Masters of Science / Viral genomes consist of either deoxyribonucleic acid (DNA) or ribonucleic acid (RNA). The viral RNA molecules are responsible for two functions, firstly, their sequences contain the genetic code, which encodes the viral proteins, and secondly, they may form structural elements important in the regulation of the viral life-cycle. Using a host of computational and bioinformatics techniques we investigated how predicted secondary structure may influence the evolutionary dynamics of a group of single-stranded RNA viruses from the Picornaviridae family. We detected significant and marginally significant correlations between regions predicted to be structured and synonymous substitution constraints in these regions, suggesting that selection may be acting on those sites to maintain the integrity of certain structures. Additionally, coevolution analysis showed that nucleotides predicted to be base paired, tended to co-evolve with one another in a complimentary fashion in four out of the eleven species examined. Our analyses were then focused on individual structural elements within the genome-wide predicted structures. We ranked the predicted secondary structural elements according to their degree of evolutionary conservation, their associated synonymous substitution rates and the degree to which nucleotides predicted to be base paired coevolved with one another. Top ranking structures coincided with well characterized secondary structures that have been previously described in the literature. We also assessed the impact that genomic secondary structures had on the recombinational dynamics of picornavirus genomes, observing a strong tendency for recombination breakpoints to occur in non-coding regions. However, convincing evidence for the association between the distribution of predicted RNA structural elements and breakpoint clustering was not detected.

>Magister Scientiae - MSc / Insect-derived baculoviruses have been used extensively as a safe and versatile research model for transgenic protein expression. Preclinical studies have revealed the promising potential of Baculoviruses as a delivery vector for a variety of therapeutic applications, including vaccination, tissue engineering and cancer treatments. Coronaviruses are enveloped viruses containing linear, non-segmented ribonucleic acid. Human coronavirus NL63 was first discovered in the Netherlands in January 2004, where a 7-month-old girl presented with an acute respiratory tract infection that was later established to predominantly infect infants, the elderly and immunocompromised individuals. In addition to the known non-structural and structural proteins of coronaviruses, an accessory protein known as open reading frame 3 which is conserved in the Coronaviridae family has not been extensively researched. Open reading frame 3 encodes a putative membrane-bound protein. This study cloned the open reading frame 3 viral gene of 741 base pairs into the baculovirus expression construct via competent bacterial cell lines. Open reading frame 3-Baculovirus particles were generated in Spodoptera frugiperda insect cells. Recombinant cells containing the viral protein gene were used to infect healthy Spodoptera frugiperda 9 cells at varying ratios of multiplicity of infection over a fixed time-course. The open reading frame 3 viral protein was not detected by quantification methods at a molecular weight of 26 kilo Dalton, due to polyclonal antibody degradation.

Master of Science / Department of Plant Pathology / Harold Trick / The object of this study was to find a target sequence for the known Heterodera glycines Y25 sequence that contained no homology to any known Glycine max genes so homologous endogenous soybean gene expression will not be effected. In addition, in attempt to improve the accuracy of SCN bioassays performed in greenhouse settings, applications of a variety of insecticides with differing modes of action were applied to screen for any detectable effects on the SCN populations. The full-length sequence of the Y25 gene was blasted against the G. max genome using the National Center for Biotechnology Information blast database and a portion of the gene was found to contained no homology to the G. max genome. A rapid hairy root assay was used to screen for resistance to H. glycines. The sequence was transformed into Agrobacterium rhizogenes using a modified heat shock method. The transformed A. rhizogenes were used to inoculate soybean seedlings. The inoculated seedlings developed hairy roots expressing the target sequence. Upon finishing the hairy root assay it was discovered that there were no detectable differences across any of the treatments or the controls. It was neither proved nor disproved that the new target sequence containing no homology to the G. max genome was as effective as the original target. Further investigation will need to be conducted to show the level of control for the new target sequence.

α2 subunit-containing GABAA receptors (α2-GABAARs) are abundantly expressed in the nucleus accumbens (NAc), a region thought to be important in mediating cocaine's reinforcing properties. This thesis develops viral-based RNAi tools in efforts to investigate the functional role of mesoaccumbal α2-GABAARs in mediating cocaine's ability to facilitate conditioned behaviours (i.e. behavioural sensitisation and conditioned reinforcement). RNA interference (RNAi)-mediated knockdown of the α2 subunit expression in the NAc core neither affected appetitive Pavlovian learning nor instrumental learning maintained by the conditioned reinforcer, but blocked cocaine facilitation of conditioned reinforcement. This behavioural phenotype was also observed upon α2 knockdown specifically in NAc core dopamine D2 receptor (D2R)-containing neurons, whereas α2 knockdown in mesoaccumbal D1R-containing neurons reduced the level of discriminated approach during Pavlovian learning. Further, α2 knockdown in the NAc core or shell did not block cocaine-induced sensitisation as previously observed in the constitutive knockouts (Dixon et al., 2010), but the latter increased acute locomotor responses to cocaine. Data presented within this thesis indicate that GABAergic signalling via α2-GABAARs within the NAc is involved in some of the motivation-enhancing properties of cocaine, most likely via interactions with the dopaminergic system.

Orientador: Maria Isabel Nogueira Cano / Resumo: Os protozoários do gênero Leishmania causam leishmaniose, uma doença tropical negligenciada, que se apresenta de diferentes formas clínicas e que acomete milhões de pessoas no Brasil e no mundo. Até o momento não existe nenhuma vacina ou tratamento eficientes para leishmaniose e por isso, estudos que contribuam para o entendimento da biologia e fisiologia do parasito podem fornecer uma possibilidade de encontrar novos alvos terapêuticos. Este é o caso dos telômeros, cuja função principal é manter a estabilidade do genoma que se perturbada pode afetar diretamente a proliferação ou multiplicação dos parasitos. Os telômeros são estruturas nucleoprotéicas localizadas nas extremidades dos cromossomos, mantidos pela enzima telomerase. Eles são regulados por diversos processos entre os quais se encontram alguns longos RNAs não codificadores (lncRNA). Entre os lncRNAs com função telomérica está o TER (RNA Telomerase) o qual é um dos principais componentes do complexo telomerase, pois contém uma pequena sequência molde a qual é copiada pela telomerase durante a replicação dos telômeros, o TER foi recentemente identificado em Leishmania spp., porém se desconhece a sua função e biogênese. Outro RNA não codificante com função telomérica é o TERRA (Repetições Teloméricas contendo RNA), os quais são essenciais para a manutenção dos telômeros. Até o momento, identificamos a presença do TERRA expressos a partir das extremidades cromossômicas nas diferentes fases de desenvolvimento (amastigot... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Protozoan from Leishmania genus are the etiologic agents of leishmaniasis, a tropical disease that presents different clinical manifestations and affect million people in Brazil and in the world. There are no eficiente vacines nor treatment protocols against leishmaniasis, therefore, it is crucial to improve the knowledge about Leishmania molecular biology and physiology for the development of new therapies. Actually, telomeres have been considered potential molecular targets as they are responsible to maintain genome stability. Leishmania telomeres similarly to other eukaryotes, are nucleoprotein structures found at the end of the chromosomes maintained by telomerase. They can be regulated by different mechanisms such as the action of long non-coding telomeric RNAs (lncRNAs). Among the telomeric lncRNAs are the telomerase RNAcomponent (TER) which is crucial for telomerase activity because it contains the template sequence that is copied by telomerase during telomere elongation. TER was recently identified in Leishmania although there is no information about its function and biogenesis.TERRA, the Telomere Repeat containing RNA is other telomeric RNA that it is involved with telomere length regulation telomere damage response and alterations in the composition of telomeric chromatin and is essential for telomere maintenance. In this work, we identified TERRA transcripts in the three Leishmania developmental stages (amastigote, promastigote e metacyclic). We interrogate three i... (Complete abstract click electronic access below) / Doutor

Thesis (Ph.D. in Biochemistry) -- University of Colorado Denver, 2007. / Typescript. Includes bibliographical references (leaves 191-200). Free to UCD affiliates. Online version available via ProQuest Digital Dissertations;

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Made available in DSpace on 2014-06-11T19:32:55Z (GMT). No. of bitstreams: 0 Previous issue date: 2008-12-16Bitstream added on 2014-06-13T20:24:24Z : No. of bitstreams: 1 oliveira_am_dr_rcla.pdf: 1319026 bytes, checksum: b6ad03694a53b696678fbabde842876e (MD5) / O presente trabalho teve por objetivo otimizar a autólise de levedura fresca de cervejaria (Saccharomyces cerevisiae), visando a extração máxima de ácido ribonucléico da biomassa na produção do extrato de levedura. As variáveis estudadas foram pH, temperatura, % de NaCl, % de NH3, tempo de processo e, métodos de recuperação de RNA do autolisado. Os experimentos foram realizados por meio de quatro ensaios delineados segundo Box & Benken (1989) e avaliado pela Metodologia da Superfície de Resposta, utilizando-se o Software Statística 5.1 e a análise estatística ANOVA. A otimização foi concluída por meio do quinto ensaio com a produção do extrato nas condições otimizadas (55,2ºC, 9,8% de NaCl em pH=5,1 por 24 horas e, 12,2% de NH3 a 60ºC sob agitação a 200 rpm/15minutos. Três métodos foram avaliados para recuperação do RNA e das frações de extrato e parede celular: 1) autólise/plasmólise; 2) choque térmico por 1 minuto a 68ºC seguido da autólise/plasmólise 3) hidrólise química alcalina. Pelo processo de autólise em combinação com 9,8% de NaCl, a taxa de extração de RNA em 24 horas foi de 89,7%, com um rendimento de 51,3% em massa de extrato com 57,9% de proteína e, 48,7% de parede celular desidratada com 21,7 % de proteína. A utilização de 12,2% de NH3 em base seca de levedura permitiu o aumento na taxa de extração de RNA de 89,7 para 93,6%, mas um forte escurecimento foi verificado no extrato obtido. Na recuperação do RNA após precipitação protéica em pH 4,3 com posterior uso de 2 volumes de etanol em pH=2, recuperou-se 15,47%, 13,80% e 7,42% de RNA respectivamente com purezas de 49,85%, 51,70% e 38,70%. As taxas de extração de RNA da biomassa foram de 87,45% para o método 1; 91,40% para o método 2 e 78,80% para o terceiro método, indicando uma boa alternativa para redução do teor de RNA da biomassa e produção do extrato rico... / The present work had for objective to optimize the autolysis of fresh brewery’s yeast (Saccharomyces cerevisiae), aiming the maximum extraction of ribonucleic acid of biomass in the yeast extract production. The studied variables were pH, temperature, % of NaCl, % NH3, processing time and RNA recovering methods from autolysed. The experiments were accomplished by mean of four delineated assays according to Box & Benken (1989) and evaluated by Surface Methodology of Answer, utilizing the software Statistica 5.1. and the analysis statistics “ANOVA”. The optimization was concluded by mean of the fifth assay with an extract production in the optimized conditions (55.2ºC, 9.8% of NaCl in pH 5.1 for 24 hours and, 12.2% of NH3 at 60ºC under agitation at 200 rpm/15 minutes. Tree methods were evaluated for RNA recovering and of the extract fractions and cell wall: 1) autolysis/plasmolysis; 2) thermic shock during 1 minute at 68ºC followed of autolysis/plasmolysis; 3) alkaline chemical hydrolysis. The process of autolysis in combination with 9.8% of NaCl, the RNA extraction yield in 24 hours was of 89.7%, with a yield of 51.3% in extract mass with 57.9% of protein and, 48.7% of dehydrated cell wall with 21.7% of protein. The utilization of 12.2% of NH3 in dried base of yeast allowed the increase in the RNA yield extraction from 89.7 to 93.6%, but a strong darkness was observed in the obtained extract. The RNA recovering after 4.3 pH proteic precipitation with posterior use of 2 ethanol volumes in pH 2.0, it was recovered 15.47%, 13.8% and 7.42% of RNA respectively with purities of 49.85%, 51.70% and 38.70%. The RNA extraction yields of biomass were of 87.45% for the method 1; 91.40% for the method 2 and 78.80% for the third method, indicating a good alternative for RNA content reduction of biomass and rich extract production in nucleotides. The extract fractions were evaluated... (Complete abstract click electronic access below)