1.1: Syllabus

Welcome to 20.109!

For many of you this will be the first time in a research lab and for others it will not, but it is our goal to make this class a useful and fun introduction to experiments and techniques in biological engineering. There is not time enough to show you everything you'll need to know if you go on to do research, but after taking this class you should feel confident and familiar with some fundamental experimental approaches and lab protocols. You will develop good habits at the bench, ones that will increase the likelihood of success in your work and ensure the health and safety of you and those around you. By the end of the semester, you should also be aware of good scientific practice, having had some experience with report writing, notebook keeping and publicly presenting your data. All of us involved in teaching 20.109 hope you will find it a satisfying challenge and an exciting experience that has lasting value.

Prerequisites

• Biology GIR (One of 7.012, 7.013, or 7.014)
• Chemistry GIR (One of 3.091, 5.111, or 5.112);
• 6.00 Introduction to Computer Science and Programming
• 18.03 Differential Equations
• 20.110J Thermodynamics of Biomolecular Systems or 20.111J Physical Chemistry of Biomolecular Systems

How 20.109 Varies from Term to Term

20.109 is offered twice per year in the fall and spring semesters, with rotating instructor responsibilities. Reflecting the instructors' specific expertise and the evolving biological engineering field, the topics covered will change over time. The fall term classes, led by Natalie Kuldell, emphasize her molecular genetics, microbiology, and synthetic biology expertise. The spring term reflects Agi Stachowiak's biomaterial and tissue engineering background.

Coursework Requirements

You will perform three series of experiments (called "modules") over the course of the semester. The modules differ in both intellectual and experimental content, and in the ways that your learning will be assessed.

You will be working as pairs throughout the semester in lab, but you must submit individual written work (for both daily homeworks and major assignments) and give individual journal club presentations. You will close out the course by developing and presenting a novel research idea as a two-person team. Please read the 20.109 statement on collaboration and integrity for more detail about academic honesty in our class.

We appreciate that time management can be a difficult skill to develop, and that learning takes place on many time-scales. However, when assignments are turned in at wildly disparate times, it creates additional logistical burdens for the teaching faculty. Therefore, late work (both daily and culminating assignments) will be penalized 1/3 of a letter grade for each day late and will not be accepted after a week. We strongly recommend that you plan ahead and space out your work when possible.

Assignments and Grading

See the Assignments page for more details on these items.

MAJOR ASSIGNMENTS
MODULE	TOPICS	ASSIGNMENTS	% OF FINAL GRADE
1	RNA Engineering	Laboratory report	15
		Computational analysis	5
		Journal club presentation	10
2	Protein Engineering	Research article	25
3	Cell-Biomaterial Engineering	Research idea presentation	20
		Data summary	5

In addition to the module major assignments listed above, there are several other forms of required coursework.

• Daily Lab Quizzes (5% of final grade)
• Homework Assignments (8% of final grade)
• Laboratory Notebooks (5% of final grade)
• Participation (2% of final grade)

OpenWetWare Wiki

Since 20.109 is a lab class, we think the students, TAs and instructors would benefit from having a shared space in which to discuss experimental protocols and results. By putting all the course materials on an OpenWetWare wiki, they can be updated and improved instantly by everyone (not just the instructors).

More about OpenWetWare use in 20.109

Calendar

SES #	MODULE DAY	LECTURES	LABS	KEY DATES
1			Orientation (Dr. Stachowiak)
Module 1: RNA Engineering (Prof. Niles)
2	1	Introduction	Amplify aptamer-encoding DNA
3	2	SELEX I: Building a Library	Purify aptamer-encoding DNA
4	3	SELEX II: Selecting RNA with target functionality	Prepare RNA by IVT
5	4	SELEX III: Technical advances & problem-solving	Purify RNA and run affinity column
6	5	Characterizing aptamers	RNA to DNA by RT-PCR
7	6	Introduction to porphyrins:chemistry & biology	Post-selection IVT Journal Club 1
8	7	Aptamer applications in biology & technology	Aptamer binding assay
9	8	Aptamers as therapeutics	Journal Club 2
Module 2: Protein Engineering (Prof. Jasanoff)
10	1	Introduction	Start-up protein engineering	Module 1 draft report due
11	2	Rational protein design	Site-directed mutagenesis
12	3	Fluorescence and sensors	Bacterial amplification of DNA
13	4	Protein expression	Prepare expression system
14	5	Review & gene analysis	Induce protein and evaluate DNA
15	6	Purification and protein analysis	Characterize protein expression	Module 1 final report due
16	7	Binding & affinity measurements	Assay protein behavior
17	8	High throughput engineering	Data analysis
Module 3: Cell-Biomaterial Engineering (Dr. Stachowiak)
18	1	Introduction	Start-up biomaterials engineering	Module 2 draft report due
19	2	Introduction to biomaterials; cartilage composition	Initiate cell culture
20	3	Basic statistics; standards in scientific communities I	Testing cell viability
21	4	Standards in scientific communities II; cell viability	Preparing cells for analysis
22	5	Assays for transcription and protein levels	Transcript-level analysis
23	6	Cartilage TE: from in vitro and in vivo models to the clinic	Protein-level analysis	Module 2 final report due
24	7	Creating your proposal presentation	Wrap-up analysis	Module 3 final report due
25	8	Drug and gene delivery; clinical progress in engineering tissues besides cartilage	Student presentations
26			Evaluations and celebratory luncheon