Date of Award

Summer 2020


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Document Type


Degree Name

Master of Science (MS) in Biology




Helicobacter pylori is a common microaerophilic gram-negative bacterium that infects approximately 50% of the human population. Although all H. pylori infections result in inflammation of the gastric epithelium, only 10-15% of infections are symptomatic and progress to severe gastric diseases such as gastric and duodenal ulcers, MALT lymphoma and gastric cancer. Different disease outcomes are due in part to genetic variations among H. pylori strains. Helicobacter pylori strains with a genomic region called the cytotoxin-associated pathogenicity island (cagPAI) are associated with an increased risk of severe disease. The cagPAI region encodes a type IV secretion system that transports the CagA effector into host gastric epithelial cells. Regulation of the cagPAI is a vital area of research. Previous studies on H. pylori and other bacteria have found that small RNAs (sRNAs) play a role in gene regulation. These transcripts are 50-300 nucleotides in length and act independently on expressed targets. sRNAs serve to regulate and fine-tune gene expression by interacting with target mRNA molecules to inhibit or accelerate gene translation or function. Understanding how cagPAI genes are regulated is key to understanding how they promote disease. Herein, I investigate three cagPAI located sRNAs HPnc2525, HPnc2600, and HPnc2645 identified in previous studies. Using bioinformatics, conservation, and visual inspection, I predicted promoters and terminators for HPnc2525, HPnc2600, and HPnc2545. I devised an RT-PCR primer walking strategy to delimit the 5' end of HPnc2525 further. I analyzed the sRNA sequences defined by this and previous research using the TargetRNA2 program and predicted these sRNAs regulate virulence (e.g., cagL, hopZ, and fliA) and other genes. Due to CoVID-19, I was unable to verify sRNA interactions with their predicted targets using a plasmid-based GFP expression system.