BioE 506 Molecular and Cellular Bioengineering
http://imaging.bioen.uiuc.edu/yingxiao_wang/classes.htm
Course Description
To introduce the cutting-edge engineering technologies applied in the molecular and cellular biology research, i.e. how can the properties of genes, molecules, and cells be monitored, measured, manipulated, and modeled to advance our understanding of the complex biological system. Special emphasis will also be placed on how cells interact with each other and external environment to shed light on the molecular mechanisms governing tissue engineering and regenerative medicine.
Grade will be based on 30% from three quizzes, 30% from Class Presentation, 30% from final exam, 10% from class attendance.
Instructors: Yingxiao Wang
Beckman 4261
333-6727
Email:
Credit: 4 hours
Meeting Times: MW 9:00-10:50am
Office Hour: Thu 4-5pm Beckman Institute 4261
Location: 3211 DCL
Prerequisite: MCB 150
Proposed Texts: On Line Literature and Notes
Recommended Book: 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
Exams and Homeworks: 3 Quizzes 30 points
In Class Presentation 30 points
Final Exam, 30 points
Class attendance 10 points
Total Points 100 points
All quizzes and examinations are cumulative.
Grading Criteria for Oral Presentation:
1. Content: Purpose/subject defined clearly, information and logics are self consistent.
2. Organization: Introduction, Topic, Closing.
3. Delivery: Poise/Appearance, Body Language, Eye Contact, Voice, Pacing
4. Awareness of Audience: Persuasion
5. Quality of Visual Aids: Texts and Figures are clear, not overcrowded,
Content: 12 points. Organization: 12 points. Delivery/Awareness of Audience/Quality of Visual Aids: 2/2/2 points
Grading: Letter Grade
A 100-90
B 89-80
C 79-70
D 69-60
F 59-0
The instructors reserve the right to shift the grades slightly based on score distribution.
Mon / WedWeek 1 (Jan 19-23) / Class rules, Introduction to the class
Week 2 (Jan 26-30) / Cells and Genomes
(chap 1, recommended text) / Cell Chemistry and Biosynthesis
(chap 2, recommended text)
Week 3(Feb 2-6) / Proteins
(chap 3, recommended text) / Chromosomes, Genomes (chap 4, recommended text)
Week 4 (Feb 9-13) / DNA, DNA replication, repair, recombination (chap 5, recommended text) / From DNA to protein
(chap 6, recommended text)
(Ms. Jie Sun)
Week 5 (Feb 16-20) / Single Molecular Detection of DNA and Protein interactions, Prof. Taekjip Ha;
Quiz 1 / Student Presentation 1;
Directed Evolution1, 2
Andrew Goodrich & Charles Feng
Week 6 (Feb 23-27) / Control of Gene Expression
(chap 7, recommended text) / Cell Membrane and Its Functions (chap 10-11, recommended text)
Week 7 (Mar 2-6 ) / Intracellular Trafficking
(chap 12-13, recommended text) / Cell Signaling (chap 15, recommended text),
Week 8 (Mar 9-13) / Cell Signaling (chap 15, recommended text),
Quiz 2 / Cytoskeleton (chap 16, recommended text),
Week 9 (Mar 16-20) / Cell-ECM Adhesion (chap 19, recommended text), / Cell-Cell Adhesion
(chap 19, recommended text),
Week 10 (Mar 23-27) / Spring Break
Week 11 (Mar 30-Apr 3) / Biotechnology I (chap 8, recommended text) / Biotechnology II (chap 9, recommended text)
Week 12 (Apr 6-10) / Biotechnology III (Bio-Nanotechnology), Prof. Gang Logan Liu;
Quiz 3 / Fluorescent Proteins 3-8, Live Cell Imaging of Signaling Transduction with Fluorescence Proteins 7, 9-11,
Week 13 (Apr 13-17) / Student Presentation 2;
Cell-Environment Interaction (outside-in)12, 13;
Cell-Environment Interaction (inside-out)14, 15
Yuan Liu & Wagner Nishitani / Student Presentation 3;
Mechanical Force Effects on Cellular Functions16, 17;
Cell Effects on Mechanical Properties of Environment18, 19
Kyle Wallenberg & Eric Salm & Will Leinweber
Week 14 (Apr 20-24) / Student Presentation 4;
Cell and Tissue Engineering, 3D effects20, 21;
Cell and Tissue Engineering, Nanotechnology22, 23
Muqeem Qayyum & Vincent Chan / Student Presentation 5;
Stem Cells, General Concepts 24, 25;
Stem Cells and Cell Signaling26, 27
Sarah Holton & Helen Hwang
Week 15 (Apr 27-May 1) / Student Presentation 6;
Stem Cells and Tissue Engineering28, 29
Stephanie Pasquesi & Deepika Chitturi & Tongcheng Qian / Student Presentation 7;
Cell Signaling, migration30, 31;
Cell Signaling, junction32, 33
Erich Lidstone & Piyush Bajaj
Week 16 (May 4-8) / Final Exam (9-12pm)
1. Arnold, F.H. When blind is better: protein design by evolution. Nat Biotechnol 16, 617-618 (1998).
2. Schmidt-Dannert, C. Directed evolution of single proteins, metabolic pathways, and viruses. Biochemistry 40, 13125-13136 (2001).
3. Baird, G.S., Zacharias, D.A. & Tsien, R.Y. Circular permutation and receptor insertion within green fluorescent proteins. Proc Natl Acad Sci U S A 96, 11241-11246 (1999).
4. Campbell, R.E. et al. A monomeric red fluorescent protein. Proc Natl Acad Sci U S A 99, 7877-7882 (2002).
5. Shaner, N.C. et al. Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein. Nat Biotechnol 22, 1567-1572 (2004).
6. Shaner, N.C., Steinbach, P.A. & Tsien, R.Y. A guide to choosing fluorescent proteins. Nat Methods 2, 905-909 (2005).
7. Wang, Y. et al. Visualizing the mechanical activation of Src. Nature 434, 1040-1045 (2005).
8. Matz, M.V. et al. Fluorescent proteins from nonbioluminescent Anthozoa species. Nat Biotechnol 17, 969-973 (1999).
9. Mochizuki, N. et al. Spatio-temporal images of growth-factor-induced activation of Ras and Rap1. Nature 411, 1065-1068 (2001).
10. Zhang, J., Campbell, R.E., Ting, A.Y. & Tsien, R.Y. Creating new fluorescent probes for cell biology. Nat Rev Mol Cell Biol 3, 906-918 (2002).
11. Zhang, J., Ma, Y., Taylor, S.S. & Tsien, R.Y. Genetically encoded reporters of protein kinase A activity reveal impact of substrate tethering. Proc Natl Acad Sci U S A 98, 14997-15002 (2001).
12. Chen, C.S., Mrksich, M., Huang, S., Whitesides, G.M. & Ingber, D.E. Geometric control of cell life and death. Science 276, 1425-1428 (1997).
13. Whitesides, G.M., Ostuni, E., Takayama, S., Jiang, X. & Ingber, D.E. Soft lithography in biology and biochemistry. Annu Rev Biomed Eng 3, 335-373 (2001).
14. Arnaout, M.A., Goodman, S.L. & Xiong, J.P. Structure and mechanics of integrin-based cell adhesion. Curr Opin Cell Biol 19, 495-507 (2007).
15. Meshel, A.S., Wei, Q., Adelstein, R.S. & Sheetz, M.P. Basic mechanism of three-dimensional collagen fibre transport by fibroblasts. Nat Cell Biol 7, 157-164 (2005).
16. Bershadsky, A., Kozlov, M. & Geiger, B. Adhesion-mediated mechanosensitivity: a time to experiment, and a time to theorize. Curr Opin Cell Biol 18, 472-481 (2006).
17. Johnson, C.P., Tang, H.Y., Carag, C., Speicher, D.W. & Discher, D.E. Forced unfolding of proteins within cells. Science 317, 663-666 (2007).
18. Beningo, K.A., Dembo, M., Kaverina, I., Small, J.V. & Wang, Y.L. Nascent focal adhesions are responsible for the generation of strong propulsive forces in migrating fibroblasts. J Cell Biol 153, 881-888 (2001).
19. Dobereiner, H.G., Dubin-Thaler, B.J., Giannone, G. & Sheetz, M.P. Force sensing and generation in cell phases: analyses of complex functions. J Appl Physiol 98, 1542-1546 (2005).
20. Cukierman, E., Pankov, R., Stevens, D.R. & Yamada, K.M. Taking cell-matrix adhesions to the third dimension. Science 294, 1708-1712 (2001).
21. Yamada, K.M. & Cukierman, E. Modeling tissue morphogenesis and cancer in 3D. Cell 130, 601-610 (2007).
22. Barnes, C.P., Sell, S.A., Boland, E.D., Simpson, D.G. & Bowlin, G.L. Nanofiber technology: designing the next generation of tissue engineering scaffolds. Adv Drug Deliv Rev 59, 1413-1433 (2007).
23. Dalby, M.J. et al. The control of human mesenchymal cell differentiation using nanoscale symmetry and disorder. Nat Mater 6, 997-1003 (2007).
24. Donovan, P.J. & Gearhart, J. The end of the beginning for pluripotent stem cells. Nature 414, 92-97 (2001).
25. Engler, A.J., Sen, S., Sweeney, H.L. & Discher, D.E. Matrix elasticity directs stem cell lineage specification. Cell 126, 677-689 (2006).
26. Jian, H. et al. Smad3-dependent nuclear translocation of beta-catenin is required for TGF-beta1-induced proliferation of bone marrow-derived adult human mesenchymal stem cells. Genes Dev 20, 666-674 (2006).
27. Mishra, L., Derynck, R. & Mishra, B. Transforming growth factor-beta signaling in stem cells and cancer. Science 310, 68-71 (2005).
28. Huang, N.F., Lee, R.J. & Li, S. Chemical and physical regulation of stem cells and progenitor cells: potential for cardiovascular tissue engineering. Tissue Eng 13, 1809-1823 (2007).
29. Leach, J.K., Kaigler, D., Wang, Z., Krebsbach, P.H. & Mooney, D.J. Coating of VEGF-releasing scaffolds with bioactive glass for angiogenesis and bone regeneration. Biomaterials 27, 3249-3255 (2006).
30. Balasubramanian, N., Scott, D.W., Castle, J.D., Casanova, J.E. & Schwartz, M.A. Arf6 and microtubules in adhesion-dependent trafficking of lipid rafts. Nat Cell Biol 9, 1381-1391 (2007).
31. Ridley, A.J. et al. Cell migration: integrating signals from front to back. Science 302, 1704-1709 (2003).
32. Halbleib, J.M. & Nelson, W.J. Cadherins in development: cell adhesion, sorting, and tissue morphogenesis. Genes Dev 20, 3199-3214 (2006).
33. Yamada, S., Pokutta, S., Drees, F., Weis, W.I. & Nelson, W.J. Deconstructing the cadherin-catenin-actin complex. Cell 123, 889-901 (2005).