deuer (2012) Predator-Induced Fleeing Behaviors in Phytoplankton: A New Mechanism for Harmful Algal Bloom Formation? PLoS ONE 7(9): e46438. doi:10.1371/journal.pone.0046438

This research focuses on toxic phytoplankton Heterosigma akashiwo, a known cause of harmful algal blooms (HABs; for a fairly recent review of HABs and their effects on human health, see Backer and McGillicuddy Jr., 2006). (more…)

Friday Film: Powerful Plants

by Charis Cook

Categories: teaching resources

Tags: Friday film, teaching resources

Comments: No Comments

Published on: October 12, 2012

If you thought that plants were stationary, lazy beings, think again. Bladderworts are water-dwelling carnivorous plants that trap prey by storing elastic energy in the trap body and releasing it by very fast opening and closing of a water-tight trap door. This video was made by Phillippe Marmottant and his research group from Grenoble, who published the mechanism of bladderwort action in their 2011 paper.

Another super fast plant is the dogwood species, Cornus canadensis, whose flowers explode faster than a rifle shot as they disperse their pollen.

While exploding plants and super-suction make for exciting viewing, they happen too fast for the human eye to see without the benefit of slow motion footage. It is possible to show slightly slower plant reflexes to students in schools, though – SAPS have a carnivorous plants information page and worksheets.

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