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…)

FESPB-EPSO Plant Congress 2012

Ruth Bastow has put together an excellent Storify on the recent Plant Biology Congress in Freiburg. Here are just a few snippets from the first two days – go to the Storify for the complete story, including insights from diverse speakers like Professor Richard Dixon, farmer Helmut Bonn, and Joachim Schneider from Bayer.

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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…)

Structural colour

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Published on: July 25, 2012

Guest poster Anne Osterrieder discusses iridescence, caused by ‘structural colour’. This article was originally posted on the Annals of Botany blog as My favourite colour is structural colour on July 11th, 2012.

Hibiscus trionum

What do peacocks, CDs and certain plants have in common? They all have multi-coloured parts – feathers, surfaces or petals – which change their hue depending on the angle you look at them. This physical phenomenon in which an ordered repeating surface structure rather than a pigment gives an object its colour is called iridescence.

Iridescence has evolved multiple times in plants and occurs in a lot of land plant families, from angiosperms to algae and ferns. It can impact on how insects and animals see plants. Dr Heather Whitney, a plant scientist from Bristol University, was awarded the President’s Medal of the Society of Experimental Biology (SEB) last week for her novel and interdisciplinary work. Heather studies how plant surfaces become iridescent and how iridescence influences plant-animal interactions. (more…)

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