Post‐genomic virology: the impact of bioinformatics, microarrays and proteomics on investigating host and pathogen interactions

Abstract

Post-genomic research encompasses many diverse aspects of modern science. These include the two broad subject areas of computational biology (bioinformatics) and functional genomics. Laboratory based functional genomics aims to measure and assess either the messenger RNA (mRNA) levels (transcriptome studies) or the protein content (proteome studies) of cells and tissues. All of these methods have been applied recently to the study of host and pathogen interactions for both bacteria and viruses. A basic overview of the technology is given in this review together with approaches to data analysis. The wealth of information produced from even these preliminary studies has shown the generalities, subtleties and specificities of host-pathogen interactions. Such research should ultimately result in new methods for diagnosing and treating infectious diseases.

Integrated Proteomics and Genomics Strategies Bring New Insight into Candida albicans Response upon Macrophage Interaction

“…In this situation, we combined the complementary data from gene-and protein-based assays, thus providing more information about the response of Candida upon macrophage interaction. The ability to conduct these correlation analyses represents an additional and novel means to generate discrete and testable biological hypotheses from these global and discovery-driven measurements (41)(42)(43)(44)(45).…”

Viral Bioinformatics: Computational Views of Host and Pathogen

“…The e¡ects of viral infection on the transcriptome of cells in vitro and in vivo has been determined for viruses as diverse as retroviruses, herpesviruses, orthomyxoviruses, enteroviruses, adenoviruses, hepatitis B and C viruses, and papilloma viruses. These initial studies show that viruses cause both common and unique changes in cellular gene expression pro¢les during their replication cycle (Fruh et al 2001, Kellam 2000, 2001. However, the degree of host 242 KELLAM ET AL transcriptional modulation is likely to be more complicated than a simple re£ection of the type of virus causing the infection.…”

“…Immunoinformatics should therefore encompass pathogen bioinformatics. Post genomic research therefore allows us to take an overarching view of how a ¢nite human genome facilitates and maintains essential biological functions and homeostasis whilst guarding against and responding appropriately to acute, persistent or commensal infections (Kellam 2001). …”

Secreted Immunomodulatory Viral Proteins as Novel Biotherapeutics

“…Through the unraveling of discoveries made by viruses, a new class of therapeutic agents has been revealed based upon virus-engineered immunomodulatory proteins. Viruses were the first organisms for which complete genome sequences were deduced, beginning a quarter of a century ago, and the science of "virogenomics" has been expanding rapidly ever since (177)(178)(179). The repertoire of novel viral gene products that are devoted to host modulation has also been proliferating at an astounding rate, and there are reasons to suspect that we have uncovered only the tip of the virus iceberg.…”