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You searched for subject:(RNA viruses). Showing records 1 – 30 of 200 total matches.
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2017 – 2021 (30)
University of Adelaide (17)
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1. Prescott, Meagan A. Host-pathogen Interactions of Respiratory RNA Viruses and the Application of Recombinase Polymerase Amplification for Viral Diagnostics.
Degree: PhD, Microbiology, 2015, Oregon State University
URL: http://hdl.handle.net/1957/57270
► Humans and viral disease are inextricably intertwined. Viral disease plays an immeasurable role in human life, from the disease and economic burden associated with every… (more)
▼ Humans and viral disease are inextricably intertwined. Viral disease plays an immeasurable role in human life, from the disease and economic burden associated with every facet of contending with human viral disease, to managing the consequences of viral disease in organisms important to our food supply, economy, and entertainment. The studies within this dissertation encompass crucial areas of viral research: host-pathogen interactions and diagnostics. Chapters 2 and 3 of this dissertation describe both the study and manipulation of viral-pathogen interactions. The next two chapters describe the application of recombinase polymerase amplification (RPA) for the detection of two prominent viral pathogens in need of improved diagnostic strategies. In Chapter 2, a host-viral pathogen interaction was exploited in an effort to develop a method for increasing influenza virus in the context of cell culture-based viral propagation for vaccine production purposes. PPMO antisense technology was employed to target and suppress the expression of the host gene Interferon alpha (IFNα), which is mainly involved in innate immune response against viral infection, in chicken embryo fibroblast (DF-1) cells. Suppression of IFNα by PPMO resulted in significantly reduced levels of IFNα protein in treated wells measured by ELISA and was shown to not have any cytotoxicity to DF-1 cells at the effective concentrations tested. Treatment of the self-directing PPMO increased the ability of the influenza virus to replicate in DF-1 cells. Over a three-fold increase in viral production was observed in PPMO treated wells compared to those of untreated controls, which was observed to be independent of the initial viral input. Our results indicate that the use of PPMOs to target host protein expression can result in increased production of influenza virus; a technology that could be used on its own for improvement of vaccine production strategies or as a screening tool for subsequent permanent alterations in cell culture lines that would have similarly increased influenza virus production. In Chapter 3, host-viral pathogen interactions were examined in an attempt to understand an aspect of the host response to Respiratory Syncytial Virus (RSV) infection. The host gene, Myeloid Cell Leukemia 1 (Mcl-1), is upregulated early in RSV infection and is thought to have anti-apoptotic function. Mcl-1 knockout and wild type (WT) mouse embryonic fibroblast (MEF) cells were used to characterize the viral response to the absence of the host protein Mcl-1. The lack of Mcl-1 caused MEF cells to become highly permissive to RSV infection and resulted in extremely high levels of RSV compared to viral replication in WT MEF cells. Mcl-1 knockout cells also exhibited uncharacteristic morphology during RSV infection with increased and enlarged syncytial formation. Interestingly, apoptosis, which Mcl-1 helps regulate, was not induced in knockout cells until late in infection. The work presented in Chapter 3 provides evidence that Mcl-1 upregulation in RSV infection… Advisors/Committee Members: Pastey, Manoj K. (advisor), Lowry, Malcolm B. (committee member).
Subjects/Keywords: RNA viruses
Prescott, M. A. (2015). Host-pathogen Interactions of Respiratory RNA Viruses and the Application of Recombinase Polymerase Amplification for Viral Diagnostics . (Doctoral Dissertation). Oregon State University. Retrieved from http://hdl.handle.net/1957/57270
Prescott, Meagan A. "Host-pathogen Interactions of Respiratory RNA Viruses and the Application of Recombinase Polymerase Amplification for Viral Diagnostics." 2015. Doctoral Dissertation, Oregon State University. Accessed January 16, 2021. http://hdl.handle.net/1957/57270.
Prescott, Meagan A. "Host-pathogen Interactions of Respiratory RNA Viruses and the Application of Recombinase Polymerase Amplification for Viral Diagnostics." 2015. Web. 16 Jan 2021.
Prescott MA. Host-pathogen Interactions of Respiratory RNA Viruses and the Application of Recombinase Polymerase Amplification for Viral Diagnostics. [Internet] [Doctoral dissertation]. Oregon State University; 2015. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/1957/57270.
Prescott MA. Host-pathogen Interactions of Respiratory RNA Viruses and the Application of Recombinase Polymerase Amplification for Viral Diagnostics. [Doctoral Dissertation]. Oregon State University; 2015. Available from: http://hdl.handle.net/1957/57270
California State University – East Bay
2. Chu, Wally. Optimized UV Melting as a Tool for Conformational Studies on Virla [i.e. Viral] RNA Motifs: Optimized UV Melting as a Tool for Conformational Studies on Viral RNA Motifs.
Degree: 2013, California State University – East Bay
URL: http://hdl.handle.net/10211.5/52
► UV melting study has been instrumental in investigating the thermodynamic characteristics of various biologically important RNA conformations. In my master???s degree thesis research, I have… (more)
▼ UV melting study has been instrumental in investigating the thermodynamic characteristics of various biologically important RNA conformations. In my master???s degree thesis research, I have optimized the in-house UV melting experimental system by establishing a calibration method which addresses the issue of temperature variation between different UV cuvettes. Using the optimized melting method, I have investigated the thermodynamic characteristics of two important viral RNA motifs ??? Subgenomic RNA promoter of Brome Mosaic Virus (BMV) and the kissing complex of H2 and H3 RNA motifs of Moloney Murine Leukemia Virus (MMLV). My results have shown that 1) BMV subgenomic promoter seems to form an usually flexible C???G base pair in its loop region. 2) The conformational stability of kissing complexes of both H2 and H3 RNA motifs of MMLV are significantly affected by the identity of its loop-closing base pair only when the wild-type base pair is changed to 5???C???G3???. In addition, both the base composition and the length of its stem region also seem to contribute to its conformational stability. I have also established a protocol for purification of T7 RNA polymerase as a part of my thesis work since preparation of pure, active T7 RNA polymerase was crucial in preparing RNA samples in a large scale for my thesis work. Advisors/Committee Members: McPartland, Dr. Ann A. (advisor), Kim, Dr. Chul-Hyun (primaryAdvisor).
Chu, W. (2013). Optimized UV Melting as a Tool for Conformational Studies on Virla [i.e. Viral] RNA Motifs: Optimized UV Melting as a Tool for Conformational Studies on Viral RNA Motifs . (Thesis). California State University – East Bay. Retrieved from http://hdl.handle.net/10211.5/52
Chu, Wally. "Optimized UV Melting as a Tool for Conformational Studies on Virla [i.e. Viral] RNA Motifs: Optimized UV Melting as a Tool for Conformational Studies on Viral RNA Motifs." 2013. Thesis, California State University – East Bay. Accessed January 16, 2021. http://hdl.handle.net/10211.5/52.
Chu, Wally. "Optimized UV Melting as a Tool for Conformational Studies on Virla [i.e. Viral] RNA Motifs: Optimized UV Melting as a Tool for Conformational Studies on Viral RNA Motifs." 2013. Web. 16 Jan 2021.
Chu W. Optimized UV Melting as a Tool for Conformational Studies on Virla [i.e. Viral] RNA Motifs: Optimized UV Melting as a Tool for Conformational Studies on Viral RNA Motifs. [Internet] [Thesis]. California State University – East Bay; 2013. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/10211.5/52.
Chu W. Optimized UV Melting as a Tool for Conformational Studies on Virla [i.e. Viral] RNA Motifs: Optimized UV Melting as a Tool for Conformational Studies on Viral RNA Motifs. [Thesis]. California State University – East Bay; 2013. Available from: http://hdl.handle.net/10211.5/52
3. Yarlagadda, Sandeep. Optimizing Two Separation Methods for Characterizing the Conformation of the N-Terminal Region of the Coat Protein of Brome Mosaic Virus ??? PAGE & HPLC.
URL: http://hdl.handle.net/10211.3/98456
► Brome Mosaic Virus (BMV) is a RNA virus that infects granary plants. Its three separate genomic RNAs are produced in a timely manner through the… (more)
▼ Brome Mosaic Virus (BMV) is a RNA virus that infects granary plants. Its three separate genomic RNAs are produced in a timely manner through the regulatory function of the viral coat protein (CP), which is required for efficient viral replication. In my master???s thesis, I tried to investigate the conformational characteristics of the N-terminal region of CP and its binding characteristics with BMV RNA promoter motifs. 1D NMR and Circular Dichroism (CD) spectroscopy were used to explore the conformational characteristics of two peptides (CPNT-1 & CPNT-2) mimicking the N-terminal region of the coat protein, which is crucial for binding to the genomic RNA. The results had shown that CPNT-1 has more random or flexible conformation, whereas the CPNT-2 has a flexible conformation, yet with higher percentage of alpha helix. While trying to use both native and denaturing PolyAcrylamide Gel Electrophoresis (PAGE) for the purification of the required BMV RNA sequences, I ran into a problem of poor resolution of PAGE, which led me to discover an interesting pH effect on the resolution of gels. My systemic investigation on the pH effect has shown that lowering the pH of the gel solution even by 0.5 would negatively affect the resolution of both denaturing and native gel, though more drastic negative effect was observed on a denaturing gel. The pH effect was reversible, evidenced by the addition of NaOH recovering the normal resolution of a gel. The possible mechanism behind this mysterious pH effect was proposed. Once I resolved the issue, I successfully purified two RNA motifs used for their binding ability and investigated the possibility of using HPLC as a way to quantify CPNT-RNA complex as well as a way to separate unbound RNA and peptide from to peptide-RNA complexes. I performed systemic optimization experiments with different columns on HPLC 1100 instrument on CPNT-1 & 2 in order to establish optimal procedures for running HPLC experiments on CPNT peptide and the RNA samples. I found the solvent conditions and retention time of CPNT-2 and for peptide mixtures (CPNT-1 & 2). Advisors/Committee Members: McPartland, Dr. Ann A. (advisor), Kim, Dr. Chul-Hyun (primaryAdvisor).
Yarlagadda, S. (2013). Optimizing Two Separation Methods for Characterizing the Conformation of the N-Terminal Region of the Coat Protein of Brome Mosaic Virus ??? PAGE & HPLC. (Thesis). California State University – East Bay. Retrieved from http://hdl.handle.net/10211.3/98456
Yarlagadda, Sandeep. "Optimizing Two Separation Methods for Characterizing the Conformation of the N-Terminal Region of the Coat Protein of Brome Mosaic Virus ??? PAGE & HPLC." 2013. Thesis, California State University – East Bay. Accessed January 16, 2021. http://hdl.handle.net/10211.3/98456.
Yarlagadda, Sandeep. "Optimizing Two Separation Methods for Characterizing the Conformation of the N-Terminal Region of the Coat Protein of Brome Mosaic Virus ??? PAGE & HPLC." 2013. Web. 16 Jan 2021.
Yarlagadda S. Optimizing Two Separation Methods for Characterizing the Conformation of the N-Terminal Region of the Coat Protein of Brome Mosaic Virus ??? PAGE & HPLC. [Internet] [Thesis]. California State University – East Bay; 2013. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/10211.3/98456.
Yarlagadda S. Optimizing Two Separation Methods for Characterizing the Conformation of the N-Terminal Region of the Coat Protein of Brome Mosaic Virus ??? PAGE & HPLC. [Thesis]. California State University – East Bay; 2013. Available from: http://hdl.handle.net/10211.3/98456
4. Roth, Caroline Julie Maeva. Creating a Bacterial Clone Expressing NS5B, the RNA-dependent RNA Polymerase from the Pegivirus GBV-C.
Degree: MSin Biological Sciences, 2015, California State University – East Bay
URL: http://hdl.handle.net/10211.3/158619
► The GB virus Type-C (GBV-C) is a member of the Flaviviridae family, which is characterized by a positive-sense single-stranded RNA genome, whose replication is dependent… (more)
▼ The GB virus Type-C (GBV-C) is a member of the Flaviviridae family, which is characterized by a positive-sense single-stranded RNA genome, whose replication is dependent on the viral RNA-dependent RNA polymerase (RdRp) called NS5B. The Flaviviridae consist of animal and human pathogens, such as the Hepatitis C virus (HVC) and the Dengue virus responsible for hemorrhagic fever, unlike GBV-C, which itself is non-pathogenic and primarily infects peripheral blood mononuclear cells (PBMCs). The co-infection by GBV-C with HIV-1 has a favorable effect on HIV-1 positive patient, as it slows the replication of HIV-1 and delays progression to the Acquired Immunodeficiency Syndrome (AIDS). Nevertheless, the mechanism by which GBV-C slows HIV-1 replication is still unknown. To understand the viral lifecycle, it is important to understand the mechanism by which the virus replicates. This project is focused on creating a bacterial clone expressing NS5B for the further characterization of the RdRp. For this, NS5B coding sequence was predicted, amplified by PCR, sequenced, and inserted into an expression vector, pFN6K. The plasmid construct was then transformed into bacteria in order to induce the expression of NS5B. So far, the clones created do not show signs of expression of NS5B, as checked by SDS-PAGE in the soluble protein extract as well as in the insoluble pellet fraction. The results from this research could eventually aid in developing inhibitors against other pathologic members of the Flaviviridae family, as well as obtaining a clearer picture as to how GBV-C replicates its own genome. Advisors/Committee Members: Baysdorfer, Dr. Christoph W. (advisor), Uhde-Stone, Dr. Claudia (committee member).
Subjects/Keywords: RNA viruses – Genetics
Roth, C. J. M. (2015). Creating a Bacterial Clone Expressing NS5B, the RNA-dependent RNA Polymerase from the Pegivirus GBV-C . (Masters Thesis). California State University – East Bay. Retrieved from http://hdl.handle.net/10211.3/158619
Roth, Caroline Julie Maeva. "Creating a Bacterial Clone Expressing NS5B, the RNA-dependent RNA Polymerase from the Pegivirus GBV-C." 2015. Masters Thesis, California State University – East Bay. Accessed January 16, 2021. http://hdl.handle.net/10211.3/158619.
Roth, Caroline Julie Maeva. "Creating a Bacterial Clone Expressing NS5B, the RNA-dependent RNA Polymerase from the Pegivirus GBV-C." 2015. Web. 16 Jan 2021.
Roth CJM. Creating a Bacterial Clone Expressing NS5B, the RNA-dependent RNA Polymerase from the Pegivirus GBV-C. [Internet] [Masters thesis]. California State University – East Bay; 2015. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/10211.3/158619.
Roth CJM. Creating a Bacterial Clone Expressing NS5B, the RNA-dependent RNA Polymerase from the Pegivirus GBV-C. [Masters Thesis]. California State University – East Bay; 2015. Available from: http://hdl.handle.net/10211.3/158619
5. Kurath, Gael. Molecular characterization of infectious hematopoietic necrosis virus transcription and genome organization.
► The transcription process of infectious hematopoietic necrosis virus (IHNV), a rhabdovirus of salmonid fish, was studied both in vivo and in vitro. Polyadenylated RNA from… (more)
▼ The transcription process of infectious hematopoietic necrosis virus (IHNV), a rhabdovirus of salmonid fish, was studied both in vivo and in vitro. Polyadenylated RNA from IHNV infected-salmon cells was resolved electrophoretically into five bands, one of which was found to contain two mRNA species. The molecular weights and intracellular molar ratios of these bands were determined. Coding assignments were made by hybrid selection and in vitro translation of individual mRNA species using cloned plasmids carrying cDNA to each viral mRNA. Species of mRNA were identified which encode each of the five known virion proteins. In addition, a sixth viral mRNA species which encodes a previously unrecognized non-virion protein was discovered. This protein, designated NV, is the first non-virion protein reported for a rhabdovirus. Transcription by the RNA polymerase of IHNV was also examined in vitro. Studies of the optimal reaction conditions revealed that the use of HEPES buffer rather than Tris, and the addition of S-adenosyl methionine to the reactions led to a six-fold increase in enzyme activity. The products of in vitro transcription were found to contain polyadenylated species which co-migrated electrophoretically with IHNV mRNA bands 2, 3, 4, and 5 from IHNV infected-cells. These transcripts were shown to be functional mRNA species by the ability to direct the synthesis of viral proteins in vitro. The construction of cloned plasmids carrying cDNA to viral mRNA species is described. A set of 21 cloned plasmids was characterized by mRNA blot hybridizations and cross-hybridization studies, which identified subsets of plasmids with cDNA to each of the six viral mRNA species. The molecular weight of the genome RNA of IHNV was determined to be 3.7 x 10 ⁶. The cDNA clones were used to construct a physical map of the viral genome by heteroduplex analyses. Measurements of R-loops formed between viral genome RNA and cDNA cloned plasmids determined that the gene order on the viral genome is 3' N-Ml-M2-G-NV-L 5'. Advisors/Committee Members: Leong, JoAnn C. (advisor).
Kurath, G. (1984). Molecular characterization of infectious hematopoietic necrosis virus transcription and genome organization . (Doctoral Dissertation). Oregon State University. Retrieved from http://hdl.handle.net/1957/40697
Kurath, Gael. "Molecular characterization of infectious hematopoietic necrosis virus transcription and genome organization." 1984. Doctoral Dissertation, Oregon State University. Accessed January 16, 2021. http://hdl.handle.net/1957/40697.
Kurath, Gael. "Molecular characterization of infectious hematopoietic necrosis virus transcription and genome organization." 1984. Web. 16 Jan 2021.
Kurath G. Molecular characterization of infectious hematopoietic necrosis virus transcription and genome organization. [Internet] [Doctoral dissertation]. Oregon State University; 1984. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/1957/40697.
Kurath G. Molecular characterization of infectious hematopoietic necrosis virus transcription and genome organization. [Doctoral Dissertation]. Oregon State University; 1984. Available from: http://hdl.handle.net/1957/40697
6. To, Richard Yue-leung. Studies on the transforming gene of avian myeloblastosis virus.
Degree: PhD, Biochemistry and Biophysics, 1981, Oregon State University
To, R. Y. (1981). Studies on the transforming gene of avian myeloblastosis virus . (Doctoral Dissertation). Oregon State University. Retrieved from http://hdl.handle.net/1957/41736
To, Richard Yue-leung. "Studies on the transforming gene of avian myeloblastosis virus." 1981. Doctoral Dissertation, Oregon State University. Accessed January 16, 2021. http://hdl.handle.net/1957/41736.
To, Richard Yue-leung. "Studies on the transforming gene of avian myeloblastosis virus." 1981. Web. 16 Jan 2021.
To RY. Studies on the transforming gene of avian myeloblastosis virus. [Internet] [Doctoral dissertation]. Oregon State University; 1981. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/1957/41736.
To RY. Studies on the transforming gene of avian myeloblastosis virus. [Doctoral Dissertation]. Oregon State University; 1981. Available from: http://hdl.handle.net/1957/41736
7. Jauka, Tembisa Innocencia. Generation of polyclonal antibodies against Theiler's Murine Encephalomyelitis virus protein 2C, and their use in investigating localisation of the protein in infected cells.
Degree: Faculty of Science, Biochemistry, Microbiology and Biotechnology, 2010, Rhodes University
URL: http://hdl.handle.net/10962/d1004018
► The Picornavirus family of positive sense RNA viruses includes some significant human and animal pathogens including Poliovirus (PV), Foot-and-Mouth disease virus (FMDV) and Human Rhinovirus… (more)
▼ The Picornavirus family of positive sense RNA viruses includes some significant human and animal pathogens including Poliovirus (PV), Foot-and-Mouth disease virus (FMDV) and Human Rhinovirus (HRV). The genome is translated within the host cell into a polyprotein that is proteolytically cleaved into the structural and nonstructural proteins. The highly conserved, non-structural protein 2C has numerous roles during the virus life cycle and is essential for virus replication. Although the protein has been well studied in the case of PV, its interactions with the host cell during picornavirus infection is poorly understood. Theiler's Encephalomyelitis virus (TMEV) is a picornavirus that infects mice, and is being used in our laboratory as a model in which to study the 2C protein. In this study, polyclonal antibodies against the TMEV 2C protein were generated and used to localise the protein in infected cells by indirect immunofluorescence. To produce antigen for immunisation purposes, the TMEV-2C protein sequence was analysed to identify hydrophilic and antigenic regions. An internal region of the 2C representing amino acid residues 31-210 was selected, expressed in bacteria and purified by nickel NTA affinity chromatography. Time course analysis of 2C (31-210) showed that the peptide was maximally expressed at 5 hours post induction. The peptide was solubilised using a mild detergent and 1.5 mg of purified antigen was used for immunisation of rabbits. Western blot analysis confirmed that the antibodies could detect both bacteriallyexpressed antigen, and virally-expressed 2C. Examination of virus-infected baby hamster kidney cells by immunofluorescence and confocal microscopy using the antiserum (anti-TMEV 2C antibodies) showed that the protein had a diffuse distribution upon early infection and at later stages it was located in a large perinuclear structure representing the viral replication complex. Furthermore, 2C localised to the Golgi apparatus as revealed by dual-label immunofluorescence using anti-TMEV 2C antibodies and wheat germ agglutinin (WGA). Furthermore, it was shown that TMEV infection results in changes in cell morphology and a redistribution of the cytoskeletal protein, β-actin. The successful production of antibodies that recognise TMEV 2C opens the way for further studies to investigate interactions between 2C and hostencoded factors.
Subjects/Keywords: Picornaviruses; RNA viruses; Immunoglobulins; Encephalomyelitis
Jauka, T. I. (2010). Generation of polyclonal antibodies against Theiler's Murine Encephalomyelitis virus protein 2C, and their use in investigating localisation of the protein in infected cells . (Thesis). Rhodes University. Retrieved from http://hdl.handle.net/10962/d1004018
Jauka, Tembisa Innocencia. "Generation of polyclonal antibodies against Theiler's Murine Encephalomyelitis virus protein 2C, and their use in investigating localisation of the protein in infected cells." 2010. Thesis, Rhodes University. Accessed January 16, 2021. http://hdl.handle.net/10962/d1004018.
Jauka, Tembisa Innocencia. "Generation of polyclonal antibodies against Theiler's Murine Encephalomyelitis virus protein 2C, and their use in investigating localisation of the protein in infected cells." 2010. Web. 16 Jan 2021.
Jauka TI. Generation of polyclonal antibodies against Theiler's Murine Encephalomyelitis virus protein 2C, and their use in investigating localisation of the protein in infected cells. [Internet] [Thesis]. Rhodes University; 2010. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/10962/d1004018.
Jauka TI. Generation of polyclonal antibodies against Theiler's Murine Encephalomyelitis virus protein 2C, and their use in investigating localisation of the protein in infected cells. [Thesis]. Rhodes University; 2010. Available from: http://hdl.handle.net/10962/d1004018
8. Bruslind, Linda D. Pathogenic and molecular characterization of three closely related isolates of infectious pancreatic necrosis virus (IPNV).
► Three closely related isolates belonging to the A₁ serotype of infectious pancreatic necrosis virus (IPNV) were selected for comparison, to provide insight into the nature… (more)
▼ Three closely related isolates belonging to the A₁ serotype of infectious pancreatic necrosis virus (IPNV) were selected for comparison, to provide insight into the nature of variation in the virulence of IPN viruses. Brook trout fry (Salvelinus fontinalis) were experimentally infected with the three isolates by immersion. Cumulative mortalities over a 62 day period for the three isolates were 67%, 78%, and 93%. The negative control was 3%. Virus titers from whole fish homogenates sampled at peak mortality for each isolate were statistically similar, indicating that quantity of virus does not account for virulence differences. For the two least virulent isolates, the virus titer was inversely correlated with fish weight, whereas for the most virulent isolate, no correlation was observed. Amino acid sequences of the viral capsid protein VP2 were determined using the reverse transcriptase polymerase chain reaction (RT-PCR). There were two amino acid changes at residue 217 and 288 between the two least virulent isolates and the most virulent isolate. These changes might provide a specific molecular basis for the variations in virulence among isolates. The progression of IPN virus infection in the experimentally infected fry was followed using histopathology, in situ cDNA hybridization, and alkaline phosphatase immunohistochemistry (APIH). While microscopic lesions were limited almost exclusively to necrosis of the pyloric caeca and pancreas, positive reactions with in situ hybridization and APIH were observed in tissues throughout infected fish. An IPNV infection appeared to be established in the fish by two routes: by entering the skin/lateral line and diffusing through the muscle, and from the oral region into the gastrointestinal tract by ingestion. In a second experiment, within a group of experimentally infected brook trout fry, external and behavioral signs of IPN disease in moribund fish disappeared, with the fish becoming healthy in appearance. Several of these fish were sampled, along with dead, moribund, and asymptomatic fish (never showed signs of IPN disease). Very few differences were observed among the fish sampled, using histopathology and in situ hybridization. Fish that appeared to recover after displaying signs of IPN disease died within a 2 week period. Advisors/Committee Members: Reno, Paul W. (advisor), Leong, Jo-Ann (committee member).
Bruslind, L. D. (1997). Pathogenic and molecular characterization of three closely related isolates of infectious pancreatic necrosis virus (IPNV) . (Doctoral Dissertation). Oregon State University. Retrieved from http://hdl.handle.net/1957/34139
Bruslind, Linda D. "Pathogenic and molecular characterization of three closely related isolates of infectious pancreatic necrosis virus (IPNV)." 1997. Doctoral Dissertation, Oregon State University. Accessed January 16, 2021. http://hdl.handle.net/1957/34139.
Bruslind, Linda D. "Pathogenic and molecular characterization of three closely related isolates of infectious pancreatic necrosis virus (IPNV)." 1997. Web. 16 Jan 2021.
Bruslind LD. Pathogenic and molecular characterization of three closely related isolates of infectious pancreatic necrosis virus (IPNV). [Internet] [Doctoral dissertation]. Oregon State University; 1997. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/1957/34139.
Bruslind LD. Pathogenic and molecular characterization of three closely related isolates of infectious pancreatic necrosis virus (IPNV). [Doctoral Dissertation]. Oregon State University; 1997. Available from: http://hdl.handle.net/1957/34139
9. Daughenbaugh, Katie Finney. The role of VPg in translation of calicivirus RNA.
Degree: PhD, College of Agriculture, 2005, Montana State University
URL: https://scholarworks.montana.edu/xmlui/handle/1/1141
► Molecular mechanisms of Norovirus replication remain for the most part undefined, primarily due to the lack of cell culture and small animal model systems. However,… (more)
▼ Molecular mechanisms of Norovirus replication remain for the most part undefined, primarily due to the lack of cell culture and small animal model systems. However, sequence comparisons and studies using cultivable caliciviruses have lead to the description of many features of the viral genome. Genomes are positive sense RNA, where the genome itself serves as mRNA for the production of viral protein. Additionally, viral RNA is covalently attached at the 5α end to the viral protein VPg. VPg is required for infectivity of the RNA by transfection, and removal of VPg by proteinase K treatment reduces the ability of the RNA to be translated in vitro. Because of these data, and because viral RNA is presumably not translated by an IRES mechanism, it has been suggested that VPg plays a role in translation of viral RNA. Studies described herein were initiated to investigate the potential role for Norwalk virus (NV) VPg in this process. It was found that NV VPg binds translation initiation factor 3 (eIF3) directly and in cell lysates, and is present in complexes with other eIFs including the cap-binding protein eIF4E, the large scaffolding protein eIF4G, the S6 ribosomal protein, and eIF2á, a component of the ternary complex. VPg also inhibits translation of reporter RNAs in vitro, suggesting that the interactions observed between VPg and eIFs are relevant to translation. Regions of VPg responsible for interactions with eIFs were mapped, and it was found that interaction between VPg and the 40S ribosome is most likely that which is responsible for translation inhibition of the reporter RNAs. VPg directly binds 40S ribosomal subunits by sucrose density gradient centrifugation, and this interaction is likely mediated by the central domain of VPg, similar to binding properties observed for the universally conserved factor eIF1A. Finally, a recently discovered, cultivable murine norovirus ₁ 1 (MNV-1) was used to ask if interactions between VPg and eIFs occur in infected cells. It was found that VPg of MNV ₁ 1 coprecipitates with eIF4GI, the d subunit of eIF3, and eIF4E from infected cells, and that this VPg has similar binding properties as the NV VPg. Together the data support the hypothesis that VPg plays a role in translation of viral RNA during infection, and suggets a third mechanism of ribosome recruitment dependent upon protein-protein interactions between VPg and eIFs. These studies also highlight the possibility of using MNV ₁ 1 as a molecular model for the study of human norovirus infection. Advisors/Committee Members: Chairperson, Graduate Committee: Michele Hardy. (advisor).
Subjects/Keywords: RNA.; Viruses.
Daughenbaugh, K. F. (2005). The role of VPg in translation of calicivirus RNA . (Doctoral Dissertation). Montana State University. Retrieved from https://scholarworks.montana.edu/xmlui/handle/1/1141
Daughenbaugh, Katie Finney. "The role of VPg in translation of calicivirus RNA." 2005. Doctoral Dissertation, Montana State University. Accessed January 16, 2021. https://scholarworks.montana.edu/xmlui/handle/1/1141.
Daughenbaugh, Katie Finney. "The role of VPg in translation of calicivirus RNA." 2005. Web. 16 Jan 2021.
Daughenbaugh KF. The role of VPg in translation of calicivirus RNA. [Internet] [Doctoral dissertation]. Montana State University; 2005. [cited 2021 Jan 16]. Available from: https://scholarworks.montana.edu/xmlui/handle/1/1141.
Daughenbaugh KF. The role of VPg in translation of calicivirus RNA. [Doctoral Dissertation]. Montana State University; 2005. Available from: https://scholarworks.montana.edu/xmlui/handle/1/1141
University of Missouri – Columbia
10. Fasina, Olufemi. Alternative translation and alternative RNA processing mechanism in parvovirus RNA processing.
Degree: 2014, University of Missouri – Columbia
URL: http://hdl.handle.net/10355/45905
► [ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT AUTHOR'S REQUEST.] Viruses as obligate intracellular metabolic parasite require the capacity to orchestrate and modulate the host… (more)
▼ [ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT AUTHOR'S REQUEST.] Viruses as obligate intracellular metabolic parasite require the capacity to orchestrate and modulate the host environment either in the nucleus or cytoplasm for their efficient reproductive life cycle. This warrants the use of diverse range of proteins expressed from the viral genome with the ability of regulating viral genome replication, transcription and translation, in addition antagonizing host factors inhibitory to the virus. Therefore, in order to achieve these goals, viruses utilizes gene expression strategies to expand their coding capacity. Gene expression mechanism such as transcription initiation, capping, splicing and 3�-end processing afford viruses the opportunities to utilize the eukaryotic metabolic machineries for generating proteome diversity. Parvoviruses and other DNA viruses effectively capitalize on their use of nuclear eukaryotic metabolic machineries to co-opt host cell factors for optimal replication and gene expression. Parvoviruses with small genome size and overlapping open reading frames utilize alternative transcription initiation, alternative splicing and alternative polyadenylation to co-ordinate the expression of its non-structural and structural proteins. In this work, we have characterized how two parvoviruses; Dependovirus AAV5 and Bocavirus Minute virus of canine (MVC) utilize alternative gene expression mechanisms and strategies to optimize expression of viral proteins from their genome. Advisors/Committee Members: Pintel, David (advisor).
Subjects/Keywords: RNA; Viruses; Eukaryotic cells; Microbiology
Fasina, O. (2014). Alternative translation and alternative RNA processing mechanism in parvovirus RNA processing . (Thesis). University of Missouri – Columbia. Retrieved from http://hdl.handle.net/10355/45905
Fasina, Olufemi. "Alternative translation and alternative RNA processing mechanism in parvovirus RNA processing." 2014. Thesis, University of Missouri – Columbia. Accessed January 16, 2021. http://hdl.handle.net/10355/45905.
Fasina, Olufemi. "Alternative translation and alternative RNA processing mechanism in parvovirus RNA processing." 2014. Web. 16 Jan 2021.
Fasina O. Alternative translation and alternative RNA processing mechanism in parvovirus RNA processing. [Internet] [Thesis]. University of Missouri – Columbia; 2014. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/10355/45905.
Fasina O. Alternative translation and alternative RNA processing mechanism in parvovirus RNA processing. [Thesis]. University of Missouri – Columbia; 2014. Available from: http://hdl.handle.net/10355/45905
11. 王寶珍. Genomic characterization of novel picobirnaviruses in camels.
Degree: 2016, University of Hong Kong
URL: http://hdl.handle.net/10722/236299
► Due to the recent emergency of Middle East Respiratory Coronavirus (MERS-CoV), the study of novel viruses in dromedaries has given rise to an enormous interest.… (more)
▼ Due to the recent emergency of Middle East Respiratory Coronavirus (MERS-CoV), the study of novel viruses in dromedaries has given rise to an enormous interest. In this study, the molecular epidemiology of picobirnaviruses (PBVs) in dromedary fecal samples and the complete genome sequencing of genogroup I and genogroup II PBVs were carried out. Camel fecal samples (n=229) were collected in Dubai for detection of PBVs using newly designed PCR primers targeting the RdRp gene in which 94 of 229 (41%) were confirmed for positive genogroup I PBVs while 50 of 229 (22%) were confirmed positive for genogroup II PBVs. Among these 121 positive samples, 23 (19%) were positive for both genogroup I and genogroup II PBVs, while 98 (81%) were positive for either genogroup I or genogroup II PBVs. Marked nucleotide polymorphisms were observed in most of the RdRp sequences of both genogroup I and genogroup II PBVs, suggesting the possible existence of multiple strains in the same specimen. Phylogenetic analysis based on 205-bp or 207-bp fragment in the RdRp gene revealed that high diversity of PBVs observed in dromedaries. In addition, 5 genogroup I and 3 genogroup II PBVs among the positive samples were selected for whole genome sequencing. In genogroup I, 2 complete and near-complete genomes of segment 1 and 3 complete and near-complete genomes of segment 2 were sequenced. In genogroup II, 2 partial genomes of segment 1 and 3 partial genomes of segment 2 were sequenced as well. During the process of genome sequencing, two different sequence types of segment 1 were found in one camel sample (103C) positive for genogroup I PBV, sharing only 43% amino acid identity. The genome organization of the PBVs camel samples were compared with PBV genome references in Genbank; genome characteristic including the sequence length, G+C content, the conserved motif in segment 1(ExxRxNxxxE) and three conserved motifs in segment 2 (DxT/SxxD, SFxxxT,GDD) are typical to existing PBVs genomes. Phylogenetic analysis was also performed based on the amino acid sequence of capsid and RdRp proteins respectively. Overall; the topology of the phylogenetic tree based on capsid sequence was concordant with that based on RdRp sequence. However, further confirmation requires to be studied by having more availability of capsid sequences. PBV probably evolves through mechanisms similar to other segmented RNA viruses, as it was observed that two different sequences types of segment 1 can be present in the same specimen which may provide a good opportunity for reassortment.
王寶珍. (2016). Genomic characterization of novel picobirnaviruses in camels . (Thesis). University of Hong Kong. Retrieved from http://hdl.handle.net/10722/236299
Author name may be incomplete
王寶珍. "Genomic characterization of novel picobirnaviruses in camels." 2016. Thesis, University of Hong Kong. Accessed January 16, 2021. http://hdl.handle.net/10722/236299.
王寶珍. "Genomic characterization of novel picobirnaviruses in camels." 2016. Web. 16 Jan 2021.
王寶珍. Genomic characterization of novel picobirnaviruses in camels. [Internet] [Thesis]. University of Hong Kong; 2016. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/10722/236299.
王寶珍. Genomic characterization of novel picobirnaviruses in camels. [Thesis]. University of Hong Kong; 2016. Available from: http://hdl.handle.net/10722/236299
12. Combe, Marine. Variability and host-dependency of RNA virus mutation rates .
Degree: 2015, Universitat de Valencia
► Los virus de ARN pueden infectar todo tipo de organismos, desde los procariotas a los eucariotas superiores, y estos agentes infecciosos parecen particularmente propensos a… (more)
▼ Los virus de ARN pueden infectar todo tipo de organismos, desde los procariotas a los eucariotas superiores, y estos agentes infecciosos parecen particularmente propensos a causar enfermedades emergentes tanto en humanos, animales, como en plantas. Su habilidad para escapar del sistema inmunitario, evadir estrategias antivirales o infectar a nuevas especies son aspecto más de su rápida evolución. Por lo tanto, comprender los procesos básicos del la evolución de los virus de ARN podría ayudar en el diseño de nuevas estrategias antivirales. Una de las principales características de los virus de ARN es su tasa de mutación extremadamente alta. De hecho, la alta diversidad genética de las poblaciones virales da lugar a una nube de variantes que interactúan y contribuyen colectivamente, conocido también por el término de cuasiespecies, y que permite a las poblaciones virales adaptarse rápidamente a entornos dinámicos. Estudios anteriores han demostrado que la tasa de mutaciones espontáneas de los virus de ARN varía de 10-6 a 10-4 sustituciones por nucleótido por célula infectada (s/n/c) y puede variar considerablemente, incluso para el mismo virus, aunque se sabe poco sobre las causas de esta variabilidad. Consecuentemente, el conocimiento de la tasa de mutación y el espectro molecular de mutaciones espontáneas son importantes para entender la evolución de la composición genética de las poblaciones virales. En los virus de ARN las tasas de mutación están determinadas por factores codificados por el virus, como la fidelidad de la polimerasa viral, la presencia/ausencia de mecanismos correctores, o el modo de replicación viral. Sin embargo, sólo unos pocos estudios se han centrado en las características celulares que podrían explicar la variabilidad en la producción de la diversidad genética viral, o si esta variabilidad pudiera ser distribuida heterogéneamente entre células únicas. En este estudio, se propuso analizar algunos de los factores subyacentes a la variabilidad en las tasas de mutación de los virus de ARN. En primer lugar, se estudió el efecto del tipo de célula que se infecta, y la variación en función del huésped en el que el virus se replica. A continuación, nos centramos en la variabilidad que ocurre a nivel de una célula única, mediante la caracterización de la diversidad genética de los virus liberados a partir de células individuales. Por último, nos fijamos en el potencial efecto de factores celulares de tipo ADAR, mediante la determinación del tipo de mutaciones espontáneas que se acumulan en el genoma de un norovirus. Se utilizó la prueba de fluctuación de Luria-Delbrück para comprobar la variabilidad en la tasa de mutación del virus de la estomatitis vesicular (VSV) entre diferentes células de mamíferos, así como entre diferentes condiciones de cultivo. Se encontró una tasa de mutación similar entre las células BHK-21, así como en células embrionarias de ratón (MEF), células MEF inmortalizadas mediante deleción del gen p53, células de cáncer de colon murino (CT26) y de neuroblastoma… Advisors/Committee Members: Sanjuán Verdeguer, Rafael (advisor).
Subjects/Keywords: RNA viruses; viral mutation rates
Combe, M. (2015). Variability and host-dependency of RNA virus mutation rates . (Doctoral Dissertation). Universitat de Valencia. Retrieved from http://hdl.handle.net/10550/46762
Combe, Marine. "Variability and host-dependency of RNA virus mutation rates ." 2015. Doctoral Dissertation, Universitat de Valencia. Accessed January 16, 2021. http://hdl.handle.net/10550/46762.
Combe, Marine. "Variability and host-dependency of RNA virus mutation rates ." 2015. Web. 16 Jan 2021.
Combe M. Variability and host-dependency of RNA virus mutation rates . [Internet] [Doctoral dissertation]. Universitat de Valencia; 2015. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/10550/46762.
Combe M. Variability and host-dependency of RNA virus mutation rates . [Doctoral Dissertation]. Universitat de Valencia; 2015. Available from: http://hdl.handle.net/10550/46762
13. Hicks, Allison, 1988-. Cell tropism predicts long-term nucleotide substitution rates of mammalian RNA viruses.
Degree: MS, Microbial Biology, 2013, Rutgers University
URL: https://rucore.libraries.rutgers.edu/rutgers-lib/41786/
► The high rates of RNA virus evolution are generally attributed to replication with error-prone RNA-dependent RNA polymerases. However, these long-term nucleotide substitution rates span three… (more)
▼ The high rates of RNA virus evolution are generally attributed to replication with error-prone RNA-dependent RNA polymerases. However, these long-term nucleotide substitution rates span three orders of magnitude and do not correlate well with mutation rates or selection pressures. This substitution rate variation may be explained by differences in virus ecology or intrinsic genomic properties. We generated long-term nucleotide substitution rate estimates for mammalian RNA viruses and compiled comparable published rates, yielding a dataset of 118 substitution rates of structural genes from 51 different species, as well as 40 rates of non-structural genes from 28 species. Through multiple regression analyses, we evaluated the relationships between these rates and four ecological factors: target cell, transmission route, host range, infection duration; and three genomic properties: genome length, genome sense, genome segmentation. Of these seven factors, we found target cells to be the only significant predictors of viral substitution rates, with tropisms for epithelial cells (P<2x10-5 for the structural genes) or neurons (P<3x10-7 and P<0.01 for the structural genes and non-structural genes, respectively) as the most significant predictors. Further, one-tailed t-tests showed that viruses primarily infecting epithelial cells evolve significantly faster than neurotropic viruses (P=1.83x10-10 and P=6.30x10-4 for the structural genes and non-structural genes, respectively). These results provide strong evidence that the fastest evolving mammalian RNA viruses infect cells with the highest turnover rates: the highly proliferative epithelial cells. Estimated viral generation times suggest that epithelial-infecting viruses replicate more quickly than viruses with different cell tropisms. Our results indicate that cell tropism is a key factor in viral evolvability. Advisors/Committee Members: Duffy, Siobain (chair), Hillman, Bradley (internal member), Kahn, Peter C. (internal member).
Subjects/Keywords: RNA viruses; Nucleotides; Mammals – Cytology
Hicks, Allison, 1. (2013). Cell tropism predicts long-term nucleotide substitution rates of mammalian RNA viruses . (Masters Thesis). Rutgers University. Retrieved from https://rucore.libraries.rutgers.edu/rutgers-lib/41786/
Hicks, Allison, 1988-. "Cell tropism predicts long-term nucleotide substitution rates of mammalian RNA viruses." 2013. Masters Thesis, Rutgers University. Accessed January 16, 2021. https://rucore.libraries.rutgers.edu/rutgers-lib/41786/.
Hicks, Allison, 1988-. "Cell tropism predicts long-term nucleotide substitution rates of mammalian RNA viruses." 2013. Web. 16 Jan 2021.
Hicks, Allison 1. Cell tropism predicts long-term nucleotide substitution rates of mammalian RNA viruses. [Internet] [Masters thesis]. Rutgers University; 2013. [cited 2021 Jan 16]. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/41786/.
Hicks, Allison 1. Cell tropism predicts long-term nucleotide substitution rates of mammalian RNA viruses. [Masters Thesis]. Rutgers University; 2013. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/41786/
14. Short, James Roswell. An investigation into the replication biology of Helicoverpa armigera stunt virus.
Degree: PhD, Faculty of Science, Biochemistry, Microbiology and Biotechnology, 2011, Rhodes University
► 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… (more)
▼ 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.
Subjects/Keywords: Helicoverpa armigera; RNA viruses; Viruses – Reproduction; Lepidoptera – Viruses
Short, J. R. (2011). An investigation into the replication biology of Helicoverpa armigera stunt virus . (Doctoral Dissertation). Rhodes University. Retrieved from http://hdl.handle.net/10962/d1004026
Short, James Roswell. "An investigation into the replication biology of Helicoverpa armigera stunt virus." 2011. Doctoral Dissertation, Rhodes University. Accessed January 16, 2021. http://hdl.handle.net/10962/d1004026.
Short, James Roswell. "An investigation into the replication biology of Helicoverpa armigera stunt virus." 2011. Web. 16 Jan 2021.
Short JR. An investigation into the replication biology of Helicoverpa armigera stunt virus. [Internet] [Doctoral dissertation]. Rhodes University; 2011. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/10962/d1004026.
Short JR. An investigation into the replication biology of Helicoverpa armigera stunt virus. [Doctoral Dissertation]. Rhodes University; 2011. Available from: http://hdl.handle.net/10962/d1004026
15. Chen, Jiao (Graduate of Michigan State University). Inference of viral strains using metagenomics data.
Degree: 2018, Michigan State University
URL: http://etd.lib.msu.edu/islandora/object/etd:19664
Thesis Ph. D. Michigan State University. Computer Science 2018
RNA Viruses, such as human immunodeficiency virus (HIV), influenza, and hepatitis C virus (HCV), have a… (more)
RNA Viruses, such as human immunodeficiency virus (HIV), influenza, and hepatitis C virus (HCV), have a great impact on human health. The high mutation rate of RNA viruses can produce a population of different but closely related virus sequences called viral quasispecies. To develop prevention and treatment strategies for viral pathogens, an essential and fundamental step is to characterize their sequences and abundances at the strain-level for a viral quasispecies. Advances in next-generation sequencing (NGS) technologies have opened up new opportunities to study viruses. Viral metagenomic data, which contains the genetic information for a bunch of viruses in the same habitat, have become the major resource for characterizing RNA viruses. Although there are many pipelines for analyzing viruses in metagenomic data, they usually lack three functions. First, novel viruses or viruses that lack closely related reference genomes cannot be detected with high sensitivity. Second, strain-level analysis is usually missing. Although there are several assembly tools specifically designed for viral haplotypes, de novo assembly of virus genomes is still a computationally challenge task due to the error-prone short reads, high similarities between related strains, and unknown number or abundance of virus haplotypes. Third, it is hard to estimate the number of haplotypes and their abundances in a quasispecies. In this dissertation, we have developed a pipeline with three tools, TAR-VIR PEHaplo and VirBin to address the challenges existing for viral metagenomic assembly and analysis. TAR-VIR is a tool for classifying and enriching viral reads from metagenomic data without relying on complete or high-quality reference genomes. It is optimized for identifying RNA viruses from metagenomic data with an efficient Burrows-Wheeler Transform (BWT) based overlapping method. TAR-VIR was tested on both simulated and real viral metagenomic datasets. The results demonstrated TAR-VIR competes favorably with benchmarked tools. PEHaplo is a de novo haplotype reconstruction tool, which employs paired-end reads to distinguish highly similar strains for viral quasispecies data. It was applied on both simulated and real quasispecies data, and the results were benchmarked against several recently published de novo haplotype reconstruction tools. The comparison shows that PEHaplo outperforms the benchmarked tools in a comprehensive set of metrics. With assembled viral contigs, VirBin focuses on estimating the number of haplotypes and clustering the contigs to different haplotypes. VirBin firstly identifies windows from contigs alignment profile to estimate haplotype number and better calculate the contig abundances. Then, it applies an Expectation-Maximization method to cluster the contigs based on contig abundance levels. The experimental results of VirBin on both simulated and real data sets show that the window-based method can precisely estimate the haplotype number, and generate more…
Advisors/Committee Members: Sun, Yanni, Arnosti, David, Liu, Kevin, Chen, Jin.
Subjects/Keywords: RNA viruses; Metagenomics; RNA viruses – Identification; Computer science; Bioinformatics
Chen, J. (. o. M. S. U. (2018). Inference of viral strains using metagenomics data . (Thesis). Michigan State University. Retrieved from http://etd.lib.msu.edu/islandora/object/etd:19664
Chen, Jiao (Graduate of Michigan State University). "Inference of viral strains using metagenomics data." 2018. Thesis, Michigan State University. Accessed January 16, 2021. http://etd.lib.msu.edu/islandora/object/etd:19664.
Chen, Jiao (Graduate of Michigan State University). "Inference of viral strains using metagenomics data." 2018. Web. 16 Jan 2021.
Chen J(oMSU. Inference of viral strains using metagenomics data. [Internet] [Thesis]. Michigan State University; 2018. [cited 2021 Jan 16]. Available from: http://etd.lib.msu.edu/islandora/object/etd:19664.
Chen J(oMSU. Inference of viral strains using metagenomics data. [Thesis]. Michigan State University; 2018. Available from: http://etd.lib.msu.edu/islandora/object/etd:19664
16. Tomasicchio, Michele. Assembly of Omegatetravirus virus-like particles in the yeast Saccharomyces cerevisiae.
► 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… (more)
▼ 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…
Subjects/Keywords: Helicoverpa armigera; Imbrasia cytherea; Viruses; RNA viruses; Insects – Viruses; Lepidoptera – Viruses; Saccharomyces cerevisiae
Tomasicchio, M. (2008). Assembly of Omegatetravirus virus-like particles in the yeast Saccharomyces cerevisiae . (Doctoral Dissertation). Rhodes University. Retrieved from http://hdl.handle.net/10962/d1003989
Tomasicchio, Michele. "Assembly of Omegatetravirus virus-like particles in the yeast Saccharomyces cerevisiae." 2008. Doctoral Dissertation, Rhodes University. Accessed January 16, 2021. http://hdl.handle.net/10962/d1003989.
Tomasicchio, Michele. "Assembly of Omegatetravirus virus-like particles in the yeast Saccharomyces cerevisiae." 2008. Web. 16 Jan 2021.
Tomasicchio M. Assembly of Omegatetravirus virus-like particles in the yeast Saccharomyces cerevisiae. [Internet] [Doctoral dissertation]. Rhodes University; 2008. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/10962/d1003989.
Tomasicchio M. Assembly of Omegatetravirus virus-like particles in the yeast Saccharomyces cerevisiae. [Doctoral Dissertation]. Rhodes University; 2008. Available from: http://hdl.handle.net/10962/d1003989
17. Huang, Manley T. F. Molecular cloning of infectious pancreatic necrosis virus and characterization of the coding capacity of the complementary DNA.
► The two segments of double-stranded RNA (dsRNA) from infectious pancreatic necrosis virus (IPNV) were cloned into plasmid vector pUC8. Two distinct sets of overlapping clones… (more)
▼ The two segments of double-stranded RNA (dsRNA) from infectious pancreatic necrosis virus (IPNV) were cloned into plasmid vector pUC8. Two distinct sets of overlapping clones were identified by restriction enzyme and Southern blot analysis. Each of these sets was shown, by Northern blot analysis, to be exclusively related to either segment A or B of genomic RNA. The synthesis of complementary DNA (cDNA) from viral RNA segments A and B was less than full-length. Continuous sequences from each segment were represented by two overlapping inserts which were ligated together at a common restriction site. The entire lengths of the cloned segments A and B were estimated to be 2.9 and 2.6 kilobases, respectively. The cDNA sequences from segements A and B were subcloned into the T7 RNA polymerase vectors, pT71 and pT72 and used to transcribe single-stranded RNA (ssRNA). This RNA was used to indirectly compare the lengths of the cloned sequences to those of the viral dsRNA by glyoxal denaturation and agarose gel electrophoresis. The electrophoretic mobilities of the single-stranded RNA's originating from cloned viral sequences were identical to those of the individual strands of ds genomic RNA. The coding capacity of the viral cDNA was determined by cell-free translation analysis. The single-stranded RNA described above was active in a rabbit reticulocyte lysate translation system and did not require either 5'-capping or 3'-polyadenylation. The electrophoretic mobility of the proteins originating from the cloned viral segments was compared to those produced from viral dsRNA as well as the proteins found in purified virus. The four proteins reportedly encoded by the genome of IPNV were identified among the translation products of the individual cloned segments by immunoprecipitation and SDS-polyacrylamide gel electrophoresis. The coding assignments of the proteins produced from cloned segments A and B are shown to be identical to those previously reported for IPNV. Advisors/Committee Members: Leong, JoAnn Ching (advisor).
Subjects/Keywords: RNA viruses – Reproduction
Huang, M. T. F. (1985). Molecular cloning of infectious pancreatic necrosis virus and characterization of the coding capacity of the complementary DNA . (Doctoral Dissertation). Oregon State University. Retrieved from http://hdl.handle.net/1957/40674
Huang, Manley T F. "Molecular cloning of infectious pancreatic necrosis virus and characterization of the coding capacity of the complementary DNA." 1985. Doctoral Dissertation, Oregon State University. Accessed January 16, 2021. http://hdl.handle.net/1957/40674.
Huang, Manley T F. "Molecular cloning of infectious pancreatic necrosis virus and characterization of the coding capacity of the complementary DNA." 1985. Web. 16 Jan 2021.
Huang MTF. Molecular cloning of infectious pancreatic necrosis virus and characterization of the coding capacity of the complementary DNA. [Internet] [Doctoral dissertation]. Oregon State University; 1985. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/1957/40674.
Huang MTF. Molecular cloning of infectious pancreatic necrosis virus and characterization of the coding capacity of the complementary DNA. [Doctoral Dissertation]. Oregon State University; 1985. Available from: http://hdl.handle.net/1957/40674
18. Guo, Yi. Interplay between microRNA and Hepatitis B virus replication.
Degree: 2013, Drexel University
URL: http://hdl.handle.net/1860/4239
Chronic infection with the hepatitis B virus (HBV), which affects 350 million people worldwide, is an important global health issue. Virus-mediated changes in normal cellular… (more)
Chronic infection with the hepatitis B virus (HBV), which affects 350 million people worldwide, is an important global health issue. Virus-mediated changes in normal cellular physiology of hepatocytes, the main target cell of HBV, are considered to facilitate persistent and chronic infection of HBV, potentially leading to the development of HBV-associated liver cancer. Recent work with microRNAs (miRNAs) has shown that many cell types express distinct profiles of miRNAs specifically suited for regulating normal cellular function. This is particularly apparent in hepatocytes, where a single miRNA, mircoRNA-122 (miR-122), makes up at least 50% of the total miRNAs in the cell. Given the important role of miRNAs in regulating cellular function, and the particular importance of miR-122 to hepatocytes, we hypothesize that the levels of miR-122 in the cell may directly influence HBV replication, which may in turn regulate levels of miR-122. To address this hypothesis, the expression levels of miR-122 in HepG2.215 cells, which stably express HBV, were compared to their parental cell line, HepG2. Levels of miR-122 were significantly higher in HepG2.215 cells compared to HepG2. We then measured miR-122 using a luciferase reporter system in which luciferase activity is directly proportional to the amount of functional miR-122. These results, however, indicated minimal alteration of levels of miR-122 between these two cell lines. Also, when HepG2 cells were transfected with a plasmid expressing the HBV genome, HBV failed to elevate miR-122 levels, despite the presence of HBV proteins. On the other hand, exploring the effects of miR-122 expression on HBV replication showed that miR-122 enhanced HBV replication in transfected HepG2 cells in a dose dependent manner. These results may help explain why HBV specifically infects hepatocytes, the only cell type known to express significant levels of miR-122. Additionally, an assay was developed to confirm the authenticity of isolated primary rat hepatocytes using real-time reverse transcription-polymerase chain reaction for hepatocyte specific markers. Future work will replicate these miR-122 experiments in this more biologically relevant system. Together, while the effect of HBV infection on miR-122 expression remains controversial, these results do suggest a potential role for miR-122 in enhancing HBV replication.
M.S., Biomedical Science – Drexel University, 2013
Advisors/Committee Members: Bouchard, Michael.
Subjects/Keywords: Biomedical engineering; Hepatitis B virus; RNA viruses
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Guo, Y. (2013). Interplay between microRNA and Hepatitis B virus replication . (Thesis). Drexel University. Retrieved from http://hdl.handle.net/1860/4239
Guo, Yi. "Interplay between microRNA and Hepatitis B virus replication." 2013. Thesis, Drexel University. Accessed January 16, 2021. http://hdl.handle.net/1860/4239.
Guo, Yi. "Interplay between microRNA and Hepatitis B virus replication." 2013. Web. 16 Jan 2021.
Guo Y. Interplay between microRNA and Hepatitis B virus replication. [Internet] [Thesis]. Drexel University; 2013. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/1860/4239.
Guo Y. Interplay between microRNA and Hepatitis B virus replication. [Thesis]. Drexel University; 2013. Available from: http://hdl.handle.net/1860/4239
19. Hermanns, Kyra. Diversität von RNA-Viren in Moskitos und Effekte von Virusinteraktionen in Vektoren und Wirten.
Degree: 2020, Freie Universität Berlin
URL: http://dx.doi.org/10.17169/refubium-27432
► Mosquitoes transmit important infectious diseases such as yellow fever or dengue fever. Understanding emergence processes and knowledge about diversity of mosquito-associated viruses can help to… (more)
▼ Mosquitoes transmit important infectious diseases such as yellow fever or dengue fever. Understanding emergence processes and knowledge about diversity of mosquito-associated viruses can help to identify control strategies for these viruses. As part of this thesis, novel mosquito viruses were characterized, and the impact of ecological changes and mixed infections was assessed. A large diversity of 49 viruses from the families Flavi-, Rhabdo-, Reo-, Toga-, Mesoni- and Iflaviridae and the order Bunyavirales was detected in mosquitoes that were sampled in Côte d'Ivoire along an anthropogenic disturbance gradient. The majority of these viruses occurred at a low level, but nine viruses were detected frequently. Five of those viruses showed a clear increase in prevalence towards the disturbed habitats. It was shown that virus prevalence was determined by abundance rates of the main mosquito host species and not by changes in host infection rates. In the mosquitoes from Côte d'Ivoire, a previously unknown alphavirus (Taï Forest alphavirus, TALV) was discovered. The complete genome of TALV was sequenced. TALV represents a suggested novel alphavirus species which belongs to the same phylogenetic clade as the only previously detected insect-specific alphavirus Eilat virus (EILV). Since alphaviruses are rarely found in mosquitoes, additional mosquitoes from Panama were tested. Another novel alphavirus (Agua Salud alphavirus, ASALV) was detected in these samples. ASALV was isolated and characterized in cell culture. As ASALV was temperature-sensitive and could not infect cell lines derived from poikilothermic vertebrates, ASALV is likely an insect-specific alphavirus. Phylogenetic analyses placed ASALV on a solitary branch in basal relationship to EILV and TALV as well as to the arboviruses of the Western equine encephalitis complex. Mosquitoes can be simultaneously infected with different viruses possibly resulting in virus interactions. Mixed infections in cell culture with two co-occurring bunyaviruses as well as ASALV and a negevirus detected in the same mosquito showed no effect on replication. However, the cytopathogenicity of ASALV and the negevirus was increased in mixed infections from which the viruses might profit in vivo. In contrast, herbeviruses inhibited a superinfection with another herbevirus. This ability to restrict infections with a related virus might also influence vector competence for arboviruses. When arboviruses infect humans, they can interact with antibodies that were produced against previous virus infections. These antibodies can cross-react with closely related viruses and enhance the infection. This mechanism was suspected after the Zika virus (ZIKV) outbreak in South America as the seroprevalence of the related dengue virus (DENV) was high and a new ZIKV symptom in neonates (microcephaly) was observed. Placenta explants were infected with ZIKV that was pre-incubated with DENV-immune sera or control sera. It was shown that pre-incubation with DENV-immune sera resulted in a faster ZIKV… Advisors/Committee Members: female (gender), Junglen, Sandra (firstReferee), McMahon, Dino (furtherReferee).
Subjects/Keywords: RNA viruses; mosquitoes; virus interactions; ddc:579
Hermanns, K. (2020). Diversität von RNA-Viren in Moskitos und Effekte von Virusinteraktionen in Vektoren und Wirten . (Thesis). Freie Universität Berlin. Retrieved from http://dx.doi.org/10.17169/refubium-27432
Hermanns, Kyra. "Diversität von RNA-Viren in Moskitos und Effekte von Virusinteraktionen in Vektoren und Wirten." 2020. Thesis, Freie Universität Berlin. Accessed January 16, 2021. http://dx.doi.org/10.17169/refubium-27432.
Hermanns, Kyra. "Diversität von RNA-Viren in Moskitos und Effekte von Virusinteraktionen in Vektoren und Wirten." 2020. Web. 16 Jan 2021.
Hermanns K. Diversität von RNA-Viren in Moskitos und Effekte von Virusinteraktionen in Vektoren und Wirten. [Internet] [Thesis]. Freie Universität Berlin; 2020. [cited 2021 Jan 16]. Available from: http://dx.doi.org/10.17169/refubium-27432.
Hermanns K. Diversität von RNA-Viren in Moskitos und Effekte von Virusinteraktionen in Vektoren und Wirten. [Thesis]. Freie Universität Berlin; 2020. Available from: http://dx.doi.org/10.17169/refubium-27432
20. Lancaster, Karen. Mechanisms Controlling Virulence Thresholds of Mixed Viral Populations and Identification of Novel Host Barriers to Poliovirus Neuropathogenesis.
Degree: 2012, University of Texas Southwestern Medical Center
URL: http://hdl.handle.net/2152.5/1030
► Neurotropic viruses comprise some of the worlds most widespread and deadly pathogens, including West Nile virus, rabies virus, and poliovirus. Poliovirus, as a model neurotropic… (more)
▼ Neurotropic viruses comprise some of the worlds most widespread and deadly pathogens, including West Nile virus, rabies virus, and poliovirus. Poliovirus, as a model neurotropic virus, is also an RNA virus. RNA viruses have high mutation rates and a propensity to revert attenuating mutations, contributing to disease and complicating treatment and vaccine development. Despite worldwide epidemics in the early nineteenth century, paralysis from poliovirus is a rare event occurring in less than 1% of poliovirus infections. This suggests the presence of viral and host barriers limiting disease. Here we examined viral barriers by exploring the concept of virulence thresholds using mixtures of virulent and attenuated viruses in a transgenic mouse model of poliovirus infection. We determined that 1000-fold excess of an attenuated strain of poliovirus was protective against disease induced by the virulent strain. Protection was induced locally, was a poliovirus specific effect, and inactivated virus conferred protection. Treatment with a poliovirus receptor-blocking antibody phenocopied the protective effect of inactivated viruses in vitro and in vivo, suggesting virulence thresholds may be modulated by competition for viral receptor. Furthermore, we found the attenuated virus became virulent in immune-deficient mice due to enhanced replication and reversion of attenuating mutations. We also identified additional host barriers limiting pathogenesis using a novel hybridization-based viral diversity assay to quantify the efficiency of poliovirus transport from the periphery to the central nervous system. We found viral replication in peripheral axons is limited and the type I interferon response limits viral replication in peripheral tissues, protecting against disease. Significantly, we discovered that retrograde axonal transport of poliovirus in the sciatic nerve was inefficient and only 20% of viral pool members reaching the brain. The efficiency of viral transport increased upon muscle damage, leading to increased viral diversity and pathogenesis. In summary, we identified a viral induced mechanism controlling virulence of mixed viral populations, and characterized three host barriers that restrict poliovirus pathogenesis in the nervous system. The identification of these barriers restricting virulence may help explain the rare incidence of neurological complications following poliovirus infection and aid in our understanding of viral population dynamics and pathogenesis. Advisors/Committee Members: Pfeiffer, Julie K..
Subjects/Keywords: RNA Viruses; Poliomyelitis; Antibodies; Disease Models, Animal
Lancaster, K. (2012). Mechanisms Controlling Virulence Thresholds of Mixed Viral Populations and Identification of Novel Host Barriers to Poliovirus Neuropathogenesis . (Thesis). University of Texas Southwestern Medical Center. Retrieved from http://hdl.handle.net/2152.5/1030
Lancaster, Karen. "Mechanisms Controlling Virulence Thresholds of Mixed Viral Populations and Identification of Novel Host Barriers to Poliovirus Neuropathogenesis." 2012. Thesis, University of Texas Southwestern Medical Center. Accessed January 16, 2021. http://hdl.handle.net/2152.5/1030.
Lancaster, Karen. "Mechanisms Controlling Virulence Thresholds of Mixed Viral Populations and Identification of Novel Host Barriers to Poliovirus Neuropathogenesis." 2012. Web. 16 Jan 2021.
Lancaster K. Mechanisms Controlling Virulence Thresholds of Mixed Viral Populations and Identification of Novel Host Barriers to Poliovirus Neuropathogenesis. [Internet] [Thesis]. University of Texas Southwestern Medical Center; 2012. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/2152.5/1030.
Lancaster K. Mechanisms Controlling Virulence Thresholds of Mixed Viral Populations and Identification of Novel Host Barriers to Poliovirus Neuropathogenesis. [Thesis]. University of Texas Southwestern Medical Center; 2012. Available from: http://hdl.handle.net/2152.5/1030
21. Bradford, Emma Louise. Transmission of deformed wing virus (DWV) between Varroa destructor and the European honeybee (Apis mellifera) : in vitro and in vivo studies.
Degree: PhD, 2019, University of Aberdeen
URL: https://eu03.alma.exlibrisgroup.com/view/delivery/44ABE_INST/12152387330005941  ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.767351
► The European honeybee (Apis mellifera) is a managed insect pollinator of global economic importance. Over the last few decades honeybees have been undergoing a major… (more)
▼ The European honeybee (Apis mellifera) is a managed insect pollinator of global economic importance. Over the last few decades honeybees have been undergoing a major health crisis, with one of the biggest causes the parasitic mite, Varroa destructor and its role in changing the viral landscape of deformed wing virus (DWV), which consists of two major variants: DWV-A and DWV-B. Prior to the start of this project there was limited information known about the mechanisms behind the relationships between Varroa, DWV and honeybees. The overarching aim of this project was to further enhance our understanding of these complex relationships, focusing on the impact of Varroa DWV transmission and differences between the main DWV variants. One of the initial obstacles to understanding these complex interactions was the inability to accurately quantify DWV variants. Prior to the start of this project, there was a need for an accurate assay for the quantification of DWV-A, DWV-B and total DWV, allowing the role of both variants in viral transmission and establishment to be investigated. While primers did exist for DWV quantification, the majority did not distinguish between variants, or provide accurate levels of DWV. Given these challenges in variant detection, a new assay for the quantification of DWV-A, DWV-B and total DWV was designed and validated. The assay consists of an external plasmid standard with distinct sections, for the detection of variants and total DWV. This DWV variant plasmid assay was essential for further transmission studies in this project. DWV variant transmission was explored using a variety of different methods. A new in vitro feeding system was used, to allow investigations into Varroa DWV variant transmission in isolation. The feeding system utilises locust haemolymph, allowing changes in DWV transmission to be detected. In multiple feeding experiments significant changes in DWV transmission were detected. Significant changes in DWV composition within feeding Varroa were detected with decreased levels of DWV, and changing variant levels. Switches in variant composition within mites and transmission rates occurred during Varroa in vitro feeding. These variant switches occurred in both directions from DWV-A to DWV-B, and DWV-B to DWV-A dominance. These changes in mite variant composition corresponded to changes in levels of replicating strands. iv These changes in DWV transmission, composition and replicating strand detection were only seen due to the use of this in vitro feeding system. The in vitro work provided valuable information about Varroa variant transmission and composition changes during feeding but this is not a natural system. Honeybee pupae from a Varroa-free area with extremely low DWV titres provided the opportunity to investigate Varroa variant transmission and pupal DWV establishment. Over 96 hours total DWV levels underwent a 1339408X fold increase, within pupae following Varroa feeding, with a sharp increase after 12 hours, followed by a plateau after 60 hours. Within this time…
Subjects/Keywords: 570; Honeybee; Varroa destructor; RNA viruses
Bradford, E. L. (2019). Transmission of deformed wing virus (DWV) between Varroa destructor and the European honeybee (Apis mellifera) : in vitro and in vivo studies . (Doctoral Dissertation). University of Aberdeen. Retrieved from https://eu03.alma.exlibrisgroup.com/view/delivery/44ABE_INST/12152387330005941 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.767351
Bradford, Emma Louise. "Transmission of deformed wing virus (DWV) between Varroa destructor and the European honeybee (Apis mellifera) : in vitro and in vivo studies." 2019. Doctoral Dissertation, University of Aberdeen. Accessed January 16, 2021. https://eu03.alma.exlibrisgroup.com/view/delivery/44ABE_INST/12152387330005941 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.767351.
Bradford, Emma Louise. "Transmission of deformed wing virus (DWV) between Varroa destructor and the European honeybee (Apis mellifera) : in vitro and in vivo studies." 2019. Web. 16 Jan 2021.
Bradford EL. Transmission of deformed wing virus (DWV) between Varroa destructor and the European honeybee (Apis mellifera) : in vitro and in vivo studies. [Internet] [Doctoral dissertation]. University of Aberdeen; 2019. [cited 2021 Jan 16]. Available from: https://eu03.alma.exlibrisgroup.com/view/delivery/44ABE_INST/12152387330005941 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.767351.
Bradford EL. Transmission of deformed wing virus (DWV) between Varroa destructor and the European honeybee (Apis mellifera) : in vitro and in vivo studies. [Doctoral Dissertation]. University of Aberdeen; 2019. Available from: https://eu03.alma.exlibrisgroup.com/view/delivery/44ABE_INST/12152387330005941 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.767351
22. Fei, Yue. Investigating RNA silencing-mediated epigenetic modifications in virus-infected plants.
Degree: PhD, 2018, University of Edinburgh
► Plant viruses can cause many plant diseases, which result in substantial damage to crop production. To overcome viral infections, plants evolved RNA silencing which can… (more)
▼ Plant viruses can cause many plant diseases, which result in substantial damage to crop production. To overcome viral infections, plants evolved RNA silencing which can recognise viral RNAs during their replications and slice them into small RNA (sRNA) using antiviral nucleases called DICER or Dicer-like (DCL). The resulting virus-derived small interfering RNA (vsiRNA, 21-24 nucleotides) then guides effector nucleases, namely ARGONAUTE (AGO), to cleave viral RNAs in the cytoplasm in a nucleotide-specific manner. However, the activity of vsiRNA is not restricted to the control of viral RNA accumulation. Virus-derived sRNAs can regulate host gene expression if host mRNAs share sequence complementarity with vsiRNAs. Interestingly, vsiRNAs are also able to target and methylate homologous DNA sequences in the nucleus indicating that vsiRNAs have potential to regulate endogenous genes at transcriptional level by modifying the epigenetic status of gene promoter sequences. This mechanism is referred to as transcriptional gene silencing (TGS). Thus, RNA silencing opens up new strategies to stably and heritably alter gene expression in plants. However, the mechanisms and efficacy of plant virus-induced TGS are largely unknown. The aim of my PhD was to investigate the molecular and environmental factors that are involved in virus-induced epigenetic modifications in the infected plants and in their progeny. First, I examined the required sequence complementary between sRNAs and their nuclear target sequence. I demonstrated for the first time that nuclear-imported vsiRNAs can induce RNA-directed DNA methylation (RdDM) and subsequently heritable virus-induced transcriptional gene silencing (ViTGS) even when they do not share 100% nucleotide sequence complementarity with the target DNA. This finding reveals a more dynamic interaction between viral RNAs and the host epigenome than previously thought. Secondly, I explored how environmental stimuli such as light and temperature can affect the efficacy of ViTGS. I found that ViTGS is greatly inhibited at high temperature. Using RNA-seq, I established that inefficient ViTGS at high temperature is due to the limited production of secondary sRNAs that may limit the initiation, amplification and spreading of virus-induced DNA methylation to neighbouring cells and down generations. Lastly, I studied the link between the viral suppressors of RNA silencing (VSRs): viral proteins that can interfere with plant RNA silencing and ViTGS. I established that VSRs of certain viruses can impair TGS in infected tissues, suggesting that viruses may alter the epigenome and consequently plant gene expression in the infected plants and their progeny. Collectively, my work reveals how viruses can re-program the epigenome of infected plants, and deepens our knowledge of how we can harness pathogens to modify the epigenome for plant breeding.
Subjects/Keywords: 579.2; plant viruses; RNA silencing; epigenetics
Fei, Y. (2018). Investigating RNA silencing-mediated epigenetic modifications in virus-infected plants . (Doctoral Dissertation). University of Edinburgh. Retrieved from http://hdl.handle.net/1842/33125
Fei, Yue. "Investigating RNA silencing-mediated epigenetic modifications in virus-infected plants." 2018. Doctoral Dissertation, University of Edinburgh. Accessed January 16, 2021. http://hdl.handle.net/1842/33125.
Fei, Yue. "Investigating RNA silencing-mediated epigenetic modifications in virus-infected plants." 2018. Web. 16 Jan 2021.
Fei Y. Investigating RNA silencing-mediated epigenetic modifications in virus-infected plants. [Internet] [Doctoral dissertation]. University of Edinburgh; 2018. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/1842/33125.
Fei Y. Investigating RNA silencing-mediated epigenetic modifications in virus-infected plants. [Doctoral Dissertation]. University of Edinburgh; 2018. Available from: http://hdl.handle.net/1842/33125
23. Brian, David Alvin, 1941-. Analysis of ribonucleic acid from feline leukemia virus.
Subjects/Keywords: Oncogenic viruses; RNA
Brian, David Alvin, 1. (1974). Analysis of ribonucleic acid from feline leukemia virus . (Thesis). Michigan State University. Retrieved from http://etd.lib.msu.edu/islandora/object/etd:18049
Brian, David Alvin, 1941-. "Analysis of ribonucleic acid from feline leukemia virus." 1974. Thesis, Michigan State University. Accessed January 16, 2021. http://etd.lib.msu.edu/islandora/object/etd:18049.
Brian, David Alvin, 1941-. "Analysis of ribonucleic acid from feline leukemia virus." 1974. Web. 16 Jan 2021.
Brian, David Alvin 1. Analysis of ribonucleic acid from feline leukemia virus. [Internet] [Thesis]. Michigan State University; 1974. [cited 2021 Jan 16]. Available from: http://etd.lib.msu.edu/islandora/object/etd:18049.
Brian, David Alvin 1. Analysis of ribonucleic acid from feline leukemia virus. [Thesis]. Michigan State University; 1974. Available from: http://etd.lib.msu.edu/islandora/object/etd:18049
24. Aguilera, Elizabeth Renata. Factors That Influence Mammalian Enteric Virus Infection.
► RNA viruses are a common cause of emerging diseases due to their vast genetic diversity. This diversity is largely attributed to mutations generated by the… (more)
▼ RNA viruses are a common cause of emerging diseases due to their vast genetic diversity. This diversity is largely attributed to mutations generated by the error-prone viral RNA-dependent RNA polymerase during replication. Despite the ability to acquire mutations beneficial to the virus, most mutations are deleterious and reduce viral fitness. This poses an obstacle for RNA viruses to successfully infect the host. In addition, a subset of RNA viruses are also enteric pathogens. In particular, these viruses must navigate several environments for transmission and subsequent infection through the fecal-oral route. In this work, I used poliovirus, an enteric RNA virus from the Picornaviridae family, as a model system to study mechanisms of RNA virus co-infection and how bacteria influence picornavirus infection. Recent studies determined several modes of RNA virus transmission exist outside of canonical pathways, including en bloc transmission of multiple viruses into a single cell via bacteria or host-derived membrane vesicles. Co-infection of RNA viruses is important since it can enhance viral fitness. I determined that multiple polioviruses are found within a single plaque even at low multiplicity of infection. I also showed that poliovirus stocks contain virion aggregates and that aggregates induce co-infection. Furthermore, I found that co-infection frequency was increased when polioviruses were heavily mutagenized. This work suggests that co-infection can contribute to plaque formation and that co-infection may assist plaque formation in situations with high genomic damage. This work contributes to mechanisms that influence co-infection of RNA viruses and potentially drive viral evolution. Infection by members of the Picornaviridae family can cause respiratory, cardiac, gastrointestinal, and neurological disease. These and other viruses encounter various bacteria within the host and in the environment. Despite these close encounters, the effects of bacteria on picornaviruses is not completely understood. Previous work determined that poliovirus has enhanced virion stability when exposed to bacteria or bacterial polysaccharides. Therefore, I investigated whether bacteria broadly enhance stability of picornaviruses from three different genera: Enterovirus (PV and coxsackievirus B3 (CVB3)), Kobuvirus (Aichi virus) and Cardiovirus (Mengo virus). I determined that specific bacterial strains enhance thermal stability of subset of viruses, while others were stable in the absence of bacteria. Additionally, I determined that bacteria can stabilize the entire picornavirus panel when individually exposed to bleach. These effects are likely mediated through direct interactions with bacteria since viruses bound to bacteria in vitro. Overall, this work reveals shared and distinct effects of bacteria on a panel of picornaviruses with implications on viral transmission. Advisors/Committee Members: Schoggins, John W., Pfeiffer, Julie K., Reese, Tiffany A., Winter, Sebastian E..
Subjects/Keywords: Bacteria; Coinfection; Enterovirus Infections; RNA Viruses
Aguilera, E. R. (2018). Factors That Influence Mammalian Enteric Virus Infection . (Thesis). University of Texas Southwestern Medical Center. Retrieved from http://hdl.handle.net/2152.5/9300
Aguilera, Elizabeth Renata. "Factors That Influence Mammalian Enteric Virus Infection." 2018. Thesis, University of Texas Southwestern Medical Center. Accessed January 16, 2021. http://hdl.handle.net/2152.5/9300.
Aguilera, Elizabeth Renata. "Factors That Influence Mammalian Enteric Virus Infection." 2018. Web. 16 Jan 2021.
Aguilera ER. Factors That Influence Mammalian Enteric Virus Infection. [Internet] [Thesis]. University of Texas Southwestern Medical Center; 2018. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/2152.5/9300.
Aguilera ER. Factors That Influence Mammalian Enteric Virus Infection. [Thesis]. University of Texas Southwestern Medical Center; 2018. Available from: http://hdl.handle.net/2152.5/9300
25. Jarvie, Rachel Anne. Unravelling the replication biology of Providence virus in a cell culturebased model system.
► There has been an increase in the number of viral outbreaks in the last decade; the majority of these are attributed to insect-human or animal-human… (more)
▼ There has been an increase in the number of viral outbreaks in the last decade; the majority of these are attributed to insect-human or animal-human transfer. Despite this awareness, there is limited understanding of the replication biology of the viruses causing the outbreaks and there are few model systems that are available to study RNA virus replication and viral persistence. In this study, we describe a Providence (PrV)-based model system to study virus replication biology. PrV is a single-stranded RNA virus that can cross Kingdom boundaries; it is capable of establishing a productive infection in insect and mammalian cell culture and it is also capable of replicating in plants. Only one other virus has been reported to infect a similar host range - the Nodavirus, Flock House virus (FHV). First, we performed a bioinformatic analysis of the PrV genome and validated the tools that were currently available to work with this model system in mammalian cells. Our data indicate that PrV infection of human cervical cancer (HeLa) cells results in the production of p130, p104/p40 and VCAP, albeit at low levels. While PrV replication in insect cells is associated with the Golgi apparatus and secretory vesicles, in HeLa cells, PrV replication is associated with the mitochondria. It is interesting to note that FHV replication factories are located on the outer mitochondrial membrane. In an attempt to study PrV virus replication in vitro, we adapted the BioID system reported by Roux et al. (2012). Here a promiscuous biotin ligase enzyme (BirA) was fused to a protein of interest and the expression of the fusion protein in mammalian cells resulted in the proximitybased biotinylation of proteins associated with the protein of interest. Using p40 as the protein of interest, we studied the fusion protein (BirA-p40) in transiently transfected HeLa cells and in a stable cell line, using western blot analysis and confocal microscopy. We faced challenges comparing the data collected using the two antibody-based detection techniques and the lack of BirA-p40 detection when using western analysis was attributed to the associated of p40 with detergent resistant membranes. BirA-p40 was subsequently expressed using in vitro coupled transcription/translation reactions, in the presence of excess biotin. While BirA-p40 was robustly expressed under these conditions, biotinylation of BirA-p40 was not detected. We attributed this to the conditions used in the experiments and given additional time, we would extend the duration of biotinylation, in vitro. PrV replication in mammalian cells was detectable using confocal microscopy however the levels of fluorescence were relatively low. The knowledge that p40 was associated with detergent resistant membranes led us to question the impact of detergent treatment of live cells on the detection of PrV replication. PrV-infected HeLa cells were treated with detergents with varying biochemical characteristics and the impact of these treatments on the detection of PrV replication were evaluated. We observed…
Subjects/Keywords: Virology – Research; RNA viruses; Viruses – Reproduction; Providence virus
Jarvie, R. A. (2020). Unravelling the replication biology of Providence virus in a cell culturebased model system . (Thesis). Rhodes University. Retrieved from http://hdl.handle.net/10962/142339
Jarvie, Rachel Anne. "Unravelling the replication biology of Providence virus in a cell culturebased model system." 2020. Thesis, Rhodes University. Accessed January 16, 2021. http://hdl.handle.net/10962/142339.
Jarvie, Rachel Anne. "Unravelling the replication biology of Providence virus in a cell culturebased model system." 2020. Web. 16 Jan 2021.
Jarvie RA. Unravelling the replication biology of Providence virus in a cell culturebased model system. [Internet] [Thesis]. Rhodes University; 2020. [cited 2021 Jan 16]. Available from: http://hdl.handle.net/10962/142339.
Jarvie RA. Unravelling the replication biology of Providence virus in a cell culturebased model system. [Thesis]. Rhodes University; 2020. Available from: http://hdl.handle.net/10962/142339
26. Armenteros, Yordanka Medina. Avaliação da resposta imune contra as proteínas L e G do vírus respiratório sincicial humano.
Degree: PhD, Microbiologia, 2012, University of São Paulo
URL: http://www.teses.usp.br/teses/disponiveis/42/42132/tde-19092012-093646/  ;
As formulações vacinais contra o Vírus Respiratório Sincicial Humano, HRSV, estão associadas à indução de eosinofilia pulmonar mediada por uma resposta de células TCD4+ Th2,… (more)
As formulações vacinais contra o Vírus Respiratório Sincicial Humano, HRSV, estão associadas à indução de eosinofilia pulmonar mediada por uma resposta de células TCD4+ Th2, após exposição ao HRSV selvagem. Foi identificado um peptídeo da proteína viral G, que modificado perde a capacidade de predispor à eosinofilia, tornando-o um imunógeno atraente. Células T CD8+ específicas para HRSV reduzem a resposta Th2, mediam resistência a desafio com o vírus, e estão relacionadas à redução dos sintomas. Assim, neste trabalho buscamos e identificamos epítopos de células TCD8+ na polimerase viral, utilizando programas de predição, imunização com peptídeos e avaliação da resposta celular. Também construímos vacinas de DNA contendo a seqüência nucleotídica do peptídeo da proteína G modificado. A caracterização da resposta imune estimulada por essas vacinas e por peptídeos purificados revelou que o plasmídio pTGMCTB, bem como os peptídeos GM e GMCTB, foram capazes de induzir anticorpos que, porém, não se mostraram neutralizantes de HRSV e protetores frente a desafio.
Vaccines against human respiratory syncytial virus (HRSV) are associated with pulmonary eosinophilia induction mediated by a TCD4+ Th2 response, after exposition to wild HRSV. A peptide from the viral protein G was identified to predispose to eosinophilia and loses this ability when mutated, making it an interesting immunogen. CD8+ T cells specific to HRSV reduce the Th2 response, mediate resistance to virus challenge, and are related to symptom-reduction. Thus, in the present work, we searched for and identified CD8+ T cell epitopes in the viral polymerase; using prediction programs, peptide immunization and evaluation of the cellular response. We also constructed DNA vaccines containing the nucleotide sequence of the mutated peptide from G protein mentioned above. The characterization of the immune response elicited by these vaccines and purified peptides showed that the pTGMCTB plasmid, as well as GM and GMCTB peptides were able to induce antibody response; however they are not neutralizing and protective against HRSV challenge.
Advisors/Committee Members: Ventura, Armando Morais.
Subjects/Keywords: Epitopes; Epítopos; RNA viruses; Vaccine; Vacinas; Virologia; Virology; Vírus de RNA
Armenteros, Y. M. (2012). Avaliação da resposta imune contra as proteínas L e G do vírus respiratório sincicial humano. (Doctoral Dissertation). University of São Paulo. Retrieved from http://www.teses.usp.br/teses/disponiveis/42/42132/tde-19092012-093646/ ;
Armenteros, Yordanka Medina. "Avaliação da resposta imune contra as proteínas L e G do vírus respiratório sincicial humano." 2012. Doctoral Dissertation, University of São Paulo. Accessed January 16, 2021. http://www.teses.usp.br/teses/disponiveis/42/42132/tde-19092012-093646/ ;.
Armenteros, Yordanka Medina. "Avaliação da resposta imune contra as proteínas L e G do vírus respiratório sincicial humano." 2012. Web. 16 Jan 2021.
Armenteros YM. Avaliação da resposta imune contra as proteínas L e G do vírus respiratório sincicial humano. [Internet] [Doctoral dissertation]. University of São Paulo; 2012. [cited 2021 Jan 16]. Available from: http://www.teses.usp.br/teses/disponiveis/42/42132/tde-19092012-093646/ ;.
Armenteros YM. Avaliação da resposta imune contra as proteínas L e G do vírus respiratório sincicial humano. [Doctoral Dissertation]. University of São Paulo; 2012. Available from: http://www.teses.usp.br/teses/disponiveis/42/42132/tde-19092012-093646/ ;
27. York, Ashley D. A study of viral and cellular factors in the regulation of the influenza virus RNA-dependent RNA polymerase.
Degree: PhD, 2014, University of Oxford
URL: http://ora.ox.ac.uk/objects/uuid:5958fafd-4c91-4434-910e-29e2dd0539b9  ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.627879
► The segmented negative-sense vRNA genome of influenza A virus is replicated via a complementary RNA (cRNA) intermediate by the viral RNA-dependent RNA polymerase (RdRP). The… (more)
▼ The segmented negative-sense vRNA genome of influenza A virus is replicated via a complementary RNA (cRNA) intermediate by the viral RNA-dependent RNA polymerase (RdRP). The replicative intermediate has been thought to exist as a complementary ribonucleoprotein (cRNP) complex. Development of an RNA-based affinity-purification strategy for the isolation of viral ribonucleoprotein complexes enabled the structural and functional characterisation of the previously uncharacterised cRNP complex. The cRNP exhibits a filamentous double-helical organisation with defined termini, containing the viral RdRP at one end and a loop structure at the other end. In vitro characterisation of cRNP activity led to a proposal of a model of vRNA synthesis that relies on a trans-activating RdRP. The viral RdRP is an important host range determinant indicating that its function is affected by interactions with cellular factors. However, the identities and the roles of most of these factors remain unknown. Affinity-purification followed by mass spectrometry was performed to identify cellular proteins that interact with the viral RdRP. 171 cellular proteins were found to co-purify with the viral RdRP, the most abundant of which were chaperones, cytoskeletal proteins, importins, proteins involved in ubiquitination, kinases and phosphatases, mitochondrial and ribosomal proteins. Among the phosphatases, three subunits of the cellular serine/threonine-protein phosphatase 6 (PP6) were identified. PP6 was found to interact directly with the PB1 and PB2 subunits of the viral RdRP, and siRNA-mediated knockdown of the catalytic subunit of PP6 in infected cells resulted in the reduction of viral RNA accumulation and the attenuation of virus growth. Taken together, these results suggest that PP6 interacts with and positively regulates the activity of the influenza virus RdRP.
Subjects/Keywords: 572.8; Biochemistry; Biology; Microbiology; Viruses; influenza; RNA polymerase; RNA synthesis
York, A. D. (2014). A study of viral and cellular factors in the regulation of the influenza virus RNA-dependent RNA polymerase . (Doctoral Dissertation). University of Oxford. Retrieved from http://ora.ox.ac.uk/objects/uuid:5958fafd-4c91-4434-910e-29e2dd0539b9 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.627879
York, Ashley D. "A study of viral and cellular factors in the regulation of the influenza virus RNA-dependent RNA polymerase." 2014. Doctoral Dissertation, University of Oxford. Accessed January 16, 2021. http://ora.ox.ac.uk/objects/uuid:5958fafd-4c91-4434-910e-29e2dd0539b9 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.627879.
York, Ashley D. "A study of viral and cellular factors in the regulation of the influenza virus RNA-dependent RNA polymerase." 2014. Web. 16 Jan 2021.
York AD. A study of viral and cellular factors in the regulation of the influenza virus RNA-dependent RNA polymerase. [Internet] [Doctoral dissertation]. University of Oxford; 2014. [cited 2021 Jan 16]. Available from: http://ora.ox.ac.uk/objects/uuid:5958fafd-4c91-4434-910e-29e2dd0539b9 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.627879.
York AD. A study of viral and cellular factors in the regulation of the influenza virus RNA-dependent RNA polymerase. [Doctoral Dissertation]. University of Oxford; 2014. Available from: http://ora.ox.ac.uk/objects/uuid:5958fafd-4c91-4434-910e-29e2dd0539b9 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.627879
28. Hull, Stacey Lynn. Identification and characterization of new and distinct functional roles of posttranscriptional control elements in cytoplasmic expression of retroviral RNA.
Degree: PhD, Graduate School, 2002, The Ohio State University
URL: http://rave.ohiolink.edu/etdc/view?acc_num=osu1486463803603145
Subjects/Keywords: Biology; RNA; RNA viruses; Retroviruses
Hull, S. L. (2002). Identification and characterization of new and distinct functional roles of posttranscriptional control elements in cytoplasmic expression of retroviral RNA . (Doctoral Dissertation). The Ohio State University. Retrieved from http://rave.ohiolink.edu/etdc/view?acc_num=osu1486463803603145
Hull, Stacey Lynn. "Identification and characterization of new and distinct functional roles of posttranscriptional control elements in cytoplasmic expression of retroviral RNA." 2002. Doctoral Dissertation, The Ohio State University. Accessed January 16, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=osu1486463803603145.
Hull, Stacey Lynn. "Identification and characterization of new and distinct functional roles of posttranscriptional control elements in cytoplasmic expression of retroviral RNA." 2002. Web. 16 Jan 2021.
Hull SL. Identification and characterization of new and distinct functional roles of posttranscriptional control elements in cytoplasmic expression of retroviral RNA. [Internet] [Doctoral dissertation]. The Ohio State University; 2002. [cited 2021 Jan 16]. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=osu1486463803603145.
Hull SL. Identification and characterization of new and distinct functional roles of posttranscriptional control elements in cytoplasmic expression of retroviral RNA. [Doctoral Dissertation]. The Ohio State University; 2002. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=osu1486463803603145
29. Martin, James Arthur. Investigation of Ribonuclease HI handle region dynamics using Solution-state nuclear magnetic resonance spectroscopy, Molecular Dynamic simulations and X-ray crystallography.
Degree: 2020, Columbia University
URL: https://doi.org/10.7916/d8-t0wr-yr67
► Ribonuclease HI (RNase HI), a ubiquitous, non-sequence-specific endonuclease, cleaves the RNA strand in RNA/DNA hybrids. The enzyme has roles in replication, genome maintenance, and is… (more)
▼ Ribonuclease HI (RNase HI), a ubiquitous, non-sequence-specific endonuclease, cleaves the RNA strand in RNA/DNA hybrids. The enzyme has roles in replication, genome maintenance, and is the C-terminal domain of retroviral multi-domain reverse transcriptase (RT) proteins. Murine Leukemia Virus (MLV) and Human Immunodeficiency Virus (HIV) are two such retroviruses and their RNase HI (RNHI) domains are necessary for viral replication, making it an attractive drug target. RNase HI has a "handle region", an extended loop with a large cluster of positive residues, that is critical for substrate recognition. MLV-RNHI is active in isolation and contains a handle region, but, HIV-RNHI is inactive in isolation and does not contain a handle region. HIV-RT, however, has a region in its polymerase domain (positive charge cluster and aromatic cluster) that makes contact with the RNHI domain that may be serving as a "pseudo" handle region; additionally, insertion of a handle region into isolated HIVRNHI restores its activity. Overall, a breadth of information exists on this region's dynamics, but important gaps remain unfilled; gaps that may potentially lead to creating effective drugs to treat the above-mentioned viruses. Solution-state nuclear magnetic resonance (NMR) spectroscopy combined with Molecular Dynamic (MD) simulations suggest a model in which the extended handle region domain of the mesophilic Escherichia coli RNHI (EcRNHI) populates "open" (substrate-bindingcompetent) and "closed" (substrate-binding incompetent) states, while the thermophilic Thermus thermophilus RNHI (TtRNHI) mainly populates the closed state at 300 K. In addition, an in silico designed mutant Val98Ala (V98A) EcRNHI was predicted to populate primarily the closed state. Understanding the structural features and internal motions that lead RNase HI to adopt these various conformers is of central importance to better understanding RNase HI's role in retroviral infection. To formulate a comprehensive model on handle region dynamics, an integrative approach of NMR spectroscopy, X-ray crystallography, and MD simulations is employed. The sensitivity to internal conformational dynamics at multiple time scales of NMR spectroscopy, molecular range and resolution of X-ray crystallography, and structural interpretations of dynamic processes by MD simulations create a synergistic trio capable of tackling this issue. First, the in silico 2-state Kinetic model is validated through NMR observables that correlate with the respective conformers, thus serving as experimental analogs. The NMR parameters also correlate with the Michaelis constants (KM) for RNHI homologs and help to confirm the in silico predictions of V98A EcRNHI. This study shows the important role of the handle region in modulation of substrate recognition. It also illustrates the power of NMR spectroscopy in dissecting the conformational preferences underlying enzyme function. Next, a deeper dive is taken into handle region dynamics, specifically focusing on residue 88 and the…
Subjects/Keywords: Biophysics; Biochemistry; HIV (Viruses); Mouse leukemia viruses; RNA; Endonucleases; Nuclear magnetic resonance spectroscopy
Martin, J. A. (2020). Investigation of Ribonuclease HI handle region dynamics using Solution-state nuclear magnetic resonance spectroscopy, Molecular Dynamic simulations and X-ray crystallography . (Doctoral Dissertation). Columbia University. Retrieved from https://doi.org/10.7916/d8-t0wr-yr67
Martin, James Arthur. "Investigation of Ribonuclease HI handle region dynamics using Solution-state nuclear magnetic resonance spectroscopy, Molecular Dynamic simulations and X-ray crystallography." 2020. Doctoral Dissertation, Columbia University. Accessed January 16, 2021. https://doi.org/10.7916/d8-t0wr-yr67.
Martin, James Arthur. "Investigation of Ribonuclease HI handle region dynamics using Solution-state nuclear magnetic resonance spectroscopy, Molecular Dynamic simulations and X-ray crystallography." 2020. Web. 16 Jan 2021.
Martin JA. Investigation of Ribonuclease HI handle region dynamics using Solution-state nuclear magnetic resonance spectroscopy, Molecular Dynamic simulations and X-ray crystallography. [Internet] [Doctoral dissertation]. Columbia University; 2020. [cited 2021 Jan 16]. Available from: https://doi.org/10.7916/d8-t0wr-yr67.
Martin JA. Investigation of Ribonuclease HI handle region dynamics using Solution-state nuclear magnetic resonance spectroscopy, Molecular Dynamic simulations and X-ray crystallography. [Doctoral Dissertation]. Columbia University; 2020. Available from: https://doi.org/10.7916/d8-t0wr-yr67
30. Hsu, Nai-Yun, 1976-. Building plus strand viral RNA replication platforms.
Degree: Biology, 2013, Rutgers University
Subjects/Keywords: Phosphoinositides; RNA viruses; RNA – Synthesis; Viruses – Reproduction
Hsu, Nai-Yun, 1. (2013). Building plus strand viral RNA replication platforms . (Thesis). Rutgers University. Retrieved from https://rucore.libraries.rutgers.edu/rutgers-lib/41482/
Hsu, Nai-Yun, 1976-. "Building plus strand viral RNA replication platforms." 2013. Thesis, Rutgers University. Accessed January 16, 2021. https://rucore.libraries.rutgers.edu/rutgers-lib/41482/.
Hsu, Nai-Yun, 1976-. "Building plus strand viral RNA replication platforms." 2013. Web. 16 Jan 2021.
Hsu, Nai-Yun 1. Building plus strand viral RNA replication platforms. [Internet] [Thesis]. Rutgers University; 2013. [cited 2021 Jan 16]. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/41482/.
Hsu, Nai-Yun 1. Building plus strand viral RNA replication platforms. [Thesis]. Rutgers University; 2013. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/41482/

redpajama_set_name: RedPajamaCommonCrawl