This course syllabus outlines the topics, schedule, and requirements for a graduate level Molecular and Cellular Bioengineering course. Over 50 contact hours, the course will cover topics such as DNA engineering, gene regulation, molecular and cellular techniques, cellular functions, cell-environment interactions, tissue engineering, and advanced topics including stem cell biology and fluorescence proteins/biosensors. Students will be evaluated based on five quizzes, a class presentation, and a final exam. Recommended textbooks and research papers are provided as additional references for each major topic.

1. Course Syllabus
Subject and Course Number: BIOE 506
Title: Molecular & Cellular Bioengrg
Proposed Texts: On Line Lecture Notes
Recommended 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, 2002
Credit: 4 graduate hours.
Contact Hours: Two 90-minute lectures-discussions per week. 3.5 contact hours per week.
Topics Contact Hours
I. Introduction to Molecular and Cellular Engineering
• Introduction and review of DNA, RNA, Protein, Organelles, Cells 4
II. DNA Engineering and Technologies
• PCR, RT-PCR, DNA Mutagenesis, DNA Shuffling, Directed Evolution 2
• Northern Blot, Southern Blot, Microarray 2
III. Gene Regulation and Genetic Engineering
• Transcription, RNA, SiRNA, Gene Therapy 2
IV. Molecular Engineering and Technologies
• Antibodies, Electrophoresis, Immunoblotting, Immunostaining 2
• Kinase assay, Yeast Two-Hybrid Assay, Flow Cytometry 2
V. Cellular Functions
• Cytoskeleton 2
• Signaling Transduction, Phosphorylation, GTPases, Protein-Protein interaction 4
• Cell-Extracellular Matrix Adhesions 2
• Cell-Cell adhesions 2
VI. 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
VII. Cellular and Tissue Engineering
• Biomaterials, Nanofabrication 2
• Cell-Material Interaction, Tissue Engineering, 3D Culture 2
• Signaling and Regulation 2
VIII. Advanced Topics: (I) Stem Cell Biology
• Maintenance, Differentiation, Proliferation 2
• Stem cells for tissue engineering 4
IX. Advanced Topics: (II) Fluorescence Proteins and Biosensors

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 50
Grading: Grade will be based on five quizzes (40%), class presentation (30%), and final exam (30%).
Proposed By: Dr. Yingxiao Wang

3. References Addendum
Topics Class Time References
X. 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 hr
Total 50 hr

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
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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
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18. Holmbeck K, Bianco P, Yamada S, Birkedal-Hansen H. 2004. J Cell Physiol 200: 11-9
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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
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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
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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
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37. Lippincott-Schwartz J, Patterson GH. 2003. Science 300: 87-91
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