Sistema computacional para o estudo da estrutura primária e redesenho de genes

Doutoramento em Engenharia InformáticaUm dos maiores avanços científicos do século XX foi o desenvolvimento de tecnologia que permite a sequenciação de genomas em larga escala. Contudo, a informação produzida pela sequenciação não explica por si só a sua estrutura primária, evolução e seu funcionamento. Para esse fim novas áreas como a biologia molecular, a genética e a bioinformática são usadas para estudar as diversas propriedades e funcionamento dos genomas. Com este trabalho estamos particularmente interessados em perceber detalhadamente a descodificação do genoma efectuada no ribossoma e extrair as regras gerais através da análise da estrutura primária do genoma, nomeadamente o contexto de codões e a distribuição dos codões. Estas regras estão pouco estudadas e entendidas, não se sabendo se poderão ser obtidas através de estatística e ferramentas bioinfomáticas. Os métodos tradicionais para estudar a distribuição dos codões no genoma e seu contexto não providenciam as ferramentas necessárias para estudar estas propriedades à escala genómica. As tabelas de contagens com as distribuições de codões, assim como métricas absolutas, estão actualmente disponíveis em bases de dados. Diversas aplicações para caracterizar as sequências genéticas estão também disponíveis. No entanto, outros tipos de abordagens a nível estatístico e outros métodos de visualização de informação estavam claramente em falta. No presente trabalho foram desenvolvidos métodos matemáticos e computacionais para a análise do contexto de codões e também para identificar zonas onde as repetições de codões ocorrem. Novas formas de visualização de informação foram também desenvolvidas para permitir a interpretação da informação obtida. As ferramentas estatísticas inseridas no modelo, como o clustering, análise residual, índices de adaptação dos codões revelaram-se importantes para caracterizar as sequências codificantes de alguns genomas. O objectivo final é que a informação obtida permita identificar as regras gerais que governam o contexto de codões em qualquer genoma.Sequencing of several genomes. However, the raw data alone produced from these genome sequencing efforts does not explain its primary structure, its evolution or its functioning. In order to do this, molecular biology, genetics and bioinformatics approaches have to be used for genome analysis. We are particularly interested in understanding the general rules that govern accurate decoding by the ribosome and gene evolution through global analysis of genome primary structure features, such as codon context and usage. However, the general rules that govern codon usage and codon context remain largely elusive, raising the question: can those rules be unraveled using genomic scale approaches by combining bioinformatics, statistical and computer visualization tools? Traditional methods, used for codon usage and context analysis, do not provide the tools to carry out detailed gene primary structure analysis at a genomic scale. Codon usage tables, using absolute metric, are available in public databases for any sequenced gene or genome and free-ware software for multivariate analysis of codon and amino acid usage is also readily available, however sophisticated statistical and data visualization tools are clearly missing. We developed a model supported by mathematical and statistical tools for automated analysis of codon context and codon usage and also to find trinucleotide repeats within coding regions on a genomic scale. A sophisticated graphical application system has also been developed to help data visualization and interpretation. The statistical tools incorporated in the system for data clustering, residual analysis and codon adaptation index determination will allow the obtention of global views of the important sequence features. It is expected that the data obtained will allow the identification of general rules that govern codon context and codon usage in any genome

Sistema de rastreio de doenças metabólicas

Mestrado em Engenharia Electrónica e TelecomunicaçõesO objectivo principal deste trabalho é desenhar e implementar um sistema de suporte à decisão, apoiado num conjunto de ferramentas matemáticas e estatísticas, que permita rastrear doenças metabólicas em recém-nascidos. O sistema terá que reduzir ao máximo o número recém-nascidos com diagnósticos de falsos positivos e negativos. Para tal, o sistema apoia-se na análise dos valores obtidos em recém-nascidos saudáveis/validados para obter, através do cálculo dos percentis, os valores máximos e mínimos dos limites necessários ao diagnóstico. A concepção da interface está baseada num paradigma familiar que permite ao utilizador um manejo amigável e de fácil utilização, permitindo um rápido rastreio. O sistema de informação proporciona também um controlo diário sobre as amostras submetidas, possibilitando a detecção de valores anormais originados por algum mau manuseamento dos espectrómetros ou uma anómala preparação das amostras para análise.The main goal of this work is the development of an information system supported by a set of mathematical and statistical tools necessary to the screening of metabolic diseases in new born offspring. The system will have to minimize the number of newborns with fake positive and negative diagnosis. To achieve this goal, the system is based upon the analysis of the obtained values of healthy newborns in order to get, through the calculation of the percentis, the maximum and minimum values of the necessary limits to the diagnosis. The layout of the operator interface is constructed upon familiar paradigms allowing for increased user friendliness. The information system also permits a daily control of the submitted samples, allowing the detection of abnormal values originated by some improper usage of the mass spectrometers or an unsuitable preparation of the samples to be analyzed

Transcriptomes analysis of Aeromonas molluscorum Av27 cells exposed to tributyltin (TBT) : unravelling the effects from the molecular level to the organism

This work was supported by FCOMP-01-0124-FEDER-010630 project, co-funded by FEDER, European Funds through COMPETE and FCT within project PEst-C/MAR/LA0017/2013. Andreia Cruz was funded by the PhD grant SFRH/BD/36047/2007 from FCT and by a post-doctoral grant (BPD/UI88/2886/2013), from the project “Sustainable Use of Marine Resources” - MARES (CENTRO-07-ST24-FEDER-002033), funded by QREN, Mais Centro - Programa Operacional Regional do Centro e UE/Fundo Europeu de Desenvolvimento Regional. Bioinformatics support was provided by Miguel Pinheiro from the Bioinformatics Unit at St Andrews University funded by a Wellcome Trust ISSF grant (097831/Z/11/Z).Aeromonas molluscorum Av27 cells were exposed to 0, 5 and 50 μM of TBT and the respective transcriptomes were obtained by pyrosequencing. Gene Ontology revealed that exposure to 5 μM TBT results in a higher number of repressed genes in contrast with 50 μM of TBT, where the number of over-expressed genes is greater. At both TBT concentrations, higher variations in gene expression were found in the functional categories associated with enzymatic activities, transport/binding and oxidation-reduction. A number of proteins are affected by TBT, such as the acriflavin resistance protein, several transcription-related proteins, several Hsps, ABC transporters, CorA and ZntB and other outer membrane efflux proteins, all of these involved in cellular metabolic processes, important to maintain overall cell viability. Using the STRING tool, several proteins with unknown function were related with others involved in degradation processes, such as the pyoverdine chromophore biosynthetic protein, that has been described as playing a role in the Sn-C cleavage of organotins. This approach has allowed a better understanding of the molecular effects of exposure of bacterial cells to TBT. Furthermore it contributes to the knowledge of the functional genomic aspects of bacteria exposed to this pollutant. Furthermore, the transcriptomic data gathered, and now publically available, constitute a valuable resource for comparative genome analysis.Publisher PDFPeer reviewe

Transcriptome of the deep-sea black scabbardfish, Aphanopus carbo (Perciformes: Trichiuridae) : tissue-specific expression patterns and candidate genes associated to depth adaptation

Deep-sea fishes provide a unique opportunity to study the physiology and evolutionary adaptation to extreme environments. We carried out a high throughput sequencing analysis on a 454 GS-FLX titanium plate using unnormalized cDNA libraries from six tissues of A. carbo. Assemblage and annotations were performed by Newbler and InterPro/Pfam analyses, respectively. The assembly of 544,491 high quality reads provided 8,319 contigs, 55.6% of which retrieved blast hits against the NCBI nonredundant database or were annotated with ESTscan. Comparison of functional genes at both the protein sequences and protein stability levels, associated with adaptations to depth, revealed similarities between A. carbo and other bathypelagic fishes. A selection of putative genes was standardized to evaluate the correlation between number of contigs and their normalized expression, as determined by qPCR amplification. The screening of the libraries contributed to the identification of new EST simple-sequence repeats (SSRs) and to the design of primer pairs suitable for population genetic studies as well as for tagging and mapping of genes. The characterization of the deep-sea fish A. carbo first transcriptome is expected to provide abundant resources for genetic, evolutionary, and ecological studies of this species and the basis for further investigation of depth-related adaptation processes in fishes.Publisher PDFPeer reviewe

MOSAL : software tools for multiobjective sequence alignment

Multiobjective sequence alignment brings the advantage of providing a set of alignments that represent the trade-off between performing insertion/deletions and matching symbols from both sequences. Each of these alignments provide a potential explanation of the relationship between the sequences. We introduce MOSAL, a software tool that provides an open-source implementation and an on-line application for multiobjective pairwise sequence alignment.Publisher PDFPeer reviewe

Transcriptomes analysis of Aeromonas molluscorum Av27 cells exposed to tributyltin (TBT): unravelling the effects from the molecular level to the organism (dataset)

SRA BioProject accession number PRJNA18260