Talk:20.109(S13): Spring 2013 schedule

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20.109(S13): Laboratory Fundamentals of Biological Engineering

S13 109-OWW-frontpage.jpg

Home        Schedule Spring 2013        Assignments       
DNA Engineering        Protein Engineering        Cell Engineering              

Lecture: T/R 11-12 (4-237)
Lab: T/R 1-5 or W/F 1-5 (56-322)
People: Instructor and student web pages may be found at the linked People page.

Welcome to 20.109! For some of you this will be the first time in a research lab and for others it will not; either way, 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 data and your 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.


You will perform three series of experiments (hereafter “modules”) over the course of the semester. The modules differ in both conceptual and technical content, and in the ways that your learning will be assessed. Links to the experiments and assignments are provided below.

Although your lab work will be done in pairs, most assignments will be submitted individually (as summarized below) and should reflect your personal understanding. Please read the 20.109 statement on collaboration and integrity for more detail about academic honesty in our class. You are encouraged to ask the teaching faculty any questions you have about what constitutes appropriate collaboration.

  • Individual assignments (60% of grade): all lab notebooks, quizzes, and homeworks (unless otherwise noted in directions); Module 1 primer design summary and journal club presentation; Module 2 research article.
  • Team assignments (40% of grade): Module 1 laboratory report (draft and revision), Module 3 data summary, and Module 3 research proposal.

We appreciate that time management can be a difficult skill to develop, and that learning takes place on many time-scales. However, assignments turned in at wildly disparate times create 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.

We will endeavor to provide equal access to subject 20.109 for students with disabilities, in accordance with the Americans with Disabilities Act (ADA) of 1990. Please see the teaching faculty as soon as possible regarding needed accommodations.


N/A 0 Tue/Wed Feb 5/6 Orientation
1 1 Thur/Fri Feb 7/8 Context-setting and primer design
1 2 Tue/Wed Feb 12/13 DNA extraction
1 3 Thur/Fri Feb 14/15 PCR and paper discussion
President's Day Feb 18 No lab Feb 19 or Feb 20
1 4 Thur/Fri Feb 21/22 DNA cloning
1 5 Tue/Wed Feb 26/27 DNA sequencing and primer analysis
1 6 Thur/Fri Feb 28/ Mar 1 Journal club I
1 7 Tue/Wed Mar 5/6 Phylogenetic analysis
1 8 Thur/Fri Mar 7/8, No lecture today Journal club II
2 1 Tue/Wed Mar 12/13 Design mutant
Module 1 Draft Due
2 2 Thur/Fri Mar 14/15 Site-directed mutagenesis
2 3 Tue/Wed Mar 19/20 Bacterial amplification of DNA
Module 1 Primer Summary Due
2 4 Thur/Fri Mar 21/22 Prepare expression system
Spring Break Mar 25-29 No lab all week
2 5 Tue/Wed Apr 2/3 Induce protein and evaluate DNA
2 6 Thur/Fri Apr 4/5 Purify protein
Module 1 Revision Due
2 7 Tue/Wed Apr 9/10 Characterize protein expression
2 8 Thur/Fri Apr 11/12 Assess protein function
Patriot's Day April 15-16 No lab Apr 16 or Apr 17
3 1 Thur/Fri Apr 18/19 Design experiment
3 2 Tue/Wed Apr 23/24 Initiate cell culture
Module 2 Report Due MONDAY APRIL 22 by 5 pm for all.
3 3 Thur/Fri Apr 25/26 Testing cell viability
3 4 Tue/Wed Apr 30/May 1 Preparing cells for analysis
3 5 Thur/Fri May 2/3 Initiating transcript and protein assays
3 6 Tue/Wed May 7/8 Transcript-level analysis
3 7 Thur/Fri May 9/10 Protein-level and wrap-up analysis
Module 3 Summary Due
3 8 Tue/Wed May 14/15 Student presentations