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1
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.
2
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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Najmabadi, Hossein. "Characterization of the Self-Replicating Kirsten Murine Leukemia Viral DNA: Replication and Tetracycline Resistance". Thesis, University of North Texas, 1989. https://digital.library.unt.edu/ark:/67531/metadc798479/.
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This research project deals with the characterization of self-replicating Kirsten murine viral DNA. The replication of this viral DNA and tetracycline resistance conferred to bacteria by this viral DNA will be studied. The restriction endonuclease and Southern blot analysis revealed a fragment of pBR322 from the Hind III and Pst I site that is located in the 3' end of the MLV-K:E molecule. Single stranded sequencing of the two terminal ends of this fragment verified that the 3' end of MLV-K:E contains identical sequence homology to pBR322. The presence of this pBR322 fragment explains the unusual properties of the MLV-K:E molecule. However, tetracycline resistance is less in E. Coli containing MLV-K:E than E. coli containing pBR322 as determined by zone of inhibition assay. This may be due to alteration in the promoter region of the tetracycline gene.
4
Yip, Chi-wai, i 葉志偉. "Characterization of the cell entry mechanism of infectious bursal disease virus". Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2010. http://hub.hku.hk/bib/B44756306.
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Ong, Jamie. "In bed with viruses: The partnership between orchids, fungi and viruses". Thesis, Ong, Jamie (2016) In bed with viruses: The partnership between orchids, fungi and viruses. PhD thesis, Murdoch University, 2016. https://researchrepository.murdoch.edu.au/id/eprint/37275/.
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The Orchidaceae is the largest and most diverse angiosperm family comprising of five subfamilies, over 800 genera and over 26,000 species. In Western Australia, there are over 450 indigenous orchid species across 40 genera, concentrated predominately within the South West Australian Floristic Region, but with a few species in the tropical Kimberley. The southern species are all terrestrial and most belong to the Diurideae tribe, which are primarily restricted to Australia and New Zealand. To varying degrees, orchids rely on associations with other organisms, particularly fungi for nutrient provision and insects for pollination. The partnerships between the orchids, their fungal symbionts and insect pollinators are quite well studied in some cases. However, the ecological influence of viruses, in particular indigenous viruses, within these symbiotic partnerships remains largely unexplored. Orchids cultivated for their flowers or vanilla are frequently infected by viruses, which are spread from plant to plant by vectors, husbandry tools and through vegetative propagation, and from place to place in infected propagules by trade. Only recently have wild orchids been shown to also harbour viruses.
In this research, we used a combination of high throughput sequencing approach, traditional techniques and informatics to examine the leaf tissues of indigenous terrestrial orchid plants growing in their natural habitats for virus infection. Further, we isolated fungi that form mycorrhizal associations within cortical root cells of these plants and examined them for the presence of viruses. Terrestrial orchids and their fungal symbionts were sampled from 17 species across six genera (Caladenia, Diuris, Drakaea, Microtis, Paraceleana and Pterostylis) during the winter (June to August) and spring (September to November) growing seasons. This study represents the first of viruses from the indigenous orchids and fungal species examined.
Thirty-two viruses, representing seven viral families and eight genera (Alphapartitivirus, Betapartitivirus, Endornavirus, Goravirus, Hypovirus, Mitovirus, Platypuvirus and Totivirus), were identified and characterised from wild plants of Drakaea, Microtis and Pterostylis orchids and their fungal symbionts. Four of the viruses were identified from leaves of Drakaea species and Pterostylis sanguinea orchids and the remaining 28 viruses were from six isolates of orchid mycorrhizal fungi of the genus Ceratobasidium. All but one of the viruses found were novel, and most were from taxonomic groups not previously described in the Australian continent.
In three Ceratobasidium isolates studied, there were 5-13 virus species present in each. The presence of several closely-related bi-partite partitiviruses within the one host presented challenges in determining the numbers of species present and accurate pairing of virus segments. This study proposes solutions to address these problems, which will no doubt also arise in future metagenomics studies.
Two of the new viruses described formed the bases of new genera (Goravirus and Platypuvirus), while other viruses could be tentatively classified within known taxa, but were often genetically divergent from existing members. For example, two novel partitiviruses represent a lineage basal to existing members of Alphapartitivirus, pointing to Australia as an important location in partitivirus evolution. The richness and uniqueness of viruses found in this study are likely a reflection of the orchid and fungal diversity of the region, itself a consequence of over 25 million years of relative geological and climatic stability. The surprisingly high numbers of mycoviruses detected from only a few fungal samples indicate that there is a rich virus association with fungal component of orchid biology and that orchid flora might represent a potentially enormous reservoir of novel viruses. geological and climatic stability. The surprisingly high numbers of mycoviruses detected from only a few fungal samples indicate that there is a rich virus association with fungal component of orchid biology and that orchid flora might represent a potentially enormous reservoir of novel viruses.
6
Griffin, Jennifer Shoener. "Torque Teno Virus: A Potential Indicator of Enteric Viruses". Worcester, Mass. : Worcester Polytechnic Institute, 2009. http://www.wpi.edu/Pubs/ETD/Available/etd-031509-151117/.
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Thesis (M.S.)--Worcester Polytechnic Institute.Keywords: cell culture; PCR; coliphage; coliform; fecal indicator; enteric virus; waterborne disease outbreak; TTV; torque teno virus. Includes bibliographical references (leaves 96-117).
7
Chan, Yuk-on. "Impact of respiratory viruses on mortality". Click to view the E-thesis via HKUTO, 2005. http://sunzi.lib.hku.hk/hkuto/record/b39724025.
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Del, Valle Mendoza Juana, Tapia Ángela Cornejo, Pablo Weilg, Eduardo Verne, Fuertes Ronald Nazario, Claudia Ugarte, Valle Luis J. del i Toma´ s. Pumarola. "Incidence of Respiratory Viruses in Peruvian Children With Acute Respiratory Infections". John Wiley & Sons, 2015. http://hdl.handle.net/10757/347016.
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jdelvall@upc.edu.peAcute respiratory infections are responsible for high morbi–mortality in Peruvian children. However, the etiological agents are poorly identified. This study, conducted during the pandemic outbreak of H1N1 influenza in 2009, aims to determine the main etiological agents responsible for acute respiratory infections in children from Lima, Peru. Nasopharyngeal swabs collected from 717 children with acute respiratory infections between January 2009 and December 2010 were analyzed by multiplex RT-PCR for 13 respiratory viruses: influenza A, B, and C virus; parainfluenza virus (PIV) 1, 2, 3, and 4; and human respiratory syncytial virus (RSV) A and B, among others. Samples were also tested with direct fluorescent-antibodies (DFA) for six respiratory viruses. RT-PCR and DFA detected respiratory viruses in 240 (33.5%) and 85 (11.9%) cases, respectively. The most common etiological agents were RSV-A (15.3%), followed by influenza A (4.6%), PIV-1 (3.6%), and PIV-2 (1.8%). The viruses identified by DFA corresponded to RSV (5.9%) and influenza A (1.8%). Therefore, respiratory syncytial viruses (RSV) were found to be the most common etiology of acute respiratory infections. The authors suggest that active surveillance be conducted to identify the causative agents and improve clinical management, especially in the context of possible circulation of pandemic viruses
9
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
10
Bieker, Jill M. "Chemical inactivation of viruses". Diss., Manhattan, Kan. : Kansas State University, 2006. http://hdl.handle.net/2097/226.
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Liu, X. Q. (Xingquan). "Differentiation of garlic viruses". Thesis, McGill University, 1985. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=63286.
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Thomas, Joanne Marie. "Assembly of influenza viruses". Thesis, University of Reading, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.326757.
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Hale, Benjamin G. "Influenza A viruses and PI3K signalling /". St Andrews, 2008. http://hdl.handle.net/10023/483.
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Pulford, David J. "Expression of porcine transmissible gastroenteritis virus genes with recombinant viruses". Thesis, University of Reading, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.305024.
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Ngamyeesoon, Nualphan. "Studies of viruses and virus-like agents infecting woody ornamentals". Thesis, University of Bath, 1989. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.329558.
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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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Davis, Adam James. "Transcriptional analysis of human immunodeficiency virus type 1 infection following cell-to-cell transmission /". Title page, contents and abstract only, 1997. http://web4.library.adelaide.edu.au/theses/09PH/09phd2609.pdf.
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Chan, Yuk-on, i 陳旭安. "Impact of respiratory viruses on mortality". Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2005. http://hub.hku.hk/bib/B39724025.
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Yama, Ninon Ines. "Viruses in rodents : from field work to virus discovery and characterization". Thesis, Aix-Marseille, 2012. http://www.theses.fr/2012AIXM5037.
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Les maladies émergentes représentent actuellement 65% de toutes les pathologies infectieuses récentes. Récemment, un nombre croissant de nouveaux virus a été associé à de petits mammifères terrestres, plus particulièrement à des rongeurs, désignant ce groupe comme étant l'une des possibles sources de dangereuses pathologies émergentes et ré-émergentes. Actuellement, la réaction en chaîne par polymérase (PCR) est l'outil principal utilisé pour la détection d'agents pathogènes dans la diagnostique de routine et dans la recherche. Or, plusieurs recherches ont montré que certaines substances inhibent la PCR, causant de faux résultats. Aussi, nous avons lancé un programme de capture de rongeurs pour le dépistage de virus connus et non identifiés. Au total 1441 rongeurs ont été capturés pendant des campagnes organisées en Europe et Afrique entre 2002 et 2011. Tout d'abord, nous avons examiné l'inhibition de la PCR et étudié les différentes techniques de traitement d'échantillons qui favorisent la réduction de la quantité d'inhibiteurs dans les échantillons de rongeurs. Parmi les techniques d'extraction évaluées, l'EZ1 virus mini kit et le réactif d'extraction RNAnow se sont avéré plus efficaces que le NucleoSpin virus kit ou le réactif d'extraction TRIzol. De même, l'utilisation des poumons et de reins était préférable à l'utilisation du foie et de la rate. Aucune différence significative n'a été observée entre le stockage à -80°C et le stockage dans le réactif RNAlater. Nous avons conduit le dépistage des virus, en utilisant les tests moléculaires et la culture cellulaire. Deux nouvelles souches de virus ont été isolées, séquencées et caractériséesEmerging diseases currently represent 65% of recent major disease outbreaks. Of them, 75% are associated with wildlife. Recently, an increasing number of newly discovered viruses have been associated with small terrestrial mammals, particularly with rodents, pointing at this group as one of the most dangerous potential sources of emerging or re-emerging diseases. To meet these challenges for public health, a proper surveillance becomes necessary, which passes by detection of pathogens in human and risky groups of animals, including field investigations. Yet this can be achieved only by using proper techniques of samples treatment and pathogen detection. Currently, polymerase chain reaction (PCR) is the main tool used for the detection of pathogens in routine diagnostic and research. Yet, several researches showed that some substances can inhibit PCR, causing false-negative results. Therefore, we initiated a screening program targeting rodents for the presence of known and unidentified viruses. A total of 1441 rodents were trapped during field campaigns organized in Europe and Africa, between 2002 and 2011. At first we investigated on PCR inhibitors and discussed techniques of treatment of samples allowing reducing the influence of inhibitors in rodent samples. Among the extraction techniques tested, EZ1 virus mini kit and RNAnow extraction reagent were more effective than NucleoSpin virus kit or TRIzol extraction reagent. Also, the use of lungs and kidneys was preferable to the use of liver and spleen, the quantity of inhibitors being higher in the last two organs. No significant difference was observed between storage at -80°C, or in RNAlater RNA stabilization reagent
20
Nagano, Hideaki. "Studies on Plant-Virus Cell-to-Cell Movement Using Chimeric Viruses". Kyoto University, 2000. http://hdl.handle.net/2433/78105.
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Kyoto University (京都大学)0048
新制・課程博士
博士(農学)
甲第8438号
農博第1122号
新制||農||801(附属図書館)
学位論文||H12||N3395(農学部図書室)
UT51-2000-F342
京都大学大学院農学研究科農林生物学専攻
(主査)教授 古澤 巌, 教授 泉井 桂, 教授 津田 盛也
学位規則第4条第1項該当
21
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.
22
Wang, Yuan Min. "In vivo and in vitro dynamics of HIV-1 in patients with and without antiretroviral treatment". Thesis, The University of Sydney, 2002. https://hdl.handle.net/2123/27848.
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Highly active antiretroviral therapy (HAART) successfully reduces plasma levels of HIV-1 RNA and improves the quality of life for HIV-infected patients. However, these clinical benefits may be limited by the emergence of multiple drug- and cross drug resistance in HIV-1, and also by the concealment of these viral variants in other sanctuary sites such as
tissues, brain, lung and other blood cell types. Furthermore, the persistence of HIV reservoirs, including latently infected resting CD4 cells, brain, lymph tissue, bone marrow and genital tract, have posed a challenge to the long—term control or eradication of HIV infected patients received HAART. To determine the effect of HAART on the distribution
of viral variants, drug resistance variants, co-receptor surface expression and co—receptormediated viral entry in treated and untreated patients, we have carried out a detailed longitudinal and a comparative study on 6 seroconverters receiving HAART, in addition to 6 antiretroviral naive patients, and four patients receiving structured treatment interruption (STI). All treated patients were followed for 26 to 36 months from the initiation of HAART. In this study we have compared the interrupted and non-interrupted HAART patients to analyze the overall molecular, biological and cellular receptor dynamics over time, and highlight the advantages and disadvantages of the two therapies.
23
Plevka, Pavel. "Structure of Small Icosahedral Viruses". Doctoral thesis, Uppsala universitet, Strukturell molekylärbiologi, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-99933.
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This thesis presents structural studies on the plant virus Ryegrass mottle virus (RGMoV), the bacteriophage φCb5, and the icosahedral particles and octahedral crystal assembly of a bacteriophage MS2 coat protein mutant. In contrast to other sobemoviruses, the RGMoV coat protein is missing several residues in two of the loop regions important for capsid assembly. The first loop contributes to contacts between subunits around the quasi-three fold symmetry axis. The altered contact interface results in tilting of the subunits towards the quasi-threefold axis. The assembly of the T=3 capsid of sobemoviruses is controlled by the N-termini of the C subunits. The second and smaller RGMoV loop does not interact with the N-terminus of the C subunit as do the corresponding loops of other sobemoviruses. The loss of interaction has been compensated for by additional interactions between the N-terminal arms of RGMoV C subunits. The bacteriophage MS2 belongs to the Leviviridae family of small RNA phages. Covalent dimers of the coat protein with insertions in the surface loops are known to be highly immunogenic epitope carriers. We crystallized the icosahedral particle assembled from covalent coat protein dimers in space group P213. At 4.7Å resolution the structure resembles the wildtype MS2 virion except for the intersubunit linker regions. The covalent dimer also crystallized in the cubic space group F432. The organization of the asymmetric unit in combination with the F432 symmetry results in an arrangement of subunits that corresponds to T=3 octahedral particles. Our crystal structure of the bacteriophage φCb5 capsid showed that it is stabilized by four calcium ions per icosahedral asymmetric unit. One ion is located between the quasi-threefold related subunits and is important for formation of a network of hydrogen bonds stabilizing the interface. The remaining calcium ions stabilized the contacts within the coat protein dimer. There was electron density of three putative RNA nucleotides per icosahedral asymmetric unit in the φCb5 structure. The nucleotides mediated contacts between two subunits forming a dimer and a third subunit in another dimer. On the basis of these findings, we have proposed a model for φCb5 capsid assembly in which addition of coat protein dimers to the forming capsid is facilitated by interaction with the RNA genome. The structure of RGMoV increases our understanding of mechanisms controlling sobemovirus assembly. This knowledge could be used to create genetically modified plants resistant to sobemovirus infection. The modified capsids of leviviruses can be used in immunization and as vehicles for gene or therapeutic compound delivery.
24
Dunlop, K. A. "Respiratory viruses and meningococcal disease". Thesis, Queen's University Belfast, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.446133.
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Rahnama, Leila. "Phylodynamics of Influenza A Viruses". Thesis, Université d'Ottawa / University of Ottawa, 2015. http://hdl.handle.net/10393/31904.
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Human populations are constantly exposed to emerging pathogens such as influenza A viruses that result from cross-species transmissions. Generally these sporadic events are evolutionary dead-ends, but occasionally, viruses establish themselves in a new host that offers a novel genomic context to which the virus must adjust to avoid attenuation. However, the dynamics of this process are unknown. Here we present a novel method to characterize the time it takes to G+C composition at third codon positions (GC3 content) of influenza viruses to adjust to that of a new host. We compare the inferred dynamics in two subtypes, H1N1 and H3N2, based on complete genomes of viruses circulating in humans, swine and birds between 1900-2009. Our results suggest that both subtypes have the same fast-adjusting genes, which are not necessarily those with the highest absolute rates of evolution, but those with the most relaxed selective pressures. Our analyses reveal that NA and NS2 genes adjust the fastest to a new host and that selective pressures of H3N2 viruses are relaxed faster than for H1N1. The asymmetric nature of these processes suggests that viruses with the greatest adjustment potential to humans are coming from both birds and swine for H3N2, but only from birds for H1N1.
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Stubbs, M. T. "Structural investigations of certain viruses". Thesis, University of Oxford, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.376951.
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Etherington, Graham John. "Computational analysis of foodborne viruses". Thesis, University of East Anglia, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.423473.
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Luke, James Steven. "Detecting previously unseen computer viruses". Thesis, University of Southampton, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.274015.
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Sun, Yunming. "Ribonucleotide reductase of herpes viruses". Thesis, Glasgow Caledonian University, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.364779.
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Gage, Zoe O. "Interferon, viruses and drug discovery". Thesis, University of St Andrews, 2017. http://hdl.handle.net/10023/10127.
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The interferon (IFN) response is a crucial component of cellular innate immunity, vital for controlling virus infections. Dysregulation of the IFN response however can lead to serious medical conditions including autoimmune disorders. Modulators of IFN induction and signalling could be used to treat these diseases and as tools to further understand the IFN response and viral infections. We have developed cell-based assays to identify modulators of IFN induction and signalling, based on A549 cell lines where a GFP gene is under the control of the IFN-β promoter (A549/pr(IFN-β).GFP) and the ISRE containing MxA promoter (A549/pr(ISRE).GFP) respectively. The assays were optimized, miniaturized and validated as suitable for HTS by achieving Z' Factor scores >0.6. A diversity screen of 15,667 compounds using the IFN induction reporter assay identified 2 hit compounds (StA-IFN-1 and StA-IFN-4) that were validated as specifically inhibiting IFNβ induction. Characterisation of these molecules demonstrated that StA-IFN-4 potently acts at, or upstream, of IRF3 phosphorylation. We successfully expanded this HTS platform to target viral interferon antagonists acting upon IFN-signalling. An additional assay was developed where the A549/pr(ISRE).GFP.RBV-P reporter cell line constitutively expresses the Rabies virus phosphoprotein. A compound inhibiting viral protein function will restore GFP expression. The assay was successfully optimized for HTS and used in an in-house screen. We further expanded this assay by placing the expression of RBV-P under the control of an inducible promoter. This demonstrates a convenient approach for assay development and potentiates the targeting of a variety of viral IFN antagonists for the identification of compounds with the potential to develop a novel class of antiviral drugs.
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Romijn, Phyllis Catharina. "Studies on porcine influenza viruses". Thesis, University of Surrey, 1989. http://epubs.surrey.ac.uk/847965/.
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A number of different cell cultures were examined for their susceptibility to the influenza virus A/swine/Weybridge/86(H1N1) and A/swine/Weybridge/87(H3N2). PK1 (porcine kidney) was found to be the most susceptible to the viruses, and MDCK (canine kidney), the best cell line for primary isolation. A method of infectivity assay by immunoperoxidase in microplate cultures of MDCK cells was developed which was simple enough for routine use and practically as sensitive as the egg infectivity test. The potential risks of accidental importation of influenza infection in pig was assessed by determining the survival time of the porcine influenza virus H1N1 in pig tissues. It was found that the virus may keep its infectivity in frozen (-20°C) pig tissues for up to 15 days. The interspecies transmission of porcine influenza viruses was studied using turkeys infected with porcine influenza isolates. Although both A/swine/Weybridge/86 and A/swine/Weybridge/87 were transmitted from infected turkeys to pigs, only A/swine/Weybridge/86(H1N1) infected turkeys presented clinical signs of disease. More than 50% of the pigs presented the virus in the nostrils and/or faeces, at some time during the experiment, and all seroconverted. Transmission from these pigs to newly introduced turkeys was not observed, nor was seroconversion detected. Influenza epidemiology in Brazil was investigated by serological studies using pig sera collected in different areas of that country, using human, porcine and avian isolates of influenza viruses. Highest antibody titres were found against A/Leningrad/86(H3N2) (19%) and A/Port Chalmers/73(H3N2) (17%), but not against specific porcine isolates. Only serological evidence was found to suggest that reassortant influenza viruses occur in English pig herds. However, interspecies transmission of influenza viruses between man and pigs, and the maintenance of human strains in English pig herds was demonstrated by the isolation of two H3N2 influenza viruses very similar to A/Port Chalmers/73, present in the human population in the 1970s.
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Pereira, Pagarete Antonio Joaquim. "Functional Genomics of Coccolithophore Viruses". Paris 6, 2010. http://hal.upmc.fr/tel-01111009v1.
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L’Emiliania huxleyi virus (EhV) est un NCLDV. Il appartient à la famille des virus algaux, les Phycodnaviridae. Il infect Emiliania huxleyi, le coccolithophore le plus abondant dans les océans modernes. Nous avons montré sur une base phylogénétique le transfert de 29 gènes entre le génome d’Emiliania huxleyi et de EhV, notamment 7 gènes impliqués dans la biosynthèse des sphingolipides (SBP). C’est le premier cas patent, dans un système de virus et phytoplancton eucaryotes, de transfert horizontal de multiples gènes d’enzymes liées fonctionnellement. Pour deux des plus importantes enzymes de la SBP, la sérine palmitoyl transférase et la dihydroceramide désaturase, l’étude transcriptomique a permis de définir trois étapes au cours de la formation et de la disparition des blooms de E. Huxleyi, pendant lesquelles on registre une activation progressive des transcrits de coccolithovirus, culminant avec leur contrôle de la SBP au cours des étapes 2 et 3. En utilisant la technique de puce à ADN on a réalisé la première étude transcriptomique globale entre l’hôte le virus au sein d’une communauté océanique naturel. Nos résultats montrent que durant les efflorescences de E. Huxleyi il y a un épisode synchrone de dominance virale qui est clairement visible à travers les signaux transcriptomiques qui en résultent. Parmi les gènes dont la quantité de transcrits augmentent significativement entre la pre et la post dominance virale on a trouvé des fonctions impliquées dans le transfert de l’information génétique, mais aussi des gènes probablement impliqués dans le contrôle post-transitionnel, dans les mécanismes de déplacement intracellulaires, ou même dans le contrôle de l’apoptoseEmiliania huxleyi Virus (EhV) is a giant nucleo-cytoplasmic double stranded DNA virus that belongs to the Phycodnavirus family. It has the capacity to infect Emiliania huxleyi, the most abundant coccolithophore in today’s oceans. Population dynamics of these eukaryotic microalgae is clearly controlled by the severe lytic action of EhV. After an extended bibliographic review on the current knowledge existing on these viruses, we present a series of bioinformatic and experimental analyses conducted to unveil important functional genomic features of the EhV. Evidence for the transfer of 29 genes between E. Huxleyi’s and the EhV genomes is presented. In particular, we investigate the origin of seven genes involved in the unique viral sphingolipid biosynthesis pathway (SBP) encoded in EhV genome. This is the first clear case of horizontal gene transfer of multiple functionally-linked enzymes in a eukaryotic host-virus system. We then focus on a field E. Huxleyi/EhV system from a mesocosm experiment in Norway. The dynamics of expression for two of the most important homologous, host and virus, genes of this pathway, serine palmitoyl transferase and dihydroceramide desaturase is investigated. Three defined transcriptional stages are reported during the bloom, with the coccolithovirus transcripts taking over and controlling the SBP. Finally, host and virus global transcript abundance occurring along the mesocosm experiment was investigated. The majority of the genes that significantly increased in abundance from pre to post viral takeover corresponded to viral sequences for which there is so far no match in the protein databases. Nonetheless, novel transcription features associated with EhV infection were discovered, namely the utilization of genes potentially related to genetic information processing, posttranslational control, intracellular trafficking mechanisms, and control of programmed cell death. As a conclusion, the entire dataset analysed herein is discussed, followed by the potential implications of these findings and future research perspectives in the field of plankton virology
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Costa, Liliana Andreia dos Santos. "Photoinactivation of viruses by porphyrins". Doctoral thesis, Universidade de Aveiro, 2012. http://hdl.handle.net/10773/10869.
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Doutoramento em BiologiaA inativação fotodinâmica tem sido usada com sucesso na inativação de microorganismos. Diversos aspetos da inativação fotodinâmica foram já estudados para diferentes microrganismos, contudo, existe ainda pouca informação disponível no que diz respeito à inativação de bacteriófagos por processos fotodinâmicos. Este trabalho pretendeu elucidar e avaliar vários aspetos da fotoinativação de vírus, em particular de bacteriófagos, incluindo (i) o efeito de diversos parâmetros de luz utilizados na fotoinativação de bacteriófagos; (ii) a eficiência da inativação fotodinâmica de diferentes tipos de bacteriófagos (fagos do tipo DNA e RNA); (iii) o principal mecanismo através do qual a inativação fotodinâmica tem lugar; (iv) o efeito da fotoinativação nas proteínas do bacteriófago; e (v) o possível desenvolvimento de resistência e recuperação da viabilidade após vários tratamentos fotodinâmicos consecutivos. Para avaliar o efeito dos diferentes parâmetros de luz, suspensões fágicas com 107 UFP mL-1 foram irradiadas com diferentes fontes e doses de luz, intensidades luminosas e tempos de irradiação (30,90 e 270 min) na presença de 0,5; 1,0 e 5,0 μM dos derivados porfirínicos catiónicos Tri- Py+-Me-PF e Tetra-Py+-Me. A eficiência da fotoinativação de diferentes fagos do tipo DNA e RNA, foi avaliada através da irradiação da suspensão fágica com luz branca (40 W m-2) durante 270 min na presença de 0,5 e 5,0 μM do derivado porfirínico Tri-Py+-Me-PF, respetivamente para os fagos do tipo RNA e DNA. O mecanismo através do qual a fotoinativação de fagos de DNA (fago do tipo T4) e de RNA (fago Qb) tem lugar foi avaliado por exposição da suspensão fágica à luz branca com uma potência de 40 W m-2, na presença de fotossensibilizador (Tri-Py+-Me-PF e Tetra-Py+-Me) e inibidores, quer do oxigénio singuleto (azida de sódio e L-histidina) quer de radicais livres (Dmanitol e L-cisteína). Os danos nas proteínas do fago do tipo T4, induzidos pelas espécies reativas de oxigénio geradas por 5,0 μM Tri-Py+-Me-PF, foram avaliados pelo método convencional de SDS-PAGE e por espectroscopia de infravermelho. O possível desenvolvimento de resistência e recuperação da viabilidade após a inativação fotodinâmica dos bacteriófagos foi avaliado após dez ciclos consecutivos de tratamento fotodinâmico incompletos (120 min sob irradiação de luz branca a uma potência de 40 W m-2) na presença de 5,0 μM do derivado porfirínico Tri-Py+-Me-PF. Os resultados deste trabalho mostraram que (i) quando uma quantidade de energia (dose de luz) determinada foi aplicada numa suspensão fágica, a partir de uma mesma fonte irradiação, a fotoinactivação do fago foi tanto mais eficiente quanto mais baixa foi a potência luminosa aplicada; (ii) os bacteriófagos foram eficientemente inativados até ao limite de deteção (redução de 6-7 log); (ii) os fagos do tipo RNA foram inativados mais facilmente do que os fagos do tipo DNA (tempos de exposição mais curtos e com concentração de fotossensibilizador dez vezes menor do que a usada para inativar os fagos do tipo DNA); (iii) o mecanismo do tipo II (via produção de oxigénio singuleto) foi o principal mecanismo através do qual a fotoinativação dos bacteriófagos teve lugar; (iv) foi possível detectar danos no perfil proteico após tratamento fotodinâmico e a espectroscopia de infravermelho apresentou-se como uma metodologia promissora de screening para avaliação dos danos induzidos pela inativação fotodinâmica em proteínas; e (v) após dez ciclos consecutivos de tratamento fotodinâmico, o fago do tipo T4 não revelou nenhum tipo de resistência ao tratamento fotodinâmico nem recuperou a sua viabilidade. Como conclusão, a inativação fotodinâmica microbiana é uma tecnologia bastante eficaz para a fotoinativação de bacteriófagos do tipo DNA e RNA sem invólucro, a qual pode ser considerada como uma alternativa ao tratamento convencional com agentes antivíricos, mesmo com intensidades luminosas baixas, sem o risco associado de desenvolvimento de mecanismos de resistência.
Microbial photodynamic inactivation (PDI) has been successfully used to inactivate microorganisms. PDI has already been studied under different conditions for different microorganisms; however, there is still scarce information about bacteriophage inactivation by photodynamic procedures. The goal of this study was to elucidate and evaluate several aspects of viral PDI which include (i) the effect of different light sources, doses and intensities on phage inactivation; (ii) the photoinactivation efficiency on different types of bacteriophages (DNA- and RNA-type phages), (iii) the main mechanism by which phage photosensitization takes place, (iv) the effect of PDI on phage proteins; and (v) the possibility of resistance development and viability recovery after consecutive phototreatments. To evaluate the efficiency of photoinactivation, T4-like phage suspensions of 107 PFU mL-1 were exposed to different light sources(fluorescent PAR lamps, solar light and halogen lamp), and fluence rates (40 W m-2, 600 W m-2 and 1690 W m-2) during 30, 90 and 270 min in the presence of 0.5, 1.0 and 5.0 μM of the cationic porphyrin derivatives Tri-Py+-Me-PF and Tetra-Py+-Me. DNA- and RNA-type phages were exposed to white light (40 W m-2) during 270 min in the presence of Tri-Py+-Me-PF at the concentrations of 0.5 and 5.0 μM, respectively for RNA- and DNA-type phages. The mechanism of phage inactivation was evaluated for DNA- (T4-like) and RNA-type (Qb) phages, in the presence of photosensitizer (Tri-Py+-Me-PF and Tetra-Py+-Me) and singlet oxygen quenchers (sodium azide and L-histidine) and free radicals scavengers (D-mannitol and L-cysteine). The damages on T4- like phage proteins, induced by the ROS generated by Tri-Py+-Me-PF, were assessed by the conventional SDS-PAGE analysis and by IR spectroscopy. Ten consecutive and incomplete (120 min of irradiation at 40 W m-2) cycles of T4-like phage photosensitization by 5.0 μM Tri-Py+-Me-PF were also performed in order to determine the possible development of resistance and viability recovery after phage PDI. From this study it can be concluded that (i) considering the same light source and a fixed light dose, applied at different fluence rates, phage photoinactivation was significantly higher when low fluence rates were used at long irradiation times; (ii) the phages were efficiently inactivated to the detection limit (reductions of 6-7 log); (ii) RNA-type phages were much more easily inactivated than the DNA-type ones (sooner and with ten times less porphyrin concentration than that used for DNA-type phages); (iii) type II mechanism (production of singlet oxygen) was the main mechanism by which phage photosensitization took place; (iv) IR spectroscopy represents a promising and fast-screening methodology when the damages induced by photosensitization on phage proteins are to be studied; and (v) after ten consecutive photodynamic cycles, T4-like phage did not exhibit any resistance to PDI nor recovered its viability. In conclusion, viral PDI is a very efficient technology for the inactivation of non-enveloped DNA- and RNA-type phages, which may be used as an alternative to the conventional antiviral treatments, even at low light fluence rates, without the problem of viral resistance.
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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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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.
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Besozzi, M. "RESPIRATORY VIRUSES IN ALPINE CHAMOIS". Doctoral thesis, Università degli Studi di Milano, 2016. http://hdl.handle.net/2434/351709.
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In the heterogeneous ecosystem of the Alps an interdisciplinary approach is necessary to prevent, survey and control wildlife diseases in order to ensure the biological integrity, the environmental conservation and so the biodiversity. In this contest the matter of livestock-wildlife interface is of particular importance for the presence of grazing domestic herds and the increase of wild ruminants populations, that lead to novel cohabitation situations with a possible “spill-over” of diseases from livestock or vice versa. Livestock-wildlife interfaces are dynamic and bidirectional and pathogens could be transmitted freely within and between the species. Mountain ungulates appear as a good biological model to study inter-species transmission and in particular, respiratory infections of wild ruminants. Chamois has already been subjected in the past to demographic decreases due to respiratory viruses’ circulation. In this study a total of 394 chamois sera hunted in two different areas of North Western Italian Alps were analysed by virus-neutralization test to detect antibody against Bovine Respiratory Syncytial virus (BRSV), Bovine Viral Diarrhea virus (BVDV) and Mammalian Orthoreovirus (MRV). Seroprevalence of viruses and statistical analysis of antibody titres suggest that infection of pestivirus in chamois populations is sporadic as a spill-over from livestock; BRSV has a high adaptation level in wildlife and can be considered endemic in this two areas; high MRV seroprevalence has been observed and confirms the spread of MRV, that has been identified in a previous study in three chamois lungs. Furthermore, in this study PCR and phylogenetic analysis showed that chamois MRV strains belong to serotype 3 and are closely related to Italian dog and Italian bats strains.
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Szeto, Wai-chi. "Computer virus prevention and control in Hong Kong /". [Hong Kong] : University of Hong Kong, 1993. http://sunzi.lib.hku.hk/hkuto/record.jsp?B13302371.
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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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Goffin, Véronique. "Etude de la région cis-régulatrice positive associée à un site hypersensible aux nucléases et localisée dans le gène pol du virus HIV-1 (Human Immunodeficiency virus type 1)". Doctoral thesis, Universite Libre de Bruxelles, 2005. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/210907.
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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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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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Goka, Edward Anthony Chilongo. "Influenza A viruses dual and multiple infections with other respiratory viruses and risk of hospitalization and mortality". Thesis, University of Manchester, 2014. https://www.research.manchester.ac.uk/portal/en/theses/influenza-a-viruses-dual-and-multiple-infections-with-other-respiratory-viruses-and-risk-of-hospitalization-and-mortality(256eb122-a52a-4276-8dc1-28b5a2cc6662).html.
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Introduction: Epidemiological studies have indicated that 5-38% of influenza like illnesses (ILI) develop into severe disease due to, among others, factors such as; underlying chronic diseases, age, pregnancy, and viral mutations. There are suggestions that dual or multiple virus infections may affect disease severity. This study investigated the association between co-infection between influenza A viruses and other respiratory viruses and disease severity. Methodology: Datum for samples from North West England tested between January 2007 and June 2012 was analysed for patterns of co-infection between influenza A viruses and ten respiratory viruses. Risk of hospitalization to a general ward ICU or death in single versus mixed infections was assessed using multiple logistic regression models. Results: One or more viruses were identified in 37.8% (11,715/30,975) of samples, of which 10.4% (1,214) were mixed infections and 89.6% (10,501) were single infections. Among patients with influenza A(H1N1)pdm09, co-infections occurred in 4.7% (137⁄2,879) vs. 6.5% (59⁄902) in those with seasonal influenza A virus infection. In general, patients with mixed respiratory virus infections had a higher risk of admission to a general ward (OR: 1.43, 95% CI: 1.2 – 1.7, p = <0.0001) than those with a single infection. Co-infection between seasonal influenza A viruses and influenza B virus was associated with a significant increase in the risk of admission to ICU/ death (OR: 22.0, 95% CI: 2.21 – 219.8 p = 0.008). RSV/seasonal influenza A viruses co-infection also associated with increased risk but this was not statistically significant. For the pandemic influenza A(H1N1)pdm09 virus, RSV and AdV co-infection increased risk of hospitalization to a general ward, whereas Flu B increased risk of admission to ICU/ death, but none of these were statistically significant. Considering only single infections, RSV and hPIV1-3 increased risk of admission to a general ward (OR: 1.49, 95% CI: 1.28 – 1.73, p = <0.0001 and OR: 1.34, 95% CI: 1.003 – 1.8, p = 0.05) and admission to ICU/ death (OR: 1.5, 95% CI: 1.20 – 2.0, p = <0.0001 and OR: 1.60, 95% CI: 1.02 – 2.40, p = 0.04). Conclusion: Co-infection is a significant predictor of disease outcome; there is insufficient public health data on this subject as not all samples sent for investigation of respiratory virus infection are tested for all respiratory viruses. Integration of testing for respiratory viruses’ co-infections into routine clinical practice and R&D on integrated drugs and vaccines for influenza A&B, RSV, and AdV, and development of multi-target diagnostic tests is encouraged.
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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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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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Leung, Lok Chun Rogen. "Novel fluorescence and fluorine labelling methods for viruses and virus-like particles". Thesis, University of Oxford, 2016. https://ora.ox.ac.uk/objects/uuid:26f1f546-367a-4a6d-8d01-8b05ef24ac74.
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Molecular imaging involves the development of probes which can specifically label a certain object in the body at cellular or subcellular level. This thesis consists of three parts, each involving the development of novel labelling methods for viruses or virus-like particles with specific applications. Virus-like particles (VLP) derived from the E. coli bacteriophage Qβ are widely employed as a nano-carrier for drugs and vaccines, but a powerful method for tracing its circulation without affecting its structure is yet to be developed. In the first part of the thesis, the electrophilic fluorine source 19F-SelectfluorTM was employed for introducing single fluorine atoms on Qβ VLPs. For the 'tag-and-modify' approach, site-selective electrophilic C-F bond formation was achieved on the dehydroalanine (Dha) amino acid tag of VLPs under aqueous conditions. Chemoselective electrophilic aromatic fluorination on tyrosine residues were also achieved using the same reagent by manipulating the amino acid sequence. Similar results were observed in conditions required for 18F-Selectfluor™ reaction, indicating the potential of this technique for positron emission tomography (PET) imaging. In addition, there is a lack of in situ technique for tracking the functional status of Qβ VLPs and hence the release of cargos. In the second part of the thesis, a simple way to monitor the disassembly of 19F-labelled Qβ VLPs by 19F NMR spectrosocpy is reported. Analysis of resonances, using experiments under a range of conditions, allowed determination not only of the intact particle but also the disassembled multimeric species and even smaller peptides upon digestion by cells. This in turn allowed mutational redesign of disassembly and testing in both bacterial and mammalian systems as a strategy for the creation of putative, targeted-VLP delivery systems. In the third part of the thesis, a new type of rhodamine B fluorescent dye functionalised with a 2-imino-2-methoxyethyl (IME) group is reported. The amidine linkage formed between the IME group and lysine residue retains the pKaH of the original side chain, which cannot be achieved using commercially available conjugating dyes. This in turn minimises the change in net charge hence virus infectivity following virus labelling. By employing adenovirus (AV) as an example, the IME dye was shown to be a better choice in retaining virus infectivity compared to dyes linked with other coupling groups. In addition, preliminary experiments on dengue virus with the synthesised dyes were also performed.
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Perkins, Colin J. "A study of some viruses and virus-like agents infecting woody ornamentals". Thesis, University of Bath, 1987. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.376333.
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Enriquez-Enriquez, Carlos. "Detection and survival of selected viruses in water". Diss., The University of Arizona, 1994. http://hdl.handle.net/10150/186948.
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Nucleic acid hybridization (gene probe) and polymerase chain reaction (PCR) techniques have been used to detect viral nucleic acid in water. However, gene probe and PCR may not distinguish between infectious and noninfectious viruses. This study evaluated the ability of gene probe to detect viable poliovirus 1 (polio 1), from sterile and nonsterile groundwater, and the ability of PCR to detect infectious human immunodeficiency virus (HIV-1) from tap and wastewater. The plaque forming (BGM cells), and the tissue culture infectious dose fifty (TCID₅₀) (PLC/PRF/5 cells) procedures were used to detect infectious polio 1 and HIV-1, respectively. Detection of polio 1 by gene probe and cell culture was similar in nonsterile water and in filter sterilized water, but not in autoclaved water. These results suggest that in some natural waters, detection of polio 1 by gene probe may correlate to detection by cell culture procedures. Although detection of infectious HIV-1 by cell culture decreased gradually, until no virus could be found, detection by PCR remained positive throughout the study. Therefore, it was concluded that the use of PCR to assess the risk associated to the presence of HIV-1 in polluted waters, may not be adequate. The enteric adenovirus types 40 (Ead 40) and 41 (Ead 41) are considered the second most important cause of viral gastroenteritis in children, but their role as waterborne pathogens is uncertain. This study compared the survival of Ead 40 and Ead 41 with polio 1, and hepatitis A virus (HAV) in different types of water. The Enteric adenoviruses survived longer in tap and sea water than either polio 1 or HAV, but only slightly better in wastewater. These results suggest that the enteric adenoviruses may survive for prolonged periods in water, representing a potential route of transmission. This study evaluated also the concentration of Ead 40 by the filter adsorption-elution method. With negatively-charged filters, recovery efficiencies of 22, 36, and 38% were obtained from secondary sewage, tap and sea water, respectively. Using electropositive filters, Ead 40 was recovered from tap water with an efficiency of 26.5%. These results show that Ead 40 can be concentrated, from water, with an efficiency comparable to that of other enteric viruses.
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De, Silva Naomi Samantha. "Targeting Tumour Vasculature with Oncolytic Viruses". Thesis, Université d'Ottawa / University of Ottawa, 2014. http://hdl.handle.net/10393/31735.
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Oncolytic viruses (OVs) have been engineered or selected for cancer cell-specific infection; however, we have found that following intravenous administration of vesicular stomatitis virus (VSV), tumour cell killing rapidly extends far beyond the initial sites of infection. This Bystander Effect is due to the virus’ ability to specifically target tumour vasculature through tumour-specific infection of tumour endothelium and the induction of an inflammatory response resulting in tumour-restricted coagulation, acute vascular disruption, apoptosis and necrosis of the tumour core. VSV-infected tumours, reconstructed in three-dimensions from serial histological sections, revealed that the majority of the tumour mass lacks significant blood flow in contrast to uninfected tumours, which exhibit relatively uniform perfusion. VSV infection rapidly induced intravascular coagulation within 6 hours of intravenous
administration. The induction of coagulation was dependent on neutrophils and could be prevented with inhibitors of the coagulation pathway. Normal vasculature was not infected by VSV and no increase in coagulation was observed. Vascular collapse was also observed with the oncolytic poxvirus, JX-594, in patients and preclinical models. Biopsies from patients enrolled in a dose escalation trial for JX-594 were immunoreactive for vaccinia antigens and transgene products in high dose cohorts. Tumour-associated vessels from patients treated with JX-594 were infected with JX-594 and expressed virally encoded transgenes. A decrease in blood flow was also observed 5 days post infection. Several viruses, VSV, JX-594, vvDD, Maraba, and Sindbis, were able to rapidly induce widespread bystander cell death in a subset of mouse models. Tumours responded to OV therapy in three ways, and the type of response was determined by two factors - susceptibility to infection and
the heterogeneity of the tumour microenvironment. Heterogeneity correlated with E-cadherin expression. Among tumours that supported viral replication, cancers with low E-cadherin expression were susceptible to vascular collapse. E-cadherin positive tumours were susceptible to infection and direct cell killing but resistant to vascular disruption or bystander cell death. If poorly-differentiated tumours were resistant to infection, no acute cell killing was observed. These histological subtypes provide a potential framework for the rational selection of patients, the integration of combination therapies and the creation of designer viruses to improve the success of OV therapy.
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Caddy, Sarah. "Characterisation of enteric viruses in dogs". Thesis, Imperial College London, 2015. http://hdl.handle.net/10044/1/39793.
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Human noroviruses (HuNoV) are a significant cause of viral gastroenteritis in man worldwide. Noroviruses are also associated with intestinal disease in multiple species, including dogs. Canine norovirus (CNV) was initially discovered in 2007 and the first aim of this thesis was to determine the prevalence of CNV in the UK dog population. qPCR screening of canine stool samples did not identify CNV RNA, but canine astroviruses (CaAstV) were serendipitously identified and subsequently characterized according to the second aim of this work. For serological screening, CNV virus-like particles (VLPs) to three CNV strains were produced. CNV circulation in the UK was confirmed by identification of CNV-specific antibodies in 60% of canine serum samples collected in 2012-2013. The third aim of this thesis was investigate to CNV interactions with host cells by identifying the cellular attachment factor for CNV. Synthetic carbohydrates and canine tissue samples were used to assess the binding specificity of CNV VLPs, and it was shown that antigens of the HBGA family were recognized. Phenotyping studies then demonstrated expression of HBGAs in dogs. As HuNoV also uses HBGAs to attach to cells, this raised concerns that dogs may be susceptible to HuNoV. Evaluating the zoonotic risk of enteric viruses in dogs was the final aim of this thesis. The susceptibility of dogs to HuNoV and hepatitis E virus (HEV) was determined by screening canine samples for the presence of HuNoV or HEV RNA and HuNoV or HEV-specific antibodies. Antibodies to both HuNoV and HEV were identified in dogs, and results confirmed HuNoV VLPs can bind to canine gastrointestinal samples. This data indicates that dogs are susceptible to HuNoV and HEV infections. In conclusion, this thesis has provided epidemiological and molecular characterization of CNV and CaAstV, in addition to highlighting the zoonotic potential for CNV, HuNoV and HEV in dogs.