20.109(F17):Module 1

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20.109(F17): Laboratory Fundamentals of Biological Engineering

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Fa17 Schedule        Announcements        Assignments        Homework        Communication
       1. Measuring Genomic Instability        2. Manipulating Metabolism        3. Engineering Biomaterials              

Module 1

Lecturer: Bevin Engelward
Instructors: Noreen Lyell, Leslie McClain and Josephine Bagnall
TA: Eric Lehnhardt
Lab manager: Hsinhwa Lee


In this module you will measure genomic instability using two techniques: the CometChip and immunofluorescence. Your first task is to critically think through the development of the CometChip assay and determine which conditions provide the best results for loading mammalian cells into the device. To this end, you will consider variables that affect cell loading into the microwells of the CometChip. The data you collect will be used to determine the conditions for subsequent assays.

Next, you will use the CometChip assay to measure DNA damage in response to chemical treatments. Specifically, you will study the mechanisms of DNA damage in response to two chemical treatments that are known to induce DNA damage: H2O2 and MMS. Then, you will consider the effect of these chemical treatments on the abundance of double-strand breaks and compare the results to the CometChip data.

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Lab links: day by day

M1D1: Prepare microwell array and practice tissue culture
M1D2: Develop experiment to optimize cell loading
M1D3: Evaluate cell loading results
M1D4: Test role of biochemical factors in genomic stability
M1D5: Complete biochemical experiment and apply chemical treatments for sub-nuclear foci assay
M1D6: Examine sub-nuclear foci abundance to measure DNA damage
M1D7: Visualize and analyze data for sub-nuclear foci assay


See all M1 student data on the Discussion page.


Data summary


CometChip: A high-throughput 96-well platform for measuring DNA damage in microarrayed human cells. Journal of Visualized Experiments 92: 1-11. A video of the procedure can be found here.

CometChip: Single-cell microarray for high-throughput detection of DNA damage. Methods in Cell Biology 112: 247-268.

Notes for teaching faculty

F17 notes for M1

F17 notes for orientation day