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Masters by Research: Genome-based phylogenetic and functional analysis of industrially significant actinobacteria


School of Applied Sciences

About the Project

Actinobacteria are known to produce a multitude of secondary metabolites and demonstrate diverse metabolic capabilities. One distinct evolutionary line within this phylum includes an array of interesting species that synthesise mycolic acids in their cell walls, including members of the closely relate genera Gordonia and Rhodococcus. Members of these taxa have attracted much attention for their degradation and synthesis pathways with various strains applied in full-scale industrial and biotechnological applications.

This study will focus on genome sequence investigations of unknown actinobacteria that possess mycolic acids to establish their phylogenetic positions by comparative analyses of single genes such as 16SSU and gyrB and whole genomes with those available in bioinformatics databases. Further, whole genome data will be explored via bioinformatics analyses for degradation and synthesis pathways of potential biotechnological interest for future investigation.

This will primarily be an in silico study but may have an element of laboratory work, including bacteriology and molecular biology, depending on progress.


Academic qualifications
A first degree (at least a 2.1) ideally in Microbiology or Biomedical Science with a good fundamental knowledge of bacteriology and bioinformatics.

English language requirement
IELTS score must be at least 6.5 (with not less than 6.0 in each of the four components). Other, equivalent qualifications will be accepted. Full details of the University’s policy are available online.

Essential attributes:
• Experience of fundamental laboratory skills in bacteriology
• Competent in bioinformatics and PCR
• Knowledge of whole genome sequence analysis
• Good written and oral communication skills
• Strong motivation, with evidence of independent research skills relevant to the project
• Good time management

Desirable attributes:
Knowledge of bacterial taxonomy, genomic DNA extraction and sequence analysis

Please quote project code SAS0076 in your enquiry and application.

APPLICATION CHECKLIST
• Completed application form
• CV
• 2 academic references, using the Postgraduate Educational Reference Form (Found on the application process page)
• A personal research statement (This should include (a) a brief description of your relevant experience and skills, (b) an indication of
what you would uniquely bring to the project and (c) a statement of how this project fits with your future direction.)
• Evidence of proficiency in English (if appropriate)


Funding Notes

This is a self-funded position.
For informal enquiries about this MRes project, please contact Dr Fiona Stainsby:

References

Zampolli, J., Zeaiter, Z., Di Canito, A. et al. Genome analysis and - omics approaches provide new insights into the biodegradation potential of Rhodococcus. Appl Microbiol Biotechnol 103, 1069–1080 (2019).

Ma, Q., Gao, X., Bi, X., Tu, L., Xia, M., Shen Y., & Wang, M. (2020).
Isolation, characterisation, and genome sequencing of Rhodococcus equi: a novel strain producing chitin deacetylase. Scientific Reports
10: 4329

Sangal, V., Goodfellow, M., Jones, A.L., Seviour, R.J. & Sutcliffe, I.C. (2019). Refined Systematics of the Genus Rhodococcus Based on Whole Genome Analyses. In Alvarez, H.M. (Ed) Biology of Rhodococcus. Springer, Cham

Schneider, K., Graf, E., Irran, E.E., Nicholson, G., Stainsby, F.M., Goodfellow, M., Borden, S.A., Keller, S., Süssmuth, R.D., & Feidler, H-
P. (2008). Biosynthetic capabilities of Actinomycetes No. 43: Bendigoles A~C, new steroids from Gordonia australis Acta 2299. The Journal of Antibiotics 61, 356-364.

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