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.

Journals

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.
garnet2014 1

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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.

Arabidopsis Research Round-up

Categories: Arabidopsis, Global, Round-up
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Published on: August 28, 2014

Here’s your UK Arabidopsis Research Round-up for this week.  Today we feature a mixed bag of new work from the Universities of CambridgeLeicesterLeeds andLiverpool. One of the Leeds authors, Emily Hawkes, has been selected to present her work at GARNet 2014, which takes place in just two weeks’ time (9–10 September 2014)! If you haven’t already registered for this conference – the largest Arabidopsis conference in Europe this year, we might add! – it’s not too late to do so. Simply browse our website for more information at www.garnet2014.org and click the ‘Registration’ tab to sign up and join us in Bristol!

 

  • Rennie EA, Ebert B, Miles GP, et alIdentification of a sphingolipid a-glucuronosyltransferase that is essential for pollen function in Arabidopsis. The Plant Cell, 1 August 2014. DOI: 10.1105/tpc.114.129171. [Open Access]

Scientists from the Universities of Cambridge and Leicester worked with American colleagues on this Plant Cell paper. It has been known for some times that glycosyl inositol phosphorylceramide (GIPC) sphingolipids make up a large proportion of the lipids in the plant plasma membrane, and that they are often decorated with glycan residues. However, until now, no glycosylating proteins have been discovered that are responsible for these residues. This group shows that the Arabidopsis thalianaprotein INOSITOL PHOSPHRYLCERAMIDE GLUCURONOSYLTRANSFERASE1 (IPUT1) transfers glucuronic acid A (GlcA) from UDP-GlcA to GIPCs. Furthermore, mutations in IPUT1 are not transmitted through pollen, suggesting that sphingolipids are essential in plants.

 

  • Watson M, Hawkes E and Meyer P. Transmission of epi-alleles with MET1-dependent dense methylation in Arabidopsis thalianaPLOS ONE, 19 August 2014. DOI: 10.1371/journal.pone.0105338. [Open Access]

This is a neat paper by three researchers at the University of Leeds, in which they describe an unusual pattern of ‘dense methylation’ under the control of METHYLTRANSFERASE1 (MET1). This protein is found to be responsible for three different methylation contexts: CG, CHG and CHH (where H represents A, C or T). Epi-alleles of dense methylation at non-coding RNA loci are stably maintains and transmitted in genetic crosses, suggesting that at certain loci MET1 is able to create transcriptional diversity based on the generation of independent epi-alleles. Though rare in Arabidopsis, it will be interesting to explore the possibility that MET1 is a contributor to epigenetic diversity in other plant species.

Emily Hawkes, middle author on this paper, was selected to give an oral presentation of her abstract at GARNet 2014. So, if you haven’t already registered, do so today and join us in Bristol to hear more about her work!

 

  • Parry G. Components of the Arabidopsis nuclear pore complex play multiple diverse roles in control of plant growth. Journal of Experimental Botany, 27 August 2014. DOI: 10.1093/jxb/eru346. [Open Access]

Geraint Parry from the University of Liverpool here presents evidence to suggest that nucleoporins – involved in nuclear pore complexes (NPCs) that facilitate movement of RNA and protein between the nucleus and cytoplasm – may play distinct roles in nuclear transport. In Arabidopsis lines with defective nucleoporins in NPCs, it was noted that nuclear export of mRNA is differentially affected.

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.

 

Arabidopsis Research Round-up

Categories: Arabidopsis, Global, Round-up
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Published on: August 21, 2014

These Arabidopsis Research Round-ups are usually posted on the main GARNet website (and still will be) but we’re also going to start posting them here. We were recently approached by the Arabidopsis Information Portal to ask if we could make the Round-ups available for their website too, and it’s easier for us to do that from the blog. Long story…but enjoy!

This week we have 10 new papers published from the end of July to the middle of August, including one by our very own Charis Cook!

  • De Jong M, George G, Ongaro V, Williamson L, Willetts B, Ljung K, McCulloch H and Leyser O. Auxin and strigolactone signaling are required for modulation of Arabidopsis shoot branching by N supply. Plant Physiology, 21 July 2014. DOI: 10.1104/pp.114.242388. [Open Access]

Led by GARNet’s founder Ottoline Leyser from the University of Cambridge, this paper also involved UK plant science researchers from The Sainsbury Laboratory, Cambridge, the University of York and the Swedish University of Agricultural Sciences. Here the finding is presented that nitrate limitation results in increased auxin export from active buds, leading to reduced shoot branching and a characteristic shift in relative biomass allocation to the root.

  • Rautengarten C, Ebert B, Moreno I et alThe golgi localized bifunctional UDP-rhamnose/UDP-galactose transporter family of Arabidopsis.Proceedings of the National Academy of Sciences of the USA, 22 July 2014. DOI: 10.1073/pnas.1406073111. [Open Access]

Paul Dupree and Jennifer Mortimer from the University of Cambridge are listed as authors on this PNAS paper. In order to understand more about nucleotide sugar transporting (NST) proteins and their substrate-specific actions, this team have developed a novel approach to reconstitute NSTs into liposomes and subsequently analyse nucleotide sugar uptake  by mass spectrometry. Using this approach, and by synthesizing UDP-L-rhamnose in a newly developed two-step reaction, it has been possible to identify and characterize six bifunctional UDL-L-Rha/UDP-D-galactose transporters. This work is supported by evidence from loss-of-function and overexpression Arabidopsis lines.

  • Yang H, Howard M and Dean C. Antagonistic roles for H3K36me3 and H3K27me3 in the cold-induced epigenetic switch at Arabidopsis FLCCurrent Biology, 24 July 2014. DOI: 10.1016/j.cub.2014.06.047. [Open Access]

Led by Professor Caroline Dean at the John Innes Centre, this paper in Current Biology unpicks the epigenetic mechanism behind the switching on and off of the FLCgene, which is responsible for the onset of vernalisation after a period of cold. It is found that the histone modification H3K36me3 causes the FLC gene to be active, while an alternate modification, H3K27me3, switches the gene off again. It is thought that accumulation of these opposing histone modifications allow the plant to register how long it has been exposed to cold, so that it knows when to start flowering.

You can read more about this research on our Latest News page here: How Plants Remember Winter, and Other Stories.

  • Smith S, Osman K and Franklin FCH. The condensin complexes play distinct roles to ensure normal chromosome morphogenesis during meiotic division in Arabidopsis. The Plant Journal, 26 July 2014. DOI: 10.1111/tpj.12628.

In a collaboration between the University of Birmingham and Durham University, this paper in The Plant Journal presents new information about meiosis in Arabidopsis. Specifically, the group looked at condensins – proteins involved in the organization of chromosomes during meiosis – and found distinct roles for condensin I and condensin II.

  • Bardou F, Ariel F, Simpson CG, Romero-Barrios N, Laporte P, Balzergue S, Brown JWS and Crespi M. Long noncoding RNA modulates alternative splicing regulators in Arabidopsis. Developmental Cell, 28 July 2014. DOI: 10.1016/j.devcel.2014.06.017.

In this article, Craig Simpson and John Brown from the James Hutton Institute in Scotland worked with French colleagues to present the finding that nuclear speckle RNA-binding protein (NSR) and the alternative splicing competitor long noncoding RNA (ASCO-lncRNA) work together as a regulatory module to control alternative splicing patterns of transcription in Arabidopsis.  Furthermore, it is found that auxin induces a major change in the alternative splicing patterns of many genes, a response largely dependent on NSRs.

  • Rasool B, Karpinska B, Konert G, Durian G, Denessiouk K, Kangasjärvi S and Foyer CH. Effects of light and the regulatory Beta subunit composition of protein phosphatase 2A on the susceptibility of Arabidopsis thaliana to aphid (Myzus persicae) infestation. Frontiers in Plant Science, 29 July 2014. DOI: 10.3389/fpls.2014.00405. [Open Access]

The Foyer Lab at the University of Leeds takes the helm on this new research paper investigating the effects of light and the composition of the regulatory B-subunit of protein phosphatase 2A on aphid fecundity and plant susceptibility to Pseudomonas syringae infection. Low light-grown Arabidopsis thaliana mutant lines were used, defective in phosphatase regulatory subunit B’γ (gamma; pp2a-b’γ), B’ζ (zeta; pp2a-b’ζ1-1 and pp2a-b’ζ 1-2) or gamma zeta double mutants (pp2a-b’γζ), in the presence or absence of a high light pre-treatment. Findings suggest that pre-exposure of plants to high light, and the composition of B-subunits are important in regulating plant resistance to aphids.

  • Becker JD, Takeda S, Borges F, Dolan L and Feijó JA. Transcriptional profiling of Arabidopsis root hairs and pollen defines an apical cell growth signature. BMC Plant Biology, 1 August 2014. DOI: 10.1186/s12870-014-0197-3. [Open Access]

Researchers working on this paper, including those from the John Innes Centre and the University of Oxford, developed a new method for isolating growing and mature root hair cells to better analyse their transcriptomes my microarray analysis. By comparing the transcriptomes of these root hair cells with those of pollen tubes, the team found a statistical relationship between the datasets, suggesting a common transcriptional profile pattern for the apical growing cells in a plant. This study will underpin the further genetic and physiological dissection of the mechanisms underlying apical growth of plant cells.

  • Cook C, Francocci F, Cervone F, Bellincampi D, Bolwell PG, Ferrari S and Devoto A. Combination of pretreatment with white rot fungi and modification of primary and secondary cell walls improves saccharification. BioEnergy Research, 5 August 2014. DOI: 10.1007/s12155-014-9512-y. [Open Access]

Here’s a paper from GARNet’s very own communication and liaison officer, Charis Cook! The final paper to be published from her PhD in the Devoto lab at Royal Holloway, here Charis et al describe how pre-treating biomass with two types of white rot fungi can improve saccharification and thus increase the accessibility of cellulose in the cell wall. The work was done in tobacco and in Arabidopsis thaliana lines with reduced de-esterified homogalacturonan content.

  • Mitchell K, Brown I, Knox P and Mansfield J. The role of cell wall-based defences in the early restriction of non-pathogenic hrp mutant bacteria in Arabidopsis. Phytochemistry, 6 August 2014. DOI: 10.1016/j.phytochem.2014.07.015.

Scientists from the Universities of KentLeeds and Imperial College London studied the effects of challenging Arabidopsis leaves with an hrp mutant strain ofPseudomonas syringae. It was found that, although they remained viable, hrp mutant bacteria were restricted in growth within 6 hours, and the plant accumulated for H2Oand peroxidase around the mutant than in the wild type. The results suggest that the generation of H2Ocould be a likely target for effector proteins injected into plant cells by the wild-type bacteria.

  • Koster T, Meyer K, Weinholdt C, Smith LM, Lummer M, Speth C, Grosse I, Weigel D and Staiger D. Regulation of pri-miRNA processing by the hnRNP-like protein AtGRP7 in Arabidopsis. Nucleic Acids Research, 7 August 2014. DOI: 10.1093/nar/gku716.

Lisa Smith from the University of Sheffield worked with German colleagues on this Nucleic Acids Research paper. It is already known that the hnRNP-like glycine-rich RNA-binding protein AtGRP7 regulates pre-mRNA splicing in Arabidopsis, but here it is shown the AtGRP7 as has an effect on miRNA levels in the plant. Arabidopsis lines overexpressing AtGRP7 showed a significant reduction in the level of 30 different miRNAs, and an increase in a further 14; RNA immunoprecipitation also revealed that AtGRP7 interacts directly wit the pri-miRNAs in vivo.

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