20.109(S18): Spring 2018 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 (4-149)
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 6/7	NLL Orientation Lecture	Orientation and laboratory tour T/R Prelab W/F Prelab
1	1	R/F Feb 8/9	AK M1D1 Lecture	In silico cloning and confirmation digest of protein expression vector T/R Prelab W/F Prelab	Orientation quiz Homework due
1	2	T/W Feb 13/14	AK M1D2 Lecture	Complete small microarray analysis and induce protein expression T/R Prelab and ligation calculation W/F Prelab	Homework due
1	3	R/F Feb 15/16	AK M1D3 Lecture	Purify protein for secondary assays T/R Prelab W/F Prelab	Homework due
		T/W Feb 20/21		President's day holiday
1	4	R/F Feb 22/23	AK M1D4 Lecture	Evaluate protein purity and concentration T/R Prelab W/F Prelab Methods Tips	Laboratory quiz Homework due
1	5	T/W Feb 27/28	AK M1D5 Lecture	Test protein activity using peptidyl-prolyl cis-trans isomerase assay T/R Prelab W/F Prelab	Homework due
1	6	R/F Mar 1/2	AK M1D6 Lecture	Confirm ligand binding using differential scanning fluorimetry assay T/R Prelab W/F Prelab	Homework due
1	7	T/W Mar 6/7	AK M1D7 Lecture	Complete data analysis T/R Prelab W/F Prelab	Laboratory quiz Homework due
2	1	R/F Mar 8/9	NLL M2D1 Lecture	Practice tissue culture techniques and prepare cells for RNA purification T/R Prelab W/F Prelab	Homework due
2	2	T/W Mar 13/14	NLL	Induce DNA damage and apply drug treatments for RNA purification T/R Prelab W/F Prelab	Homework due Data summary draft due Mon, Mar 12 at 10 pm
2	3	R/F Mar 15/16	EF M2D3 Lecture	Purify RNA and practice RNA-seq data analysis methods T/R Prelab W/F Prelab	Homework due Mini-presentation due Sat, Mar 17 at 10 pm Blog post due Sun, Mar 18 at 10 pm
2	4	T/W Mar 20/21	EF M2D4 Lecture	Analyze RNA-seq data and prepare for quantitative PCR experiment T/R Prelab W/F Prelab	Laboratory quiz Homework due
2	5	R/F Mar 22/23	EF M2D5 Lecture	Investigate RNA-seq data using public databases T/R Prelab W/F Prelab	Homework due
		T/W Mar 27/28		Spring vacation	Data summary revision due Mon, Mar 26 at 10 pm
		R/F Mar 29/30		Spring vacation
2	6	T/W Apr 3/4	Comm Lab	Journal club I presentations
2	7	R/F Apr 5/6	NLL M2D7 Lecture	Journal club II presentations	Blog post due Sat, Apr 7 at 10 pm
2	8	T/W Apr 10/11	EF M2D8 Lecture	Induce DNA damage and apply drug treatments for cell viability and identification of regulatory motifs in RNA-seq data T/R Prelab W/F Prelab	Homework due
2	9	R/F Apr 12/13	EF M2D9 Lecture	Complete cell viability assay T/R Prelab W/F Prelab	Laboratory quiz Homework due
		T/W Apr 17/18		Patriots' day holiday
3	1	R/F Apr 19/20	AB	Grow phage-based active (cathode) material Quiz Review&T/R Prelab Quiz Review&W/F Prelab	Homework due Research article due Sat, Apr 21 at 10 pm Blog post due Sun, Apr 22 at 10 pm
3	2	T/W Apr 24/25	AB	Purify phage-based active (cathode) material T/R Prelab W/F Prelab	Homework due
3	3	R/F Apr 26/27	AB M3D3 Lecture	Construct cathode with phage-based active material T/R Prelab W/F Prelab	Laboratory quiz Homework due
3		T/W May 1/2		Lecture, but no laboratory
3	4	R/F May 3/4	AB M3D4 Lecture	Visualize phage nanowires using transmission electron microscopy T/R Prelab W/F Prelab	Homework due
3	5	T/W May 8/9	AB	Assemble and test batteries T/R Prelab W/F Prelab	Laboratory quiz Homework due
		R/F May 10/11		Research proposal presentations	Blog post due Sat, May 12 at 10 pm
		T May 15		Feedback and celebratory lunch	Mini-report due Mon, May 14 at 10 pm