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20.106

Applied Microbiology

3-0-9 units · Undergraduate

Introductory microbiology from a systems perspective - considers microbial diversity and the integration of data from a molecular, cellular, organismal, and ecological context to understand the interaction of microbial organisms with their environment. Special emphasis on specific viral, bacterial, and eukaryotic microorganisms and their interaction with animal hosts with focus on contemporary problems in areas such as vaccination, emerging disease, antimicrobial drug resistance, and toxicology.

Fall 2006 · Systems Microbiology

This course covers introductory microbiology from a systems perspective, considering microbial diversity, population dynamics, and genomics. Emphasis is placed on the delicate balance between microbes and humans, and the changes that result in the emergence of infectious diseases and antimicrobial resistance. The case study approach covers such topics as vaccines, toxins, biodefense, and infections including Legionnaire’s disease, tuberculosis, Helicobacter pylori, and plague.

Readings

  • Many of the readings come from the course textbook, “Brock”: Madigan, Michael, and John Martinko. Brock Biology of Microorganisms . 11th ed. Upper Saddle River, NJ: Pearson Prentice Hall, 2005. ISBN: 9780131443297.
    Listed reading
  • LEC #: 1 · TOPICS: Early Earth/Microbial Evolution · LECTURERS: Prof. Ed DeLong · READINGS: Chapter 11 in Brock
    Reading assignment
  • LEC #: 2 · TOPICS: Cell Structure/Function · LECTURERS: Prof. Ed DeLong · READINGS: Chapter 4 in Brock
    Reading assignment
  • LEC #: 3 · TOPICS: Biological Energy Conservation · LECTURERS: Prof. Ed DeLong · READINGS: Chapters 5 and 17 in Brock
    Reading assignment
  • LEC #: 4 · TOPICS: Microbial Growth · LECTURERS: Prof. David Schauer · READINGS: Chapter 6 in Brock
    Reading assignment
  • LEC #: 6 · TOPICS: Virology · LECTURERS: Prof. David Schauer · READINGS: Chapter 9 in Brock
    Reading assignment
  • LEC #: 7 · TOPICS: Information Flow in Biological Systems · LECTURERS: Prof. Ed DeLong · READINGS: Chapter 10 in Brock
    Reading assignment
  • LEC #: 8 · TOPICS: Regulation of Cell Activity · LECTURERS: Prof. Ed DeLong · READINGS: Chapter 8 in Brock
    Reading assignment
  • LEC #: 10 · TOPICS: Experimental Evolution: Optimization of Metabolic Systems · LECTURERS: Guest Lecturer, Prof. Christopher Marx from Harvard · READINGS: Marx, Christopher J., Stephen J. Van Dien, and Mary E. Lidstrom. “Flux Analysis Uncovers Key Role of Functional Redundancy in Formaldehyde Metabolism.” PLOS Biology 3 (2005): 244-253. ( PDF ) ↗
    Reading assignment
  • LEC #: 11 · TOPICS: Genomics I · LECTURERS: Prof. Ed DeLong · READINGS: Chapter 15 in Brock
    Reading assignment
  • LEC #: 12 · TOPICS: Genomics II · LECTURERS: Prof. Ed DeLong · READINGS: Chapter 15 in Brock
    Reading assignment
  • LEC #: 13 · TOPICS: Metabolic Diversity I · LECTURERS: Prof. Ed DeLong · READINGS: Chapter 17 in Brock
    Reading assignment
  • LEC #: 14 · TOPICS: Metabolic Diversity II · LECTURERS: Prof. Ed DeLong · READINGS: Chapter 17 in Brock
    Reading assignment
  • LEC #: 15 · TOPICS: Microbial Ecology · LECTURERS: Prof. Ed DeLong · READINGS: Chapter 19 in Brock
    Reading assignment
  • LEC #: 16 · TOPICS: Microbial Growth Control · LECTURERS: Prof. David Schauer · READINGS: Chapter 20 in Brock
    Reading assignment
  • Chapter 21 in Brock
    Listed reading
  • Backhed, Fredrik, et al. “Host-Bacterial Mutualism in the Human Intestine.” Science 307 (2005): 1915-1920.
    Listed reading
  • LEC #: 18 · TOPICS: Immunology I · LECTURERS: Megan McBee · READINGS: Chapters 22 and 23 in Brock
    Reading assignment
  • LEC #: 20 · TOPICS: Diagnostic Microbiology · LECTURERS: Prof. David Schauer · READINGS: Chapters 21 and 24 in Brock
    Reading assignment
  • LEC #: 21 · TOPICS: Person-to-person Transmission · LECTURERS: Prof. David Schauer · READINGS: Chapter 25 in Brock
    Reading assignment
  • LEC #: 22 · TOPICS: Epidemiology · LECTURERS: Megan McBee · READINGS: Chapter 26 in Brock
    Reading assignment
  • LEC #: 23 · TOPICS: Animal- and Arthropod-transmitted Diseases · LECTURERS: Prof. David Schauer · READINGS: Chapter 27 in Brock
    Reading assignment
  • LEC #: 24 · TOPICS: Review · LECTURERS: Prof. David Schauer · READINGS: Chapters 28 and 29 in Brock
    Reading assignment
  • Berg, Howard. “ Motile Behavior of Bacteria .” Physics Today on the Web (January 2000). ↗
    Listed reading
  • Galan, Jorge E., and Hans Wolf-Watz. “Protein Delivery into Eukaryotic Cells by Type III Secretion Machines.” Nature 444 (2006): 567-573.
    Listed reading
  • Jetten, Mike S. M., et al. “Microbiology and Application of the Anaerobic Ammonium Oxidation (‘Anammox’) Process.” Environmental Biotechnology 12 (2001): 283-288.
    Listed reading
  • Lovley, Derek R. “Bug Juice: Harvesting Electricity with Microorganisms.” Nature Reviews Microbiology 4 (2006): 497-508.
    Listed reading
  • Marx, Christopher J., Stephen J. Van Dien, and Mary E. Lidstrom. “Flux Analysis Uncovers Key Role of Functional Redundancy in Formaldehyde Metabolism.” PLOS Biology 3 (2005): 244-253. ( PDF ) ↗
    Listed reading
  • Moran, Nancy A., Fordon R. Plague, Jonas P. Sandstro, and Jennifer L. Wilcox. “A Genomic Perspective on Nutrient Provisioning by Bacterial Symbionts of Insects.” PNAS 100 (2003): 14543-14548.
    Listed reading
  • Nakabachi, Atsushi, et al. “The 160-Kilobase Genome of the Bacterial Endosymbiont Carsonella.” Science 314 (2006): 267.
    Listed reading
  • Pace, Norman R. “Time for a Change.” Nature 441 (2006): 289.
    Listed reading
  • Purcell, E. M. “Life at Low Reynolds Number.” American Journal of Physics 45 (1977): 3-11.
    Listed reading
  • Santiago, F. Elena, and Richard E. Lenski. “Evolution Experiments with Microorganisms: The Dynamics and Genetic Bases of Adaptation.” Nature Reviews Genetics 4 (2003): 457-469.
    Listed reading
  • Tamas, Ivica, et al. “50 Million Years of Genomic Stasis in Endosymbiotic Bacteria.” Science 296 (2002): 2376-2379.
    Listed reading
  • Wu, Dongying, et al. “Metabolic Complementarity and Genomics of the Dual Bacterial Symbiosis of Sharpshooters.” PLOS Biology 4 (2006): 1079-1092. ( PDF - 1.0 MB ) ↗
    Listed reading
  • Madigan, Michael, and John Martinko. Brock Biology of Microorganisms . 11th ed. Upper Saddle River, NJ: Pearson Prentice Hall, 2005. ISBN: 9780131443297.
    Listed reading

Prerequisites & course information

Same subject as 1.084[J] Prereq: Biology (GIR) and Chemistry (GIR) U (Fall) 3-0-9 units

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