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You searched for subject:(GORS). Showing records 1 – 3 of 3 total matches.

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University of Rochester

1. Priore, Salvatore F. (1983 - ). Discovery and characterization of influenza virus RNA secondary structures.

Degree: PhD, 2013, University of Rochester

PART I: Influenza virus is a significant public health threat, partially because of its capacity to readily exchange gene segments between different host species to form novel pandemic strains. Even though influenza virus uses RNA exclusively throughout its entire life cycle, little is known about the structure of the Influenza A genome and transcriptome. This works presents bioinformatics efforts to discover and characterize RNA secondary structures in both the (+) and (−)RNA orientations of influenza A virus. All available unique influenza A sequences from the NCBI database were used to identify 20 likely structured regions, primarily in the (+)RNA. One of these predictions is verified and refined using small molecule mapping and isoenergetic microarrays for a conserved region of the Segment 8 (NS1/NEP) intron. Part II: In addition to locally conserved structure, this work examines the global RNA secondary structure in coding regions of both Influenza A and B. For Influenza A, segments 1, 5, 7 and 8 show evidence of wide-spread structure conservation. This phenomenon is referred to as Global Ordered RNA Structure, or GORS. On average the predicted thermodynamic stability of each coding region segregated based on the host species with avian having the most stable folding free energies followed by swine and then human. Similarly, a study of Influenza B virus, which infects primarily humans, showed GORS in Segments 1, 2, 5 and 8. In silico codon mutations that maintained the amino acid sequence for each segment demonstrate the relatively unstable folding free energies of influenza B coding regions. Together these results highlight some of the molecular similarities and differences between influenza A and B and demonstrate the evolutionary adaptation of Influenza

Subjects/Keywords: GORS; Influenza; RNA; Secondary structure; Structure prediction; Virology

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APA (6th Edition):

Priore, S. F. (. -. ). (2013). Discovery and characterization of influenza virus RNA secondary structures. (Doctoral Dissertation). University of Rochester. Retrieved from http://hdl.handle.net/1802/27156

Chicago Manual of Style (16th Edition):

Priore, Salvatore F (1983 - ). “Discovery and characterization of influenza virus RNA secondary structures.” 2013. Doctoral Dissertation, University of Rochester. Accessed August 14, 2020. http://hdl.handle.net/1802/27156.

MLA Handbook (7th Edition):

Priore, Salvatore F (1983 - ). “Discovery and characterization of influenza virus RNA secondary structures.” 2013. Web. 14 Aug 2020.

Vancouver:

Priore SF(-). Discovery and characterization of influenza virus RNA secondary structures. [Internet] [Doctoral dissertation]. University of Rochester; 2013. [cited 2020 Aug 14]. Available from: http://hdl.handle.net/1802/27156.

Council of Science Editors:

Priore SF(-). Discovery and characterization of influenza virus RNA secondary structures. [Doctoral Dissertation]. University of Rochester; 2013. Available from: http://hdl.handle.net/1802/27156


Macquarie University

2. Abbassi, Soumaya. Hydrocarbon potential characterisation and kinetic models for source rocks in the Bonaparte and Gippsland Basins, Australia.

Degree: 2014, Macquarie University

Empirical thesis.

Research was cofunded by Macquarie University and GFZ, Helmholtz Centre Potsdam.

1. Introduction  – 2. Methods and approaches  – 3. Petroleum potential and kinetic models for hydrocarbon generation from the Upper Cretaceous to Paleogene Latrobe Group coals and shales in the Gippsland Basin, Australia  – 4. Predicted bulk chemical and isotopic signature of petroleum generated from Jurassic and Cretaceous source rocks in the Vulcan Sub-basin, Bonaparte Basin, North West Shelf of Australia  – 5. Generation characteristics of Mesozoic syn- and post-rift resource rocks, Bonaparte Basin, Australia : new insights from compositional kinetic modelling  – 6. On the filling and leakage of petroleum from traps in the Laminaria high region of the northern Bonaparte Basin, Australia  – 7. Discussion and summary.

A detailed geochemical study was performed on potential source rocks in the Bonaparte Basin (Australian North West Shelf) and the Gippsland Basin (Australian southeastern margin). Both of these basins have been the focus of attention for extensive exploration activity that has led to the discovery of numerous economic gas and oil accumulations. The hydrocarbon generation characteristics of potential source rocks in each of these two basins remain uncertain. This study involved the integration of several techniques and approaches, such as Rock-Eval pyrolysis and open-system pyrolysis-gas chromatography (Py-GC) to assess the petroleum potential and to define petroleum organo-facies. Pyrolysis experiments under open-system conditions were applied to simulate the timing of hydrocarbon formation for a range of source rocks in these Australian basins. The bulk kinetics of petroleum formation were determined by pyrolysis experiments under closed-system conditions to predict and provide insights on phase behaviour and compositional properties of generated hydrocarbons. Two case studies were carried out within the Bonaparte Basin (the Vulcan Sub-basin and the Laminaria High), from which 61 and 14 source rock samples were analysed, respectively. Py-GC results indicate that the overall molecular compositions of the organic matter preserved in the Bonaparte Basin do not differ significantly between the Upper Jurassic and Lower Cretaceous kerogens. The low abundance of phenolic compounds in these kerogens indicates a contribution from marine material. In contrast, the Middle Jurassic Plover Formation is more enriched in straight chain hydrocarbons with a higher carbon-number range and exhibits higher phenolic and aromatic content, suggesting high input of terrigenous organic matter in the source facies. Additionally, there is a significant variation in petroleum-type organofacies, which ranges from gas/condensates to Paraffinic-Naphthenic-Aromatic. This variability in organic richness, petroleum potential and organic facies type is interpreted to be a direct result of the varied sedimentary environments in which these facies were deposited, reflecting the transition from fluvial-deltaic during the…

Advisors/Committee Members: Macquarie University. Department of Earth and Planetary Sciences, GeoForschungsZentrum Potsdam.

Subjects/Keywords: Petroleum  – Geology  – Victoria; Petroleum  – Geology  – Western Australia; Vulcan sub-basin; Laminaria High; GORs; isotopes

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APA (6th Edition):

Abbassi, S. (2014). Hydrocarbon potential characterisation and kinetic models for source rocks in the Bonaparte and Gippsland Basins, Australia. (Doctoral Dissertation). Macquarie University. Retrieved from http://hdl.handle.net/1959.14/1184868

Chicago Manual of Style (16th Edition):

Abbassi, Soumaya. “Hydrocarbon potential characterisation and kinetic models for source rocks in the Bonaparte and Gippsland Basins, Australia.” 2014. Doctoral Dissertation, Macquarie University. Accessed August 14, 2020. http://hdl.handle.net/1959.14/1184868.

MLA Handbook (7th Edition):

Abbassi, Soumaya. “Hydrocarbon potential characterisation and kinetic models for source rocks in the Bonaparte and Gippsland Basins, Australia.” 2014. Web. 14 Aug 2020.

Vancouver:

Abbassi S. Hydrocarbon potential characterisation and kinetic models for source rocks in the Bonaparte and Gippsland Basins, Australia. [Internet] [Doctoral dissertation]. Macquarie University; 2014. [cited 2020 Aug 14]. Available from: http://hdl.handle.net/1959.14/1184868.

Council of Science Editors:

Abbassi S. Hydrocarbon potential characterisation and kinetic models for source rocks in the Bonaparte and Gippsland Basins, Australia. [Doctoral Dissertation]. Macquarie University; 2014. Available from: http://hdl.handle.net/1959.14/1184868

3. Blundell, Richard James. Investigation into genome-scale ordered RNA structure (GORS) in murine norovirus and other positive-stranded RNA viruses.

Degree: PhD, 2010, University of Edinburgh

Genome-scale ordered RNA structure (GORS) was first identified in 2004. It refers to the presence of secondary structure throughout the length of the RNA genomes of certain genera of RNA virus families, as predicted by bioinformatic analysis. It was also observed that the viruses containing GORS were able to establish persistent infections in their natural hosts, raising the possibility that the presence of GORS could play a role in viral avoidance of the innate immune system. This thesis describes the first study of GORS and its possible role in persistence. Two GORS viruses have been studied, equine rhinitis A virus (ERAV) and murine norovirus (MNV). A 55% seroprevalence of ERAV has been determined in a cohort of Scottish horses indicating a wide exposure to the virus. Equine faecal samples were screened for ERAV by PCR with the intention of identifying a virus, possibly from a persistently infected animal, which would not have undergone any cell culture adaptations as laboratory strains have. Newly identified viruses would then be sequenced, their secondary structures predicted and further studies carried out. Unfortunately, none of the 50 faecal samples screened were positive and clinical isolates of ERAV provided by the Animal Health Trust were sequenced but were identical to laboratory strains, so the study then focussed on MNV. Prevalence of MNV in laboratory mice was determined by PCR of faecal samples to be 67%. MNV was also discovered in the faeces of a pet shop mouse and a wild wood mouse (Apodemus sylvaticus). The complete genomes of 4 laboratory mouse MNVs, the pet shop mouse and wood mouse MNVs were sequenced. Phylogenetic analysis showed the wood mouse MNV had a p distance of 23% from other MNVs, although the laboratory mice and pet shop mouse were closely related to other MNVs. Structural analysis of the genomes of 6 sequenced MNVs, including the wood mouse virus, showed all were GORS viruses. A laboratory strain of MNV, MNV-3, was serially passaged in RAW 264.7 cells to test the hypothesis that in an animal with an intact immune system, there is a pressure for GORS viruses to maintain their genomic RNA structure as a means of immune avoidance, and that cell culture adaptation would attenuate the degree of secondary structure. The complete genome of passage 33 was sequenced, which revealed 7 base mutations, a mutation rate of 0.1 %, which was not considered significant enough to have affected the degree of secondary structure. In order to assess if structured and unstructured RNA behaved differently in cells, replication deficient RNA transcripts were made from the infectious clones of a panel of GORS and non-GORS viruses. These transcripts were electroporated into cells and their rate of decay measured, but there was no difference between the GORS and non-GORS transcripts. The full length and 4 kilobase transcripts were transfected into NIH3T3 cells and the degree of interferon-β induction measured by quantitative PCR and a luciferase reporter assay. The IFN-β response differed across the panel of…

Subjects/Keywords: 636.089; Genome-scale ordered RNA structure; immune system; equine rhinitis A virus; murine norovirus; RNA; GORS

…133 Chapter 5 A Study of the Interactions of GORS and non-GORS RNA Transcripts With… …5.3.1 Stability of GORS and non-GORS RNA transcripts in NIH3T3 cells . 147… …5.3.2 IFN-β induction by full length/truncated RNA transcripts of GORS and non-GORS viruses in… …NIH3T3 cells and A549 cells …... 155 5.3.3 IFN-β induction by GORS and… …non-GORS viral RNA transcripts pre- and post-phosphatase treatment .. 162 5.3.4 IFN-β… 

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Blundell, R. J. (2010). Investigation into genome-scale ordered RNA structure (GORS) in murine norovirus and other positive-stranded RNA viruses. (Doctoral Dissertation). University of Edinburgh. Retrieved from http://hdl.handle.net/1842/4411

Chicago Manual of Style (16th Edition):

Blundell, Richard James. “Investigation into genome-scale ordered RNA structure (GORS) in murine norovirus and other positive-stranded RNA viruses.” 2010. Doctoral Dissertation, University of Edinburgh. Accessed August 14, 2020. http://hdl.handle.net/1842/4411.

MLA Handbook (7th Edition):

Blundell, Richard James. “Investigation into genome-scale ordered RNA structure (GORS) in murine norovirus and other positive-stranded RNA viruses.” 2010. Web. 14 Aug 2020.

Vancouver:

Blundell RJ. Investigation into genome-scale ordered RNA structure (GORS) in murine norovirus and other positive-stranded RNA viruses. [Internet] [Doctoral dissertation]. University of Edinburgh; 2010. [cited 2020 Aug 14]. Available from: http://hdl.handle.net/1842/4411.

Council of Science Editors:

Blundell RJ. Investigation into genome-scale ordered RNA structure (GORS) in murine norovirus and other positive-stranded RNA viruses. [Doctoral Dissertation]. University of Edinburgh; 2010. Available from: http://hdl.handle.net/1842/4411

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