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7.548

Advances in Biomanufacturing

1-0-2 units · Graduate

Seminar examines how biopharmaceuticals, an increasingly important class of pharmaceuticals, are manufactured. Topics range from fundamental bioprocesses to new technologies to the economics of biomanufacturing. Also covers the impact of globalization on regulation and quality approaches as well as supply chain integrity. Students taking graduate version complete additional assignments.

Spring 2006 · Perspectives in Biological Engineering

Topics

  • Introduction - Quantitative/Integrative Systems Approach to Biology
  • Genomics Technologies - Sequencing
  • Genomics Technologies - Gene Expression
  • Genomics Technologies - Computational Analysis
  • Genes and Disease - Analysis and Statistics I
  • Genes and Disease - Analysis and Statistics II
  • Genomics and Gene Expression - Pathophysiological Applications
  • Genomics to Proteomics - mRNA to Protein Relationships
  • Proteins and Proteomics - Flow Cytometry Approaches
  • Proteins and Proteomics - Protein Network Dynamics
  • Proteins and Proteomics - Arrays and Gels
  • Proteins and Proteomics - Mass Spectrometry Approaches
  • Proteins and Proteomics - Protein Network Topologies
  • Project Planning Presentations
  • Project Planning Presentations (cont.)
  • Tissues and Animals - Technologies for Cellular Analysis
  • Tissues and Animals - Pathophysiological Application
  • Ethics and Responsible Conduct of Research
  • Ethics and Responsible Conduct of Research (cont.)
  • Tissues and Animals - Transgenic Animal Models
  • Tissues and Animals - Metabolomics
  • Tissues and Animals - Tissue Engineering Models
  • Project Presentations

Readings

  • Lodish, Harvey, Matthew P. Scott, Paul Matsudaira, James Darnell, Lawrence Zipursky, Chris A. Kaiser, Arnold Berk, and Monty Krieger. Molecular Cell Biology . New York, NY: W.H. Freeman, 2003. ISBN: 9780716743668.
    Listed reading
  • Lodish, Harvey, Matthew P. Scott, Paul Matsudaira, James Darnell, Lawrence Zipursky, Chris A. Kaiser, Arnold Berk, and Monty Krieger. Molecular Cell Biology . New York, NY: W.H. Freeman, 2003. ISBN: 9780716743668.
    Required
  • Drmanac, R., S. Drmanac, G. Chui, R. Diaz, A. Hou, H. Jin, P. Jin, S. Kwon, S. Lacy, B. Moeur, J. Shafto, D. Swanson, T. Ukrainczyk, C. Xu, and D. Little. “Sequencing by hybridization (SBH): advantages, achievements, and opportunities.” Adv Biochem Eng Biotechnol 77 (2002): 75-101.
    Listed reading
  • Graves, D. J. “Powerful tools for genetic analysis come of age.” Trends Biotechnol 17, no. 3 (March 1999): 127-34.
    Listed reading
  • Shendure, J., R. D. Mitra, C. Varma, and G. M Church. “Advanced sequencing technologies: methods and goals.” Nat Rev Genet 5, no. 5 (May 2004): 335-44.
    Listed reading
  • Lipshutz, R. J., S. P. Fodor, T. R. Gingeras, and D. J. Lockhart. “High density synthetic oligonucleotide arrays.” Nat Genet 21, no. 1 (January 1999): 20-4. (Supplementary)
    Listed reading
  • Schulze, A., and J. Downward. “Navigating gene expression using microarrays-a technology review.” Nat Cell Biol 3, no. 8 (August 2001): E190-5.
    Listed reading
  • Wong, M. L., and J. F. Medrano. “Real-time PCR for mRNA quantitation.” Biotechniques 39, no. 1 (July 2005): 75-85.
    Listed reading
  • Baldwin, D. N., V. Vanchinathan, P. O. Brown, and J. A. Theriot. “A gene-expression program reflecting the innate immune response of cultured intestinal epithelial cells to infection by Listeria monocytogenes.” Genome Biol 4, no. 1 (2003): R2; Epub (December 23, 2002).
    Listed reading
  • Kuruvilla, F. G., P. J. Park, and S. L. Schreiber. “Vector algebra in the analysis of genome-wide expression data.” Genome Biol 3, no. 3 (2002): RESEARCH0011; Epub (February 13, 2002).
    Listed reading
  • Sherlock, G. “Analysis of large-scale gene expression data.” Curr Opin Immunol 12, no. 2 (April 2000): 201-5.
    Listed reading
  • SES #: 5 · TOPICS: Genes and Disease - Analysis and Statistics I · READINGS: Morgenthaler, Stephan, and William G. Thilly. “A strategy to discover genes that carry multi-allelic and multigenic risk for common diseases: a cohort allelic sums test (CAST).” Submitted to Mutation Research (January 20, 2006).
    Reading assignment
  • Haugen, A. C., R. Kelley, J. B. Collins, C. J. Tucker, C. Deng, C. A. Afshari, J. M. Brown, T. Ideker, and B. Van Houten. “Integrating phenotypic and expression profiles to map arsenic-response networks.” Genome Biol 5, no. 12 (2004): R95; Epub (November 29, 2004).
    Listed reading
  • Huang, C., Q. Ke, M. Costa, and X. Shi. “Molecular mechanisms of arsenic carcinogenesis.” Mol Cell Biochem 255, no. 1-2 (January 2004): 57-66.
    Listed reading
  • Kitchin, K. T. “Recent advances in arsenic carcinogenesis: modes of action, animal model systems, and methylated arsenic metabolites.” Toxicol Appl Pharmacol 172, no. 3 (May 1, 2001): 249-61.
    Listed reading
  • Rossman, T. G. “Mechanism of arsenic carcinogenesis: an integrated approach.” Mutat Res 533, no. 1-2 (December 10, 2003): 37-65.
    Listed reading
  • Chou, W. C., C. Jie, A. A. Kenedy, R. J. Jones, M. A. Trush, and C. V. Dang. “Role of NADPH oxidase in arsenic-induced reactive oxygen species formation and cytotoxicity in myeloid leukemia cells.” Proc Natl Acad Sci USA 101, no. 13 (March 30, 2004): 4578-83; Epub (March 15, 2004).
    Listed reading
  • White, S. L., S. Gharbi, M. F. Bertani, H. L. Chan, M. D. Waterfield, and J. F. Timms. “Cellular responses to ErbB-2 overexpression in human mammary luminal epithelial cells: comparison of mRNA and protein expression.” Br J Cancer 90, no. 1 (January 12, 2004): 173-81.
    Listed reading
  • Cox, B., T. Kislinger, and A. Emili. “Integrating gene and protein expression data: pattern analysis and profile mining.” Methods 35, no. 3 (March 2005): 303-14; Epub (January 12, 2005).
    Listed reading
  • Krutzik, P. O., J. M. Irish, G. P. Nolan, and O. D. Perez. “Analysis of protein phosphorylation and cellular signaling events by flow cytometry: techniques and clinical applications.” Clin Immunol 110, no. 3 (March 2004): 206-21.
    Listed reading
  • Perez, O. D., D. Mitchell, G. C. Jager, S. South, C. Murriel, J. McBride, L. A. Herzenberg, S. Kinoshita, and G. P. Nolan. “Leukocyte functional antigen 1 lowers T cell activation thresholds and signaling through cytohesin-1 and Jun-activating binding protein 1.” Nat Immunol 4, no. 11 (November 2003): 1083-92; Epub (October 5, 2003).
    Listed reading
  • Sachs, K., O. Perez, D. Pe’er, D. A. Lauffenburger, and G. P. Nolan. “Causal protein-signaling networks derived from multiparameter single-cell data.” Science 308, no. 5721 (April 22, 2005): 523-9.
    Listed reading
  • Eddy, S. R. “What is Bayesian statistics?” Nat Biotechnol 22, no. 9 (September 2004): 1177-8.
    Listed reading
  • Sitek, B., O. Apostolov, K. Stuhler, K. Pfeiffer, H. E. Meyer, A. Eggert, and A. Schramm. “Identification of dynamic proteome changes upon ligand activation of Trk-receptors using two-dimensional fluorescence difference gel electrophoresis and mass spectrometry.” Mol Cell Proteomics 4, no. 3 (March 2005): 291-9; Epub (January 15, 2005).
    Listed reading
  • Ptacek, J., G. Devgan, G. Michaud, H. Zhu, X. Zhu, J. Fasolo, H. Guo, G. Jona, A. Breitkreutz, R. Sopko, R. R. McCartney, M. C. Schmidt, N. Rachidi, S. J. Lee, A. S. Mah, L. Meng, M. J. Stark, D. F. Stern, C. De Virgilio, M. Tyers, B. Andrews, M. Gerstein, B. Schweitzer, P. F. Predki, and M. Snyder. “Global analysis of protein phosphorylation in yeast.” Nature 438, no. 7068 (December 1, 2005): 679-84.
    Listed reading
  • Somiari, R. I., A. Sullivan, S. Russell, S. Somiari, H. Hu, R. Jordan, A. George, R. Katenhusen, A. Buchowiecka, C. Arciero, H. Brzeski, J. Hooke, and C. Shriver. “High-throughput proteomic analysis of human infiltrating ductal carcinoma of the breast.” Proteomics 3, no. 10 (October 2003): 1863-73.
    Listed reading
  • Kolkman, A., E. H. Dirksen, M. Slijper, and A. J. Heck. “Double standards in quantitative proteomics: direct comparative assessment of difference in gel electrophoresis and metabolic stable isotope labeling.” Mol Cell Proteomics 4, no. 3 (March 2005): 255-66; Epub (January 4, 2005).
    Listed reading
  • Patton, W. F. “A thousand points of light: the application of fluorescence detection technologies to two-dimensional gel electrophoresis and proteomics.” Electrophoresis 21, no. 6 (April 2000): 1123-44.
    Listed reading
  • Glish, G. L., R. W. Vachet. “The basics of mass spectrometry in the twenty-first century.” Nat Rev Drug Discov 2, no. 2 (February 2003): 140-50.
    Listed reading
  • Bhat, V. B., M. H. Choi, J. S. Wishnok, and S. R. Tannenbaum. “Comparative plasma proteome analysis of lymphoma-bearing SJL mice.” J Proteome Res 4, no. 5 (September-October, 2005): 1814-25.
    Listed reading
  • Hoffmann, A., A. Levchenko, M. L. Scott, and D. Baltimore. “The IkappaB-NF-kappaB signaling module: temporal control and selective gene activation.” Science 298, no. 5596 (November 8, 2002): 1241-5.
    Listed reading
  • Aggarwal, B. B. “Nuclear factor-kappaB: the enemy within.” Cancer Cell 6, no. 3 (September 2004): 203-8.
    Listed reading
  • Ting, A. Y., and D. Endy. “Signal transduction. Decoding NF-kappaB signaling.” Science 298, no. 5596 (November 8, 2002): 1189-90.
    Listed reading
  • Saghatelian, A., and B. F. Cravatt. “Global strategies to integrate the proteome and metabolome.” Curr Opin Chem Biol 9, no. 1 (February 2005): 62-8.
    Listed reading
  • Saghatelian, A., S. A. Trauger, E. J. Want, E. G. Hawkins, G. Siuzdak, and B. F. Cravatt. “Assignment of endogenous substrates to enzymes by global metabolite profiling.” Biochemistry 43, no. 45 (November 16, 2004): 14332-9.
    Listed reading
  • Nicholson, J. K., J. Connelly, J. C. Lindon, and E. Holmes. “Metabonomics: a platform for studying drug toxicity and gene function.” Nat Rev Drug Discov 1, no. 2 (February 2002): 153-61.
    Listed reading
  • Mortishire-Smith, R. J., G. L. Skiles, J. W. Lawrence, S. Spence, A. W. Nicholls, B. A. Johnson, and J. K. Nicholson. “Use of metabonomics to identify impaired fatty acid metabolism as the mechanism of a drug-induced toxicity.” Chem Res Toxicol 17, no. 2 (February 2004): 165-73.
    Listed reading
  • Lindon, J. C., E. Holmes, and J. K. Nicholson. “So what’s the deal with metabonomics?” Anal Chem 75, no. 17 (September 1, 2003): 384A-391A.
    Listed reading
  • Martinson, B. C., M. S. Anderson, and R. de Vries. “Scientists behaving badly.” Nature 435, no. 7043 (June 9, 2005): 737-8.
    Listed reading
  • Grinnell, F. “Misconduct: acceptable practices differ by field.” Nature 436, no. 7052 (August 11, 2005): 776.
    Listed reading
  • Taylor, I. “Academia’s ‘misconduct’ is acceptable to industry.” Nature 436, no. 7051 (August 4, 2005): 626.
    Listed reading
  • Clouthier, S. G. “Misconduct: lower ranks take most of the blame.” Nature 436, 7050 (July 28, 2005): 460.
    Listed reading
  • Wadman, M. “One in three scientists confesses to having sinned.” Nature 435, no. 7043 (June 9, 2005): 718-9.
    Listed reading
  • Deichmann, U., and B. Muller-Hill. “The fraud of Abderhalden’s enzymes.” Nature 393, no. 6681 (May 14, 1998): 109-11.
    Listed reading
  • Bonetta, Laura, ed. “Mentoring and Being Mentored.” Chapter 5 in Making the Right Moves: A Practical Guide to Scientific Management for Postdocs and New Faculty . Chevy Chase, Maryland: Howard Hughes Medical Institute and Research; Triangle Park, North Carolina: Burroughs Wellcome Fund, 2004. ↗
    Listed reading
  • Editors of the Publications Division of the American Chemical Society. “ Ethical Guidelines to Publication of Chemical Research .” American Chemical Society (January, 2000).
    Listed reading
  • Important Questions for Collaborations. Template developed by the NIH Ombudsman for establishing collaborations . ↗
    Listed reading
  • Publication practices, authorship, peer-review, and collaborations. NIH Web site on Ethical Conduct . ↗
    Listed reading
  • Branda, C. S., and S. M. Dymecki. “Talking about a revolution: The impact of site-specific recombinases on genetic analyses in mice.” Dev Cell 6, no. 1 (January 2004): 7-28.
    Listed reading
  • Andreu, P., S. Colnot, C. Godard, S. Gad, P. Chafey, M. Niwa-Kawakita, P. Laurent-Puig, A. Kahn, S. Robine, C. Perret, and B. Romagnolo. “Crypt-restricted proliferation and commitment to the Paneth cell lineage following Apc loss in the mouse intestine.” Development 132, no. 6 (March 2005): 1443-51; Epub (February 16, 2005).
    Listed reading
  • Kucherlapati, M. H., A. A. Nguyen, R. T. Bronson, and R. S. Kucherlapati. “Inactivation of conditional Rb by Villin-Cre leads to aggressive tumors outside the gastrointestinal tract.” Cancer Res 66, no. 7 (April 1, 2006): 3576-83.
    Listed reading
  • Gillespie, J. W., G. Gannot, M. A. Tangrea, M. Ahram, C. J. Best, V. E. Bichsel, E. F. Petricoin, M. R. Emmert-Buck, and R. F. Chuaqui. “Molecular profiling of cancer.” Toxicol Pathol 32, no. 1 (March-April, 2004): 67-71. (Supplement)
    Listed reading
  • Kunz, G. M., Jr., and D. W. Chan. “The use of laser capture microscopy in proteomics research-a review.” Dis Markers 20, no. 3 (2004): 155-60.
    Listed reading
  • Petricoin, E. F., K. C. Zoon, E. C. Kohn, J. C. Barrett, and L. A. Liotta. “Clinical proteomics: translating benchside promise into bedside reality.” Nat Rev Drug Discov 1, no. 9 (September 2002): 683-95.
    Listed reading
  • Paweletz, C. P., L. Charboneau, V. E. Bichsel, N. L. Simone, T. Chen, J. W. Gillespie, M. R. Emmert-Buck, M. J. Roth, E. F. Petricoin, III, and L. A. Liotta. “Reverse phase protein microarrays which capture disease progression show activation of pro-survival pathways at the cancer invasion front.” Oncogene 20, no. 16 (April 12, 2001): 1981-9.
    Listed reading
  • Sivaraman, A., J. K. Leach, S. Townsend, T. Iida, B. J. Hogan, D. B. Stolz, R. Fry, L. D. Samson, S. R. Tannenbaum, L. G. Griffith. “A microscale in vitro physiological model of the liver: predictive screens for drug metabolism and enzyme induction.” Curr Drug Metab 6, no. 6 (December 2005): 569-91.
    Listed reading
  • Griffith, L. G., and M. A. Swartz. “Capturing complex 3D tissue physiology in vitro.” Nat Rev Mol Cell Biol 7, no. 3 (March 2006): 211-24.
    Listed reading

Prerequisites & course information

Same subject as 10.53[J] Subject meets with 7.458[J] , 10.03[J] Prereq: None G (Spring; second half of term) 1-0-2 units

Sources