20.109(S22):Spring 2022 schedule

From Course Wiki
Jump to: navigation, search
20.109(S22): Laboratory Fundamentals of Biological Engineering

Sp17 20.109 M1D7 chemical structure features.png

Spring 2022 schedule        FYI        Assignments        Homework        Class data        Communication        Accessibility

       M1: Drug discovery        M2: Metabolic engineering        M3: Project design       


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 enough time 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: Tuesday (T) and Thursday (R) 11 - 12 pm in 1-390
Laboratory section times: Tuesday (T) and Thursday (R) 1 - 5 pm or Wednesday (W) and Friday (F) 1 - 5 pm in 56-322

ABSENCE POLICY:
Absences from lecture: Attendance will be recorded for participation points throughout the semester. If absent, student is responsible for all information provided in lecture.
Absences from laboratory: Excused absences should be discussed with the Instructors as soon as possible. Because make-up laboratory time is not provided, attendance in another section may be required to complete the necessary experiments. Unexcused absences will result in a 1/3 of a letter grade deduction from the final grade on the major assignment for the module (for example, a B+ would become a B).

MODULE DATE LECTURER LABORATORY EXPERIMENTS ASSIGNMENTS
T/W Feb 1/2 NLL
Lecture slides
Orientation and laboratory tour
T/R prelab
W/F prelab
M1D1 R/F Feb 3/4 AK
Lecture slides
Review small molecule microarray (SMM) technology
T/R prelab
W/F prelab
Orientation quiz
Homework due
M1D2 T/W Feb 8/9 AK
Lecture slides
Examine SMM data collected using TDP43 protein
T/R prelab
W/F prelab
Homework due
M1D3 R/F Feb 10/11 AK
Lecture slides
Induce and purify TDP43 protein
T/R prelab
W/F prelab
Homework due
M1D4 T/W Feb 15/16 AK
Lecture slides
Assess purity and concentration of purified TDP43 protein
T/R prelab
W/F prelab
Laboratory quiz
Homework due
M1D5 R/F Feb 17/18 AK
Lecture slides
Perform aggregation assay using TDP43 protein and draft data slide for Data summary
T/R prelab
W/F prelab
Homework due
T/W Feb 22/23 Presidents' day holiday Research talk due Wed, Feb 23 at 10 pm
M1D6 R/F Feb 24/25 AK
Lecture slides
Learn best practices for mammalian cell culture and seed CAD cells for TDP43-localization experiment
T/R prelab
W/F prelab slides
W/F prelab video and notes for due M1D7 homework
Homework due
M1D7 T/W Mar 1/2 AK
Lecture slides
Complete staining for TDP43-localization assay
T/R prelab
W/F prelab
Homework due
M1D8 R/F Mar 3/4 Comm Lab workshop
Image TDP43-localization experiment and complete data analysis
prelab slides [T/R prelab video] W/F prelab
W/F prelab video
Laboratory quiz
Homework due
M2D1 T/W Mar 8/9 NLL
Lecture slides
Complete in-silico cloning of pdCas9 expression plasmid
T/R prelab
W/R prelab
Homework due
M2D2 R/F Mar 10/11 NLL
Lecture slides
Design gRNA sequence for CRIPSRi system
T/R prelab
W/F prelab
Homework due
Data Summary draft due Sat, Mar 12 at 10 pm
M2D3 T/W Mar 15/16 NLL
Lecture slides
Clone psgRNA expression plasmid
T/R prelab
W/F prelab
Homework due
Blog post due Mon, Mar 14 at 10 pm
M2D4 R/F Mar 17/18 NLL
Lecture slides
Confirm gRNA sequence in psgRNA expression plasmid
T/R Prelab JC Notes
W/F Prelab
Laboratory quiz
Homework due
Data Summary revision due Sun, Mar 20 at 10 pm
T/W Mar 22/23 Spring break
R/F Mar 24/25 Spring break
T/W Mar 29/30 Journal club presentations
R/F Mar/Apr 31/1 Journal club presentations Blog post due Fri, Apr 1 at 10 pm
M2D5 T/W Apr 5/6 NLL
Lecture slides
Prepare for induction of CRISPRi system
T/R prelab
W/F prelab
Homework due
M2D6 R/F Apr 7/8 NLL
Lecture slides
Complete CRISPRi experiment and measure fermentation products
T/R prelab
W/F prelab
Homework due
M2D7 T/W Apr 12/13 NLL
Lecture slides
Examine features in gRNA-targeted genomic sequences
T/R prelab
W/F prelab
Homework due
M2D8 R/F Apr 14/15 Comm Lab workshop
Organize figures and outline text for Research article
prelab
Laboratory quiz
Homework due
T/W Apr 19/20 Patriots' Day holiday
M3D1 R/F Apr 21/22 NLL
Lecture slides
Brainstorm ideas for Research proposal presentation
T/R prelab
W/F prelab
Homework due
Research article due Sat, Apr 23 at 10 pm
T/W Apr 26/27 AB Research proposal pitches
T/R prelab
W/F prelab

Blog post due Mon, Apr 25 at 10 pm
M3D2 R/F Apr 28/29 Comm Lab workshop Develop ideas for Research proposal presentation
T/R prelab
W/F prelab
Homework due
M3D3 T/W May 3/4 NLL
Lecture slides
Participate in Research proposal peer reviews
T/R prelab
W/F prelab
Homework due
R/F May 5/6 Research proposal presentations Blog post due Fri, May 6 at 10 pm
T May 10 Feedback session