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…)

Publication trends in Arabidopsis

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Published on: September 18, 2014

Pete McQuilton and Richard Smith of Nowomics have pulled a load of information on Arabidopsis trends for us to write this fascinating guest blog post. Nowomics is a new website that fetches data from many biological databases every day and works out what’s changed, and finds genes and species names mentioned in new PubMed abstracts. This lets users (this can be anyone – it’s free!) to follow genes and gene ontology terms to create a personalised news feed of new papers and data. 

Arabidopsis thaliana, the humble model organism for flowering plants, has been studied for over 140 years. Discovered by Johannes Thal (hence the name thaliana), the mouse-ear cress is a member of the mustard family (Brassicaceae), alongside such luminaries as cabbage and radish. With it’s relatively small sequenced genome (114.5mb/125Mb total), rapid life cycle (about 6 weeks from germination to mature seed), prolific seed production and many genetic tools and mutants, Arabidopsis is a wonderful model organism for basic research in genetics and molecular biology.

As part of a series of blog posts at Nowomics we have examined the publication trends in Arabidopsis-related research. We’ve extracted data on primary research papers from PubMed (excluding reviews and clinical trials) for a ten year range from 2004-2013 and have identified those that mention Arabidopsis in the title or abstract. These papers are defined as Arabidopsis papers (further details of the method are given below).

From this analysis, it is clear that the Arabidopsis community is thriving, having produced just over 3500 papers in 2013, up from 1847 in 2004. This represents a 91% increase in article number, keeping pace with the overall rise in number of journal articles published, which has grown by 95% since 2004.


Figure 1. The top Arabidopsis-publishing journals 2004-2013.
Figure 1. The top Arabidopsis-publishing journals 2004-2013.

From 2004 to 2011, Plant Physiology (Plant Physiol.), Plant Journal (Plant J.) and Plant Cell made up the top three journals publishing Arabidopsis research (see figure 2). Plant Signal Behaviour (Plant Signal Behav.) has risen rapidly from it’s inception in 2006 to join the top five in 2008. By far the strongest trend, however, is the rise of PLoS ONE from outside the top ten in 2010 with just 66 Arabidopsis papers, to topping the chart with 315 in 2013. That figure represents 9% of all Arabidopsis articles in 2013. The meteoric rise of PLoS ONE can be seen for other organisms, such as in Drosophila, as described in a previous blog post. (more…)

GARNet 2014: In pictures

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Published on: September 16, 2014

GARNet 2014, Arabidopsis: The Ongoing Green Revolution, is over! We had a great two days of discussions, networking, speciality cupcakes, and of course excellent talks from researchers at all career stages, from ‘one of the fathers of Arabidopsis research’ to a few of the UK’s brightest young PhD students.

There is a report on the conference on our website, and also a Storify of Tweets. Thank you to everyone who attended and contributed to discussions in situ and on Twitter – we’re delighted to work with such a supportive, enthusiastic community!

Here are a some pictures from the event – they’re mostly of the speakers (Maarten Koorneef, Andrew Millar, Cyril Zipfel, Kerry Franklin, and Miriam Gifford) and panel sessions, with a few pictures of the networking sessions towards the end.
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GARNet and CGR Liverpool present Software Carpentry

Categories: GARNet, Workshops
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Published on: September 9, 2014

SWC Liverpool v1


On 17th-18th November 2014, GARNet and the University of Liverpool’s Centre for Genomic Research are teaming up with Software Carpentry in Liverpool for the second Software Carpentry for Plant Scientists bootcamp.

Software Carpentry teaches principles of good programming applicable to any coding language or application, whether sequencing data, phenotypic trait analysis or biochemical assays. Tutorials will start from first principles and cover using Command Line, Python programming including data manipulation with Python, and version control using Git and GitHub. Teaching will be a combination of live coding guided by the trainer and independent practical exercises.

Although the content is suitable for complete beginners, researchers with some experience of programming will also benefit from being taught good practice like version control and test-driven development. These practices will make your programs more sustainable, vastly reducing replication in your code over time, and make them easier to share with team members, collaborators and even in publications.

The programme and tutorials from the first Software Carpentry for Plant Scientists bootcamp is here. This information is to give potential delegates an idea of what the Liverpool event will be like – please be aware that the upcoming bootcamp event will be run by different trainers and therefore will not be exactly the same as the previous one.

To apply for a place on the bootcamp, email charis@garnetcommunity.org.uk between 9th and 23rd September 2014. In your email, please include:

  • Your name
  • Whether you are a student, post-doc, PI or hold another position
  • A brief description of your research interests (less than 50 words)
  • Why you would like to attend the bootcamp (less than 50 words)

Successful applicants will then be invited to register for the workshop from 29th September.

Training and skills in the UK plant sciences community: Have your say

Categories: UKPSF
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Published on: September 4, 2014

The UK Plant Sciences Federation have set up working groups to follow up the recommendations made in their report, which was launched in January. The Training and Skills Working group is tackling school, university, post-graduate and early career issues in the plant science – definitely a broad scope. The Chair Simon Leather is trying out ‘crowd-sourcing’ with his working group, asking anyone who wants to contribute for their opinions and suggestions about the way forward.

In a post on his personal website, Simon Leather has given a lot of information about the current status of training and skills in the UK plant science community, the main problems highlighted in the report, comments from the first Working Group meeting and some ideas to help solve the problem.

Leather argues that action is imperative: Without a well-trained cadre of plant scientists that are able to recognise whole organisms and are able to interact with industry we will see more problems arising with invasive species, our crop production industry will be severely compromised and biodiversity loss will accelerate. 

Some of the ideas to improve training and skills in plant science discussed at the Working Group are:

  • Working with teachers to encourage children and young people to take an interest in plant science
  • Raising awareness in schools and universities of the opportunities provided by a background in plant sciences
  • Working with the Society of Biology degree accreditation scheme to make sure plant science is a part of accredited courses
  • Building stronger training links between academia and industry to ensure HE courses are fit for purpose

What do you think? Do you think these are the right areas to focus on? The Working Group has come up with reasonable actions to begin making progress. I strongly encourage you to read the whole article, and to have your say on the action plan and challenges by commenting on the article.

Along with the Working Groups on Funding, Regulation and Translation, the Training and Skills group will report at the UKPSF AGM on 20 November.

Go here to read the article and comment: http://simonleather.wordpress.com/2014/09/02/how-do-we-save-uk-plant-sciences/

Arabidopsis Research Round-up

Categories: Global, Round-up
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Published on: September 2, 2014

There are some really interesting Arabidopsis papers in the Round-up this week, including one from GARNet’s Chair, Jim Murray, a review on the role of sugar–hormone interactions in the regulation of floral signal transduction from the University of Bolton, and a fascinating Science paper describing how sieve element cells become enucleated. Enjoy!


  • Mammarella ND, Cheng Z, Qing Fu Z, Daudi A, Bolwell GP, Dong X and Ausubel FM. Apoplastic peroxidases are required for salicylic acid-mediated defense against Psuedomonas syringaePhytochemistry, 2 August 2014. DOI: 10.1016/j.phytochem.2014.07.010.

Arsalan Daudi and Paul Bolwell from Royal Holloway worked with American colleagues on this Phytochemistry paper, which provides further detail to some previous findings regarding the effect of reduced expression of peroxidase genes. This newly published work shows that some, but not all aspects of pattern-triggered immunity in Arabidopsis are diminished in lines with reduced peroxidase expression. It was also found that salicylic acid signaling is impaired in these lines.

This paper is dedicated to the memory of Paul Bolwell, who sadly died from motor neurone disease before publication.


  • Matsoukas IG. Interplay between sugar and hormone signaling pathways modulate floral signal transduction. Frontiers in Genetics, 13 August 2014.DOI: 10.3389/fgene.2014.00218. [Open Access]

This useful review by Ianis Matsoukas at the University of Bolton highlights potential roles of sugar–hormone interactions in the regulation of floral signal transduction. It particularly emphasises Arabidopsis thaliana mutant phenotypes, and suggests possible directions for future research.


  • Forzani C, Aichinger E, Willemsen V, Laux T, Dewitte W and Murray JAH. WOX5 suppresses CYCLIN D activity to establish quiescence at the center of the root stem cell niche. Current Biology, 18 August 2014. DOI: 10.1016/j.cub.2014.07.019. [Open Access]

This paper was led by GARNet Chair Jim Murray at Cardiff University and describes findings that provide new information about the role of the transcription factor WOX5. WOX5 is known to be involved in the maintenance of a pool of stem cells at the quiescent centre (QC) of the Arabidopsis root, but the molecular mechanisms underpinning this, as well as whether WOX5 in involved in proliferation of the QC cells, has not been previously well understood. Here Jim et al propose a specific role for WOX5 in initiating and maintaining the quiescence of QC cells.


  • Miyashima Furata K, Ram Yadav S, Lehesranta S, et alArabidopsis NAC45/86 direct sieve element morphogenesis culminating in enucleation. Science, 22 August 2014. DOI: 10.1126/science.1253736.

Led by a Finnish group, this fascinating Science paper also involves colleagues from Belgium, more scientists from Cardiff, and from the Sainsbury Lab at the University of Cambridge. The researchers used electron microscope imaging and 3D-reconstructions to follow the development of sieve element cells and observe the regulation of the self-destruction of the nucleus. If you can get through the paywall, check out the images and movies in the supplementary data files!


  • El Zawily AM, Schwarzländer M, Finkmeier I, et alFRIENDLY regulates mitochondrial distribution, fusion, and quality control in Arabidopsis. Plant Physiology, 27 August 2014. DOI: 10.1104/pp.114.243824. [Open Access]

This paper presents findings for the role of FRIENDLY, a protein responsible for the correct distribution of mitochondria within the cell. Scientists from Imperial College London were involved in this international work, which identified that FRIENDLY is likely to have a role in mediating inter-mitochondrial associations. Disruption of mitochondrial associations, motility and chondriome structure affects mitochondrial quality control, which in turn has repercussions for mitochondrial stress, cell death and strong growth phenotypes.

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