Expression analyses of viral (frog virus 3 and channel catfish virus) and host cell genes following in vitro infection

The goals of this dissertation were to determine the temporal class of frog virus 3 (FV3) genes, identify the transcriptional response of channel catfish B cells and fibroblasts to channel catfish virus (CCV) infection, and ascertain the temporal class of CCV genes.;The temporal class of FV3 genes was identified using an oligonucleotide array containing probes targeted to each of the 98 putative FV3 ORFs. Based on microarray and PCR analyses 33 immediate early (IE) genes, 22 delayed early (DE) genes and 36 late (L) viral genes were identified. Among genes with known or putative function, the majority of IE and DE genes were shown to encode regulatory, catalytic, and immune evasion proteins, whereas L gene products were mainly involved with virion assembly and DNA packaging.;In a second study, a cDNA microarray comprised of ∼1000 catfish genes and 61 of the 79 putative CCV open reading frames was used. Host and viral gene expression were analyzed at 2, 6 and 9 hr after infection of channel catfish ovary (CCO) fibroblasts and 3B11 B cells. Using microarray and qPCR analyses, qualitatively and quantitatively different responses were observed among the two cell types. Differentially expressed genes were classified into various functional categories. Cell line specific differences were noted among genes involved with apoptosis and immune-related functions. Lastly, to determine the temporal class of CCV genes, viral genes expressed in CCO cells were analyzed at 2, 6 and 9 hr following infection and in the presence of cycloheximide, which limits viral expression to only IE genes. Based on microarray analyses, 14 IE (alpha), 24 E (beta) and 22 L (gamma) genes were identified. Collectively, these studies advance our understanding of viral replication and anti-viral immunity in lower vertebrates.