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Categories: Brassica, conferences, funding, GARNet, UKPSF

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Published on: January 24, 2014

GARNet news

Lisa and I went to the Brassica Growers Association Conference on Tuesday. I wrote two posts on it over on the UK-BRC website, and Lisa put together a very informative Storify of tweets on the #BGAconference stream.

The UK Plant Sciences Federation has been collecting opinions, facts and data for the past year or so and is now ready to launch a report entitled UK Plant Science: Current Status and Future Challenges. Lisa and I helped out with this report so keep an eye out for it on Tuesday and let us know what you think!

I went to the SEB Synthetic Biology conference last week and have written a short report for the SEB Bulletin about it – I’ll share it when it is published. There was some excellent plant science there. Antonio Scialdone presented the plant-arithmatic work from Martin Howard’s lab – you can read his open access 2013 paper modelling starch degredation over night here (Scialdone et al., eLife 2013;2:e00669). Oliver Ebenhoeh discussed how mathematical models for photosynthesis and plant metabolism can help synthetic biology be done in plants and other photosynthetic organisms.

On the GARNet website

If you missed some January funding deadlines, there are plenty more opportunities to submit your proposal – take a look at the funding round-up on our website for ideas for fellowships, travel, collaborations or straightforward research grants.

Lisa is continuing to write her weekly Arabidopsis research round-up, which you can find on the GARNet news pages. It’s the best way to keep informed of what fellow UK Arabidopsis researchers are up to. This week, papers from GARNet committee members Heather Knight and Cyril Zipfel feature.

Your chance to present your work

PlantSci 2014 is in York on 31 March/1 April, and abstract submission is open until the end of February. There are two £200 cash prizes to be won by early career researchers giving short talks, so make sure you submit an abstract! There won’t be a traditional poster session, but delegates are invited to bring mini-posters to discuss during the networking sessions. Abstracts for the mini-posters will be included in the abstract book.

Further away in September, GARNet 2014 is your second chance to present your work at either a poster session or as a short talk. Registration and abstract submission are both open, and news about special opportunities for students will be coming very soon.

Finally, I’ve been reliably informed that the FSPB/EPSO Plant Biology Conference organisers are looking for proposals for short talks for the Big Data in Plant Science session, so if you’re planning on going and do ‘big data,’ think about submitting an abstract!

How do plants remember winter?

by Guest Blogger

Categories: Arabidopsis, Celebrating Basic Plant Science, guest blogger, synthetic biology, systems biology

Tags: Arabidopsis, celebrating basic plant science, John Innes Centre, mathematical modelling

Comments: 4 Comments

Published on: January 14, 2014

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…)

This much is known…Arabidopsis science-art

by Guest Blogger

Categories: Arabidopsis, Friday Film, something fun

Tags: 25 years, Andrew Stryan, animation, Arabidopsis, art, Gordon Simpson, movie, plantsci, Science, scientific research, University of Dundee, video, vimeo

Comments: 1 Comment

Published on: January 10, 2014

Proving that science and art aren’t mutually exclusive, check out this gorgeous animation that has recently been produced by engineer-turned-Fine Art student Andrew Styan.

this much is known from Andrew Styan on Vimeo.

Andrew recently took part in a science-art course, tutored in part by Dr Gordon Simpson, an Arabidopsis researcher who works within Dundee’s Department of Plant Sciences.

Inspired by Dr Simpson’s work, Andrew’s animation This Much is Known represents 25 years of Arabidopsis research and demonstrates how our understanding of this little weed has expanded in such a relatively short time.

Using the Scopus database, he searched for all Arabidopsis papers published in the last 25 years, and the keywords associated with them. Each bubble that appears on the screen represents a different keyword, with the size of the bubble growing as more papers on that topic are published.

I think it’s very clever and very beautiful! Thanks Andrew, and Gordon!

If there are any other budding science-artists out there who have produced some cool work on Arabidopsis or other plant science, we’d love to see it so please email lisa@garnetcommunity.org.uk.

Register now for GARNet’s 2014 events

by Charis Cook

Categories: Arabidopsis, bioinformatics, conferences, GARNet, Workshops

Tags: conferences, GARNet, GARNet workshop, Software Carpentry

Comments: No Comments

Published on: January 6, 2014

We have been busy arranging two great events for 2014! Registration for both Software Carpentry for Plant Scientists (9-10 April) and Arabidopsis: The Ongoing Green Revolution (9-10 September) is now open.

On 9-10 April we are hosting a Software Carpentry bootcamp for plant scientists – an Introduction to Programming for Biologists. For those of you who don’t know about Software Carpentry, it is a foundation that teaches good practice in scientific computing, with the aim of providing all scientists with basic, but reliable and transferable, programming skills. If you’ve ever run through the rain to Computing to have a large ChIP-chip dataset split so you can attempt an Excel analysis on it, you’ll know how valuable that is (based on real events – feel free to insert your own experiences there …)!

We’ve worked with the Software Sustainability Institute to develop a programme suitable for both complete beginners and scientists how know their way around the Terminal/Command Prompt but want to improve their skills and learn how to write reliable, re-usable code they can share with their colleagues and collaborators. Registration is £50 and discounted on-campus accommodation is available.

Later in the year, the GARNet general meeting is returning for one time only on 9-10 September at the University of Bristol. Our theme is ‘Arabidopsis: The Ongoing Green Revolution’. We have a line up of excellent speakers, including plenary talks from Alistair Hetherington (University of Bristol), Andrew Millar (University of Edinburgh), Rob Martienssen from Cold Spring Harbor Laboratories, and Paul Schulze-Lefert and Maarten Koornneef from the Max Planck Institute for Plant Breeding Research.

The full line-up and registration details can be found by visiting www.garnet2014.org. More information will appear on there closer to the time of the conference. Registration costs £150 for two days, lunch and refreshments on both days, and a drinks reception on the afternoon of 9 September. We’d also love to see you at our conference dinner on the evening of the 9 September at the Bristol Marriott Royal Hotel (£44 per head for three courses and wine on the tables).

What makes one species different from another?

by Guest Blogger

Categories: Celebrating Basic Plant Science, guest blogger

Tags: Begonia, genomics, guest blogger

Comments: No Comments

Published on: December 10, 2013

In the third of our series of blog posts Celebrating Basic Plant Science, Catherine Kidner from Edinburgh’s Royal Botanic Garden explains how she pinpoints what makes a species a species. This sheds light onto what drove that species’ evolution. Catherine spoke about her research at a conference earlier in the year – you can see her talk in this video.

Catherine Kidner uses genomic data to understand why Begonia like these have evolved into different species

There are likely to be about 9 million species on Earth (not counting bacteria). Each species has traits which define it and allow it to thrive in its niche. My research group at the Royal Botanic Garden in Edinburgh is trying to understand the diversity around us, so we need to know what these traits are and how they contribute to the success, or otherwise, of the species.

There are difficulties with this approach to understanding diversity. For a start, traits we think are important may not be that important to the species concerned. Also, some traits critical to a species’ success might be difficult to measure, for example phosphate uptake by roots; or be seen only on very specific occasions, like response to a particular pathogen.

Using genetics to define differences between species

We get around these problems by looking at genetic differences between species. New sequencing technologies make it relatively quick and easy to sequence the genome of an individual.

In a typical genome, around 25 000-50 000 genes code for proteins. If we want to know how two species differ we can compare sequences of these protein coding genes and see which types of gene differ the most between species. These changes in gene sequences mean the proteins work differently.

Not all genes are expressed, that is translated into proteins, all the time, and we can see which sets of genes are expressed at particular times and in different organs, like petal or leaf. So when looking at how species differ, we can also look at which genes show the biggest changes in expression level, which would mean one species having more of a particular protein than the other.

Having a list of which genes show sequence changes and which show expression changes is not much help if it’s just a list of genes xzy, abc and rst. What really makes this a useful technique are the huge databases which have been built up over the past 20 years. Work in model species such as yeast, Arabidopsis, mouse and Drosophila have determined functions for many genes in typical genomes. We can match the genes in our ‘interesting genes’ lists to sequences from these model organisms to find out that, for example, gene xzy looks like a disease resistance gene, or gene abc looks like a gene that controls root growth rates.

A typical comparative study might highlight hundreds of genes which differ between species, so even with good descriptions of function we still have a lot of data to sift though to find patterns. We can simplify the lists by using GO (Gene Ontology) terms. This is a way of describing what genes do in a very defined way.

(more…)

A tale of two models

by Guest Blogger

Categories: Arabidopsis, guest blogger, Summary for non-specialists

Tags: guest blogger, moss, summary for non-specialists

Comments: No Comments

Published on: November 19, 2013

James Lloyd (University of Leeds) was the lead author on last month’s Plant Journal paper on nonsense-mediated mRNA decay, which demonstrated that working on a model plant can sometimes be a hinderance rather than a help. In this guest post he explains how he and his supervisor Brendan Davies overturned widely held assumptions about NMD in plants – by working on moss.

Physcomitrella patens, the model moss, growing on agar.

Plant biology has been greatly advanced by the use of Arabidopsis thaliana as a model. Fantastic community resources, such as mutant collections and numerous genome sequences from natural accessions have aided researchers in all areas of plant sciences. However, A. thaliana is far from perfect. Nonsense-mediated mRNA decay (NMD) is a little heard of pathway to regulate transcript stability and it has recently been shown to be involved in pathogen response in A. thaliana (Rayson et al., 2012).

The mechanism of mRNA decay has largely been worked out in animals and revolves around the phosphorylation of an RNA helicase called UPF1 by a kinase SMG1. However, fungi and A. thaliana both lack the SMG1 kinase, so it has been a mystery how the fungal and plant proteins are phosphorylated. We have recently shown that SMG1 is not animal specific but is an ancient component of the NMD machinery, appearing in the genomes of all plants examined, with the exception of A. thaliana. SMG1 is even found in the genome of A. lyrata, a close relative of A. thaliana.

Arabidopsis thaliana, the model plant.

The lack of SMG1 in the genome of A. thaliana meant that we had to use another plant as our model to understand the role of SMG1 in the plant kingdom. Enter moss! Physcomitrella patens is the model moss, with a sequenced genome and a high rate of homologous recombination it is a relatively simple task to identify and delete any gene in the genome. The rate of homologous recombination is much lower in flowering plants than it is in moss, meaning that short (around 1 Kb) of moss genomic DNA from upstream and downstream of a gene of interest can be cloned around an antibiotic selection gene and then transformed into moss cells and a large proportion of antibiotic resistant plants have the gene of interest deleted.

We deleted SMG1 from moss and found that NMD was compromised thus placing plant SMG1 in the NMD pathway (Lloyd and Davies, 2013). Therefore, many plants including crops like rice and maize are likely to rely on SMG1 to control gene expression through NMD. Future research will hopefully reveal why A. thaliana has lost SMG1 and if another kinase has replaced SMG1 in this plant.

A. thaliana has been useful in characterising other components of the NMD pathway in plants, such as UPF1 and understanding the biological role in plants (such as controlling the pathogen response). However, it was limited in helping us understand the NMD pathway of commercially important crops and it was moss to the rescue!

Animal researchers have long used multiple, evolutionarily diverse models, including but not limited to fruit flies, C. elegans, zebrafish, frogs and mice. Despite big differences between invertebrates like fruit flies and vertebrates like humans, a great deal about human biology has been learnt by using these organisms in the lab.

Many important questions cannot be answered by simply studying A. thaliana, big differences in fundamental processes exist between accessions. Therefore, multiple models are needed in plant sciences. Moss is just one plant that can help compliment research in other plant species, using the powerful genetic tool of homologous recombination.

References:

Lloyd JPB and Davies B (2013) SMG1 is an ancient nonsense-mediated mRNA decay effector. The Plant Journal 1365-313X http://dx.doi.org/10.1111/tpj.12329

Rayson S, Arciga-Reyes L, Wootton L, De Torres Zabala M, Truman W, et al. (2012) A Role for Nonsense-Mediated mRNA Decay in Plants: Pathogen Responses Are Induced in Arabidopsis thaliana NMD Mutants. PLoS ONE 7(2): e31917. doi:10.1371/journal.pone.0031917

Images courtesy of James Lloyd.

Research funding: What strategy is best?

by Charis Cook

Categories: funding

Tags: funding

Comments: No Comments

Published on: November 14, 2013

I was invited to the EPIC Planning Committee meeting after October’s Epigenomes of Plants and Animals conference at the John Innes Centre, and during the meeting we discussed what I think is the biggest issue in research strategy. That inspired this post, and a probably series of posts on the EPIC website – I’ll share them when they’re up.

Is it best to spread resources and support/fund/promote as wide a breadth of research as possible, or focus on a few areas in more depth?

The problem with the ‘catch-all’ approach to research funding is that it inevitably does not catch all. In the UK plant science is funded via the BBSRC, and a large part of that funding is allocated through a committee-determined responsive mode structure. As the committees, made up of jobbing scientists, are only gently guided by broad strategic priorities, this is essentially catch-all. However, some plant science areas now occupy very small niches and are in danger of extinction. Plant and pathogen taxonomy, physiology, soil science and some plant species, even those of economic value like ornamental flowers, soft fruits and many vegetables, have all been neglected.

The alternative is to try and deliver an effective strategy for a few areas, ensuring that these areas have a healthy, broad basic research base from which any innovations that arise can efficiently be turned into commercial product. The difficulty is, of course, deciding which areas to focus on. The decision cannot be driven by fashions or trends, nor unduly influenced by current strengths and expertise, which are all reasons for gaps in the catch-all approach. Modelling and predicting global and local challenges, other countries’ research strategies, risk of failure and impact of success, existing expertise and facilities – these and many more factors should all be considered.

It would be a cop-out to write this post and not say what my opinion is. This issue is of course far more complex than this article allows, and there has to be flexibility in any system. There are big, bad consequences of choosing the wrong areas to invest in, but there are similar, unpredictable, ramifications to accidental skills gaps in both basic and translational science caused by thinly spread funding. So my inclination is to think that within a hypothetical altruistic and infinitely flexible innovation ecosystem, the world would be better served by a focused, in-depth strategy.

What do you think? Leave a comment or get in touch on Twitter.

Staying together: green beginnings

by Guest Blogger

Categories: Celebrating Basic Plant Science, guest blogger

Tags: algae, genomics, guest blogger

Comments: No Comments

Published on: November 5, 2013

This seaweed, Ulva linza, would only exist as undifferentiated cells if not for bacterial signals

The second of our series of blog posts Celebrating Basic Plant Science is written by Juliet Coates, Lecturer in Molecular Genetics at the University of Birmingham.

Living organisms can be categorised in a number of ways, but one very obvious “either/or” distinction is between organisms that are made up of a single cell – unicellular organisms – and those that are many-celled, or multicellular.

The multicellular state arose many times during evolution: animals, plants, algae, amoebae, fungi and bacteria can all be multicellular. Multicellular organisms completely underpin life on Earth as we know it today – and they all must have evolved from single-celled ancestors. We understand a little of why they might have done so, as being multicellular gives a number of competitive advantages: increased size and improved nutrient collection being just two. Yet how multicellular organisms came to be is a key biological problem that is still largely unanswered.

I am a plant scientist, so I am particularly interested in the origins of multicellular green things: plants and algae. Without becoming multicellular, plants would never have colonised the land, and the evolution of multicellular plants and algae was key in shaping our climate, our ecosystems and our oxygen-rich atmosphere. How green multicellularity arose seems to me to be a really fundamental thing to understand, but it is a little-addressed question. Here I’ll give an overview of the important findings to date about the evolution of multicellularity.

(more…)

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