Cultures of the ciliate <i>Tetrahymena</i> grow into dense colonies overnight in chemically defined medium, when seeded above a ‘critical’ density.  Below this density, the cells all die within hours. The diverging pathways leading to survival and death are investigated in this thesis. Rescuing activity is demonstrated in conditioned medium (and buffer) and a novel, cell-produced survival factor, TCSF1, is isolated from this, by means of PAGE and HPLC with commercially available and custom made columns.  The active factor is investigated through mass spectrometry, amino acid analysis and Edman degradation.  It is shown to have a mass of ~10kDa, but the rescuing activity can be located to a ~1.5kDa motif of 15 amino acid residues.  The peptide, cellular or synthetic, rescues the cells from LDD.  Changes to the primary structure of the synthetic motif result in partial or total loss of activity, suggesting that the motif may be conserved.  The intact cellular factor stimulates DNA synthesis as measured by incorporation of labelled Thymidine; an activity not observed in the synthetic peptide, and it is suggested that the cellular protein may comprise active sites lacking in the synthetic peptide.  The peptide is demonstrated to exert a rescuing effect on other types of <i>Tetrahymena, Colpidium </i>and fibroblasts.  The regulation of cultures entering the stationary phase is investigated, with focus on a hypothesised inhibitory factor.  Results indicate that entry into the stationary phase is not caused by depletion of any nutrients, yet do not suggest that any cell released inhibitory component is readily obtainable.  The possible role of TCSF1 on the regulation of lipolysis and protein kinase activity is discussed.  Another component from the extracellular medium of ~23kDa is observed, but not purified.  Its relation to TCSF1 is discussed.

The main thrust of this thesis was to characterize P.falciparum genetic diversity in northern Ghana. To do this, I used simple techniques to purify P. falciparum DNA from clinical samples across a rural setting for whole-genome sequencing. The goal was to provide a framework for exploring host-parasite genetic interactions. Utilizing Illumina deep sequencing data for 277 isolates I analyzed P. falciparum genetic diversity and described within-host diversity across this area. I observed random mating (ie no population structure) in the local parasite population, and a high genetic diversity indicative of high out-crossing. Moreover, when I aggregated my data with similar published data from Burkina Faso and Mali (sites ≈500km apart), no population structure was evident. In contrast, sites sampled in Cambodia and Thailand (≈ 800km apart) were found to have greater population structure and high potential for inbreeding. This may be driven by differences in transmission intensity between the sites sampled in West Africa and southeast Asia. To demonstrate the utility of deep sequencing data, I focused on the genomic regions of pfdhfr, pfdhps and pfcrt, known to be under antimalarial drug selection. I surveyed the full diversity of point mutations already characterized in these genes and discovered previously unknown variants. However, in order to provide a means to follow up on new variants or interesting candidate regions in large clinical samples with limited parasite DNA, I assessed the Sequenom iPLEX platform for high-throughput genotyping of P. falciparum polymorphisms. This necessitated developing a method appropriate for assigning genotypes in haploid genome mixtures common in natural infections. Finally, I used this method to type host and parasite markers in a case-control sample set from this region for exploring host-parasite genetic interactions. I found that children who have the sickle-cell trait and carry parasites that have pfdhfr resistant alleles lose their protection against severe malaria as compared to children who have normal haemoglobin and are infected with parasites with these resistant alleles.