MicroRNAs as modulators of water deficit responses in Medicago truncatula

Dissertação para a obtenção do grau de doutor em Biologia pelo Instituto de Tecnologia Química e Biológica. Universidade Nova de Lisboa

The Relevance of Ribonuclease III in Pathogenic Bacteria

Dissertation presented to obtain the Ph.D degree in Biology.

Controlling gene expression in enterobacteriaceae: studies on sRNAs and strategies for synthetic biology

Dissertation presented to obtain the Master Degree in Molecular, Genetics and Biomedicine

Previsão da estrutura temporal da taxa de juro na zona Euro : aproximação paramétrica e por métodos de aprendizagem automática

A estrutura temporal das taxas de juro, também conhecida por yield curve ou curva de rendimentos define a relação entre as taxas de juros e o prazo de vencimento (ou maturidades) dos investimentos feitos. Assim, o desenvolvimento de modelos que possibilitem a obtenção de previsões precisas sobre a estrutura temporal das taxas de juro e que permitam estudar a dinâmica da evolução das taxas de juro é de crucial importância em diversas áreas de financiamento. Neste estudo investigou-se a performance de diferentes métodos de previsão para obter a estrutura temporal das taxas de juro da Zona Euro, considerando o período entre 2009 e 2015. Em termos mais específicos, foi analisada a capacidade preditiva do modelo de Nelson-Siegel & Svensson assumindo que os parâmetros resultantes da estimação da especificação paramétrica podem ser modelizados através de métodos de séries temporais univariados (modelos ARIMA, Random walk) e multivariados (modelos VAR) e Redes Neuronais Artificiais (RNA) individuais e conjuntas. Os resultados deste estudo mostram que (i) as RNA com a previsão dos parâmetros em simultâneo exibem os valores de erro mais baixos para as maturidades de curto e médio prazo (3 meses a 5 anos); (ii) As RNAs individuais são melhores para prever as taxas de juro nas maturidades compreendidas entre os 7 e os 10 anos, e que (iii) para as maturidades de longo e muito longo prazo (15 e 30 anos respetivamente) deverá ser escolhido o modelo VAR(1). Estes resultados são robustos e consistentes para todos os horizontes de previsão analisados (1,2 e 3 meses). Contudo, no período analisado nenhum dos modelos testados apresenta valores de erro inferiores aos obtidos com o modelo Random Walk.

Hair coloration by gene regulation: fact or fiction?

The unravelling of hair pigmentation genetics and robust delivery systems to the hair follicle (HF) will allow the development of a new class of colouring products. The challenge will be changing hair colour from inside out by safely regulating the activity of target genes through the specific delivery of synthetic/natural compounds, proteins, genes, or small RNAs.

Desenvolvimento de rede neuronal artificial para o diagnóstico de doenças neurodegenerativas

Dissertação de mestrado integrado em Engenharia Eletrónica Industrial e Computadores

Reconstruction of the regulatory network for Bacillus subtilis and reconciliation with gene expression data

The Supplementary Material for this article can be found online at: http://journal.frontiersin.org/article/10.3389/fmicb. 2016.00275

MicroRNAs: um novo paradigma no tratamento e diagnóstico da insuficiência cardíaca?

MicroRNAs (miRNAs) são um grupo recém-descoberto de pequenos RNAs, não codificantes, que representam uma das áreas mais estimulantes da ciência médica moderna por modularem uma enorme e complexa rede regulatória da expressão dos genes.Recentemente, linhas de evidências sugerem que os miRNAs desempenham um papel crucial na patogênese da insuficiência cardíaca. Alguns miRNAs altamente expressos no coração como o miR-1, miR-133 e miR-208 estão fortemente associados ao desenvolvimento da hipertrofia cardíaca, enquanto o exato papel de miR-21 no sistema cardiovascular permanece controverso. Os níveis séricos de miRNAs circulantes como o miR-423-5p estão sendo avaliados como potenciais biomarcadores no diagnóstico e prognóstico da insuficiência cardíaca.Por outro lado, a manipulação dos níveis de miRNAs usando técnicas como os mimetizadores de miRNAs (miRmimics) e miRNAs antagônicos(antagomiRs) está tornando cada vez mais evidente o enorme potencial dos miRNAs como promissoras estratégias terapêutica sna insuficiência cardíaca.

Exercício físico e microRNAs: novas fronteiras na insuficiência cardíaca

Embora recentemente tenha sido questionado o impacto do exercício na sobrevida de pacientes com insuficiência cardíaca, o treinamento físico melhora a qualidade de vida, a capacidade funcional, a inflamação, a função autonômica e a função endotelial. Nos últimos anos, vem crescendo o interesse em um grupo de pequenos RNAs não codificadores de proteína chamados microRNAs. Estudos têm demonstrado que a expressão dessas moléculas se modifica em diversas condições patológicas, como a hipertrofia miocárdica, a isquemia miocárdica e a insuficiência cardíaca, e, quando ocorre melhora clínica, elas parecem se normalizar. Com o potencial de aplicabilidade prática, já foram identificados marcadores que poderão ser úteis na avaliação diagnóstica e prognóstica da insuficiência cardíaca, como o miR-423-5p. Além disso, resultados de estudos experimentais indicam haver possíveis efeitos terapêuticos dos microRNAs. Implicados na regulação da expressão genética durante o desenvolvimento fetal e no indivíduo adulto, os microRNAs aumentam ou diminuem no coração em resposta a estresse fisiológico, injúria ou sobrecarga hemodinâmica. Assim, o estudo do comportamento dessas moléculas no exercício físico vem trazendo informações importantes quanto aos efeitos dessa modalidade terapêutica e representa uma nova era no entendimento da insuficiência cardíaca. Esta revisão tem por objetivo integrar as evidências sobre microRNAs na insuficiência cardíaca com maior relevância no estudo do exercício físico.

mRNA metabolism: nonsense mediated mRNA decay as a tool for gene therapy and the role of human DIS3L2 in transcript degradation

Tese de mestrado em Biologia Humana e Ambiente, apresentada à Universidade de Lisboa, através da Faculdade de Ciências, 2015

Comprehensive Expression Analyses of Neural Cell-Type-Specific miRNAs Identify New Determinants of the Specification and Maintenance of Neuronal Phenotypes.

MicroRNAs (miRNAs) have been shown to play important roles in both brain development and the regulation of adult neural cell functions. However, a systematic analysis of brain miRNA functions has been hindered by a lack of comprehensive information regarding the distribution of miRNAs in neuronal versus glial cells. To address this issue, we performed microarray analyses of miRNA expression in the four principal cell types of the CNS (neurons, astrocytes, oligodendrocytes, and microglia) using primary cultures from postnatal d 1 rat cortex. These analyses revealed that neural miRNA expression is highly cell-type specific, with 116 of the 351 miRNAs examined being differentially expressed fivefold or more across the four cell types. We also demonstrate that individual neuron-enriched or neuron-diminished RNAs had a significant impact on the specification of neuronal phenotype: overexpression of the neuron-enriched miRNAs miR-376a and miR-434 increased the differentiation of neural stem cells into neurons, whereas the opposite effect was observed for the glia-enriched miRNAs miR-223, miR-146a, miR-19, and miR-32. In addition, glia-enriched miRNAs were shown to inhibit aberrant glial expression of neuronal proteins and phenotypes, as exemplified by miR-146a, which inhibited neuroligin 1-dependent synaptogenesis. This study identifies new nervous system functions of specific miRNAs, reveals the global extent to which the brain may use differential miRNA expression to regulate neural cell-type-specific phenotypes, and provides an important data resource that defines the compartmentalization of brain miRNAs across different cell types.

Results of An International Study of Quantitative BCR/ABL Assays Using Defined RNA Samples

Molecular monitoring of BCR/ABL transcripts by real time quantitative reverse transcription PCR (qRT-PCR) is an essential technique for clinical management of patients with BCR/ABL-positive CML and ALL. Though quantitative BCR/ABL assays are performed in hundreds of laboratories worldwide, results among these laboratories cannot be reliably compared due to heterogeneity in test methods, data analysis, reporting, and lack of quantitative standards. Recent efforts towards standardization have been limited in scope. Aliquots of RNA were sent to clinical test centers worldwide in order to evaluate methods and reporting for e1a2, b2a2, and b3a2 transcript levels using their own qRT-PCR assays. Total RNA was isolated from tissue culture cells that expressed each of the different BCR/ABL transcripts. Serial log dilutions were prepared, ranging from 100 to 10-5, in RNA isolated from HL60 cells. Laboratories performed 5 independent qRT-PCR reactions for each sample type at each dilution. In addition, 15 qRT-PCR reactions of the 10-3 b3a2 RNA dilution were run to assess reproducibility within and between laboratories. Participants were asked to run the samples following their standard protocols and to report cycle threshold (Ct), quantitative values for BCR/ABL and housekeeping genes, and ratios of BCR/ABL to housekeeping genes for each sample RNA. Thirty-seven (n=37) participants have submitted qRT-PCR results for analysis (36, 37, and 34 labs generated data for b2a2, b3a2, and e1a2, respectively). The limit of detection for this study was defined as the lowest dilution that a Ct value could be detected for all 5 replicates. For b2a2, 15, 16, 4, and 1 lab(s) showed a limit of detection at the 10-5, 10-4, 10-3, and 10-2 dilutions, respectively. For b3a2, 20, 13, and 4 labs showed a limit of detection at the 10-5, 10-4, and 10-3 dilutions, respectively. For e1a2, 10, 21, 2, and 1 lab(s) showed a limit of detection at the 10-5, 10-4, 10-3, and 10-2 dilutions, respectively. Log %BCR/ABL ratio values provided a method for comparing results between the different laboratories for each BCR/ABL dilution series. Linear regression analysis revealed concordance among the majority of participant data over the 10-1 to 10-4 dilutions. The overall slope values showed comparable results among the majority of b2a2 (mean=0.939; median=0.9627; range (0.399 - 1.1872)), b3a2 (mean=0.925; median=0.922; range (0.625 - 1.140)), and e1a2 (mean=0.897; median=0.909; range (0.5174 - 1.138)) laboratory results (Fig. 1-3)). Thirty-four (n=34) out of the 37 laboratories reported Ct values for all 15 replicates and only those with a complete data set were included in the inter-lab calculations. Eleven laboratories either did not report their copy number data or used other reporting units such as nanograms or cell numbers; therefore, only 26 laboratories were included in the overall analysis of copy numbers. The median copy number was 348.4, with a range from 15.6 to 547,000 copies (approximately a 4.5 log difference); the median intra-lab %CV was 19.2% with a range from 4.2% to 82.6%. While our international performance evaluation using serially diluted RNA samples has reinforced the fact that heterogeneity exists among clinical laboratories, it has also demonstrated that performance within a laboratory is overall very consistent. Accordingly, the availability of defined BCR/ABL RNAs may facilitate the validation of all phases of quantitative BCR/ABL analysis and may be extremely useful as a tool for monitoring assay performance. Ongoing analyses of these materials, along with the development of additional control materials, may solidify consensus around their application in routine laboratory testing and possible integration in worldwide efforts to standardize quantitative BCR/ABL testing.

Mutation screening of the glutamate cysteine ligase modifier (GCLM) gene in patients with schizophrenia.

BACKGROUND: Experimental evidences show that glutathione and its rate-limiting synthesizing enzyme, the glutamate-cysteine ligase (GCL), are involved in the pathogenesis of schizophrenia. Furthermore, genetic association has been previously reported between two single nucleotide polymorphisms lying in noncoding regions of glutamate cysteine ligase modifier (GCLM) gene, which specifies for the modifier subunit of GCL and schizophrenia. OBJECTIVE: We wanted to investigate the presence of GCLM true functional mutations, likely in linkage disequilibrium with the previously identified single nucleotide polymorphism alleles, in the same set of cases that allowed the detection of the original association signal. METHODS: We screened all the coding regions of GCLM and their intronic flanking vicinities in 353 patients with schizophrenia by direct DNA sequencing. RESULTS: Ten sequence variations were identified, five of which were not previously described. None of these DNA changes was within the GCLM coding sequence and in-silico analysis failed to indicate functional impairment induced by these variations. Furthermore, screening of normal controls and downstream statistical analyses revealed no significant relationship of any of these DNA variants with schizophrenia. CONCLUSION: It is unlikely that functional mutations in the GCLM gene could play a major role in genetic predisposition to schizophrenia and further studies will be required to assess its etiological function in the disease.

Conserved microRNA editing in mammalian evolution, development and disease.

BACKGROUND: Mammalian microRNAs (miRNAs) are sometimes subject to adenosine-to-inosine RNA editing, which can lead to dramatic changes in miRNA target specificity or expression levels. However, although a few miRNAs are known to be edited at identical positions in human and mouse, the evolution of miRNA editing has not been investigated in detail. In this study, we identify conserved miRNA editing events in a range of mammalian and non-mammalian species. RESULTS: We demonstrate deep conservation of several site-specific miRNA editing events, including two that date back to the common ancestor of mammals and bony fishes some 450 million years ago. We also find evidence of a recent expansion of an edited miRNA family in placental mammals and show that editing of these miRNAs is associated with changes in target mRNA expression during primate development and aging. While global patterns of miRNA editing tend to be conserved across species, we observe substantial variation in editing frequencies depending on tissue, age and disease state: editing is more frequent in neural tissues compared to heart, kidney and testis; in older compared to younger individuals; and in samples from healthy tissues compared to tumors, which together suggests that miRNA editing might be associated with a reduced rate of cell proliferation. CONCLUSIONS: Our results show that site-specific miRNA editing is an evolutionarily conserved mechanism, which increases the functional diversity of mammalian miRNA transcriptomes. Furthermore, we find that although miRNA editing is rare compared to editing of long RNAs, miRNAs are greatly overrepresented among conserved editing targets.

Molecular analysis of yellow fever virus 17DD vaccine strain

The Oswaldo Cruz Foundation produces most of the yellow fever (YF) vaccine prepared world wide. As part of a broader approach to determine the genetic variability in YF l7D seeds and vaccines and its relevance to viral attenuation the 17DD virus was purifed directly from chick embryo homogenates which is the source of virus used for vaccination of millions of people in Brazil and other countries for half a century. Neutralization and hemagglutination tests showed that the purified virus is similar to the original stock. Furthermore, radioimmune precipitation of 35S-methionine-labeled viral proteins using mouse hyperimmune ascitic fluid revealed identical patterns for the purified 17DD virus and the YF l7D-204 strain except for the 17DD E protein which migrated slower on SDS-PAGE. This difference is likely to be due to N-linked glycosylation. Finally, comparison by northern blot nybridization of virion RNAs of purified 17DD with two other strains of YF virus only fenome-sized molecules for all three viruses. These observations suggest that vaccine phenotype is primarily associated with the accumulation of mutations.