20.109(S18): Laboratory Fundamentals of Biological Engineering
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
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DAY
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DATE
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LECTURER
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LABORATORY EXPERIMENTS
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ASSIGNMENTS
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|
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T/W Feb 6/7
|
NLL Orientation slides
|
Orientation and laboratory tour T/R Prelab W/F Prelab
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|
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1
|
1
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R/F Feb 8/9
|
AK
|
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
|
Complete small microarray analysis and induce protein expression T/R Prelab, and File:Sp18 M1D2 nll lig calc.pdf W/F Prelab
|
Homework due
|
1
|
3
|
R/F Feb 15/16
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AK
|
Purify protein for secondary assays
|
Homework due
|
|
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T/W Feb 20/21
|
|
President's day holiday
|
|
1
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4
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R/F Feb 22/23
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AK
|
Evaluate protein purity and concentration
|
Laboratory quiz Homework due
|
1
|
5
|
T/W Feb 27/28
|
AK
|
Test protein activity using peptidyl-prolyl cis-trans isomerase assay
|
Homework due
|
1
|
6
|
R/F Mar 1/2
|
AK
|
Confirm ligand binding using differential scanning fluorimetry assay
|
Homework due
|
1
|
7
|
T/W Mar 6/7
|
AK
|
Complete data analysis
|
Laboratory quiz Homework due
|
|
2
|
1
|
R/F Mar 8/9
|
NLL
|
Practice tissue culture techniques and prepare cells for RNA purification
|
Homework due
|
2
|
2
|
T/W Mar 13/14
|
NLL
|
Induce DNA damage and apply drug treatments for RNA purification
|
Homework due Data summary draft due Mon, Mar 12 at 10 pm
|
2
|
3
|
R/F Mar 15/16
|
EF
|
Purify RNA and practice RNA-seq data analysis methods
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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
|
Analyze RNA-seq data and prepare for quantitative PCR experiment
|
Laboratory quiz Homework due
|
2
|
5
|
R/F Mar 22/23
|
EF
|
Investigate RNA-seq data using public databases
|
Homework due
|
|
|
T/W Mar 27/28
|
|
Spring vacation
|
Data summary revision due Mon, Mar 26 at 10 pm
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|
|
R/F Mar 29/30
|
|
Spring vacation
|
|
2
|
6
|
T/W Apr 3/4
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Comm Lab
|
Journal club I presentations
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|
2
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7
|
R/F Apr 5/6
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NLL
|
Journal club II presentations
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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
|
|
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R/F May 10/11
|
|
Research proposal presentations
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Blog post due Sat, May 12 at 10 pm
|
|
|
T May 15
|
|
Feedback and celebratory lunch
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Mini-report due Mon, May 14 at 10 pm
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