May 2013 - Weeding the Gems

Plant synthetic biology round-up

Categories: bioinformatics, conferences, GARNet, resource, synthetic biology

Tags: BBSRC, GARNet workshop, synthetic biology

Comments: 1 Comment

Published on: May 24, 2013

Well, I’ve just about recovered from this week’s GARNet meeting, An Introduction to Opportunities in Plant Synthetic Biology. It was a great two days. For a report of the meeting through the medium of Twitter, including links to resources and papers from the speakers, see this Storify I made – thanks to everyone who Tweeted throughout the meeting!

I’ve rounded up a few of the resources and papers I think would be most helpful for plant scientists below. The Storify of the meeting contains more, and keep an eye on the Journal of Experimental Botany for a series of perspectives and a meeting report over the coming months.

Tools and resources:

CellModeller is an open source software from Jim Haseloff’s lab, which allows users to model multicellular systems. It has been used to model the growth and behavious of synthetic microbial biofilms (Rudge et al. 2012, ACS SynBio 1:345), and plant cell division and expansion (Dupuy et al. 2010, PNAS 107:2711). For toll-free links to both papers, go to the CellModeller website.
TAL effectors were mentioned in a number of talks, and were presented to the audience by Sebastian Schornack, who declared them fool-proof means of DNA editing. For protocols, papers, and more information see the TAL effectors website, and you can order custom TALs from Life Technologies. Sebastian is keeping a database of papers using TAL effectors on Scoop.it.
Golden Gate cloning and its variants are extremely powerful tools for DNA assembly and combinatorial library construction. Speakers Giles Oldroyd and Tom Ellis have used it to great effect. Sylvestre Marrillionet explained to delegates how Golden Gate cloning was invented and what it can be used for – to find out how to use it, see his papers or get in touch with him. This website also gives a good overview and selection of useful papers.
Gibson Assembly is another powerful DNA assembly tool, which was presented by Jim Ajioka at the meeting. There is a very comprehensive guide to using it, including sequences and protocols, online here.
The Infobiotics Workbench was designed by speaker Natalio Krasnagor. It is a freely available framework for carrying out in silico experiments, from design to results visualisation.

Inspirational plant synthetic biology projects

June Medford presented the most complete plant synthetic biology project, the plants which de-colour in the presence of toxins – the synthetic signal transduction pathway that the ‘plant sentinels’ contain is published in PLOS ONE. You can see her papers, many with toll-free links, on her website. Also, if you’re looking for an adventurous post-doc position, she’s recruiting!
Last year Giles Oldroyd received funding from the Bill and Melinda Gates Foundation to build synthetic signalling pathways into wheat to enable sybmiosus between this global food crop and nitrogen fixing bacteria. You can see his progress so far in papers on his website.

More information and sites of interest

To keep up to date with synthetic biology news and funding, and to link up with possible collaborators, join the Synthetic Biology Special Interest group from the Bisosciences Knowledge Transfer Network.
Many of the speakers at the meeting were also at last year’s New Phytologist workshop on synthetic biology. You can see videos of the talks on YouTube, and the meeting report in New Phytologist 3:617.
If you’re interested in synthetic biology and want to get plugged into the community, think about going to the 2^nd International Synthetic Yeast Genome Consortium Meeting. True, it’s not about green leafy things, but the techniques discussed will be relevant and you’ll make good connections.

Review papers

Speaker Tom Ellis recommended this recent review article from Kahl and Endy (Open Access; JBE 7:13) for an overview of available DNA assembly methods.
This open access 2012 review by Richard Kitney is an overview of the current situation in synthetic biology – Kitney and Freemont 2012; FEBS Letters 587:2029).

Synthetic biology has arrived

by Charis Cook

Categories: conferences, funding, GARNet, synthetic biology

Tags: BBSRC, funding, GARNet, GARNet workshop

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Published on: May 20, 2013

GARNet’s An Introduction to Opportunities in Plant Synthetic Biology conference couldn’t have come at a better time – it feels like synthetic biology has officially arrived. Over the last week or so, some long-anticipated synbio news was announced.

First of all, there are the two synbio funding opportunities from BBSRC and other funders:

BBSRC and EPSRC announced a call for proposals for multidisciplinary research centres in synthetic biology. At the moment they want interested groups to express their interest, and on 6^th June the call will officially be launched at an information workshop. The final deadline for applications is 18 July 2013. The research centres will focus on strategic areas that could include life science technologies, agriculture and food, and environment.
The synthetic biology ERA-NET, ERASynBio, launched a call for transnational synthetic biology research projects on Monday. Thirteen European funding agencies, including BBSRC, expect to invest €15.5M. The submission period ends on 26^th August. Proposals have to be able to demonstrate an interface between biology and chemistry, informatics, mathematics, physics, or engineering, and may originate from metabolic engineering, bionanoscience, minimal genomes, or other sub-fields of science.

One of the important aspects of synthetic biology is the potential for application and commercial impact, so it’s important to think about synthetic biology products in the context of public opinion and current markets. The BBSRC and EPSRC started a synthetic biology dialogue in 2010, and have just released a report describing the impact it has. If you’re interested in the ethics and communication of synthetic biology, see what RCUK have been doing in this area in the report:

While it received less fanfare than the multi-national, multi-million pound investments in synthetic biology, the patenting of TAL-effector technology (for anything except commercial use in plants) by Life Technologies is important news for wet-lab synthetic biologists. For the GARNet community, it means that UK plant scientists can use TALEN technology as easily as using any other molecular biology kit. You can buy the GeneArt Precision TALs kit from the Life Technologies website.

Life Technologies Corporation said in a press release, “The GeneArt® Precision TALs are supplied as Gateway® compatible entry clones encoding a DNA binding protein for a specific customer-submitted sequence fused to a range of effector domains. Custom TALs are typically delivered within two weeks after orders are placed.”

Sebastian Schornack (@dromius), one of the inventors of TALEN technology, will be speaking at An Introduction to Opportunities in Plant Synthetic Biology on Wednesday. Follow his and other talks on Twitter #plantsynbio.

Finally (and it’s not really news), just for geeky kicks take a look at this Kickstarter synbio project for glowing plants. They’ve already reached their initial goal, but you can still support the project to the ‘stretch’ goal to get your very own glowing Arabidopsis thaliana, or other less exciting goodies. There’s a very informative write-up about the project and science on Kickstarter on a blog called Splasho.

Monogram 2013

by Guest Blogger

Categories: conferences, guest blogger

Tags: conferences, Monogram

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Published on: May 17, 2013

Laura Dixon

This is a guest post from Laura Dixon, post-doc at the John Innes Centre.

Monogram, the UK small grains conference, was hosted by the James Hutton Institute in Dundee. The conference, which was attended by scientists, breeders and companies showcased the research projects and technologies recently developed for small grains research. In particular, the conference was used to discuss the best approaches the community could use for utilising the rapid advances in sequencing technologies, such as the wheat affymetric chips and the how to approach more controversial topics including the genetic modification of cereals.

The talks ranged from reporting the latest scientific developments to promoting new technologies and resources including huge germplasm collections. The conference had a strong theme of the progress being made in sequencing and constructing a consensus genetic map in wheat and the complexities faced through the highly repetitive hexaploid genome. This theme was established in the keynote talk from Catherine Feuillet, which linked Monogram and to PlantSci 2013. The conference also played host to the first annual Early Career Researcher in Cereals Award, which was presented to Dr. Christopher Burt from the John Innes Centre for his work on understanding disease resistance in wheat.

Next year’s Monogram conference will be hosted by Rothamsted.

Starting your interdisciplinary journey

by Guest Blogger

Categories: guest blogger, resource, systems biology, Workshops

Tags: No Tags

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Published on: May 14, 2013

This is a guest post by Susie Lydon, Outreach Officer at the University of Nottingham

Plant science is becoming increasingly interdisciplinary, and for early career researchers, gaining experience in working across the traditional subject boundaries can be very useful. A common problem is that many of the training opportunities in relevant areas of maths and computer science assume a level of background knowledge which many biologists do not have (or do not feel confident about).

The Centre for Plant Integrative Biology at the University of Nottingham has been running ‘summer schools’ (which actually take place in early September!) for six years now which aim to bridge the gap for interdisciplinary ‘beginners’.

Mathematical Modelling for Biologists is a four-day residential course which provides an introduction to biological modelling. The course comprises integrated lectures and computer practical classes, and the background knowledge assumed is ‘rusty A-level maths’ or equivalent. Participants learn from examples taken from gene regulation, biochemical reactions, population dynamics, and epidemiology.

Image Analysis for Biologists is a three-day residential course running for the second time in September 2013. The aims of this course are to allow participants gain an understanding of image analysis approaches commonly used in the biological sciences, and confidence in applying them. Like the modelling course, it comprises integrated lectures and practicals using relevant software. Many of the examples are drawn from CPIB’s work in plant image analysis, but the course is open to biologists from any discipline.

For more information about these courses, and to apply to attend in September 2013, visit the CPIB events page, or contact CPIB’s Outreach Officer, Dr Susie Lydon.

Image credits: Centre for Plant Integrative Biology

Celebrating basic plant science with David Baulcombe

by Charis Cook

Categories: UKPSF

Tags: celebrating basic plant science, UK PlantSci 2013, UKPSF

Comments: No Comments

Published on: May 10, 2013

Barbara McClintock discovered transposable elements when investigating irregular colouring in maize.

It’s now nearly a month since UK PlantSci 2013, and high time I wrote something about it on this blog. Rebecca Nesbit has written two posts about it already on the Society of Biology blog, and a New Phytologist meeting report will be coming out soon. The Weeding the Gems contribution to this collection of UK PlantSci nostalgia is a write-up of the second keynote talk by David Baulcombe.

David Baulcombe’s talk was a rallying cry in defence of basic research and plant science. He kicked it off with a whistle-stop history of important scientific achievements, all by scientists carrying out basic research on plants: Robert Hooke, who identified and labelled ‘cells’ for the first time when studying woody plant biomass in 1665; 19^th century monk Gregor Mendel, whose peas were the first genetic model system; Russian botanist Dmitri Iwanowsk, who in 1892 was the first scientist to identify and characterise a virus; and Barbara McClintock, who discovered transposable elements in maize. More recently even than McClintock’s work, Argonaute proteins, tumour formation, and cellular totipotency were all identified first in plants (Bohmert et al. 1998, EMBO 17:170; Sussex 2008, Plant Cell 20:1189).

The scientists involved in the discoveries listed above were carrying out what they presumably viewed as interesting work, simply because they wanted to know the answer – pure science, but all with far-reaching consequences. Baulcombe commented than in the 21^st Century research is impact-driven, so some of these pioneers may have struggled to get funding via today’s funding mechanisms.

Now, it is unfair to say that research today is all end-product focussed and impact driven. I know that the BBSRC and other funders worldwide fund basic plant science research regularly, and I highlight some of it here on this blog. Baulcombe’s main point in this first half of the talk was that basic excellent plant science research has to be celebrated in its own right rather than as a half-way point to a useful product in the future. (more…)

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