Atomic force microscopy assisted with electron and ion beam microscopy for the direct measurement of biostructures and DNA samples

Dissertation to obtain a Master degree in Biotechnology

The role of electron transfer in DNA building blocks: evaluation of strand breaks and their implications

Dissertação para obtenção do Grau de Doutor em Engenharia Física

Functional and structural studies of two enzymes: membrane bound kinase and Z-DNA/Z-RNA-binding protein

Dissertação para obtenção do Grau de Doutor em Sistemas de Bioengenharia

Arte em Construção: Análise Documental Sobre o Projecto “DNA – District of New Art”, Lisboa

Trabalho de Projecto realizado para cumprimento dos requisitos necessários à obtenção do grau de Mestre em Ciências da Comunicação – Cinema e Televisão

Optimization of randomly amplified polymorphic DNA-polymerase chain reaction for molecular typing of Salmonella enterica serovar Typhi

Optimization of the RAPD reaction for characterizing Salmonella enterica serovar Typhi strains was studied in order to ensure the reproducibility and the discriminatory power of this technique. Eight Salmonella serovar Typhi strains isolated from various regions in Brazil were examined for the fragment patterns produced using different concentrations of DNA template, primer, MgCl2 and Taq DNA polymerase. Using two different low stringency thermal cycle profiles, the RAPD fingerprints obtained were compared. A set of sixteen primers was evaluated for their ability to produce a high number of distinct fragments. We found that variations associated to all of the tested parameters modified the fingerprinting patterns. For the strains of Salmonella enterica serovar Typhi used in this experiment, we have defined a set of conditions for RAPD-PCR reaction, which result in a simple, fast and reproducible typing method.

Phenetic studies on randomly amplified polymorphic DNA-polymerase chain reaction-variability of four geographical populations of Lutzomyia whitmani (Diptera: Psychodidae) in Brazil

Previous evaluation of the genetic variability of four biogeographical populations of Lutzomyia whitmani from known foci of cutaneous leishmaniasis in Brazil demonstrated two main spatial clusters: Corte de Pedra-BA, Ilhéus-BA and Serra de Baturité-CE in the first cluster, and Martinho Campos-MG in the second. Further analysis showed a high degree of homogeneity in Corte de Pedra population but not in the others, which presented a significant percentage of specimens displaced from their phenon of origin (discrepant individuals). In the present work we analyzed the frequencies of association coefficients in the matrixes of similarity per population of Lutzomyia whitmani from both sexes and the general phenograms obtained, in a more detailed study of those discrepant specimens. Populational stability was observed for Corte de Pedra population, whereas the three remaining populations showed varying degrees of heterogeneity and different displacements according to sex. Our results strongly suggested the existence of a genetic flow between the lineages North-South/North-East and Ilhéus/Serra do Baturité of Lutzomyia whitmani.

DNA-Protein interaction: a response regulatory protein associated with Mo homeostasis in Desulfovibrio alaskensis G20.

Dissertation for a degree in Doctor in Sustainable Chemistry

Efetividade das vacinas anti-VHB (DNA-recombinante) em doadores de sangue de uma região endêmica para hepatite B no sul do Brasil

O objetivo deste estudo foi de estimar a efetividade das vacinas anti-VHB em um estudo longitudinal, retrospectivo composto por 1.012 doadores de sangue que completaram o esquema padrão de vacinação (três doses, incluindo doses de reforço nos doadores com títulos de anti-HBs <10UI/L) durante o período entre 1998 e 2002. Os resultados mostram que a taxa de soroconversão foi significativamente menor nos doadores cujo título de anti-HBs foi mensurado após seis meses decorridos do término do esquema de vacinação e nos doadores com mais de 50 anos. A efetividade média correspondeu a 88,7%, variando de 80,6% nos com maior idade (50 anos ou mais) a 91,4% nos doadores mais jovens (18 a 30 anos). O regime de dose de reforço foi efetivo, principalmente por reduzir o percentual de não-respondedores. Conclui-se que a efetividade da vacina foi significativamente maior nos doadores mais jovens e que o tempo decorrido entre a vacinação e a testagem interferiu na taxa de soroconversão.

Estudo da ação danificadora do 2,2'-Bipyridyl no DNA na presença de radiação UV

Em 2008, foram estimados no mundo, cerca de 12.7 milhões de novos casos de cancro e 7,6 milhões de mortes por cancro, sendo que 56% dos casos e 64% das mortes ocorreram nos países em desenvolvimento. Estes números indicam que é necessário se encontrar novos meios de combater este flagelo. Uma das possibilidades é encontrar moléculas intercalantes do ácido desoxirribonucleico (DNA) que se degradem na presença de radiação ou partículas carregadas de baixa energia que criem condições de induzir lesões no DNA, inibidoras da replicação e que portanto contribuam para a não proliferação de células cancerígenas. Assim, nesta dissertação analisou-se a influência do agente intercalante 2,2'-Bipyridyl do DNA em presença de radiação UV, 254 nm, na degradação do DNA. Os danos criados no DNA foram analisados pelas técnicas de espectroscopia de ultravioleta-visível e de infravermelho. Os resultados obtidos permitiram inferir que a cinética de degradação do DNA é mais eficiente na presença do composto 2,2'-Bipyridyl e que o ataque pelos produtos da decomposição do 2,2'-Bipyridyl é feito a todas as bases, embora com constantes características diferentes, sendo a ataque à guanina com uma constante de tempo maior. Estes resultados permitem concluir que este composto pode ser um possível candidato a indutor de lesões no DNA.

Identification and differentiation of Candida species from pediatric patients by random amplified polymorphic DNA

Thirty-four Candida isolates were analyzed by random amplified polymorphic DNA using the primer OPG-10:24 Candida albicans; 4 Candida tropicalis; 2 Candida parapsilosis; 2 Candida dubliniensis; 1 Candida glabrata and 1 Candida krusei. The UPGMA-Pearson correlation coefficient was used to calculate the genetic distance between the different Candida groupings. Samples were classified as identical (correlation of 100%); highly related samples (90%); moderately related samples (80%) and unrelated samples (< 70%). The results showed that the RAPD proposed was capable of classifying the isolates coherently (such that same species were in the same dendrogram), except for two isolates of Candida parapsilosis and the positive control (Netherlands, 1973), probably because they are now recognized as three different species. Concerning the only fluconazole-resistant Candida tropicalis isolate with a genotype that was different to the others, the data were insufficient to affirm that the only difference was the sensitivity to fluconazole. We concluded that the Random Amplified Polymorphic DNA proposed might be used to confirm Candida species identified by microbiological methods.

Alteração da metilação do DNA após exposição prolongada a fitoquímicos

Parte do trabalho efetuado durante este projeto de dissertação foi publicado na revista Chemico-Biological Interactions. E apresentado no “50th Congress of the European Societies of Toxicology 7th - 10th September 2014 Edinburgh International Conference Centre, Edinburgh, Scotland” em forma de poster.

Gold nanoparticles for the detection of DNA adducts as biomarkers of exposure to acrylamide

The main objective of this thesis was the development of a gold nanoparticle-based methodology for detection of DNA adducts as biomarkers, to try and overcome existing drawbacks in currently employed techniques. For this objective to be achieved, the experimental work was divided in three components: sample preparation, method of detection and development of a model for exposure to acrylamide. Different techniques were employed and combined for de-complexation and purification of DNA samples (including ultrasonic energy, nuclease digestion and chromatography), resulting in a complete protocol for sample treatment, prior to detection. The detection of alkylated nucleotides using gold nanoparticles was performed by two distinct methodologies: mass spectrometry and colorimetric detection. In mass spectrometry, gold nanoparticles were employed for laser desorption/ionisation instead of the organic matrix. Identification of nucleotides was possible by fingerprint, however no specific mass signals were denoted when using gold nanoparticles to analyse biological samples. An alternate method using the colorimetric properties of gold nanoparticles was employed for detection. This method inspired in the non-cross-linking assay allowed the identification of glycidamide-guanine adducts and DNA adducts generated in vitro. For the development of a model of exposure, two different aquatic organisms were studies: a goldfish and a mussel. Organisms were exposed to waterborne acrylamide, after which mortality was recorded and effect concentrations were estimated. In goldfish, both genotoxicity and metabolic alterations were assessed and revealed dose-effect relationships of acrylamide. Histopathological alterations were verified primarily in pancreatic cells, but also in hepatocytes. Mussels showed higher effect concentrations than goldfish. Biomarkers of oxidative stress, biotransformation and neurotoxicity were analysed after prolonged exposure, showing mild oxidative stress in mussel cells, and induction of enzymes involved in detoxification of oxygen radicals. A qualitative histopathological screening revealed gonadotoxicity in female mussels, which may present some risk to population equilibrium.

Extração de DNA a partir de sangue humano coagulado para aplicação nas técnicas de genotipagem de antígenos leucocitários humanos e de receptores semelhantes à imunoglobulina

O objetivo deste estudo foi padronizar uma metodologia de extração de DNA de alta qualidade a partir de amostras de sangue coagulado. Quarenta e oito amostras de sangue humano coagulado foram utilizadas para a extração de DNA pelo kit comercial EZ-DNA® (Biological Industries, Beit Haemek, Israel), pelo kit de coluna Neoscience® (One Lambda Inc., San Diego, CA) e pelo método modificado de salting out. Apenas o método de salting out foi capaz de extrair altas concentrações de DNA (média, 180ng/µL), as quais foram medidas pelo detector de fluorescência Qubit® (Invitrogen, USA). Este método permitiu a amplificação dos genes HLA (human leukocyte antigens) pela tecnologia PCR-SSO (polymerase chain reaction - specific sequence of oligonucleotides) Luminex, a qual exige DNA de boa qualidade, e de genes KIR (killer cell immunoglobulin-like receptors) pela técnica made in house PCR-SSP (polymerase chain reaction-sequence specific of primers), a qual demanda uma concentração específica de DNA (10ng/µL). Concluímos que a técnica de salting out modificada foi muito eficiente, simples e rápida para a extração de DNA de amostras de sangue humano coagulado, com o objetivo de realizar a genotipagem de genes HLA e KIR.

PCR-RFLP of 16S ribosomal DNA to confirm the identification of Enterococcus gallinarum and Enterococcus casseliflavus isolated from clinical and food samples

INTRODUCTION: This study aimed to confirm the identification of Enterococcus gallinarum and Enterococcus casseliflavus isolated from clinical and food samples by PCR-RFLP. METHODS: Fifty-two strains identified by conventional biochemical exams were submitted to PCR amplification and digested with HinfI. Only 20 (38.5%) of the 52 strains showed a DNA pattern expected for E. gallinarum and E. casseliflavus. RESULTS: Analysis of the results of this study showed that E. gallinarum and E. casseliflavus are occasionally erroneously identified and confirmed the potential application of 16S rDNA analysis for accurate identification of these species. CONCLUSIONS: A correct identification is important to distinguish between intrinsic and acquired vancomycin resistance.