20.109(S18): Spring 2018 schedule

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20.109(S18): Laboratory Fundamentals of Biological Engineering

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Spring 2018 schedule        FYI        Assignments        Homework        Class data        Communication
       1. Assessing ligand binding        2. Measuring gene expression        3. Engineering biomaterials              


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 (4-149)
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 6/7 NLL
Orientation Lecture
Orientation and laboratory tour
T/R Prelab
W/F Prelab
1 1 R/F Feb 8/9 AK
M1D1 Lecture
In silico cloning and confirmation digest of protein expression vector
T/R Prelab
W/F Prelab
Orientation quiz
Homework due
1 2 T/W Feb 13/14 AK
M1D2 Lecture
Complete small microarray analysis and induce protein expression
T/R Prelab and ligation calculation
W/F Prelab
Homework due
1 3 R/F Feb 15/16 AK
M1D3 Lecture
Purify protein for secondary assays
T/R Prelab
W/F Prelab
Homework due
T/W Feb 20/21 President's day holiday
1 4 R/F Feb 22/23 AK
M1D4 Lecture
Evaluate protein purity and concentration
T/R Prelab
W/F Prelab
Methods Tips
Laboratory quiz
Homework due
1 5 T/W Feb 27/28 AK
M1D5 Lecture
Test protein activity using peptidyl-prolyl cis-trans isomerase assay
T/R Prelab
W/F Prelab
Homework due
1 6 R/F Mar 1/2 AK
M1D6 Lecture
Confirm ligand binding using differential scanning fluorimetry assay
T/R Prelab
W/F Prelab
Homework due
1 7 T/W Mar 6/7 AK
M1D7 Lecture
Complete data analysis
T/R Prelab
W/F Prelab
Laboratory quiz
Homework due
2 1 R/F Mar 8/9 NLL
M2D1 Lecture
Practice tissue culture techniques and prepare cells for RNA purification
T/R Prelab
W/F Prelab
Homework due
2 2 T/W Mar 13/14 NLL
Induce DNA damage and apply drug treatments for RNA purification
T/R Prelab
W/F Prelab
Homework due
Data summary draft due Mon, Mar 12 at 10 pm
2 3 R/F Mar 15/16 EF
M2D3 Lecture
Purify RNA and practice RNA-seq data analysis methods
T/R Prelab
W/F Prelab
Homework due
Mini-presentation due Sat, Mar 17 at 10 pm
Blog post due Sun, Mar 18 at 10 pm
2 4 T/W Mar 20/21 EF
M2D4 Lecture
Analyze RNA-seq data and prepare for quantitative PCR experiment
T/R Prelab
W/F Prelab
Laboratory quiz
Homework due
2 5 R/F Mar 22/23 EF
Investigate RNA-seq data using public databases
T/R Prelab
Homework due
T/W Mar 27/28 Spring vacation Data summary revision due Mon, Mar 26 at 10 pm
R/F Mar 29/30 Spring vacation
2 6 T/W Apr 3/4 Comm Lab
Journal club I presentations
2 7 R/F Apr 5/6 NLL
Journal club II presentations
Blog post due Sat, Apr 7 at 10 pm
2 8 T/W Apr 10/11 EF
Induce DNA damage and apply drug treatments for cell viability and identification of regulatory motifs in RNA-seq data Homework due
2 9 R/F Apr 12/13 EF
Complete cell viability assay
Laboratory quiz
Homework due
T/W Apr 17/18 Patriots' day holiday
3 1 R/F Apr 19/20 AB
Grow phage-based active (cathode) material
Homework due
Research article due Sat, Apr 21 at 10 pm
Blog post due Sun, Apr 22 at 10 pm
3 2 T/W Apr 24/25 AB
Purify phage-based active (cathode) material
Homework due
3 3 R/F Apr 26/27 AB
Construct cathode with phage-based active material
Laboratory quiz
Homework due
3 T/W May 1/2 Lecture, but no laboratory
3 4 R/F May 3/4 AB Visualize phage nanowires using transmission electron microscopy
Homework due
3 5 T/W May 8/9 AB Assemble and test batteries
Laboratory quiz
Homework due
R/F May 10/11 Research proposal presentations Blog post due Sat, May 12 at 10 pm
T May 15 Feedback and celebratory lunch Mini-report due Mon, May 14 at 10 pm