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Comparative genomic analysis of variant features within the Neisseria spp.

  • Full or part time
  • Application Deadline
    Applications accepted all year round
  • Self-Funded PhD Students Only
    Self-Funded PhD Students Only

Project Description

The availability of rapid genome sequencing had generated an explosion of bacterial genome sequence data, much of which has not been fully explored and investigated. Using computer-based genome sequence data analysis, bioinformatics, and comparative genomic investigations, the genome sequence data available for the human pathogens Neisseria gonorrhoeae, cause of the sexually transmitted disease gonorrhoea, and Neisseria meningitidis, cause of meningococcal meningitis and septicaemia, will be compared to non-pathogenic Neisseria spp. The bacteria within this genus are closely related and naturally competent for transformation, meaning that horizontal gene transfer between them is possible and has been observed in previous research studies.

Based on previous genomic research into the Neisseria species genome sequences, this project will explore the diversity and variation in gene presence across the genus. Genes with likely roles in virulence and within host survival will be explored in detail, with the aim of understanding their presence in the context of the rest of the genome and whether they are potential targets for antimicrobial interventions. In addition, non-coding genetic features that influence the expression of genes will be comparatively assessed and investigated as potential targets for pharmaceutical control of virulence. During the PhD, existing genome sequence data will be re-annotated and analysed and new data will be generated, assembled, annotated, and analysed. Shared features in the core genome will be used to show phylogenetic relationships, against which accessory genome features present in only a few datasets can be better understood.

Funding Notes

No funding is available - only self-funded applications can be considered

References

Churchward, C.P., Calder, A. and Snyder, L.A.S. (2018). Mutations in Neisseria gonorrhoeae grown in sub-lethal concentrations of monocaprin do not confer resistance. PLoS One 13(4): e0195453.

Spencer-Smith, R., Gould, S.W., Pulijala, M. and Snyder, L.A.S. (2018) Investigating potential chromosomal rearrangements during laboratory culture of Neisseria gonorrhoeae. Microorganisms 6: 10.

Elbeyioglu, F., Roberts, S.B., Spencer-Smith, R., Pulijala, M., Zelewska, M.A., Nebel, J-C. and Snyder, L.A.S. (2017). Inversion of Correia Repeat Enclosed Elements in Neisseria gonorrhoeae. Microbiology 163: 31-36.

Roberts, S.B., Spencer-Smith, R., Shah, M., Nebel, J-C., Cook, R.T. and Snyder, L.A.S. (2016). Correia Repeat Enclosed Elements and non-coding RNAs in the Neisseria spp. Microorganisms 4(3): 31.

Zelewska, M.A., Pulijala, M., Spencer-Smith R., Mahmood H.A., Norman B., Churchward, C.P., Calder, C. and Snyder, L.A.S. (2016). Phase variable DNA repeats in Neisseria gonorrhoeae influence transcription, translation, and protein sequence variation. Microbial Genomics 2.

Spencer-Smith*, R., Roberts*, S.B., Gurung, N. and Snyder, L.A.S. (2016). DNA uptake sequences in Neisseria gonorrhoeae as intrinsic transcriptional terminators and markers of horizontal gene transfer. Microbial Genomics 2.

Karlyshev, A., Snyder, L.A.S., Griffin, R. and McFadden, J. (2015). Insight to proteomic investigations provided by the analysis of the genome sequence of Neisseria meningitidis serogroup C strain L91543. FEMS Microbiol. Letters 362(9).


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FTE Category A staff submitted: 17.22

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