Arabidopsis Research Roundup: August 27th

The Arabdopsis Research Roundup broadens its remit this week. As well as including three original research papers, which look at casparian strip formation, light and hormone signaling, we also highlight an important viewpoint article that aims to set standards for synthetic biology parts. In addition we include a meeting report from a plant synthetic biology summer school and interviews with plant scientists at the JIC, Caroline Dean and Anne Osbourn.

Kamiya T, Borghi M, Wang P, Danku JM, Kalmbach L, Hosmani PS, Naseer S, Fujiwara T, Geldner N, Salt DE (2015) The MYB36 transcription factor orchestrates Casparian strip formation Proc Natl Acad Sci USA Open Access

GARNet Advisory Board Chairman David Salt (Aberdeen) leads this international collaboration that looks at the (relatively) poorly understood Casparian strip (CS), a lignin-based filter that lies in root endodermal cells. Formation of the CS is initiated by Casparian strip domain proteins (CASPs) that recruit other proteins, which begin the process of lignin deposition. In this study the authors look upstream this process and identify the transcription factor MYB36 that directly regulates expression of CASPs and is essential for CS formation. Ectopic expression of MYB36 in root cortical tissues is sufficient to stimulate expression of CASP1-GFP and subsequent deposit a CS-like structure in the cell wall of cortex cells. These results have implications for the design of future experiments that aim to control how nutrients are taken up by the plant as even though myb36 mutants have a ‘root-defect’, they also have changes to their leaf ionome.

Sadanandom A, Ádám É, Orosa B, Viczián A, Klose C, Zhang C, Josse EM, Kozma-Bognár L, Nagy F (2015) SUMOylation of phytochrome-B negatively regulates light-induced signaling in Arabidopsis thaliana Proc Natl Acad Sci USA Open Access

Ari Sadanandom (Durham) and Ferenc Nagy (Edinburgh) are the leaders of this study that investigates the precise function of the PhyB photoreceptor protein. PhyB interacts with a wide range of downstream signaling partners including the PHYTOCHROME INTERACTING FACTOR (PIF) transcription factors. The small ubiquitin-like modifier (SUMO) peptide is conjugated to larger proteins to bring about a variety of signaling outcomes. In this case the authors find that SUMO is preferentially attached to the C-term of PhyB under red light conditions, a relationship that occurs in a diurnal pattern. SUMOylation of PhyB prevents interaction with PIF5 whilst the OVERLY TOLERANT TO SALT 1 (OTS1) protein likely de-SUMOlyates PhyB in vivo. Altered levels of PhyB SUMOylation cause distinct light-responsive phenotypes and as such this paper adds another level of regulation to the already complex known network that controls light signaling.

Schuster C, Gaillochet C, Lohmann JU (2015) Arabidopsis HECATE genes function in phytohormone control during gynoecium development Development. Open Access

Christopher Schuster who is now a postdoc based at the Sainsbury lab in Cambridge is the lead author on this investigation into the role of the HECATE (HEC) family of bHLH transcription factors on fruit development in Arabidopsis. During this process HEC proteins are involved in the response to both the phytohormones auxin and cytokinin, the authors proposing that HEC1 plays an essential role in Arabidopsis gynoecium formation.

Patron N et al (2015) Standards for plant synthetic biology: a common syntax for exchange of DNA parts New Phytologist Open Access

Carmichael RE, Boyce A, Matthewman C Patron N (2015) An introduction to synthetic biology in plant systems New Phytologist Open Access

Although not strictly based on Arabdopsis work, there are a couple of articles in New Phytologist that have broad relevance to plant scientists who are interested in plant synthetic biology. In the first of these Nicola Patron (The Sainsbury Laboratory) leads a wide consortium that aims to set parameters for the standardisation of parts in plant synthetic biology. It is hoped that as the principles of synbio are used more widley in the plant sciences that the proposals in this paper will serve as a useful guide to standidise part production. GARNet has recently written a blog post on this topic.
The associated meeting report looks at the use of plant synthetic biology in a teaching context with a synopsis of the ERASynBio summer school hosted by John Innes Centre. In this event, young researchers from a range of backgrounds were introduced to the power and potential of plant synthetic biology through a diverse course of lectures, practical session and group projects.


Vicente C (2015) An interview with Caroline Dean Development Open Access

An interview with Anne Osbourn (2015) New Phytologist Open Access

These are interviews with eminent female plant molecular biologists who both work at the John Innes Centre. Caroline Dean’s lab focuses on the epigenetic mechanisms that regulate vernalisation whilst Anne Osbourn is interested in using synthetic biology approaches to engineer metabolic pathways for the production of novel compounds.

Optimising photosynthesis

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Published on: September 25, 2014
Perennial grass Alloteropsis semialata (image c/o Marjorie Lundgren)
Perennial grass Alloteropsis semialata (image c/o Marjorie Lundgren)

Angela White (University of Sheffield) spoke to some photosynthesis researchers at the SEB annual conference in July – this is what she found out! Find Angela on Twitteronline and at the blog.

This post was originally published on the UK Plant Sciences Federation blog

Photosynthesis is a major target area for crop improvement. In July 2014, I caught up with three plant scientists researching photosynthesis to discover their latest findings, which were presented at the Society for Experimental Biology’s annual main meeting in Manchester.

Understanding evolutionary intermediates between two photosynthetic pathways

Marjorie Lundgren, a PhD student at the University of Sheffield, is researching how different photosynthetic mechanisms evolve. She works on the grass Alloteropsis semialata, which is unique in having both C3 and C4 photosynthetic pathways within this single species. Excitingly, her work has discovered populations of this species with intermediate photosynthetic phenotypes (known as C2 plants), helping us to understand how C4 evolves from the C3 pathway.

Marjorie’s research has three main findings. Firstly, she’s confirmed the existence of intermediate photosynthetic states using a range of physiological techniques.  Secondly, she’s established that this intermediacy arose in Central Africa.  And finally, Marjorie has elucidated clear links between environment, leaf anatomy and physiology. Together, her preliminary work suggests that leaf anatomical traits which are important for the C3 to C4 transition respond to environmental changes. This responsiveness is known as phenotypic plasticity and may affect the evolution of photosynthetic types.

“There’s a huge amount of variation within this species,” says Marjorie. “It’s a brilliant system.” Marjorie hopes that her research will inform the multinational C4 rice consortium, which aims to introduce the efficient C4 photosynthetic pathway into rice. She is working to identify important anatomical turning points in the evolutionary process which leads from C3 to C4 photosynthesis.

The next challenge is to use this wild grass species to identify the genetic variation that underpins evolution of the C4 photosynthetic pathway, and see how it affects physiology. This understanding is crucial if we are to successfully engineer C4 traits into C3 plants to improve crop efficiency and yield.  (more…)

Female Plant Scientists on ‘Women in Science’

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Published on: September 6, 2012
A snapshot of the Smithsonian Institute’s Women In Science archives

This post on ‘Women in Science’ is ghost written by several women working in science, either in research or in science policy. I asked them to give me their thoughts, and as some of them wanted to be anonymous, I collected the common ideas and put them into this blog post. Thank you to everyone who contributed.

Why are there so few women at the highest levels of academia, for example as Heads of School, Directors of Institutes, or Fellows of the Royal Society?

As in many other pieces on women in science, a common response to this question was that an academic career is not family friendly. Day-to-day working life is difficult to manage with a family as a very successful academic career involves unsociable hours and a huge workload. In fact, a study out last week showed that many scientists work all night and through weekends. For many reasons, women are more likely than men to see their families as a more important focus for their time and energy than their careers.

Two of the women I asked pointed out very practical problems of combining family life and research. Firstly, if a woman takes a career break for her children, when she returns to work she may be excluded from grants and fellowships for early career scientists, which set a maximum number of years from PhD graduation to be eligible for the funding. Secondly, a woman who takes ordinary maternity leave and returns to work straight away will probably find maintaining the same level of output as before her pregnancy difficult. Strength of publication record is important for senior scientific positions, so a drop and/or gap in publications caused by maternity leave and subsequent out-of-hours time devoted to a baby may delay or prevent her making applications for more senior positions.

A second theme, again commonly discussed and relevant whether a woman has family commitments or not, is that male dominance at the highest levels of academia is self-perpetuating. Some women, consciously or otherwise, are put off staying in research and aiming for the top positions by the very fact that there are few women at those high levels. Equally, women may not be recommended or headhunted for top positions, not maliciously but automatically, simply because they do not fit the norm.

As in many professions, in academia the lack of women in senior positions is partially due to more men than women forcing their way to the top. The scientists who contributed to this piece thought that women are less likely than men to self-promote, to ask for a promotion, or to apply for the top job. This is the feeling of successful women in other professions too. One of the women I asked felt that women are judged more harshly than men by men and women alike, being seen as aggressive or manipulative if they use the same methods as men to get to the top.

Do you think the programs and awards that encourage ‘women in science’ in some way are necessary, and doing a good job? (more…)

Links for Women in Science (and family men too)

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Published on: August 28, 2012
Some institutions which support women in science and family-friendly working practices

At the University where I did my PhD, male PIs far outnumbered female PIs in the School of Biological Sciences. The Head of School and all the Heads of Departments were male. The faculty lists of other universities show a similar story – and this is in life sciences, the science subject most dominated by girls at A-level. Gender balance among fellows of Royal Society is even more skewed, perhaps reflecting the wider scope of the Society, at 5% female.

These unbalanced ratios are not seen at school, university or even at post-doc level, so there is a time early in academic careers when more women than men leave academic research. The UK Resource Centre for Women in SET and the Royal Society of Chemistry commissioned a report to find out why. The report concluded that the lack of women in many areas of academia can seem isolating and off-putting; and an academic career demands a working life dictated by experiments and deadlines, with no room for part-time work or career breaks. The report also notes that both men and women are put off by the difficulties of life in academia, but more men than women are happy to make the sacrifices.

There are organisations and individuals calling for change, and providing support for female researchers at all stages of their careers. I have collected them below – feel free to get in touch if you know of any others.

Please note that many of these funds are available to men who require flexible working times and support for dependants. Most of them are not open now, but call for proposals annually or bi-annually. (more…)

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