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).

The many advantages of chloroplasts

Chloroplasts are a major advantage to doing synthetic biology in plants. They produce starch and some amino acids as well as hosting photosynthesis, all fully separated from other cellular functions going on in the rest of the cell. Synthetic biology approaches could turn them into individualised micro-factories inside plant cells, synthesising whatever compound you fancy without poisoning the cell and with almost no risk of any transgenes escaping into other plants.

Stable plastid transformation was first achieved in tobacco in 1990.  Since then, chloroplast transformation has been successful in many plant species – a 2009 review by Huan-Hyan Wang et al. (JGG 36:387) contains a nice table summarizing the methods used in each species. Plastid-based biosynthesis of biopharmaceuticals has been researched for years, but synthetic biology technologies make it possible to consider moving beyond synthesis of antigens and relatively simple molecules (for examples see Daniell et al. 2009, Trends in Plant Sci 14:669) to more complex structures.

In today’s highlighted paper, Nielson et al. successfully built the P450-dependant dhurrin pathway into tobacco chloroplast cells. This in itself does not have a major benefit to science, as dhurrin has no real value, but as a proof of concept this is worthy of note. The three-step biosynthesis of dhurrin from L-tyrosine is normally based on the endoplasmic reticulum, and its rate is limited by low concentrations of NADPH. By building the pathway in a chloroplast, the authors have proven not only the feasibility of chloroplast pathway engineering, but also the potential of using reducing power from photosynthesis to run biosynthesis pathways.

For more information about chloroplast engineering, this 2011 paper reviews chloroplast transformation markers and this paper is another example of pathway engineering in chloroplasts.

More generally, to find out about synthetic biology approaches please register for our Synthetic Biology meeting, which aims to introduce synthetic biology to plant scientists. It is £250 for academics, and includes overnight accommodation and meals – there is a reduced rate for students and post-docs.

Highlighted paper: Agnieszka Zygadlo Nielsen, Bibi Ziersen, Kenneth Jensen, Lærke Münter Lassen, Carl Erik Olsen, Birger Lindberg Møller, and Poul Erik Jensen (2013) Redirecting Photosynthetic Reducing Power toward Bioactive Natural Product Synthesis. ACS Synthetic Biology DOI: 10.1021/sb300128r

Image credit: Martin Bahmann, via Wikimedia Commons.

Impact through the Biosciences: Plant Synthetic Biology

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Published on: February 28, 2013

The phrase ‘synthetic biology’ doesn’t naturally pair with ‘plant science’ for most plant researchers. Yet at the Biosciences KTN Annual Conference 2012, Impact through the Biosciencesof five talks on synthetic biology, one was an introduction, one was about photosynthesis, and one was about synthesising high value plant compounds in microalgae. You can view all the videos from the meeting here if you are a member of connect_, which is free to join.

Expertise in molecular pathways, plant hormones, bioinformatics, and modelling, could all be applied to synthetic biology. It’s true that currently most synthetic biology, even the plant synthetic biology in the two videos highlighted above, is done in microorganisms or inorganic systems, but plants are the obvious choice for a multi-cellular synthetic biology system.

If you want to find out more about the synthetic biology approach, current plant synthetic biology projects, and the range of synthetic biology tools and resources available, come to our meeting An Introduction to Opportunities in Plant Synthetic Biology. It is an introduction to synthetic biology to plant scientists, and we hope it will encourage the UK plant science community to benefit from the emphasis the governmentBBSRCEPSRC and TSB are placing on synthetic biology.

Video credit: Biosciences KTN, via their YouTube channel. 

An Introduction to Synthetic Biology for Plant Researchers

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Published on: February 20, 2013

 

Synthetic biology is a fast-growing research area both in the UK and further afield and UK policy makers and funders are taking it very seriously. In November last year, George Osborne announced a £20 million investment for Synthetic Biology and as a result Synthetic Biology is one of the few research areas in the BBSRC portfolio to receive an increase in funding. This is in addition to the numerous schemes that are already supporting Synthetic Biology (including BBSRC, EPSRC and TSB). 

To make sure that UK plant researchers can make the most of these funding opportunities, GARNet is hosting a meeting to introduce the concept of Synthetic Biology and the many and varied applications of Synthetic Biology at the molecular, cell and whole plant level.

Like Systems Biology before it, Synthetic Biology can be viewed as both a tool and a scientific approach for understanding and furthering basic science and as a means of developing commercially important plant products. Synthetic Biology in plants is under-researched, but has enormous potential and it is time for UK scientists of all disciplines to explore it.

So to make sure you understand what Synthetic Biology is and how you might apply to your research area, make sure you register for An Introduction to Opportunities in Plant Synthetic Biology. For more information go to: http://www2.warwick.ac.uk/fac/sci/lifesci/news/synbio. Please note that registration fee covers the cost of accommodation and meals during the meeting

To help us promote the meeting, please print out this poster and put it up in your department. Please also forward this email to anyone from other departments you think will be interested.


GARNet Workshop: Plant Synthetic Biology

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Published on: January 22, 2013

It is important for UK plant scientists to consider synthetic biology, both as a tool for understanding and furthering basic science and as a means of producing commercially important plant products – the BBSRC has even chosen synthetic biology as an important emerging scientific sphere. To demonstrate the potential of synthetic biology in plant science and introduce synbio methods, tools, and resources to researchers new to the field, GARNet is having a workshop on Plant Synthetic Biology. Go to  http://www2.warwick.ac.uk/fac/sci/lifesci/news/synbio for more information.

From systems biology to digital organism

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.

NIAB Innovation Farm GM workshop 2: Public Good Programme?

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Published on: September 25, 2012
Cows and maize, a major GM cattle feed.

For responses to last week’s news story about the GM maize feeding trial that appeared to cause tumours in rats, GARNet suggests: New Scientist,  the Science Media Centre, UKPSF, or for a rather more biting commentary, Forbes.

As discussed in the previous post, GM plant products are commonly used worldwide for food and for animal feedstock. But strict European regulations mean growing a GM crop and bringing its product to market is very difficult in Europe. Any progress toward GM products on the European market, especially under a public good programme, is dependent on a relaxation of EU regulations for GM. The consensus view from the NIAB Innovation farm workshop GM: Is it time for a public good programme? was that if GM was treated as another breeding method, and GM crops were subject to the same regulations as conventionally bred plant varieties, industry would be far more likely to invest in GMOs.

Anti-GM feeling in the general public has reduced recently, but governments still implement anti-GM legislation. This in itself makes a government-supported public good programme unlikely in a European country. A public good programme would also have to overcome several technical and legal barriers. A framework would be needed to allow open access to technology and outputs, therefore a unique intellectual property arrangement would have to be implemented. A wide stakeholder steering group, independent of any one institution, to deal with these and other issues would be essential. Several people wondered what exactly a public good programme would look like – there is a successful public GMO programme in China, but it depends almost entirely on government funding and a similar financial commitment from the UK government is unlikely, at least in the near future. (more…)

NIAB Innovation Farm GM workshop 1: Background to GM discussions

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Published on: September 18, 2012


On 12th September, I attended a workshop at NIAB Innovation Farm entitled ‘GM – Is it time for a public good programme?’ There were some very good points made throughout the day, and instead of a chronological account of the presentations, two blog posts on the workshop will outline the main themes that came out of the discussions. The programme is on the Innovation Farm website.

The CEO and Director of NIAB TAG, Tina Barsby, kicked off proceedings by outlining the definition of public good: a ‘good’ that is non-excludable and non-rivalrous, and therefore not produced primarily for profit. Making it clear that the workshop was to be very much focussed on the UK and Europe, Barsby argued that as a market for GM products has failed to materialise, it is time for a non-profit, public good programme, perhaps supported by the government. However throughout the day, it became clear that a commercial market for GM cannot yet be written off.

Barsby went on to describe why GM technology in agriculture is necessary. Farmers battling  crop diseases and world leaders trying to ensure a reliable food supply both have the same problem – crop productivity is too low for the demands placed upon it. GM is one of the solutions to this problem, and while in Europe transgenic crops are not farmed, genetic modification is universally used in conventional breeding; from mutagenesis to marker assisted selection. Genetic engineering has the potential to make crops resistant to disease, contain increased nutrition, and withstand extreme weather conditions. (more…)

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