20.109(S19): Spring 2019 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 lecture slides	Orientation and laboratory tour Prelab T/R Prelab W/F
1	1	R/F Feb 7/8	AK M1D1 lecture slides	In silico cloning and confirmation digest of protein expression vector Prelab T/R Prelab W/F	Orientation quiz Homework due
1	2	T/W Feb 12/13	AK M1D2 lecture slides	Purify protein for secondary assays Prelab T/R Prelab W/F	Homework due
1	3	R/F Feb 14/15	AK M1D3 lecture slides	Analyze small molecule microarray (SMM) data Prelab T/R Prelab W/F	Homework due
		T/W Feb 19/20		President's day holiday
1	4	R/F Feb 21/22	AK M1D4 lecture slides	Evaluate protein purity and concentration Prelab T/R Prelab W/F	Laboratory quiz Homework due
1	5	T/W Feb 26/27	AK M1D5 lecture slides	Test protein activity using peptidyl-prolyl cis-trans isomerase assay Prelab T/R Prelab W/F	Homework due
1	6	R/F Feb/Mar 28/1	AK M1D6 lecture slides	Confirm ligand binding using differential scanning fluorimetry assay Prelab T/R Prelab W/F	Homework due
1	7	T/W Mar 5/6	AK M1D7 lecture slides	Complete data analysis Prelab T/R Prelab W/F	Laboratory quiz Homework due
2	1	R/F Mar 7/8	NLL M2D1 lecture slides	Practice tissue culture techniques and prepare cells for RNA purification Prelab T/R Prelab W/F	Homework due
2	2	T/W Mar 12/13	NLL M2D2 lecture slides	Etoposide treat cells for RNA purification Prelab T/R Prelab W/F	Homework due Data summary draft due Mon, Mar 11 at 10 pm
2	3	R/F Mar 14/15	EF M2D3 lecture slides	Purify RNA and practice RNA-seq data analysis methods Prelab T/R Prelab W/F	Homework due Mini-presentation due Sat, Mar 16 at 10 pm Blog post due Sun, Mar 17 at 10 pm
2	4	T/W Mar 19/20	EF M2D4 lecture slides	Analyze RNA-seq data and prepare for quantitative PCR experiment Prelab T/R Prelab W/F	Laboratory quiz Homework due
2	5	R/F Mar 21/22	NLL M2D5 lecture slides	Perform quantitative PCR experiment and explore additional RNA-seq datasets Prelab T/R Prelab W/F	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 M2D6 lecture slides	Design cell viability experiment and complete RNA-seq data analysis Prelab T/R Prelab W/F	Homework due
2	7	R/F Apr 4/5	Comm Lab	Journal club I presentations	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 Prelab T/R Prelab W/F	Laboratory quiz Homework due
		T/W Apr 16/17		Patriots' day holiday
3	1	R/F Apr 18/19	AB M3D1 lecture slides	Grow phage-based active (cathode) material Prelab T/R Prelab W/F	Homework due Research article due Sat, Apr 20 at 10 pm Blog post due Sun, Apr 21 at 10 pm
3	2	T/W Apr 23/24	AB M3D2 lecture slides	Purify phage-based active (cathode) material Prelab T/R Prelab W/F	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 Prelab T/R Prelab W/F	Laboratory quiz Homework due
3	4	R/F May 2/3	AB M3D4 lecture slides	Visualize phage nanowires using transmission electron microscopy Prelab T/R Prelab W/F	Homework due
3	5	T/W May 7/8	AB	Assemble and test batteries Prelab T/R Prelab W/F	Laboratory quiz Homework due
		R/F May 9/10		Research proposal presentations	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