Photosynthesis for fresh water

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Published on: February 10, 2014

Annegret Honsbein is a post-doc in Anna Amtmann‘s lab at the University of Glasgow. As she explains in this guest post, she is working on an EPSRC project that hopes to harness the power of photosynthesis to desalinate sea water. 

Water covers more than 70% of Earth’s surface but less than 2% of it is available as freshwater. Many of the driest regions of our planet are close to the sea but irrigating fields with seawater – even if diluted – leads to build-up of salt in the soil to levels toxic to all common food crops. Current desalination technologies, such as membrane-based reverse osmosis, are successfully used in large-scale desalination plants, but they are expensive and energy inefficient.

desalinationOur multi-disciplinary EPSRC-funded project takes a synthetic biology approach to the development of an innovative desalination technology based on biological processes. We are a team of biologists and engineers from the Universities of Glasgow, Sheffield, Newcastle, Robert Gordon University at Aberdeen and Imperial College London, led by Dr. Anna Amtmann from Glasgow University.

Our idea is solar energy-fuelled desalination – with a twist. Instead of using solar panels we intend to let photosynthetic microorganisms desalinate the sea water. Cyanobacteria are ideal candidates, and we are currently working with two strains that are naturally able to adapt to a wide range of salt concentrations from fresh to sea water.

In principle, salt is toxic to all living cells, which is why most living systems have developed means to actively export sodium. In some cyanobacteria species that grow to very high densities, this ability means they actually form a low-salt reservoir within their saline environment.

We intend to use this low-salt reservoir as ion exchanger to extract the salt from the surrounding seawater. We aim to engineer cyanobacteria so we can switch off the endogenous salt export mechanism towards the end of their growth cycle, and activate a synthetic intracellular sodium accumulation unit. This synthetic unit will be assembled from membrane transport proteins evolved by different organisms to import sodium and chloride ions.

Our team’s engineers are developing techniques to manipulate the surface properties of the cyanobacteria and effectively separate the ‘salty’ cells from the desalinated water before they die, preventing release of the accumulated salt back into the ‘fresh’ water.

The final stage of the project will be to build a model version of the actual plant that could house our photosynthesis-driven bio-desalination process.

This work is published in: Jaime M. Amezaga, Anna Amtmann, Catherine A. Biggs, Tom Bond, Catherine J. Gandy, Annegret Honsbein, Esther Karunakaran, Linda Lawton, Mary Ann Madsen, Konstantinos Minas and Michael R. Templeton (2014) Biodesalination: A Case Study for Applications of Photosynthetic Bacteria in Water Treatment. Plant Physiology 164: 1661-1676; doi: http:/​/​dx.​doi.​org/​10.​1104/​pp.​113.​233973.

Image c/o Annegret Honsbein.

How do plants remember winter?

Martin Howard is a Professor at the John Innes Centre, one of a small cluster of research institutes in Norwich. In the fourth of our Celebrating Basic Plant Science series, he explains how he uses mathematical modelling to understand how plants remember winter cold and respond to it throughout the year. 

How do plants ‘know’ the correct time to flower? Getting this timing right is vital for reproductive success; flowering in the middle of winter is unlikely to be optimal! Many factors are integrated together to make this critical decision, including the day length.

We have been studying one aspect of this question: How the plant Arabidopsis thaliana perceives and then remembers exposure to winter cold. This fundamental mechanism ensures that flowering doesn’t occur until winter has passed. Interestingly, this memory is quantitative – a longer winter means flowering is faster once it starts (see the image below).  This process is a very nice example of what’s called an epigenetic phenomenon, as the plants store information about winter cold exposure even after the environmental stimulus (cold) has been removed.

So how is this information about cold stored? In Arabidopsis, this is centred on a gene called FLC (Flowering Locus C). When the plant is cold, the FLC gene is turned off. The products of this gene prevent flowering, so turning it off actually stimulates the plant to flower. Over recent years, we have learned a great deal about the operation of FLC and associated genes through genetics and biochemistry, in large part through the work of my experimental collaborator, Caroline Dean. However, despite all this knowledge it was still not clear overall how the epigenetic memory system worked. This was partly due to feedback among the different components, which made arriving at an intuitive understanding a very difficult task. For these reasons, we began to model the dynamics of FLC mathematically in the hope of making sense of these interactions and, we hoped, revealing some underlying simplicity in how the system operated.

Mathematical modelling turned out to be very informative and suggested that FLC gene silencing occurred in an all or nothing fashion inside each cell. (more…)

Collaborations and training in integrative biology

The prevalence of first systems and then synthetic biology in BBSRC and wider UK research funding calls, the establishment of The Genome Analysis Centre (TGAC), the fact that the term ‘big data’ is mentioned in nearly every meeting of any type about the biological sciences … all these point to the irreversible integration of mathematics into biology.

This blog post is for two groups of people: plant scientists who feel they lack the expertise to confidently maneuver in the world of integrative biology; and theoreticians either interested in plant science, or who would rather not have to spend quite as much time dealing with the mathematical problems of the plant scientists in their professional or non-professional circles. (more…)

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.

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
  • 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.


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.

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