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

• 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

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

Reference: 1. Bruce Alberts AJ, Julian Lewis, Martin Raff, Keith Roberts, Peter Walter. 2002. Garland

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