UCSF

This graduate work consists of projects concerned with functions of RNA, use of high throughput sequencing technology, and the molecular biology of the malaria parasite Plasmodium falciparum. The intricacies of recognition of mRNA molecules by yeast transport machinery were explored in an unbiased manner, leading to identification of both primary sequence and secondary structural motifs. High throughput sequencing was used to recover a new type of bornavirus associated with proventricular dilatation disease in psittacine birds. High throughput sequencing was again used to find leads as to the genetic determinant of artemisinin resistance in Plasmodium falciparum, finding an amplification on chromosome 10 as the most promising lead. Parasite response to artemisinin was also studied at the transcriptional level using microarrays to document the entry into and recovery from the ring-like dormant state induced in Plasmodium falciparum by artemisinin. Finally, splicing in Plasmodium falciparum was investigated by sequencing mRNA from four timepoints in the blood stages of the parasite. Specific software was written to extract all exon-exon junctions within that dataset and higher order analysis revealed previously unknown splice sites, hundreds of alternative splicing events, and the presence of spliced antisense RNAs in the transcriptome.