Synthetic biology has arrived

by Charis Cook
Categories: conferences, funding, GARNet, synthetic biology
Tags: , , ,
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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: http://ht.ly/l2NXR 

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: ,
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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: resource, systems biology, Workshops
Tags: No Tags
Comments: No Comments
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: , ,
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; 19th 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 21st 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…)

A model tree?

by Charis Cook
Categories: Arabidopsis, Summary for non-specialists
Tags: ,
Comments: No Comments
Published on: April 30, 2013

Just how many things can we really use Arabidopsis thaliana as a ‘model’ for? Certainly our favourite weed has an historic advantage for genomic research. As the first plant genome to be fully sequenced, it has had a long head start for all sorts of ‘omics databases and projects. The A. thaliana databases have proved useful for researchers working on other plant species too; even today Arabidopsis genomic sequences are used to fish un-annotated genomes for genes and motifs. A recent paper questions how appropriate it is to transfer in vivo Arabidopsis research on xylem and water flow to woody plant species. Yes, how useful is weedy (in all senses of the word), tiny A. thaliana to understand massive woody trees? The answer? It’s not perfect, but it’s OK.

Tixier et al. (JXB, doi:10.1093/jxb/ert087, Open Access) carried out a series of experiments to test A. thaliana’s value as a model for wood development. It turns out wildtype Arabidopsis is a good xylem hydraulic model, with tissue structure and vessel dimensions that are reliably representative of larger woody plants. To quote Tixier et al., “A. thaliana can be used to measure specific conductivity and cavitation resistance in an accurate and reliable approach,” and far more conveniently than trying to use an 8 metre tall tree to do it. However, the model plant is not appropriate for some xylem parameters, such as end-wall sensitivity. A. thaliana xylem also responded differently to abnormal environmental conditions and cell wall structure manipulation.

As an aside, Wendrich and Weijers present another system for which A. thaliana is an appropriate model in this month’s Tansley review in New Phytologist (doi: 10.1111/nph.12267). They describe current understanding of morphogenesis in the early A. thaliana embryo, and identify five key questions that still remain to be answered.

Image credit: Climbing plant by Heriberto Herrera, via stock.xchng.

CellSet confocal image analysis

by Guest Blogger
Categories: resource
Tags: , , ,
Comments: No Comments
Published on: April 25, 2013

Michael Pound is an image analyst at CPIB. He kindly agreed to write a guest post for GARNet on his recent project, confocal image analysis software CellSeT. 

CellSeT, which was recently published in Plant Cell (24:1353), is open source software which analyses confocal images of plant cells. CellSeT can extract information including fluorescence and membrane polarity objectively and quickly. A simple workflow begins with the program filtering noise out of the image, and then it segments the image into individual cells. Confocal images can produce excellent slices through root meristems, however some incorrect segmentation is inevitable deeper into the root tissue. CellSeT was designed with this in mind, and the user can then manually refine the cell segments. This optional manual step is followed by an automatic refinement using active contours, aimed at improving accuracy and reducing subjectivity. Finally the cells can be manually assigned semantic tags and measured. Plugins, which are also open source, allow users to carry out more specialised functions, or cell geometries can be exported into modelling packages such as OpenAlea.

CellSeT will be useful to researchers who produce confocal images at a cell scale, usually of root tissue, although CellSeT has been shown to work on other regions such as the plant leaf. The plugin architecture allows anyone with a basic programming knowledge to perform additional image analysis within each cell. For example, an existing plugin is used to detect and quantify nuclear fluorescence in a separate colour channel to the cell walls.

You can download CellSeT from Sourceforge. Due to its use of Windows graphics libraries, CellSeT only runs in Windows. If you don’t use Windows, you will have to run a virtual windows environment to use it. CellSeT works successfully on software such as parallels if this is necessary.

Image credits: CPIB 

Dundee’s week of plant science conferences

by Charis Cook
Categories: conferences, UKPSF
Tags: , ,
Comments: 1 Comment
Published on: April 23, 2013

Well, what felt like the biggest week of the year for UK plant science is now over. Last week, the UK Plant Phenomics Network meeting, UK PlantSci 2013, and Monogram all happened at the University of Dundee. It was a whirlwind week of inspirational talks, updates, people, and a drop or two of Scottish whiskey.

PlantSci 2013 was the second annual conference organised by the UK Plant Sciences Federation. Representatives from fields as wide-ranging as basic and applied research, industry, molecular biology, ecology, and science communication spoke to an auditorium packed with people from all stages of their careers.

I have committed myself to no less than 3 write-ups of PlantSci 2013, so I won’t blog about it here, but I will do my best to write up David Baulcombe’s keynote talk as soon as I can. As far as I know, it hasn’t had a write-up yet and was very inspirational. However, until I can share my reports, there are plenty of PlantSci-related media to immerse yourself in.

The extraordinarily talented Rebecca Nesbit of the Society of Biology managed to write-up two sessions of PlantSci 2013 while live-tweeting. Her post on the first keynote talk, ‘Feeding 10 Billion People on a Finite Planet’ is here and her second post, on the Inspiring Future Generations session, is here.

At one point the conference hashtag #plantsci2013 was one of the most used phrases on Twitter! Twitter coverage of the conference extended well beyond the lecture theatre in Dundee as people all over the world followed the conference by the live-tweets and interacted with delegates who were present. For a fairly comprehensive overview of all the talks and the conference in general, take a look at the Storify I made of the Twitter feed. The shortlinks in the tweets will take you to papers or resources the speakers mentioned in their talks.

Monogram is the annual conference on UK small grain cereal and grass research, again attended by breeders and other stakeholders as well as basic and applied researchers. The Monogram blog will soon have a post about the conference, but in the mean time the Storify of tweets from the meeting is here.

Image credit: left image, Anne Osterrieder, right image, Charis Cook

 

Mathematics in the Plant Sciences

by Charis Cook
Categories: bioinformatics, Workshops
Tags: , ,
Comments: No Comments
Published on: April 17, 2013

After the ELIXIR/GOBLET workshop before Easter, I headed to Nottingham for another workshop, this time as an onlooker. In a brilliantly eccentric set-up there were actually two parallel workshops, and the participants hopped between the two and had lunch, dinner, and tea breaks in the same rooms. The event I was officially attending was the final meeting of the ‘Systems approaches to study hormone regulated root growth’ US Partnering Award (USPA). The Sixth Mathematics in the Plant Sciences Study Group was in its final two days during the USPA workshop, and some of its attendees presented their research at the USPA meeting or sat in on a session they were particularly interested in.

The Study Groups are hackathon-style workshops at which mathematicians and computer scientists take on problems set by plant scientists. This year’s problems included analysing 300 standing-electron microscopy images of cell walls, and modelling nitrogen release from the symbiosome. As someone with a traditional science background, of course the solutions the teams came up with were a bit beyond me – which is, after all, the whole point of the Study Group. I was impressed by the solutions that had appeared after just four days of work, which ranged from programmes to quantify subtle differences in images, to a model which predicted the optimum light input for photosynthesis and explained plant acclimatisation to variable light sources.

There will be another Study Group and when it is announced, we’ll keep you informed. If you know any mathematicians or computer scientists with a liking for academic science problems and who likes hackathon events, let them know about Study Groups and encourage them to send their details to Susie Lydon, who organises the events. Similarly if your plant research has thrown up a thorny problem which needs specialist expertise, think about submitting it for the next Study Group.
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  • Synthetic biology has arrived by Charis Cook

    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 [...]

  • Monogram 2013 by Guest Blogger

    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 [...]

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