Welcome to 20.109 Laboratory Fundamentals of Biological Engineering

1. Welcome to 20.109Laboratory 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. 20.109 Laboratory Fundamentals of Biological Engineering Course Mission • 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

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

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

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

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

8. Round covers cannot be dropped down the manhole, no matter how you turn them. They were triplets! Puzzles: hindsight bias Why is it better to have round manhole covers than square ones? 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? (cf. invention of PCR)

9. 31 36 1128 108 48 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!

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

11. - + ? Appropriate controls Reluctant interpretation Community vigilance - + ? 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)

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

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

14. DNA Engineering: EGFP recombination web.mit.edu/engelward-lab/animations/DSBR.html Recombocell image from Dominika Wiktor, Engelward lab. • 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

15. Protein Engineering: Calcium sensor redesign • 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 • 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. Biomaterials Engineering: Cartilage gel • 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.

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

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

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