Molecular and Cellular Biology for Engineers

BioE 598 Molecular and Cellular Fundamentals of Bioengineering
http://imaging.bioen.uiuc.edu/yingxiao_wang/classes/
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 40% from five quizzes, 30% from Class Presentation, 30% from final
exam.
Instructors: Yingxiao Wang
Beckman 4261
333-6727
Email: [email protected]
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:
5 Quizzes
In Class Presentation
Final Exam,
Total Points
All quizzes and examinations are cumulative.
40 points
30 points
30 points
100 points
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:
Week 1 (Jan 14-18)
Week 2(Jan 21-25)
Week 3 (Jan 28-Feb 1)
Week 4 (Feb 4-8)
Week 5 (Feb 11-15)
Week 6 (Feb 18-22)
Week 7 (Feb 25-29)
Week 8 (Mar 3-7)
Week 9 (Mar 10-14)
Week 10 (Mar 17-21)
Week 11 (Mar 24-28)
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
Class rules, Introduction to
the class, Cells and Genomes
(chap 1, recommended text)
MLK Holiday
Wed
Cell Chemistry and Biosynthesis
(chap 2, recommended text)
Proteins
(chap 3, recommended text)
DNA replication, repair,
Quiz 1, DNA,
recombination (chap 5,
Chromosomes, Genomes
(chap 4, recommended text) recommended text)
From DNA to protein
Control of Gene Expression
(chap 6, recommended text) (chap 7, recommended text)
Quiz 2, Cell Membrane and Cell Signaling (chap 15,
recommended text)
Its Functions (chap 10-11,
recommended text)
Cell Signaling (chap 15,
Cytoskeleton (chap 16,
recommended text),
recommended text),
Cell-ECM Adhesion (chap
Cell-Cell Adhesion
19, recommended text),
(chap 19, recommended text),
Biotechnology II (Directed DNA
Quiz 3, Biotechnology I
(chap 8, recommended text) Evolution) Prof. Huimin Zhao
Biotechnology III (chap 9,
Live Cell Imaging of Signaling
recommended text),
Transduction with Fluorescence
Fluorescence Proteins 1-6
Proteins 7-10, Quiz 4
Spring Break
Cell-Environment
Interaction (outside-in)
(Chien-Chun Chen)11, 12
Week 12 (Mar 31-Apr 4) Mechanical Force Effects on
Cellular Functions (James
Eddy)15, 16
Week 13 (Apr 7-11)
Cell and Tissue Engineering,
3D effects
(John Eichorst)19, 20
Cell-Environment Interaction
(inside-out) (Brian Dorvel)13, 14
Cell Effects on Mechanical
Properties of Environment (Sherine
George)17, 18
Cell and Tissue Engineering,
Nanotechnology
(Mark Hwang)21, 22
Week 14 (Apr 14-18)
Cell and Tissue Engineering, Stem Cells, General Concepts
Biomaterials
(Jason Ip)23, 24
Professor Hyun Joon Kong,
Quiz 5
Week 15 (Apr 21-25)
Stem Cells and Cell Signaling Stem Cells and Tissue Engineering
(David Mahr)25, 26
(Aaron Maki)27, 28
Week 16 (Apr 28-May 2) Cell Signaling, migration
(Samantha Polak)29, 30
Cell Signaling, junction
(Yue Zhuo)31, 32
Final Exam: DCL 3211, May 1st, 7-10pm
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
12.
13.
14.
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, 1124111246 (1999).
Campbell, R.E. et al. A monomeric red fluorescent protein. Proc Natl Acad Sci U
S A 99, 7877-7882 (2002).
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).
Shaner, N.C., Steinbach, P.A. & Tsien, R.Y. A guide to choosing fluorescent
proteins. Nat Methods 2, 905-909 (2005).
Tsien, R.Y. The green fluorescent protein. Annu Rev Biochem 67, 509-544
(1998).
Matz, M.V. et al. Fluorescent proteins from nonbioluminescent Anthozoa species.
Nat Biotechnol 17, 969-973 (1999).
Mochizuki, N. et al. Spatio-temporal images of growth-factor-induced activation
of Ras and Rap1. Nature 411, 1065-1068 (2001).
Wang, Y. et al. Visualizing the mechanical activation of Src. Nature 434, 10401045 (2005).
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).
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).
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).
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).
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).
Meshel, A.S., Wei, Q., Adelstein, R.S. & Sheetz, M.P. Basic mechanism of threedimensional collagen fibre transport by fibroblasts. Nat Cell Biol 7, 157-164
(2005).
15.
16.
17.
18.
19.
20.
21.
22.
23.
24.
25.
26.
27.
28.
29.
30.
31.
32.
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).
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).
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).
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).
Cukierman, E., Pankov, R., Stevens, D.R. & Yamada, K.M. Taking cell-matrix
adhesions to the third dimension. Science 294, 1708-1712 (2001).
Yamada, K.M. & Cukierman, E. Modeling tissue morphogenesis and cancer in
3D. Cell 130, 601-610 (2007).
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).
Dalby, M.J. et al. The control of human mesenchymal cell differentiation using
nanoscale symmetry and disorder. Nat Mater 6, 997-1003 (2007).
Donovan, P.J. & Gearhart, J. The end of the beginning for pluripotent stem cells.
Nature 414, 92-97 (2001).
Engler, A.J., Sen, S., Sweeney, H.L. & Discher, D.E. Matrix elasticity directs
stem cell lineage specification. Cell 126, 677-689 (2006).
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).
Mishra, L., Derynck, R. & Mishra, B. Transforming growth factor-beta signaling
in stem cells and cancer. Science 310, 68-71 (2005).
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).
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).
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).
Ridley, A.J. et al. Cell migration: integrating signals from front to back. Science
302, 1704-1709 (2003).
Halbleib, J.M. & Nelson, W.J. Cadherins in development: cell adhesion, sorting,
and tissue morphogenesis. Genes Dev 20, 3199-3214 (2006).
Yamada, S., Pokutta, S., Drees, F., Weis, W.I. & Nelson, W.J. Deconstructing the
cadherin-catenin-actin complex. Cell 123, 889-901 (2005).