Welcome to 20.109 Laboratory Fundamentals of Biological Engineering Orientation Lecture Fall 2007 20.109 Laboratory Fundamentals of Biological Engineering Course Mission  To prepare students to be thefuture of Biological Engineering  To teach cutting edge research skill and technology through an authentic research experience  To inspire rigorous data analysis and its thoughtful communication Module 1 Genome Engineering Module 2 Expression Engineering Module 3 Biomaterials Engineering Cite as: Angela Belcher, Drew Endy, Natalie Kuldell and Agi Stachowiak. Course materials for 20.109 Laboratory Fundamentals in Biological Engineering, Fall 2007. MIT OpenCourseWare (http://ocw.mit.edu), Massachusetts Institute of Technology. Downloaded on [DD Month YYYY].1Genome Engineering: M13 redesign . http://www.sciencedirect.com. Used with permssion.Expression Engineering: siRNA Biomaterial Engineering: phage nanowires Lab skills Experiments Build prototype electrochromic device Phage material production • Grow iridium nanowires on phage surface TEM • Pattern indium tin oxide slide Fabrication of bio-based device • Electrodeposit phage nanowires Design and variation of • Overlay solid polymer electrolytes experimental conditions Cite as: Angela Belcher, Drew Endy, Natalie Kuldell and Agi Stachowiak. Course materials for 20.109 Laboratory Fundamentals in Biological Engineering, Fall 2007. MIT OpenCourseWare (http://ocw.mit.edu),2 Massachusetts Institute of Technology. Downloaded on [DD Month YYYY].Left: Firefly photo courtesy of Eloise Mason. Used with permission. Center: Plasmid map courtesy of Promega Corporation. Used with permission. Right: “Sea pansy” (Renilla reniformis) courtesy of NOAA. Used with permission. Experiments Lab skills Silence expression of a gene using Genetic and physical manipulations RNAi of mouse ES cells • siRNA design • transfection Luciferase measurements • RNA and protein measurements siRNA design Assess intended and unintended Microarray analysis consequences Courtesy of Elsevier, IncSource: Specthrie, L., et al. “Construction of a Microphage Variant of Filamentous Bacteriophage.” J Mol Biol 228, no. 3 (December 5, 1992): 720-4. Experiments Lab skills DNA manipulations Modify existing genome to tag one coat protein • digests Refactor genome, order its synthesis and test • transformation • electrophoresis Compare infection of minimal and robust E. coli genome Western analysis Cell & phage cultureState-of-the-Art Laboratory Classroom Space for 12 students • Demonstration Area • 20 Computer Drops • Gas/Vacuum/Air/Water • Modern Equipment • Cell and Tissue Culture Facility HEPA Filtered Air • 3 Sterile Hoods • 6 incubators • 2 inverted microscopes • Modern Culture Equipment Support Room Autoclave • Dishwasher • Ice Machine • CO2 Source •Vacuum Source Cite as: Angela Belcher, Drew Endy, Natalie Kuldell and Agi Stachowiak. Course materials for 20.109 Laboratory Fundamentals in Biological Engineering, Fall 2007. MIT OpenCourseWare (http://ocw.mit.edu),3 Massachusetts Institute of Technology. Downloaded on [DD Month YYYY].Course Details Lecture Tuesdays and Thursdays 11-12 Lab Tuesdays and Thursdays 1-5 Wednesdays and Fridays 1-5 There are no “make-up” labs Work must be turned in on time lab reports, homework: at beginning of lab lab notebook pages: at end of lab You will perform experiments in pairs Assignments can be worked ontogether but submitted individually Grading 50% Written Work Modules 1 and 2 30% Oral Presentations Modules (1 or 2) and 3 10% Homework Assignments 5% Daily Lab Quizzes 5% Lab Notebooks Foundations/Skills • Basic Laboratory Skills following and designing protocols first-hand experience with equipment and procedures how to keep a lab notebook • Robust Quantitative Analysis of Data statistical analysis when appropriate repetition of protocols to assess quality of findings effect of experimental perturbations on outcome • Verbal and Written Communication two oral presentations two written reports • Critical Thinking Analysis and discussion of primary scientific literature Cite as: Angela Belcher, Drew Endy, Natalie Kuldell and Agi Stachowiak. Course materials for 20.109 Laboratory Fundamentals in Biological Engineering, Fall 2007. MIT OpenCourseWare (http://ocw.mit.edu),4 Massachusetts Institute of Technology. Downloaded on [DD Month