Analysis of HIV-1 and foraminiferal molecular evolution

Wade, Chris

Abstract

This thesis presents work examining aspects of both HIV- 1 and foraminiferal evolution. The thesis is set out accordingly into two sections, each of which contains an introduction with individual chapters presented as a series of papers.
In section A, five papers are presented which examine the evolution of HIV-1 both within and between patients. The first paper presented examines the molecular epidemiology of HIV-1 within Scotland, Northern England, and Ireland (paper I), with attention focused on identifying risk group associated differences within the cohort. This work also provides important background information for the interpretation of molecular data from transmission clusters. The main focus of the work on HIV-1 evolution has been on the transmission of IIIV-1, with particular emphasis placed on mother-child transmission. Four papers are presented which examine evolutionary aspects of HIV-1 transmission. The first of these (paper II) examines the viral variants transmitted from mother to child in four mother-child transmission pairs. The second (paper ffi) analyses similar data from five mother-child transmission pairs, focussing predominantly on viral evolution within the child over the first year of life. The final two papers investigating l{IV-1 transmission examine viral variation within two transmission sets. Paper IV examines the vertical transmission of lily-i to two infected children born to the same mother at an approximately two year interval, while paper V examines the heterosexual transmission of lily- 1 from a male index to two female contacts and the subsequent vertical transmission of H1V-1 to their two children. The phylogenetic placement of these transmission sets within the Edinburgh cohort is also assessed.
In section B, four papers are presented which examine aspects of foraminiferal evolution. The first paper (paper I) focuses on the problems inherent in the amplification of foraminiferal DNA due to the association of large numbers of symbionts, commensals and food particles with each foraminifer. The amplification of foraminiferal sequences for the small subunit ribosomal RNA gene is then described, and the phylogenetic placement of the foraminifera within eukaryote evolution examined (papers II and ifi). Finally, the phylogenetic relationships within the foraniinifera, in particular planktic foraininiferal evolution and the relationships between benthic and planktic foraminiferal species, are described (paper V).

Citation

Wade, C. (1997). Analysis of HIV-1 and foraminiferal molecular evolution. (Dissertation). University of Edinburgh. Retrieved from https://nottingham-repository.worktribe.com/output/34111093

• Thesis Type: Dissertation
• Deposit Date: May 7, 2024
• Public URL: https://nottingham-repository.worktribe.com/output/34111093
• Award Date: Dec 1, 1997