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. 

Spring funding round-up

Categories: funding, UKPSF
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Published on: February 28, 2013

Spring 2013 is full of deadlines for various plant science funding opportunities. I compiled a list of calls that close in the next few months here. For up-to-date funding news, check the UKPSF website.

Research funding, partnering awards, and fellowships

BBSRC Strategic Longer and Larger Grants: Outline proposal deadline 18 April. Selected applicants will then be invited to submit full applications by January 2014. These sLoLa grants are worth over £2M and can last up to 5 years. The proposed projects must be in line with BBSRC Strategic Priorities, and in this round proposals are particularly encouraged in ‘innovative routes to fine and platform chemicals’ and ‘mechanisms for enhancing cellular productivity.’

BBSRC Responsive Mode: Deadline 24 April. Proposals are accepted to the four research committees for projects in line with BBSRC Strategic Priorities. Remember that plant scientists may apply to Committees B and D. For non-plant specific generic genes, development, technology, engineering, and maths approaches to biology, consider Committee C.

BBSRC Synthetic Biology China Partnering Award: Deadline 30 April. Up to 5 awards will be co-funded with the Chinese Academy of Sciences (CAS). The funds are to form collaborations between UK- and China- based groups who are current BBSRC or CAS grant holders. The four key areas highlighted in the call are fairly well suited to plant science, so if you have Chinese contacts and are open to synthetic biology, do give this partnering award consideration.

BBSRC Enterprise fellowships: Deadline 17 May. This enterprise-driven award provides a salary for a year spent on developing a business plan and seeking investment, access to mentors and business experts, and business training. Academics, research staff, or post-grads may apply. (more…)

Were you there? Arabidopsis as a model plant

Categories: Arabidopsis
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Published on: February 26, 2013
A reproduction of a painting by C. A. M. Lindman (1856–1928)

The history of Arabidopsis as a model organism and of the Arabidopsis Genome Project is the story of the birth of modern plant science, full of visionaries and phenomenal teamwork. No doubt some readers of this blog were present at the dawn of the Age of Arabidopsis, but many others think of Arabidopsis as an established part of the plant science landscape. I myself can’t imagine pre-Arabidopsis plant research, before seed stock catalogues, genome sequences, and BLAST. For all you early career Arabidopsis researchers  this is your opportunity to catch up on the history of this most-researched weed. For those of you who remember it, I hope I got most of it right!

German scientist Friedrich Laibach first suggested Arabidopsis as a plant model species in 1943. He noted that A. thaliana was easy and fast to grow, showed a lot of natural variation, was amenable to cross-breeding between varieties, and generated a lot of progeny. By the 1960s a number of researchers in Germany and a few elsewhere were working on Arabidopsis.

The first annual Arabidopsis Information Service was put together by Gerhard Röbbelen in 1964, and you can read an electronic version of it on TAIR. It is interesting to see the kind of research going on in the ’60s – authors report X-ray and biochemical mutants, growth and development under certain conditions, and methods to induce mutations and grow sterile seedlings on agar. A year later, the first Arabidopsis Symposium met in Göttingen. You can see a picture of the delegates here.

It took twenty more years for Arabidopsis to became widely used worldwide. Albert Kranz, at the Botanical Institute of the Johann Wolfgang Goethe University, collected and maintained Arabidopsis seed stock for the community and took over the Arabidopsis Information Service in 1974. During this time, early identification of embryo-lethal mutants and the small genome size, and by the end of the 1980s, reliable Agrobacterium-mediated gene transfer, were all added to the list of benefits to working with Arabidopsis.

In 1989, James Watson, by then the Director of Cold Spring Harbour Laboratory, called a meeting to discuss the use of Arabidopsis as a model for genetic research. A year later, the newly formed Multinational Arabidopsis Steering Committee (Marc van Montagu, Caroline Dean, Richard Flavell, Howard Goodman, Maarten Koornneef, Elliot Meyerowitz, Jim Peacock, Yoshiro Shimura and Chris Somerville) published a report outlining plans to sequence the whole Arabidopsis thaliana genome. At the time, the project sounded overly ambitious and unlikely to be completed – A. thaliana has a relatively small genome, but at around 120 million base pairs long it was a mammoth project. (more…)

Ash Dieback News

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Published on: February 21, 2013


This video is an introduction to a series of filmed talks from the Forestry Commission Plant Health Conference. It introduces the ash dieback problem nicely and places it in a wider context. A number of experts give their opinions on how to approach combatting the disease.

Another new tree health resource is the UKPSF’s Ash Dieback web resource, which was launched this week. Mimi Tanimoto, Executive Officer of the UKPSF, said, “Speaking to scientists who wanted to do something to help combat ash dieback, I found a recurring problem that they were unsure of what else was happening. It was clear that by joining up the various projects we could better tackle the disease.” The website will be updated regularly with news, and it is possible to sign up on the site to receive these updates via email. Anyone who has news that they would like added to the site can contact Mimi at

The final piece of ash dieback news is that the Open Ash Dieback project, which crowdsources genome analysis of ash trees and the fungal pathogen Chalara fraxinea,published their first paper last week. Crowdsourcing genomic analyses of ash and ash dieback – power to the people by researchers from several UK universities, lead by two groups at the Sainsbury Laboratory, was published in GigaScience 2:2 doi:10.1186/2047-217X-2-2.

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: 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.

Transpiration is perfectly in tune

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Published on: February 19, 2013

Plants contain a continuous water column from the roots, where water is absorbed, to the leaves, where water is lost through evaporation via the stomata. When a plant’s cells require water, opening stomata makes water potential in the xylem strongly negative and water is pulled from the soil into the roots and into the xylem strongly and quickly. However, the water potential gradient can be too steep, causing cavitation (bubbles) in the xylem, which slows down water transport. The optimum transpiration rate occurs when water potential and cavitation are balanced in the right way. According to research published recently in New Phytologist, plants are able to maintain a transpiration rate very close to the maximum theoretical transpiration potential, allowing partial cavitation but not letting it limit hydraulic conductivity.

Here, Manzoni et al. from Amilcare Porporato’s group at Duke University, compared the theoretical optimum transpiration rate with actual transpiration ates in a number of tree species (grouped into boreal, temperate, Mediterranean, tropical dry, and tropical moist species). Their parameters for calculating the theoretical optimum were extensive, including soil water potential, xylem hydraulic conductivity, and canopy height.

The actual maximum transpiration rate of these species was then collected from published papers, and sorted according to climate and the conditions under which the analysis was done. Only the data from well-irrigated systems was used. The average observed peak transpiration rate was close to the theoretical maximum transpiration rate, and both were fairly conserved among plant types of a similar size in a particular climate. (more…)

Corpse Flower

Categories: Friday Film, something fun
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Published on: February 15, 2013

If you have even been close to a hawthorn tree, you will know that yesterday’s post about pretty roses and petunias didn’t tell the whole story about floral smells. Today, lets consider a flower far smellier than mildly unpleasant hawthorn blossoms – the fascinating titan arum, Amorphophallus titanum, sometimes also known as the corpse flower. It has the largest unbranched inflorescence in the world, emits a powerful, horrible smell like rotting flesh, and is thermogenic.

Shirashi et al. (2010, Biosci Biotechnol Biochem 74:2550) published observations of a titan arum in flower. When the petal-like spathe began to open, the plant emitted a smell like rotten fruit. As time went on, the smell became stronger and more unpleasant. When the spathe opened fully, revealing the tall spadix, the spadix became up to to 5°C hotter than the ambient temperature and secreted a strong smelling fluid like rotton flesh. The spathe was open for around 12 hours.

Shirashu et al. identified the odorous chemical emitted by the titan arum as dimethyl trisulphate, a product of bacterial decomposition of mammalian flesh. It is emitted by a few other plants, all of which, like the corpse flower, are pollinated by insects that feed on rotting flesh.

The titan arum is an impressive, but rather gruesome, plant. And like all gruesome things, it attracts visitors to science outreach events! The video above is about the Corpse Flower attraction at the Museum of Natural Science in Houston.

Video credit: VOA News, via YouTube. 


Valentine’s Volatiles

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Published on: February 14, 2013

Plenty of flowers are beautiful and expensive, but the lovely rose scent makes roses the perfect traditional gift to your Valentine. And since it is Valentine’s Day today, and this is a plant science blog, here’s a brief review of the science of floral scents and a recently published paper on the topic (roses not included).

Despite rose breeders managing to come up with flowers with stronger, subtle, or new scents from new rose varieties, the science of floral scents is not well understood. Floral scent can be under stronger natural phenotypic selection than flowers (Parachnowitsch et al. 2012; New Phyt. 195:667), but the agents of selection may be any number of organisms including pollinators and herbivores and the main influencing factor on scent evolution is not known (Theis and Adler 2012; Ecology 93:430). 

The molecular mechanism and regulation of biosynthesis of the volatile, low-molecular weight compounds that cause floral scent is also fairly uncharacterised. They are mainly products of the terpenoid, fatty acid, and phenylpropanoid pathways. Recently a group from the Hebrew University of Jerusalem characterised a regulation mechanism of the phenylpropanoid volatile biosynthesis pathway (Spitzer-Rimon et al. 2012; Plant Cell 24:5089).

All phenylpropanoids share the same precursor, Phe, which is biosynthesized via the shikimate pathway. A transcriptional regulator ODORANT1 (ODO1) regulates shikimate pathway enzymes and affects metabolic flow toward phenylpropanoid production. Another transcriptional regulator, EMISSION OF BENZENOIDS II (EOBII) directly regulates ODO1’s expression, indirectly affecting the shikimate pathway and the biosynthesis of phenylpropanoid volatiles. (Van Moerkercke et al. 2001, Plant J 67:917; Verdonk et al. 2005, Plant Cell 17:1612).

Working on petunia, Spitzer-Rimon et al. identified EOBI, another regulator of floral scent. (more…)

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