DOI
https://doi.org/10.25772/F1JT-WH11
Author ORCID Identifier
https://orcid.org/0000-0002-7982-7718
Defense Date
2023
Document Type
Thesis
Degree Name
Master of Science
Department
Bioinformatics
First Advisor
Dr. Ping Xu
Second Advisor
Dr. Allison Johnson
Third Advisor
Dr. Peter Uetz
Abstract
The oral cavity hosts hundreds of bacterial species, amongst them are the Streptococci family. More specifically, S. sanguinis is a benign bacteria in the oral cavity to protect the tooth surface from S. mutans. which is a pathogen causing dental caries. While S. sanguinis is harmless in the oral cavity, it becomes pathogenic once entering the bloodstream and causing Infective Endocarditis (IE). To further study S. sanguinis and eventually develop an effective drug to treat IE caused by S. sanguinis, a gene expression study was conducted. In order to study gene expression, RNA-sequencing was conducted, and appropriate methods to remove rRNA were used. A knockout of the F1Fo gene was also discovered in the lab for further study of the gene’s conditional essentiality. Different media growth conditions were used to test under which conditions the F1Fo becomes essential. A gene expression analysis was conducted using EDGE-Pro, the first and so far most efficient tool used for estimating gene expression in Prokaryotes. Study of differentially expressed genes was conducted to test which genes are expressed on different levels between conditions, and co-expression genes were identified to show which genes have a coordinated expression across all samples.
The study of differential expressed genes (DEG) showed that treatment with LA causes the WT to have a higher number of DEG and make the WT act more like the mutant. In contrast, for the mutant, treatment with NaOH and PEG (osmotic) conditions causes the mutant to act more like WT. Co-expressed genes were used to identify seven hub genes (SSA_0201, SSA_0434, SSA_0435, SSA_0453, SSA_0500, SSA_0537, SSA_2091). These hub genes play an essential role in gene regulation and are targets for further evaluation.
Rights
© The Author
Is Part Of
VCU University Archives
Is Part Of
VCU Theses and Dissertations
Date of Submission
8-8-2023