BS05-05 Developing tools to integrate transcriptomic and metabolomic data for understanding plant adaptation

(NERC/EPSRC Special Environmental Genomics Studentship).
Supervisors: Dr. Nick Smirnoff and Professor Mark Macnair (School ofBiosciences, University of Exeter) and Dr. John Newbury and Dr. BrianFord-Lloyd (School of Biosciences, University of Birmingham). Contact:N.Smirnoff@exeter.ac.uk.

Application deadline: Thursday 30th June, 2005.

Summary
Transcriptomics (DNA microarrays) and metabolomics (measurement of manymetabolites simultaneously by mass spectroscopy and NMR) are tools thatare being applied to understanding the response and adaptation oforganisms to their environment on a genome-wide scale. This projectaims to develop bioinformatic tools to integrate transcriptomic andmetabolomic data from plants that differ in their ability to tolerateand accumulate zinc, a potentially toxic metal. The project will bebased at Exeter and candidates should be interested in combiningcomputational/systems biology with laboratory work.

Details
Arabidopsis halleri and A. petraea are close relatives of the modelplant A. thaliana. A. halleri is highly tolerant to zinc andhyperaccumulates in its leaves, while A. petraea does not. Crossesbetween these species produce offspring that inherit zinc tolerance andhyperaccumulation independently. In a current project we are usinggenetics combined with DNA microarrays to identify genes that determinehyperaccumulation. Metabolic traits potentially involved in zincaccumulation (such as organic acid accumulation) also differ betweenthe parent species and offspring In this project we will identify genesthat control these metabolic traits by combining DNA microarray datawith comprehensive metabolic profiling of the plants using massspectroscopy and nuclear magnetic resonance spectroscopy (NMR). Thestudent will produce new microarray data, produce metabolic profilesand develop bioinformatic methods to integrate these so as to identifygenes that determine plant adaptation. The project will be based atExeter.

For further project details email: N.Smirnoff@exeter.ac.uk

To apply please send the following:
1)A covering letter (headed with Project title and Supervisor Name)
2)Your CV
3)Two letters of reference to:

Sarah Mudge (PG Studentships)
School of Biological and Chemical Sciences
Hatherly Laboratories
University of Exeter Exeter EX4 4PS

Source: NERC/EPSRC Special Environmental Genomics Studentship