Data Mining with iPlant: Published

Categories: GARNet
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Published on: October 20, 2014

Data mining with iPlant

We have a new paper published! Lisa is first author on the report from last year’s Data Mining with iPlant workshop, published last week in the Journal of Experimental Botany.

As noted in the abstract, the paper ‘provides an overview of the workshop, and highlights the power of the iPlant environment for lowering barriers to using complex bioinformatics resources, furthering discoveries in plant science research and providing a platform for education and outreach programmes.’

The full reference for the paper is: Martin L, Cook C, Matasci N, Williams J and Bastow R (2014) Data Mining with iPlant: A meeting report from the 2013 GARNet workshop ‘Data Mining with iPlant’, Journal of Experimental Botany, DOI: 10.1093/jxb/eru402

You can view the paper via this toll-free link.

Don’t forget, all the tutorials from the workshop are available for anyone to use on the iPlant Wiki pages.

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.

 

A model tree?

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Published on: April 30, 2013

Just how many things can we really use Arabidopsis thaliana as a ‘model’ for? Certainly our favourite weed has an historic advantage for genomic research. As the first plant genome to be fully sequenced, it has had a long head start for all sorts of ‘omics databases and projects. The A. thaliana databases have proved useful for researchers working on other plant species too; even today Arabidopsis genomic sequences are used to fish un-annotated genomes for genes and motifs. A recent paper questions how appropriate it is to transfer in vivo Arabidopsis research on xylem and water flow to woody plant species. Yes, how useful is weedy (in all senses of the word), tiny A. thaliana to understand massive woody trees? The answer? It’s not perfect, but it’s OK.

Tixier et al. (JXB, doi:10.1093/jxb/ert087, Open Access) carried out a series of experiments to test A. thaliana’s value as a model for wood development. It turns out wildtype Arabidopsis is a good xylem hydraulic model, with tissue structure and vessel dimensions that are reliably representative of larger woody plants. To quote Tixier et al., “A. thaliana can be used to measure specific conductivity and cavitation resistance in an accurate and reliable approach,” and far more conveniently than trying to use an 8 metre tall tree to do it. However, the model plant is not appropriate for some xylem parameters, such as end-wall sensitivity. A. thaliana xylem also responded differently to abnormal environmental conditions and cell wall structure manipulation.

As an aside, Wendrich and Weijers present another system for which A. thaliana is an appropriate model in this month’s Tansley review in New Phytologist (doi: 10.1111/nph.12267). They describe current understanding of morphogenesis in the early A. thaliana embryo, and identify five key questions that still remain to be answered.

Image credit: Climbing plant by Heriberto Herrera, via stock.xchng.

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