PhD: Using mass spectrometry and computational methods to measure environmental chemicals and disco

In 2005, Professor Chris Wild at the University of California, Berkeley, introduced the concept of the EXPOSOME – representing all environmental exposures from conception onwards – as a quantity of critical interest to human and environmental health. This launched a series of major international research programs. With >70,000 synthetic chemicals used by industry, from pharmaceuticals to agrichemicals to consumer products, the challenge to measure the exposome is colossal. Since many of these chemicals enter our environment it is essential to understand the potential impacts of complex chemical mixtures, typically at low levels, on environmental and human health. Specifically, to what extent do these mixtures perturb organism health, and which chemicals are predominantly responsible? Knowing this is essential to strengthen regulation under the European Union’s landmark legislation – the Water Framework Directive – the law that governs the monitoring of freshwater across the UK and Europe.

METABOLOMICS is a transformative technology that measures 1000’s of metabolites in organisms, yielding information-rich molecular signatures that describe the responses to pollution. Building on the University of Birmingham’s decade-long track record in metabolomics, we will adapt mass spectrometry metabolomics approaches to measure both the exposome (‘exposure’) and metabolome (‘effect’). We will then undertake the first ecological Exposome Wide Association Study (EWAS) to discover associations between environmental pollution and health of a sentinel freshwater species, Daphnia magna. This species has multiple benefits: it is a sentinel organism in freshwater ecology and ecotoxicology; lifetime exposures are feasible due to the rapid life cycle; chemically unexposed lab populations exist as negative controls; and all components of the Daphnia’s environment can be controlled, including nutrition and pollutant exposure. Overall, this studentship will provide the community with novel methods to characterise the exposome, and build weight of evidence to support the application of EWAS approaches to discover links between pollution and health.

Partners and collaboration:
Our CASE PARTNER, Thermo Fisher Scientific (TFS), is a world leader in the development of liquid chromatography and mass spectrometry (LC-MS) and has identified metabolomics as a priority area. In 2013, TFS formed a Technology Alliance Partnership with the University of Birmingham, the first such partnership within Europe. This proposal builds upon four existing iCASE awards with TFS as part of their commitment to graduate training.

Training and skills:
Collectively this team will provide SPECIALIST TRAINING: in LC-MS, including unparalleled access to current and pre-released metabolomics technologies; in metabolomics, toxicology and analytical sciences (Viant lab; the largest group in environmental metabolomics nationally).

TRANSFERABLE SKILLS will be taught at both Birmingham, through the extensive courses in the Biosciences Graduate Research School, and at TFS, including business awareness, project management and financial training. This training will be truly MULTIDISCIPLINARY to enrich the student experience. Furthermore the main supervisor is highly experienced, having completed 9 PhDs in the past five years and with 4 current students, several of which are/were NERC CASE.

The student will be integrated within three pre-existing communities of PhD students and researchers, providing an exceptional TRAINING ENVIRONMENT: the growing Environmental Systems Biology network at Birmingham, comprising 7 research groups; the Computational Toxicology community, a network of several research groups from Birmingham and internationally; and the community of ca. 30 scientists who constitute the Partnership with TFS.

Importance of this science:
The IMPACTS of this research will be great: economically to TFS through developing and marketing their technologies to study the exposome; socio-economically by developing EWAS approaches that enable a more rigorous assessment of the effects of chemicals on health, of relevance to risk regulation; and by training a scientist who is competent in molecular and computational ‘Big Data’ science.

Are you the right person for this PhD?
We seek an exceptional candidate with a high quality undergraduate or Masters degree (can be pending) in fields such as analytical chemistry, environmental chemistry or forensics, who has a passion to develop bioanalytical approaches and importantly to apply them to a highly relevant 21st century challenge in the environmental sciences.

Funding Notes

This studentship is for 3.5 years and is funded by the NERC and Thermo Fisher Scientific. The studentship covers tuition fees and an annual stipend of ca. £15,000 per annum for UK and EU nationals (where the EU nationals have resided in the UK for 3 years or more), as per NERC funding rules.

Please apply through the University of Birmingham application portal at http://www.birmingham.ac.uk/postgraduate/courses/research/bio/biosciences.aspx

When applying specifically include the name of the supervisor (MARK VIANT), state the funding source (NERC iCASE PhD) and the project title above.

References

Various references from Viant laboratory, and others relevant to the project:
1. A. Southam, A. Lange, R. Al-Salhi, E. Hill, C. Tyler, M. R. Viant, Distinguishing between the metabolome and xenobiotic exposome in environmental field samples analysed by direct-infusion mass spectrometry based metabolomics and lipidomics. Metabolomics 10, 1050-1058 (2014).
2. K. L. Poulson-Ellestad, C. M. Jones, J. Roy, M. R. Viant, F. M. Fernández, J. Kubanek, B. L. Nunn, Metabolomics and proteomics reveal impacts of chemically mediated competition on marine plankton. PNAS 111, 9009-9014 (2014).
3. M. R. Viant, and U. Sommer, Mass spectrometry based environmental metabolomics: A primer and review. Metabolomics 9, S144-158 (2013).
4. C. P. Wild, Complementing the Genome with an “Exposome”: The Outstanding Challenge of Environmental Exposure Measurement in Molecular Epidemiology. Cancer Epidemiol Biomarkers Prev 14, 1847 (2005).
5. C. P. Wild, The exposome: from concept to utility. Int. J. Epidemiol. 41, 24-32 (2012).
6. J.K. Colbourne, M.E. Pfrender, D. Gilbert, W.K. Thomas et al. The ecoresponsive genome of Daphnia pulex. Science 331: 555-561 (2011).

Please contact Mark Viant - attaching your CV to the email - for further information.