Thesis (Ph. D.)--West Virginia University, 2000. / Title from document title page. Document formatted into pages; contains x, 231 p. : ill. (some col.). Vita. Includes abstract. Includes bibliographical references (p. 188-203).

Thesis (M.Med.Sc.)--University of Hong Kong, 2002. / Includes bibliographical references (leaves 42-47). Also available in print.

Thesis (M.S.) -- University of Tennessee, Knoxville, 2005. / Title from title page screen (viewed on Feb. 7, 2006). Thesis advisor: Larry D. McKay. Vita. Includes bibliographical references.

Thesis (Ph. D.)--University of Washington, 2005. / Vita. Includes bibliographical references (leaves 112-127).

abstract: Telomerase is a specialized enzyme that adds telomeric DNA repeats to the chromosome ends to counterbalance the progressive telomere shortening over cell divisions. It has two essential core components, a catalytic telomerase reverse transcriptase protein (TERT), and a telomerase RNA (TR). TERT synthesizes telomeric DNA by reverse transcribing a short template sequence in TR. Unlike TERT, TR is extremely divergent in size, sequence and structure and has only been identified in three evolutionarily distant groups. The lack of knowledge on TR from important model organisms has been a roadblock for vigorous studies on telomerase regulation. To address this issue, a novel in vitro system combining deep-sequencing and bioinformatics search was developed to discover TR from new phylogenetic groups. The system has been validated by the successful identification of TR from echinoderm purple sea urchin Strongylocentrotus purpuratus. The sea urchin TR (spTR) is the first invertebrate TR that has been identified and can serve as a model for understanding how the vertebrate TR evolved with vertebrate-specific traits. By using phylogenetic comparative analysis, the secondary structure of spTR was determined. The spTR secondary structure reveals unique sea urchin specific structure elements as well as homologous structural features shared by TR from other organisms. This study enhanced the understanding of telomerase mechanism and the evolution of telomerase RNP. The system that was used to identity telomerase RNA can be employed for the discovery of other TR as well as the discovery of novel RNA from other RNP complex. / Dissertation/Thesis / Ph.D. Biochemistry 2011

Eukaryotic initiation factor 5A, eIF5A, is a ubiquitous eukaryotic protein that has been shown to influence the translation initiation of a specific subset of mRNAs. It is the only protein known to undergo hypusination in a two-step post translational modification process involving deoxyhypusine synthase (DHS) and deoxyhypusine hydroxylase (DOHH) enzymes. Hypusination has been shown to influence translation of HIV-1 and HTLV-1 nuclear export signals, while the involvement of active hypusinated eIF5A in induction of IRES mediated processes that initiate pro-apoptotic process have inspired studies into the manipulation of eIF5A in anti-cancer and anti-diabetic therapies. eIF5A oligomerisation in eukaryotic systems has been shown to be influenced by hypusination and the mechanism of dimerisation is RNA dependent. Nuclear magnetic resonance spectroscopy approaches were proposed to solve the structure of the hypusinated eIF5A in solution in order to understand the influence of hypusination on the monomeric arrangement which enhances dimerisation and activates the protein. Cleavage of the 18 kDa protein monomer by introduction of thrombin cleavage site within the flexible domain was thought to give rise to 10 kDa fragments accessible to a 600 MHz NMR spectrometer. Heteronuclear single quantum correlation experiments of the mutated isotopically labelled protein expressed in E. coli showed that the eIF5A protein with a thrombin cleavage insert, eIF5AThr (eIF5A subscript Thr), was unfolded. In silico investigations of the behaviour of eIF5A and eIF5AThr (eIF5A subscript Thr) models in solution using molecular dynamics showed that the mutated model had different solution dynamics to the native model. Chemical shift predictors were used to extract atomic resolution data of solution dynamics and the introduction of rigidity in the flexible loop region of eIF5A affected solution behaviour consistent with lack of in vivo function of eIF5AThr (eIF5A subscript Thr) in yeast. Residual dipolar coupling and T₁ relaxation times were calculated in anticipation of the extraction of experimental data from RDC and relaxation dispersion experiments based on HSQC measurable restraints.

abstract: Telomerase enzyme is a truly remarkable enzyme specialized for the addition of short, highly repetitive DNA sequences onto linear eukaryotic chromosome ends. The telomerase enzyme functions as a ribonucleoprotein, minimally composed of the highly conserved catalytic telomerase reverse transcriptase and essential telomerase RNA component containing an internalized short template region within the vastly larger non-coding RNA. Even among closely related groups of species, telomerase RNA is astonishingly divergent in sequence, length, and secondary structure. This massive disparity is highly prohibitive for telomerase RNA identification from previously unexplored groups of species, which is fundamental for secondary structure determination. Combined biochemical enrichment and computational screening methods were employed for the discovery of numerous telomerase RNAs from the poorly characterized echinoderm lineage. This resulted in the revelation that--while closely related to the vertebrate lineage and grossly resembling vertebrate telomerase RNA--the echinoderm telomerase RNA central domain varies extensively in structure and sequence, diverging even within echinoderms amongst sea urchins and brittle stars. Furthermore, the origins of telomerase RNA within the eukaryotic lineage have remained a persistent mystery. The ancient Trypanosoma telomerase RNA was previously identified, however, a functionally verified secondary structure remained elusive. Synthetic Trypanosoma telomerase was generated for molecular dissection of Trypanosoma telomerase RNA revealing two RNA domains functionally equivalent to those found in known telomerase RNAs, yet structurally distinct. This work demonstrates that telomerase RNA is uncommonly divergent in gross architecture, while retaining critical universal elements. / Dissertation/Thesis / Doctoral Dissertation Molecular and Cellular Biology 2015

Made available in DSpace on 2014-06-11T19:29:32Z (GMT). No. of bitstreams: 0 Previous issue date: 2007-06-22Bitstream added on 2014-06-13T18:39:11Z : No. of bitstreams: 1 figueiredo_as_me_botfmvz.pdf: 290159 bytes, checksum: 38ae46f390705b8d387a7ef9c78d6040 (MD5) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / O Vírus da Imunodeficiência Felina (FIV) é um lentivírus que causa uma síndrome de imunodeficiência em gatos domésticos. O FIV tem sido particularmente utilizado em estudos de resistência viral aos análogos de nucleosídeos devido a Transcriptase Reversa (TR) apresentar propriedades físicas, catalíticas e sensibilidade às drogas semelhantes à TR do HIV. Os objetivos desse trabalho foram tratar com AZT gatos naturalmente infectados com o FIV, fazer o monitoramento da carga viral e DNA proviral por PCR em tempo real e monitoramento genético por seqüenciamento. Dos 12 animais infectados, 6 receberam o AZT na dose de 10mg/kg/dia e 6 receberam placebo. Durante 96 dias de tratamento, o plasma e sangue destes animais foram analisado com relação à carga viral e concentração relativa de DNA proviral utilizando-se a técnica de quantificação relativa por PCR em tempo real com SYBR Green, desenvolvida por nossa equipe. Além disso, foi realizado o sequenciamento genético da região que codifica a TR de 3 dos animais. Foi realizada com sucesso a padronização da PCR em tempo real para quantificação relativa do FIV. Não houve diferença estatisticamente significativa da carga viral ou do DNA proviral entre os grupos tratado e controle. O seqüenciamento genético revelou a presença de lisina na posição 41 do sítio ativo da TR. A presença deste aminoácido confere até 4 vezes menor sensibilidade ao AZT em mutantes do HIV. Por possuir alta estabilidade genética, supomos que os vírus dos demais animais não sequenciados possuem também a 41-lisina A presença da 41-lisina pode ser uma das possíveis explicações para a falha do tratamento com AZT. Outra hipótese é a de que a dose fornecida não foi adequada. / Feline Immunodeficiency Virus (FIV) is a lentivirus which causes a progressive disruption of the host's immune functions. FIV has been particularly used as a model for studies in retroviral resistance to nucleoside analogs because its similarities in physical properties, catalytic and sensitivity in comparison with HIV/RT. The aims of this work were to treat cats naturally infected with FIV, quantify viral load and proviral DNA by real time quantitative PCR with SYBR Green and analyze the viral nucleotide sequence. From 12 animals naturally infected, 6 received AZT at a dose of 10mg/kg/day and 6 received placebo. During 96 days of treatment, viral load and concentration of proviral DNA were measured by relative quantitative real time PCR developed by our staff. The nucleotide sequence of the RT encoding region was also achieved for 3 animals. The real time PCR relative quantification was successfully standardized for FIV. There was no significant statistical difference between treated and control groups. The nucleotide sequence revealed a lysine at position 41 on the enzyme active site. This lysine confers 4-fold decreased sensitivity to AZT in HIV RT-mutants. FIV subtype B has high genetic stability and we purposed that the other virus not sequenced have the same amino acid and hypothesized that this mutations can be one of the reasons determining the failure of the treatment. The other hypothesis is that the dose was not adequate.

Orientador: Renata de Oliveira Mattos-Graner / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Odontologia de Piracicaba / Made available in DSpace on 2018-08-06T06:24:36Z (GMT). No. of bitstreams: 1 Stipp_RafaelNobrega_M.pdf: 1453482 bytes, checksum: 75a8c7b14bc2c1994765a8fd89ae2d9f (MD5) Previous issue date: 2006 / Resumo: Streptococcus mutans são os principais patógenos da cárie dentária, pois são capazes de se acumular no biofilme dentário na presença de sacarose, e sob condições altamente acidogênicas, promovem a desmineralização dentária. As glucosiltransferases B (GtfB) e C (GtfC) produzidas por S. mutans são fundamentais neste processo, porque catalisam a síntese de glucanos extracelulares insolúveis, a partir da sacarose. A proteína ligante de glucano B (GbpB) parece também participar do acúmulo de S. mutans nos biofilmes, embora por processos ainda não compreendidos. Pouco se sabe sobre os mecanismos que regulam a expressão dos genes que codificam essas proteínas de virulência (gtfB, gtfC e gbpB). Neste sentido, objetivamos caracterizar o padrão de expressão dos genes gtfB, gtfC e gbpB e de seus possíveis genes regulatórios (vicR, comE, ciaR e rr11) em genótipos distintos de S. mutans. Para isso, foram realizadas análises de transcrição reversa-PCR semi-quantitativa (RT-PCR) dos genes alvo em diferentes fases de curvas de crescimento planctônico, em meio Brain Heart Infusion, a 37°C, em condições de anaerobiose. RNAs das células nas diferentes fases de crescimento foram extraídos e submetidos a reações de transcriptase reversa com primers arbitrários, para obtenção dos cDNAs totais. Análises de PCR semi-quantitativas dos cDNAs foram então realizadas com primers específicos e normalizados pela expressão do gene housekeeping 16SRNA, cuja expressão foi constante nas condições experimentais estudas. Os padrões de transcrição de gtfB e gtfC foram específicos ao background genético da cepa estudada. Os níveis de transcritos de gtfB e de gtfC foram coordenados durante fases específicas de crescimento, mas divergências nas curvas expressão dos mesmos ocorreram em grande parte dos genótipos. Os níveis de transcritos de gbpB foram também variáveis entre cepas, mas assumiram padrão independente de genes gtf e foi caracterizado por menores variações entre as diferentes fases de crescimento. Os genes regulatórios demonstraram picos de expressão nas fases log e/ou estacionária de crescimento, de acordo com o genótipo testado. Os resultados indicam que o padrões de expressão dos genes estruturais (gtfB, gtfC e gbpB) e regulatórios são cepa-específicos e que gtfB e gtfC são regulados por sistemas independentes, os quais parecem ser ativados em fases distintas de crescimento / Abstract: Streptococcus mutans, the main pathogen of dental caries, have the capacity to accumulate in the dental biofilm in the presence of sucrose, under highly acidic conditions that are responsible for teeth demineralization. The glucosyltransferases B (GtfB) and C (GtfC) produced by S. mutans are essential in this process, because catalyze the synthesis of water-insoluble from sucrose. The Glucan-binding protein B (GbpB) appears to also participate in S. mutans accumulation, but under processes that are still unclear. Little is known about the mechanisms that regulate expression of genes encoding these proteins (gtfB, gtfC and gbpB). In this sense, we aimed to characterize the patterns of transcription of gtfB, gtfC and gbpB in distinct S. mutans genotypes. For that purpose, semi-quantitative analysis of reverse transcription¿PCR (RT-PCR) were performed in strains at different phases of the growth curves in Brain Heart Infusion broth bath cultures at 37°C, under anaerobiosis. RNAs were extracted from cells at different growth phases, and applied in reactions of reverse transcription with arbitrary primers to yield total cDNAs. Semi-quantitative PCR reactions were then performed with the cDNAs using specific primers to each target gene, and normalized by the expression of the housekeeping gene 16SRNA, whose expression remained constant at the experimental conditions. Patterns of expression of gtfB and gtfC were specific to the strain background. Transcriptions of gtfB e de gtfC were coordinated in specific phases of growth, but the curves of transcription diverged at different phases in the majority of the genotypes studied. The levels of gbpB transcripts were variable between strains and assumed an independent pattern when compared with gtf genes. The levels of gbpB transcripts were characterized by lesser variations between the different phases of growth. The regulatory genes have shown peaks of expression at log and/or stationary phases of growth and the curves of transcript levels were strain-dependent. The results indicate that patterns of expression of gtfB, gtfC and gbpB and regulatory genes are strain-specific, and that gtfB and gtfC are regulated by distinct systems that may be activated at distinct phases of growth / Mestrado / Microbiologia e Imunologia / Mestre em Biologia Buco-Dental

Submitted by Cláudia Bueno (claudiamoura18@gmail.com) on 2016-04-04T18:58:10Z No. of bitstreams: 2 Dissertação - Antônio Silva Machado - 2015.pdf: 1923171 bytes, checksum: 991e35e30785c0ac34b0f9290b2fc249 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2016-04-05T10:37:58Z (GMT) No. of bitstreams: 2 Dissertação - Antônio Silva Machado - 2015.pdf: 1923171 bytes, checksum: 991e35e30785c0ac34b0f9290b2fc249 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Made available in DSpace on 2016-04-05T10:37:58Z (GMT). No. of bitstreams: 2 Dissertação - Antônio Silva Machado - 2015.pdf: 1923171 bytes, checksum: 991e35e30785c0ac34b0f9290b2fc249 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Previous issue date: 2015-03-10 / Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPq / AIDS is considered an epidemic disease shaping up as a serious public health problem. Since its discovery in 1981, considerable efforts have been made to better understand the HIV infection mechanism thus, propelling the research and drug development process. According to their mechanism of action, HIV drugs can be classified into six mainly subgroups: nucleoside reverse transcriptase inhibitors (NRTIs), protease inhibitors (PI), non-nucleoside reverse transcriptase inhibitors (NNRTIs), nucleotide reverse transcriptase inhibitors (NtRTI ), entry inhibitors and integrase inhibitors. Currently, searching for safer and more effective drugs showing less collateral effects remains an encouraging pace. In this context, our work describes a synthesis of a new family of heterocyclic compounds, chemically related to delavirdine, a NNRTIs currently used in AIDS treatment. Bioisosterism strategy was applied to obtain synthetic products (54a-54h) in four steps only. Conventional heating method (A) and optimized microwave reactor (B) methodology were both compared by means of their intermediate products yields. Results showed increased yields of partial products (20a-20h [91-98%]); (29a-29h [69-88%]); (37a-37h [82-92%]) for microwave reactor methodology, as well a gain in the time spent during the procedure. All compounds (20a-20h; 29a-29h; 37a-37h e 54a-54h) were characterized by Nuclear Magnetic Resonance of Hydrogen (1H NMR), Carbon (13 C NMR) and Infrared spectroscopy (IR). / A Aids é considerada uma epidemia de cunho global, se configurando como um grave problema de saúde pública. Desde de sua descoberta em 1981, foram realizados esforços consideráveis para a melhor compreensão do mecanismo pelo qual o HIV propicia a infecção, iniciando o processo de pesquisa e desenvolvimento de fármacos. Sendo estes classificados de acordo com os seus mecanismos de ação, apresentados em 6 grupos i.e inibidores nucleosídicos da transcriptase reversa (NRTI), inibidores da protease (PI), inibidores não nucleosídicos da transcriptase reversa (NNRTI), inibidores nucleotídeos da transcriptase reversa (NtRTI), inibidores de entrada e inibidores de integrase. Logo, a busca por novos fármacos que sejam mais efetivos, seguros e com menos efeitos coletareis é de grande relevância. Neste contexto, o trabalho descreve a síntese de uma nova família de compostos heterocíclicos, planejados estruturalmente a partir do fármaco delavirdina - atualmente empregada no tratamento da AIDS, atuando como inibidor não nucleosídico da transcriptase reversa. Os compostos finais sintetizados (54a-54h) são obtidos em quatro etapas sintéticas. Estas foram planejadas e seus rendimentos comparadas a partir da estratégia de bioisosterismo. Seus intermediários foram sintetizados tanto por metodologia de aquecimento convencional (A) assim como, por reator de micro-ondas (B). Os resultados obtidos demonstraram aumento do rendimento parcial (20a-20h [91-98%]); (29a-29h [69-88%]); (37a-37h [82-92%]) e ganho de tempo na síntese dos intermediários, pela metodologia otimizada por reator de microondas. Todos os compostos (20a-20h; 29a-29h; 37a-37h e 54a-54h) foram caracterizados por meio de ressonância magnética nuclear de Hidrogênio (RMN 1H), de Carbono (RMN 13C) e espectroscopia de infravermelho (IV).