Single-molecule DNA flow-stretching assays have been a powerful approach to study various aspects on the mechanism of DNA replication for more than a decade. This technique depends on flow-induced force on a bead attached to a surface-tethered DNA. The difference in the elastic property between double-strand DNA (long) and single-strand DNA (short) at low regime force allows the observation of the beads motion when the dsDNA is converted to ssDNA by the replisome machinery during DNA replication. Here, I aim to develop an assay to track in real-time the encounter of the bacteriophage T7 replisome with abasic lesion site inserted on the leading strand template. I optimized methods to construct the DNA substrate that contains the abasic site and established the T7 leading strand synthesis at the single molecule level. I also optimized various control experiments to remove any interference from the nonspecific interactions of the DNA with the surface. My work established the foundation to image the encounter of the T7 replisome with abasic site and to characterize how the interactions between the helicase and the polymerase could influence the polymerase proofreading ability and its direct bypass of this highly common DNA damage type.

Porcine reproductive and respiratory syndrome (PRRS) is a viral disease that has devastated the global swine industry since the mid 1980s. Although modified live vaccines (MLVs) are typically used for the prevention of clinical disease, they are not always fully effective. Additionally, acute PRRS outbreaks, characterized by more severe clinical signs, have appeared in herds that were previously vaccinated. In this dissertation, we further analyzed the pathogenesis of PRRSV through genetic characterization, assay development, and quasispecies evaluation using the PRRSV ORF5 gene while also attempting to develop an improved PRRS vaccine. To explore the possible mechanism for the emergence of acute PRRS, the open reading frame 5 (ORF5) gene encoding the major envelope protein (GP5) of acute PRRSV isolates was characterized. Sequence and phylogenetic analyses revealed that seven of the acute PRRS virus (PRRSV) isolates were related to other N. American PRRSV isolates while one isolate, 98-37120-2, was very closely related to and may have been derived from the MLV, RespPRRS. We also developed a heteroduplex mobility assay (HMA) for quickly identifying PRRSV field isolates with significant nucleotide sequence identities (â d98%) with the MLVs based on the amplification, denaturation, and reannealing of the ORF5 gene of the field isolates with those of MLV reference strains. All of the field isolates that were highly related to RespPRRS (â T2% nucleotide sequence divergence) were identified by the HMA to form homoduplexes with the reference RespPRRS MLV. We also developed a unique strategy for infecting pigs with PRRSV, known as in vivo transfection, by bypassing the traditional in vitro cell culture step required for in vivo studies. We demonstrated that inoculation of RNA transcripts of a PRRSV infectious cDNA clone directly into the lymph nodes and tonsils of pigs produces active PRRSV infection. Using this method, we also examined the quasispecies populations of PRRSV. Finally, we evaluated the ability of Salmonella choleraesuis to express the PRRSV GP5, and tested its immunogenicity in mice. Based on our data, there was no indication of Salmonella replication in the mice or any evidence of antibody production against S. choleraesuis or PRRSV GP5. / Ph. D.

Porcine reproductive and respiratory syndrome virus (PRRSV) is the cause of a pandemic that has been devastating the U.S. and global swine industry for more than twenty years. PRRSV vaccine development is challenging due to virus heterogeneity. Evidence indicates that the major envelope protein, GP5, is the primary target for a subunit vaccine. In native virions GP5 primarily exists as a disulfide linked complex with the membrane protein, M, which also possesses immunogenic properties. Recent studies report that the GP5/M complex is a more significant vaccine candidate. Currently, no bulk purification methods have been reported for PRRSV proteins. The objective of this research was to develop a purification process for GP5 or GP5/M from native virions. PRRS virions were isolated and concentrated through sucrose cushion ultracentrifugation and target envelope proteins were solubilized with Triton X-100 detergent for further processing. GP5/M was not consistently identified in samples and was therefore abandoned. GP5 was identified by Western blot throughout processing with a αORF5 antibody. Cation exchange chromatography (CEX) was utilized for partial fractionation of GP5, although the viral nucleocapsid protein, N, was a major impurity in CEX elution fractions. As a second chromatographic step, hydrophobic interaction chromatography (HIC) further purified GP5 by means of a two-stage elution scheme. Pure GP5 was eluted from the HIC resin in the second HIC elution stage by Triton X-100 displacement; however the protein is present as a homodimeric/tetrameric aggregate. This process will be useful in PRRSV vaccine development and the purified GP5 product could be used as much needed positive controls in animal studies. / Master of Science

Made available in DSpace on 2014-06-12T15:51:41Z (GMT). No. of bitstreams: 2 arquivo2823_1.pdf: 9037757 bytes, checksum: fa5b9563e9f3a0baec78ac68dd1bc1a2 (MD5) license.txt: 1748 bytes, checksum: 8a4605be74aa9ea9d79846c1fba20a33 (MD5) Previous issue date: 2009 / Conselho Nacional de Desenvolvimento Científico e Tecnológico / As infecções causadas por papilomavírus humanos (HPV) destacam-se por sua elevada frequência, implicações clínicas e interpessoais, além de serem identificadas como fatores relacionados à oncogenese. A infeção pelo HPV é considerada uma doença sexualmente transmissível relatada entre 10% a 20% da população adulta mundial. O HPV DNA está prevalente em 2% a 68% dos adultos. O HPV é considerado o agente etiológico essencial no desenvolvimento de neoplasias de colo uterino, que é a segunda causa mais importante de mortes em mulheres. A infecção pelo HPV tem sido correlacionada também com o câncer de anus, em 85% dos casos (Palesfsky, 1998), 35% a 50% dos casos de cânceres de vulva, vagina e pênis e em 10% dos casos de neoplasias de laringe, trato respiratório e digestivo (zur Hausen, 2009). O câncer gástrico é uma das principais causas de óbitos em todo mundo. Sua heterogeneidade o transforma em modelo para estudos em carcinogênese. A identificação de papilomavírus humano em neoplasias gástricas e esofágicas sugere a possibilidade de seu envolvimento na oncogênese destas neoplasias. Normalmente, amostras oriundas de biópsias diagnósticas e exéreses cirúrgicas são inclusas em parafina para posterior estudo histopatológico. Estas amostras podem servir de fonte para identificação genômica, através de técnicas adequadas. A presente Tese buscou o desenvolvimento de uma nova técnica de identificação de genes a partir de materiais biológicos conservados em parafina. Foram utilizadas amostras provenientes de pacientes portadores de adenocarcinoma gástrico e carcinoma epipermóide perianal. Os fragmentos do gene da proteína viral L1 foram amplificados através de PCR com o primer GP5+/6+ e o primer MY09/11, identificados com o uso dos equipamentos Bioanalyzer e Papillocheck. A técnica desenvolvida demonstrou-se eficiente na identificação do gene da proteína viral L1, em amostras fixadas em parafina