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Welcome to 20.109 Laboratory Fundamentals of Biological Engineering Orientation Lecture Spring 2008 Introducing 20.109 • Why you’re here – course mission – the art of investigation • What you’ll do – three experimental modules – assessments/communication – course logistics 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 20.109 Laboratory Fundamentals of Biological Engineering Course Mission To prepare students to be the future of Biological Engineering 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? Engineering Principles + Modern Biology Make stuff! Measure Model Manipulate pdb.org How Doctors(*) People Think …even engineers! Scientists are like detectives Bias leads investigations astray Hindsight bias Attribution error Framing effect (*) J. Groopman Puzzles: hindsight bias Why is it better to have round manhole covers than square ones? Round covers cannot be dropped down the manhole, no matter how you turn them. 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? They were triplets! (cf. invention of PCR) 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? 31 36 1128 108 48 Most popular answer: 31 remainder 12! Framing effect Politics: “tax cuts” vs. “tax relief” vs. “tax responsibility” Science: what carries and controls genetic information? (The Canon, N. Angier; Images all from public domain) 2 4 1 3 Science policy: GM foods or nanotechnology benefits frame vs. risks frame ?5? How Engineers Succeed Bias leads investigations astray How do we fight bias? Appropriate controls - + ? - + ? Reluctant interpretation Community vigilance “Your data should be true even if your story is wrong.” ~ Darcy Kelley, Columbia (The Canon, N. Angier) 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 Module 1 Module 2 Module 3 DNA Engineering (B. Engelward) Protein Engineering (A. Jasanoff) Biomaterials Engineering (A. Stachowiak) openwetware.org/wiki/20.109(S08) DNA Engineering: EGFP recombination web.mit.edu/engelward-lab/animations/DSBR.html Recombocell image from Dominika Wiktor, Engelward lab. 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 Lab+Analytical Skills DNA manipulation: PCR, recombination, gels Cell culture bacterial ( DNA) mammalian ( protein) Flow cytometry statistical analysis Discuss primary research article 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 Biomaterials Engineering: Cartilage gel Experimental Goals Design: Culture conditions Study how cell environment affects viability and morphology. Measure collagen contents for chondrocytes cultured differently. Lab+Analytical Skills 3D cell culture Fluorescence microscopy Measure message isolate RNA RT-PCR Measure one protein (from mixture) ELISA Communication and Grading Major Assessments 50% Written Work Module 1 - lab report Module 2 - portfolio Module 3 - essay 30% Oral Presentations Module 2 - journal article Module 3 - research proposal Day-to-day Assessments 10% Homework Assignments 5% In-lab Daily Quizzes 5% Lab Notebooks Neal Lerner Atissa Banuazizi 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 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