Difference between revisions of "20.109(F20):Module 3"
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Revision as of 23:42, 27 July 2020
Contents
Module 3
Lecturer: Noreen Lyell
Instructors: Noreen Lyell, Leslie McClain, and Becky Meyer
TAs:
Overview
At the core of scientific discovery is building on the research of others to push the field forward. To accomplish this an iterative process is used to answer research questions: manipulate, measure, mine and model, and modify.
Manipulate: Often, the first step in answering a research question is designing and performing an experiment. The existing literature is an important resource at this stage as it provides information on what has already been done. In addition, the literature is useful in identifying which types experimental methods are appropriate for answering your specific research question. After the experiment is designed, the fun part of actually doing the benchwork can start.
Measure: It is not enough to just do an experiment. For the work to be meaningful, the data need to be collected and analyzed.
Mine and Model:
Modify:
In Module 3 you will use this process to expand on the research completed by previous 109ers. In past iterations of this module students used a modified Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) system to modulate transcription in E. coli strain MG1655. Specifically, they used a CRISPR-based interference system (CRISPRi) to target genes within the anaerobic fermentative pathway in an effort to increase ethanol yield.
Research goal: Improve ethanol yield in E. coli MG1655 using the CRISPRi system by using previous research to design an optimized sgRNA targeting sequence.
Lab links: day by day
M3D1: Research project scope and experimental strategy
M3D2: Align gRNA sequences with genomic targets
M3D3: Analyze ethanol yield data
M3D4: Examine features in gRNA-targeted genomic sequences
M3D5: Design optimized gRNA sequence for enhanced ethanol production
Assignments
Research proposal presentation
Mini-report
References
CRISPR interference (CRISPRi) for sequence-specific control of gene expression. Nature Methods. (2013) 8: 2180-2196.
Metabolic engineering of Escherichia coli for production of mixed-acid fermentation end products. Frontiers in Bioengineering and Biotechnology. (2014) 2:1-12.