Lipinski, Emma
(2024)
RNA SEQUENCING ANALYSIS TO DISCOVER DIFFERENTIALLY EXPRESSED OPEN READING FRAMES IN MULTICELLULAR VS UNICELLULAR S. CEREVISIAE.
Master's Thesis, University of Pittsburgh.
(Unpublished)
Abstract
Multicellular yeast biofilms can pose a risk to patients when formed on implanted medical devices or when presented as skin infections in immunosuppressed patients. Because the Saccharomyces cerevisiae species of yeast can exist in a multicellular or unicellular form, it is ideal for studying the genetic differences between the two phenotypes. Insights about the genetic mechanisms behind the multicellular phenotype in yeast can aid in combatting multicellular yeast infections and improving public health. To explore the open reading frame (ORF) expression differences between multicellular and unicellular strains of S. cerevisiae, I conducted a differential expression analysis with RNA sequencing data of the strains using DESeq2 and annotated the up- and down-regulated ORFs to known genes where possible. I identified 798 differentially expressed ORFs and investigated the functions of 14 with the greatest differentiation that had known functions. To gain insight into involved biological processes, I identified the most prominent Gene Ontology terms enriched with differentially expressed genes in the multicellular vs the unicellular strains. In the multicellular strain, I found enriched biological processes including reproduction, sporulation, and meiosis. Genes most up-regulated in the multicellular strain encoded proteins involved in chromosome synapsis, recombination, and the MAPK pathway. Biological processes enriched in the unicellular yeast included protein folding, response to heat, and transmembrane transport of sugars and carbohydrates. Genes that were down-regulated in the multicellular strain when compared to the unicellular included a glucose transporter and an RNA stabilizer that can affect gene expression. With improved annotation of novel ORFs and further exploration of the differentially expressed genes and significant biological pathways enriched for the differential expression between the two phenotypes, researchers may be able to target factors that pro-mote multicellular yeast biofilm development. Therapies that inhibit the formation of the multi-cellular phenotype could mitigate infections in the skin or on implants.
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| Item Type: |
University of Pittsburgh ETD
|
| Status: |
Unpublished |
| Creators/Authors: |
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| ETD Committee: |
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| Date: |
14 May 2024 |
| Date Type: |
Publication |
| Defense Date: |
18 April 2024 |
| Approval Date: |
14 May 2024 |
| Submission Date: |
24 April 2024 |
| Access Restriction: |
2 year -- Restrict access to University of Pittsburgh for a period of 2 years. |
| Number of Pages: |
72 |
| Institution: |
University of Pittsburgh |
| Schools and Programs: |
School of Public Health > Human Genetics |
| Degree: |
MS - Master of Science |
| Thesis Type: |
Master's Thesis |
| Refereed: |
Yes |
| Uncontrolled Keywords: |
Open reading frame, Saccharomyces cerevisiae, multicellularity, differential expression, RNA sequencing, gene expression |
| Date Deposited: |
14 May 2024 18:54 |
| Last Modified: |
21 May 2024 17:31 |
| URI: |
http://d-scholarship.pitt.edu/id/eprint/46274 |
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