The Dynamic Structural Genome of Plasmodium falciparum

Plasmodium falciparum is the causative agent of the most severe and deadly form of malaria in humans causing significant amounts of human suffering. These intracellular parasites are spread between vertebrate hosts by the bites of infected Anopheles mosquitoes. A campaign to eradicate malaria initiated by the World Health Organization in the 1950s had some initial success but the goal of global eradication was eventually abandoned as it was determined to be unrealistic. Currently there is no approved vaccine to combat malaria, and drug resistance of parasites to antimalarial drugs is a real and growing concern. Genome sequencing projects have been completed for humans, the mosquito vector, and the causative parasite with the prospects and expectations of breakthroughs in combating malaria. These genome sequences, in addition to being substantial technical achievements, are significant and meaningful enabling resources of information. The challenge to the research community is to devise useful applications, leading to discoveries from this wealth of information. The parasite has shown a remarkable ability to adapt to novel antimalarial drugs. Microarrays -- which have enabled by the information from sequencing projects -- afford a global view of changes in the parasite over time and following selection pressures. Depending on the target (RNA or DNA), this includes the ability to monitor gene expression levels, large copy number variations in the genomic DNA, and even allows for the identification of smaller polymorphisms (e.g. SNPs, indels, and tandem repeats). The first aim of this thesis is to assess the SNP detection performance of a first- generation P. falciparum microarray and to identify optimal probe features for polymorphism detection to be incorporated in future designs. By adjusting specific probe design parameters identified through this study, we can build high specificity while improving sensitivity. The second aim is to use CGH microarrays to monitor genomic changes that have occurred in a parasite line under chloroquine pressure. This approach identifies significant genomic changes of various types which may have implications for drug response and genome evolvability. The final aim is to globally characterize tandem repeat sequences in the P. falciparum genome initially identified by CGH. This previously unrecognized variation is ubiquitous and impacts the coding structures of hundreds of genes, underscoring their potential role in genome evolution. General characteristics of these sequences including their genome-wide distribution, their size distribution, and common features in the tandem repeat flanking regions are described.