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actual physical memory images, and C language code for the program itself.

The role of biotic mechanisms in baculovirus (BV) dispersal was investigated using three Lepidopteran pests; Plodia interpunctella (Hubner), Ephestia cautella Walker and Mamestra brassicae L. and their respective BVs. The first two, pyralid moths, are pests of stored products, and the third is a pest of brassicas. Detailed host biology and virus mortality studies were undertaken to provide background information for the main investigation of virus dispersal using P.interpunctella. BV infectionincreased larval activity and thus BV dispersal in all three species until the disease at an advanced stage caused sluggish behaviour and mortality. However, larva to larva virus transmission was limited, especially as the integuments of diseased pylarids did not rupture and cannibalism was rare when a suitable food supply was available. P.interpunctella adults which received a sub-lethal BV dose in the larval stages appeared normal but the proportion of eggs oviposited, the viability of the eggs and the survival of the progeny were reduced. However, no BV was detected in the adult stage. Transovum transmission occurred if the adults were externally contaminated with BV. Scavangers, predators and adult parasitoids which fed on diseased prey voided viable BV in their faeces. This contaminated the larval medium and resulted in larval infection. The predators tested readily fed on diseased prey but the parasitoids were less able to compete with BV for hosts, Bracon hebetor Say preferentially avoided diseased hosts. There was little evidence to indicate that BV can be mechanically vectored between host larvae on the ovipositor of a parasitoid or the mouthparts of a predator. The relative potential of the host and other biotic mechanisms to cause BV dispersal is discussed.

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Cassava (Manihot esculenta Crantz) is affected by two major viral diseases, namely Cassava brown streak disease (CBSD) and Cassava mosaic disease (CMD). Two of the most widely distributed begomoviruses in East Africa associated with CMD, are East African cassava virus- Uganda2 (EACMV-UG2) and African cassava mosaic virus (ACMV). Despite efforts of generating improved Tropical Manihot Series (TMS) by traditional breeding and using highly resistant geminivirus cassava landraces such as Tropical Manihot Esculenta1 (TME1) and Tropical Manihot Esculenta3 (TME3), more recently two circular single stranded (ss) satellite-like DNA molecules (episomal DNA-II and DNA-III) have been found to be associated with CMD and are able to break resistance to EACMV-UG2 and enhance virus symptoms. The nature of these satellite-like DNA molecules is unknown, and furthermore, the discovery of integration of partial copies of DNA molecules (DNA-II and III fragments), and evidence for transcription from cassava Expressed Sequence Tag (EST) database screening, has led to an even more perplexing disease complex. In the present study, we attempted to further explore the interaction between the satellite-like DNAs and their associated cassava-infecting begomoviruses by investigating the impact of these DNA molecules on disease development in TME3 (tolerant) and cv. 60444 (susceptible) cassava cultivars, and to also gather biological evidence for transcription of integrated genomic and episomal (putative predicted ORFs) sequences in the ACMV and EACMV-UG2-associated DNA-II and DNA-III. Biolistic inoculation of EACMV-UG2, ACMV, and in co-bombardment with DNA-II, DNA-III, DNA-II + DNA-III was successfully performed. CMD symptoms were developed earlier on cassava plants inoculated with ACMV + DNA-II, ACMV + DNA-III, ACMV + DNA-II + DNA-III and EACMV-UG2 + DNA-II, EACMV-UG2 + DNA-III, EACMV-UG2 + DNA-II + DNA-III molecules compared with cassava plants inoculated with begomoviruses alone. Additionally, CMD symptoms were more severe in cv.60444 compared to TME3 when inoculated with begomoviruses alone, or in combination with DNA-II, DNA-III and DNA-II + DNA-III molecules. DNA-II and III were able to break resistance to the highly CMD-tolerant cassava landrace, TME3, and enhance virus symptoms. In order to confirm EST-generated evidence for transcription of DNA-II and III fragments, cDNA was subjected to RT-PCR. RT-PCR of transcripts was successful for only three putative ORFs: ORF C4 of the antisense DNA-II strand, ORF V1 on sense DNA-II strand, and ORF C2 on antisense strand for DNA-III. Primers for transcripts amplified 250 bp and 220 bp for ORF C4 of DNA-II and ORF V1 of DNA-III, respectively. Transcribed ORFs were confirmed by sequencing, and the sequences were similar to the published sequences of Begomovirus associated DNA-II satellite and Begomovirus associated DNA-III satellite, respectively. These results showed that at least two putative ORFs for DNA-II and one (the largest ORF VI) DNA-III can be transcribed. Furthermore, surveys were undertaken in order to ascertain the distribution of episomal and integrated DNA-II and III in cassava germplasm from several countries, namely Tanzania, Uganda, Kenya and Rwanda. Results from this research successfully established genetic diversity and wide geographical distribution of integrated DNA-II and DNA-III molecules. Two primer pairs were designed from a central conserved sequence found in all the integrated DNA-II or III fragments identified from the cDNA libraries (EST database). These primers also amplified integrated sequences of expected size in cassava accessions and wild Manihot species which were similar to satellite-like sequence occurrences in the ESTs. Using designed primers, PCR amplification yielded integrated DNA-II and DNA-III products of ~895 bp and ~306 bp, respectively. Analysis of 363 field leaf samples detected the presence of DNA-II or DNA-III from Kenya (3.3% or 8.3%), Uganda (18% or 2.5%), Rwanda (6.5% or 19.6%) and Tanzania (5.7% or 11.9%) , results which were confirmed by analysis of the sequenced PCR amplicons. Detection of both DNA-II and DNA-III molecules on the samples collected was also found from Kenya (73%), Uganda (69.1%), Rwanda (50%) and Tanzania (69.3%). Interestingly integrated DNA-II and II copies were amplified from healthy, symptomless and infected cassava samples. DNA-II sequences did not vary significantly (93.3% - 99.8%) and were highly similar to the sequences of Begomovirus associated sat DNA-II (AY836366) and 99% with mentha leaf deformity disease associated satellite DNA-II, while DNA-III sequences and Begomovirus associated DNA-II satellite (AY833667). In conclusion, this study has provided useful information that contributes to a further understanding of the biological function of integrated and episomal DNA-II and III molecules in begomoviruses infected cassava plant. However the relationship, if any between episomal and integrated forms needs to be established in future, and investigation into whether the transcribed ORFs can produce functional proteins, needs to be undertaken. How DNA-II and III interact with EACMV-UG2 and ACMV in disease modulation remains to be explored, and the replication of episomal DNA-II and III by these associated begomoviruses needs to be confirmed if these DNA molecules are to truly show a satellite-like relationship. Furthermore, the findings in this study that partial and varied-sized integrated DNA-II and III fragments occur widely in healthy and infected cassava germplasm will enable researchers (plant virologists and breeders) working on cassava in Sub Saharan Africa (SSA) to explore this complex more deeply in order to develop durable management strategies for CMD.

The European honeybee (Apis mellifera) is a managed insect pollinator of global economic importance. Over the last few decades honeybees have been undergoing a major health crisis, with one of the biggest causes the parasitic mite, Varroa destructor and its role in changing the viral landscape of deformed wing virus (DWV), which consists of two major variants: DWV-A and DWV-B. Prior to the start of this project there was limited information known about the mechanisms behind the relationships between Varroa, DWV and honeybees. The overarching aim of this project was to further enhance our understanding of these complex relationships, focusing on the impact of Varroa DWV transmission and differences between the main DWV variants. One of the initial obstacles to understanding these complex interactions was the inability to accurately quantify DWV variants. Prior to the start of this project, there was a need for an accurate assay for the quantification of DWV-A, DWV-B and total DWV, allowing the role of both variants in viral transmission and establishment to be investigated. While primers did exist for DWV quantification, the majority did not distinguish between variants, or provide accurate levels of DWV. Given these challenges in variant detection, a new assay for the quantification of DWV-A, DWV-B and total DWV was designed and validated. The assay consists of an external plasmid standard with distinct sections, for the detection of variants and total DWV. This DWV variant plasmid assay was essential for further transmission studies in this project. DWV variant transmission was explored using a variety of different methods. A new in vitro feeding system was used, to allow investigations into Varroa DWV variant transmission in isolation. The feeding system utilises locust haemolymph, allowing changes in DWV transmission to be detected. In multiple feeding experiments significant changes in DWV transmission were detected. Significant changes in DWV composition within feeding Varroa were detected with decreased levels of DWV, and changing variant levels. Switches in variant composition within mites and transmission rates occurred during Varroa in vitro feeding. These variant switches occurred in both directions from DWV-A to DWV-B, and DWV-B to DWV-A dominance. These changes in mite variant composition corresponded to changes in levels of replicating strands. iv These changes in DWV transmission, composition and replicating strand detection were only seen due to the use of this in vitro feeding system. The in vitro work provided valuable information about Varroa variant transmission and composition changes during feeding but this is not a natural system. Honeybee pupae from a Varroa-free area with extremely low DWV titres provided the opportunity to investigate Varroa variant transmission and pupal DWV establishment. Over 96 hours total DWV levels underwent a 1339408X fold increase, within pupae following Varroa feeding, with a sharp increase after 12 hours, followed by a plateau after 60 hours. Within this time period, DWV-A underwent a similar increase, while DWV-B increased at a much slower rate (33X fold change). In contrast to the in vitro work, mite DWV levels did not decrease during feeding. The impact of natural Varroa cell infestation on L5 larvae was investigated, showing no significant effects between pupal total DWV levels and mite density, and DWV levels between infested and none-infested larvae. However, this lack of significance could be attributed to the use of L5 larvae, which had only undergone a maximum of 24 hours Varroa feeding within the cell. Additionally, the use of two drug treatments (ribavirin and hydroxyurea) to reduce DWV levels was explored. Both drug treatments were tested against Varroa and honeybees, using a variety of methods: immersion (Varroa), injections (honeybees) and feeding (both). While neither drug treatment resulted in consistent DWV decreases, some reduction in DWV levels were seen following Varroa soaking in drug solutions. A significant decrease in DWV was seen in honeybees following bolus and ad libitum feeding of drug treatments. Overall, information and insights have been gained regarding the complex relationship between Varroa, honeybees and DWV. A new DWV variant qPCR assay was developed and utilised in subsequent studies. DWV variant switches in both transmission rates and mite composition were found to occur in in vitro studies. Differences in DWV variant establishment within honeybees were detected following Varroa in vivo feeding, in low DWV pupae. Though the tested drug treatments did not affect DWV levels, this highlights the difficultly facing the establishment of any DWV treatment.

Plant viruses can cause many plant diseases, which result in substantial damage to crop production. To overcome viral infections, plants evolved RNA silencing which can recognise viral RNAs during their replications and slice them into small RNA (sRNA) using antiviral nucleases called DICER or Dicer-like (DCL). The resulting virus-derived small interfering RNA (vsiRNA, 21-24 nucleotides) then guides effector nucleases, namely ARGONAUTE (AGO), to cleave viral RNAs in the cytoplasm in a nucleotide-specific manner. However, the activity of vsiRNA is not restricted to the control of viral RNA accumulation. Virus-derived sRNAs can regulate host gene expression if host mRNAs share sequence complementarity with vsiRNAs. Interestingly, vsiRNAs are also able to target and methylate homologous DNA sequences in the nucleus indicating that vsiRNAs have potential to regulate endogenous genes at transcriptional level by modifying the epigenetic status of gene promoter sequences. This mechanism is referred to as transcriptional gene silencing (TGS). Thus, RNA silencing opens up new strategies to stably and heritably alter gene expression in plants. However, the mechanisms and efficacy of plant virus-induced TGS are largely unknown. The aim of my PhD was to investigate the molecular and environmental factors that are involved in virus-induced epigenetic modifications in the infected plants and in their progeny. First, I examined the required sequence complementary between sRNAs and their nuclear target sequence. I demonstrated for the first time that nuclear-imported vsiRNAs can induce RNA-directed DNA methylation (RdDM) and subsequently heritable virus-induced transcriptional gene silencing (ViTGS) even when they do not share 100% nucleotide sequence complementarity with the target DNA. This finding reveals a more dynamic interaction between viral RNAs and the host epigenome than previously thought. Secondly, I explored how environmental stimuli such as light and temperature can affect the efficacy of ViTGS. I found that ViTGS is greatly inhibited at high temperature. Using RNA-seq, I established that inefficient ViTGS at high temperature is due to the limited production of secondary sRNAs that may limit the initiation, amplification and spreading of virus-induced DNA methylation to neighbouring cells and down generations. Lastly, I studied the link between the viral suppressors of RNA silencing (VSRs): viral proteins that can interfere with plant RNA silencing and ViTGS. I established that VSRs of certain viruses can impair TGS in infected tissues, suggesting that viruses may alter the epigenome and consequently plant gene expression in the infected plants and their progeny. Collectively, my work reveals how viruses can re-program the epigenome of infected plants, and deepens our knowledge of how we can harness pathogens to modify the epigenome for plant breeding.

This thesis provides an examination of how Papuan university students in eastern Indonesia react to Indonesian governance. Qualitative interviews investigate students' understandings of HIVIAIDS, an emerging threat in Papua around which the state makes moral claims and promotes development. Media discourse analysis reveals the way that "development" is used by the state for control, evaluation, regulation, and to make assertions about the quality and qualities of local people. Papuan students in Manado, Sulawesi are strongly influenced by development ideology. As they negotiate their way through state discourse, they show conformity and resistance to Indonesian development ideology, and by extension, governance.