Guest post: Plantwise Knowledge Bank Map

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Published on: October 25, 2012

Tim Holmes works for CABI, a not-for-profit international organization that improves people’s lives by providing information and applying scientific expertise to solve problems in agriculture and the environment. Plantwise is an initiative, led by CABI, to improve food security and the lives of the rural poor by reducing crop losses. It is for the Plantwise Knowledge Bank, that Tim tackles the challenge of presenting species distribution data to a diverse group of users.

Plantwise is the biggest project that the whole of CABI has ever been engaged in together. It brings together all the strands of our work, from the publishing business, through scientific research, to international development. The Knowledge Bank is my bit of the programme, and something I’m immensely proud of. We’ve been developing a suite of data and information tools over the last few years, and it’s to one of these that I’d like to introduce you now.

The Plantwise Knowledge Bank Map was the first tool concept that we presented back in 2010, and straight away it was our number one priority to make it a reality. The genesis was a crude, but cool looking, Google Earth presentation of CABI’s plant pest distribution data. The globe spun and zoomed impressively, but it wasn’t going to be the useful scientific tool that we were after. For starters you couldn’t see the whole of the Earth’s surface at once; problematic if you wanted to get a Baumgartner’s-Eye view of the worldwide range of a pest! It was problematic too if you wanted to build it into a website that would fling around large datasets AND do so for users with restricted internet bandwidth. So we trialled many different bits of mapping software and settled on something that would display a Google Maps-style projection and would let us do as much of the map production leg-work on our servers. It would be familiar and fast. (more…)

Transcription factor-like effectors (TALEs)

Ubud, Bali by Mee Lin Woon; DNA Sequence by schulergd. Via stock.chng

Background

Xanthomonas spp. are plant pathogens that modulate their host’s gene expression in order to facilitate infection. They do this using transcription activator-like effectors (TALEs). Two domains are conserved in TALEs: an N-terminus, required for type III secretion into the plant cells; and a C-terminus with transcription factor activity. In the middle is a set of tandem repeats of amino acids, which mediates binding to host DNA.

As the binding and effector domains of TALEs can be customised, the possibility of using them for molecular and synthetic biology has been explored for some time. They have been used to change gene expression in plants, yeast, and even human cells.

TALEs have been adapted by researchers to make TALE nucleases (TALENs) – TALEs attached to a FOK1 nuclease domain. TALENs work in pairs that flank either side of the target site so that the nuclease domains meet at the point of cleavage. The nucleases cause a double-stranded DNA break, which is fixed imperfectly, causing an insertion or deletions.

In May this year, a paper was published demonstrating the huge impact TALEs could have on agriculture. Li et al. prove that transcription activator-like effector nucleases (TALENs) can be used to render rice resistant to the major agricultural pathogen, Xanthomonas oryzae pv. Oryzae (Xoo). (more…)

Warwick Systems Biology at SEB 2012

It’s time for another guest post today – Katherine Denby writes about the SEB 2012 conference.

Warwick Systems Biology Centre was well represented at the recent SEB conference in Salzburg, with 4 presentations in sessions on Biotic Stress, Environmental Control of Development and Generating New Biological Insights from Complex Data.

Arabidopsis leaf cells, stained to visualise the cell wall and Botrytis cinerea mycelia. Credit: Katherine Denby

First up was Katherine Denby who presented analysis of a gene expression time series from Arabidopsis leaves infected with the fungal pathogen Botrytis cinerea generated in the PRESTA project. Using a variety of network inference algorithms, the group has generated models of the gene regulatory networks underlying the Arabidopsis response to this pathogen. These network models have highlighted specific regulatory interactions, and led to identification of transcription factors with a novel role in defence. Modelling using gene expression time series from other biotic and abiotic stresses has predicted a core regulatory network underlying multiple stress responses with differential flux through the network under different environmental conditions. Katherine also described a novel tool, Wigwams, to identify groups of genes significantly co-expressed across multiple stresses. Integrating this with the network models enables prediction of the upstream regulators of these groups. (more…)

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