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1
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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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.
3
Choudhury, Md Abu Hasnat Zamil. "Population Dynamics of RNA viruses." Thesis, Queensland University of Technology, 2013. https://eprints.qut.edu.au/60866/1/Md._Choudhury_Thesis.pdf.
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Between 50 and 100 million people are infected with dengue viruses each year and more than 100,000 of these die. Dr Choudhury has demonstrated that populations of dengue viruses in individual patients are genetically and functionally very diverse and that this diversity changes significantly at the time of major outbreaks of disease. The results of his studies may inform strategies which will make dengue vaccines far more effective.
4
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.
5
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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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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7
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.
8
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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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.
11
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.
12
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.
13
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.
14
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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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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Repass, John F. "Studies of murine coronavirus cis-acting RNA elements that affect RNA synthesis /." Digital version accessible at:, 2000. http://wwwlib.umi.com/cr/utexas/main.
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17
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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18
Fusaro, Alice. "Evolutionary dynamics of RNA viruses with zoonotic potential." Doctoral thesis, Università degli studi di Padova, 2014. http://hdl.handle.net/11577/3423562.
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RNA viruses with zoonotic potential represent a public health threat throughout the world. High mutation rates, short generation times and large population sizes are three factors responsible for their high genetic variability and enormous adaptive capacity to new environmental conditions. Understanding the genetic properties and the evolutionary dynamics of RNA viruses with zoonotic potential is crucial to prevent, control, treat and lessen the damage to animal and human health.
This thesis investigates the most essential aspects related to the evolution and epidemiology of two widespread zoonotic diseases caused by two RNA viruses: Avian Influenza and rabies. Through the application of bioinformatics tools, I analysed a large amount of sequence data, generated using both first and second generation sequencing technology, from viruses collected during four distinct epidemics: a fox-rabies virus epidemic occurred in north-eastern Italy between 2008 and 2011, highly pathogenic H5N1 avian influenza outbreaks reported in Egypt between 2006 and 2010, and two avian influenza epidemics caused by two distinct subtypes that took place in northern Italy from 1999 to 2001 and 2002 to 2004.
Through phylogenetic and Bayesian phylogeographic analyses of viral sequences sampled over multiple discrete spatio-temporal scales, the studies in this thesis reveal the co-circulation of multiple viral lineages, explore the viral gene flows and investigate the evolutionary dynamics of viruses under different selection pressures. In addition, to better understand the pattern of transmission of viral subpopulations from host to host, the intra-host variability and the evolution of viral pathogenicity, I employed an ultra-deep sequencing approach to assess the diversity of viral populations.
The data generated in this thesis provide important insights into the a) impact and efficacy of surveillance strategies and control measures implemented during an outbreak, b) differences in the evolutionary dynamics and spatial spread between distinct genetic groups, c) emergence of amino acid mutations that may increase viral fitness, d) inter-host transmission of viral variants and e) gain of virulence determinants.
Finally, this thesis shows the great opportunity offered by next generation sequencing technology for dramatic advancement in our understanding of the complicated evolutionary dynamics of these pathogensI virus a RNA con potenziale zoonosico rappresentano una seria minaccia per la salute pubblica a livello mondiale. L’elevato tasso di mutazione, i rapidi tempi di replicazione e le ingenti dimensioni della popolazione sono tre peculiarità all’origine delle potenzialità di questi patogeni in termini di variabilità genetica e capacità di adattamento a diverse condizioni ambientali. Comprendere le caratteristiche genetiche e le dinamiche evolutive dei virus a RNA con potenziale zoonosico è fondamentale al fine di prevenire, controllare, curare e ridurre i danni che provocano alla salute degli animali e dell’uomo. Questa tesi si occupa dello studio dell’epidemiologia e dell’evoluzione molecolare di due zoonosi di origine virale diffuse a livello mondiale: l’influenza aviaria e la rabbia. Un elevato numero di dati genetici, generati con l’utilizzo di tecniche di sequenziamento di prima (sequenziamento Sanger) e seconda (Next Generation Sequencing) generazione, sono stati analizzati mediante l’utilizzo di strumenti bioinformatici. Tali sequenze sono state ottenute da campioni raccolti nel corso di quattro diverse epidemie: un’epidemia di rabbia silvestre verificatasi nel nord-est Italia tra il 2008 e il 2011, focolai epidemici di influenza aviaria causati dal sottotipo H5N1 ad alta patogenicità descritti in Egitto tra il 2006 e il 2010, e due ondate epidemiche provocate da due diversi sottotipi influenzali aviari H7N1 e H7N3 che hanno colpito l’Italia settentrionale nei periodi 1999 - 2001 e 2002 - 2004. Attraverso l’analisi filogenetica e filogeografica di sequenze virali rappresentative a livello spazio-temporale delle varie epidemie, è stato possibile identificare la co-circolazione di diversi gruppi genetici, determinare il flusso genico e studiare le dinamiche evolutive di virus sottoposti a pressioni selettive di varia natura, come ad esempio la vaccinazione. Inoltre, grazie all’applicazione di un approccio di tipo deep sequencing, questo studio ha permesso di comprendere meglio i meccanismi di trasmissione delle sottopopolazioni virali da un ospite all’altro, la variabilità intra-ospite della popolazione virale e l’evoluzione della patogenicità. I risultati presentati in questa tesi permettono di ampliare le nostre conoscenze a) sull’impatto e l’efficacia delle misure di sorveglianza e controllo applicate nel corso delle epidemie studiate, b) sulle dinamiche evolutive e sulla diffusione spaziale di virus appartenenti a diversi gruppi genetici, c) sull’emergenza di mutazioni amminoacidiche potenzialmente correlate a un aumento della fitness virale, d) sulla trasmissione a livello inter-ospite di varianti virali e e) sull’acquisizione di determinanti di virulenza. Infine, il presente studio evidenzia le enormi potenzialità della tecnologia di Next Generation Sequencing nel favorire la comprensione delle complicate dinamiche evolutive dei patogeni emergenti
19
Upton, John H. "The role of RNA secondary structure in replication of Nodamura virus RNA2." 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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Croci, R. "RNA DEPENDENT RNA POLYMERASE: A VALUABLE TARGET TO BLOCK VIRAL REPLICATION IN SINGLE-STRANDED (+)SENSE RNA VIRUSES." Doctoral thesis, Università degli Studi di Milano, 2014. http://hdl.handle.net/2434/243352.
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The (+)strand RNA viruses include a very large group of viruses that cause epidemic diseases in humans, including dengue fever and gastroenteritis. The human (+)RNA viruses include Flaviviruses (FV) and Norovirus (NV). Both encode for proteins essential for viral replication, such as the RNA dependent RNA polymerase (RdRp). Since human cells lack RdRp, it appears as one of the most promising targets for antivirals development. I worked on the identification of new non-nucleotide inhibitors against FV and NV, using RdRp as the main target. In this context, suramin and NF023 have been identified in my lab as NV RdRp inhibitors that, however both are hampered in their application by pharmacokinetics problems. To overcome such problems, I analyzed the potential inhibitory role of Naf2, a fragment derived from these two molecules. Although Naf2 showed a low inhibitory activity, the crystal structures of NV RdRp/Naf2 complex revealed a new binding site. To further map this new site, I tested a Naf2 related molecule, PPNDS. The crystal structures of the RdRp/PPNDS complex revealed interesting features about the new binding site. I also focused on structurally related molecules synthesized following structure-driven information. NV RdRp crystal structures in complex with one of these compounds (Cpd6) were analyzed, providing new knowledge on the interactions between a small fragment and NV RdRps, establishing a platform for structure-guided drug optimization. In parallel to the NV work, I screened in silico a library of compounds against FV RdRp. One of the best compounds identified (HeE1-2Tyr) was able to inhibit the RdRp activity and several FVs in cell-based assays. Although the crystallographic analyses don't reveal clear enough electron density for the inhibitor, indirect evidence suggests that HeE1-2Tyr interferes with the RdRp priming loop that appears disordered.
21
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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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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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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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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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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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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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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Wang, Andrew C. "Recombination of Two RNA Viruses: Red Clover Necrotic Mosaic Virus and Carnation Ringspot Virus." Thesis, The University of Arizona, 2010. http://hdl.handle.net/10150/146250.
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In this research project, two plant RNA viruses, Red clover necrotic mosaic virus (RCNMV) and Carnation Ringspot Virus (CRSV) were studied and two recombinants were created using RNA1 of RCNMV and RNA2 of CRSV (R1+C2) for one recombinant and RNA2 of RCNMV and RNA1 of CRSV (C1+R2) for the other recombinant. Nicotiana clevelandii and Nicotiana benthamiana were inoculated with the wild types and the two recombinants. The tissues of the plants were extracted for total RNA and a reverse transcription polymerase chain reaction was performed on the total RNA. Using specific primers, the RCNMV wild type from the 12/1/09 total RNA extraction showed the presence of both R1 and R2, while the CRSV wild type from the 12/1/09 total RNA extraction also showed the presence of both C1 and C2. The recombinant C1+R2 from the 12/8/09 total RNA extraction showed the presence of both C1 and R2 and the recombinant of R1+C2 from the 12/1/09 total RNA extraction also showed the presence of both R1 and C2. The next step in this study would be to clone the terminal ends to find out where exactly recombination occurs.
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Talló, Parra Marc 1992. "Circular RNAs : from host RNA molecules to novel broad-spectrum antivirals." Doctoral thesis, Universitat Pompeu Fabra, 2019. http://hdl.handle.net/10803/668309.
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La rellevància clínica dels virus transmesos per mosquits, com el virus del dengue (DENV), el virus del zika (ZIKV), el virus del chikungunya (CHIKV) i el virus del Nil Occidental (WNV), ha augmentat dràsticament durant els darrers anys, provocant un problema de salut global. Actualment, no hi ha cap tractament disponible ni cap vacuna efectiva per tractar aquestes infeccions. Tots aquests virus causen infeccions agudes que han de ser tractades ràpidament després de l’aparició dels símptomes inicials perquè els medicaments siguin efectius. Tot i això, el diagnòstic precoç continua sent un repte no resolt. Això evidencia la necessitat de descobrir noves interaccions essencials entre el virus i la cèl·lula que podrien ser utilitzades com a noves dianes terapèutiques; i la necessitat de desenvolupar teràpies antivirals d’ampli espectre, eficients, que puguin ser administrades abans que s’aconsegueixi un diagnòstic precís. En aquesta tesi hem abordat aquests dos grans problemes centrant-nos en els ARNs circulars (circRNAs).
Els circRNAs són una classe d’ARN generats a partir de progenitors lineals d'ARN mitjançant un mecanisme alternatiu de splicing anomenat back-splicing. En comparació amb els seus homòlegs lineals, els circRNAs són molt estables a causa de la seva resistència a les exonucleases. Actualment, s’ha descrit la implicació dels circRNAs en les infeccions virals, tanmateix, no es coneix el seu rol precís. El primer capítol de la tesi intenta respondre a aquest buit de coneixement utilitzant el virus de l’hepatitis C (HCV) com a sistema model i analitza l'efecte dels circRNAs identificats en altres virus de la mateixa família, en concret, els virus transmesos per mosquits. Mitjançant anàlisis de seqüenciació d’ARN, hem identificat 73 circRNAs cel·lulars induïts pel HCV. Aquest canvi en l’expressió dels circRNAs no pot ser explicat a través de canvis paral·lels en els ARNs lineals. A més a més, hem identificat que el silenciament de cinc d’aquests circRNAs provoca canvis en la infectivitat viral, actuant com a molècules pro- o anti- virals. Un d’aquests circRNAs, cPSD3, és clau per a la infectivitat del virus del dengue.
El segon capítol de la tesi se centra en desenvolupament d’una nova plataforma basada en circRNAs que sigui versàtil, dificulti l’aparició de mutants resistents i permeti desenvolupar antivirals d’ampli espectre. En contrast amb altres teràpies basades en ARN, els circRNAs són molècules altament estables, una característica que simplificarà el seu ús terapèutic. Els circRNAs sintètics dissenyats contenen seqüències llargues que s’hibriden a regions del genoma viral implicades en formar estructures d’RNA essencials per a la supervivència del virus. Com a prova de concepte, hem validat amb èxit circRNAs que inhibeixen el HCV, el DENV, el CHIKV o el WNV. A més, hem generat circRNAs amb capacitat antiviral d’ampli espectre i hem optimitzat la producció in vitro d’aquestes molècules per obtenir quantitats elevades a baix preu.
En conclusió, els nostres resultats (i) emfatitzen la complexitat de la interacció entre els circRNAs cel·lulars i els virus i (ii) descobreixen el gran potencial dels circRNAs artificials com a noves plataformes per al desenvolupament de fàrmacs.The clinical importance of the mosquito-borne viruses, such as dengue virus (DENV), zika virus (ZIKV) chikungunya virus (CHIKV) and West Nile virus (WNV), has dramatically increased over the last years, resulting in a global health problem. Currently, there are no available treatments or effective vaccines to treat these infections. All these viruses produce acute infections that require to be treated early after the onset of the symptoms for drugs to be effective. However, an early diagnosis remains still as an unsolved challenge. This brings to the spotlight the need to uncover novel fundamental virus-cell interactions that could be targeted and to develop efficient broad-spectrum antiviral therapies that could be administered before an accurate diagnosis is achieved. In this thesis we addressed these two major concerns with a focus in circular RNAs (circRNAs). CircRNAs are a class of RNAs generated from linear RNA progenitors by an alternative splicing mechanism termed back splicing. They are highly stable relative to their linear spliced counterparts due to exonuclease resistance. Currently, cellular circRNAs are described to be involved in viral infections. However, their precise role is mainly unknown. The first chapter of the thesis addresses this intriguing issue using HCV as a model system and analyzing the effect of the identified circRNAs in mosquito-borne viruses that belong to the same viral group. By RNA-Seq analyses we identified 73 HCV-differentially expressed circRNAs whose changes could not be explained by parallel changes in linear mRNAs. Silencing of five selected HCV-induced up-regulated circRNAs altered viral infectivity, acting either as anti-viral or pro-viral molecules. Further characterization of one of the selected circRNAs, cPSD3, show, that it also impaired DENV infections. The second chapter focuses on the generation of a novel circRNA-based platform that is versatile, hampers the emergence of resistant mutants, and allows developing broad-spectrum antivirals. In contrast to other RNA-based therapies, circRNAs are highly stable molecules, a trait that will simplify their therapeutic use. The designed synthetic circRNAs contain long sequences that hybridize to multiple target sequences in the viral RNA genome involved in forming RNA structures essential for virus survival. As a proof of concept, we have successfully validated circRNAs that inhibit HCV, DENV, CHIKV or WNV. Furthermore, we have generated circRNAs with broad-spectrum antiviral capacity and optimized the production in vitro of these molecules to obtain high amounts at low price. In conclusion, our results (i) emphasize the complexity of the interaction between cellular circRNAs and viruses and (ii) uncover the great potential of artificial circRNAs as novel platforms for drug development.
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Killip, Marian J. "RNA virus modulation of IFN, PI3K and apoptosis." Thesis, St Andrews, 2009. http://hdl.handle.net/10023/777.
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Phosiwa, Maanda Noaxe. "Molecular characterization of a porcine picobirnavirus RNA-dependent RNA polymerase." Diss., Pretoria : [s.n.], 2009. http://upetd.up.ac.za/thesis/available/etd-07152009-175205/.
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Ford, Robert John. "The roles of RNA in the assembly and disassembly of single-stranded RNA icosahedral viruses." Thesis, University of Leeds, 2012. http://etheses.whiterose.ac.uk/4135/.
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Single-stranded, positive-sense icosahedral viruses are major pathogens in every kingdom of life. Despite this, their capsid assembly and uncoating mechanisms remain poorly understood. This work describes these processes in two model systems; satellite tobacco necrosis virus and turnip crinkle virus. For satellite tobacco necrosis virus, several aptamers were previously raised against the coat protein, where each aptamer folded into stem-loops displaying the motif AXXA. Aptamer B3 contained the strongest sequence similarity to the cognate genome, including a 10/10 contiguous stretch. Capsid assembly using the purified coat protein shows that RNA is critical for capsid assembly, and that stem-loops displaying the motif AXXA can efficiently trigger this process. There is a clear preference for this loop motif, which is unaffected by the sequence of the base paired stem. The structure of the B3-encapsidated virus-like particle has been solved by X-ray crystallography to 2.3 Å, together with a lower resolution map encompassing the RNA. The presence of B3 results in an extension of the N-terminal helices by roughly one and a half turns, such that residues 8-11 that are disordered in all previous X-ray structures are now visualised, including R8 and K9. The binding of B3 facilitates charge neutralisation and trimer formation in the coat protein, resulting in the assembly of a T=1 capsid. This assembly mechanism is consistent with additional assembly studies using longer RNAs, in which the first step in assembly is genomic compaction. This compaction event is driven by multiple binding events of coat proteins with packaging signals in the form of stem-loops displaying the preferred loop sequence. In turnip crinkle virus, a putative disassembly mechanism has been suggested. Expansion and proteolysis mediates extrusion of the viral genome, such that the formation of “striposomes”, which are thought to be polysomal arrays of ribosomes on extruding RNA, can be visualised by TEM. Purification of proteolysed capsids revealed that the cleaved coat proteins become dissociated and the remaining protein shells lose their icosahedral symmetry, often appearing to begin release of RNA from unique sites in the absence of ribosomes. These results explain why coat proteins are essential for wild-type infections because they facilitate a ribosome-mediated uncoating mechanism avoiding host RNA silencing. The results in this thesis suggest new paradigms for capsid assembly and uncoating, which may be exploited by other members of the same family of viruses, especially those having similar coat protein folds.
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Treutler, Eva [Verfasser], and Peter [Akademischer Betreuer] Beyer. "Untersuchungen zur Isolierung von eps-RNA-Polymerase-Komplexen des Hepatitis-B-Viruses durch RNA-Affinitätsreinigung." Freiburg : Universität, 2012. http://d-nb.info/1123472637/34.
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Wright, Sam Mathew. "Structural and biophysical studies of RNA-dependent RNA polymerases." Thesis, University of Oxford, 2010. http://ora.ox.ac.uk/objects/uuid:d5c2a16d-e1e2-4c22-aca5-70f72aa96853.
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RNA-dependent RNA polymerases (RdRps) play a vital role in the life cycle of RNA viruses, being responsible for genome replication and mRNA transcription. In this thesis viral RdRps (vRdRps) of dsRNA bacteriophage phi6 (phi6 RdRp) and Severe Acute Respiratory Syndrome (SARS) coronavirus [non structural protein 12 (NSP-12)] are studied. For SARS polymerase NSP-12, a library-based screening method known as ESPRIT (Expression of Soluble Protein by Random Incremental Truncation) was employed in an attempt to isolate domains of NSP-12 that express solubly in Escherichia coli (E. coli) and are thereby suitable for structural studies. This experiment identified for the first time in a systematic fashion, conditions under which the SARS polymerase could be solubly expressed at small scale and allowed mapping of domain boundaries. Further experiments explored different approaches for increasing expression levels of tractable fragments at large scale. Bacteriophage phi6 RdRp is one of the best studied vRdRps. It initiates RNA synthesis using a de novo mechanism without the need for a primer. Although formation of the de novo initiation complex has been well studied, little is known about the mechanism for the transition from initiation to elongation (i.e. extension of an initiated dinucleotide daughter strand). In the phi6 RdRp initiation complex the C-terminal domain (CTD) blocks the exit path of the newly synthesised dsRNA which must be displaced for the addition of the third nucleotide. The crystal structure of a C-terminally truncated phi6 RdRp (P2T1) reveals the strong non-covalent interactions between the CTD and the main body of the polymerase that must be overcome for the elongation reaction to proceed. Comparing new crystal structures of complexes of both wild-type (WT) and a mutant RdRp (E634 to Q, which removes a salt-bridge between the CTD and main body of the polymerase) with various oligonucleotides (linear and hairpin), nucleoside triphosphates (NTPs) and divalent cations, alongside their biophysical and biochemical properties, provides an insight into the precise molecular details of the transition reaction. Thermal denaturation experiments reveal that Mn2+ acquired from the cell and bound at the phi6 RdRp non-catalytic ion site sufficiently weakens the polymerase structure to facilitate the displacement of the CTD. Our crystallographic and biochemical data also indicate that Mn2+ is released during this displacement and must be replaced for the elongation to proceed. Our data explain the role of the non-catalytic divalent cation in vRdRps and pinpoint the Mn2+-dependent step in viral replication. In addition, by inserting a dysfunctional Mg2+ at the non-catalytic ion site for both WT and E634Q RdRps we captured structures with two NTPs bound within the active site in the absence of Watson-Crick base pairing with template and could map movements of divalent cations during preinitiation through to initiation. Oligonucleotides present on the surface of phi6 RdRp allowed mapping of key residues involved in template entry and unwinding of dsRNA; these preinitiation stages have not been observed previously. Considering the high structural homology of phi6 RdRp with other vRdRps, particularly from (+)ssRNA hepatitis C virus (HCV), insights into the mechanistic and structural details of phi6 RdRp are thought to be relevant to the general understanding of vRdRps.
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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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Worobey, Michael. "The occurrence and impact of viral recombination." Thesis, University of Oxford, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.249612.
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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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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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Bamford, Anona Isabelle. "Interactions between cytotoxic effector cells and bovine parainfluenza type 3 virus." Thesis, Queen's University Belfast, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.241326.
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Williams, Claire Amy. "The role of RNA helicases in HIV-1 replication." Thesis, University of Cambridge, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.610047.
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McCauley, Sephen Jude. "The annotation and evolutionary analysis of overlapping CDS in ssRNA viral genomes." Thesis, University of Oxford, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.670151.
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Palasingam, Kampan. "Homologous Recombination in Q-Beta Rna Bacteriophage." Thesis, University of North Texas, 1992. https://digital.library.unt.edu/ark:/67531/metadc500683/.
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Q-Beta phage RNAs with inactivating insertion (8 base) or deletion (17 base) mutations within their replicase genes were transfected into Escherichia coli spheroplasts containing QB replicase provided in trans by a resident plasmid. Replicase-defective (Rep~) Q3 phage produced by these spheroplasts were unable to form plaques on cells lacking this plasmid. When individual Rep~ phage were isolated and grown to high titer in cells containing plasmid derived Q3 replicase, revertant Q3 phage (Rep'), with the original mutation (insertion or deletion) repaired, were obtained at a frequency of ca. 1 x 108. RNA recombination via a "template switching" mechanism involving Q3 replicase, the mutant phage genome, and the plasmid-derived replicase mRNA was shown to be the primary means by which these mutant phages reverted to wild type.
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Dudas, Gytis. "Inference of evolutionary and ecological processes from reticulate evolution in RNA viruses." Thesis, University of Edinburgh, 2016. http://hdl.handle.net/1842/20442.
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RNA viruses have the fastest evolutionary rates amongst protein-coding organisms on the planet. Ease of sequencing, advanced techniques of analysis and global health and economic concerns have all contributed to the recognition of RNA viruses as a robust research platform. Phylogenetic methods have been at the forefront of analytical techniques used to understand the dynamics of RNA viruses - during natural circulation in populations and in individual hosts, within epidemics, across species barriers and over billions of years that viruses have been around. Most of the work presented in this thesis employs phylogenetic incongruity arising from reassortment and recombination to gain insights into the genomes and populations of RNA viruses. Chapter 2 explores the selection regimes Ebola virus has experienced following a year of circulation in humans inWest Africa, as well as its recent history. Chapter 3 investigates the extent of recombination in MERS-CoV, a novel human pathogen with an obscure epidemiology, which is suggestive of frequent co-infection of some hosts. Chapter 4, on the other hand, documents a pattern of non-intuitive linkage between some segments of the human-endemic influenza B virus genome and explores its potential to speciate. Chapter 5 builds upon chapter 4 and attempts to describe small-scale reassortment between two segments of influenza B virus and the overall migration patterns of influenza B virus in Scotland. Chapter 6 exploits the independence of segments of influenza D virus, a recently described cattle pathogen, and coalescent theory to disentangle the origins of this virus. This thesis exemplifies the success of modern sequencing methods, which, together with the use of sophisticated analytical techniques, have uncovered a wealth of information hidden away in molecular sequences of RNA viruses. The work presented herein demonstrates how reticulate evolution can be exploited as a reliable, and sometimes indispensable, marker to improve inference of evolutionary forces in RNA viruses.
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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’ADNMosquitoes 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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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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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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Williams, Rhys Harold Verdon George. "Further studies on the structure and function of the cucumber mosaic virus genome : a thesis submitted to the University of Adelaide, South Australia for the degree of Doctor of Philosophy." 1988, 1988. http://web4.library.adelaide.edu.au/theses/09PH/09phw7261.pdf.
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Hengrung, Narin. "Structure of the RNA-dependent RNA polymerase from influenza C virus." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:694e16a6-f94e-4375-a1f9-7e250aea7343.
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The influenza virus causes a disease that kills approximately 500,000 people worldwide each year. Influenza is a negative-sense RNA virus that encodes its own RNA-dependent RNA polymerase. This protein (FluPol) carries out both genome replication and viral transcription. Therefore, like the L-proteins of non-segmented negative-sense RNA (nsRNA) viruses, FluPol also contains mRNA capping and polyadenylation functionality. In FluPol, capping is achieved by snatching cap structures from cellular mRNAs, so requiring cap-binding and endonuclease activities. This makes FluPol a substantial machine. It is a heterotrimeric complex, composed of PB1, PB2 and PA/P3 subunits, with a total molecular weight of 255 kDa. PB1 houses the polymerase active site, whereas PB2 and PA contain, respectively, cap-binding and endonuclease domains. Currently, we only have high resolution structural information for isolated fragments of FluPol. This severely hampers our understanding of influenza replication and consequently inhibits the development of therapies against the virus. In this DPhil project, I have determined a preliminary structure for the heterotrimeric FluPol of influenza C/Johannesburg/1/66, solved by x-ray crystallography to 3.6 Å. Overall, FluPol has an elongated structure with a conspicuous deep groove. PB1 displays the canonical right-hand-like polymerase fold. It sits at the centre of the particle, sandwiched between the two domains of P3, and with PB2 stacked against one side of this dimer. In the structure, the polymerase and endonuclease catalytic sites are both ~40 Å away from the cap-binding pocket. This pocket also faces a tunnel leading to the polymerase core. This suggests a mechanism for how capped cellular mRNAs are cleaved and then fed into the polymerase active site to prime transcription. The structure also hints at a unique trajectory for template RNA, in which the RNA exits at an angle ~180° from which it came in. This provides an explanation for how the polymerases of influenza, and other nsRNA viruses, can copy templates that are packaged into ribonucleoprotein complexes. My work reveals the first molecular structure of any polymerase from an nsRNA virus. It uncovers the arrangement of functional domains within FluPol, illuminating the mechanisms of this and related viral polymerases. This work will help focus future experiments into FluPol biology, and should hopefully spur the development of novel antiviral drugs.
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Liu, Chunyu. "Quinic Acid-Mediated Induction of Hypovirulence and a Hypovirulence-Associated Double-Stranded RNA in Rhizoctonia Solani." Fogler Library, University of Maine, 2001. http://www.library.umaine.edu/theses/pdf/LiuC2001.pdf.
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Rajendran, KS. "Dissecting the functions of carmovirus replicase proteins dissecting the functions of carmovirus tombusvirus replicase proteins dissecting." Lexington, Ky. : [University of Kentucky Libraries], 2004. http://lib.uky.edu/ETD/ukyplpa2004d00150/Rajendra.pdf.
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Thesis (Ph. D.)--University of Kentucky,2004.Title from document title page (viewed Oct. 12, 2004). Document formatted into pages; contains ix, 111 p. : ill. Includes abstract and vita. Includes bibliographical references (p. 97-110).