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Funded PhD Opportunity

Naturally-occurring microbial biosynthetic pathways for propane

This project is funded by: DfE CAST award in Collaboration with Calor UK Ltd

Subject: Biomedical Sciences


Summary

Replacement of fossil fuels with sustainable energy sources has become an environmental priority due to climate change issues. Energy companies, including Calor UK Ltd, are committed to reducing fossil fuel usage through alternative technologies. Current solutions would include biopropane production using sustainable resources. Some researchers have genetically engineered bacteria capable of producing propane. However, yield restrictions due to product or substrate toxicity, and maintaining cell integrity at high product concentrations remain major challenges. It is likely that naturally occurring microorganisms capable of propane production are better adapted to maintain cell integrity at high product concentration. There is geochemical evidence for the biological formation of ethane and propane. However, to date no natural biosynthetic pathways for propane have been reported, and a biochemical pathway is potentially novel and of great interest. We have succeeded in obtaining mixed propane-producing microbial cultures from environmental samples.

A longterm aim is the development of an industrially relevant process that could be scaled for commercial production. In this project we aim to identify further microbial biosystems capable of propane biosynthesis and investigate the biosynthetic pathways involved, identifying key genes and enzymes.

Successful outcomes of the project would include:

i)   Identifying microbial species capable of producing high propane yields

ii)  Elucidating the biochemical biosynthesis pathway(s)

iii)  The identification of genetic resources for novel metabolically-engineered organisms.

iv)  Obtaining pure cultures/consortia for potential commercial biopropane fermentation

Objectives

1. To identify propane production in microbial cultures obtained from 40 UK environmental samples. Positive individual microbial species will be isolated and identified by 16S rRNA gene sequencing.

2. Use a Systems Biology approach (metabolomic and transcriptomic experiments) to elucidate the biochemical pathway(s) involved in propane biosynthesis. To identify metabolites and upregulated gene expression associated with increased propane production and the key genes / enzymes involved. Metabolomics profiling experiments will utilize uHPLC-high resolution mass spectrometry (HRMS) platforms including Orbital traps and FT-ICR-MS. Statistical analysis of the LC-MS data will allow the identification of altered metabolite concentrations that are correlated with propane production. Pathway analysis will be carried out using XCMS, MetaCyc, and KEGG Pathway Mapping. Transcriptomics experiments will utilize nanopore long read direct RNA-seq – a highly parallel realtime method that enables direct detection of RNA. Statistical analysis will allow the identification of significant alterations in gene expression.

3. To carry out targeted experiments to test generated hypotheses, including quantitative and qualitative analysis of metabolites, stable isotope labelling of precursors to track metabolite conversions by mass spectrometry, or gene deletion and metabolomics analysis. Microbial culture and propane analysis can be undertaken in Year 1 while Metabolomics and Transcriptomics investigation during Years 2 and 3.  The Systems Biology experiments will follow the Metabolomics Society guidelines and best practices for RNA-seq experiments and data analysis, and will provide suitable training for a PhD in the areas of microbiology and in Systems Biology, analytical analysis and statistical analysis. It will also provide valuable knowledge on propane microbial biosynthesis that is of environmental and industrial relevance.


Essential criteria

  • To hold, or expect to achieve by 15 August, an Upper Second Class Honours (2:1) Degree or equivalent from a UK institution (or overseas award deemed to be equivalent via UK NARIC) in a related or cognate field.
  • Sound understanding of subject area as evidenced by a comprehensive research proposal

Desirable Criteria

If the University receives a large number of applicants for the project, the following desirable criteria may be applied to shortlist applicants for interview.

  • Completion of Masters at a level equivalent to commendation or distinction at Ulster
  • Experience using research methods or other approaches relevant to the subject domain
  • Work experience relevant to the proposed project
  • Publications - peer-reviewed
  • Publications record appropriate to career stage
  • Experience of presentation of research findings
  • A comprehensive and articulate personal statement
  • Use of personal initiative as evidenced by record of work above that normally expected at career stage.
  • Relevant professional qualification and/or a Degree in a Health or Health related area

Funding

This project is funded by: DfE CAST award in Collaboration with Calor UK Ltd

The scholarship will cover tuition fees at the Home rate and a maintenance allowance of £ 16,009 per annum for three years. EU applicants will only be eligible for the fee’s component of the studentship (no maintenance award is provided). For Non-EU nationals the candidate must be "settled" in the UK. This scholarship also comes with £900 per annum for three years as a research training support grant (RTSG) allocation to help support the PhD researcher.


Other information


The Doctoral College at Ulster University


Reviews

Profile picture of Kieran O'Donnell

My experience has been great and the people that I have worked with have been amazing

Kieran O'Donnell - 3D printing of biological cells for tissue engineering applications

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Profile picture of Michelle Clements Clements

Completing the MRes provided me with a lot of different skills, particularly in research methods and lab skills.

Michelle Clements Clements - MRes - Life and Health Sciences

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Profile picture of William Crowe

Throughout my PhD I’ve been provided with continuous support and guidance by my supervisors and the staff at the University.I’ve also received many opportunities to further enhance my professional development in the form of teaching experience and presenting my work at conferences which will aid in my pursuit of a career in academia or industry.

William Crowe


Key dates

Submission deadline
Friday 7 February 2020

Interview Date
9 to 20 March 2020


Applying

Apply Online  


Campus

Coleraine campus

Coleraine campus
The feeling of community at our Coleraine campus makes for a warm and welcoming student experience.


Contact supervisor

Professor Ibrahim Banat


Other supervisors

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