Premium
A research‐based biochemistry lab focused on gene expression and RNA degradation: design, implementation and outcomes
Author(s) -
Callahan Kevin Patrick,
Butler Scott
Publication year - 2016
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.30.1_supplement.880.7
Subject(s) - gene expression , rna , gene , biology , mutant , exoribonuclease , nucleic acid , saccharomyces cerevisiae , yeast , computational biology , biochemistry , genetics , rnase p
Biochemistry II (CHEM 408) is an upper level course that focuses on the structure, production and regulation of DNA and RNA, as well as the synthesis, manipulation and detection of these nucleic acids. To complement the lecture, a research‐based laboratory sequence was developed that utilized quantitative real‐time polymerase chain reaction (qRT‐PCR) to evaluate gene expression changes in Saccharomyces cerevisiae (baker's yeast). The goal of this lab is to reinforce the dynamic nature of gene regulation while providing students an opportunity to be involved in authentic research aimed at better understanding the role that RNA degradation plays in controlling gene expression. The initial stages of the project had students isolate RNA from a wild‐type strain, as well as a strain lacking an enzyme that affects gene expression, the 3′‐5′ exoribonuclease Rrp6p. The students evaluated how the expression of both non‐coding and coding RNAs changed in the rrp6‐ Δ cells relative to the wild‐type using the ΔΔ Ct method for quantification. These initial experiments helped establish an in‐depth understanding of qPCR and the corresponding data analysis. Working in pairs the students were asked to develop experimental conditions that they believed would modulate gene expression, and design a well‐controlled experiment to test if RNA levels change in the wild‐type and mutant strains. Students chose a variety of conditions such as nutrient source, different phases of cell growth, exposure to reactive oxygen species and UV‐light. Students were expected to complete three replicates of the experiment. After each experiment the students would present their data to the instructor and modify the protocol if necessary. To reinforce scientific writing and analysis skills the culmination of this project was a manuscript describing their results and a final class lab meeting where each group presented their data and conclusions. Informal assessments indicated that participating in this lab increased students’ interest in attending graduate school and pursing careers in biomedical research.