Banca de DEFESA: JORGE DOS SANTOS OLIVEIRA

Uma banca de DEFESA de DOUTORADO foi cadastrada pelo programa.
DISCENTE : JORGE DOS SANTOS OLIVEIRA
DATA : 29/04/2018
HORA: 09:00
LOCAL: Instituto de Engenharia de Sistemas e Computadores - Investigação e Desenvolvimento (INESC-ID)
TÍTULO:

Prospecting of genes applied to hydrocarbon biodegradation and surfactant production using computational approaches

PALAVRAS-CHAVES:

Bioinformatics, Metagenomics, Biosurfactants, Biodegradation, Bioremediation, Petroleum, Hydrocarbons.

PÁGINAS: 153
GRANDE ÁREA: Ciências Biológicas
ÁREA: Genética
RESUMO:

Crude oil extraction, transportation and use provoke the contamination of countless ecosystems. Therefore, bioremediation through hydrocarbon biodegradation or surfactants mobilization is an important subject, both economically and environmentally. Bioremediation research had a great boost with the recent advances in Metagenomics, as it enabled the sequencing of uncultured microorganisms providing new insights on surfactant producing and/or oil-degrading bacteria. Countless research studies are making available genomic data from unknown organisms obtained from metagenomics analysis of oil contaminated environmental samples. These new datasets are presently demanding the development of new tools and data repositories tailored for the biological analysis in a context of bioremediation data analysis. This work presents new bioinformatic tools and protocols for the domain of hydrocarbon biodegradation and surfactant production. The first tool created was BioSurfDB, http://www.biosurfdb.org/, acurated relational information system integrating data from: (i) metagenomes; (ii) organisms; (iii) biodegradation relevant genes; proteins and their metabolic pathways; (iv) bioremediation experiments results; and (v) a biosurfactant-curated list. The main goal of this repository is to gather information on the characterization of biological compounds and mechanisms involved in biosurfactant production and/or hydrocarbon biodegradation and make it available in a curated way and associated with a number of computational tools to support studies of genomic and metagenomic data. Secondly, a biogeographical distribution analysis of hydrocarbon degrading and biosurfactant producing genes was performed. It was of great importance for our reseach as it confirmed the correlation of surfactation and degradation, and therefore, the need for analysis of these events together. The results also suggested that terrestrial biomes have higher abundance of biodegradation genes, when compared to water biomes and that near-equatorial biomes have higher abundance of genes with potential for bioremediation. With more than 70 metagenomes analysed, this work was an extensive test to BioSurfDB and its publication validated the database and tools relevance. Meanwhile, the massive amount of data generated by metagenomics, presents specific computational challenges, demanding the development of new collaborative research platforms. In this thesis the Oil and Gas Virtual Research Environment (OGVRE), available at http://aleph.inesc-id.pt/vre/, was developed. The OGVRE that can support studies using metagenomic data with application to the oil and gas field through a responsive web-based working environment, providing: (ii) workflow sharing, both bioinformatics and bench; (ii) access to algorithms and tools; (iii) access to databases and datasets related with biodegradation and biosurfactants; (iv) access to processing resources; (v) access to storage resources; and (vi) access to social tools. The sharing of tailor-made computational and bench workflows is very useful in metagenomics research due to the novelty, heterogeneity and size of the data that is being generated. The final stage of this thesis corresponds to the selection of consortia enhanced for biodegradation of hydrocarbons ans surfactant production, using oil from the pre-salt layer of Brazil. The best consortium, together with a sample of pure oil were sequenced in a 16S amplicon approach and analysed for a taxonomic classification of this still largely unknown oil type, obtaining a research base for this economical important layer.

MEMBROS DA BANCA:
Interno - 1549705 - ADRIANA FERREIRA UCHOA
Externo à Instituição - Ana Tereza Ribeiro de Vasconcelos - LNCC
Presidente - 1149647 - LUCYMARA FASSARELLA AGNEZ
Externo à Instituição - SUSANA VINGA - Inesc-ID
Externo ao Programa - 2261797 - TIRZAH BRAZ PETTA LAJUS