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
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.
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. thalianadatabases 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 vivoArabidopsis 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. thalianacan 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. thalianaxylem 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. thalianaembryo, and identify five key questions that still remain to be answered.
Over the past thirty years the Multinational Arabidopsis Steering Committee (MASC) has represented the global Arabidopsis community through its collaborative oversight of the annual International Conference on Arabidopsis Research (ICAR), production of a MASC annual report and preparation of the series of decadal Roadmaps that have helped coordinate the future activities of the community. In[…]
https://meetings.embo.org/event/20-plant-systems This EMBO Workshop on international Plant Systems Biology (iPSB) is the central gathering of plant systems biology researchers from across the world. Climate change poses unique challenges for how to feed and power humanity without further degrading the environment. Plant science therefore is a key discipline in meeting the challenge of adapting food and[…]
The spring season of #UKPlantSciPresents begins on January 12th and we have a strong schedule set until the end of April! Each webinar is at Tuesday afternoon at 3pm GMT (or BST)! Registration is free and webinars will be made freely available soon after the event. Although closed captioning/subtitles are not available for live webinars,[…]
The previously awesome #GARNetPresents webinar series is morphing into the #UKPlantSciPresents webinar series. This series has the aim of promoting plant science excellence across the UK! UK plant science research uses many different experimental organisms such as Arabidopsis, Wheat, Brassicas, Brachypodium, Marchantia, Physomitrella and many others. This webinar series is supported by both GARNet and[…]
Contents: – Society Updates– Introducing Quantitative Plant Biology– Congratulations to Ottoline Leyser– Conference Updates– Bacterial Plant Diseases Programme– Introducing CHAP– Twenty Years of GARNet– GARNet Research Roundup– MASC Publication Update– Plant RNA Interactome Capture– Update on new BBSRC Projects– Spotlight on University of Nottingham Download here: https://www.garnetcommunity.org.uk/sites/default/files/newsltr/GARNish33_Online_Final_0.pdf
Marcel Bach-Pages works with Gail Preston at the University of Oxford and we discuss a new protocol to identify the RNA-Binding Proteome from Arabidopsis leaves. This community-focused work includes full instructions for use of the protocol and they provide an accessible list of proteins that they have identified. This research is published in Biomolecules and[…]
This edition of GARNet Research Roundup begins with a remarkable four papers that include work from Caroline Dean’s lab at the John Innes Centre. The first two papers are collaborations with members of Martin Howard’s lab and look at the molecular mechanisms that control long-term cold sensing or the antisense regulation of FLC respectively. The[…]
Christos Velanis works at the University of Edinburgh and discusses work published in PloS Genetics entitled ‘The domesticated transposase ALP2 mediates formation of a novel Polycomb protein complex by direct interaction with MSI1, a core subunit of Polycomb Repressive Complex 2 (PRC2)‘. http://blog.garnetcommunity.org.uk/wp-content/uploads/2020/07/Velanis_edit-13072020-09.32.mp3 Pumi Perera is co-first author on this work from the Goodrich lab[…]
This has been a challenging time for both conference organisers and conference venues. Most 2020 plant science conferences have cancelled, postponed or majorly changed their events. Below is a non-exhaustive list of the changes that have been made to different conferences. Up to date as July 6th 2020. (download)
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