BME 510 BIOLOGY FOR ENGINEERS FALL 2007
Mon, Wed & Fri 9:00-9:50, AHSC 8403
3 Credits

Course Description and Overview:
The goal of this course is to introduce students to fundamental concepts in molecular and cellular biology in a Lecture/Discussion format. The course will cover basic biological principles governing biomolecular and cellular processes and link these to applications in medicine, engineering, and applied sciences. The course will emphasize technical approaches, experimental design, and data interpretation.

Readings:
The text for the course is Molecular Cell Biology, 6th edition, editors Lodish, Berk, Krieger, Scott, Bretscher, Ploegh, and Matsudaira (W. H. Freeman and Co). A copy is on reserve in the Health Sciences Library and the Medical Bookstore has copies for purchase.

Grading Policies:
Grades for the course will be determined based on three examinations and presentation of a journal article. The grading distribution is as follows: Examinations (3) 75%; Presentation 25%.

Presentations: Students, singly or in pairs, will present to the class a journal article selected from the primary literature and each presentation should include a brief description of the question being examined, the methods used, the findings and the discussion points of the article. In addition, a brief summary of the article will be turned in by each of the presenting students at the time of the presentation. Students may additionally be asked to present short summaries of journal articles in class.

Syllabus (as of 080707)

Recommended articles for presentations
1. Xiao, Q., L.Zeng, Z.Zhang, Y.Hu, and Q.Xu. 2006. Stem Cell-derived Sca-1+ Progenitors Differentiate into Smooth Muscle Cells, which is Mediated by Collagen IV-Integrin {alpha}1/{beta}1/{alpha}v and PDGF Receptor Pathways. Am. J. Physiol Cell Physiol.

2. Alberti, P. and J.L.Mergny. 2004. DNA structural changes as the basis for a nanomolecular device. Cell Mol. Biol. (Noisy. -le-grand) 50:241-253.

3. Brown, D.L., P.J.Meagher, K.R.Knight, E.Keramidaris, R.Romeo-Meeuw, A.J.Penington, and W.A.Morrison. 2006. Survival and function of transplanted islet cells on an in vivo, vascularized tissue engineering platform in the rat: A pilot study. Cell Transplant. 15:319-324.

4. Edgar, R., M.McKinstry, J.Hwang, A.B.Oppenheim, R.A.Fekete, G.Giulian, C.Merril, K.Nagashima, and S.Adhya. 2006. High-sensitivity bacterial detection using biotin-tagged phage and quantum-dot nanocomplexes. Proc. Natl. Acad. Sci. U. S. A 103:4841-4845.

5. Hollander, A.P., S.C.Dickinson, T.J.Sims, P.Brun, R.Cortivo, E.Kon, M.Marcacci, S.Zanasi, A.Borrione, L.C.De, A.Pavesio, C.Soranzo, and G.Abatangelo. 2006. Maturation of tissue engineered cartilage implanted in injured and osteoarthritic human knees. Tissue Eng 12:1787-1798.

6. Isenberg, B.C., C.Williams, and R.T.Tranquillo. 2006. Endothelialization and flow conditioning of fibrin-based media-equivalents. Ann. Biomed. Eng 34:971-985.

7. Kobayashi, K., Y.Nomoto, T.Suzuki, Y.Tada, M.Miyake, A.Hazama, S.Kanemaru, T.Nakamura, and K.Omori. 2006. Effect of Fibroblasts on Tracheal Epithelial Regeneration in Vitro. Tissue Eng.

8. Ng, L., H.H.Hung, A.Sprunt, S.Chubinskaya, C.Ortiz, and A.Grodzinsky. 2006. Nanomechanical properties of individual chondrocytes and their developing growth factor-stimulated pericellular matrix. J. Biomech.

9. Oka, C., H.Matsuda, N.Sarai, and A.Noma. 2006. Modeling the calcium gate of cardiac gap junction channel. J. Physiol Sci. 56:79-85.

10. Paek, H.J., A.B.Campaner, J.L.Kim, L.Golden, R.K.Aaron, D.M.Ciombor, J.R.Morgan, and M.J.Lysaght. 2006. Microencapsulated cells genetically modified to overexpress human transforming growth factor-beta1: viability and functionality in allogeneic and xenogeneic implant models. Tissue Eng 12:1733-1739.

11. Platt, M.O., R.F.Ankeny, and H.Jo. 2006. Laminar shear stress inhibits cathepsin L activity in endothelial cells. Arterioscler. Thromb. Vasc. Biol. 26:1784-1790.

12. Schwartz, M.A. and A.R.Horwitz. 2006. Integrating adhesion, protrusion, and contraction during cell migration. Cell 125:1223-1225.

13. Sun, H., C.Wu, K.Dai, J.Chang, and T.Tang. 2006. Proliferation and osteoblastic differentiation of human bone marrow-derived stromal cells on akermanite-bioactive ceramics. Biomaterials.

14. Sun, N., R.J.Carroll, and H.Zhao. 2006. Bayesian error analysis model for reconstructing transcriptional regulatory networks. Proc. Natl. Acad. Sci. U. S. A 103:7988-7993.

15. Varani, J., M.K.Dame, L.Rittie, S.E.Fligiel, S.Kang, G.J.Fisher, and J.J.Voorhees. 2006. Decreased collagen production in chronologically aged skin: roles of age-dependent alteration in fibroblast function and defective mechanical stimulation. Am. J. Pathol. 168:1861-1868.

16. Volgraf, M., P.Gorostiza, R.Numano, R.H.Kramer, E.Y.Isacoff, and D.Trauner. 2006. Allosteric control of an ionotropic glutamate receptor with an optical switch. Nat. Chem. Biol. 2:47-52.

17. Krantz, M., Becit, E., and S. Hohmann.  2006. Comparitive genomics of the HOG-signalling system in fungi. Curr. Genet. 49:137-151.

18. Gibbs, M., Armstrong, J., and A. Gibbs. 2001. Recombination in the Hemagglutinin Gene of the 1918 “Spanish Flu”. Science 293:1842-1845.

19. Prochnow, D. Riedel, N., Agutter, P., and H. Fasold. 1990. Poly(A) Binding Proteins Located at the Inner Surface of Resealed Nuclear Envelopes. J. Biol. Chem. 265:6536-6539.

20. Li, S.-C., Pan, C.-Y., and W.-C. Lin. 2006. Bioinformatic discovery of microRNA precursors from human ESTs and introns. BMC Genomics 7:164.

21. Cheng, J. et al. 2005. Transcriptional Maps of 10 Human Chromosomes at 5-Nucleotide Resolution. Science 308:1149-1154.

Links
Genome Links: www.ensembl.org/
PubMed literature search: www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed
BLAST: www.ncbi.nlm.nih.gov/BLAST/
Genbank: http://www.ncbi.nlm.nih.gov/Tools/index.html
Institute for Systems Biology: http://www.systemsbiology.org/
Programs in Genomic Applications: http://www.nhlbi.nih.gov/resources/pga/index.htm
The J. Craig Venter Institute:http://www.tigr.org

Journals

American Association for the Advancement of Science (Science): www.sciencemag.org/
Nature: www.nature.com
Biomed Central: http://www.biomedcentral.com/
Public Library of Science Journals: http://www.plos.org/
The Lancet: http://www.thelancet.com/

Bioinformatics Tools

Sequence visualization, alignment, etc.
Bioedit: http://www.mbio.ncsu.edu/BioEdit/bioedit.html
CLC Free Workbench: www.clcbio.com/free/
Geneious: http://www.geneious.com/
Protein-Protein Interaction Networks
Osprey: http://www.thebiogrid.org/