Date of Defense
9-4-2025 1:30 PM
Location
F3-0120
Document Type
Thesis Defense
Degree Name
Master of Science in Molecular Biology and Biotechnology
College
COS
Department
Biology
First Advisor
Dr. Mohammad Tauqeer Alam
Keywords
Thermophiles, psychrophiles, genomic characteristics, metabolic network, metabolite exchange.
Abstract
Thermophiles and psychrophiles are extremophilic microorganisms that thrive in harsh conditions. Thermophiles are mostly located in hot springs, prosper in high temperatures. Psychrophiles thrive in extremely cold environments, including polar regions and deep-sea habitats. Although they play a crucial role in biotechnology and environmental research, their mechanisms of adaptation are still not well understood. The main objective of this thesis is to understand the genomic characteristics and metabolic network features in thermophiles and psychrophiles compared to mesophiles. The genomes of 59 species among thermophiles, psychrophiles, and mesophiles were collected from the NCBI database. These genomes were used to analyze their key features such as genome length, CDS counts, and G+C content at both whole-genome and codon-specific levels. Codon usage and amino acid abundance were analyzed, and genome-scale metabolic models were constructed using the ModelSEED platform. Additional analysis included model simulation, evaluation of metabolite production rates, pathway enrichment analysis of unique active reactions, and the generating of a metabolic network for all species. The study suggests that psychrophiles have larger genomes, more genes, larger metabolic networks, less metabolite exchange, and greater growth rates compared to thermophiles. Both groups have specific codon and amino acid preferences where thermophiles favor GC-rich codons, and psychrophiles prefer AT-rich codons. These bioinformatic analysis gives us deeper understanding of thermophiles and psychrophiles adaptation mechanisms, which enables their advanced application in biotechnology for industrial processes that requires stability in either extremely high or low temperatures. They also support biofuel production by leveraging their efficient metabolic networks and offer advanced applications in environmental industries.
GENOMIC AND METABOLIC NETWORK PROPERTIES IN THERMOPHILES AND PSYCHROPHILES COMPARED TO MESOPHILES
F3-0120
Thermophiles and psychrophiles are extremophilic microorganisms that thrive in harsh conditions. Thermophiles are mostly located in hot springs, prosper in high temperatures. Psychrophiles thrive in extremely cold environments, including polar regions and deep-sea habitats. Although they play a crucial role in biotechnology and environmental research, their mechanisms of adaptation are still not well understood. The main objective of this thesis is to understand the genomic characteristics and metabolic network features in thermophiles and psychrophiles compared to mesophiles. The genomes of 59 species among thermophiles, psychrophiles, and mesophiles were collected from the NCBI database. These genomes were used to analyze their key features such as genome length, CDS counts, and G+C content at both whole-genome and codon-specific levels. Codon usage and amino acid abundance were analyzed, and genome-scale metabolic models were constructed using the ModelSEED platform. Additional analysis included model simulation, evaluation of metabolite production rates, pathway enrichment analysis of unique active reactions, and the generating of a metabolic network for all species. The study suggests that psychrophiles have larger genomes, more genes, larger metabolic networks, less metabolite exchange, and greater growth rates compared to thermophiles. Both groups have specific codon and amino acid preferences where thermophiles favor GC-rich codons, and psychrophiles prefer AT-rich codons. These bioinformatic analysis gives us deeper understanding of thermophiles and psychrophiles adaptation mechanisms, which enables their advanced application in biotechnology for industrial processes that requires stability in either extremely high or low temperatures. They also support biofuel production by leveraging their efficient metabolic networks and offer advanced applications in environmental industries.
