20.109(F19): Fall 2019 schedule

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20.109(F19): Laboratory Fundamentals of Biological Engineering

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Fall 2019 schedule        FYI        Assignments        Homework        Class data        Communication
       1. Measuring genomic instability        2. Modulating metabolism        3. Testing chemical probes              


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: T/R 11 - 12 pm (16-220)
Laboratory section times: T/R 1 - 5 pm or W/F 1 - 5 pm (56-322)

MODULE DAY DATE LECTURER LABORATORY EXPERIMENTS ASSIGNMENTS
R/F Sept 5/6 NLL
Orientation slides
Orientation and laboratory tour
Prelab T/R
Prelab W/F
1 1 T/W Sept 10/11 BE Learn optimal methods for culturing mammalian cells and initiate repair foci analysis experiment
Prelab T/R
Prelab W/F
Laboratory orientation quiz
Homework due
1 2 R/F Sept 12/13 BE Perform cell exposures for repair foci experiment and perform high-throughput genome damage pilot
Prelab T/R
Prelab W/F
Homework due
1 3 T/W Sept 17/18 BE Perform immunofluorescence assay for repair foci and optimize high-throughput genome damage assay
Prelab T/R
Prelab W/F
Homework due
R/F Sept 19/20 Comm Lab Lecture, but no laboratory
Career fair student holiday
1 4 T/W Sept 24/25 BE Perform immunofluorescence imaging for repair foci and expose cells for high-throughput genome damage assay
Prelab T/R
Prelab W/F
Laboratory quiz
Homework due
1 5 R/F Sept 26/27 BE Quantify repair foci via network algorithm and complete high-throughput genome damage assay
Dushan's Talk
TR Prelab
WF Prelab
Homework due
1 6 T/W Oct 1/2 BE Perform quantitative image analysis for the high-throughput genome damage assay
TR Prelab
WF Prelab
Homework due
1 7 R/F Oct 3/4 BE Complete data analysis and apply statistical methods
TR Prelab
WF Prelab
Laboratory quiz
Homework due
2 1 T/W Oct 8/9 NLL
Lecture slides
Complete in silico cloning of pdCas9
TR Prelab
WF Prelab
Homework due
2 2 R/F Oct 10/11 NLL
Lecture slides
Design gRNA sequence for CRISPRi
TR Prelab
WF Prelab
Homework due
T/W Oct 15/16 Columbus day holiday Data Summary draft due Mon, Oct 14 at 10 pm
Blog post due Fri, Oct 18 at 10 pm
2 3 R/F Oct 17/18 NLL
Article Figures
Lecture slides
Generate gRNA plasmid
TR Prelab
WF Prelab
Homework due
Mini-presentation due Sat, Oct 19 at 10 pm
2 4 T/W Oct 22/23 NLL
Lecture slides
Journal club I
2 5 R/F Oct 24/25 NLL
Lecture slides
Confirm gRNA sequence in pgRNA
TR Prelab
WF Prelab
Laboratory quiz
Homework due
Data Summary revision due Sat, Oct 26 at 10 pm
2 6 T/W Oct 29/30 NLL
Lecture slides
Journal club II
2 7 R/F Oct/Nov 31/1 NLL
Lecture slides
Induce CRISPRi system
TR Prelab
WF Prelab
Homework due
Blog post due Fri, Nov 1 at 10 pm
2 8 T/W Nov 5/6 NLL
Measure fermentation products
TR Prelab
WF Prelab
Laboratory quiz
Homework due
3 1 R/F Nov 7/8 AK
Lecture slides
Prepare for cellular thermal shift assay
TR Prelab
WF Prelab
Homework due
T/W Nov 12/13 Veterans' day holiday Research article due Mon, Nov 11 at 10 pm
Blog post due Tue, Nov 12 at 10 pm
3 2 R/F Nov 14/15 AK
Lecture slides
Incubate with ligand and apply heat treatment for protein denaturation
TR Prelab
WF Prelab
Homework due
3 3 T/W Nov 19/20 AK
Lecture slides
Begin Western blot analysis
TR Prelab
WF Prelab
Laboratory quiz
Homework due
3 4 R/F Nov 21/22 AK
Lecture slides
Complete antibody staining for Western blot analysis
TR Prelab
WF Prelab
Homework due
T/W Nov 26/27 Lecture: research proposal pitch, but no laboratory
R/F Nov 28/29 Thanksgiving holiday
3 5 T/W Dec 3/4 AK
Lecture slides
Data analysis and assignment preparation
TR Prelab
WF Prelab
Laboratory quiz
Homework due
R/F Dec 5/6 Research proposal presentations Blog post due Fri, Dec 6 at 10 pm
T Dec 10 Feedback and celebratory lunch Mini-report due Mon, Dec 9 at 10 pm