20.109(S20): Spring 2020 schedule

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 (32-124)
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 5/6	NLL	Orientation and laboratory tour
1	1	R/F Feb 7/8	AK	In silico cloning and confirmation digest of protein expression vector	Orientation quiz Homework due
1	2	T/W Feb 12/13	AK	Purify protein for secondary assays	Homework due
1	3	R/F Feb 14/15	AK	Analyze small molecule microarray (SMM) data	Homework due
		T/W Feb 19/20		President's day holiday
1	4	R/F Feb 21/22	AK	Evaluate protein purity and concentration	Laboratory quiz Homework due
1	5	T/W Feb 26/27	AK	Test protein activity using peptidyl-prolyl cis-trans isomerase assay	Homework due
1	6	R/F Feb/Mar 28/1	AK	Confirm ligand binding using differential scanning fluorimetry assay	Homework due
1	7	T/W Mar 5/6	AK	Complete data analysis	Laboratory quiz Homework due
2	1	R/F Mar 7/8	NLL	Practice tissue culture techniques and prepare cells for RNA purification	Homework due
2	2	T/W Mar 12/13	NLL	Etoposide treat cells for RNA purification	Homework due Data summary draft due Mon, Mar 11 at 10 pm
2	3	R/F Mar 14/15	EF	Purify RNA and practice RNA-seq data analysis methods	Homework due Mini-presentation due Sat, Mar 16 at 10 pm [https:// Blog post due] Sun, Mar 17 at 10 pm
2	4	T/W Mar 19/20	EF	Analyze RNA-seq data and prepare for quantitative PCR experiment	Laboratory quiz Homework due
2	5	R/F Mar 21/22	NLL	Perform quantitative PCR experiment and explore additional RNA-seq datasets	Homework due
		T/W Mar 26/27		Spring vacation	Data summary revision due Mon, Mar 25 at 10 pm
		R/F Mar 28/29		Spring vacation
2	6	T/W Apr 2/3	EF	Design cell viability experiment and complete RNA-seq data analysis	Homework due
2	7	R/F Apr 4/5	Comm Lab	Journal club I presentations	[https:// Blog post due] Sat, Apr 6 at 10 pm
2	8	T/W Apr 9/10	EF	Journal club II presentations
2	9	R/F Apr 11/12	EF	Complete data analysis	Laboratory quiz Homework due
		T/W Apr 16/17		Patriots' day holiday
3	1	R/F Apr 18/19	AB	Grow phage-based active (cathode) material	Homework due Research article due Sat, Apr 20 at 10 pm [https:// Blog post due] Sun, Apr 21 at 10 pm
3	2	T/W Apr 23/24	AB	Purify phage-based active (cathode) material	Homework due
3		R/F Apr 25/26		Lecture, but no laboratory
3	3	T/W Apr/May 30/1	AB	Construct cathode with phage-based active material	Laboratory quiz Homework due
3	4	R/F May 2/3	AB	Visualize phage nanowires using transmission electron microscopy	Homework due
3	5	T/W May 7/8	AB	Assemble and test batteries	Laboratory quiz Homework due
		R/F May 9/10		Research proposal presentations	[https:// Blog post due] Sat, May 11 at 10 pm
		T May 14		Feedback and celebratory lunch	Mini-report due Mon, May 13 at 10 pm