Modelling acetogen metabolism

Overview

There is currently much interest in expanding the range of organisms used in industrial biotechnology and the range of products made with them, both at the low value end for biofuels and the mid-value range of chemical feed-stocks. One option, of broad application, is to use one carbon precursors, such as syngas (CO, CO2 and H2) or waste gases from e.g. steel plants. These can be exploited by organisms such as the acetogens, which use the Woods-Ljungdahl pathway to convert 1C compounds to acetate and other low-value products. These organisms would need to be engineered to produce more complex, higher value products, but a limitation is that their metabolism has not been extensively studied.

Since a number of the acetogens have now been sequenced, the possibility arises of modelling their metabolic networks with the emerging technique of genome-scale metabolic modelling. This can determine the metabolic capabilities encoded in the genome, and be used as a tool to design modifications to produce novel products whilst maintaining the viability of the organism. The modelling process involves extracting the metabolic network from databases and analysing it by techniques including linear programming (also called flux balance analysis). The aim of this project is to construct a metabolic model of the representative acetogen Acetobacter woodii and to use it to assess its potential for industrial biotechnology.

This systems biology project has a theoretical and experimental component. The theoretical component is the construction and analysis of the metabolic model within the Cell Systems Modelling Group (http://mudshark.brookes.ac.uk/) at Oxford Brookes University. The group has previously used its metabolic modelling package, ScrumPy, to build a number of bacterial and plant metabolic models. The experimental component will consist of two three month placements at BioSyntha for obtaining the fermentation data needed to formulate and test the model.

Application Information

Applicants should have the equivalent of a good Honours degree (minimum 2.1 or higher) that includes some coverage of at least one, but preferably more, of the following topics: metabolism, microbiology, computer programming and linear algebra. Applications from graduates of Systems Biology courses are welcomed. The student appointed will be provided with opportunities for complementary studies as required.

To apply, please complete the Faculty of Health and Life Sciences PhD Research Studentship Application Form, which you can download from http://www.hls.brookes.ac.uk/images/research/phd-studentship-application-form-jan-14.doc

Applications will only be accepted by e-mail to the following e-mail address: [Email Address Removed]

Additionally with your e-mail application you should enclose a CV.

Please refer to guidance notes that accompany the downloadable application form.

Applicants who are chosen to attend a final selection interview, will be asked to supply two academic references. Our standard referee form will be provided AT THIS STAGE, when we will also require copies of degree certificate/s and transcript/s.

For further information on the project description please e-mail: Professor David Fell ([Email Address Removed]) or Dr Mark Poolman ([Email Address Removed]) in Department of Biological and Medical sciences, Faculty of Health and Life Sciences, Oxford Brookes University.

PLEASE NOTE NO APPLICATIONS - CV or QUERIES MUST BE SENT VIA FINDAPHD

PLEASE NOTE Potential applicants must check that they satisfy the BBSRC requirements described at http://www.bbsrc.ac.uk/funding/studentships/studentships-index.aspx.