Bioe506

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Bioe506

  1. 1. Course SyllabusSubject and Course Number: BIOE 506Title: Molecular & Cellular BioengrgProposed Texts: On Line Lecture NotesRecommended Texts: Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., Walter, P.:Molecular Biology of the Cell. 4th ed., Garland Science, Taylor & Francis Group, 2002Credit: 4 graduate hours.Contact Hours: Two 90-minute lectures-discussions per week. 3.5 contact hours per week.Topics Contact HoursI. Introduction to Molecular and Cellular Engineering• Introduction and review of DNA, RNA, Protein, Organelles, Cells 4II. DNA Engineering and Technologies• PCR, RT-PCR, DNA Mutagenesis, DNA Shuffling, Directed Evolution 2• Northern Blot, Southern Blot, Microarray 2III. Gene Regulation and Genetic Engineering• Transcription, RNA, SiRNA, Gene Therapy 2IV. Molecular Engineering and Technologies• Antibodies, Electrophoresis, Immunoblotting, Immunostaining 2• Kinase assay, Yeast Two-Hybrid Assay, Flow Cytometry 2V. Cellular Functions• Cytoskeleton 2• Signaling Transduction, Phosphorylation, GTPases, Protein-Protein interaction 4• Cell-Extracellular Matrix Adhesions 2• Cell-Cell adhesions 2VI. Cell-Environment Interactions• Outside-in: Receptors, Cell Signaling and Cytoskeleton; Inside-out: Cell Traction Force, Extracellular Matrix remodeling; The measurement of intracellular strain using marker displacement, of external traction force using beads-embedded elastic gels and nanofabricated elastic poles. The effects of mechanical properties. 6VII. Cellular and Tissue Engineering• Biomaterials, Nanofabrication 2• Cell-Material Interaction, Tissue Engineering, 3D Culture 2• Signaling and Regulation 2VIII. Advanced Topics: (I) Stem Cell Biology• Maintenance, Differentiation, Proliferation 2• Stem cells for tissue engineering 4IX. Advanced Topics: (II) Fluorescence Proteins and Biosensors
  2. 2. • Fluorescence Proteins 3• Genetically-encoded Biosensors based on Fluorescence Proteins. The application of biosensors for measuring cell-environment interactions 2 Five quizzes, 40 minutes for each quiz 3 Total 50Grading: Grade will be based on five quizzes (40%), class presentation (30%), and final exam (30%).Proposed By: Dr. Yingxiao Wang
  3. 3. References Addendum Topics Class Time ReferencesX. Introduction to Molecular and Cellular Engineering• Introduction and review of DNA, RNA, Protein, Organelles, Cells 4 hr (1)XI. DNA Engineering and Technologies• PCR, RT-PCR, DNA Mutagenesis, DNA Shuffling, Directed Evolution 2 hr (2, 3)• Northern Blot, Southern Blot, Microarray 2 hr (1, 3, 4)XII. Gene Regulation and Genetic Engineering• Transcription, RNA, SiRNA, Gene Therapy 2 hr (1, 5)XIII. Molecular Engineering and Technologies• Antibodies, Electrophoresis, Immunoblotting, Immunostaining 2 hr (1, 3, 6)• Kinase assay, Yeast Two-Hybrid Assay, Flow Cytometry 2 hr (3)XIV. Cellular Functions• Cytoskeleton 2 hr (1)• Signaling Transduction, Phosphorylation, GTPases, Protein-Protein interaction 4 hr (7-9)• Cell-Extracellular Matrix Adhesions 2 hr (10-13)• Cell-Cell adhesions 2 hr (14-17)XV. Cell-Environment Interactions• Outside-in: Receptors, Cell Signaling and Cytoskeleton; Inside-out: Cell Traction Force, Extracellular Matrix remodeling; The measurement of intracellular strain using marker displacement, of external traction force using beads-embedded elastic gels and nanofabricated elastic poles. The effects of mechanical properties. 6 hr (1, 18-20)XVI. Cellular and Tissue Engineering• Biomaterials, Nanofabrication 2 hr (21, 22)• Cell-Material Interaction, Tissue Engineering, 3D Culture 2 hr (23-25)• Signaling and Regulation 2 hr (26, 27)XVII. Advanced Topics: (I) Stem Cell Biology• Maintenance, Differentiation, Proliferation 2 hr (1)• Stem cells for tissue engineering 4 hr (28-32)XVIII. Advanced Topics: (II) Fluorescence Proteins and Biosensors• Fluorescence Proteins 3 hr (33-35)• Genetically-encoded Biosensors based on Fluorescence Proteins, The application of biosensors for measuring cell-environment interactions 2 hr (36-38) Five quizzes, 40 minutes for each quiz 3 hrTotal 50 hr
  4. 4. Reference: 1. Bruce Alberts AJ, Julian Lewis, Martin Raff, Keith Roberts, Peter Walter. 2002. Garland Science, Taylor & Francis Group 2. James D. Watson MG, Jan A. Witkowski, Mark Zoller 1992. W. H. Freeman 3. Joseph Sambrook DWR. 2001. Cold Spring Harbor Laboratory Press 4. Jares P. 2006. Ultrastruct Pathol 30: 209-19 5. Tuschl T. 2001. Chembiochem 2: 239-45 6. Ed Harlow DL. 1988. Cold Spring Harbor Laboratory Press 7. Janin J, Wodak SJ. 2002. Adv Protein Chem 61: 1-8 8. Karin M, Hunter T. 1995. Curr Biol 5: 747-57 9. Stelzl U, Wanker EE. 2006. Curr Opin Chem Biol 10: 551-8 10. Calderwood DA. 2004. J Cell Sci 117: 657-66 11. Manso AM, Elsherif L, Kang SM, Ross RS. 2006. Cardiovasc Res 69: 574-84 12. Seiki M. 2003. Cancer Lett 194: 1-11 13. Springer TA, Wang JH. 2004. Adv Protein Chem 68: 29-63 14. Braga VM. 2002. Curr Opin Cell Biol 14: 546-56 15. Gumbiner BM. 2005. Nat Rev Mol Cell Biol 6: 622-34 16. Halbleib JM, Nelson WJ. 2006. Genes Dev 20: 3199-214 17. Sallee JL, Wittchen ES, Burridge K. 2006. J Biol Chem 281: 16189-92 18. Holmbeck K, Bianco P, Yamada S, Birkedal-Hansen H. 2004. J Cell Physiol 200: 11-9 19. Larsen M, Artym VV, Green JA, Yamada KM. 2006. Curr Opin Cell Biol 18: 463-71 20. Wang YL. 2007. Sci STKE 2007: pe10 21. Holmes TC. 2002. Trends Biotechnol 20: 16-21 22. Shin H. 2007. Biomaterials 28: 126-33 23. Kirkpatrick CJ, Krump-Konvalinkova V, Unger RE, Bittinger F, Otto M, Peters K. 2002. Biomol Eng 19: 211-7 24. Minuth WW, Schumacher K, Strehl R, Kloth S. 2000. J Biomater Sci Polym Ed 11: 495- 522 25. Wilson CJ, Clegg RE, Leavesley DI, Pearcy MJ. 2005. Tissue Eng 11: 1-18 26. Even-Ram S, Yamada KM. 2005. Curr Opin Cell Biol 17: 524-32 27. Cukierman E, Pankov R, Stevens DR, Yamada KM. 2001. Science 294: 1708-12 28. Niwa H. 2001. Cell Struct Funct 26: 137-48 29. Noggle SA, James D, Brivanlou AH. 2005. Stem Cell Rev 1: 111-8 30. Feng GS. 2007. Cell Res 17: 37-41 31. Kleber M, Sommer L. 2004. Curr Opin Cell Biol 16: 681-7 32. Zhang J, Li L. 2005. Dev Biol 284: 1-11 33. Lukyanov KA, Chudakov DM, Lukyanov S, Verkhusha VV. 2005. Nat Rev Mol Cell Biol 6: 885-91 34. Shaner NC, Steinbach PA, Tsien RY. 2005. Nat Methods 2: 905-9 35. Tsien RY. 1998. Annu Rev Biochem 67: 509-44 36. Giepmans BN, Adams SR, Ellisman MH, Tsien RY. 2006. Science 312: 217-24 37. Lippincott-Schwartz J, Patterson GH. 2003. Science 300: 87-91 38. Zhang J, Campbell RE, Ting AY, Tsien RY. 2002. Nat Rev Mol Cell Biol 3: 906-18

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