Senior Design Projects

ECS193 A/B Winter & Spring 2020

RNA-seq analysis of Vibrio parahaemolyticus in summer and winter seawater

Email chaliao@ucdavis.edu
Name Chao Liao
Affiliation Food Science and Technology, UCD

Project's details

Project title RNA-seq analysis of Vibrio parahaemolyticus in summer and winter seawater
Background Vibrio parahaemolyticus is a foodborne pathogen that presents ubiquitously in seawaters. It has caused significant numbers of human diseases due to the consumption of contaminated raw or uncooked seafood, particular raw oysters. In the U.S., approximately 72.8% of the Vibrio infection cases occur during summer months, when seawater water temperatures are higher than 20oC. Seawater temperatures usually reach their annual highest levels from July to September and are at their lowest levels (about 10oC) from December to February.
Description Two pathogenic V. parahaemolyticus strain (one with the virulent tdh gene (ATCC 43996) and one with the virulent trh gene (ATCC 17802)) were inoculated into sterile seawater and stored at 10oC and 30oC for 5 days. The RNA were extracted from samples and carried out with RNA sequencing. The comparative transcriptomic data analyses of the two V. parahaemolyticus in seawater under two different temperature condition over five day storage needs to be conducted. Especially, the expression of virulent genes will be focused on.
Deliverable Differential gene expression analysis (DGE)
Skill set desirable RNA-seq data analysis experience, Bioinformatics knowledge, and R or Python
Phone number 3343293450
Client time availability 30-60 min weekly or more
IP requirement Client wishes to keep IP of the project
Attachment N/A