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 | |||
