Dissertations / Theses: 'RNA viruses Plant viruses'

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Chare, Elizabeth R. "Recombination in RNA viruses and plant virus evolution." Thesis, University of Oxford, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.433381.

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Keese, Paul Konrad. "Structures of viroids and virusoids and their functional significance." Title page, contents and summary only, 1986. http://web4.library.adelaide.edu.au/theses/09PH/09phk268.pdf.

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Afsharifar, Alireza. "Characterisation of minor RNAs associated with plants infected with cucumber mosaic virus." Title page, table of contents and abstract only, 1997. http://web4.library.adelaide.edu.au/theses/09PH/09pha2584.pdf.

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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.

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Jeffries, Alex Craig. "The study at the molecular level of the New Zealand isolate of Lucerne transient streak sobemovirus and its satellite RNA." Title page, contents and summary only, 1993. http://web4.library.adelaide.edu.au/theses/09PH/09phj47.pdf.

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5

Naylor, Martin. "The effects of salicylic acid on RNA plant viruses." Thesis, University of Cambridge, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.624519.

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Rohozinski, J. "Studies of velvet tobacco mottle virus RNA replication by enzyme-template complexes in extracts from infected leaves /." Title page, contents and summary only, 1985. http://web4.library.adelaide.edu.au/theses/09PH/09phr738.pdf.

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7

Liu, Yuan Yi. "A study of a satellite RNA from arabis mosaic nepovirus." Thesis, University of Oxford, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.335830.

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Bustamante-Gallardo, Pedro. "Molecular studies on Rice hoja blanca virus (RHBV)." Thesis, University of East Anglia, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.338096.

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9

Sheldon, Candice Claire. "Hammerhead mediated self-cleavage of plant pathogenic RNAs /." Title page, contents and summary only, 1992. http://web4.library.adelaide.edu.au/theses/09PH/09phs544.pdf.

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10

Fei, Yue. "Investigating RNA silencing-mediated epigenetic modifications in virus-infected plants." Thesis, University of Edinburgh, 2018. http://hdl.handle.net/1842/33125.

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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.

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11

Wahyuni, Wiwiek Sri. "Variation among cucumber mosaic virus (CMV) isolates and their interaction with plants." Title page, contents and summary only, 1992. http://web4.library.adelaide.edu.au/theses/09PH/09phw137.pdf.

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Includes appendix containing journal publications co-authored by the author. Includes bibliographical references (leaves 130-151). Eighteen strains of Cucumber mosaic virus, including forteen from Australia, two from the USA, and two from Japan were used in this study.

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12

Linnik, Volha. "Functional analysis of a plant virus replication 'factory' using live cell imaging." Thesis, University of Edinburgh, 2010. http://hdl.handle.net/1842/4639.

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Plant viruses have developed a number of strategies that enable them to become obligate intracellular parasites of many agricultural crops. Potato virus X (PVX) belongs to a group of positive-sense, single-stranded plant RNA viruses that replicate on host membranes and form elaborate structures known as viral replication complexes (VRCs) that contain viral RNA (vRNA), proteins and host cellular components. VRCs are the principal sites of viral genome replication, virion assembly and packaging of vRNA for export into neighbouring cells. For many animal viruses, host membrane association is crucial for RNA export. For plant viruses, it is not yet known how vRNA is transported to and through plant plasmodesmata. PVX encodes genetic information required for its movement between cells; three viral triple gene block (TGB) movement proteins and a viral coat protein are essential for viral trafficking. This research project studies the relationship between PVX and its host plants, Nicotiana benthamina and Nicotiana tabacum. A particular focus of this project is exploration of the structural and functional significance of the PVX VRC and how the virus recruits cell host components for its replication and movement between cells. The role of specific viral proteins in establishing the VRC, and the ways in which these interact with host organelles, was investigated. A combination of different approaches was used, including RNA-binding dyes and a Pumilio-based bimolecular fluorescence complementation assay for detection of the vRNA, fluorescent reporters for virusencoded proteins, fluorescent reporters for host organelles involved in viral replication, and also transgenic tobacco plants expressing reporters for specific plant components (endoplasmic reticulum, Golgi, actin, microtubules and plasmodesmata). In addition, mutagenesis was used to study the functions of individual viral proteins in replication and movement. All of these approaches were combined to achieve live-cell imaging of the PVX infection process. The PVX VRC was shown to be a highly compartmentalised structure; (+)-stranded vRNA was concentrated around the viral TGB1 protein, which was localised in discrete circular compartments within the VRC while coat protein was localised to the external edges of the VRC. The vRNA was closely associated with host components (endoplasmic reticulum and actin) shown to be involved in the formation of the VRC. The TGB2/TGB3 viral proteins were shown to colocalise with the host endomembranes (ER) and to exit these compartments in the form of motile granules. vRNA, TGB1, TGB2 and CP localised to plasmodesmata of the infected cells. TGB1 was shown to move cell-to-cell and recruit ER, Golgi and actin in the absence of viral infection. In the presence of virus, TGB1 targeted the VRCs in several neighbouring cells. A model of PVX replication and movement is proposed in which TGB1 functions as a key component for recruitment of host components into the VRC to enable viral replication and spread.

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13

Hacker, Caroline Victoria. "The molecular characterisation and phylogeny of double-stranded RNA viruses in plant pathogenic fungi and oomycetes." Thesis, Imperial College London, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.412503.

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14

Du, Preez Jacques. "The construction of an infectious clone of grapevine virus A (GV A)." Thesis, Link to the online version, 2005. http://hdl.handle.net/10019/1012.

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15

Lennefors, Britt-Louise. "Molecular breeding for resistance to rhizomania in sugar beets /." Uppsala : Department of Plant Biology and Forest Genetics, Swedish University of Agricultural Sciences, 2006. http://epsilon.slu.se/2006106.pdf.

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16

Avelar, Ana Sofia. "Single and Mixed Infections of Plant RNA and DNA Viruses are Prevalent in Commercial Sweet Potato in Honduras and Guatemala." Thesis, The University of Arizona, 2015. http://hdl.handle.net/10150/578609.

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Sweet potato is one of the 15 most important food crops worldwide. At least 30 different virus species, belonging to different taxonomic groups affect sweet potato. Little is known about the viruses present in sweet potato crops in Central America, which is the primary origin of sweet potato. The objective of this study was to design and implement primers for use in polymerase chain reaction (PCR) and Reverse transcription-PCR (RT-PCR) to identify and survey the diversity of plant viruses infecting sweet potato in Honduras and Guatemala. Primers were designed and used to amplify, clone, and sequence a taxonomically informative fragment of the coat protein (CP) gene for whitefly-transmitted geminiviruses (herein, sweepoviruses) and potyviruses, and of the heat shock protein 70 (HSP70) for the Crinivirus, Sweet potato chlorotic stunt virus (SPCSV). The partial genome sequences were used for identification based on phylogenetic relationships with reference sequences available in the GenBank database. All three of the plant virus groups identified in this study were found to occur either in single or in multiple infections. Results of the sequence analyses indicated that the genomic regions amplified in this study were capable of discriminating among potyvirus species, and strains of SPCSV. With respect to potyvirus, all isolates were identified as Sweet potato feathery mottle virus (SPFMV) species, except for two, which grouped phylogenetically with Sweet potato virus G (SPVG) and Sweet potato virus C (SPVC). All sweepoviruses detected in sweet potato plants belonged to a single phylogenetically, well-supported group that contains all other previously described geminiviruses (sweepoviruses) associated with sweet potato or closely related host species. These results demonstrate that the primers designed for amplification of plant virus species commonly recognized to infect sweet potato, effectively detected the viruses singly and in mixtures from symptomatic plants, and that the resultant fragment, when subjected to cloning and DNA sequenced, was phylogenetically informative at the species and/or strain levels, depending on the virus group.

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17

Kasumba, Muhandwa Dacquin. "A plant-derived nucleic acid protects mice from respiratory viruses in an IFN-I-dependent and independent manner." Kyoto University, 2017. http://hdl.handle.net/2433/228258.

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18

Mulot, Michaël. "Analyse fonctionnelle du récepteur de l'éphrine de Myzus persicae et mise en évidence de son rôle dans la transmissino du virus de la jaunisse du navet." Thesis, Strasbourg, 2018. http://www.theses.fr/2018STRAJ004/document.

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Les polérovirus infectent une large gamme de plantes d’intérêt économique. Ils sont transmis par un insecte vecteur, le puceron, selon le mode circulant non-multipliant. Le virus, acquis par le puceron lors de l’ingestion de sève sur une plante infectée, traverse l’épithélium des cellules intestinales puis celui des glandes salivaires par un mécanisme de transcytose impliquant des récepteurs encore inconnus. Le récepteur de l’éphrine (Eph) est une protéine membranaire dont un domaine est capable de se lier dans la levure aux protéines structurales des polérovirus. En développant des techniques basées sur l’ARN interférence, nous avons montré que l’acquisition orale d’ARN double brin ciblant Eph chez le puceron Myzus persicae permet de réduire de manière reproductible l’internalisation des polérovirus dans le corps du puceron. Les pucerons ainsi traités transmettent le virus avec une efficacité réduite. Eph pourrait donc assurer la fonction de récepteur des polérovirus chez M. persicae
Poleroviruses infect a wide range of economically important plants. They are transmitted in a circulative and non-propagative mode by an insect vector, the aphid. The virus particles are acquired by aphids when ingesting the sap from an infected plant and cross successively the epithelia of the midgut and the salivary gland cells by a transcytosis mechanism that relies on the presence of unknown receptors.The ephrin receptor (Eph) is a membrane protein which contains a domain able to bind in yeast to the structural proteins of poleroviruses. By developing methods based on RNA interference, we have shown that oral acquisition of double-stranded RNA targeting Eph in the aphid Myzus persicae can reproducibly reduce polerovirus internalization into the aphid's body. Such treated aphids transmit the virus to plants with a lower efficiency. Eph could therefore function as a receptor for poleroviruses in M. persicae

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Olabode, Abayomi. "The evolution of RNA viruses." Thesis, University of Manchester, 2017. https://www.research.manchester.ac.uk/portal/en/theses/the-evolution-of-rna-viruses(ac87e71c-e9ce-44c6-8dc1-6adbb01e5efb).html.

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This thesis analyzes the evolutionary trajectories that drive the evolution of several RNA viruses. These viruses have been identified to be the leading causes of viral outbreaks and deaths in humans. Studying the mechanisms influencing their evolution could therefore produce vital information for controlling the spread of these viruses or for their eradication. The availability of huge sequence repositories and advancement in computing and sequencing technologies allows for the development of novel methods for understanding the evolution of viruses even during an on-going outbreak, epidemic or pandemic. In this study, I developed a method that incorporates phylogenetic and structural based techniques to study the evolution of drug resistance in (A) HIV-1 Pol proteins, (B) the evolutionary dynamics of the 2013 - 2016 EBOV outbreak and (C) the evolution of the A(H1N1) influenza virus amongst human, avian and swine species. Findings from this thesis show that though HIV-1 evolves differently in the presence and absence of drug selection pressure, the virus is generally constrained by the need to maintain viral protein structure stability. The virus achieves this by accumulating enabling mutations early in its evolutionary history in order to accommodate the emergence of drug resistance associated mutations, which are mostly destabilizing. I also show that although the 2013 - 2016 EBOV was evolving rapidly, early data indicated that it was not changing at the functional level and not adapting to the human host. This is because most of the mutations occur in either inter genic or intrinsically disordered regions, which are less constrained, while the structured bits are characterized by neutral impact mutations. This again suggests that the virus needs to maintain a stable protein structure in order to remain functional. I show that EBOV is relatively stably evolving and the major force driving its evolution is more of an epidemiologic rather than a molecular factor whereas HIV-1 is evolving adaptively and its evolution is driven by molecular processes. However, one residue change, A82V seems to have altered the ability of the virus to bind its human receptor. This suggests that adaptive or functional mutations (which are mostly destabilizing in nature) work hand in hand with enabling mutations in such a way that a virus can acquire a mutation that confers drug resistance or leads to a gain of function without compromising its fitness while also retaining its functions such as infectivity and transmissibility. This indicates that the mechanisms described above may be a general way through which viruses evolve. The methods developed in the study can easily be applied to studying the evolution of other viruses and other systems e.g. microorganisms and cancer cells. Even if selection analysis does not show positive selection or any mutations in functional site, my thesis has demonstrated that structural analysis will be very useful for identifying and also predicting mutations that could facilitate adaptation of viruses. Also the influenza study shows that though the A(H1N1) is evolving somewhat differently in the humans, avian and swine species, one thing they seem to have in common is that stability constrains their evolution. I also show that my findings based on the human A(H1N1) influenza virus is consistent with the other human viruses (HIV and EBOV) analyzed in this project work.

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20

Wain, Louise V. "Origins of diversity of RNA viruses." Thesis, University of Nottingham, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.440123.

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21

Willcocks, Margaret Mary. "Small RNA viruses associated with diarrhoea." Thesis, University of Newcastle Upon Tyne, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.287271.

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22

Mcmenemy, Lindsay Sara. "Raspberry viruses manipulate plant–aphid interactions." Thesis, University of Sussex, 2011. http://sro.sussex.ac.uk/id/eprint/7465/.

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Plants come under attack by a variety of organisms, including insects and pathogenic microorganisms such as viruses. Plant viruses can interact indirectly with their vectors by inducing changes to plant chemistry which may alter its attractiveness as a host for herbivore vectors. Using red raspberry as a study system, this study aimed to investigate the host plant mediated interactions occurring between the large raspberry aphid, Amphorophora idaei, and two of the viruses that it transmits, Black raspberry necrosis virus (BRNV) and Raspberry leaf mottle virus (RLMV). In whole plant bioassays, BRNV and RLMV-infected plants were shown to be initially more attractive to A. idaei and aphids remained on the initially selected host plant for a period of approximately 30 minutes. In addition, A. idaei took three days longer to reach reproductive maturity compared with those feeding on non-infected plants, suggesting a virally-induced manipulation of aphid behaviour whereby a deceptive attraction of the vector to a host plant found to be nutritionally poor, presumably acts to promote virus transmission. Investigations of the underlying plant chemistry revealed that raspberry viruses may be capable of facilitating aphid feeding by reducing leaf phenolic concentration when aphids are feeding and that infection with BRNV and RLMV resulted in significantly elevated levels of carbon and free amino acids in the leaves. While increased concentrations of amino acids might be expected to promote aphid performance, the amino acid composition was dominated by glutamate (77% of total content of infected plants), a previously suggested indicator of reduced host-plant suitability for aphids. Volatile entrainments from virus-infected plants showed elevated levels of the green leaf volatile (Z)-3-hexenyl acetate. Bioassays subsequently revealed that this compound acted as an aphid attractant at a concentration of 50 ng ml-1 but that aphid behaviour was unaffected by lower concentrations. The combined utilisation of PCR diagnostics developed from newly sequenced viral genomes and the implementation of a non-invasive, targeted method of sampling plant headspace volatiles enabled this study to provide novel insights into the nature of host plant mediated interactions between aphids and the viral pathogens that they transmit.

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23

Wu, Chuang. "Phenotype Inference from Genotype in RNA Viruses." Research Showcase @ CMU, 2014. http://repository.cmu.edu/dissertations/457.

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The phenotype inference from genotype in RNA viruses maps the viral genome/protein sequences to the molecular functions in order to understand the underlying molecular mechanisms that are responsible for the function changes. The inference is currently done through a laborious experimental process which is arguably inefficient, incomplete, and unreliable. The wealth of RNA virus sequence data in the presence of different phenotypes promotes the rise of computational approaches to aid the inference. Key residue identification and genotype-phenotype mapping function learning are two approaches to identify the critical positions out of hitchhikers and elucidate the relations among them. The existing computational approaches in this area focus on prediction accuracy, yet a number of fundamental problems have not been considered: the scalability of the data, the capability to suggest informative biological experiments, and the interpretability of the inferences. A common scenario of inference done by biologists with mutagenesis experiments usually involves a small number of available sequences, which is very likely to be inadequate for the inference in most setups. Accordingly biologists desire models that are capable of inferring from such limited data, and algorithms that are capable of suggesting new experiments when more data is needed. Another important but always been neglected property of the models is the interpretability of the mapping, since most existing models behave as ’black boxes’. To address these issues, in the thesis I design a supervised combinatorial filtering algorithm that systematically and efficiently infers the correct set of key residue positions from available labeled data. For cases where more data is needed to fully converge to an answer, I introduce an active learning algorithm to help choose the most informative experiment from a set of unlabeled candidate strains or mutagenesis experiments to minimize the expected total laboratory time or financial cost. I also propose Disjunctive Normal Form (DNF) as an appropriate assumption over the hypothesis space to learn interpretable genotype-phenotype functions. The challenges of these approaches are the computational efficiency due to the combinatorial nature of our algorithms. The solution is to explore biological plausible assumptions to constrain the solution space and efficiently find the optimal solutions under the assumptions. The algorithms were validated in two ways: 1) prediction quality in a cross-validation manner, and 2) consistency with the domain experts’ conclusions. The algorithms also suggested new discoveries that have not been discussed yet. I applied these approaches to a variety of RNA virus datasets covering the majority of interesting RNA phenotypes, including drug resistance, Antigenicity shift, Antibody neutralization and so on to demonstrate the prediction power, and suggest new discoveries of Influenza drug resistance and Antigenicity. I also prove the extension of the approaches in the area of severe acute community disease.

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Bowden, Gregory David. "Novel acyclic nucleotide phosphonates against RNA viruses." Master's thesis, University of Cape Town, 2012. http://hdl.handle.net/11427/10258.

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Includes bibliographical references.
Acyclic nucleotide phosphonates (ANPs) have been used for years as successful anti-viral agents against diseases such as HIV/AIDS and hepatitis while the drug ribavirin is one of the only drugs available for the treatment of RNA-viral infections which mainly affect the developing world. The large and unmet need for anti-RNA viral treatments has prompted this study into the design and synthesis of a range of ANPs, which includes a series of ribavirin-based ANP derivatives. The series of compounds was synthesised from a diisopropyl protected phosphonomethoxyethyl (PME) synthon and included an arylethynyltriazole derivative which was produced via a Sonogashira palladium catalysed cross-coupling reaction. A selection of these compounds was then deprotected to their corresponding phosphonic acids via a bromotrimethylsilane mediated phosphonate ester hydrolysis. In one example, a bis(pivaloyloxymethyl) prodrug variant was produced in order to probe a general synthesis for prodrug protected ANP derivatives. All new compounds were characterised by NMR, IR, and Mass spectroscopic techniques.

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25

Ward, Melissa Jayne. "Evolutionary analysis of rapidly evolving RNA viruses." Thesis, University of Edinburgh, 2013. http://hdl.handle.net/1842/11748.

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Recent advances in sequencing technology and computing power mean that we are in an unprecedented position to analyse large viral sequence datasets using state-of-the-art methods, with the aim of better understanding pathogen evolution and epidemiology. This thesis concerns the evolutionary analysis of rapidly evolving RNA viruses, with a focus on avian influenza and the use of Bayesian methodologies which account for uncertainty in the evolutionary process. As avian influenza viruses present an epidemiological and economic threat on a global scale, knowledge of how they are circulating and evolving is of substantial public health importance. In the first part of this thesis I consider avian influenza viruses of haemagglutinin (HA) subtype H7 which, along with H5, is the only subtype for which highly pathogenic influenza has been found. I conduct a comprehensive phylogenetic analysis of available H7 HA sequences to reveal global evolutionary relationships, which can help to target influenza surveillance in birds and facilitate the early detection of potential pandemic strains. I provide evidence for the continued distinction between American and Eurasian sequences, and suggest that the most likely route for the introduction of highly pathogenic H5N1 avian influenza to North America would be through the smuggling of caged birds. I proceed to apply novel methods to better understand the evolution of avian influenza. Firstly, I use an extension of stochastic mutational mapping methods to estimate the dN/dS ratio of H7 HA on different neuraminidase (NA) subtype backgrounds. I find dN/dS to be higher on the N2 NA background than on N1, N3 or N7 NA backgrounds, due to differences in selective pressure. Secondly, I investigate reassortment, which generates novel influenza strains and precedes human influenza pandemics. The rate at which reassortment occurs has been difficult to assess, and I take a novel approach to quantifying reassortment across phylogenies using discrete trait mapping methods. I also use discrete trait mapping to investigate inter-subtype recombination in early HIV-1 in Kinshasa, the epicentre of the HIV-1 group M epidemic. In the final section of the thesis, I describe a method whereby epidemiological parameters may be inferred from viral sequence data isolated from different infected individuals in a population. To conclude, I discuss the findings of this thesis in the context of other evolutionary and epidemiological studies, suggest future directions for avian influenza research and highlight scenarios in which the methods described in this thesis might find further application.

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Bakker, Saskia. "RNA packaging and uncoating in simple single-stranded RNA viruses." Thesis, University of Leeds, 2012. http://etheses.whiterose.ac.uk/2801/.

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Simple (non-enveloped) small, positive-sense single-stranded RNA viruses infect hosts from all kingdoms of life. However, their assembly and uncoating processes remain poorly understood. For turnip crinkle virus (TCV), 3D reconstructions by cryoelectron microscopy (cryo-EM) are shown for the native and the expanded form. The expanded form is a putative disassembly intermediate and exhibits pores that are large enough to allow exit of single-stranded RNA. Biochemical experiments revealed the expanded form is protease-sensitive, although the RNA genome remains protected from ribonuclease. Virus particles complexed with ribosomes are shown by negative stain EM. Proteolysis causes release of some coat protein from the capsid, while the capsid remains largely intact. Proteolysed particles have lost their icosahedral symmetry and show a protuberance in negative stain EM. Taken together, these results suggest expansion and subsequent proteolysis are essential steps in the uncoating process of TCV, and that the capsid plays multiple roles consistent with ribosome-mediated genome uncoating to avoid host anti-viral activity. Similarly, 3D cryo-EM reconstructions are presented for native equine rhinitis A virus (ERAV) an expanded particle containing no RNA. The native virus fits well with the ERAV crystal structure. The empty particle is a putative disassembly intermediate representing a stage after the release of the RNA genome. A mechanism is suggested that is consistent with the RNA release from the endosome without exposure to the endosomal contents. A crystal structure is presented of satellite tobacco necrosis virus (STNV) virus-like particles containing a small RNA fragment. The coat protein structure is identical to that of native STNV. Although density internal to the coat protein shell has been observed in the experiment that corresponds to earlier experiments, no unambiguous RNA structure can be built into the density. Together, the results presented here shed some light on the life cycle of three of these viruses.

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Fu, S. F. "Salicylic acid induced resistance to plant viruses." Thesis, University of Cambridge, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.599252.

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Mitochondrial alternative oxidase (AOX) plays a role in protecting plant cells against reactive oxygen species. The SA-inducible RNA-directed RNA polymerase 1 (RDR1), contributes to viral RNA degradation via RNA interference. Previous data suggested that these enzymes comprise separately regulated, redundant elements in SA-induced resistance to viruses. To test this hypothesis, I constructed transgenic tobacco (Nicotiana tabacum) and N. benthamiana plants compromised simultaneously in AOX function and RDR1 activity. Transgenic tobacco and N. benthamiana plants were characterised by measuring alternative respiratory pathway (AP) capacity and RDR enzyme activity. The resistance/susceptibility status of the transgenic plants was assessed by analysing Tobacco mosaic virus (TMV) accumulation in the chemically treated, directly-inoculated tissues. Antimycin A (AA)-induced resistance to TMV was inhibited in transgenic N. benthamiana with increased AP capacity, and SA- and AA-induced resistance was enhanced in transgenic N. benthamiana with decreased AP capacity. However, SA-induced resistance to TMV in directly-inoculated leaves was still unaffected in transgenic tobacco and N. benthamiana compromised in AOX function and RDR1 activity. This suggests that SA-induced resistance to viruses involves additional, unknown mechanisms. Surprisingly, SA can enhance RDR activity in transgenic 35S-MtRDR1 N. benthamiana but not wild-type and vector-control plants (natural mutants of RDR1). This SA-enhanced RDR activity resulted from increased MtRDR1 protein level, indicating the post-transcriptional regulation of MtRDR1 enzyme activity. SA-induced resistance to systemic movement was enhanced in transgenic 35S-MtRDR1 N. benthamiana plants, suggesting that SA-induced increase in RDR1 activity plays a role in induced resistance to systemic movement of viruses. Basal resistance to viruses was studied in transgenic tobacco (nn or NN genotype) and N. benthamiana plants with modified AP capacity or RDR activity. Modification of AP capacity had no effect on TMV accumulation in HR lesions from transgenic tobacco plants overexpressing the Aoxla construct (NN background). Notably, transgenic N. benthamiana plants with increased AP capacity were more susceptibility to Potato virus X (PVX) than non-transgenic plants. This was seen in the transgenic plant with increased AP capacity that PVX accumulated to higher level in both directly-inoculated and systemic leaf tissues. It was also nearly discovered that transgenic 35S-MtRDR1 N. benthamiana plants were more resistant to Potato virus Y ordinary strain. The results suggest that altering AP capacity has effect on basal resistance to some viruses and confirms that RDR1 plays a role on basal resistance.

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28

Aw, D. W. J. "Analysis of methods for screening plant viruses." Thesis, University of Glasgow, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.328786.

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29

Boz, Mustafa Burak. "Modeling and simulations of single stranded rna viruses." Diss., Georgia Institute of Technology, 2012. http://hdl.handle.net/1853/44815.

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The presented work is the application of recent methodologies on modeling and simulation of single stranded RNA viruses. We first present the methods of modeling RNA molecules using the coarse-grained modeling package, YUP. Coarse-grained models simplify complex structures such as viruses and let us study general behavior of the complex biological systems that otherwise cannot be studied with all-atom details. Second, we modeled the first all-atom T=3, icosahedral, single stranded RNA virus, Pariacoto virus (PaV). The x-ray structure of PaV shows only 35% of the total RNA genome and 88% of the capsid. We modeled both missing portions of RNA and protein. The final model of the PaV demonstrated that the positively charged protein N- terminus was located deep inside the RNA. We propose that the positively charged N- terminal tails make contact with the RNA genome and neutralize the negative charges in RNA and subsequently collapse the RNA/protein complex into an icosahedral virus. Third, we simulated T=1 empty capsids using a coarse-grained model of three capsid proteins as a wedge-shaped triangular capsid unit. We varied the edge angle and the potentials of the capsid units to perform empty capsid assembly simulations. The final model and the potential are further improved for the whole virus assembly simulations. Finally, we performed stability and assembly simulations of the whole virus using coarse-grained models. We tested various strengths of RNA-protein tail and capsid protein-capsid protein attractions in our stability simulations and narrowed our search for optimal potentials for assembly. The assembly simulations were carried out with two different protocols: co-transcriptional and post-transcriptional. The co-transcriptional assembly protocol mimics the assembly occurring during the replication of the new RNA. Proteins bind the partly transcribed RNA in this protocol. The post-transcriptional assembly protocol assumes that the RNA is completely transcribed in the absence of proteins. Proteins later bind to the fully transcribed RNA. We found that both protocols can assemble viruses, when the RNA structure is compact enough to yield a successful virus particle. The post-transcriptional protocol depends more on the compactness of the RNA structure compared to the co-transcriptional assembly protocol. Viruses can exploit both assembly protocols based on the location of RNA replication and the compactness of the final structure of the RNA.

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30

Jenkins, Gareth. "Determinants of the molecular evolution of RNA viruses." Thesis, University of Oxford, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.365413.

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Exline, Colin Michael Stoltzfus C. Martin. "The positive regulation of HIV-1 Vif mRNA splicing is required for efficient virus replication." [Iowa City, Iowa] : University of Iowa, 2009. http://ir.uiowa.edu/etd/356.

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32

Rosskopf, John J. "CIS-acting signals for replication of Nodamura virus RNA1." To access this resource online via ProQuest Dissertations and Theses @ UTEP, 2009. http://0-proquest.umi.com.lib.utep.edu/login?COPT=REJTPTU0YmImSU5UPTAmVkVSPTI=&clientId=2515.

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33

Short, James Roswell. "An investigation into the replication biology of Helicoverpa armigera stunt virus." Thesis, Rhodes University, 2011. http://hdl.handle.net/10962/d1004026.

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Tetraviruses are a family of small non-enveloped positive sense RNA viruses that exclusively infect members of the order Lepidoptera. Their replication biology is poorly studied because, with the exception of Providence virus (PrV), tetraviruses are unable to replicate in tissue culture cells. The overall aim of the research described in this thesis was to develop a fundamental understanding of the replication of tetraviruses, focussing on the site of replication within host cells and in particular, the subcellular localisation of the viral replicase. Helicoverpa armigera stunt virus (HaSV, Genus: Omegatetravirus) was chosen for this study because it is the only tetravirus for which the cDNAs have been shown to be infectious. In the absence of tissue culture cell lines susceptible to HaSV infection, the approach was to use confocal fluorescence microscopy to examine the subcellular localisation of the HaSV replicase fused to enhanced green fluorescent protein (EGFP) in mammalian and insect tissue culture cells. The replicase (with EGFP fused at its C-terminus) localised to punctate structures throughout the cytoplasm of transfected HeLa and Sf9 cells. These structures were then shown – using live cell imaging and time lapse photography – to behave similarly to cellular endocytic organelles and fluorescence partially overlapped with membranes containing the late endosomal marker protein CD63. Biochemical fractionation of Sf9 cells expressing the replicase via a recombinant baculovirus (as well as transfected HeLa and Sf9 cells expressing EGFP-replicase fusion proteins) demonstrated that the replicase was strongly associated with detergentresistant membranes (DRMs) in these cells. Deletion analysis of the replicase coding sequence revealed two regions involved in the generation of the punctuate structures. Firstly, the C-terminal half of the replicase RNAdependant RNA polymerase domain was found to be essential for targeting and the tight association with DRMs while the second region, within the Nterminal 44 amino acids, enhanced localisation through a combination of secondary structural elements and sequence-specific functions. A comparative immunofluorescence study on PrV, which replicates as a persistent infection in an insect midgut cell line, showed that the PrV replicase also localised to punctate structures in the cytoplasm. Biochemical fractionation showed that the replicase was also strongly associated with DRMs. This thesis describes the development of new experimental systems for the study of tetravirus replication biology and the data lead to the conclusion that the HaSV replicase associates with DRMs derived from alternate endocytic pathway organelles.

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Groen, Simon Cornelis. "Manipulation of plant-insect interactions by insect-borne plant viruses." Thesis, University of Cambridge, 2013. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.648187.

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Topley, Elize Lindsay. "Molecular detection and characterisation of RNA viruses of honeybees." Thesis, University of the Western Cape, 2009. http://etd.uwc.ac.za/index.php?module=etd&action=viewtitle&id=gen8Srv25Nme4_6220_1298349602.

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Propagation methods for honeybee viruses have not changed since these viruses were discovered. There are no suitable cell lines or cell culture techniques available for honeybee viruses. Honeybee viruses have to be manually injected with virus in order for the virus to multiply and be extracted. With the presence of inapparent viruses which could co-infect pupae, a method for pure virus propagations needs to be found. Recombinant baculovirus systems have been used extensively to produce foreign proteins from different viruses using vectors and recombinant technology. In this chapter we inserted the capsid gene from BQCV into a transfer vector under the control of the p10 promoter of Autographa californica. Fractions of the sucrose gradient containing the virus like particles (VLPs) were seen under the electron microscope. A Western blot showed the four capsid proteins at the expected sizes for BQCV capsid. This study therefore has shown that a heterologous system such as baculovirus can be used for virus like particle production. Infectious virus technology has helped gain insight into how viruses work. Using this technology altering honeybee viruses could be used to observe different functionalities of the viruses. An attempt was made to interchange the open reading frames of ABPV and BQCV to observe any changes in virus assembly and infectivity. A fusion PCR strategy was employed to interchange the 5&rsquo
and 3&rsquo
ORFs of APBV and BQCV. The strategy however was unsuccessful. Alternative strategies could improve the chances of obtaining a chimeric virus.

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36

Zeng, Yingying. "Modeling and structural studies of single-stranded RNA viruses." Diss., Georgia Institute of Technology, 2013. http://hdl.handle.net/1853/47630.

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My research focuses on structures of the genomes of single-stranded RNA viruses. The first project is concerned with the sequence and secondary structure of HIV-1 RNA. Based on the secondary structure that Watts et al. determined, I performed a series of analysis and the results suggested that the abundance of Adenosines at the wobble position of the codons leads to an unusual structure with numerous unpaired nucleotides. The findings indicated how the virus balances evolutionary pressures on the genomic RNA secondary structure against pressures on the sequence of the viral proteins. The second project is the modeling of satellite tobacco mosaic virus (STMV). STMV is a T=1 icosahedral virus with a single piece of RNA that has 1058 nucleotides. X-ray crystallography studies of this RNA have revealed a structure containing 30 helices. The linkers between the helices, the possible structures at the interior of the icosahedron, and the sequence of the RNA were all missing in the crystal structure. To explore how the genome is organized within the protein capsid, I built a 3D model based on the RNA secondary structure predicted by Susan Schroeder. Being the first all-atom model of any virus, this model is highly correlated with the crystal structure; and the comparison with the in vitro structure of the same RNA supports the hypothesis that capsid protein plays an important role in RNA folding during assembly. The third project includes the modeling of bacteriophage MS2 (MS2) and the examination of the compactness of RNA in different viruses. MS2 is a T=3 RNA virus, and the cryo-EM studies have revealed a double-shell conformation of the genome. My final model of MS2 recaptures the double-shell structure of the RNA presented in the cryo-EM density. In addition, the predicted secondary structure that I used for the construction of the model shares a strong similarity with the in vitro structure determined in 1980s. This similarity contrasts with the striking difference between in vivo and in vitro RNA structures observed in STMV. Inspired by this finding, I examined the compactness of the RNA of several different viruses. The results strongly suggest that the RNAs of viruses requiring packaging signals have evolved to be structurally compact, which facilitates post-replicational RNA packaging. In contrast, viruses that do not depend on packaging signals probably adopt co-replicational RNA packaging.

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Hershan, Almonther A. "Identification and analysis of conserved structures in RNA viruses." Thesis, University of Essex, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.572803.

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The family Picornaviridae includes many important human pathogens. RNA structures play important roles in picornavirus molecular biology and recent evidence suggests that these are more extensive than previously thought. In this project we identified a number of potential RNA structures in picornavirus genomes and started to analyse one of these structures. The work focussed on human parechoviruses (HPe V). The structure of the HPe V 5' untranslated region (UTR) was analysed by obtaining several new sequences and using an alignment of 60 sequences to identify covariant changes. This allowed the previously predicted structure to be confirmed and refined. Aligned sequences representing most picornavirus species were then analysed for suppression of synonymous codon variation (SSCV). Strong SSCV was seen in several cases and this was often related to the presence of RNA structures including the Cre and novel potential structures. Patterns of conserved dinucleotides were also used to identify regions of importance in the picornavirus genome. A new program, Dinucleotider (1.0) was developed and used, which allows a graphical output of conserved dinucleotides in aligned sequences. CG was found to be the most informative dinucleotide and could be used to identify regions of the picornavirus genome, which corresponded to the 5'UTR, 3'UTR and Cre, as well as further new structures. Genetic analysis of a predicted structure in the 3D-encoding region of HPe V s, was carried out by making two mutants, with 3 or 6 mutations in one of the structural domains. Both sets of mutations had little effect on virus growth in cultured cells, suggesting that the structure does not play a critical role in replication and other possible roles need to be identified. Overall, this project has allowed several RNA structures to be identified in picornaviruses. These are conserved between related viruses and presumably play important roles in the biology of picornaviruses. They need to be studied further in order to improve understanding of how picornaviruses infect cells, which is required to improve diagnosis and control of these pathogens.

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Kallender, Howard. "Characterisation and molecular biology of two plant viruses." Thesis, Imperial College London, 1990. http://hdl.handle.net/10044/1/46375.

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39

Li, Tin-wai Olive. "Influenza polymerase subunit compatibility between human H1 and H5 viruses." Click to view the E-thesis via HKUTO, 2009. http://sunzi.lib.hku.hk/hkuto/record/B41896890.

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40

Kok, Tuckweng. "Early events in the replication cycle of human immunodeficiency virus /." Title page, contents and abstract only, 1998. http://web4.library.adelaide.edu.au/theses/09PH/09phk79.pdf.

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Thesis (Ph. D.)--University of Adelaide, Dept. of Microbiology & Immunology, 1998.
Copy of author's previously published article on back end-paper. Includes bibliographical references (leaves 105-158).

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41

Li, Tin-wai Olive, and 李天慧. "Influenza polymerase subunit compatibility between human H1 and H5 viruses." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2009. http://hub.hku.hk/bib/B41896890.

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42

Chan, Annie Yee-Man. "Interactions between the influenza virus RNA polymerase and cellular RNA polymerase II." Thesis, University of Oxford, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.670083.

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43

Tomasicchio, Michele. "Assembly of Omegatetravirus virus-like particles in the yeast Saccharomyces cerevisiae." Thesis, Rhodes University, 2008. http://hdl.handle.net/10962/d1003989.

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The Tetraviridae are a family of ss (+) RNA viruses that specifically infect lepidopteran insects. Their icosahedral capsids are non-enveloped and approximately 40 nm in diameter with T=4 quasi-equivalent symmetry. The omegatetraviruses, which are structurally the best characterised in the family, include Helicoverpa armigera stunt virus (HaSV) and Nudaurelia capensis omega virus (NwV). The omegatetravirus procapsid is composed of 240 identical copies of the capsid precursor proteins, which undergo autoproteolytic cleavage at its carboxyl-terminus generating the mature capsid protein (b) and γ-peptide. This process occurs in vitro following a shift from pH 7.6 to pH 6.0. The viral capsid encapsidates two ss genomic RNAs: The larger RNA1 encodes the viral replicase as well as three small ORFs while RNA2 encodes the capsid precursor protein together with an overlapping ORF designated P17. While a wealth of structural data pertaining to the assembly and maturation of omegatetraviruses is available, little is known about how this relates to their lifecycle. The principle aim of the research described in this thesis was to use an experimental system developed in the yeast, Saccharomyces cerevisiae, to investigate the assembly of HaSV and NwV virus-like particles (VLPs) in terms of maturation and encapsidation of viral RNAs, in vivo. The yeast expression system used two promoter systems for expression of capsid precursor protein: in the first, a hybrid promoter (PGADH) was used for high-level expression, while the second, PGAL1, produced substantially lower levels of the virus capsid protein precursors. An increase in the level of HaSV capsid protein precursor (p71) via the PGADH promoter resulted in a dramatic increase in VLP assembly as compared with the PGAL system. A protein equivalent to the mature capsid protein (p64) appeared at later time intervals following induction of transcription. Transmission electron microscopic studies showed that p64 correlated with the presence of mature VLPs as opposed to procapsids in cells containing p71. This confirmed that the presence of p64 denoted maturation of VLPs in vivo. Further investigation indicated that maturation correlated with cell aging and the onset of apoptosis. It was shown that induction of apoptosis resulted in VLP maturation while inhibition of apoptosis prevented maturation. These results suggested that the process of apoptosis might be the trigger for maturation of virus procapsids in their host cells. The increase in the efficiency of VLP assembly observed in the high-level expression system was proposed to be due to an increase in the cellular concentrations of viral RNA. To test this hypothesis, HaSV P71 was co-expressed with either P71 mRNA or full length RNA2. An increase in the solubility of p71 was observed in cells expressing increased levels of both RNAs, but there was no increase in the efficiency of VLP assembly. Northern analysis of encapsidated RNAs revealed that there was no selective encapsidation of either P71 mRNA or viral RNA2. This data indicated that the increase in viral RNA was not the reason for increased efficiency of VLP assembly, but most likely resulted from higher concentrations of p71 itself. It was decided to determine whether a highly efficient nodavirus replication system developed in yeast for heterologous production of proteins, could be used as a method for expressing the capsid protein precursor. The aim of using this system was to determine if VLPs assembled in a replication system specifically encapsidated viral RNA. Transcripts encoding the NwV capsid protein precursor (p70) were generated in yeast cells by replication of a hybrid RNA template by the Nodamura virus (NoV) replicase. Western analysis confirmed the presence of p70 as well as a protein of 62 kDa corresponding to the mature NwV capsid protein. Northern analysis of purified VLPs showed that NoV RNA1 and RNA3 were encapsidated, but no RNA2 was detected. Taken together, the data lead to the conclusion that specific encapsidation of tetraviral RNAs required more than close proximity of the viral RNAs and assembling virus-like particles. Encapsidation specificity in the omegatetraviruses may require additional viral proteins such as p17 during encapsidation or specific viral RNA encapsidation was replication-dependent. Replication-dependent assembly has been shown in the nodaviruses.

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44

Zeicher, Marc. "Oncolytic viruses cancer therapy." Doctoral thesis, Universite Libre de Bruxelles, 2008. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/210439.

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Wild-type viruses with intrinsic oncolytic capacity in human includes DNA viruses like some autonomous parvoviruses and many RNA viruses. Recent advances in molecular biology have allowed the design of several genetically modified viruses, such as adenovirus and herpes simplex virus that specifically replicate in, and kill tumor cells. However, still several hurdles regarding clinical limitations and safety issues should be overcome before this mode of therapy can become of clinical relevance. It includes limited virus spread in tumor masses, stability of virus in the blood, trapping within the liver sinusoids, transendothelial transfer, and/or vector diffusion of viral particles to tumor cells, limited tumor transduction, immune-mediated inactivation or destruction of the virus. For replication-competent vectors without approved antiviral agents, suicide genes might be used as fail-safe mechanism. Cancer stem cells are a minor population of tumor cells that possess the stem cell property of self-renewal. Therefore, viruses that target the defective self-renewal pathways in cancer cells might lead to improved outcomes.

In this thesis, data we generated in the field of oncolytic autonomous parvoviruses are presented.

We replaced capsid genes by reporter genes and assessed expression in different types of human cancer cells and their normal counterparts, either at the level of whole cell population, (CAT ELISA) or at the single cell level, (FACS analysis of Green Fluorescent Protein). Cat expression was substantial (up to 10000 times background) in all infected tumor cells, despite variations according to the cell types. In contrast, no gene expression was detected in similarly infected normal cells, (with the exception of an expression slightly above background in fibroblasts.). FACS analysis of GFP expression revealed that most tumor cells expressed high level of GFP while no GFP positive normal cells could be detected with the exception of very few (less than 0.1%) human fibroblast cells expressing high level of GFP. We also replace capsid genes by genes coding for the costimulatory molecules B7-1 and B7-2 and show that, upon infection with B7 recombinant virions, only tumor cells display the costimulatory molecules and their immunogenicity was increased without any effect on normal cells. Using a recombinant MVM containig the Herpes Simplex thymidine kinase gene, we could get efficient killing of most tumor cell types in the presence of ganciclovir, whithout affecting normal proliferating cells. We also produced tetracycline inducible packaging cell lines in order to improve recombinant vectors yields. The prospects and limitations of these different strategies will be discussed.

An overview is given of the general mechanisms and genetic modifications by which oncolytic viruses achieve tumor cell-specific replication and antitumor efficacy. However, as their therapeutic efficacy in clinical trials is still not optimal, strategies are evaluated that could further enhance the oncolytic potential of conditionally replicating viruses in conjunction with other standard therapies.

Another exciting new area of research has been the harnessing of naturally tumor-homing cells as carrier cells to deliver oncolytic viruses to tumors. The trafficking of these tumor-homing cells (stem cells, immune cells and cancer cells), which support proliferation of the viruses, is mediated by specific chemokines and cell adhesion molecules and we are just beginning to understand the roles of these molecules. Finally, we will explore some ways deserving further study in order to be able to utilize various oncolytic viruses for effective cancer treatment.

Doctorat en sciences, Spécialisation biologie moléculaire
info:eu-repo/semantics/nonPublished

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45

Nanfack, Minkeu Ferdinand. "Interaction of novel natural RNA viruses with Anopheles malaria vectors." Electronic Thesis or Diss., Sorbonne université, 2018. https://accesdistant.sorbonne-universite.fr/login?url=https://theses-intra.sorbonne-universite.fr/2018SORUS442.pdf.

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Les moustiques sont colonisés par un virome très peu étudié. Comme les bactéries, le virome influence probablement la biologie et l'immunité des populations de moustiques vecteurs, mais les modèles expérimentaux sont rares. Nous avons récemment découvert deux nouveaux virus chez le virome des vecteurs sauvages du paludisme, anophèles et des colonies d’Anopheles coluzzii : Anopheles C virus (AnCV) et Anopheles cypovirus (AnCPV). L’un ou les deux virus sont présents dans toutes les colonies de laboratoire d’An. gambiae et An. coluzzii. La prévalence des virus varie en fonction des stades du moustique. L'abondance des deux virus est négativement corrélée chez les moustiques individuels. L'analyse fonctionnelle révèle l'implication des voies de signalisation immunitaire des moustiques sur la réplication du virus, avec une influence différentielle sur les deux virus. Un modèle expérimental a été développé pour l'infection d’AnCPV chez les anophèles non porteurs de ces virus, en utilisant du sang infecté afin d'étudier les réponses antivirales chez ces moustiques. Les séquences de l'AnCPV sont hautement polymorphiques chez les moustiques individuels, alors que l'AnCV est pratiquement dépourvue de mutations. AnCPV entraine une plus grande mortalité chez An. stephensi, mais certaines mutations semblent impliquées dans son adaptation à cette espèce. AnCPV peut être potentiellement transmis comme un arbovirus à travers un hôte mammifère à des moustiques non infectés, ce qui suggère une voie évolutive relativement simple. Le virome d’An. stephensi contient un chaq-like virus et un partiti-like virus. Ce dernier appartenant à la famille des Partitiviridae a des formes d’ADN
Mosquitoes are colonized by a little-studied natural virome. Like the bacterial microbiome, the virome also probably influences the biology and immunity of mosquito vector populations, but tractable experimental models are lacking. We recently discovered two novel viruses in the virome of wild Anopheles and in colonies of the malaria vector Anopheles coluzzii: Anopheles C virus and Anopheles cypovirus. One or both viruses are present in all tested laboratory colonies of An. coluzzii and An. gambiae. Viral abundance varies reproducibly during mosquito development. Relative abundance of the two viruses is inversely correlated in individual mosquitoes. Functional genomic analysis reveals the implication of mosquito immune signaling pathways on virus replication, with differential influence on the two viruses. An experimental model was developed for AnCPV infection of Anopheles by bloodmeal, in order to study mosquito antiviral responses. Sequences of AnCPV are highly polymorphic in individual mosquitoes, while AnCV is virtually devoid of variation. AnCPV is pathogenic to An. stephensi but some viral mutations seem to be involved in its adaption to this species. AnCPV can be transmitted like an arbovirus through a vertebrate host to uninfected mosquitoes, suggesting that the evolutionary pathway from vertical “insect specific” to infective blood transmission may be remarkably simple. The Anopheles stephensi virome harbors a chaq-like virus and partiti-like virus. This latter belonging to Partitiviridae is present in An. stephensi as DNA forms of the virus genome

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46

Haley, Ann. "Characterisation of the movement proteins of two plant viruses." Thesis, University of Cambridge, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.308317.

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47

Murray, Rose Rebecca. "Investigating the interactions between plant viruses and host stomata." Thesis, University of Bristol, 2015. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.686167.

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Stomata are microscopic pores located in the epidermis of most terrestrial plants. As well as serving as gateways for gas exchange and transpiration, stomata have recently become known to have increasingly complex relationships with pathogens, with many pathogens utilising stomata as entry portals. However, the research so far has largely focussed on bacterial and fungal pathogens, leaving a gap in the knowledge about the interactions between plant viruses and stomata. This study aims to investigate the interactions and relations between stomata and viruses by investigating potential for stomata to act as entry portals for viruses and the developmental changes which occur under virus infection. In order to test the hypothesis that stomata can act as entry portals for plant viruses, a series of experiments was performed which altered stomatal apertures before applying purified virus suspended in solution in an aerosol. It was found that Nicotiana tabacum plants were more likely to become infected when TMV virus solution was applied when stomata were open. Natural and chemical factors were used to manipulate stomatal apertures prior to virus application. Stomatal development was investigated following a virus infection. A range of host-virus systems was used and it was found that susceptible host types had a general reduction in stomatal index and density when infected with a virus. Transcripts of genes involved in stomatal development were also tested for changes in healthy and infected plants and were found to vary upon infection. Knock-out mutants of various stomatal developmental or functional genes showed varying developmental responses to a virus infection, with notable changes in rin4 which resulted in an increase in stomatal development post infection. The results presented in this project provide an insight into a relatively new field of research which has so far been neglected in the field of plant pathology.

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48

Walter, Cheryl Tracy. "Development of experimental systems for studying the biology of Nudaurelia capensis ß virus." Thesis, Rhodes University, 2005. http://hdl.handle.net/10962/d1004007.

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After 20 years, Nudaurelia ß virus (NßV) was re-isolated from a population of Nudaurelia capensis larvae exhibiting similar symptoms to those described in 1974 for a tetravirus infection. NßV is a member of the Tetraviridae, a family of positive sense insect RNA viruses that exclusively infect Lepidopteran insects. In addition to NbV, there was evidence that the insects were infected with another small RNA virus. SDS-PAGE and Western analysis revealed two proteins (p56 and p58), that cross-reacted with anti-NbV antibodies. Transmission Electron Microscopy (TEM) analysis showed the presence of particles exhibiting a morphology described for NbV and majority of particles of a diameter of 37 nm. In addition there was a second, minor population of particles with a diameter of 34 nm, which also exhibited the characteristic pitted surface of NßV, raising the possibility of two species of NßV in the N. capensis population. To further investigate this, cDNA corresponding to the 3` end of the replicase gene as well as the entire capsid gene of NbV was synthesized and sequenced. Alignments of the cDNA sequence showed a 99.46 % identity to the published sequence of NbV. Two amino acid substitutions were observed in the capsid coding sequence, one of which was a conservative substitution. Both of these substitutions were found in the b-sandwich domain of the capsid protein. Inspection of the capsid coding sequence showed a second methionine (Met50) at the VCAP amino terminus raising the possibility that p56 might arise from a translation product starting at this site. To investigate this, a full length and truncated capsid coding sequence starting at Met50, were expressed in a baculovirus expression system. VLPs were examined by TEM and Western analysis showed the presence of virus like particles with NßV morphology, but smaller in diameter than the wild-type with an average of 33.33 nm, similar to the smaller particles observed in the virus preparations of NßV. This result supported the hypothesis that NßV translates a smaller coat protein from the second in-frame methionine residue.

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Hodge, Brian Allen. "Occurrence, Diversity, and Impact of Viruses in Ohio." The Ohio State University, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=osu1606307407425512.

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50

Ali, Akhtar. "Pathology and molecular comparison of a range of pea seed-borne mosaic virus isolates." Title page, contents and summary only, 1999. http://web4.library.adelaide.edu.au/theses/09ACP/09acpa398.pdf.

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Copies of author's previously published articles inserted. Bibliography: leaves 128-143. This thesis describes the development of serological and nucleic acid based diagnostic methods for pea-seed borne mosaic virus (PSbMV), the isolation of specific effects on infected pea plants, the collection and biological comparison of new PSbMV isolates from Pakistan, the cloning and sequencing of specific parts of the genome of selected isolates, nucleotide and amino acid sequence comparisons between selected isolates, and the development of a ribonuclease protection assay (RPA) for identifying genomic differences among the PSbMV isolates. It is the first comparison of a range of geographically different isolates of PSbMV on the basis of both biological and molecular properties.

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Dissertations / Theses on the topic 'RNA viruses Plant viruses'

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