BEE 3600. Molecular and Cellular Bioengineering Spring Semester 2007 Credit: 3 hours Catalogue description: Biotechnology viewed at the cellular and molecular level. Advances in biotechnology will be broken down to their functional parts using the tools of biological engineering (thermodynamics, transport, kinetics, etc.) to understand how and why they work with an emphasis on design. Particular attention paid to gene therapy, synthetic biology, protein engineering and nucleic acid engineering. Case studies in biomedical, bioprocess, and bioenvironmental engineering. Required or elective: Core-curriculum course: Required” Prerequisites: Biochemistry (for BEE students) or AEP 252 (for students from Applied and Engineering Physics, Chemical and Biomolecular Engineering, etc.) or permission of instructor. Textbook(s) and other required materials: Research papers/handouts. Course objectives: This course is being taught as an upper level introduction to cutting edge topics of interest to biological engineers. The focus will be on connecting relevant themes and concepts from the BEE curriculum to recent developments in the areas of cellular and molecular engineering. Rather than rely on a one-t i me review of relevant background material at the beginning of the course, we will review pertinent information as we progress with the focus being always on how the concepts are relevant to the technology under study. The goals for the course will be to make relevant and lasting connections between the fundamental concepts (such as biology, genetics, biochemistry, transport, thermodynamics, etc.) and biotechnological applications. We will pull equally from industrial and academic examples and attempt to make a clear connection between advances in basic science and their importance to engineering. Topics covered: 1. Cloning and engineering gene expression: a. Basic cloning: WC base pairing, DNA as genetic material, plasmids, PCR b. PCR: designing primers, restriction endonucleases, ligases, high/low copy c. High yield gene expression, bacteria d. Plant, animal cloning and gene expression 2. Metabolic Engineering/synthetic biology: a. Metabolic engineering: prokaryotes, networks, fluxes b. (cont.) fluxes, example: linear algebra c. Metabolic engineering: eukaryotes, signal transduction d. (cont.) signal transduction, gut signaling e. (cont.) signal transduction, other pathways, quorum sensing f. (cont.) signal transduction, other pathways, cell cycle g. (cont.) signal transduction, other pathways, RNAi h. (cont.) signal transduction, other pathways, insulin signaling i. Synthetic biology: functional decomposition, applications 5. Nucleic acid engineering: a. Ribozymes, microRNA, etc. b. DNA as a generic rather than genetic material 4. Vaccines/protein engineering: a. Vaccines: concepts, techniques for producing, gene shuffling 1 b. (cont.) Protein engineering: Targets for change, error-prone PCR other techs. 3. Gene therapy/drug delivery: a. Gene therapy: host genes and cancer, therapies b. Drug delivery: one lecture 6. Plant and biomass engineering: a. Biopharming, biofuels b. (cont.) cell yields, power density, etc. 7. Bioremediation/environmental biotechnology: a. Bioremediation: pathways, contaminants b. (cont.) successes, failures, techniques, new approaches Class/laboratory schedule: Two 75 min lectures per week Contribution of course to meeting the professional component: Required BEE course; BME elective; M. Eng course (both BEE and BME) Course outcomes and their relation to ABET program outcomes a-m: 1. Understand molecular biology as it relates to recombinant protein synthesis and be able to design recombinant protein expression systems. (a, c, e, k, l) 2. Use flux analysis and pathway mapping to design organisms for biotechnological applications. (a, c, k) 3. Understand the complications associated with high yield product synthesis systems and the kinetic equations describing these systems can be used to improve their design. (a, c, k) 4. Understand how cutting edge techniques used in molecular and cellular biology can be used in the design of biotechnologies for use in medicine, bioprocessing, and environmental engineering. (a, c, j, k, l) 5. To employ engineering design methodologies (such as Quality Functional Deployment) that are traditionally used in mechanical design in the development of biotechnologies. (a, c, e, k) 6. To use all the resource material available to define a real problem to society and to propose a feasible solution to that problem in a short research proposal and presentation. (a, c, e, g, h, j, k, l) 7. Understand ethical issues related to biological engineering such as impact of cloning or stem cell research. (h, j, l) Assessment of course outcomes: 3 Midterms: 15 points each = 45 6 Homeworks: 5 points each = 30 1 Project: 20 points = 20 Random quizzes: 15 points = 15 ________________________________ 110 total Person preparing this description and date: John March, 4/28/07 Ethical behavior statement: You may get a failing grade if you violate the Cornell University Code of Academic Integrity, whether intentionally or “un-intentionally”. 2 .