Perseverance and community: The opening session of Plant Biology 2013

Categories: conferences
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Published on: July 21, 2013

Follow Plant Biology 2013 on #plantbiology2013

Plant Biology 2013 is in full flow here in Providence, Rhode Island. It kicked off on Saturday afternoon with an impressive Awards Ceremony recognising fifteen plant scientists (see the list here) from across the world, and of all ages – from graduate students to emeritus professors. Celebrating the huge breadth and depth of plant science today and over lifetimes was an inspirational way to start the conference.

The first major conference talks began directly after the Awards Ceremony with lectures from two of last year’s award winners, Lisa Ainsworth and Ian Sussex, and the Science Perspective Speaker Robert Zeigler. These three lectures were each very different, but represented three major themes of ASPB and the conference: an overview of excellent research, a celebration of plant science, and an update on the reason most plant scientists do what they do: the food security challenge.

Lisa Ainsworth’s work on ozone damage and ozone resistance in soybean is remarkable for its quality (publications here) and its potential impact, but for me the stand out message was the reminder that US science is just on another scale to UK plant science. Ainsworth carries out most of her experiments in the open air at SoyFACE in Illinois – not a growth chamber or glass house in sight. UK scientists constantly struggle with the difference between results obtained in ‘lab conditions’ and the field phenotype, even when working on crop species. Ainsworth’s results, although they are very much in the experimental stage, already show realistic field phenotypes.

Ian Sussex, an Emeritus Professor from Yale, gave a perspective on experimental plant morphogenesis and how it evolved from what was essentially surgery on plants in the 18th century into modern molecular biology in the 1970s. It was an interesting talk, and some of the ideas are in this paper by Sussex in Plant Cell vol. 20.

The CEO of the International Rice Research Institute (IRRI), Robert Zeigler, gave the last of the three diverse opening lectures. He gave an overview of the food security challenge, but with an understandable focus on rice and the work of IRRI. Rice is the staple food for 50% of the global population, but of a staggering 70% of people living in poverty worldwide. Zeigler presented an impressive and typical case study demonstrating the objectives of IRRI: submergence-tolerant rice. Using an integrated research approach, including soil scientists, genetics, and physiology, IRRI scientists bred ‘scuba rice’ and tested it in 2009.

A theme that ran through these three talks was perseverance and the importance of seeing the long view. Ainsworth is part of a long-running research programme that she joined as a post-grad student, and no doubt in the next few years, her ozone-tolerant soybean will be having a big impact. Sussex’s history of plant biology, in which he highlighted the decades before the Arabidopsis genomics revolution in the 1970s as a dry spell for cell and molecular plant science reminded us that modern plant scientists are part of a long tradition of strong community and modernisation. Zeigler summed it up when anticipating a second Green Revolution: “You can do what people say can’t be done.”

Biology by design

Categories: synthetic biology
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Published on: July 11, 2013

 

At the moment I’m reading a lot about synthetic biology (GARNet report and paper to come in the next few months) and it’s all technical stuff – genome assembly, online resources, transformation methodologies. Synthetic biology is the application of engineering principles to biology, so it’s natural that the technical challenges and ingenious solutions take centre stage.

But engineering isn’t all about building things that work. It’s also about the way things look. How much do synthetic biologists consider the aesthetics of their product? Do they need to?

In May, Daisy Ginsberg gave a talk at Warwick and argued strongly that aesthetics are a crucial part of synthetic biology. She is an artist and designer who works with scientists, including iGEM teams, to develop design principles in scientific research.

I think the idea of bringing art and science together to create beautiful, functional plant products is exciting in itself, and certainly another perspective to consider when planning a plant synthetic biology project. But a great aesthetic experience will also be very important when it comes to marketing and selling synthetic biology products, which is the ultimate goal for synthetic biology investors, and many scientists too.

Have a look at Synthetic Aesthetics, a joint project including scientists and artists run by the University of Edinburgh and Stanford University, in you are interested in aesthetics and design in synthetic biology. This recent article by Daisy on the ‘pre-future’ of synthetic biology is worth a read too.

The next time I blog it will be from Plant Biology 2013 – if you’re going, I hope to see you there!

Image credit: ‘Growth Assembly‘ by Alexandra Daisy Ginsberg and Sascha Pohflepp, illustration by Sion Ap Tomos.

What isn’t plant science?

Categories: synthetic biology
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Published on: July 5, 2013
Carboxymethylated nanocellulose adsorbed on a silica surface.

When does plant science stop being plant science? Here at Warwick, the Warwick Manufacturing Group made a nano-cellulose steering wheel with raw material from carrots. It resides in the Science Museum as part of the Nano-Cellulose exhibition, which features a car made entirely of biomaterials. The raw material was plant biomass, yet the scientists and engineers who work with it are not ‘plant scientists’.

This is just one of a lot of articles I’ve seen about nano-cellulose, a super-strong and light material which is conductive and absorbent too, so it has the potential to be used for pretty much everything. It is made from renewable raw material from plant or algal biomass. It sounds like a boon for plant science, a great plant synthetic biology product – but it is definitely a materials science baby.

Of course there are differences between developing super-materials from plant biomass and what we usually think of as ‘plant science’. Plant scientists aim to understand and/or improve plants and plant products, while materials scientists see plant biomass as a raw material to be worked with, not on.

Plant scientists should not let this difference stop them seizing the opportunities presented by increasing interest in nano-cellulose and other biomaterials. Now more than ever we can highlight the absolute dependence of humanity on plants, and promote the importance of plant science funding for improved crop production for food, energy, and materials. It is also the ideal time to start building and strengthening interdisciplinary connections.

Something I’ve noticed recently is a feeling among the plant science community that there is a need for more interdisciplinary networking and collaboration opportunities. Plant science is already crucial for agricultural innovations, and even here there are only a few opportunities for bench scientists and agriculturalists to talk to each other. Plant science can make a difference to biomaterials production, but first new connections need to be forged between two very different groups of researchers.

As with any supply chain, it is important that relevant groups are able to communicate their needs and capabilities to each other. If this were possible, it would improve the economic and environmental sustainability of biomaterial production.

Does anyone have any experience of working, however distantly, with a biomaterials group? I’d be interested to find out!

Image credit: Innventia, via Wikimedia Commons.

Two GARNet Events

Image by Centimedia.org for GARNet

We have some GARNet news to share!

First of all, we are pleased to finally open registration for the hands-on iPlant training workshop ‘Data Mining with iPlant‘. Unfortunately we’ve had to change the planned location, and it will now be at the University of Warwick. The date is still 17-20 September 2013.

For those who don’t know, iPlant is an incredible free resource which allows its users to access high performance computing power, large scale data storage, and analytical software needed for a variety of data- or compute- intensive research applications.

You can either come for just one day for a free hands-on introduction to iPlant, or stay for four days and get in depth training on how to analyse real data in iPlant. For more information go to: http://www.garnetcommunity.org.uk/news/13-06-19/data-mining-iplant-17-20-september-2013

Our second announcement is more of a save-the-date than an invitation. The GARNet general conference will return next year, possibly for one time only. GARNet 2014: The Past, Present and Future of the Genetic Model Revolution will be held at the University of Bristol on 9-10 September 2014. It will be a celebration of exciting new plant science, and a look at the evolving nature of model systems as well as the brilliant achievements made with them in the past.

The Journal of Experimental Botany kindly recorded and uploaded talks from the last GARNet conference in 2011. Here is Katherine Denby of the University of Warwick talking about the PRESTA project, which since this talk has produced two Plant Cell papers (1,2). You can see the rest of the talks from GARNet 2011 on the JXB website.

Open access: How much is enough?

Categories: Open Access
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Published on: June 4, 2013

Nearly everyone is behind Open Access as an idea, but when RCUK demanded that all papers published from RCUK-funded groups be published open access it became clear that widespread, truly open access publication is still an idea and not a deliverable. The problem is that while scientists see the moral case for open access, and it is to their advantage to have as wide an audience as possible for their research, open access publishing can be extremely expensive, especially when academic careers are so invested in publications in high-impact, traditionally high-profile journals.

Open Access publishing can be cheap – national journals can even be free, though according Eigenfactor, there are no UK-based free plant science journals. PloS and BMC are charging around £1200 per article. When I looked up the OA fee on the BMC website, a friendly message popped up saying that the University of Warwick would pay half the publication fee if I submitted an article to them; other institutions will have similar schemes to help with payment of publication costs. Plant Physiology charge £750 for OA publication, though this is on top of often much larger pre-existing fees for colour publication and other costs. These figures seem reasonably affordable with the planned block grants to provide funding for article processing charges.

Article processing charges (APC) funding will come into force in academic year 2013/14, and during this time research institutions are expected to make sure 45% of papers are published OA. In mid 2014 the funding mechanism will be reviewed. Over the next few years, it is expected that the proportion of OA articles will go up – the target for 2014/15 is 53% at the time of writing.

However, I have heard from several people that some journals are charging a very high fee for OA publishing – in excess of £10 000. The APC fund will not be able to cover fees as large as that. So it is good news then that in April of this year, RCUK revised the original announcement that OA publication means ‘gold’ – ‘green’ OA is acceptable. This means that you can publish your work in many journals without paying the OA fee, and self-publish the paper in a format and forum agreed to by the publisher. In most cases this means you can put a non-formatted version of the accepted article on your website and in your institutional repository.

 

While researching this post on Open Access (OA), I found these webpages which will be of use to anyone who is confused about the RCUK OA policy:

  • Sherpa is an online tool from RCUK that explains users’ options for complying with their policy in the majority of journals. For example, if you search for ‘New Phytologist’ it explains that you can pay $3000 for the gold open access option, OR archive your article in an open access repository.
  • A commentary from The Times about April’s revision to RCUK’s OA policy.
  • RCUK’s Policy on Open Access FAQs (PDF) – you might not get as must detail as you want about the future of the OA policy, but this is the first place you should check if you have questions.
  • Stephen Curry regularly blogs about open access, and is one of the reasons RCUK had to clarify their stance on the importance of impact factors as a result of their OA policy – well worth a read.

Plant synthetic biology round-up

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 2nd 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

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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 6th 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 26th 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

Categories: conferences, guest blogger
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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.

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