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Applications are now open for PhD studentships starting in October 2018. 

Please read the recruitment introduction for more information about eligibility, how to apply, and possibilities for further funding.

The deadline for applications is 8 January 2018.

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MOCK_UENV18EE

MOCK_UENV18EE - Genome editing for the exploration of biotechnological applications and evolutionary potential of microalgae

Project description

Selected other project supervisors:
Professor Cock van Oosterhout (UEA Environmental Sciences)
Professor Vincent Moulton (UEA Computing Sciences)
Dr Matthew Clark (Earlham Institute)

Background
Microalgae contribute more than 25% of global annual carbon fixation, which is equal to the carbon fixation of all tropical rainforests combined. Furthermore, microalgae are at the intersection of many different disciplines because of their interesting biology rooted in complex evolution and their key position in aquatic environments where they underpin global biogeochemical cycles and food webs.

Although many decades of research have elucidated the evolutionary forces underpinning their biology and ecology, only recently our group provided the first evidence of a previously unknown mechanism of Environmental Dependent Differential Allelic Expression discovered in a marine diatom. This evolutionary innovation seems to play a key role for how algae adapt to extreme fluctuating environments. In simple terms, allelic variants of the same genetic locus have diverged under Darwinian selection, facilitating adaptations to sometimes diametrically different environments. Evidence of this phenomenon is found throughout many microalgal communities, as well as other species with vast population sizes in the marine environment.

Research methodology

  1. Single cell DNA and allele-specific RNA-seq with model microalgae to identify gain or loss of heterozygosity and copy number variation, and assess the evolutionary forces underpinning allelic divergence and differential expression.  
  2. Selected allelic variants of single genes and entire metabolic pathways will be subjected to editing using CRISPR/Cas.
  3. Testing the ecological significance and biotechnological potential of selected alleles using phenomics.   

Training
The student will receive training at the crossroads of functional molecular biology, population genomics and bioinformatics. The work extends to environmental biotechnology. Training will take place in UEA’s School of Environmental Sciences and the Computational Biology Laboratories at UEA and the Earlham Institute. Thus, training will be highly integrative and based on cutting edge tools. Specific training will be provided in how to work collaboratively, how to prioritize and how to organize and structure a complex work flow.

Person specification
We are looking for a highly motivated student who is willing to pursue integrated work based on cutting edge technologies from neighbouring disciplines in environmental biology and biotechnology. Suitable first degree subjects are:  molecular biology, bioinformatics, population genomics, environmental biotechnology, marine biology, plant molecular biology, genetics, genomics and bio-oceanography.

Funding
This project has been shortlisted for funding by the EnvEast NERC Doctoral Training Partnership, comprising the Universities of East Anglia, Essex and Kent, with over twenty other research partners. Undertaking a PhD with the EnvEast DTP will involve attendance at mandatory training events throughout the course of the PhD.

Shortlisted applicants will be interviewed by EnvEast on 12/13 February 2018.

Selected candidates who meet RCUK’s eligibility criteria will be awarded a NERC studentship - in 2017/18, the stipend is £14,553. Ordinarily, EnvEast studentships are for 3.5 years, although longer awards may be made to applicants from quantitative disciplines who have limited experience in the environmental sciences, to allow them to take appropriate advanced-level courses in the subject area.

In most cases, UK and EU nationals who have been resident in the UK for 3 years are eligible for a stipend. For non-UK EU-resident applicants NERC funding can be used to cover tuition fees, RTSG and training costs, but not any part of the stipend. Individual institutes may, however, elect to provide a stipend from their own resources.

This PhD studentship is expected to begin in September/October 2018. Both full-time and part-time study are possible (those planning to study part-time may wish to discuss this with the supervisor before applying).

References

  1. Mock, T., Otillar, R. P., Strauss, J., McMullan, M., Paajanen, P., Schmutz, J., ... van Oosterhout, C. & Grigoriev, I.V. (2017). Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus. Nature, 541(7638), 536-540.
  2. Bentkowski, P., van Oosterhout, C., Ashby, B., & Mock, T. (2017). The effect of extrinsic mortality on genome size evolution in prokaryotes. The ISME Journal, 11(4), 1011.
  3. Hopes, A., Nekrasov, V., Kamoun, S. & Mock, T. (2016). Editing of the urease gene by CRISPR-Cas in the diatom Thalassiosira pseudonana. Plant Methods, 12, 49.
  4. Toseland A., Daines S. J., Clark J. R., Kirkham A., Strauss J., Uhlig C., Lenton T. M., Valentin K., Pearson G. A., Moulton V., Mock T. (2013) The impact of temperature on marine phytoplankton resource allocation and metabolism. Nature Climate Change, 3, 979-984
  5. Lopez-Gomollon S., Beckers M., Rathjen T., Moxon S., Maumus F., Mohorianu I., Moulton, V., Dalmay T., Mock T. (2014) Global discovery and characterization of small non-coding RNAs in marine microalgae. BMC Genomics, 15, 697