This report serves to document research conducted under a reimbursable agreement. Additional details of research can be found in the report for the parent CRIS 3625-32000-062-00D Understanding Host-Pathogen Interactions for the Diagnosis and Control of Paratuberculosis (Johne's). This project (funded by USDA-CSREES) is being done in collaboration with the University of Minnesota, and is designed to facilitate analysis of genomic diversity and gene expression in M. avium subspecies paratuberculosis (MAP). During this fiscal year, an oligonucleotide microarray was been used in genomic diversity experiments at NADC. These experiments showed distinct differences between the cattle isolates and sheep isolates. The genomic differences result mostly from insertions and deletions. Furthermore, the array has been distributed to several collaborators, both within the US and outside the US. One of these collaborators has used the array to show gene transcription differences within MAC-T cells. There are now 1200 transposon mutants of M. paratuberculosis that have been characterized by DNA sequencing. Another task is to clone most of the important genes in the MAP genome and express them to form recombinant proteins. There are currently 267 purified MAP proteins available for in depth studies. These proteins will be used in functional and immunological assays. Finally, we have hosted four investigators in our laboratory for a total of 1.5-months to train them in the use of these valuable resources.