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  • Charis Cook
  • I am Communication and Liaison Officer at GARNet, a network representing the plant science research community in the UK. I'd love to hear from you if you'd like contribute to our blog, Weeding the Gems, or GARNish, our newsletter which you can see at www. garnetcommunity.org.uk. I was previously a PhD student and extremely temporary post-doc at Royal Holloway, University of London and before that I did a Biology BSc at Imperial College London.
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Arabidopsis Information Portal at PAGXXIII

Last Monday the Arabidopsis community gathered for the Arabidopsis Information Portal workshop at PAG XXIII. The Arabidopsis Informatics Portal (AIP) was funded by NSF and BBSRC to move beyond the Arabidopsis genome resource provided by TAIR toward linking the genome to the epigenome, proteome, transcriptome and interactome.

AraportThe first talk was a short update from Eva Huala, formerly of TAIR and now of Phoenix Bioinformatics, the nonprofit company she started in order to keep TAIR going. Huala explained that after TAIR’s NSF funding ended, the pay-to-access model was chosen over the alternative pay-to-submit (open access) approach. This means TAIR is focussed on ensuring the subscribers get the best possible value for money by providing the best possible database curation, manual annotation and user experience. Most TAIR subscription fees are paid by libraries, as if it was a journal, but researchers from institutions whose libraries do not pay the fee will be able to access TAIR’s manual annotation after a year’s embargo.

Next, Sean May (NASC, University of Nottingham) explained that NASC is a module of AIP and is currently integrating with the ABRC. He is consulting the community about the development of NASC, so make sure you have your say in the NASC Strategy Survey: http://bit.ly/1J24Hgk

Chia-yi Cheng (JCVI) gave an overview of Araport, the online home of the AIP. Araport federates diverse datasets from other places, for example TAIR, UniProt and BAR, and maintains the Col-0 ‘gold standard’ annotation. It uses JBrowse as the default genome browser and hosts datasets including the CoGe epigenomics resource, which I blogged about last week. (more…)

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 (Arrayexpress@ebi.ac.uk) 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…)

CoGe at PAGXXIII

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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…)

Have a holly jolly Christmas

Categories: something fun
Tags: ,
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Published on: December 22, 2014

holly 1

In Europe holly is a spiky, festive plant that gets an annual spotlight in wreaths and garlands at Christmas. But taxonomically holly is a genus, Ilex, of 400-600 species. Ilex aquifolium (‘holly’) is the dominant species in the UK and Europe but worldwide the genus includes evergreens, deciduous trees, shrubs and climbing plants.

holly 2
Ilex asprella

One holly species, I. asprella, is known locally in its native southern China as Gang-Mei. Tea made from the roots and leaves is a traditional medicine for influenza, bacterial infections and lung abscess. Several studies have shown that extract from I. asprella contains bioactive compounds; this recent systems biology paper profiled the biosynthetic pathway for Ilex triterpinoid saponins. Others have demonstrated that root extract can inhibit flu viruses and sooth inflammation, and this year a team of researchers at the Guangzhou University of Traditional Chinese Medicine showed that I. asprella root extract is also fairly effective at reducing the impact of acute respiratory distress syndrome in mice.

A slow invasion of English holly (the festive kind), I. aquifolium, is causing a bit of a stir in the North West USA. This paper in the rather niche Northwest Science journal sampled holly in a forest in Washington state. The authors looked at spatial distribution and age data to estimate that both vegetative and seed-based spread are increasing exponentially. The paper states that the population doubling time is about 5 years, and individual holly trees grow slowly, so hopefully the situation will be controlled quite easily.

For more varied Christmas plant science, check out my Christmas post from 2012, which features frankincense, mistletoe, fir trees and more holly.

References:

Dai WP, Li G, Li X, Hu QP, Liu JX, Zhang FX, Su ZR, Lai XP. 2014. The roots of Ilex asprella extract lessens acute respiratory distress syndrome in mice induced by influenza virus. Journal of Ethnopharmacology 155 (3): 1575–1582

Zheng X, Xu H, Ma X, Zhan R, Chen W. 2014. Triterpenoid saponin biosynthetic pathway profiling and candidate gene mining of the Ilex asprella root using RNA-Seq. International Journal of Molecular Sciences 15(4): 5970-87

Stokes DL, Church ED, Cronkright DM and Lopez S. 2014. Pictures of an Invasion: English Holly (Ilex aquifolium) in a Semi-Natural Pacific Northwest Forest. Northwest Science 88(2): 75-93.

Image credits: holly after by Allie Edwards冬青科 Ilex asprella (Hook. et Arn.) Champ. 燈稱花 98特生 by 潘立傑 LiChieh Pan. Both via Flickr, shared under Creative Commons. 

Memory of seasons past controls germination

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Published on: December 18, 2014

Arabidopsis seedling germinating JIC

In research published this week in PNAS, Steve Penfield (formerly Exeter, now John Innes Centre) and Ian Graham (CNAP, York) and collaborators have shown that ‘mother’ plants remember seasons and use this memory to program germination time into their seeds.

Working on Arabidopsis thaliana, Penfield found that the mother plant plays an important role in sensing temperature and forms a long term temperature memory, which she uses to control the behaviour of her progeny seeds. These temperature memories enable seeds to determine time of year and modify their germination rates to ensure that their growth and development is coordinated with the seasons.

If the mother experiences warmer temperatures, it produces more of a protein called Flowering Locus T (FT) which in the fruit of the plant, represses production of tannins, making seed coats thinner, increasing their permeability, meaning they will germinate more quickly.

Conversely if the mother plant experiences cooler temperatures prior to flowering it will produce less FT protein in its fruit and therefore produce more tannins. Seed coats will be thicker and less permeable and will germinate later. In this way the mother plant can manipulate seed germination to be optimal for the time of year.

If the environment during seed production is not optimal this can result in poor germination. With climate change making suboptimal conditions more frequent, having a better understanding how plants program progeny dormancy and germination will help researchers optimise seed quality for crops and domestic use.

Steve Penfield said: “By understanding how the mother plant uses temperature information to influence the vigour of her seeds we can begin to develop strategies for breeding seeds with more resilience to climate change.”

Highlighted paper: Min Chen, Dana R. MacGregor, Anuja Dave, Hannah Florance, Karen Moore, Konrad Paszkiewicz, Nicholas Smirnoff, Ian A. Graham, and Steven Penfield. 2014. Maternal temperature history activates Flowering Locus T in fruits to control progeny dormancy according to time of year. PNAS published ahead of print December 16, 2014, doi:10.1073/pnas.1412274111.

This article is adapted from a news release from the John Innes Centre. The image is c/o John Innes Centre. 

Funding and networking opportunities from BBSRC plant science NIBBS

Categories: funding
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Published on: December 9, 2014

Early this year, BBSRC announced 13 new Networks in Industrial Biotechnology and Bioenergy (NIBBS). Their aim is to foster collaborations between the academic research base and industry in order to drive new ideas in specific areas of focus. Four NIBBS have plant science themes:

•   A Network of Integrated Technologies: Plants to Products: http://www.nibbp2p.org/

•   High Value Chemicals from Plants Network: https://hvcfp.net/

•   Lignocellulosic Biorefinery Network (LBNet): http://lb-net.net/

•   PHYCONET: unlocking the IB potential of microalgae: http://www.phyconet.org.uk/

Each BBSRC NIBB organises free residential networking events and awards funding in the form of Business Interaction Vouchers and Proof-of-Concept funds. You need to be a member of the NIBB to access any of these resources, but they are all free to join.

Business Interaction Vouchers are worth up to £5000 and are intended to support research done by an academic partner for an industrial partner of the NIBB. Depending on the NIBB, there are deadlines throughout the year or applications are accepted at any time.

Proof-of-concept funds are more flexible in scope and amount awarded, but have stricter deadlines. Each NIBB is dealing with their awards differently: The HvCFP deadline is 19 January 2015; and the LB-Net has organised Challenge Workshops in 2015, which will lead to funding for multi-disciplinary teams formed at the workshops. The other networks do not currently have proof-of-concept calls open.

Software Carpentry Bootcamp: An organiser’s story

Categories: resource, Workshops
Comments: 1 Comment
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.

(more…)

Natural variation in Arabidopsis, the MAGIC way

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Published on: November 24, 2014

The research: Finding the causes of variation in seed size and number

In the Arabidopsis Research Round-up a few weeks ago, Lisa highlighted a paper from a team at the University of Bath about natural variation in Arabidopsis seeds. Lead author Paula Kover and her team investigated the genetic basis of variation in seed size and number.

All plants negotiate a trade-off between the number and size of their seeds, so it was a surprise to learn that of 9 QTL for seed number and 8 for seed size, there was only 1 overlapping QTL. The strong negative correlation seen in size and number is logically due to resource use efficiency, but these data suggest that this is not determined genetically.

There is enough of a positive correlation between seed number and fruit length that fruit length is sometimes used to estimate seed number – though the correlation is not strong. Here too there was only 1 QTL overlapping between the two traits, suggesting that any correlation is not inherent and may vary according to environmental or internal factors.

Based on QTL analysis, Kover et al. identify five potential genes that underlie quantitative variation in seed size and number: AAP1 (AT1G58360) and KLUH (AT1G13710) on chromosome 1; and JAGGED LATERAL ORGANS (AT4G00220), YABBY 3 (AT4G00180), and BEL1 (AT5G41410) on chromosomes 4 and 5.

 

The tool: MAGIC Arabidopsis lines

All the above work was carried out using Mulitparent Advanced Generation Inter-Cross (MAGIC) Arabidopsis lines. Kover and others developed these lines to improve methods of identifying natural allelic variation that underlies variable phenotypic traits. The lines are recombinant, inbred over 6 generations, that originate from an intermated hereogenous stock. This pedigree means they represent a large diversity of genes in mostly homozygous lines; ideal for accurate QTL mapping. The original MAGIC paper from 2009 paper states ‘MAGIC lines occupy an intermediate niche between naturally occurring accessions and existing synthetic populations.’

The MAGIC lines are an incredible open resource for studying natural variation in Arabidopsis: they enable a researcher to map a trait to within 300kb. All lines in the 2009 paper are available from NASC. A set of digital tools, hosted at the Wellcome Trust Centre for Human Genetics, contains the (open source) software needed to run the QTL analysis and the data files associated with the lines.

 

Highlighted paper: Gnan, Priest and Kover. The genetic basis of natural variation in seed size and seed number and their trade-off using Arabidopsis thaliana MAGIC lines. Genetics, 2014. 10.1534/genetics.114.170746

Also cited: Kover et al. A multiparent advanced generation inter-cross to fine-map quantitative traits in Arabidopsis thaliana. PLOS Genetics, 2009. DOI: 10.1371/journal.pgen.1000551

For a comparison of resources for studying natural variation, see Weigel, Plant Phys, 2012 158:2-22

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