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
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
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
Homework due
1 6 T/W Oct 1/2 BE Perform quantitative image analysis for the high-throughput genome damage assay
Homework due
1 7 R/F Oct 3/4 BE Complete data analysis and apply statistical methods
Laboratory quiz
Homework due
2 1 T/W Oct 8/9 NLL
Complete in silico cloning of pdCas9
Homework due
2 2 R/F Oct 10/11 NLL
Design gRNA sequence for CRISPRi
Homework due
T/W Oct 15/16 Columbus day holiday Data Summary draft due Mon, Oct 14 at 10 pm
[ Blog post due] Tue, Oct 15 at 10 pm
2 3 R/F Oct 17/18 NLL
Generate gRNA plasmid
Homework due
Mini-presentation due Sat, Oct 19 at 10 pm
2 4 T/W Oct 22/23 NLL
Journal club I
2 5 R/F Oct 24/25 NLL
Confirm gRNA sequence in pgRNA
Laboratory quiz
Homework due
Data Summary revision due Sat, Oct 26 at 10 pm
2 6 T/W Oct 29/30 NLL
Journal club II
2 7 R/F Oct/Nov 31/1 NLL
Induce CRISPRi system
Homework due
[ Blog post due] Fri, Nov 1 at 10 pm
2 8 T/W Nov 5/6 NLL
Measure fermentation products
Laboratory quiz
Homework due
3 1 R/F Nov 7/8 AK
Prepare for cellular thermal shift assay
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
Incubate with ligand and apply heat treatment for protein denaturation
Homework due
3 3 T/W Nov 19/20 AK
Begin Western blot analysis
Laboratory quiz
Homework due
3 4 R/F Nov 21/22 AK
Complete antibody staining for Western blot analysis
Homework due
T/W Nov 26/27 Lecture, but no laboratory
R/F Nov 28/29 Thanksgiving holiday
3 5 T/W Dec 3/4 AK
Data analysis and assignment preparation
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