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1
Beier, Kevin. "Viral Tracing of Neuronal Circuitry." Thesis, Harvard University, 2012. http://dissertations.umi.com/gsas.harvard:10241.
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To understand how the nervous system processes information, a map of the connections among neurons is essential. Viral transsynaptic transmission has gained popularity as a method for labeling neural circuits. In particular, the development of retrograde monosynaptic tracing vectors has enabled visualization of the pre-synaptic inputs onto defined sets of postsynaptic neurons. This system utilized the rabies virus (RABV), in which the glycoprotein gene in the virus was deleted, and re-supplied in trans. In order to build alternative, more flexible tracers, we made recombinant VSV genomes, first developing the use of vesicular stomatitis virus (VSV) for tracing neuronal connections. Viruses encoding several different fluorescent proteins were made, giving brilliantly labeled neurons, bright enough for live imaging and characterization of the detailed morphologies of cells. Expression was very rapid, facilitating identification of neurons both in vivo and in ex vivo applications. In addition, the use of an avian glycoprotein (ASLV-A) allowed specific targeting to cells expressing an avian glycoprotein receptor (TVA). This allowed monosynaptic tracing from defined starter cells. In order to alter the direction and cell type specificity of transmission, we then fitted VSV with a glycoprotein from one of multiple other viruses. Glycoproteins such as the rabies virus glycoprotein (RABV-G) endowed VSV with the ability to spread in a retrograde transsynaptic pattern, while the glycoproteins from viruses such as the lymphocytic choriomeningitis virus (LCMV) gave an anterograde pattern of transsynaptic spread. This anterograde or retrograde spread was observed in all species tested, and even for other non-VSV viruses, such as lentiviruses. We also developed transsynaptic tracing viruses which direct viral spread between defined cell types, instead of from a defined cell type to any upstream of downstream cell. In all, we developed an extensive transsynaptic tracing repertoire for tracing neuronal connections.
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James, Katherine Louise. "Viral genetics of HIV-2 infection." Thesis, University of Oxford, 2015. https://ora.ox.ac.uk/objects/uuid:68ba022d-62e4-4cb1-8032-085ea5240b98.
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HIV-2 is a contemporary human retrovirus with the majority of infections localised to West Africa. Both HIV-1 and HIV-2 are able to cause AIDS; however, in contrast to HIV-1 infection, a common outcome following HIV-2 infection (∼ 37% of patients in this study cohort) is long-term non-progression (LTNP), where patients remain aviraemic and asymptomatic in the absence of treatment, often for decades. HIV-1 and HIV-2 both arose following zoonotic transmission of SIVs from non-human primates at around the beginning of the 20th century and when patients develop AIDS caused by HIV-2 infection, it is clinically indistinguishable from AIDS following HIV-1 infection. Whilst the estimated number of HIV-2 infections remains small in the context of the global HIV pandemic (HIV-2 ∼ 2 million, HIV-1 group M ∼75 million), the differences in pathogenicity between these two viruses has been a source of great interest, particularly the features of LTNPs that allow control of viral replication in the absence of anti-retroviral treatment. The studies described in this thesis were carried out using samples collected from a well-characterised longitudinal community cohort in Caió, Guinea-Bissau. Chapter 3 of this thesis presents an investigation into the variation and evolution present in the HIV-2 specific accessory gene vpx. The data showed significantly increased signals of positive selection pressure in vpx in viraemic when compared to non-viraemic patients and also allowed the identification of novel variations at high frequencies (up to 22%) in this cohort that were previously un-described. Chapters 4 and 5 present a novel application of shotgun RNA sequencing (RNA- Seq) to HIV ex vitro and ex vivo samples. Chapter 4 demonstrates the divergence seen in a cultured viral isolate at the level of the whole genome, in the absence of many of the biases typically involved in sequencing of RNA viruses. Chapter 5 further extends this method to show the applicability of using RNA-Seq on primary patient HIV samples for the first time. Analysis of diversity estimates over the whole genome in the context of a low bias sequencing method show a high level of diversity in HIV-2 pol and low diversity in vpx. The aim of this work was to combine traditional and novel sequencing methods to facilitate assessment of the variation and evolution acting on vpx and to generate an accurate picture of the genetic diversity over the whole genome of HIV-2.
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Mills, Ryan E. "Improving gene annotation of complete viral genomes." Thesis, Georgia Institute of Technology, 2003. http://hdl.handle.net/1853/25189.
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Wilson, Jamie Douglas Knox. "Oligoclonal expansions of T lymphocytes during viral infections." Thesis, University of Oxford, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.299227.
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Mistry, Ajay Ramanlal. "Development of non-viral gene delivery systems based on HMG1." Thesis, Imperial College London, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.368705.
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Ma, Hok-tsun, and 馬學俊. "RNA-Dependent RNA polymerase activity of the infectious bursal diseasevirus viral protein 1." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2004. http://hub.hku.hk/bib/B30408192.
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Upton, John H. "The role of RNA secondary structure in replication of Nodamura virus RNA2." To access this resource online via ProQuest Dissertations and Theses @ UTEP, 2009. http://0-proquest.umi.com.lib.utep.edu/login?COPT=REJTPTU0YmImSU5UPTAmVkVSPTI=&clientId=2515.
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Shi, Bu-Jun. "Expression and function of cucumoviral genomes." Title page, contents and summary only, 1997. http://web4.library.adelaide.edu.au/theses/09PH/09phs5546.pdf.
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Bibliography: leaves 104-130. The aim of this thesis is to characterise subgenomic RNAs of cucumoviruses and the functions of their encoding genes. Strains of cucumber mosaic virus (CMV) are classified into two major subgroups (I and II) on the basis of nucleotide sequence homology. The V strain of tomato aspermy virus (V-TAV) and a subgroup I CMV strain (WAII) are chosen to determine whether the 2b genes encoded by these viruses are expressed 'in vivo'. For further investigation of the 2b gene function, cDNA clones of three genomic RNAs of V-TAV are constructed. Using the infectious cDNA clones of V-TAV, a mutant virus containing only one of the two repeats is constructed.
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Song, Rujun. "Dimerization of human immunodeficiency virus type 1 genome : dimer maturation process and role of the 5' untranslated region in dimerization." Thesis, McGill University, 2008. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=111918.
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Human Immunodeficiency Virus type I genome consists of two identical RNA molecules that are non-covalently linked to form a dimer. HIV-1 immature and mature genomic RNA (gRNA) dimers were found in protease defective (PR -) and wild type virions, respectively, and the 5'untranslated region (5' UTR) was shown to play key roles during the genome dimerization process; but the dimerization mechanism still remains to be clarified My research project is to characterize the dimerization process and the role of 5' UTR in genome dimerization in virions produced by tissue culture cells. I'll firstly show the dimer maturation processes of HIV-1 gRNA isolated from newly released to grown-up (≥10h old) wild type, PR-, and SL1 defective (DeltaIDS) virions respectively. The results showed that HIV-1 gRNA dimer maturation process was protease-dependent and involved multiple steps: from low to high dimerization level and dimer thermostability, and from low dimer mobility to intermediate and high mobility. PR- virions did not freeze gRNA conformation in the primordial nascent state and gRNA changed from monomeric in newly released virions to half dimeric in grown-up virions, which showed that genome was packaged in the form of monomeric RNA or fragile dimers, more thermolabile than immature dimers in grown-up PR- virions. DeltaDIS inhibited gRNA dimerization by about 50% in newly released virions, though grown-up DeltaDIS gRNA was fully dimeric, which indicated that the DIS played the initiation role in gRNA dimerization in HIV-1 virions. The gRNA dimerization rate in PR- or DeltaDIS virions was much slower than that in wild type virions. These results show for the first time the whole process of dimer maturation after virion release, the gRNA conformation rearrangement in PR- virions, and the initiation role of the DIS in HIV-1 virions. Next, I'll provide a rather systematic search for the contribution of different regions in 5' UTR to HIV-1 gRNA dimerization by studying selected mutations singly or together with defective SL1. The results showed that the 5'trans-activation response element (5'TAR) was directly involved in gRNA dimerization, and a long distance base-pairing interaction between a sequence in U5 region (nts105-1l5) and another around the initiation codon of the gag gene (nts334-344) was structurally contributive to gRNA dimerization. Deletions of sequences around the 3'end of Primer Binding Site (PBS) stem-loop moderately decreased gRNA dimerization level. Other sequences in 5' UTR except DIS/SL1, which was previously known to play important roles, didn't show any systematic role. Here the results suggested that the absence of inhibition on gRNA dimerization level with defective DIS might be the compensation of the direct role of 5'TAR; and wild type-like dimerization level of DeltaTAR must be the direct contribution of the DIS.
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Lai, King-yin, and 賴景然. "Discovery and complete genome sequence of a novel group of bat picornavirus." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2010. http://hub.hku.hk/bib/B44546026.
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Dutta, Ranendra Nath. "Experimental Test of Solitary Wave Theory in Viral Populations." University of Toledo Health Science Campus / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=mco1226950654.
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Bawazir, Amin Ahmed. "Epidemiology, immunology and genetics of viral hepatitis in Aden City, Yemen." Thesis, University of Liverpool, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.507582.
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Background: Viral hepatitis is a significant public health problem with millions of humans infected worldwide. There are very few studies of hepatitis in Aden, Yemen. Aims: The study aims to determine the prevalence of viral hepatitis (A, B, e and E), their co-infection with Epstein - Barr virus (EBV), cytomegalovirus (eMV) and human herpes virus (HHV6) and the risk factors for HBV infection among individuals attending primary health care facilities. Risk factors for HBV and Hev infection were also identified in patients with chronic liver disease (eLO), multi-transfusions and those undergoing haemodialysis (HO). The genotypes of HBV are studied. The HBV vaccination coverage in children < 5 years in Aden is also described. Methodology: A cross-sectional study of individuals attending primary health care facilities in Aden was conducted to identify the prevalence of the viruses. Participants were recruited stratified by age. A case-control study of hospital patients with eLO, polytransfusion and HO was used to identify risk factors for HBV and Hf'V. Both cases and healthy participants were interviewed and blood samples were analysed using ELISA assays. A community-based survey of children < 5 years was used to identify vaccination coverage and to interview parents. peR sequencing method was used for HBV genotyping. Results: The overall seroprevalence of exposure to HAV (anti-HAV antibodies), HBV (anti-HBc antibodies), HEV (anti-HEV antibodies) and HeV (anti-Hf'V antibodies) were 86.6%, 16.2%, 10.7% and 0.4%, respectively. HBV and Hev had low prevalence in children and no HBV carriage. Perinatal transmission does not seem to be a major route of transmission for HBV. Acupuncture and cupping are risk factors for chronic liver diseases in this setting. The duration of the haemodialysis and a history of malaria were associated with increased rates ofHBV and Hev infections among polytransfusedIHO patients. This is the first report of the prevalence ofEBV, eMV and HHV6 in Yemen. The three viruses had high seroprevalences and co-infections with another herpes virus or hepatitis viruses were common. The Expanded Programme of Immunisations in Aden has achieved HBV vaccination coverage of 63% in children < 5 years old which was lower than its target (85%), but the highest reported in the country. Lack of parental education and access to health care facilities were associated with lack of vaccination. The predominant genotype of hepatitis B was genotype D. Conclusions: Viral hepatitis is a major public health problem in this community. Viruses causing hepatitis varied from hyperendemic (HAV) to low prevalence (HeV); and prevalence varies with age. None of the children < 15 years were HBV carriers or had Hev infection. The detection rates in the study would classify Aden as a low HBV endemic zone. This is the first description of HEV in Yemen revealing it to be a significant problem. Polytransfusion and HO are important risk factors for contracting HBV and Hev. The information yielded in this study on the prevalence and risk factors for HBV and Hev infection on patients with eLO would improve our understanding on the role of these viruses and the application of preventive and control measures in this population.
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Biryahwaho, B. "Analysis of RNAs and proteins of rotaviruses with rearranged genomes : A study of molecular variability." Thesis, University of Glasgow, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.380397.
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Rider, Janet Rosemary. "Isolation and characterisation of human cytomegalovirus envelope glycoproteins." Thesis, University of Reading, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.328918.
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Cornish, Julie Anne. "An investigation into the catalytic mechanism of the adenovirus type II proteinase." Thesis, University of St Andrews, 1996. http://hdl.handle.net/10023/13939.
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A series of P4 (Cbz and t-Boc) N-protected potential substrates and inhibitors, containing the P1 to P4 substrate recognition sequence of the type 2 adenovirus proteinase (Leu-Ala-Gly-Gly) were prepared by solution phase peptide coupling techniques and tested for activity against the proteinase. The potential substrates contained the amide and ester moieties at the P1 carbonyl position and the potential inhibitors contained the alcohol, acid, bromide, aldehyde, ketone, dimethylacetal, nitrile, alkenic, malonyl and epoxysuccinate moieties at the P1 carbonyl position. The esters, the t-Boc urethane and the p-nitroanilide moieties were substrates for the proteinase and the acid and the amides did not bind to the proteinase. Preliminary results show that the other inhibitors were mostly noncompetitive inhibitors for the adenovirus proteinase with approximate Ki's between 15 and 200 μmol dm-3. The test results indicate that the amides must contain a carbonyl group at P2' to bind to the proteinase; the loss of the P1' amine product is the rate limiting step for the hydrolysis of a substrate by the adenovirus proteinase; the P acid product leaves before the P' amine product, which is in complete contrast to classical cysteine proteinases such as papain; little protonation of the P1'amide nitrogen or the P1 carbonyl oxygen of the adenovirus proteinase-substrate complex occurs before the nucleophilic attack on the P1 carbonyl carbon of the adenovirus proteinase-substrate complex.
16
Monaghan, Alan. "Mechanisms of adenovirus DNA replication." Thesis, University of St Andrews, 1995. http://hdl.handle.net/10023/13935.
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The development of a cell-free system in which adenovirus DNA synthesis can be initiated in vitro by using the viral genome or plasmids containing the origin of replication as template has led to the identification of the sequences important for origin function and the isolation and purification of the proteins required for viral DNA replication. In vitro studies on adenovirus types 2 and 5 have shown that their replication requires the formation of a large nucleoprotein complex. This is composed of three virally encoded proteins: adenovirus DNA polymerase, precursor terminal protein and DNA binding protein, and two cellular proteins nuclear factor I and nuclear factor III. While the presence of DNA helicases in other eukaryotic DNA replication systems have been well characterised, this was not the case for adenovirus DNA replication. Initial attempts to identify DNA helicase activity associated with any of the adenovirus replication proteins were unsuccessful. However, a novel DNA unwinding activity was found associated with the DNA binding protein (Ad.DBP). We examined the interaction of DBP with partial DNA duplexes and demonstrated that it could displace oligonucleotides annealed to single-stranded M13 DNA. In addition, DBP could also unwind small fragments of fully duplex DNA. Unlike a DNA helicase, DBP promoted DNA unwinding was nucleoside-5'-triphosphate and Mg2+ independent and exhibited no directionality. The activity required saturating amounts of DBP and was both efficient and cooperative in nature. The helix-destabilising activity was shown to be situated in the C-terminal domain of the protein. These properties suggest a role for DBP in DNA replication in which DBP destabilises duplex DNA during origin unwinding and replication fork movement. The second part of the thesis dealt with the characterisation of the putative "active site" of the adenovirus DNA polymerase. This experimental approach was prompted by data from earlier studies which indicated that DBP could increase the processitivity of the polymerase as well as its sensitivity to nucleotide analogue inhibitors. The "active site" was labelled with pyridoxal-5'-phosphate (PLP), a substrate binding site directed reagent for DNA polymerases. Treatment of Ad.5 DNA polymerase with PLP followed by reduction of the enzyme-PLP adduct resulted in irreversible inactivation of the polymerase activity while the 3'-5' exonuclease associated with Ad.5 DNA polymerase was minimally affected. Substrate protection studies indicate that PLP inhibition is complex. Neither template-primer nor substrate dNTP alone showed any protective effect from PLP mediated inhibition. However, the presence of both template -primer and complementary dNTP significantly protected against PLP inhibition. Comparative tryptic mapping of labelled enzyme, modified in the presence and absence of substrates by PLP reaction, on a C-18 reverse phase column, indicated the protection of one peptide from pyridoxylation in the presence of substrates. Amino acid sequence analyses found no sequence to be present in this peak.
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Temperley, Simon M. "A study of the in vitro initiation of adenovirus DNA replication." Thesis, University of St Andrews, 1992. http://hdl.handle.net/10023/13929.
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The development of systems in which adenovirus DNA can be replicated in vitro has led to the elucidation of the sequences essential for origin function and to the identification of the proteins required for viral DNA replication. Much of the information currently available has been derived from investigations carried out using adenovirus types 2 and 5 which in addition to the viral proteins, adenovirus DNA polymerase, precursor terminal protein and DNA binding protein, require cellular proteins nuclear factor I and nuclear factor III for efficient initiation of DNA replication. In contrast adenovirus type 4 replicates Its DNA efficiently without these cellular proteins. Correspondingly its minimal origin of replication is remarkably simple in structure, consisting of only the terminal 18bp of the adenovirus genome ('the core sequence'). The effect of point mutations in the core region on adenovirus type 4 DNA replication in vitro was investigated and it was found that mutations within two discrete domains had a married deleterious effect on initiation of DNA replication. The crude Ad4 infected cell extracts initially used for in vitro DNA replication were fractionated and it was found that only four detectable proteins, three of which were identified as viral DNA polymerase, precursor terminal protein and DNA binding protein gave efficient DNA replication in vitro and furthermore behaved similarly to unfractionated infected cell extracts in the presence of template which contained point mutations. To examine a possible role of the core region of the origin as containing sites for specific interactions with viral replication proteins, purified adenovirus type 5 precursor terminal protein and DNA polymerase were assayed for their ability to recognise the terminal 1-18 sequence. It was found that both proteins independently and as a heterodimer bound specifically to a sequence corresponding to the core origin of replication, suggesting that sequences within this region are important for localisation of DNA replication proteins at the origin via a sequence specific DNA-protein interaction.
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Wahyuni, Wiwiek Sri. "Variation among cucumber mosaic virus (CMV) isolates and their interaction with plants." Title page, contents and summary only, 1992. http://web4.library.adelaide.edu.au/theses/09PH/09phw137.pdf.
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Includes appendix containing journal publications co-authored by the author. Includes bibliographical references (leaves 130-151). Eighteen strains of Cucumber mosaic virus, including forteen from Australia, two from the USA, and two from Japan were used in this study.
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Williams, Rhys Harold Verdon George. "Further studies on the structure and function of the cucumber mosaic virus genome : a thesis submitted to the University of Adelaide, South Australia for the degree of Doctor of Philosophy." 1988, 1988. http://web4.library.adelaide.edu.au/theses/09PH/09phw7261.pdf.
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Smith, Sarah D. "Selection of Generalists and Specialists in Viral Quasispecies." University of Toledo Health Science Campus / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=mco1224018547.
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Choudhury, Sourav Roy. "Developing an Adeno-Associated Viral Vector (AAV) Toolbox for CNS Gene Therapy: A Dissertation." eScholarship@UMMS, 2016. https://escholarship.umassmed.edu/gsbs_diss/809.
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Neurological disorders – disorders of the brain, spine and associated nerves – are a leading contributor to global disease burden with a sizable economic cost. Adeno-associated viral (AAV) vectors have emerged as an effective platform for CNS gene therapy and have shown early promise in clinical trials. These trials involve direct infusion into brain parenchyma, an approach that may be suboptimal for treatment of neurodegenerative disorders, which often involve more than a single structure in the CNS. However, overall neuronal transduction efficiency of vectors derived from naturally occurring AAV capsids after systemic administration is relatively low. We have developed novel capsids AAV-AS and AAV-B1 that lead to widespread gene delivery throughout the brain and spinal cord, particularly to neuronal populations. Both transduce the adult mouse brain >10-fold more efficiently than the clinical gold standard AAV9 upon intravascular infusion, with gene transfer to multiple neuronal sub-populations. These vectors are also capable of neuronal transduction in a normal cat. We have demonstrated the efficacy of AAV-AS in the context of Huntington's disease by knocking down huntingtin mRNA 33-50% after a single intravenous injection, which is better than what can be achieved by AAV9 at the particular dose. AAVB1 additionally transduces muscle, beta cells, pulmonary alveoli and retinal vasculature at high efficiency, and has reduced sensitivity to neutralizing antibodies in human sera. Generation of this vector toolbox represents a major step towards gaining genetic access to the entire CNS, and provides a platform to develop new gene therapies for neurodegenerative disorders.
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Choudhury, Sourav Roy. "Developing an Adeno-Associated Viral Vector (AAV) Toolbox for CNS Gene Therapy: A Dissertation." eScholarship@UMMS, 2001. http://escholarship.umassmed.edu/gsbs_diss/809.
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Neurological disorders – disorders of the brain, spine and associated nerves – are a leading contributor to global disease burden with a sizable economic cost. Adeno-associated viral (AAV) vectors have emerged as an effective platform for CNS gene therapy and have shown early promise in clinical trials. These trials involve direct infusion into brain parenchyma, an approach that may be suboptimal for treatment of neurodegenerative disorders, which often involve more than a single structure in the CNS. However, overall neuronal transduction efficiency of vectors derived from naturally occurring AAV capsids after systemic administration is relatively low. We have developed novel capsids AAV-AS and AAV-B1 that lead to widespread gene delivery throughout the brain and spinal cord, particularly to neuronal populations. Both transduce the adult mouse brain >10-fold more efficiently than the clinical gold standard AAV9 upon intravascular infusion, with gene transfer to multiple neuronal sub-populations. These vectors are also capable of neuronal transduction in a normal cat. We have demonstrated the efficacy of AAV-AS in the context of Huntington's disease by knocking down huntingtin mRNA 33-50% after a single intravenous injection, which is better than what can be achieved by AAV9 at the particular dose. AAVB1 additionally transduces muscle, beta cells, pulmonary alveoli and retinal vasculature at high efficiency, and has reduced sensitivity to neutralizing antibodies in human sera. Generation of this vector toolbox represents a major step towards gaining genetic access to the entire CNS, and provides a platform to develop new gene therapies for neurodegenerative disorders.
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Bull, James Christopher. "A study of the population genetics of nucleopolyhedrovirus infections within infected insects." Thesis, Imperial College London, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.274938.
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Lorson, Christian. "An analysis of transcriptional regulation of the MVM capsid gene promoter." free to MU campus, to others for purchase, 1997. http://wwwlib.umi.com/cr/mo/fullcit?p9841319.
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Ligat, Julio S. "Pathology and distribution in the host of pea seed-borne mosaic virus." Title page, contents and summary only, 1993. http://web4.library.adelaide.edu.au/theses/09PH/09phl723.pdf.
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Includes bibliographical references (leaves 82-92). Five isolates of pea seed-borne mosaic virus were compared by host range and symptomatology on 16 pisum sativum cultivars lines, 21 lines of Lathyrus and Lens spp. and several indicator species
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Hajimorad, Mohammad Reza. "Variation in alfalfa mosaic virus with special reference to its immunochemical properties." Title page, contents and summary only, 1990. http://web4.library.adelaide.edu.au/theses/09PH/09phh154.pdf.
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Includes Appendix listing other publications by the author. Includes bibliographical references (leaves 134-181). Alfalfa mosaic virus was isolated from lucerne (Medicago sativa) plants with a variety of disease symptoms. Experiments showed that each isolate was biologically distinct and that the host range and symptomatology of each isolate was affected by the environmental condition.
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Chilton, Jamie Meredith. "Investigation of the limitations of viral gene transfer to murine embryonic stem cells." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2008. http://hdl.handle.net/1853/29745.
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Thesis (Ph.D)--Biomedical Engineering, Georgia Institute of Technology, 2008.Committee Chair: Joseph Le Doux; Committee Member: Anthanassios Sambanis; Committee Member: David Archer; Committee Member: Michelle LaPlaca; Committee Member: Steve Stice; Committee Member: Todd McDevitt. Part of the SMARTech Electronic Thesis and Dissertation Collection.
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Bergner, Laura. "Viral communities in vampire bats : geographical variation and ecological drivers." Thesis, University of Glasgow, 2018. http://theses.gla.ac.uk/30811/.
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Microbial communities play important roles in organismal and ecosystem health. High throughput sequencing has revolutionized our understanding of host-associated microbial communities, but the viral component of these communities remains poorly characterized relative to microbes such as bacteria, particularly in non-human hosts. This knowledge gap has implications for global health, as viruses originating in wildlife are responsible for recent disease outbreaks in humans and domestic animals. Although studies have identified factors differentiating viral communities between species, we have little understanding of the variability of viral communities within species. Comparative studies of viral communities are therefore necessary to characterize novel taxa and to evaluate the ecological factors influencing intraspecific viral diversity and distribution. Bats are recognized as “special” reservoirs for viruses because they are associated with diverse viral communities and display deep evolutionary relationships with individual viral taxa. Common vampire bats (Desmodus rotundus) represent a particularly interesting system in which to investigate viral communities, as they are obligate blood feeders that interact ecologically with many different host species, providing opportunities for the acquisition of diverse viruses. The overall objective of this thesis was to advance our understanding of intraspecific wildlife-associated viral communities using an established field network of common vampire bat colonies across Peru. Specifically, I developed a novel method for comparative viral community studies, characterized the viral communities of vampire bats, and examined the ecological correlates of vampire bat viral diversity across Peru. Metagenomic sequencing is a promising technique for comparative studies of viral communities in wildlife, but there is a need to first develop standardized methods that can be applied to samples collected in the field. In Chapter 2 I developed a shotgun metagenomic sequencing approach to characterizing viral communities from non-invasive samples. Specifically, I optimized extraction and sequencing protocols using fecal and oropharyngeal swabs collected from common vampire bats in Peru. Two preliminary sequencing runs were performed, the results of which motivated four pilot studies in which I tested how different storage media, nucleic acid extraction procedures, and enrichment steps affect the viral community detected. Metagenomic sequencing revealed viral contamination of fetal bovine serum, a component of viral transport medium, suggesting that swabs should be stored in RNALater or another non-biological medium. Extraction and qPCR tests were performed on swabs inoculated with known concentrations of virus, which revealed that nucleic acid should be directly extracted from swabs rather than from supernatant or pelleted material. Metagenomic sequencing of paired samples was used to test enrichment by ribosomal RNA depletion and light DNAse treatment, which both reduced host and bacterial nucleic acid in samples and improved virus detection. A bioinformatic pipeline was developed specifically for processing vampire bat shotgun viral metagenomic data. Finally, the optimized protocol was applied to twelve pooled samples from seven localities in Peru, and read subsampling demonstrated that the viral communities detected were consistent at commonly attained depths of sequencing. The protocol developed in this chapter enables minimally biased comparative viral community studies in non-invasive samples collected from wildlife. Having a detailed understanding of viral diversity in key wildlife hosts is an important first step in evaluating the risk of zoonotic disease emergence, but we still lack a holistic view of viral communities in many species including vampire bats. In Chapter 3, I used the metagenomic sequencing protocol developed in Chapter 2 to thoroughly characterize viral communities in the saliva and feces of vampire bats captured across Peru. Viruses were detected from a range of natural host groups including vertebrate-associated taxa that were potentially infecting vampire bats, bacteriophages associated with gut bacteria, and plant- or insect-infecting viruses potentially acquired from the environment. There were broad differences between fecal and saliva viral communities, showing evidence of body habitat compartmentalization. Overall, results established that vampire bat viral communities differ between body habitats and suggested that, for the vertebrate-infecting families analyzed, novel viruses mostly fall within bat-specific clades, without evidence of livestock or humans acting as a major source of viral diversity in vampire bats. Interspecific differences in ecological and life history traits are known to impact viral richness in bats, but the factors structuring viral communities within bat species are less well understood. In Chapter 4, I examined the spatial, demographic and environmental correlates of intraspecific viral diversity in vampire bats. Three measures of viral diversity were calculated at the colony level: richness, a novel measure of taxonomic diversity, and community composition. Generalized linear models were then used to test the effects of broad scale and local ecological variables on saliva and fecal viral diversity. The results showed for the first time that ecological variables can influence intraspecific viral diversity. In summary, the work presented in this thesis advances our understanding of wildlife-associated viral communities in an ecologically important bat host. Future directions in comparative wildlife viral metagenomics, as discussed in Chapter 5, will include exploring the determinants of viral communities across host species, environments and time.
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Ramaley, Patricia A. "Host genetics of HIV-1 infection and disease progression in Uganda." Thesis, University of Oxford, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.365714.
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Carlsson, Beatrice. "Human Caliciviruses: a study of viral evolution, host genetics and disease susceptibility." Doctoral thesis, Linköpings universitet, Molekylär virologi, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-76036.
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The viruses described in this thesis are the norovirus and sapoviruses, which belong to the family of human caliciviruses and are known to cause gastroenteritis in humans. Gastroenteritis has emerged as a global health problem and is based on the large number of infected considered as one of the most common diseases today. According to estimates of the World Health Organization (WHO), gastroenteritis causes over five times more pediatric deaths compared to pediatric deaths caused by HIV/AIDS worldwide. Norovirus, the cause of the famous “winter vomiting disease”, is alone responsible for more than 200 000 deaths each year in children less than 5 years of age. The mechanism for emergence and evolution of new human calicivirus strains, as well as protective immunity in the human population is poorly understood. The main focus for this thesis was to elucidate the possible correlation between human calicivirus evolution, host genetics and disease susceptibility. One of the main findings presented in this thesis is the documentation of in vivo capsid gene evolution and quasispecies dynamics during chronic NoV GI.3 infection (Paper 1). In paper II, we reported that the G428A nonsense mutation in the FUT2 gene provides strong but not absolute protection against symptomatic GII.4 NoV infection. In my last two papers (Paper III and IV), we were the first to investigate host genetic susceptibility factors during authentic SaV infection. To summarize, the results presented in this thesis show that the success of human calicivirus infection probably is determined by a delicate interplay between virus evolution and susceptibility of the host, both genetically and immunologically.
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Fok, Yuen-kei Vivien. "Expression of human herpesvirus 6 (HHV-6) genes in virus-infected cells /." View the Table of Contents & Abstract, 2005. http://sunzi.lib.hku.hk/hkuto/record/B31385515.
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Lee, Paul. "Molecular epidemiology of human coronavirus OC43 in Hong Kong /." View the Table of Contents & Abstract, 2007. http://sunzi.lib.hku.hk/hkuto/record/B38348342.
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Fok, Yuen-kei Vivien, and 霍沅琪. "Expression of human herpesvirus 6 (HHV-6) genes in virus-infected cells." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2005. http://hub.hku.hk/bib/B45010006.
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Hampson, J. "A study of the genetics and growth of a tripartite RNA virus using ts mutants." Thesis, University of Warwick, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.380288.
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Wakeford, Laura 1956. "COMPLEMENTATION BETWEEN TEMPERATURE-SENSITIVE MUTANTS OF POLIOVIRUS." Thesis, The University of Arizona, 1987. http://hdl.handle.net/10150/276556.
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Conditional lethal mutants of poliovirus type 1 (Mahoney) were generated by treatment with the mutagen hydroxylamine. Temperature-sensitive mutants were selected by the replica plating technique at temperatures of 33°C (permissive) and 39°C (restrictive). New mutants were generated to achieve a larger population of mutants and also to generate additional RNA- mutants in this population. These mutants were characterized by two criteria: RNA synthesis and thermal stability. RNA synthesis is measured by the accumulation of labeled uridine incorporation into trichloroacetic acid (TCA) insoluble material. The thermal stability is determined by the difference in plaque forming units before and after treatment of the virion at 45°C. Complementation co-infections (5 MOI for each virus stock) were analyzed for the presence of the 150S virion particle of poliovirus after sedimentation through a linear sucrose gradient. Complementation is observed between RNA(+) mutants v.s. RNA(-) mutants, and between two RNA(-) mutants, but not between two RNA(+) mutants. Although reciprocal complementation has not been documented in this study some speculation on complementation is presented in this thesis.
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Tajbakhsh, Shahragim Carleton University Dissertation Biology. "Isolation and characterization of the Tipula Iridescent Virus capsid gene." Ottawa, 1988.
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de, Groot Saskia Elizabeth. "Genome annotation and selectional analysis of viral evolution." Thesis, University of Oxford, 2008. http://ora.ox.ac.uk/objects/uuid:9bc1f480-5556-4f44-8700-8c230a5dbda9.
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In the past few years we have witnessed an explosion in the viral genomic data available. GenBank alone holds over 80,000 close to complete viral genomes, and numbers are rising fast. For example, since the submission of the first SARS genome in May 2003, over 140 more have been published. With this genomic data at hand we hope to finally be able to improve our understanding of viruses. Several papers have been dedicated to the study of genome annotation and selection on viral genomes, in particular focusing attention on the evolutionary behaviour of overlapping reading frames. This is a feature common to viruses, where due to the three periodicity of the genetic code, up to three genes may be encoded simultaneously in one direction. The constraints placed on a nucleotide involved in such a multiple coding region will naturally have an effect on its mutational behaviour, and as a result the pattern of evolution will be more complex. Additionally, due to their fast evolution time, we observe changes in gene structure between viruses of the same family. Finally, as a result of this high divergence, alignments between two genomes will tend to be unreliable, thus complicating the issue of comparative analysis further. Our goal is to present methods which may deal with the above mentioned complications. We first introduce an ab initio pairwise comparative annotation method, which not only accounts for the presence of overlapping reading frames in genomes, but also for differences in gene structure between the two compared sequences. Secondly, we develop a hidden Markov model for the annotation of selection strengths across a viral genome accommodating for inter- as well as intragenic differences in selection. Thirdly, we investigate the effect of using a fixed alignment on the inference of selection by incorporating statistical alignment into our selection analysis. All three methods presented here improve on their respective equivalents in the field. We investigate the nature of selection in overlapping regions in several studies, in particular on the genomes of Hepatitis B and HIV2. We provide a full annotation of selection strengths on a nucleotide level for both viral sequences, highlighting fast evolving regions such as the gp120 protein. We also analyse the mutational behaviour of overlapping regions in both genomes and find that in Hepatitis B selection seems to be of equal strength for single and double coding regions. In HIV2, however, single coding regions appear to be under twice as stringent selection as double coding regions, with a tendency for a fast evolving region to overlap a slow evolving one. Each chapter of our work relates to one of our publications. We introduce in turn each method, its academic context and its results. We subsequently in chapter 5 discuss for each method its achievements, its shortcomings and future possible extensions and improvements to it.
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Deleris, Angélique. "Genetics of antiviral RNA silencing in Arabidopsis through an analysis of the P38 viral suppressor." Université Louis Pasteur (Strasbourg) (1971-2008), 2007. http://www.theses.fr/2007STR13034.
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Wong, Hoi-man Emily, and 黃凱敏. "Codon usage biases of influenza A viruses." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2009. http://hub.hku.hk/bib/B43572200.
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Wong, Hoi-man Emily. "Codon usage biases of influenza A viruses." Click to view the E-thesis via HKUTO, 2009. http://sunzi.lib.hku.hk/hkuto/record/B43572200.
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Behjatnia, Seyyed Ali Akbar. "Characterisation of DNA replication of tomato leaf curl geminivirus /." Title page, contents and abstract only, 1997. http://web4.library.adelaide.edu.au/theses/09ACP/09acpb419.pdf.
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Arnoldi, Francesca. "Interaction of rotavirus nonstructural protein NSP5 with the viral replication complex." Doctoral thesis, Scuola Normale Superiore, 2008. http://hdl.handle.net/11384/85952.
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Rotavirus morphogenesis starts in intracellular inclusion bodies called viroplasms,
where synthesis of the11 dsRNA genome segments and their packaging in new viral
particles take place. RNA replication is mediated by several viral proteins, of which
VP1, the RNA-dependent RNA polymerase, and VP2, the core scaffolding protein,
were shown to be sufficient to provide replicase activity in vitro. In vivo, however,
viral replication complexes also contain the nonstructural proteins NSP2 and NSP5,
which were shown to be essential for replication, to interact with each other and to
form viroplasm-like structures (VLS) when coexpressed in uninfected cells.
In order to gain a better understanding of the intermediates formed during viral
replication, this work focused on the interactions of NSP5 with VP1, VP2 and NSP2.
We constructed a tagged form of VP1 and by coimmunoprecipitation experiments
we demonstrated that VP1 and NSP5 interact in virus-infected cells as well as in the
absence of other viral proteins or viral RNA in cotransfected cells. Using deletion
mutants of NSP5 or different fragments of NSP5 fused to EGFP, we identified the 48
C-terminal amino acids as the region essential for interaction with VP1. On the other
hand, removal of the C-terminal 15 amino acids from tagged VP1 resulted in a less
efficient coimmunoprecipitation with NSP5, suggesting an involvement of the Cterminus
of VP1. Interaction of NSP5 with VP2 was investigated by coexpression of
the two proteins in uninfected cells, which resulted in a strong hyperphosphorylation
of NSP5 and in the formation of VLS, that we named VLS(VP2i) to distinguish them
from those induced by NSP2, here designated as VLS(NSP2i). VLS(VP2i) were shown
to assemble independently of the phosphorylation degree of NSP5 and to recruit the
viroplasm-resident proteins NSP2, VP1, VP2 and VP6 (the protein forming the middle
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layer of the virion). Attempts to coimmunoprecipitate NSP5 and VP2 failed both from
infected and cotransfected cells.
Tagged VP1 was found to localize in VLS (both VP2i and NSP2i) and in viroplasms,
and to be able to replace wild-type VP1 structurally by being incorporated into
progeny viral particles. Coexpression of different combinations of tagged VP1,
NSP5, NSP2 and VP2 showed that the interaction of VP1 with NSP5 is not affected
by the other viral proteins and is stronger than the interaction with NSP2. In addition,
an inhibitory effect of VP1 on the levels of NSP5 hyperphosphorylation induced by
both NSP2 and VP2 was observed.
Altogether, these data confirmed an important role for NSP5 in replication, related
with the interactions with the two structural proteins essentially involved in viral
genome synthesis, and suggested that NSP5 plays a key role in architectural
assembly of viroplasms and in recruitment of the other viroplasmic proteins.
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Yeung, Yin-shan. "Molecular characterization of apoptosis induced by severe acute respiratory syndrome coronavirus spike protein." Click to view the E-thesis via HKUTO, 2006. http://sunzi.lib.hku.hk/hkuto/record/B38302366.
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Burnight, Erin Rae. "Targeting therapeutic vector expression and integration for gene therapy applications." Diss., University of Iowa, 2011. https://ir.uiowa.edu/etd/2831.
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Gene therapy is an attractive treatment for many genetic diseases because rather than treat the symptoms of the disease, it has the potential to correct the underlying defect. Cystic fibrosis and hemophilia A are two monogenic disorders that are particularly well-suited to treatment with gene therapy as a relatively small increase in the function is needed to see improvement. Gene therapy has provided some correction in both diseases using a variety of vector systems but sustained expression and long term correction have yet to be demonstrated in the clinic. It is unclear in which cell type(s) correction of the underlying defect in cystic fibrosis will be most effective. Studies indicate that the majority of CFTR expression is in the submucosal glands and ciliated epithelia – a terminally differentiated cell type (Engelhardt, J.F. et al, 2004, Journal of Clinical Investigation). Therapeutic gene transfer would thus be most effective if achieved in a progenitor cell type. Additionally, the native regulation of CFTR has not been definitively elucidated. To this end, one goal of our studies is to develop a lentiviral vector system with heterologous promoters of varying strengths and cell specificity to aid in our selection of optimal reagents for appropriate CFTR expression. We show that use of novel internal promoters from the human PLUNC and WDR65 genes direct persistent expression in the airway. Additionally, disruption of the nasal epithelium with the detergent polidocanol eliminated reporter expression in mouse airway. Two weeks post-treatment, expression returned indicating targeting of a progenitor cell population with our novel vectors.
Integrating vector systems can treat chronic diseases such as cystic fibrosis because expression can persist long term from these vectors if cells with progenitor capacity are targeted (Sinn, P.L. et al, 2005, Journal of Virology). However, the potential for genotoxicity from vector-related dysregulation is a concern. Thus, a second aim of these studies was to develop a lentiviral vector that can target a specific locus in the genome. We developed a FIV vector in which the integrase was modified with a protein-binding domain that when co-delivered with a fusion consisting of the cognate protein and a DNA binding domain would tether the vector to the appropriate locus. Unfortunately, integrase modification rendered the vector catalytically inactive. Lastly, we hoped to develop a non-viral transposon vector system (piggyBac) for gene transfer applications to the liver for treatment of hemophilia A. The recent demonstration that piggyBac transposase is highly active in mammalian cells warrants further development of this vector as an alternative to other non-viral integrating vector systems currently under investigation. We showed persistent reporter and therapeutic transgene expression in the livers of mice treated with the piggyBac vector. Furthermore, we show for the first time in vivo persistence and increased expression from the recently developed hyperactive transposase. The development of integrating vectors targeted to specific tissues or genomic loci is important in for treatment of the monogenic diseases cystic fibrosis and hemophilia A.
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Lam, Suk-fun, and 林淑芬. "Discovery and complete genome sequence of a novel group ofcoronavirus." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2008. http://hub.hku.hk/bib/B41633647.
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Lam, Suk-fun. "Discovery and complete genome sequence of a novel group of coronavirus." Click to view the E-thesis via HKUTO, 2008. http://sunzi.lib.hku.hk/hkuto/record/B41633647.
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Urbani, Nicola. "Association of endogenous viral genes and myb-gene polymorphisms with disease resistance in white leghorns." Thesis, McGill University, 1992. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=56818.
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The incidences of endogenous viral genes (ev-genes) and myb-gene polymorphisms were determined in substrains of strains R, M and G which had been divergently selected or susceptibility to tumour formation induced by Rous Sarcoma virus (RSV) of type A and B. Frequencies of myb gene polymorphisms were also determined in two replicates of strains selected for high and low multiple immune response to challenge with Pasteurella multocida and Mycoplasma gallisepticum. Strains R, M and G were found to contain different sets of ev-genes reflecting their distinct genetic origins. Among eleven ev-genes identified, two showed a significantly increased frequency in the susceptible substrains. One was ev-6, which expresses the viral envelope protein of the endogenous avian leucosis, while the other was a new endogenous viral gene New-E, whose phenotype is unknown. A significant increased incidence of ev-4, reported to be a silent ev-gene, was observed in resistant rather than susceptible substrain. Myb gene polymorphisms were assessed using a cDNA probe and a genomic probe yielding 2 and 3 restriction fragment length polymorphisms (RFLPs) respectively. In strains M and G, only one polymorphism (PM5$ sp+$) observed at an Msp I site located downstream of the last of the c-myb exons was found to be significantly co-selected for susceptibility. Analysis of RFLPs of myb-gene in strains selected for high or low multiple immune response did not reveal any significant response to selection. Rather, polymorphisms seemed to reflect a founder effect as revealed by opposite frequencies obtained in the two replicates. DNA methylation, a possible epigenetic mechanism regulating gene expression, was also investigated in the myb-gene. DNA from semen, blood, spleen, liver and thymus was extracted from organs obtained from chickens at different ages.
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Dennis, Tristan Philip Wesley. "Mining genome data for endogenous viral elements and interferon stimulated genes : insights into host virus co-evolution." Thesis, University of Glasgow, 2018. http://theses.gla.ac.uk/30887/.
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Paleovirology is the study of viruses over evolutionary timescales. Contemporary paleovirological analyses often rely on sequence data, derived from organism genome assemblies. These sequences are the germline inherited remnants of past viral infection, in the form of endogenous viral elements and the host immune genes that are evolving to combat viruses. Their study has found that viruses have exerted profound influences on host evolution, and highlighted the conflicts between viruses and host immunity. As genome sequencing technology cheapens, the accumulation of genome data increases, furthering the potential for paleovirological insights. However, data on ERVs, EVEs and antiviral gene evolution, are often not captured by automated annotation pipelines. As such, there is scope for investigations and tools that investigate the burgeoning bulk of genome data for virus and and antiviral gene sequence data in the search of paleovirological insight.
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Terenius, Olle. "Anti-parasitic and anti-viral immune responses in insects." Doctoral thesis, Stockholm : Institutionen för genetik, mikrobiologi och toxikologi, Univ, 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-224.
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Geering, Andrew D. W. "The epidemiology of cucumber mosaic virus in narrow-leafed lupins (Lupinus angustifolius) in South Australia." Title page, table of contents and summary only, 1992. http://web4.library.adelaide.edu.au/theses/09PH/09phg298.pdf.
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