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Advisor(s)
Abstract(s)
A cavidade oral humana é um ecossistema complexo onde fatores do hospedeiro, microbianos e ambientais interagem num equilíbrio dinâmico. A compreensão da biologia da cavidade oral e dos distúrbios que a afetam depende de ferramentas bioinformáticas que permitam a compilação, integração e aplicação da informação gerada por técnicas de alto rendimento, como as técnicas de proteómica, que se dedica à identificação de todas as proteínas expressas.
A compreensão dos mecanismos moleculares que se desenrolam na cavidade oral assenta na interação entre as moléculas presentes. O conhecimento destes mecanismos tem aplicações na fisiologia e fisiopatologia do sistema cavidade oral.
No sentido de responder à necessidade de estudar os genes e proteínas de forma integrada, dando realce às interações estabelecidas, começaram a ser desenvolvidas bases de dados de interatómica que incluem interações conhecidas e previstas através de algoritmos, associando-lhe um índice de confiança. O nosso trabalho contribuiu para o aperfeiçoamento de um algoritmo que permite a determinação de interações proteína-proteína. É utilizada a informação estrutural e de interações anteriormente determinadas entre os vários domínios das proteínas.
Este estudo tem como objetivo analisar, interpretar e explorar os resultados da aplicação do algoritmo OralInt ao conjunto de proteínas identificado por técnicas de proteómica como presentes na cavidade oral utilizando a base de dados OralOme, assim como verificar se algumas das interações descritas na bibliografia e determinadas experimentalmente na cavidade oral, se encontram presentes nas previsões e validar os resultados através de uma análise da literatura.
O desenvolvimento de ferramentas bioinformáticas que permitam a proposta de interações proteína-proteína, na cavidade oral, pode fornecer uma enorme quantidade de informação que vai assumir implicações na compreensão dos mecanismos moleculares dos processos que ocorrem na cavidade oral em situações fisiológicas e patológicas.
Só com o conhecimento dos microrganismos que habitam a cavidade oral, das moléculas por eles produzidas e das interações destas com as do hospedeiro, podemos chegar ao entendimento molecular total.
The human oral cavity is a complex ecosystem where host, microbial and environmental factors interact in a dynamic equilibrium. Understanding the biology of oral cavity and disorders affecting it depends on bioinformatics tools to compile, integrate and apply the information generated by high-throughput techniques such as proteomics, which is dedicated to the identification of all the expressed proteins. The understanding of the molecular mechanisms that take place in the oral cavity is based on the interaction between molecules present. The knowledge of these mechanisms has applications in physiology and pathophysiology of oral cavity system. In order to address the need for studying genes and proteins in an integrated way, by emphasizing the interactions established, inteatomic databases that include known and algorithmically predicted interactions, associated to a confidence index, began to be developed. This work contributes to the improvement of an algorithm allowing the determination of protein-protein interactions based on the structural information and interactions previously described between the various domains of the proteins (OralInt). This study aims to describe the results of applying the algorithm OralInt to the set of proteins identified by proteomics techniques as in the oral cavity using the OralOme database and to check if some of the interactions described in the literature and determined experimentally in the oral cavity, are present in the predictions. The development of bioinformatics tools that allow the proposal of protein-protein interactions in the oral cavity may provide enormous information that will have implications on the understanding of the molecular mechanisms occurring in the oral cavity in physiological and pathological situations. Only with the knowledge of the microorganisms that inhabit the oral cavity, the molecules produced by them and the interactions with the host, can we reach the molecular understanding of the oral cavity.
The human oral cavity is a complex ecosystem where host, microbial and environmental factors interact in a dynamic equilibrium. Understanding the biology of oral cavity and disorders affecting it depends on bioinformatics tools to compile, integrate and apply the information generated by high-throughput techniques such as proteomics, which is dedicated to the identification of all the expressed proteins. The understanding of the molecular mechanisms that take place in the oral cavity is based on the interaction between molecules present. The knowledge of these mechanisms has applications in physiology and pathophysiology of oral cavity system. In order to address the need for studying genes and proteins in an integrated way, by emphasizing the interactions established, inteatomic databases that include known and algorithmically predicted interactions, associated to a confidence index, began to be developed. This work contributes to the improvement of an algorithm allowing the determination of protein-protein interactions based on the structural information and interactions previously described between the various domains of the proteins (OralInt). This study aims to describe the results of applying the algorithm OralInt to the set of proteins identified by proteomics techniques as in the oral cavity using the OralOme database and to check if some of the interactions described in the literature and determined experimentally in the oral cavity, are present in the predictions. The development of bioinformatics tools that allow the proposal of protein-protein interactions in the oral cavity may provide enormous information that will have implications on the understanding of the molecular mechanisms occurring in the oral cavity in physiological and pathological situations. Only with the knowledge of the microorganisms that inhabit the oral cavity, the molecules produced by them and the interactions with the host, can we reach the molecular understanding of the oral cavity.
Description
Keywords
Proteínas da cavidade oral OralOme Domínios de interação Interações proteína-proteína Interatómica Interação hospedeiro-patogéneo Oral cavity proteins Interaction domains Protein-protein interactions Interatomic Host-pathogen interaction