A Bioinformatic Framework to Assess the Genomic Response of Species to Environmental Toxins
Year: 2018
Type: dissertation
Abstract: The current ecotoxicological methods of identifying sites of biological cannot indicate the presence of hazardous chemicals before significant environmental damage has already occurred. In this thesis, I hypothesize that essential pathways and genes are conserved across the taxa and present a bioinformatic pipeline that uses genomic data for environmental monitoring. This pipeline mines chemical-gene interaction data from publicly available databases, retrieves the corresponding protein sequences and performs homology-based searches in the genome of target organisms. Afterwards, it clusters these protein sequences to obtain groups of orthologous sequences, retrieves related biological pathways and learns a Bayesian Network to show meaningful correlations between them and input chemicals. To demonstrate this pipeline, I ran a test dataset consisting of a group of phylogenetically distant taxa on it. The shared affected pathways suggested by this pipeline correspond with findings from previous studies on the toxic effects of target chemicals.
Author: Siavash Nazari
Language: English
Subfield: Health, Toxicology and Mutagenesis
Field: Environmental Science
Domain: Physical Sciences
Open Access status: green
OpenAlex ID: W2895450953