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Thesis (PhD--Biological Science)--University of Auckland, 2010. / Includes bibliographical references.

The nucleopolyhedrovirus of Epiphyas postvittana (EppoMNPV) is being studied as a potential biological control agent for leafroller insects in New Zealand. The aims of this project were for the identification of putative genes that are unique to, variant in or missing from, the EppoMNPV genome and the subsequent analysis of at least one of these genes. The purpose of this was to identify and characterise genes potentially involved in the specific host range and virulence of EppoMNPV. This was achieved in two steps. Three genome regions lacking linearity between EppoMNPV and the closely related OpMNPV were previously identified and the targeted sequencing of these three regions was the first aim of this project. The collation of the entire genome sequence of EppoMNPV and comparison to the genome sequences of 22 other baculoviruses completed the identification of genes that are unique to, variant in or missing from EppoMNPV. The EppoMNPV genome was found to be 118,584 bp in size encoding 136 putative proteins. A total of 29 genes were found to be common to all baculoviruses, while the lepidopteran baculoviruses share a total of 62 genes. The genome of EppoMNPV encodes four putative unique genes, the sequence of which offers no clues as to possible function. EppoMNPV lacks a homologue of the superoxide dismutase gene common to all other lepidopteran baculoviruses The EppoMNPV IE2 homologue was identified as a 311 amino acid protein with a truncation in the N-terminal region. We hypothesised that this truncation would lead to a loss of function, which could contribute to the virulence and/or host range of EppoMNPV For this reason, the characterisation of the EppoMNPV IE2 was taken up as the second part of this project. A comparative study between the AcMNPV and EppoMNPV IE2 proteins identified no differences in function between these two proteins in Sf21 cells. The EppoMNPV IE2 was capable of trans-activating three constitutive promoters and localised to discrete nuclear bodies. Cell cycle arrest was not achieved by either IE2 protein in our cell culture system. The role of four sequence motifs common to all IE2 proteins was studied with the aid of mutational analysis. Mutation of arginine and acidic rich sequences of EppoMNPV IE2 showed only a slight decrease in trans-activation activity while mutation of the RING-finger and coiled-coil motifs reduced trans-activation to less than half that of wild type IE2. Mutation of the coiled-coil motif resulted in reduced amounts of protein localising to discrete nuclear regions. A series of deletion mutants from the N- and C-termini of EppoMNPV IE2 identified that the C-terminal 111 amino acids of EppoMNPV IE2 was sufficient for nuclear targeting. Deletion of the C-terminal 19 amino acids resulted in an IE2 mutant completely defective in both localisation and transactivation. This demonstrates that localisation to discrete nuclear regions is essential for EppoMNPV IE2 to act as a transactivator.

Landscape heterogeneity is thought to differ among farm management types (i.e. organic and conventional), and this difference is hypothesized to result in variations in pest control by natural enemies. However, it is unclear if these variations in pest control are driven by landscape structure or by farm management practices themselves. Remotely sensed datasets were used to describe the landscape structure surrounding a group of organic and conventional caneberry farms in Oregon and Washington that have different leafroller parasitism rates attributed to farm management type. A finer scale survey was done at one of the farms using the remotely sensed data as well as field surveys. Landscape metrics of diversity, richness and percent non-crop were used to describe the landscapes surrounding the farm fields at scales ranging from 0.05 km to 5.00 km for the large scale study, and 0.05 km to 0.20 km for the fine scale study. In the fine scale study, data on parasitoid species assemblages, diversity, and parasitism rate were collected and analyzed against the calculated landscape metrics spatially and seasonally. The purpose of this study was to quantify effects of farm management type on habitat structure, effect of habitat structure on leafroller parasitism rate, and to access correlations between landscape metrics calculated at the landscape and field scale. Overall, the farms were embedded in a landscape that was broadly similar, with very few differences in landscape structure occurring between organic and conventional farms. Organic farms had higher vegetation height class diversity at the largest scale compared to conventional farms, while conventional farms had significantly higher percent non-crop area compared to organic farms. There was no significant effect of any of the calculated landscape metrics on parasitism rates. In the field scale study, no correlations were found between habitat metrics and parasitism rates, or between field based metrics and those calculated at the landscape scale. The results of this study suggest that conventional and organic caneberry farms in the Willamette Valley are broadly similar in the habitat conditions they provide parasitoids. This suggests that management changes to pesticide use alone could increase levels of leafroller biological control on conventional farms to levels that are comparable to those seen on organic farms. Our comparisons of the landscape scale and field scale landscape metrics showed no connection, this suggests that direct comparisons cannot be made with these particular metrics at these very different scales. Rather than comparing these types of data, it may be more useful to combine them in order to increase the resolution and predictive power of remotely sensed data for describing landscapes at broad scales. / Graduation date: 2013