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Abstract Gammaherpesviruses are a subfamily of the Herpesviridae, containing important viruses infecting human and animals such as Epstein-Barr viruses (EBV), Kaposi’s Sarcoma-associated herpesvirus (KSHV) and Murine Herpesvirus-68 (MHV-68) which establish latent infection within B-Lymphocytes, dentritic cells and epithelial cells. Latent infection within B-Lymphocytes macrophages, dentritic cells and epithelial cells. MHV-68 serves as a model for research of human gammaherpesviruses; is closely related to the human gammaherpesviruses. MHV-68 infects ma ny kind s of murid rodents including laboratory mice, and in addition, can replicate in many cell types in vivo. The ability to readily generate mutants of MHV-68 and their subsequent investigation contributes to the understanding of viral gene function in virus-host interactions. Identification and isolation of individual virally infected cells through long term infection will increase our knowledge of the pathogenesis of latent or persistent viruses. In order to make the study of latent or persistent viruses more efficient, the technique of marking infected cells (so they become detectable) has been developed. This technique, utilizing Cre recombines within the viral genome and the reporter gene (EGFP) in the host cells overcomes the problem of low reactivity and the effects of cells-type on the expression of the viral genes. In this study, we aimed to use a Cre-based virus with a LoxP-EGFP mouse system. The mouse line contained an enchased green fluorescent protein (EGFP) reporter gene flaked by LosP sites. Therefore, when the Cre-virus infects the cell the LoxP site is inactivated and infected cells show green. We constructed a Cre MHV-68 virus, by utilizing a Bacterial Artificial Chromosome (BASc) via a cassette (PGK promoter, Cre, Poly A signal) which was constructed and inserted in the left hand of the virus between the ORF11 and K3. In this study we aimed to analyse the locations of latent and persistent virus infection. Expression of EGFP enables the virus positive cells to be clarified by FACSorting