Defining molecular mechanisms of pathogenesis in emerging infectious diseases, development of recombinant vaccines and improved molecular diagnostics. A long-term research focus has been to understand the molecular basis for persistent infections, beginning with investigations of antigenic variation in African trypanosomes and now including persistent infections caused by rickettsias of veterinary and human importance. An important finding has been the discovery of gene sequence mosaics in trypanosomes and Anaplasma. These mosaics are formed by contribution of sequence to genomic expression sites by different functional pseudogenes. This allows extensive surface diversity to be created from the small Anaplasma genomes because of the large number of different combinatorial possibilities. With the completion of genome sequence for these organisms, this research is now extending in two main directions: 1) analysis of gene expression and variation at the whole genome level. 2) development of transformation systems to knock-out virulence genes to develop new vaccines.