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<I>Candida albicans</I>, one of the most prevalent fungal pathogens in humans, is diploid, appears to lack a natural sexual cycle and possesses a different genetic code from most other species. These features combine to make the study of its biology by traditional methods extremely difficult, particularly with respect to gene isolation and expression. A cosmid library was constructed from <I>C. albicans</I> genomic DNA which represents an 11-fold coverage of its genome. Assessments made of the breadth of library coverage and clonal stability gave favourable results and the library has already proved to be of use within the <I>Candida</I> research community. Fluorescently-labelled restriction fingerprints of the cosmid clones were used to construct a physical map consisting of 364 contigs. Screening of the library with 22 STS markers reduced the number of contigs to 353 and allowed redundancy among the fingerprinted contigs to be estimated. The fingerprinted contigs therefore represent a first generation physical map covering 86% of the <I>C. albicans</I> genome, which when complete will greatly facilitate further study of the organism and its pathology. The results obtained from a pilot sequencing project, involving several of the library clones are discussed and included in an evaluation of restriction fingerprinting as a general approach to physical mapping. Finally, as the Human genome Mapping Project reaches its conclusion, the transition to a post-genomic era and its relevance to future work with <I>C. albicans</I> are discussed.

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The development and application of a partial composite <i>S. aureus</i> virulence-associated gene micro array is described. Epidemic, pandemic and sporadic lineages of healthcare associated(HA-) and community-associated (CA-) <i>S. aureus</i> were compared. The clonal population structure was supported but further evidence for large-scale recombination events was obtained. Phage structural genes linked with the CA phenotype were identified and <i>in silico</i> analysis revealed these to be correlated with phage serogroup. CA strains generally carried a PVL-associated phage either of the A or Fb serogroup, whilst the HA strains predominantly carried sero group B phage. It is proposed that carriage of PVL associated phage rather than the specific <i>pvl</i> genes is correlated with the CA phenotype. These findings further support the role of the accessory genome in shaping the epidemiology of <i>S. aureus</i>. The microarray was used to study gene expression in isogenic strains differing by a deletion in the <i>agr</i> locus. Microarray analysis revealed significant differences between the levels of expression of several genes of the normal and mutant strains. However, RNAIII levels in the non-mutant strain were found to be cell density independent, indicating that the expected quorum sensing mechanism was not functional. Expression profiles of cells grown under biofilm simulating conditions were compared to their planktonic counterparts. Biofilm cells displayed a typical expression profile that was different from both the actively growing planktonic exponential cells and the planktonic stationary cells. The strongest feature of the biofilm state was high level expression of the haemolysin genes. This model therefore is amenable to exploitation in studies designed to improve our understanding of the mechanisms underlining biofilm survival and regulation after long periods of growth.

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