20.109(F20): Fall 2020 schedule

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20.109(F20): Laboratory Fundamentals of Biological Engineering

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Fall 2020 schedule        FYI        Assignments        Homework        Communication |        Accessibility

       M1: Genomic instability        M2: Drug discovery        M3: Metabolic engineering       


Welcome to 20.109! It is our goal to make this class a useful and fun introduction to the experiments and techniques used in biological engineering. Though there is not time enough to show you everything needed to do research, after this class you will feel confident and familiar with some fundamental experimental approaches and laboratory protocols. You will develop good habits at the bench, which will increase the likelihood of success in your work and ensure the health and safety of you and your labmates. By the end of the semester, you will also be well-versed in good scientific practices - through your experience with scientific writing, notebook keeping, and orally presenting data and novel ideas. All of us involved in teaching 20.109 hope you will find it a satisfying challenge and an exciting experience that has lasting value.

SCHEDULE DETAILS:
Lecture times: Tuesday (T) and Thursday (R) 11 - 12 pm
Laboratory section times: Tuesday (T) and Thursday (R) 3 - 5 pm or Wednesday (W) and Friday (F) 3 - 5 pm

MODULE DATE LECTURER LABORATORY EXPERIMENTS ASSIGNMENTS
T/W Sep 1/2 NLL
Zoom access
Video
Slides
Orientation and laboratory tour
T/R Zoom access, T/R prelab video, T/R prelab slides
W/F Zoom access, W/F prelab video, W/F prelab slides
M1D1 R/F Sep 3/4 BE
Zoom access
Learn best practices for mammalian cell culture
T/R Zoom access, T/R prelab video, T/R prelab slides
W/F Zoom access, W/F prelab video, W/F prelab slides
Orientation quiz
Homework due
M1D2 T/W Sep 8/9 BE
Zoom access
Prepare and treat cells for repair foci experiment
T/R Zoom access, T/R prelab video, T/R prelab slides
W/F Zoom access, W/F prelab video, W/F prelab slides
Homework due
M1D3 R/F Sep 10/11 BE
Zoom access
Use immunoflourescence staining to assess repair foci experiment
T/R Zoom access, T/R prelab video, T/R prelab slides
W/F Zoom access, W/F prelab video, W/F prelab slides
Homework due
M1D4 T/W Sep 15/16 BE
Zoom access
Image repair foci experiment and quantify results
T/R Zoom access, T/R prelab video, T/R prelab slides
W/F Zoom access, W/F prelab video, W/F prelab slides
Laboratory quiz
Homework due
M1D5 R/F Sep 17/18 BE
Zoom access
Treat cells and perform high-throughput genome damage assay
T/R Zoom access, T/R prelab video, T/R prelab slides
W/F Zoom access, W/F prelab video, W/F prelab slides
Homework due
M1D6 T/W Sep 22/23 BE
Zoom access
Image and analyze high-throughput genome damage assay
T/R Zoom access, T/R prelab video, T/R prelab slides
W/F Zoom access, W/F prelab video, W/F prelab slides
Homework due
M1D7 R/F Sep 24/25 BE
Zoom access
Complete data analysis using statistical methods
T/R Zoom access, T/R prelab video, T/R prelab slides
W/F Zoom access, W/F prelab video, W/F prelab slides
Laboratory quiz
Homework due
M2D1 T/W Sep 29/30 JN
Zoom access
Video
Slides
Complete in silico cloning of protein expression plasmid
T/R Zoom access, T/R prelab video, T/R prelab slides
W/F Zoom access, W/F prelab video, W/F prelab slides
Homework due
M2D2 R/F Oct 1/2 JN
Zoom access
Video
Slides
Perform protein purification protocol
W/F Zoom access, W/F prelab video, W/F prelab slides
Homework due
Data Summary draft due Sun, Oct 4 at 10 pm
Blog post due Mon, Oct 5 at 10 pm
M2D3 T/W Oct 6/7 JN
Zoom access
Video
Slides
Assess purity and concentration of purified protein
T/R Zoom access, T/R prelab video, T/R prelab slides purification notes
W/F Zoom access, W/F prelab video, W/F prelab slides
Homework due
M2D4 R/F Oct 8/9 JN
Zoom access
Video
Slides
Prepare small molecule microarray (SMM) slides with purified protein
T/R Zoom access, T/R prelab video, T/R prelab slides
W/F Zoom access, W/F prelab video, W/F prelab slides
Laboratory quiz
Homework due
Mini-presentation due Sun, Oct 11 at 10 pm
T/W Oct 13/14 Indigenous Peoples Day holiday Data Summary revision due Wed, Oct 14 at 10 pm
M2D5 R/F Oct 15/16 JN
Zoom access
Video
Slides
Scan SMM slides to identify putative small molecule binders
T/R Zoom access, T/R prelab video, T/R prelab slides
W/F Zoom access, W/F prelab video, W/F prelab slides
Homework due
T/W Oct 20/21 Journal club presentations
R/F Oct 22/23 Journal club presentations Blog post due Sun, Oct 25 at 10 pm
M2D6 T/W Oct 27/28 JN
Zoom access
Video
Slides
Analyze SMM data to confirm putative small molecule binders
T/R Zoom access, T/R prelab video, T/R prelab slides
W/F Zoom access, W/F prelab video, W/F prelab slides
Homework due
M2D7 R/F Oct 29/30 JN
Zoom access
Video
Slides
Examine putative small molecule binders for common features
T/R Zoom access, T/R prelab video, T/R prelab slides
W/F Zoom access, W/F prelab video, W/F prelab slides
Laboratory quiz
Homework due
M3D1 T/W Nov 3/4 NLL
Zoom access
Video
Slides
Research project scope and experimental strategy
T/R Zoom access, T/R prelab video, T/R prelab slides
W/F Zoom access, W/F prelab video, W/F prelab slides
Homework due
M3D2 R/F Nov 5/6 NLL
Zoom access
Video
Slides
Align gRNA sequences with genomic targets
T/R Zoom access, T/R prelab video, T/R prelab slides
W/F Zoom access, W/F prelab video, W/F prelab slides
Homework due
T/W Nov 10/11 Veterans day holiday Research article due Wed, Nov 11 at 10 pm
Blog post due Thu, Nov 12 at 10 pm
M3D3 R/F Nov 12/13 NLL
Zoom access
Video
Slides
Analyze ethanol yield data
T/R Zoom access, T/R prelab video, T/R prelab slides
W/F Zoom access, W/F prelab video, W/F prelab slides
Laboratory quiz
Homework due
T/W Nov 17/18 Research proposal pitches
Zoom access
Develop Research proposal ideas and presentations
T/R Zoom access
W/F Zoom access
M3D4 R/F Nov 19/20 NLL
Zoom access
Video
Slides
Examine features in gRNA-targeted genomic sequences
T/R Zoom access, T/R prelab video, T/R prelab slides
W/F Zoom access, W/F prelab video, W/F prelab slides
Homework due
T/W Nov 24/25 Thanksgiving holiday
R/F Nov 26/27 Thanksgiving holiday
M3D5 T/W Dec 1/2 NLL
Zoom access
[ Video]
Slides
Design optimized gRNA sequence for enhanced ethanol production
T/R Zoom access, [ T/R prelab video], T/R prelab slides
W/F Zoom access, [ W/F prelab video], W/F prelab slides
Laboratory quiz
Homework due
R/F Dec 3/F Research proposal presentations Blog post due Fri, Dec 4 at 10 pm
T Dec 8 Feedback session
Zoom access
Mini-report due Mon, Dec 7 at 10 pm