1. Welcome to 20.109 Laboratory Fundamentals of Biological Engineering Orientation Lecture Spring 2008

2. Introducing 20.109 Why you’re here –course mission –the art of investigation What you’ll do –three experimental modules –assessments/communication –course logistics

3. Course Mission 20.109 Laboratory Fundamentals of Biological Engineering  To teach cutting edge research skill and technology through authentic investigation  To prepare students to be the future of Biological Engineering  To inspire rigorous data analysis and its thoughtful communication

4. Course Mission 20.109 Laboratory Fundamentals of Biological Engineering  To prepare students to be the future of Biological Engineering

5. Course Mission 20.109 Laboratory Fundamentals of Biological Engineering  To prepare students to be the future of Biological Engineering We inform, you create! Your goals and interests?

6. Engineering Principles + Modern Biology Manipulate Make stuff! pdb.org Measure Model

7. How Doctors ( * ) People Think Bias leads investigations astray Hindsight bias Attribution error Framing effect Scientists are like detectives …even engineers! ( * ) J. Groopman

8. Puzzles: hindsight bias A woman had two sons who were born on the same hour of the same day of the same year. But they were not twins. How could this be so? Why is it better to have round manhole covers than square ones? They were triplets! Round covers cannot be dropped down the manhole, no matter how you turn them. (cf. invention of PCR)

9. Rote learning: attribution error Your school district must drive 1128 kids to school each day, and 36 kids can fit on a bus. How many buses do you need? Most popular answer: 31 remainder 12! 31 108 48 361128

10. Framing effect Politics: “tax cuts” vs. “tax relief” vs. “tax responsibility” Science policy: GM foods or nanotechnology benefits frame vs. risks frame Science: what carries and controls genetic information? (The Canon, N. Angier; Images all from public domain) 1 2 3 4 ?5?

11. How Engineers Succeed Bias leads investigations astray How do we fight bias? “Your data should be true even if your story is wrong.” ~ Darcy Kelley, Columbia (The Canon, N. Angier) Appropriate controls Reluctant interpretation Community vigilance - +? ?+ -

12. Course Mission 20.109 Laboratory Fundamentals of Biological Engineering  To prepare students to be the future of Biological Engineering  To teach cutting edge research skill and technology through authentic investigation  To inspire rigorous data analysis and its thoughtful communication

13. DNA Engineering (B. Engelward) Protein Engineering (A. Jasanoff) Biomaterials Engineering (A. Stachowiak) Module 1 Module 2 Module 3 openwetware.org/wiki/20.109(S08)

14. Lab+Analytical Skills  DNA manipulation: PCR, recombination, gels  Cell culture bacterial ( DNA) mammalian ( protein)  Flow cytometry statistical analysis  Discuss primary research article Experimental Goals Design: PCR primers  Truncate EGFP gene (5’)  Make and test  5 plasmid  Transfect mouse cells with EGFPs (full and  )  Test for spontaneous DNA recombination by fluorescence DNA Engineering: EGFP recombination web.mit.edu/engelward-lab/animations/DSBR.html Recombocell image from Dominika Wiktor, Engelward lab.

15. Experimental Goals Design: protein modification  Mutagenize wild-type plasmid  Express and purify protein in a bacterial host  Assess effect of mutation on protein production and behaviour Protein Engineering: Calcium sensor redesign Lab+Analytical Skills  Assess protein features  DNA mutagenesis and sequencing  Characterize protein identity, amount, fluorescence  More error analysis low vs. high-throughput MATLAB modeling

16. Lab+Analytical Skills  3D cell culture  Fluorescence microscopy  Measure message isolate RNA RT-PCR  Measure one protein (from mixture) ELISA Experimental Goals Design: Culture conditions  Study how cell environment affects viability and morphology.  Measure collagen contents for chondrocytes cultured differently. Biomaterials Engineering: Cartilage gel

17. Communication and Grading Major Assessments 30% Oral Presentations Module 2 - journal article Module 3 - research proposal 50% Written Work Module 1 - lab report Module 2 - portfolio Module 3 - essay 10% Homework Assignments 5% In-lab Daily Quizzes 5% Lab Notebooks Day-to-day Assessments Neal Lerner Atissa Banuazizi

18. After 20.109, you should be able to… Implement laboratory protocols Design novel experiments with Examine the scientific literature Communicate to various audiences, in various styles Present salient points of your own and others’ ideas appropriate controls Organize a lab notebook Interpret qualitative data Analyze quantitative data Recognize utility of models - +? ?+ -

19. Course Logistics Lecture Tuesdays and Thursdays 11-12, 13-3101 Lab Tuesdays and Thursdays 1-5, 13-3095 Wednesdays and Fridays 1-5, 13-3095 There are no “make-up” labs You will perform experiments in pairs. Collaboration with integrity is encouraged: assignments can be worked on together but must be submitted individually. Work must be turn in on time: lab notebooks - end of lab assignments - beginning of lab or lecture