20.109(S20): Spring 2020 schedule

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20.109(S20): Laboratory Fundamentals of Biological Engineering

Sp20 banner image v2.png

Spring 2020 schedule        FYI        Assignments        Homework        Class data        Communication
       1. Screening ligand binding        2. Measuring gene expression        3. Engineering antibodies              


Welcome to 20.109! It is our goal to make this class a useful and fun introduction to experiments and techniques 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: T/R 11 - 12 pm (56-154)
Laboratory section times: T/R 1 - 5 pm or W/F 1 - 5 pm (56-322)

MODULE DAY DATE LECTURER LABORATORY EXPERIMENTS ASSIGNMENTS
T/W Feb 4/5 NLL
Orientation lecture
Orientation and laboratory tour
Lab Orientation Prelab
1 1 R/F Feb 6/7 AK
M1D1 lecture
Complete in silico cloning and induce TDP43 protein expression
T/R prelab
WF Prelab
Orientation quiz
Homework due
1 2 T/W Feb 11/12 AK
M1D2 lecture
Purify TDP43 protein
T/R prelab
W/F prelab
Homework due
1 3 R/F Feb 13/14 AK
M1D3 lecture
Assess purity and concentration of TDP43 protein
T/R prelab
WF Prelab
Homework due
T/W Feb 18/19 President's day holiday
1 4 R/F Feb 20/21 AK
M1D4 lecture
Perform small molecule microarray (SMM) with TDP43 protein
T/R prelab
WF prelab
Laboratory quiz
Homework due
1 5 T/W Feb 25/26 AK
M1D5 lecture
Scan SMM slides to identify binders of TDP43 protein
T/R prelab
WF prelab
Homework due
1 6 R/F Feb 27/28 AK
M1D6 lecture
Analyze SMM data
T/R Prelab
WF Prelab
Homework due
1 7 T/W Mar 3/4 AK
M1D7 lecture
Examine TDP43 binders for chemical features
T/R prelab
WF Prelab
Laboratory quiz
Homework due
2 1 R/F Mar 5/6 NLL
M2D1 lecture
Prepare cells for RNA purification and practice RNA-seq data analysis methods
T/R prelab
W/F prelab
Homework due
Data summary draft due Sun, Mar 8 at 10 pm
2 2 T/W Mar 10/11 EF
M2D2 lecture
Treat cells with etoposide and analyze RNA-seq data
T/R prelab
WF Prelab
Homework due
2 3 R/F Mar 12/13 EF
Purify RNA from etoposide-treated cells and generate cDNA
T/R prelab
WF Prelab
First, we hope that you are all well and taking care of yourselves!! Second, we want to welcome you all back to the Sp20 semester of 20.109!! This will be an interesting endeavor for all of us and we have done / are doing our best to provide you all a positive experience. In that, several changes and modifications have been made to the remainder of the schedule. Please review the details below and, as always, feel free to share feedback...now more than ever we need your ideas to improve 20.109 and ensure a rewarding outcome for everyone! A summary of the remote teaching strategy is linked here.
2 6 T/W Mar/Apr 31/1 EF
Zoom access
M2D6 video
M2D6 slides
Analyze RNA-seq data and select gene targets for quantitative PCR (qPCR) 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
2 7 R/F Apr 2/3 EF
Zoom access
M2D7 video
M2D7 slides
Review qPCR experiment and complete statistical analysis
T/R Zoom access, T/R prelab video, T/R prelab slides
W/F Zoom access, [| WF prelab video], WF prelab slides
Laboratory quiz
Homework due
Data summary revision due Sat, Apr 4 at 10 pm
Blog post due Mon, Apr 6 at 10 pm
2 8 T/W Apr 7/8 EF
Zoom access
Complete RNA-seq data analysis
T/R Zoom access
W/F Zoom access
Homework due
2 9 R/F Apr 9/10 BE Comm Lab
Prepare M2 Major assignments: Journal club presentation and Research article
T/R Zoom access
W/F Zoom access
Laboratory quiz
Homework due
Journal club presentation due Sat, Apr 11 at 10 pm
Blog post due Mon, Apr 13 at 10 pm
3 1 T/W Apr 14/15 LM
Enrich candidate clones using fluorescence-activated cell sorter (FACS)
T/R Zoom access
W/F Zoom access
Homework due
3 2 R/F Apr 16/17 BE Comm Lab
Harvest candidate clones and prepare for sequencing
T/R Zoom access
W/F Zoom access
Homework due
T/W Apr 21/22 Patriots' day holiday Research article due Mon, Apr 20 at 10 pm
Blog post due Tue, Apr 21 at 10 pm
3 3 R/F Apr 23/24 LM
Identify clones to characterize
T/R Zoom access
W/F Zoom access
Laboratory quiz
Homework due
T/W Apr 28/29 LM Research proposal pitches, will be scheduled with each team during laboratory time
3 4 R/F Apr/May 30/1 LM
Characterize clone by titration using flow cytometry
T/R Zoom access
W/F Zoom access
Homework due
3 5 T/W May 5/6 Guest, SC Analyze titration curves
T/R Zoom access
W/F Zoom access
Homework due
R/F May 7/8 Research proposal presentations, will be scheduled with each team during laboratory time
T May 12 Feedback session, lunch will be rescheduled! Mini-report due Mon, May 11 at 10 pm
Blog post due Tue, May 12 at 10 pm