Master of Science - Molecular Medicine and Haematology / The completion of the genome sequence of Mycobacterium tuberculosis strain H37Rv revealed that 10% of the coding capacity is devoted to two, large multigene families that are characterised by repeat sequences. These are the PE and PPE families that code for acidic, glycine rich proteins. A subgroup of the PE family is the polymorphic GC rich sequence (PGRS) gene subfamily. Genome comparisons of clinical isolates of M. tuberculosis have confirmed the polymorphic character of some of these genes suggesting they may be analogous to the contingency loci found in other pathogenic bacteria. Certain PE-PGRS proteins play a direct role in virulence in M. marinum, other PE-PGRS genes are cell surface associated, and some PE-PGRS proteins are variable surface antigens, supporting a potential role in host pathogen interactions. A reporter assay designed to investigate mutations in a PE-PGRS repeat-containing sequence was used to assess mutation rates in various M. smegmatis host strains by fluctuation analysis. A wide spectrum of mutations was observed and the evidence suggests that slipped-strand mispairing between proximal and distal PGRS sequences located in cis is the predominant type of mutational event at such loci. Moreover, slipped-strand mispairing at such loci occurs at a moderately higher rate than base substitution mutagenesis and is mediated by the normal replicative polymerase.

Typically, systems biology focuses on the form and function of networks of biochemical interactions. Questions inevitably arise as to the evolutionary origin of those networks' properties. Such questions are of interest to a growing number of systems biologists, and several groups have published studies shown how varying environments can affect network topology and lead to increased evolvability. For decades, evolutionary biologists have also investigated the evolution of evolvability and its relationship to the interactions between genotype and phenotype. While the perspectives of systems and evolutionary biologists sometimes differ, their interests in patterns of interactions and evolvability have much in common. This thesis attempts to bring together the perspectives of systems and evolutionary theory to investigate the evolutionary effects of fluctuating environments. Chapter 1 introduces the necessary themes, terminology and literature from these fields. Chapter 2 explores how rapid environmental fluctuations, or "noise", affects network size and robustness. In Chapter 3, we use the Avida platform to investigate the relationship between genetic architecture, fluctuating environments and population biology. Chapter 4 examines contingency loci as a physical basis for evolvability, while chapter 5 presents a 500-generation laboratory evolution experiment which exposes E. coli to varying environments. The final discussion, concludes that the evolution of generalism can lead to genetic architectures which confer evolvability, which may arise in rapidly fluctuating environments as a by-product of generalism rather than as a selected trait.