Systems Microbiology

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.

LEC #	TOPICS	LECTURERS	READINGS
1	Early Earth/Microbial Evolution	Prof. Ed DeLong	Chapter 11 in Brock
2	Cell Structure/Function	Prof. Ed DeLong	Chapter 4 in Brock
3	Biological Energy Conservation	Prof. Ed DeLong	Chapters 5 and 17 in Brock
4	Microbial Growth	Prof. David Schauer	Chapter 6 in Brock
5	Metabolic Regulation	Prof. Ed DeLong
6	Virology	Prof. David Schauer	Chapter 9 in Brock
7	Information Flow in Biological Systems	Prof. Ed DeLong	Chapter 10 in Brock
	Midterm I
8	Regulation of Cell Activity	Prof. Ed DeLong	Chapter 8 in Brock
9	Genetic Exchange in Bacteria	Prof. Ed DeLong
10	Experimental Evolution: Optimization of Metabolic Systems	Guest Lecturer, Prof. Christopher Marx from Harvard	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)
11	Genomics I	Prof. Ed DeLong	Chapter 15 in Brock
12	Genomics II	Prof. Ed DeLong	Chapter 15 in Brock
13	Metabolic Diversity I	Prof. Ed DeLong	Chapter 17 in Brock
14	Metabolic Diversity II	Prof. Ed DeLong	Chapter 17 in Brock
15	Microbial Ecology	Prof. Ed DeLong	Chapter 19 in Brock
	Midterm II
16	Microbial Growth Control	Prof. David Schauer	Chapter 20 in Brock
17	Microbe-host Interactions	Prof. David Schauer	Chapter 21 in Brock Backhed, Fredrik, et al. “Host-Bacterial Mutualism in the Human Intestine.” Science 307 (2005): 1915-1920.
18	Immunology I	Megan McBee	Chapters 22 and 23 in Brock
19	Immunology II	Megan McBee
20	Diagnostic Microbiology	Prof. David Schauer	Chapters 21 and 24 in Brock
21	Person-to-person Transmission	Prof. David Schauer	Chapter 25 in Brock
22	Epidemiology	Megan McBee	Chapter 26 in Brock
23	Animal- and Arthropod-transmitted Diseases	Prof. David Schauer	Chapter 27 in Brock
24	Review	Prof. David Schauer	Chapters 28 and 29 in Brock
	Final Exam

Other Readings

Backhed, Fredrik, et al. “Host-Bacterial Mutualism in the Human Intestine.” Science 307 (2005): 1915-1920.

Berg, Howard. “Motile Behavior of Bacteria.” Physics Today on the Web (January 2000).

Galan, Jorge E., and Hans Wolf-Watz. “Protein Delivery into Eukaryotic Cells by Type III Secretion Machines.” Nature 444 (2006): 567-573.

Jetten, Mike S. M., et al. “Microbiology and Application of the Anaerobic Ammonium Oxidation (‘Anammox’) Process.” Environmental Biotechnology 12 (2001): 283-288.

Lovley, Derek R. “Bug Juice: Harvesting Electricity with Microorganisms.” Nature Reviews Microbiology 4 (2006): 497-508.

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)

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.

Nakabachi, Atsushi, et al. “The 160-Kilobase Genome of the Bacterial Endosymbiont Carsonella.” Science 314 (2006): 267.

Pace, Norman R. “Time for a Change.” Nature 441 (2006): 289.

Purcell, E. M. “Life at Low Reynolds Number.” American Journal of Physics 45 (1977): 3-11.

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.

Tamas, Ivica, et al. “50 Million Years of Genomic Stasis in Endosymbiotic Bacteria.” Science 296 (2002): 2376-2379.

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)