Arabidopsis Research Roundup: August 21st.

There are a wide array of topics included in this weeks Arabidopsis Research Roundup, ranging from studies on stomatal density, thylakoid transport, metabolic flux analysis, mutant detection and root development. We feature unlinked studies from three researchers from the University of Oxford Plant Science (Paul Jarvis, Lee Sweetlove and Nick Harberd), whilst the papers from Julie Gray and Brian Forde share the broad theme that investigates different mechanisms that might be used to improve nitrogen uptake, either by modifying the expression of a single gene involved in root development or by altering stomatal density.

Hepworth C, Doheny-Adams T, Hunt L, Cameron DD, Gray JE (2015) Manipulating stomatal density enhances drought tolerance without deleterious effect on nutrient uptake New Phytol.

Julie Gray (University of Sheffield) is an expert on both stomatal biology and on the potential for manipulating stomatal density to improve crop production. In this study drought tolerance and soil water retention were measured in four Arabidopsis mutants with defects in epidermal patterning and stomatal density. Nutrient uptake was measured by mass flow of 15N. Plants with less stomata had reduced transpiration and were drought-tolerant yet interestingly showed little reduction in shoot N concentrations, especially when water availability is restricted. In contrast, plants with extra stomata could take up more N except when access to water was reduced. Therefore the authors show that by altering stomatal density they can generate plants that are drought resistance yet maintain nutrient uptake or generate plants with enhancing nutrient uptake is conditions with plentiful water.

Trösch R, Töpel M, Flores-Pérez Ú, Jarvis P (2015) Genetic and Physical Interaction Studies Reveal Functional Similarities between ALB3 and ALB4 in Arabidopsis. Plant Physiol.

This German, Swedish and UK collaboration is led by Paul Jarvis at the University of Oxford and broadly investigates thylakoid protein targeting. The ALB3 complex has previously been shown to target light harvesting complex proteins (LHCP) to the thylakoid. A related Arabidopsis protein, ALB4, had been proposed to interact not the LHCPs but rather with the ATP synthase complex. However this study shows that ALB3 and ALB4 have some overlapping roles in addition to their specific functions and that they can engage with a similar set of interactor proteins to bring their substrates to the thylakoid membrane.

Cheung CY, Ratcliffe RG, Sweetlove LJ (2015) A method of accounting for enzyme costs in flux balance analysis reveals alternative pathways and metabolite stores in an illuminated Arabidopsis leaf Plant Physiol.

Lee Sweetlove (Oxford University) leads this study that looks at the Flux Balance Analysis (FBA) of plant metabolism across several metabolic pathways by attaching ‘flux weighting factors’ to allow for the variable intrinsic cost of supporting each flux. This model has been applied to the Arabidopsis leaf exposed to different light regimes to explore the flexibility of the network in meeting its metabolic requirements. The authors discover interesting trade-offs between use of different carbon storage forms and in the variable consumption of ATP and NADPH by different metabolic pathways.

Belfield EJ, Brown C, Gan X, Jiang C, Baban D, Mithani A, Mott R, Ragoussis J, Harberd NP (2014) Microarray-based optimization to detect genomic deletion mutations Genom Data Dec;2:53-54

GARNet Advisory Board member Nick Harberd (Oxford University) leads this short communication that highlights the development of a tool for detection of genomic deletion mutants in Arabidopsis. Using a NimbleGen whole genome custom tiling array they successfully identify five mutants with deletion ranging from 4bp to 5kb and therefore introduce a powerful tool for analysing this type of genetic lesion in Arabidopsis and other plant species with well-constructed genomes.

Yu C, Liu Y, Zhang A, Su S, Yan A, Huang L, Ali I, Liu Y, Forde BG, Gan Y (2015) MADS-box Transcription Factor OsMADS25 Regulates Root Development through Affection of Nitrate Accumulation in Rice PLoS One

Brian Forde (Lancaster University) is the UK lead on this Chinese collaboration that focuses on nitrate accumulation and how it regulates root development in rice. This occurs via a MADS-box transcription factor OsMADS25 that, when overexpressed in Arabidopsis, promotes primary and lateral root development. Altered expression of this gene also affects root development in transgenic rice and includes significant changes in nitrate accumulation. Therefore this gene might prove to be an important target for future attempts to improve plant growth in regions with altered nitrate concentrations.

EBI resources at PAGXXIII

Categories: conferences, resource
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Published on: January 15, 2015

I spent Sunday morning wandering in and out of the ‘Tools and Resources from EBI’ session here at PAG. Some EBI resources for plant science will be very familiar to some of our community, but the presenters gave accessible talks that included some news and advice, so I thought I’d round them up for you.

Maria Keays presented ArrayExpress and ExpressionAtlas. These are the functional genomics tools from EBI. Keays defined functional genomics as the study of gene expression, gene function and gene regulation – these tools certainly aren’t just for microarray data!

Users submit their data to ArrayExpress via the Annotare submission tool, which encourages inclusion of information about how the samples were grown all the way through to data generation. Keays acknowledged that a user may encounter an error message they can’t get around, and assured us that emails sent to the helpdesk ( are responded to quickly. Once submitted, the dataset and associated metadata is checked by a human curator before the user can upload it. The data can stay private until publication because two logins are provided; one for the submitter and one for the reviewer of the paper they hope to publish.

We’ve been encouraging our community to share data on NCBI GEO because it is able to disseminate almost any data type. But for functional genomics data, ArrayExpress is just as acceptable to journals as GEO, and the Annotare submission tool requires more extensive metadata and more stringent standards than GEO. (more…)


Comments: 1 Comment
Published on: January 11, 2015

Happy New Year! We at GARNet enjoyed a long Christmas break and some of us have returned to work via California! Ruth, Jim and I are in San Diego this week for the Plant and Animal Genome Conference (PAG).

PAG is an enormous conference – take a look at the Twitter stream (PAGXXIII) for an idea of how many sessions run at any one time. Yesterday I went to sessions on Ontologies, Brassica and Tritaceae, and I thought I’d quickly update our blog readers about a workshop about the CoGe online tool. I mentioned CoGe in this post about the EPIC conference and it’s also featured in the June 2013 edition of GARNish.

Eric Lyons, one of the creators of CoGe, began the session by explaining that CoGe is a platform for managing, visualising, analysing and comparing genomes. It can deal with unlimited numbers of genomes of unlimited size—though there is a limit for the number of annotations per genome—and while there are tools set up for ease of use, users can perform custom, on-the-fly analysis too.

Throughout the session, Lyons was clear that CoGe is ‘Powered by iPlant.’ It uses iPlant middleware to enable data storage, universal log-in and much more functionality that the user might not be aware of but which makes their experience smooth and relatively stress-free. (more…)

Software Carpentry Bootcamp: An organiser’s story

Categories: resource, Workshops
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Published on: November 27, 2014

Lisa and I have been involved in two Software Carpentry Bootcamps this year: firstly the hosts of a Bootcamp in April at the University of Warwick, and the second, just last week, at a Bootcamp co-organised with the Centre for Genomic Research at the University of Liverpool. A few people at the Liverpool event expressed interest in organising their own workshops, so we thought we would talk you through the stages of hosting a bootcamp and share our experiences to help you decide whether you want to run one of your own.


1. Early planning: Decide where the event will be, who will pay, who your audience is and what topics you want to be covered.

It is (now) not free to host a Software Carpentry event. When we organised the Warwick Bootcamp, Software Carpentry was subsidised by the Mozilla Foundation, but since the recent move to its own Software Carpentry Foundation, events now command a fee (TBC) – it’s still a non-profit organisation though.

Software Carpentry trainers are volunteers but you will need to be able to reimburse their travel, food and accommodation expenses. They can come from anywhere in the world, so budget for transatlantic flights!

Other costs you will need to think about include venue hire, and travel, food and accommodation for the workshop participants. It is also up to you whether you want to charge people to attend the workshop to recoup some or all of your costs. For our first bootcamp at Warwick we had sufficient funding to make the event free for attendees, and we paid for one nights’ accommodation too. Because it was free, we did get some last-minute drop-outs, but we had a long waiting list to fill the empty spaces. At the Liverpool event, trainees paid a small registration fee, and paid for their accommodation themselves. Both events booked up quickly and were oversubscribed, so either model works.

We provided lunch and refreshments during both workshops (caffeine breaks are definitely recommended!), and also organised a dinner on the first night of the workshop.

Both of our bootcamps were for complete beginners, but if there are specific topics you need to cover, Software Carpentry can tailor a programme to your needs.


2. First contact with Software Carpentry: If you’re in the UK, the Software Sustainability Institute (SSI) in Edinburgh is your point of contact for organising Software Carpentry events. There is information and an email address on the Software Carpentry website.

Discuss your ideas for the bootcamp with Software Carpentry. We worked with Aleksandra Pawlik and Giacamo Peru from SSI over Skype and via email. Software Carpentry requires core topics to be covered, so there may be some negotiating as you work it out. As our bootcamps were for absolute beginners, unlike most Software Carpentry events, this took some time but was not at all difficult to sort out.

Decide on a date, making sure to consider other events that might limit both trainees and instructors.

The Software Carpentry website suggests being flexible with the dates to make finding instructors easier. I think this would mean pulling a bootcamp together very quickly, which might be ok for an institutional event but was impossible for us.


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…)

Plant science podcasts: PlantSci 2014 and Radio 4

Categories: Friday Film, resource
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Published on: August 22, 2014

Just a quick blog post this week on some new plant science podcasts, for your entertainment! 

First, Radio 4’s much-retweeted Plants: From Roots to Riches. This programme has been running all month and ends today so it’s not really news, but I’ve been listening to this bit by bit and was delighted to hear a familiar voice in the ‘Signals of Growth‘ episode. Nick Harberd, one of our Advisory Committee members, discussed the Green Revolution wheat and rice varieties with presenter Kathy Willis.

This is a great series, although the episodes are quite short and only focus on a small area of plant science so I’d advise skipping any episodes on a topic you know too much about or that just isn’t of interest to you. Highlights for me so far have been the ‘Blight on the Landscape‘ episode about plant-microbe interactions, which had a very interesting section on Beatrix Potter’s work on lichens; and the episode based entirely around Kew’s Arboretum, ‘An Ill Wind‘, which gave me a new appreciation of the great value of tree science and forestry. 

Friday’s episode was about Arabidopsis – I haven’t reached that one yet though!

Second, videos of talks from the UK Plant Sciences Federation conference PlantSci 2014 are now available on the Journal of Experimental Botany YouTube channel. The talks were all excellent and the videos make good teaching resources. All the speakers pitched their science for a well-informed general audience, and all were clear about why their research is important. The highlight of the conference for me was the panel discussion about UK plant science challenges, achievements and future needs and I’m happy to see that it’s there in it’s entirety, including the comments from the floor – all 1 hour 27 minutes of it.

It’s been very quiet here on the blog recently, but we’re pretty much caught up after being away at the International Conference on Arabidopsis Research in Vancouver (you can still see the #ICAR2014 stream here). Things will be back to normal very soon.


The TREE of plant science education

Aurora Levesley is the Project Officer for the Gatsby Plant Science TREE. The TREE grew out of the Gatsby Plant Science Summer Schools as a means of sharing the valuable resources produced for and during the Schools. Here she discusses the value of the TREE’s online lectures, which are the subject of a current New Phytologist paper. 

David Beerling at the Gatsby Plant Science Summer School
David Beerling gives a lecture at the Gatsby Plant Science Summer School. This is one of many lectures that have been edited for interactive online delivery and shared on the Plant Science TREE.

The Plant Science TREE is a free online central repository of plant science educational resources. More than 90 research academics and publishers have contributed over 2000 resources, including online research lectures, research-led lecture slides, practicals, video clips and other resources on topical plant science. It was developed by the University of Leeds with funding from the Gatsby Charitable Foundation, and is currently used by scientists, educators and students from over 320 institutes worldwide.

Many students enter biological sciences courses with little interest in or knowledge of plants, and engaging students with plant science early in their studies is arguably an important step in reversing the decline in uptake of this vulnerable yet strategically important subject linked to food security and other globally important issues. Prof Alison Baker of the Centre for Plant Sciences at the University of Leeds, says of the TREE: “The aim is to put a tool in the hands of educators that will engage students in plant science and research, especially where expertise is becoming limited.”

Our recent study, published in New Phytologist, showed the online research lectures that form a large part of the TREE successfully engage undergraduates with plant science (Levesley et al 2014, New Phytologist Early View).

In this study, undergraduates from four UK universities were provided with links to online research lectures as part of their course. The lectures, filmed at the Gatsby Plant Science summer schools, were given by research leaders but pitched at a level to engage undergraduates and provided a first-hand insight into how discoveries are made and science is carried out.

Not only were the online lectures successful in engaging students with plant science and research in general, but students were unanimous in the opinion that they were a good way to learn about a subject. Interestingly the study also showed that the online viewing experience was comparable to watching the research lectures live.

These online undergraduate research lectures are freely available through the Plant Science TREE. Our study shows they represent a valuable plant science education tool to help lecturers and teachers introduce cutting-edge research examples that address globally relevant applied initiatives – as well as curiosity-driven research – to their students. As such they have the potential to change student attitudes to plant science, engage students in research and are able to reach a large and wide global student audience.

The full reference for the Plant Science TREE paper is: Levesley A, Paxton S, Collins R, Baker A and Knight CD. “Engaging students with plant science: the Plant Science TREE”, New Phytologist, published online ahead of print in June 2014.


Goldenbraid 2.0: A Standardised DNA Assembly Framework

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Published on: May 27, 2014

As promised in my posts about the Plant Engine meeting I attended a couple of weeks ago (1, 2), here is Diego Orzaez to explain his GoldenBraid cloning method and online DNA assembly framework. Diego co-leads the Plant Genomics and Biotechnology Lab at the Instituto de Biología Molecular y Celular de Plantas in Valencia, Spain. 



Engineering large multigenic constructs for Plant Synthetic Biology, such as complex metabolic pathways or intricate gene networks, requires efficient, flexible DNA synthesis and assembly technologies. Although custom gene synthesis is becoming increasingly affordable, the direct synthesis of large multigenic constructs remains prohibitive for most labs. Moreover, custom gene synthesis gives little room for combinatorial engineering, something that is highly valued by biotechnologists.

An alternative “building” strategy for multigene engineering is Modular Construction, that is, the fabrication of new devices by combination of prefabricated standard modules. Modular DNA Construction brings a number of advantages as speed, versatility, lab autonomy, combinatorial potential and often lower cost. As in any standardized methodology, the more users adopt the standard, the bigger the advantages.

GoldenBraid is a Modular DNA Construction method developed at the Plant Genomics and Biotechnology lab (IBMCP-Spain), especially designed for building exchangeable multigenic constructs for Plant Synthetic Biology. Routinely, 15-20 Kb constructs comprising 4-6 transcriptional units made of dozens of individual pre-fabricated modules (GBparts) can be created in few days. Longer constructs can be assembled with little additional effort.

To facilitate the process of genetic design using GoldenBraid, and to stimulate the exchange of genetic modules among laboratories, we have recently launched GoldenBraid2.0 (GB2.0), a web-based DNA assembly framework available at site. The GB2.0 webpage hosts the public GB2.0 database, an increasingly populated collection of pre-made “GBparts” that conform to the GB standard. An embedded software tool named GBdomesticator provides users with personalized lab protocols for creating their own collection of standard genetic parts. Users can always combine their own parts with those deposited in the public GB2.0 database. Moreover, building new GB2.0 multigenic constructs is highly facilitated by the GB assembler tool, a software package that assists in the design of new multigenic constructs.

We believe that adopting common standards and creating of public repositories of exchangeable genetic parts will speed up progress in Plant Biotechnology. If you are interested in this field, we encourage you to explore the webpages. The details of GB assembly system are described in the publications listed below, and there are tutorials online.

Comments on how to enhance community efforts towards the development of public repositories of standard DNA parts are most welcome, and can be addressed to



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