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Quantifying community metabolomes within model freshwater ecosystems and their responses to pollutants

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  • Full or part time
    Prof M Viant
    Prof J B Brown
    Prof J Colbourne
  • Application Deadline
    No more applications being accepted
  • Funded PhD Project (European/UK Students Only)
    Funded PhD Project (European/UK Students Only)

Project Description

The University of Birmingham (UoB) is an international leader in OMICS TECHNOLOGIES and SYSTEMS TOXICOLOGY, achieved by pooling its expertise and capacity in omics and bioinformatics with specialists in toxicology, systems biology and chemical regulation. Our mission statement commits to offering leadership in the development and application of omics- and bioinformatics-based solutions, enabling evidence-based chemical safety science to safeguard both human and environmental health.

Current ECOLOGICAL RISK ASSESSMENT of chemicals relies on standardised OECD tests on typically three isolated plant and animal species. This lack of realism is widely recognised as a central failure of environmental legislation. QUANTITATIVE MODEL ECOSYSTEMS have the potential to revolutionise ecological risk assessment by enabling molecularly reproducible experiments on ecologies that “develop” along predictable trajectories. Characterising the extent to which those trajectories are perturbed by pollutants would provide fundamental new metrics of pollutant impacts on ecosystems. Furthermore, when coupled with discovery-driven OMICS technologies, quantitative model ecosystems could for the first time enable discovery of stress response MECHANISMS (and subsequently diagnostic markers of pollutant impacts) within realistic environments of interacting sediment microbes, algae, higher plants, invertebrates, etc.

METABOLOMICS is a proven technology for discovering mechanisms of how organisms respond to stress. UoB is a world leader in the development and application of metabolomics to quantify pollutant impacts on isolated species, with a particular focus on aquatic organisms. Our recent NERC-funded work has for the first time utilised metabolomics to discover a toxicity pathway spanning two species across two trophic levels. Here we propose to partner with Thermo Fisher Scientific to:

(1) establish and optimise novel sampling and non-targeted LC-MS metabolomics techniques to characterise community metabolomes within model freshwater ecosystems that comprise of many species,

(2) examine the temporal stability of metabolic processes in these model systems,

(3) quantify the impacts of pollutants on baseline community metabolism, and

(4) disseminate via multiple channels including through our partnership with the European Commission’s Joint Research Centre and through our membership of OECD Extended Advisory Group on Molecular Screening and Toxicogenomics.

Our CASE PARTNER, Thermo Fisher Scientific (TFS), is a world leader in the development of LC-MS and has identified metabolomics as a priority area. Since 2013, TFS and UoB have been actively engaged in a Technology Alliance Partnership.

Collectively this team will provide SPECIALIST TRAINING: in LC-MS, including unparalleled access to current and pre-released metabolomics technologies (at TFS); in environmental metabolomics and toxicology (Viant), biostatistics and quantitative model ecosystems (Brown) and freshwater ecology (Ledger). TRANSFERABLE SKILLS will be taught at both UoB, 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 5 PhDs in the past five years and with 5 current students, most of which are/were NERC iCASE.

The student will be integrated within pre-existing cohorts of PhD students and researchers, providing an exceptional TRAINING ENVIRONMENT: the growing Environmental Systems Biology network at Birmingham, comprising 7 research groups; the community of ca. 30 scientists who constitute the technology partnership with TFS.

The IMPACTS will be far reaching: economically to TFS through developing and marketing their LC-MS technologies for metabolomics; socio-economically by facilitating the development of new methodologies to enable more rigorous quantification and mechanistic understanding of the effects of pollutants on freshwater ecosystems; and by training a scientist who is competent in molecular, analytical and computational ‘Big Data’ science.

Scientific excellence of the University:

The School of Biosciences achieved an impressive performance in the Research Excellence Framework 2014, rising up to 6th place for the quality of its research within the elite, research-focused Russell Group of UK universities.

Are you the right person for this PhD?

We seek an excellent, highly motivated candidate with a high quality undergraduate or Masters degree (can be pending) in fields such as (bio)analytical chemistry, environmental chemistry, biochemistry or toxicology, who has a passion to apply and then translate state-of-the-art metabolomics to 21st century challenges in environmental toxicology.

Funding Notes

This NERC studentship is for 4 years. In addition to the payment of tuition fees, the award provides an annual stipend and funds for the laboratory studies. Thermo Fisher Scientific are providing further funding for this PhD, as is the University of Birmingham.

NOTE that this PhD funding is for UK HOME STUDENTS ONLY, meaning it is open to UK citizens, or to EU citizens who have lived in the UK for the LAST THREE YEARS.


Representative papers from Viant’s research team:

A. D. Southam, R. J. M. Weber, J. Engel, M. R. Jones, M. R. Viant, A complete workflow for high-resolution spectral-stitching nanoelectrospray direct infusion mass spectrometry-based metabolomics and lipidomics. Nature Protocols 12(2):255-273. 10.1038/nprot.2016.156.

J. Zhang, M. A. Abdallah. T. D. Williams. S. Harrad. J. K. Chipman. M. R. Viant, Gene expression and metabolic responses of HepG2/C3A cells exposed to flame retardants and dust extracts at concentrations relevant to indoor environmental exposures. Chemosphere 144, 1996-2003 (2016).

N. S. Taylor, R. Merrifield, T. D. Williams, J. K. Chipman, J. R. Lead, M. R. Viant, Molecular toxicity of cerium oxide nanoparticles to the freshwater alga Chlamydomonas reinhardtii is associated with supra-environmental exposure concentrations. Nanotoxicology 10, 32-41 (2016).

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).

J. A. Kirwan, R. J. M. Weber, D. I. Broadhurst, M. R. Viant, Direct infusion mass spectrometry metabolomics dataset: a benchmark for data processing and quality control. Nature Publishing Group’s Scientific Data 1, Article 140012 (2014).

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. Proceedings National Academy Sciences 111, 9009-9014 (2014).

W. B. Dunn, A. Erban, R. J. M. Weber, D. J. Creek, M. Brown, R. Breitling, T. Hankemeier, R. Goodacre, S. Neumann, J. Kopka, M. R. Viant, Mass appeal: metabolite identification in mass spectrometry-focused untargeted metabolomics. Metabolomics 9, S44-66 (2013).

M. R. Viant, and U. Sommer, Mass spectrometry based environmental metabolomics: A primer and review. Metabolomics 9, S144-158 (2013).

How good is research at University of Birmingham in Biological Sciences?

FTE Category A staff submitted: 42.80

Research output data provided by the Research Excellence Framework (REF)

Click here to see the results for all UK universities

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