The Feldmannia sp. virus is a large icosahedral virus that persistently infects marine brown alga Feldmannia sp.. So far, there is no information available about viral genome replication, gene structure and gene expression in this unique viral-host system. The purpose of this study was to characterize the general features of viral transcripts in the virus producing sporophyte plants. Northern analysis, using four cosmid clones that cover the entire viral genome, showed that there were six major transcripts and at least eighteen minor transcripts in the virus producing sporophyte plants. These transcripts are not evenly distributed in the viral genome. A 5.7 kb BamHI fragment-R was found to encode a 1.5 kb and a 0.9 kb major transcript, and those two major transcripts were chosen for detailed sequence analysis. The 1.5 kb transcript was identified as the putative major capsid protein (MCP) gene. The FsV MCP has significant similarity with the major capsid protein of Chlorella virus-PBCV-1 and with iridoviruses, fish lymphocystis disease virus, frog virus 3, and with African swine fever virus. / Graduation date: 1996

Corrigendum inserted at the back. Includes bibliographical references (leaves 133-158). Ch. 1. General introduction -- ch. 2. General materials and methods -- ch. 3. Biological characterisation of Australian PSbMV isolates -- ch. 4. Developing nucleic acid based diagnostics for PSbMV -- ch. 5. Detection of PSbMV isolates by RT-PCR and RFLP analysis -- ch. 6. Developing an internal control for PSbMV RT-PCR -- ch. 7. Molecular analysis of the PSbMV VPG -- ch. 8. PSbMV sequence and phylogenetic analysis -- ch. 9. General discussion Sixteen pea seed borne mosaic virus (PSbMV) isolates were collected between 1995 and 1998. These isolates were biologically distinct yet serologically indistinguishable. The conclusion is that PSbMV is widespread and occurs at a low incidence in Australia. Reports sequence information on new isolates of PSbMV which has allowed genomic regions to be identified which distinguish PSbMV pathotypes and isolates; and, to the development of PSbMV nucleic acid hybridisation and RT-PCR assays.

Corrigendum inserted at the back. / Includes bibliographical references (leaves 133-158). / xvi, 158 leaves : ill., col. map ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Sixteen pea seed borne mosaic virus (PSbMV) isolates were collected between 1995 and 1998. These isolates were biologically distinct yet serologically indistinguishable. The conclusion is that PSbMV is widespread and occurs at a low incidence in Australia. Reports sequence information on new isolates of PSbMV which has allowed genomic regions to be identified which distinguish PSbMV pathotypes and isolates; and, to the development of PSbMV nucleic acid hybridisation and RT-PCR assays. / Thesis (Ph.D.)--University of Adelaide, Dept. of Applied and Molecular Ecology, 2001

Bibliography: leaves 127-138. This thesis studies the minor double stranded RNAs (dsRNA) and single stranded RNAs (ssRNA) which are consistently associated with plants infected with Q strain of cucumber mosaic virus (Q-CMV). The investigations are focused on the structural elucidation of new RNAs which have been observed in single stranded and double stranded RNA profiles of Q strain of CMV.

Beet yellows virus (BYV) is a filamentous, positive-strand RNA virus that belongs to the family Closteroviridae. BYV particles encapsidate a 15.5 kb RNA and posses complex polar architecture. A long virion body is formed by the major capsid protein(CP), whereas the minor capsid protein (CPm) assembles a short tail that encapsidates the 5'-terminal region of BYV RNA. In addition to proteins required for viral RNA replication and encapsidation, BYV encodes four proteins whose role in the virus life cycle was unknown. These proteins include a small, 6-kDa, hydrophobic protein (p6), a homolog of the cellular 70-kDa heat shock proteins (Hsp7Oh), a 64-kDa protein (p64), and a 20-kDa protein (p20). It was found recently that Hsp7Oh, p64, and p20 are incorporated into BYV virions, and that Hsp7Oh is required for the virus movement from cell to cell. In this study, we characterized genetic requirements for BYV assembly and cell-to-cell movement, and determined relationships between these two processes. It was demonstrated that in addition to Hsp7Oh, p6, p64, CP, and CPm are each essential, but not sufficient for virus movement. These results indicated that five-component movement machinery of BYV is the most complex among plant viruses. Extensive mutational analysis of CP and CPm revealed strong correlation between abilities of BYV to assemble tailed virions and to move from cell to cell, suggesting that formation of functional virions is a prerequisite for virus translocation. We have found that CPm, Hsp7Oh, and p64 are necessary for the efficient virion tail formation. Assembly of the virion tails and bodies was shown to occur independent of each other and likely to involve two separate packaging signals within the genomic RNA. Our work demonstrated that BYV encodes one conventional movement protein, p6, whose only known function is to mediate virus movement. The other four movement associated proteins of BYV, CP, CPm, Hsp7Oh, and p64 are the virion components, each of which is required for assembly of the tailed, movement-competent virions. Based on these and other data, we propose that BYV and other closteroviruses evolved virion tails as a specialized device for the directional cell-to-cell movement of large RNA genomes. / Graduation date: 2005 / Best scan available.

Bibliography: leaves 127-138. / v, 138 leaves : ill. ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / This thesis studies the minor double stranded RNAs (dsRNA) and single stranded RNAs (ssRNA) which are consistently associated with plants infected with Q strain of cucumber mosaic virus (Q-CMV). The investigations are focused on the structural elucidation of new RNAs which have been observed in single stranded and double stranded RNA profiles of Q strain of CMV. / Thesis (Ph.D.)--University of Adelaide, Dept. of Plant Science, 1997

Bibliography: leaves 127-138. / v, 138 leaves : ill. ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / This thesis studies the minor double stranded RNAs (dsRNA) and single stranded RNAs (ssRNA) which are consistently associated with plants infected with Q strain of cucumber mosaic virus (Q-CMV). The investigations are focused on the structural elucidation of new RNAs which have been observed in single stranded and double stranded RNA profiles of Q strain of CMV. / Thesis (Ph.D.)--University of Adelaide, Dept. of Plant Science, 1997

Viruses or viruslike particles of eukaryotic algae are ubiquitous in aquatic habitats, however, suprisingly little is known about them. The research presented here focused on one such virus which infects a multicellular filamentous brown alga of the genus Feldmannia. Although preliminary studies had been performed on the genome structure of the Feldmannia sp. Virus (FsV), little was known. The purpose of this study was to analyze the structure of the FsV genome in detail. During the experiments aimed at mapping the FsV genome, cross-hybridization was observed among five BamHI-fragments of the digested FsV DNA. Sequence analysis of one of those fragments revealed the presence of 173 by direct repeats. There are two FsV genomes of different size-classes (158 and 178 kbp). The 173 by repeats in the cross-hybridizing BamHI-fragments were confined to a small region of each virus genome. The number of these repeats in the 178 kbp genome was estimated to be about 109 and in the 158 kbp genome to be about 41. in the 178 kbp genome, the repeats are contained within a 22 kbp region and in the 1.58 kbp genome, the repeats are contained within a 10 kbp region. These viruses are actively replicated in sporophyte plants. A family of related 173 by direct repeats was discovered in an encrypted FsV genome. The family of repeats estimated to be greater than 50 kbp in length were found inserted into a protein kinase gene encoded within the 3.6 kbp viral BamHI-fragment Z. Southern analysis indicates that these repeats in the encrypted FsV genome are distinct from the previously characterized repeats in the amplified FsV genome. The translated protein kinase shares highest homologies to the SNF1 subfamily of serine/threonine protein kinases and contains a potential autophosphorylation site in a region unique to this protein kinase. A DNA polymerase gene was identified in the FsV genome. The predicted peptide sequence of the FsV DNA polymerase gene contains all of the conserved motifs found in B-family (a-like) DNA polymerases. A TTTTTNT sequence motif shown to be a transcription termination signal for Vaccinia virus early genes is found at the 3' end of the DNA polymerase gene. Phylogenetic analysis of the FsV DNA polymerase gene and other viral DNA polymerase genes indicates that FsV belongs to a group of algal viruses recently defined as Phycodnaviridae. / Graduation date: 1998

Bibliography : leaves 92-99. / v, 99, [37] leaves, [14] leaves of plates : ill. ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Thesis (Ph.D.)--University of Adelaide, Dept. of Biochemistry, 1992

Potato virus Y (PVY) is an economically important virus worldwide. In South Africa, PVY has been shown to be a major limiting factor in the production of important solanaceous crops, including potato (Solanum tuberosum L.), pepper (Capsicum annuum L.), tomato (Lycopersicon esculentum Mill.) and tobacco (Nicotiana spp). The variability that PVY displays, wherever the virus occurs, merits the study of the isolates occurring in KwaZulu-Natal (KZN) in the Republic of South Africa (RSA). This characterization will provide a clear understanding of strains/isolates from local vegetables and how they relate to the other PVY strains already identified, as well as information that can be used to manage the diseases they cause. Hence, the aim of this project was to study the biological and genetic properties of PVY isolates infecting potato, tomato and pepper in KZN. Enzyme-linked immunosorbent assay (ELISA) using monoclonal antibodies and reverse transcription polymerase chain reaction (RT-PCR) using primers specific to all PVY strains were used to detect the virus in plant material showing PVY-like symptoms collected from various locations in KZN. A total of 39 isolates (18 isolates infecting tomato, 12 infecting potato and 9 infecting pepper) were further differentiated into strains by means of ELISA using strain specific antibodies and RT-PCR using primers specific to the different strains of PVY identified around the world. All PVY isolates infecting tomato and pepper tested positive for the ordinary PVYO strain with both ELISA and RT-PCR. PVY isolates infecting potato were more diverse and comprised the PVYN, PVYNTN and PVYNWilga strains, with mixed infections noted in some cases. The biological properties were studied by mechanically inoculating Chenopodium quinoa, Nicotiana tabacum cv Xanthi, N. tabacum cv Samsun, N. glutinosa, and N. rustica with leaf extracts from plants infected with the different PVY strains detected in this study. All inoculated C. quinoa plants did not show symptoms. All tobacco plants showing symptoms were tested for the presence of PVY by means of ELISA using monoclonal antibodies targeting all strains and electron microscopy using the leaf dip technique. Not all the inoculated tobacco tested positive with ELISA. The symptoms observed were therefore divided into PVY-related and PVY non- related. PVY-related symptoms included vein clearing, mosaic chlorosis, stunting, and vein necrosis. PVY non-related symptoms included wrinkles and leaf distortions. Potyvirus-like particles of about 700 nm were observed under the transmission electron microscope (TEM) from plants showing PVY-related symptoms while rod shaped viral particles of sizes varying between 70 and 400 nm were observed from plants showing non-PVY related symptoms. A portion of the virus genome (1067 bp) covering part of the coat protein gene and the 3’ non-translated region (NTR) of three PVYO isolates infecting tomato, one PVYO isolate infecting pepper and one PVYNWilga isolate infecting potato were amplified, cloned and sequenced. The 5’ NTR, P1, HC-Pro and part of P3 regions (2559 bp) of a PVYN isolate infecting potato were also amplified, cloned and sequenced. Sequence data was compared with selected PVY sequences from different geographical locations around the world. These were available on the NCBI website and subsequently used for phylogenic analyses. The sequenced genomic regions of the PVYN isolate were found to be 99% similar to the New Zealand PVYN isolate (GenBank accession number: AM268435), the Swiss PVYN isolate CH605 (X97895) and the American PVYN isolate Mont (AY884983). Moreover, the deduced amino acid sequence comparison of the genomic regions of the PVYN isolate revealed the presence of five distinct amino acids residues. The three amino acid residues (D205, K400, and E419), which determine the vein necrosis phenotype in tobacco, were also identified. The coat protein and 3’ NTR sequences of all KZN PVYO isolates infecting pepper and tomato were closely similar to each other than to KZN PVYNWilga isolate infecting potato. The phylogenic analysis clustered the KZN PVYN isolate with the European sublineage N, PVYNWilga isolate infecting potato with the American PVYO isolate Oz (EF026074) in the O lineage and all PVYO isolates infecting tomato and pepper in a new sublineage within the O lineage. Taken together, these results point to the presence of PVY in solanaceous vegetables cultivated in KZN and they lay the foundation for the formulation of effective control measure against PVY diseases in KZN. / Thesis (M.Sc.) - University of KwaZulu-Natal, Pietermaritzburg, 2009.