April 2014 - Weeding the Gems

GARNet 2014 Early Career Researcher Bursaries

Categories: Arabidopsis, funding, GARNet

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Published on: April 29, 2014

The Easter conference season is over and some of our readers will be planning flights, talks and posters for ICAR, ASPB, MPMI or another summer conference abroad. But if that isn’t you this year, don’t worry – GARNet 2014 is much closer to home! And if you’re a student or post-doc, you might be able to win a bursary to cover all your expenses.

Arabidopsis: The Ongoing Green Revolution is in Bristol, so it doesn’t have the glamour of ICAR 2014 in Vancouver, but Bristol does have a Banksy on nearly every corner and lots of good places to eat and drink (like this bar with in-house magicians!). For two days only the city will also be able to boast our great plenary speakers Rob Martienssen, Maarten Koornneef, Andrew Millar and Paul Schulze-Lefert. Our fifth plenary speaker is Bristolian Alistair Hetherington.

Registration is only £120 for students and post-docs, but we’re offering 10 bursaries for GARNet 2014 to early career researchers. These bursaries will cover the registration fee, reasonable UK travel expenses and one night’s accommodation in Bristol. They will be awarded to 5 students or early career researchers invited to give talks, and 5 students who submit excellent abstracts but are not selected for presentations. To register and/or to apply for a bursary, go to: http://garnet2014.org/call-for-abstracts/

banksy for bursaries

Image: ghostly Banksy graffiti on the Thekla by Libby

A sweet surprise: Revealing new roles for sugars in plants

by Guest Blogger

Categories: Arabidopsis, Celebrating Basic Plant Science, guest blogger, Summary for non-specialists

Tags: Arabidopsis, guest blogger

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Published on: April 23, 2014

The fifth post of our Celebrating Basic Plant Science series comes from Mike Haydon, a lecturer at the University of York. He and his research group work on understanding signalling in plants. Here he explains some of his work on integrating sugar metabolism with light signals. You can see more about Mike and his group on his website. The work he discusses below was published in the journal Nature last year (Haydon et al. Nature 502:689-692).

Sucrose

A life based on sugar

Most of us think about sugar every day, be it consciously as we consider our calorie intake, or unconsciously when our brain tells us it’s mealtime. Sugars are among the simplest of carbohydrates and they are the raw material for cellular respiration, which produces energy for almost all living cells. Glucose, a monosaccharide, is the preferred sugar for cellular respiration. Sucrose, most familiar to us as the granulated sugar in our kitchens, is a disaccharide made of glucose and fructose. These, and other simple carbohydrates, are used to build complex carbohydrates such as starch and cellulose in plants, and glycogen and chitin in animals. Sugars are the foundation of cellular metabolism, and produce the wide array of molecules that sustain our carbon-based existence.

The most important process on the planet

Plants, along with algae and some species of bacteria, use photosynthesis to convert carbon dioxide in the air into glucose using energy from sunlight, while producing oxygen as a by-product. Photosynthetic bacteria were responsible for the Great Oxidation Event, which occurred from about 2.5 billion years ago and led to the life-sustaining atmosphere we now live in. Photosynthetic organisms are called autotrophs, because they produce their own sugars to use in cellular metabolism. All other organisms, called heterotrophs, must somehow get their sugars from their environment. For animals, this is ultimately through the plant-based component of their diet. So essentially all the carbon in our bodies was, at some point, converted from carbon dioxide into glucose by photosynthesis. Thus, photosynthesis is probably the most important metabolic process on the planet.

You might think that something so fundamental in biology would be completely understood, and we certainly do know a lot about carbohydrate metabolism. We also know that sugars have functions outside of this basic metabolism. For example in plants they can act as hormones, regulating processes such as cell growth, cell division, flowering time and disease resistance. But there is still a lot we don’t know about how plants regulate carbohydrate metabolism, and sometimes we still find entirely new functions for sugars in biological processes.

How time matters in sugar metabolism (more…)

Novel tools for reducing bias in Next Generation Sequencing of small RNAs

by Guest Blogger

Categories: guest blogger, methods, resource

Tags: guest blogger, methods, resources

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Published on: April 15, 2014

Tamas Dalmay, Professor of RNA Biology at the University of East Anglia (Norwich), has developed a robust, simple method of profiling small RNAs using next generation sequencing. Here he explains his novel HD adapters and why they are more reliable than existing commercial adapters.

Figure 1c from Sorefan et al., 2012: The structure of miR-29b with the Illumina adapters (top) and some of the structures formed by HD adapters (bottom).

Small RNAs (sRNAs) are key regulators of gene expression, and accurate representation of sRNA in sequencing experiments is critical to the interpretation of biological data. Next generation sequencing (NGS) is now the gold standard for profiling and discovering new sRNAs, so it is essential that the tools and protocols used in NGS generate accurate, reliable sequence data.

RNA ligases are essential in creating cDNA libraries prior to NGS sequencing. However, a number of recent publications reported that RNA ligases used in cDNA preparation actually mediate sequence specific ligation, so NGS approaches using these RNA ligases do not represent all sRNA present in biological samples. These publications highlighted the limitations associated with RNA ligases, questioning the reliability of currently widely used NGS approaches and the data generated from them.

Sequence specific ligation occurs because the ligases preferentially ligate ends that are more likely to be close to each other. This means that sRNAs that can efficiently anneal to the adapters have a higher chance of being ligated (Jayaprakash et al. 2011, Hafner et al. 2011 and Sorefan et al. 2012).

While identifying that cloning bias in sRNA libraries is RNA ligase dependent, our group at the School of Biological Sciences, University of East Anglia (Norwich), developed a novel, simple, robust solution to overcome this problem (Sorefan et al. 2012).

We developed a set of adapters (High Definition or HD adapters) that contain degenerated nucleotides, meaning they are a pool of many sequences instead of one fixed sequence. Consequently, many different sRNAs can form a stable duplex with them, leading to better coverage and more quantitative libraries. We have shown that using the HD adapters: (more…)

In pictures: Software Carpentry for Plant Scientists

by Charis Cook

Categories: GARNet, something fun, Workshops

Tags: GARNet workshop

Comments: 1 Comment

Published on: April 11, 2014

Over 30 plant scientists gathered at the University of Warwick this week for our Software Carpentry for Plant Scientists bootcamp. Together we learned to move through space and time using Git, how to make, explore and delete files and directories, how to use Version Control and how to program defensively. As ever we encouraged everyone to Tweet about the event and we’ve collected the tweets in a Storify, which you can access here: sfy.co/ffpW

Some photos from the event are below – enjoy! The photo on the second row is the team that made the event such a success. From left to right: Jason Piper, Charis Cook, Leonor Garcia Gutierrez, Aleksandra Pawlik, Christina Koch and Lisa Martin. Thanks especially to our trainers Aleksandra (sent to us from the Software Sustainability Institute, UK) and Christina, who came all the way from Vancouver.

PlantSci 2014 and Plant Science Careers

by Charis Cook

Categories: resource, UKPSF

Tags: plantsci, resources

Comments: 1 Comment

Published on: April 8, 2014

The GARNet team travelled up to York last week for the PlantSci 2014 conference. It was a fantastic event and I highly recommend it for future years. The variation between talks, which were all perfectly pitched for a general plant science audience, made the sessions exciting and maintained everyone’s interest.

A highlight of the conference was the Panel Discussion on the Future of UK Plant Science. The Panelists – Mike Bushell, Mark Chase, Sarah Gurr, Sandy Knapp and Dale Sanders – responded to the Status Report (download the PDF here) and spoke briefly about what they felt were the most important challenges for the UK plant science community to deal with.

To me, the most significant issues were put forward by early career researchers from the floor. The Panel and the report, which drew data from a community-wide survey, emphasised skills shortages and a lack of young talent entering the field; but several young researchers present spoke out about lack of support for those young scientists that are working in the field.

One person on a PhD program with funding for a short internship in industry or policy found it difficult to find a placement related to plant science. Two final year PhD students from very different research backgrounds spoke of their frustration in not knowing where to look for post-doctoral jobs. Despite being highly trained in areas within the ‘skills gap’ often referred to in reports, including the UKPSF report, they felt that academic post-doc positions (and the uncertain future that comes with them) were the only options they had.

If you feel passionately about education, training and/or plant science careers and career paths, see UKPSF working group call document (PDF) on information on what the UKPSF is doing to tackle these challenges. There will be UKPSF working groups on Training & Skills, Funding, Portfolio Balance, Regulation, and Translation.

Looking for a plant science job? (more…)

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