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20.109(S08): Laboratory Fundamentals of Biological Engineering

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Spring 2008

Instructors: Bevin Engelward, Alan Jasanoff, and Agi Stachowiak

Writing Instructor: Neal Lerner
Oral Presentation Instructor: Atissa Banuazizi

TAs: Bahar Edrissi,Victor Lelyveld, David Weingeist

Lecture: T/R 11-12 (13-3101) Lab: T/R 1-5 or W/F 1-5 (13-3095)

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.


  • You can find old announcements here
  • A few pieces of information that may be useful for your Methods:
    • Gels this year were made in 1X TAE buffer, which contains 40 mM Tris (pH 8), 20 mM acetic acid, and 1 mM EDTA.
    • The Qiagen kits you used are called the QIAquick PCR Purification Kit and the QIAquick Gel Extraction Kit. You may say that you used them according to the manufacturer’s instructions rather than describing the protocols step-by-step. However, you can briefly mention the principle components if you want (e.g., “DNA was purified on silica gel columns using the… kit and eluted in … buffer”).
    • Your original digests (Day 2) contained ~ 5 μg of backbone. If you don’t know the amount or concentration of something (e.g., your PCR products), it’s fine to mention a volume instead in this case. Otherwise a final amount or concentration is generally preferred.
    • Enzyme amounts are often given in terms of activity units, U. The XbaI and EcoRI enzyme stock solutions that you used are both at 20,000 U/mL.