Se validó y evaluó un método de RT-PCR en tiempo real usando cebadores y sondas específicas para los genes RdRP de SARS-CoV-2 y GAPDH de humanos; este último fue usado como control endógeno. Se evaluó la especificidad y sensibilidad; además, se evaluó otros parámetros como la robustez, la repetibilidad, reproducibilidad, comparabilidad y el límite de detección. La sensibilidad, especificidad, los valores predictivos positivo y negativo, la robustez, comparabilidad y la repetibilidad-reproducibilidad de la prueba de RT-PCR en tiempo real dúplex fue de 100%, con un límite de detección de 100 copias/μL, de acuerdo con los criterios de aceptación establecidos para validación del protocolo. Esta prueba estandarizada es una buena alternativa para el diagnóstico de COVID-19; además, la prueba fue aplicada de manera exitosa en personas sospechosas de la enfermedad permitiendo controlar el número de falsos negativos.

In the information age, media has come to be recognized as a credible mean and foreign policy tool to pursue soft power. Authoritarian states like Russia are competing in the realm of ideas through state-funded news outlets such as Russia Today (RT). This by reaching out to global and foreign public spheres and by reporting on an alternative reality of events, issues and problems. This thesis studies the role of the media news outlet RT as a mean to promote Russian soft power. This with a focus on how the channel attempts to persuade and attract an international audience based on the construction of a compelling narrative. To approach this theme empirically, a media frame analysis is conducted utilizing five news frames including; morality, human interest, responsibility, conflict and economic consequences. The overall results suggest that RT attracts and persuades largely by providing an alternative Russian perspective on events, issues or problems. It attracts by appealing both in the direction of the western- and eastern world. It appeals to the west by emphasizing how the West needs Russia to find answers to the pressing issues in global politics. It appeals to the east by suggesting an alternative model of development. RT attempts to persuade are made through the construction of counter-narratives which delegitimizes the Western approach in international affairs. The channel devotes efforts to boost these narratives by selective news porting and handpicking statements made by intellectuals from the perceived “other” western camp.

Campylobacteriosis is a leading foodborne illness worldwide, primarily caused by Campylobacter jejuni (C. jejuni) which is associated with poultry consumption. The emergence of antibiotic resistance has emphasized the need for alternative strategies to control C. jejuni colonization in poultry. To assess the prevalence of C. jejuni in poultry, 270 cloacal swab samples were collected from broilers raised under No-Antibiotics Ever system. Among these samples, 16.3% were identified as C. jejuni positive. Notably, these isolates exhibited a diverse range of virulence factors and antimicrobial resistance genes, with 61.36% of isolates showing hyper-motile and 20.45% demonstrating multidrug resistance. Following isolation, whole genome sequencing was conducted on four selected strains using a hybrid sequencing approach. Subsequently, the complete genomes of these C. jejuni strains were analyzed to identify vaccine candidates using reverse vaccinology. Three conserved potential vaccine candidates were identified as suitable targets for vaccine development, namely phospholipase A (PldA), TonB dependent transporter (ChuA), and cytolethal distending toxin (CdtB). Furthermore, the gene expression of these candidates was examined in four C. jejuni strains during host-pathogen interactions using avian macrophage cell line HD11. Significant upregulation of all three candidate genes were observed in the four tested C. jejuni strains during interaction with host cells, indicating their crucial role in C. jejuni infection. Additionally, the expression of immune genes was evaluated in avian macrophage cells to understand the immune responses during C. jejuni infection. The infection resulted in the upregulation of toll-like receptor genes (TLR-4), pro-inflammatory genes (IL-1β, IFN-γ, IL-6, IL-8L1), anti-inflammatory gene (IL-10), and iNOS2 gene expression. The observed immune response demonstrates the potential of C. jejuni to induce host immunity for protection. In conclusion, our study identifies three conserved potential vaccine candidates and provides insights into the immune responses induced by C. jejuni infection in avian macrophage cells. These findings are crucial for the development of an effective vaccine against C. jejuni, aiming to reduce C. jejuni transmission through poultry consumption and the risk of human infection.

The experiments reported within this thesis use psychophysical techniques to examine the factors which determine perceived multisensory timing in humans. Chapters 1 and 2 describe anatomical and psychophysical features of temporal processing, respectively, whilst Chapter 3 introduces the reader to psychophysical methods. Chapter 4 examines the relationship between two measures of sensory latency, reaction time (RT) and crossmodal temporal order judgment (TOJ). Despite task and attentional manipulations the two measures do not correlate, suggesting that they measure some fundamentally different aspect(s) of temporal perception. Chapter 5 examines the effects of adaptation to asynchronous stimulus pairs on perceived audiovisual (AV), audiotactile (AT) and visuotactile (VT) temporal order. Significant temporal shifts are recorded in all three conditions. Evidence is also presented showing that crossmodal TOJs are intransitive. Chapter 6 shows that concurrent adaptation to two sets of asynchronous AV stimulus pairs causes perceived AV temporal order to recalibrate at two locations simultaneously, and that AV asynchrony adaptation effects are significantly affected by observers¿ attention during adaptation. Finally, Chapter 7 shows that when observers are accustomed to a physical delay between motor actions and sensory events, an event presented at a reduced delay appears to precede the causative motor action. The data are well-described by a simple model based on a strong prior assumption of physical synchrony between motor actions and their sensory consequences.

Purpose: The aim of this study is to investigate the spectrum of neurological triad improvement in patients with diffuse intrinsic pontine glioma (DIPG) treated by reirradiation (re-RT) at first progression. Methods: We carried out a re-analysis of the SIOP-E retrospective DIPG cohort by investigating the clinical benefits after re-RT with a focus on the neurological triad (cranial nerve deficits, ataxia, and long tract signs). Patients were categorized as “responding” or “non-responding” to re-RT. To assess the interdependence between patients’ characteristics and clinical benefits, we used a chi-square or Fisher’s exact test. Survival according to clinical response to re-RT was calculated by the Kaplan–Meier method. Results: As earlier reported, 77% (n = 24/31) of patients had any clinical benefit after re- RT. Among 25/31 well-documented patients, 44% (n = 11/25) had improvement in cranial nerve palsies, 40% (n = 10/25) had improvement in long-tract signs, and 44% (11/25) had improvement in cerebellar signs. Clinical benefits were observed in at least 1, 2, or 3 out of 3 symptoms of the DIPG triad, in 64%, 40%, and 24%, respectively. Patients irradiated with a dose ≥20 Gy versus <20 Gy may improve slightly better with regard to ataxia (67% versus 23%; p-value = 0.028). The survival from the start of re-RT to death was not different between responding and non-responding DIPG patients (p-value = 0.871). Conclusion: A median re-irradiation dose of 20 Gy provides a neurological benefit in twothirds of patients with an improvement of at least one symptom of the triad. DIPG patients receiving ≥20 Gy appear to improve slightly better with regard to ataxia; however, we need more data to determine whether dose escalation up to 30 Gy provides additional benefits.

No description available.

Tunnelling in urban areas is one of the most challenging engineering activities, as it has relatively high “risk” due to various uncertainties and the intensity of the possible consequences. Numerous studies have been conducted to address the tunnelling risk, by mainly focusing on the “identification” of the causes and how to control or mitigate the risks. However, limited work has been done on how to quantify the risk by considering the multi-level uncertainties encountered in different phases of the project. The primary objective of this work is to develop a multi-scale risk management (RM) framework to address and quantify the risk of ground surface settlement, induced by tunnelling, in soft clay in urbanized areas. The specific focus is placed on quantifying the risk of tunnel-induced settlement for existing buildings, by taking into account multiple uncertainty levels (e.g. uncertainties of parameters, uncertainties of models, etc.). The framework addresses the tunnel-induced settlement risk, both during the construction of the tunnel as well as after its completion, for buildings with shallow and deep foundations. It offers different classes of assessment to quantify the risk, according to the structure’s current condition and the corresponding limit-state function, that is designated to each class. The RM framework is aligned with ISO 31000 risk management act, consisting of “risk identification”, “risk analysis” and “risk evaluation”. Risk identification includes studies on tunnelling technical reports, field observations, etc., in order to identify the causes of short-term and long-term tunnelling-induced settlement. The risk analysis involves a series of fault tree, event tree and consequence tree analyses to estimate the likelihood of the ground subsidence and subsequent events. For risk evaluation, different probabilistic methods (e.g. first-order reliability method, second-order reliability method and Monte Carlo sampling) are utilized to estimate the risk of surface buildings with shallow and deep foundations. The framework has been implemented in an example problem, to demonstrate the procedure and to address the main influential parameters in each class of assessment using the alpha importance measure. Rt risk tool has been utilized to perform reliability calculations and FORM has been used as the primary method due to its valuable balance between computational cost and accuracy. The outcomes of this RM framework are risk registers and colour-coded risk maps including the exceedance probability of a predefined settlement threshold for each building in the affected area. This framework receives technical data and provides risk-based information for higher-level managers and decision-makers to prioritize their actions and allocate their resources in the most effective way. / Thesis / Master of Applied Science (MASc) / The aim of this study is to provide a multi-level risk management (RM) framework to address and quantify the risk of surface building settlement induced by tunnelling in soft clay in urbanized areas. The focused is placed on quantifying the risk of tunnel-induced settlement of existing buildings, by taking into account multiple uncertainty levels. The framework addresses the tunnel-induced settlement risk, both during the construction of the tunnel as well as after its completion, for buildings with shallow and deep foundations. It offers different classes of assessment to quantify the risk, according to the structure’s current condition and with respect to specific limit-state functions designated for each class. The proposed framework was implemented in an example to demonstrate the procedure and outcomes.

Para obter resultados rápidos e confiáveis que permitam o monitoramento da segurança microbiológica de alimentos, seja pela indústria ou pelos órgãos de fiscalização, diversos métodos alternativos têm sido desenvolvidos para a detecção e quantificação de Salmonella. Os propósitos do estudo foram avaliar a viabilidade de emprego do QIAamp® DNA Stool Mini Kit para extração e purificação de DNA de Salmonella; validar ensaios baseados em PCR-tempo real (PCR-RT) para quantificar o DNA de Salmonella empregando ttr ou tuf e desenvolver um ensaio para quantificar Salmonella baseado na transcriptase reversa-PCR-tempo real (RT-PCR-RT). Para avaliação do QIAamp® DNA Stool Mini Kit empregaram-se fezes coletadas diretamente do reto de animais infectados ou não, sendo estas últimas artificialmente contaminadas e submetidas à extração segundo protocolo do fabricante. As amostras de DNA isoladas foram quantificadas empregando um ensaio Salmonella-específico PCR-RT utilizando como alvo o lócus ttr. O mesmo ensaio foi utilizado para células de Salmonella provenientes de meio de cultura. O ensaio PCR-RT baseado no alvo tuf foi validado empregando-se primeiramente cepas de diferentes sorotipos de Salmonella e de outras Enterobacteriaceae. A seguir sua eficiência foi avaliada para alimentos-modelo (ave e suíno) artificialmente contaminadas com elevada (&#8776; 6 log UFC/mL) e baixa (&#8776; 2 log UFC/mL) população de Salmonella Typhimurium DT 104. A validação do método quantitativo de Salmonella por RT-PCR-RT foi realizada primeiramente com células em meio de cultura e posteriormente nos mesmos alimentos-modelo utilizados para PCR-RT. Em ambos os métodos, alíquotas dos alimentos-modelo foram mantidas a 20 ºC e a 8 ºC, sendo examinadas em diferentes tempos pós-inoculação. Como controle empregou-se a enumeração de microrganismos mesófilos totais e de Salmonella por técnicas convencionais. A taxa de recuperação de Salmonella em fezes suínas artificialmente inoculadas, após tratamento com QIAamp® DNA Stool Kit, variou entre 25% a 50%, dependendo da quantidade inicial de células. Empregando o DNA extraído e submetendo-o à PCR-RT para o ttr obteve-se limite de detecção de 2,8 log UFC eq/g de fezes; método que foi menos sensível que o convencional. A quantificação de Salmonella por PCR-RT empregando tuf apresentou limite de detecção menor que 1 log UFC eq. Os resultados obtidos com este método, empregando-se células em meio de cultura ou alimentos-modelo, foram, de maneira geral, ligeiramente inferiores aos do método convencional. A eficiência de amplificação para PCR-RT e tuf foi de 94%. O método RT-PCR-RT apresentou limite de detecção semelhante ao obtido com o ttr (2 log UFC eq) e sua eficiência de amplificação foi de 100%. Observou-se que tuf é expresso na fase logarítmica de multiplicação bacteriana, o que o torna um bom indicador da viabilidade de Salmonella. / In order to get fast and trustworthy results that allow monitoring the microbiological food safety either by industries or governmental agencies, diverse alternative methods have been developed for Salmonella detection and quantification. The purposes of this study were to evaluate the viability of the use of QIAamp® DNA Stool Mini Kit for Salmonella DNA extraction and purification; to validate assays based on real time-PCR (PCR-RT) to quantify Salmonella DNA by using ttr or tuf, and to develop an assay to quantify Salmonella based on reverse transcriptase- PCR-real time (RT-PCR-RT). For QIAamp® DNA Stool Mini Kit evaluation feces taken directly from the rectum of infected or health animals were used, with the former being artificially contaminated. Samples were submitted to DNA extraction, according to manufacturers protocol. The isolated DNA were quantified using a Salmonella-specific PCR-RT targeting the ttr locus. The same assay was used for Salmonella cells originated from culture medium. The PCR-RT assay with tuf as target was first validated employing different Salmonella serovars and other Enterobacteriaceae strains. After, its efficiency was evaluated on food-models (chicken and swine) spiked with high (&#8776; 6 log CFU/mL) and low (&#8776; 2 log CFU/mL) Salmonella Typhimurium DT 104 populations. The validation of the quantitative RT-PCR-RT method was first conducted with cells grown in culture medium, and then in the same food-model used for PCR-RT. For both methods aliquots of foodmodels were maintained at 20 ºC and 8 ºC being evaluated at different incubation times. Enumeration of total mesophilic microorganisms and Salmonella based on conventional methods were used as controls. The DNA recovery rate in swine feces artificially inoculated, after QIAamp® DNA Stool Mini Kit treatment, was between 25% to 50% depending the initial amount of cells. Using the extracted DNA and submitting it to PCR-RT for ttr a detection level of 2,8 CFU eq/g of feces was obtained. This method showed lower sensitivity than the conventional. Salmonella quantification by PCR-RT employing tuf showed a detection level lower than 1 log CFU eq. The results obtained with this method and cells suspended in culture medium or in food-model systems were, in general slightly lower that those obtained with the conventional method. The efficiency of amplification for PCR-RT tuf was 94%. Detection limit of RT-PCR-RT was similar to that of ttr (2 log CFU eq) and efficiency of amplification was 100%. tuf was expressed in logarithmic phase of bacteria growth curve showing that it is a good viability indicator for Salmonella.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / CHAPTER I - Prostate cancer is a common disease in the world and in some countries it is one of the main causes of male population mortality. Some molecular markers have been associated with prostate carcinogenesis. To observe changes in transcript levels of the AR, SRD5A2, KLK2, PSMA and PCA3 genes, the mRNA was analyzed in tissues with prostatic adenocarcinoma (PCa, N= 48) and benign prostatic hyperplasia (BPH, N= 25), performed through a differential multiplex RT-PCR assay. Significant differences were observed in the relative expression of these genes between cancerous and non-cancerous tissues. The optical density ratio of the cDNA amplicons between PCa and BPH for the AR gene was 1.6-fold higher for the prostatic adenocarcinoma. On the other hand, the SRD5A2 mRNA levels were associated with BPH and were 1.4-fold higher than that of PCa. For KLK2, PSMA and PCA3, the transcriptional levels were respectively, 1.9-, 1.9- and 5-fold higher in PCa than those in BPH tissues. Of the diagnostics tests carried through individually, the PCA3 gene was that presented higher sensitivity and accuracy, and the inclusion of the serum PSA improved the sensitivity (of 76 to 92%), positive preditive value (of 85 to 94%), negative preditive value (of 60 to 62%) and accuracy (of 74 to 78%). The results suggest that the higher AR, KLK2, PSMA, and PCA3 and/or reduced SRD5A2 genes expression in prostatic tissues may indicate the occurrence of prostate adenocarcinoma; however the PCA3 and serum PSA analysis together are highly promising as auxiliary method in the diagnosis of this cancer. CHAPTER II - Purpose: Prostate cancer (PCa) is the most commonly diagnosed malignancy in men, and it consists of multifactorial and multifocal events. Due to the complexity of the disease process, which includes genome alterations, local invasion, micrometastatic cell extravasations to circulation, invasion of secondary organ tissues, and resistance to hormonal blockage, many markers must be used to represent the multiple and variable events that lead to cancer development. The low specificity of the unique serum marker for prostate cancer diagnostics, PSA, has leaded us to investigate four potential markers in the peripheral blood of patients by detecting their mRNA levels and associating them to clinical parameters. Methods: The expression levels of the KLK2, KLK3, PCA3 and PSMA transcripts were determined by Nested RT-PCR. Patients with PCa (99) and with benign prostatic hyperplasia (BPH, 36), and healthy volunteers (104) were investigated. Results: Significant differences for the RNA relative levels have been found for the KLK2, PCA3 and PSMA transcripts between PCa and BPH patients or healthy volunteers. The KLK2 and PSMA levels also presented a positive association (P<0.05) with extra-prostatic disease (pT3). The combined positive RT-PCR Nested for the KLK2, PCA3, PSMA genes with serum PSA higher than 4ng/mL presented a 10-fold higher chance of cancer occurrence than healthy controls, with sensitivity, specificity and positive predictive value of 57%, 89% and 93%, respectively. Conclusions: The combined analysis of KLK2, PCA3 and PSMA transcripts may become a useful tool for the discrimination of PCa patients from those with benign disease or healthy individuals. Additionally, the KLK2 and PSMA transcripts may also be used as prognostic markers for the presence of extra-capsular disease and assisting in the prediction of the post-operative outcome. CHAPTER III - Purpose: Transcripts of PCA3/DD3 gene are at the moment the most specific molecule found in prostate cancer specimens. This mRNA can be detected in important sample targets for clinical analyses, such as prostatic tissues, urine after prostatic massage, and the peripheral blood. Methods: The present study evaluated the PCA3 gene expression in prostatic tissues and in peripheral blood of BPH and PCa patients, by RT-PCR assays, and based on its detection together with other clinical parameters, we proposed a model for molecular monitoring in order to improve diagnosis as an auxiliary technology. Results: The concomitant use of PCA3 transcript detection in the peripheral blood and in prostate tissues has improved diagnosis, with sensitivity and an accuracy of 77%. For the molecular staging, patients have been classified as: localized disease (PBL-; negative PCA3) and circulating tumors cells disease (PBL+; positive PCA3). The higher frequencies of PBL- had been observed in T1-T2 stages (75%); on the other hand, the higher PCA3 positivity was observed for the T3-T4 staging (43%), while the T1-T2 stages presented 25% positivity. A correlation was found between the molecular staging and serum PSA < 10ng/mL before surgery, and approximately 60% of patients with T3-T4 stages that presented biochemical failure after radical prostatectomy presented a positive PCA3 result (P= 0.05), with an odds ratio of 16-fold higher for the possibility of disease recurrence in relation to the T1-T2 patients, and an accuracy of 82%. Conclusion: These data demonstrated the importance of the PCA3 gene as an auxiliary method in prostate cancer diagnosis, by distinguishing PCa from BPH patients, and also demonstrated its prognostic value in recurrent disease for post-operative patients. CHAPTER IV - Approximately 98% of all the products transcribed in the human genome correspond to non coding RNAs (ncRNA). Many ncRNA functions are attributed to this structural particularity given mainly for the secondary structures formed from its linear sequence of bases. Among the ncRNA types are tRNA, rRNA, small nuclear RNA, small nucleolar RNA, small interference RNA (siRNA), microRNA (miRNA) and catalytic RNAs (ribozymes). The bioinformatics has supplied useful tools in the prediction of optimal or suboptimal secondary structures allowing the design of interference RNA as miRNAs or siRNAs. In human, miRNAs have been associated with the development of diverse complex diseases as cancer. The PCA3 (DD3) gene was molecularly characterized as cancer and prostate specific, and its transcripts are non-coding, once no peptide products have been found. Due to its structural characteristics, the PCA3 gene belongs thus to the increasing family of ncRNA. In the present work, four new variant molecules of the PCA3 gene have been sequence characterized and their frequencies demonstrated in prostate cancer and in benign prostatic hyperplasia patients, as well as in healthy individuals. We have also investigated and predicted the putative secondary structures formed in order to elucidate its role in prostate cancer biology. No association has been found between the frequency of these molecules and prostate pathologies (PCa or BPH). On the other hand, PCA3 variants were found in 10% (12/115) of cases in the general population. Similar analyses of the possible polypeptides of these molecules demonstrated that it remains as a non-coding RNA, and introns presents in the first, second and fourth variants suggesting a possible role as a miRNA with intracellular activity to these molecules to the PCA3 gene. In prostatic tissues, 100% of the prostate cancer cases presented the RNA molecule with an exon 2 splicing. However, further investigation must be carried out to demonstrate the true role of these splicing variants in prostate tumors and in other pathologies, once these molecules have been preferentially found in the peripheral blood. / CAPÍTULO I - O câncer de próstata é uma doença comum no mundo e já assumiu em alguns países uma das principais causas de mortalidade da população masculina. Vários marcadores moleculares têm sido associados à gênese do câncer de próstata. A fim de demonstrar a expressão diferencial dos níveis transcricionais dos genes AR, SRD5A2, KLK2, PSMA e PCA3 em doenças prostáticas, o RNAm foi analisado em tecidos com adenocarcinoma prostático (CaP, N= 48) e hiperplasia prostática benigna (HPB, N= 25) por meio da técnica RT-PCR multiplex semi-quantitativa. Foram observadas diferenças significativas na expressão relativa desses genes entre os tecidos cancerosos e nãocancerosos. A taxa de densidade ótica entre os amplicons para cDNA provenientes do gene AR foi 1.6 vezes maior no adenocarcinoma prostático. Por outro lado, os níveis de RNAm do gene SRD5A2 foi associado com a HPB e foi 1.4 vezes maior do que no CaP. Para os genes KLK2, PSMA e PCA3, os níveis transcricionais foram respectivamente, 1.9, 1.9 e 5 vezes maior no câncer comparado a tecidos benignos. Dos testes diagnósticos realizados, o gene PCA3 individualmente foi o que apresentou as melhores sensibilidade e acurácia, sendo que a inclusão das medidas de PSA sérico melhorou a sensibilidade (de 76 para 92%), o valor preditivo positivo (de 85 para 94%), o valor preditivo negativo (de 60 para 62%) e a acurácia (de 74 para 78%). Os dados sugerem que a maior expressão dos genes AR, KLK2, PSMA e PCA3 ou expressão reduzida do gene SRD5A2 em tecidos prostáticos podem indicar a ocorrência do adenocarcinoma da próstata, sendo que as análises do gene PCA3 juntamente aos do PSA sérico são altamente promissores como método auxiliar no diagnóstico desse tipo de câncer. CAPÍTULO II - O câncer de próstata (CaP) e o mais comumente diagnosticado na população masculina e consiste de eventos multifatoriais e multifocais. Devido a complexidade da doença, a qual inclui alterações genômicas, invasão local, liberação de células micrometastáticas para a circulação, invasão secundaria de tecidos de outros órgãos, e resistência ao bloqueio hormonal, muitos marcadores podem ser usados para representar os eventos múltiplos e variáveis que levam ao desenvolvimento do câncer. A baixa especificidade do único marcador para diagnostico do câncer de próstata, PSA, tem nos levado a investigar quatro potenciais marcadores no sangue periférico de pacientes pela detecção de seus níveis de RNAm e associá-los a parâmetros clínicos. Os níveis de expressão dos transcritos do KLK2, KLK3, PCA3 e PSMA foram avaliados pela RT-PCR Nested, em pacientes com CaP (99), com hiperplasia prostática benigna (HPB, 36) e voluntários saudáveis (104). Diferenças significativas foram encontradas para a expressão dos genes KLK2, PSMA e PCA3 entre os pacientes com CaP e os pacientes com HPB ou voluntários saudáveis. Os níveis do KLK2 e PSMA também apresentaram associação positiva (P<0.05) com doença extra-prostática (pT3). A RT-PCR Nested positiva combinada para os genes KLK2, PCA3 e PSMA com PSA sérico maior que 4ng/mL apresentou uma chance 10 vezes maior de ocorrência do câncer comparado aos controles saudáveis, com sensibilidade, especificidade e acurácia de 57%, 89% e 93%, respectivamente. A análise combinada dos genes KLK2, PCA3 e PSMA pode ser uma ferramenta útil na distinção de pacientes com CaP daqueles com doença benigna ou de indivíduos saudáveis. Ainda, a analise dos transcritos KLK2 e PSMA podem ser usados como marcadores prognósticos para a presença de doença extra-capsular e auxiliando na predição de recidiva da doença no pós-operatório. CAPÍTULO III - Os transcritos do gene PCA3/DD3 são até o momento as moléculas mais específicas encontradas em espécimes de câncer de próstata. Esses RNAm podem ser detectados em importantes alvos para a análise clínica como tecidos prostáticos, na urina após massagem prostática e em sangue periférico. O presente estudo avaliou a expressão do gene PCA3 em tecidos prostáticos e em sangue periférico de pacientes com HPB e CaP, por técnicas de RT-PCR, e baseado na sua detecção juntamente com os parâmetros clínicos, foi proposto um modelo de estadiamento molecular como técnica assessória para melhor o diagnóstico da doença. O uso concomitante da detecção dos transcritos do gene PCA3 no sangue periférico e no tecido prostático melhorou o diagnóstico, com sensibilidade e acurácia de 77%. Para o estadiamento molecular, os pacientes foram classificados como contendo a doença localizada (PBL-) e em doença com células tumorais circulantes (PBL +). Maiores freqüências de tumor localizado pelo estadiamento molecular foram observadas nos estadios T1-T2 (75%), enquanto que 25 e 43% dos cânceres T1-T2 e T3-T4, respectivamente, apresentaram PCA3 positivo (células circulantes). Uma correlação foi encontrada para o estadiamento molecular para doença localizada e PSA sérico pré-cirúrgico < 10ng/mL, e aproximadamente 60% dos pacientes TNM T3-T4 que apresentaram falha bioquímica após a cirurgia radical apresentaram RTPCR positiva do PCA3 (P= 0.05), com um Odds Ratio 16 vezes maior para a possibilidade de recorrência da doença em relação aos pacientes T1-T2 e uma acurácia de 82%. Esses dados demonstram a importância da detecção do gene PCA3 como método no diagnóstico do câncer de próstata, por distinguir pacientes com CaP daqueles com HPB, e também demonstrando seu valor prognóstico na doença recorrente no pósoperatório dos pacientes. CAPÍTULO IV - Aproximadamente 98% de todos os produtos transcritos do genoma humano correspondem a RNAs não codificantes (RNAnc). Muitas funções dos RNAnc são atribuídas a suas particularidades estruturais dadas principalmente pelas estruturas secundárias formadas a partir da sua sequência linear de bases. Dentre os tipos de RNAnc estão os RNAt, RNAr, small nuclear RNA, small nucleolar RNA, small interference RNA (siRNA), microRNA (miRNA) e RNAs catalíticos (ribozimas). A bioinformática tem fornecido ferramentas úteis na predição de estruturas secundárias ótimas ou subótimas permitindo o design de RNAs de interferência como os miRNAs ou siRNAs. Em humanos, os miRNAs tem sido associados ao desenvolvimento de diversas doenças complexas como o câncer. O gene PCA3 (DD3) foi molecularmente caracterizado como câncer- e próstata- específico e os seus RNAs são os responsáveis por essa característica, isso porque nenhum produto protéico tem sido encontrado para esse gene. Devido às suas características estruturais, o gene PCA3, pertence assim à crescente família de RNAnc. No presente trabalho foi analisado as freqüências de quatro moléculas variantes do gene PCA3, além das anteriormente reportadas, como também foram preditas as suas estruturas secundárias na tentativa de elucidar o seu papel na biologia do câncer de próstata. Nenhuma associação foi encontrada entre a freqüência dessas moléculas e as patologias da próstata como hiperplasia benigna ou câncer, sendo que na população geral analisada essas variantes foram encontradas em apenas 10% (12/115) dos casos. As análises de homologia de possíveis polipeptídeos para essas moléculas demonstram que permanece o papel de RNA não-codificante para o gene PCA3. Ainda, a presença de introns nas variantes 1, 2 e 4 podem sugerir um papel intracelular de miRNA para essas moléculas do gene PCA3. Nos tecidos prostáticos, 100% dos casos de câncer foi representando pela molécula com splicing do exon 2. Contudo, para as variantes de splicing, novas pesquisas deverão ser realizadas incluindo outras patologias além das doenças prostáticas e outros tipos tumorais para verificar o real impacto dessas moléculas, uma vez que foram encontradas preferencialmente no sangue periférico. / Doutor em Genética e Bioquímica

Para obter resultados rápidos e confiáveis que permitam o monitoramento da segurança microbiológica de alimentos, seja pela indústria ou pelos órgãos de fiscalização, diversos métodos alternativos têm sido desenvolvidos para a detecção e quantificação de Salmonella. Os propósitos do estudo foram avaliar a viabilidade de emprego do QIAamp® DNA Stool Mini Kit para extração e purificação de DNA de Salmonella; validar ensaios baseados em PCR-tempo real (PCR-RT) para quantificar o DNA de Salmonella empregando ttr ou tuf e desenvolver um ensaio para quantificar Salmonella baseado na transcriptase reversa-PCR-tempo real (RT-PCR-RT). Para avaliação do QIAamp® DNA Stool Mini Kit empregaram-se fezes coletadas diretamente do reto de animais infectados ou não, sendo estas últimas artificialmente contaminadas e submetidas à extração segundo protocolo do fabricante. As amostras de DNA isoladas foram quantificadas empregando um ensaio Salmonella-específico PCR-RT utilizando como alvo o lócus ttr. O mesmo ensaio foi utilizado para células de Salmonella provenientes de meio de cultura. O ensaio PCR-RT baseado no alvo tuf foi validado empregando-se primeiramente cepas de diferentes sorotipos de Salmonella e de outras Enterobacteriaceae. A seguir sua eficiência foi avaliada para alimentos-modelo (ave e suíno) artificialmente contaminadas com elevada (&#8776; 6 log UFC/mL) e baixa (&#8776; 2 log UFC/mL) população de Salmonella Typhimurium DT 104. A validação do método quantitativo de Salmonella por RT-PCR-RT foi realizada primeiramente com células em meio de cultura e posteriormente nos mesmos alimentos-modelo utilizados para PCR-RT. Em ambos os métodos, alíquotas dos alimentos-modelo foram mantidas a 20 ºC e a 8 ºC, sendo examinadas em diferentes tempos pós-inoculação. Como controle empregou-se a enumeração de microrganismos mesófilos totais e de Salmonella por técnicas convencionais. A taxa de recuperação de Salmonella em fezes suínas artificialmente inoculadas, após tratamento com QIAamp® DNA Stool Kit, variou entre 25% a 50%, dependendo da quantidade inicial de células. Empregando o DNA extraído e submetendo-o à PCR-RT para o ttr obteve-se limite de detecção de 2,8 log UFC eq/g de fezes; método que foi menos sensível que o convencional. A quantificação de Salmonella por PCR-RT empregando tuf apresentou limite de detecção menor que 1 log UFC eq. Os resultados obtidos com este método, empregando-se células em meio de cultura ou alimentos-modelo, foram, de maneira geral, ligeiramente inferiores aos do método convencional. A eficiência de amplificação para PCR-RT e tuf foi de 94%. O método RT-PCR-RT apresentou limite de detecção semelhante ao obtido com o ttr (2 log UFC eq) e sua eficiência de amplificação foi de 100%. Observou-se que tuf é expresso na fase logarítmica de multiplicação bacteriana, o que o torna um bom indicador da viabilidade de Salmonella. / In order to get fast and trustworthy results that allow monitoring the microbiological food safety either by industries or governmental agencies, diverse alternative methods have been developed for Salmonella detection and quantification. The purposes of this study were to evaluate the viability of the use of QIAamp® DNA Stool Mini Kit for Salmonella DNA extraction and purification; to validate assays based on real time-PCR (PCR-RT) to quantify Salmonella DNA by using ttr or tuf, and to develop an assay to quantify Salmonella based on reverse transcriptase- PCR-real time (RT-PCR-RT). For QIAamp® DNA Stool Mini Kit evaluation feces taken directly from the rectum of infected or health animals were used, with the former being artificially contaminated. Samples were submitted to DNA extraction, according to manufacturers protocol. The isolated DNA were quantified using a Salmonella-specific PCR-RT targeting the ttr locus. The same assay was used for Salmonella cells originated from culture medium. The PCR-RT assay with tuf as target was first validated employing different Salmonella serovars and other Enterobacteriaceae strains. After, its efficiency was evaluated on food-models (chicken and swine) spiked with high (&#8776; 6 log CFU/mL) and low (&#8776; 2 log CFU/mL) Salmonella Typhimurium DT 104 populations. The validation of the quantitative RT-PCR-RT method was first conducted with cells grown in culture medium, and then in the same food-model used for PCR-RT. For both methods aliquots of foodmodels were maintained at 20 ºC and 8 ºC being evaluated at different incubation times. Enumeration of total mesophilic microorganisms and Salmonella based on conventional methods were used as controls. The DNA recovery rate in swine feces artificially inoculated, after QIAamp® DNA Stool Mini Kit treatment, was between 25% to 50% depending the initial amount of cells. Using the extracted DNA and submitting it to PCR-RT for ttr a detection level of 2,8 CFU eq/g of feces was obtained. This method showed lower sensitivity than the conventional. Salmonella quantification by PCR-RT employing tuf showed a detection level lower than 1 log CFU eq. The results obtained with this method and cells suspended in culture medium or in food-model systems were, in general slightly lower that those obtained with the conventional method. The efficiency of amplification for PCR-RT tuf was 94%. Detection limit of RT-PCR-RT was similar to that of ttr (2 log CFU eq) and efficiency of amplification was 100%. tuf was expressed in logarithmic phase of bacteria growth curve showing that it is a good viability indicator for Salmonella.