Student Theses and Dissertations


Thomas S. Oh

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RU Laboratory

Rice Laboratory


Hepatitis C virus is a small, enveloped positive‐strand RNA member of the Flaviviridae and the etiological agent of a global epidemic of chronic hepatitis C. One of the salient features of HCV is a complex regulatory scheme involving numerous viral and cellular components and which may be the key to its striking success in initiating and maintaining decades‐long chronic disease in infected individuals. Lacking any known latent or integrated form, HCV must persist through ongoing RNA replication, immune evasion, and infection of naïve cells. HCV is a highly‐studied virus, and many details of its life cycle have been worked out; however, much remains unknown. One thing lacking is an integrated model of HCV as a single dynamic system. Various viral life cycle events, such as entry, polyprotein translation and processing, RNA replication, virion morphogenesis and secretion have been studied and worked out to some extent. How these activities are coordinated and how they influence each other is less wellunderstood. We approached this problem from three angles. We developed quantitative mathematical models designed to accurately recapitulate the specific processes of virus production and accumulation and virus entry. These models were applied to gain a more detailed understanding of these systems. We studied the HCV regulatory protein NS5A through genetic and chemical perturbation to try to understand how it might be connecting different life cycle activities. These studies revealed a surprising role for the host cellular protein cyclophilin A in regulating virus assembly as well as clarifying aspects of NS5A phosphorylation. These findings suggest a complex system of regulation linking polyprotein translation, RNA replication, and virion assembly which will require further work to decipher. We also pursued a bioinformatics approach, in which we analyzed HCV multiple sequence alignments (MSAs) to identify covariant amino acid positions within HCV proteins. Some of the challenges to the study of covariation in HCV MSAs were identified, and we describe a novel method of calculating covariation which addresses some of these issues, particularly the problem of phylogenetic covariance. While an integrated dynamic model of HCV remains far from achieved, these studies are presented as incremental steps towards that goal.


A thesis presented to the faculty of The Rockefeller University in partial fulfillment of the requirements for the degree of Doctor of Philosophy.

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