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Developing a 3rd-generation genome pipeline to uncover novel metabolic activities in Galdieria: a focus on secreted enzyme activities

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  • Full or part time
    Prof S J Davis
    Dr P Ashton
  • Application Deadline
    No more applications being accepted
  • Funded PhD Project (European/UK Students Only)
    Funded PhD Project (European/UK Students Only)

Project Description

Galdieria is a red alga that exhibits wide metabolic versatility and displays enormous capacity to thrive at highly acidic conditions (down to pH 0) and temperatures above 55 ˚C, which is the limit of eukaryotic life. Its extremophile lifestyle makes it a fascinating organism to study from both a mechanistic viewpoint and to find novel species with properties that have industrial biotechnological (IB) applications. To exploit Galdieria, one must understand the constellation of diversity in metabolic capacity. We have assembled a sub-collection of lines that are strikingly different in metabolic capacity. In investigating the potential of third-generation genomics to provide rapid, affordable long-read capacity, this project develops nanopore genome sequencing to define Galdieria strains that have the greatest IB utility. In phase 1 the student will use short-read genome-sequencing as a starting point to further develop nanopore, third-generation genomics. Here it is expected that dozens of complete Galdieria genomes would be produced, and the extent of wide-scale phylogenomic diversity would be appraised. From there, full genome annotations lead to descriptions of metabolic capacities in these diverse Galdieria. In phase 2, informatic descriptions will be made for excreted enzymes that can function under very low pH and elevated temperature. From the large range of such classified enzymes, searches will be used to identify encoded enzymes, such as xylanases and other cellulases, proteases and oxidative enzymes. In phase 3, the student will perform enzyme production and characterisation. By definition, these enzymes must function at high temperature and very low pH and could be the most resistant enzymes ever isolated from a eukaryote. Taken together this project provides direct links between mechanistic biology of an interesting extremophile, with biochemical coupling to genomic-based informatics, to define exciting translational potentials for enzyme discovery.

This project will also be co-supervised by Dr Ian Carr from the Leeds Institute of Biomedical & Clinical Sciences, University of Leeds.

Funding Notes

This is a BBSRC White Rose Network studentship fully funded for 4 years and covers: (i) a tax-free stipend at the standard Research Council rate (£14,057 for 2015-2016, to be confirmed for 2016-2017 but typically increases annually in line with inflation), (ii) research costs, and (iii) tuition fees at the UK/EU rate.

The studentship is available to UK and EU students who meet the UK residency requirements.

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

FTE Category A staff submitted: 44.37

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

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