Banca de QUALIFICAÇÃO: JORGE DOS SANTOS OLIVEIRA

Uma banca de QUALIFICAÇÃO de DOUTORADO foi cadastrada pelo programa.
DISCENTE : JORGE DOS SANTOS OLIVEIRA
DATA : 21/12/2017
HORA: 09:00
LOCAL: Sala SS1 do Depto. de Biologia Celular e Genética, do Centro de Biociências
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/, a
curated 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:
Presidente - 1549705 - ADRIANA FERREIRA UCHOA
Externo ao Programa - 1507794 - RODRIGO JULIANI SIQUEIRA DALMOLIN
Externo ao Programa - 2261797 - TIRZAH BRAZ PETTA LAJUS