Weeding the Gems - Page 52 of 67 - the GARNet community blog

Starting your interdisciplinary journey

Categories: guest blogger, resource, systems biology, Workshops

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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: celebrating basic plant science, UK PlantSci 2013, UKPSF

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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; 19^th 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 21^st 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: Arabidopsis, Journal of Experimental Botany

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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: guest blogger, resource

Tags: CPIB, integrative biology, Plant Cell, resource

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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: Monogram, UK PlantSci 2013, UKPSF

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: bioinformatics, modelling, workshops

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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.

Ready for UK PlantSci 2013

by Charis Cook

Categories: Friday Film, UKPSF

Tags: Friday film, UK PlantSci 2013, UKPSF

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Published on: April 12, 2013

To whet your appetite for next week’s UK PlantSci 2013 conference in Dundee, here are clips of the keynote speakers Charles Godfray (University of Oxford) and David Baulcombe (University of Cambridge). I think that the Godfray clip can be considered a very unofficial ‘preview’ of his keynote lecture Feeding 10 Billion People on a Finite Planet, which will be on Tuesday morning. David Baulcombe’s interview probably isn’t linked to his Of maize and men or peas and people lecture on Wednesday morning, but it is still a good watch – an interesting and balanced discussion about GM.

If you’re not coming up to Dundee, you can still keep up with these talks and all the others live on the Twitter hashtag #PlantSci2013. I’ll post the blog posts and reports about the conference here once they’ve trickled out, too.

Video credits: The Oxford Martin School and LEAF

Bioinformatics and Data Analysis Training for Plant Scientists

by Charis Cook

Categories: bioinformatics, GARNet, Workshops

Tags: bioinformatics, GARNet workshop

Comments: 2 Comments

Published on: April 11, 2013

Large datasets are now the norm in modern biology. Modelling is progressing from the protein and molecular interaction level to tissue, organ, and whole-plant scales; while everything from genomics through to phenomics and, increasingly, field-level and multi-scale biology involves high throughput experiments. All of these necessitate ever greater computing power and use of complex analysis tools and software. We need you to tell us (click for extremely short survey) which areas of bioinformatics and data analysis you would benefit from training in, ahead of an upcoming GARNet workshop (in association with iPlant and the Hartree Centre).

The iPlant Collaborative is a community of researchers, educators, and students working to deliver a useful and usable cyberinfrastructure for plant science. Users are able to store and analyse their data online, and use iPlant tools for genome assembly, comparative genomics, CHiP and RNA Seq analysis, and much more. A working group is developing modelling tools at the moment, which will take advantage of the high performance computing power iPlant provides, and will support the construction, parameter estimation, sensitivity analysis, and utilization of models. All the resources are free for users worldwide and all are web based, requiring no specialist hardware at the user’s location. (more…)

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