From systems biology to digital organism

GARNet needs your help to assess the uptake, influence and future of systems biology in the plant science community. This is the second time GARNet has conducted a survey about systems biology, as in 2006 the BBSRC commissioned GARNet to produce a report on how systems biology could best be approached in UK Arabidopsis research. We believe that report and the various activities that accompanied it helped the Arabidopsis community get its foot on the ‘System Biology Ladder’ – and to win some of the associated grants.

Now, six years later, systems biology is supporting systems biology and the digital organism efforts. We feel it is time to write a follow up report to the 2006 Systems Biology report in order to advise the BBSRC and other funders on the community’s capabilities, current needs, and readiness for future initiatives that build on Systems Biology.

Please help us collect data and information for this report by filling in a questionnaire, which will take about 20 minutes of your time. Please click here to go to the questionnaire. Please contribute your ideas before the 5th November.

Video credit: Pacific Biosciences.

The cost of glucosinolate biosynthesis

Highighted article: Michaël Bekaert, Patrick P. Edger, Corey M. Hudson, J.Chris Pires, Gavin C. Conant (2012) Metabolic and evolutionary costs of herbivory defense: systems biology of glucosinolate synthesis. New Phytologist 196:596–605.

Research published in a current New Phytologist paper uses a systems biology approach to demonstrate the metabolic and evolutionary costs of producing glucosinolates for defence.  Bekart et al. used AraGEM (Oliveira Dal’Molin et al., 2010) as a starting point. They collected data on Arabidopsis glucosinolate genes by scouring published papers and downloading their expression patterns from AtGenExpress. This information was integrated into the basic dataset from AraGEM. The complete list of genes involved in glucosinolate reactions, including references, is in Supplementary Table S1 of the paper.

The team performed flux balance analysis on the integrated database to estimate metabolic and energy flux through reactions in the system both with glucosinolate biosynthesis activity and with none. They found that glucosinolate biosynthesis affected flux incidentally through 241 reactions in addition to the 196 reactions which are only active when glucosinolates are being produced.

The main finding of the research is the heavy cost of glucosinolate biosynthesis. Sulphur import dramatically increased when glucosinolates were being synthesised, and demand for water, carbon dioxide, ammonia, and photons increased too. Despite the increase in substrate import, biomass synthesis fell by around 15% during glucosinolate production. This cost is reflected in other studies demonstrating that the evolutionary competitive edge glucosinolates give to plants is a disadvantage when there are no predators around (Mauricio, 1997), and reduces the number of seeds and flowers produced per plant compared to non-producers (Stowe and Marquis, 2011). (more…)

Working with Natural Antisense Transcripts

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Published on: September 27, 2012

In January of this year Nucleic Acids Research published a paper describing a database of plant natural antisense transcripts (NATs), PlantNATsDB (Chen, Yuan et al., 2012). It contains around 2 million NATs from 69 plant species, and has a simple viewer showing the two loci involved in each NAT, any overlap, the NAT type, and an option for more detail. It is also possible for search for NATs for specific loci. It is important to note however that the database was last updated a year ago, in September 2011.

This month’s Plant Methods also features a NATs tool, a protocol for NAT identification in plant tissue (Collani and Baraccia, 2012).  It is a simple PCR based method, and relies on prior knowledge of the existence of a NAT, as specific primers are needed. Used in association with PlantNATsDB, this is a useful technique. (more…)

Online resources for sharing and viewing data

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Published on: August 15, 2012

—-  This page was updated on 17 and 21 August 2012 with recommendations from @BMC_series and others. I will make further changes if necessary so please contact me if you have any suggestions  —-

When reviewing the recent GARNet workshop Making Data Accessible to All, we thought it was a good idea to collate the important bioscience databases on the web. I set to work and came up with the table below.

GARNet are keen to get an impression of how the plant science community actually use online databases, so please use the form at the end of this post to let us know how you use these types of resources. Do you deposit data in them, use them to guide practical work, or build whole research projects around them?

You’ll notice there are some blank spaces – if you know a resource that can fill it, please let me know. Likewise if you think I’ve got something wrong (I have personally worked with only a handful of these resources!) or missed off your favourite database, please leave a comment, tweet me or use the form below to tell me about it. (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.

(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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