by Carl Zimmer
Cascales, E., S. K. Buchanan, D. Duche, C. Kleanthous, R. Lloubes, K. Postle, M. Riley, S. Slatin, and D. Cavard. 2007. Colicin biology. Microbiol Mol Biol Rev 71 (1):158-229.
Cavalieri, L. F. 1976. New strains of life—or death. New York Times Magazine, August 22, 1976.
Chang, D. E., D. J. Smalley, and T. Conway. 2002. Gene expression profiling of Escherichia coli growth transitions: An expanded stringent response model. Mol Microbiol 45 (2):289-306.
Chang, M. C., and J. D. Keasling. 2006. Production of isoprenoid pharmaceuticals by engineered microbes. Nat Chem Biol 2 (12):674-81.
Chargaff, E., and F. R. Simring. 1976. On the dangers of genetic meddling. Science 192 (4243):938.
Chen, S. L., C. S. Hung, J. Xu, C. S. Reigstad, V. Magrini, A. Sabo, D. Blasiar, T. Bieri, R. R. Meyer, P. Ozersky, J. R. Armstrong, R. S. Fulton, J. P. Latreille, J. Spieth, T. M. Hooton, E. R. Mardis, S. J. Hultgren, and J. I. Gordon. 2006. Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: A comparative genomics approach. Proc Natl Acad Sci USA 103 (15):5977-82.
Chong, Jia-Rui. 2006. 13th century text hides words of Archimedes. Los Angeles Times, December 26, 2006.
Chou, C. P. 2007. Engineering cell physiology to enhance recombinant protein production in Escherichia coli. Appl Microbiol Biotechnol, in press.
Ciccarelli, Francesca D., Tobias Doerks, Christian von Mering, Christopher J. Creevey, Berend Snel, and Peer Bork. 2006. Toward automatic reconstruction of a highly resolved tree of life. Science 311 (5765):1283-87.
Cirz, R. T., J. K. Chin, D. R. Andes, V. de Crécy-Lagard, W. A. Craig, and F. E. Romesberg. 2005. Inhibition of mutation and combating the evolution of antibiotic resistance. PLoS Biol 3 (6):e176.
Clarke, T. 2001. The stowaways. Nature 413 (6853):247-48.
Clinton, W. J. 2000. Speech by President on Completion of First Survey of Entire Human Genome. http://www.clintonpresidentialcenter.org; accessed October 24, 2007.
Cosentino Lagomarsino, M., P. Jona, B. Bassetti, and H. Isambert. 2007. Hierarchy and feedback in the evolution of the Escherichia coli transcription network. Proc Natl Acad Sci USA 104 (13):5516-20.
Crabb, W. D., and J. K. Shetty. 1999. Commodity scale production of sugars from starches. Curr Opin Microbiol 2 (3):252-56.
Crozat, E., N. Philippe, R. E. Lenski, J. Geiselmann, and D. Schneider. 2005. Long-term experimental evolution in Escherichia coli. XII. DNA topology as a key target of selection. Genetics 169 (2):523-32.
Csete, M., and J. Doyle. 2004. Bow ties, metabolism and disease. Trends Biotechnol 22 (9):446-50.
Davis, Rowland H. 2003. The microbial models of molecular biology: From genes to genomes. New York: Oxford University Press.
Delbrück, M. 1954. On the replication of desoxyribonucleic acid (DNA). Proc Natl Acad Sci USA 40:783-88.
———. 1969. Nobel lecture. http://nobelprize.org/nobel_prizes/medicine/laureates/1969/delbruck-lecture.htm.
Demerec, M. 1948. Origin of bacterial resistance to antibiotics. J Bacteriol 56 (1):63-74.
Denamur, E., O. Tenaillon, C. Deschamps, D. Skurnik, E. Ronco, J. L. Gaillard, B. Picard, C. Branger, and I. Matic. 2005. Intermediate mutation frequencies favor evolution of multidrug resistance in Escherichia coli. Genetics 171 (2):825-27.
Dethlefsen, L., P. B. Eckburg, E. M. Bik, and D. A. Relman. 2006. Assembly of the human intestinal microbiota. Trends Ecol Evol 21 (9):517-23.
Dick, Steven J. 1998. Life on other worlds: The twentieth-century extraterrestrial life debate. New York: Cambridge University Press.
Dick, Steven J., and James Edgar Strick. 2004. The living universe: NASA and the development of astrobiology. New Brunswick, N.J.: Rutgers University Press.
Dolman, Claude E. 1970. Theodor Escherich. In Dictionary of scientific biography, ed. C. C. Gillispie. New York: Scribner.
Domka, J., J. Lee, T. Bansal, and T. K. Wood. 2007. Temporal gene-expression in Escherichia coli K-12 biofilms. Environ Microbiol 9 (2):332-46.
Doolittle, W. F. 2000. Uprooting the tree of life. Sci Am 282 (2):90-95.
Doyle, J., D. L. Alderson, L. Li, S. Low, M. Roughan, S. Shalunov, R. Tanaka, and W. Willinger. 2005. The “robust yet fragile” nature of the Internet. Proc Natl Acad Sci USA 102 (41):14497-502.
Doyle, J., and M. Csete. 2005. Motifs, control, and stability. PLoS Biol 3 (11):e392.
Dutton, Diana Barbara, Thomas A. Preston, and Nancy E. Pfund. 1988. Worse than the disease: Pitfalls of medical progress. New York: Cambridge University Press.
Echols, Harrison. 2001. Operators and promoters: The story of molecular biology and its creators. Ed. Carol Gross. Berkeley: University of California Press.
Elena, S. F., and R. E. Lenski. 2003. Evolution experiments with microorganisms: The dynamics and genetic bases of adaptation. Nat Rev Genet 4 (6):457-69.
Elf, J., G. W. Li, and X. S. Xie. 2007. Probing transcription factor dynamics at the single-molecule level in a living cell. Science 316 (5828):1191-94.
Elliott, E. J., and R. M. Robins-Browne. 2005. Hemolytic uremic syndrome. Curr Probl Pediatr Adolesc Health Care 35 (8):310-30.
Elowitz, M. B., and S. Leibler. 2000. A synthetic oscillatory network of transcriptional regulators. Nature 403 (6767):335-38.
Elowitz, M. B., A. J. Levine, E. D. Siggia, and P. S. Swain. 2002. Stochastic gene expression in a single cell. Science 297 (5584):1183-86.
Endy, D. 2005. Foundations for engineering biology. Nature 438 (7067):449-53.
Escherich, T. 1989. The intestinal bacteria of the neonate and breast-fed infant. 1885. Rev Infect Dis 11 (2):352-56.
ETC Group. 2006. Global coalition sounds the alarm on synthetic biology, demands oversight and societal debate. Press release. http://www.etcgroup.org/upload/publication/8/01/nr_synthetic_bio_19th_may_2006.pdf.
Evans, P. D., N. Mekel-Bobrov, E. J. Vallender, R. R. Hudson, and B. T. Lahn. 2006. Evidence that the adaptive allele of the brain size gene microcephalin introgressed into Homo sapiens from an archaic Homo lineage. Proc Natl Acad Sci USA 103 (48):18178-83.
Favier, C. F., E. E. Vaughan, W. M. De Vos, and A. D. Akkermans. 2002. Molecular monitoring of succession of bacterial communities in human neonates. Appl Environ Microbiol 68 (1):219-26.
Feist, Adam M., Christopher S. Henry, Jennifer L. Reed, Markus Krummenacker, Andrew R. Joyce, Peter D. Karp, Linda J. Broadbelt, Vassily Hatzimanikatis, and Bernhard O. Palsson. 2007. A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol Syst Biol 3:121.
Ferens, W. A., R. Cobbold, and C. J. Hovde. 2006. Intestinal Shiga toxin–producing Escherichia coli bacteria mitigate bovine leukemia virus infection in experimentally infected sheep. Infect Immun 74 (5):2906-16.
Forster, A. C., and G. M. Church. 2006. Towards synthesis of a minimal cell. Mol Syst Biol 2:45.
Foster, J. W. 2004. Escherichia coli acid resistance: Tales of an amateur acidophile. Nat Rev Microbiol 2 (11):898-907.
Foster, K. R., K. Parkinson, and C. R. Thompson. 2007. What can microbial genetics teach sociobiology? Trends Genet 23 (2):74-80.
Francino, M. P. 2005. An adaptive radiation model for the origin of new gene functions. Nat Genet 37 (6):573-77.
Fricker, E. J., M. Spigelman, and C. R. Fricker. 1997. The detection of Escherichia coli DNA in the ancient remains of Lindow Man using the polymerase chain reaction. Lett Appl Microbiol 24 (5):351-54.
Friedmann, H. C. 2004. From Butyribacterium to E. coli: An essay on unity in biochemistry. Perspect Biol Med 47 (1):47-66.
Frost, L. S., R. Leplae, A. O. Summers, and A. Toussaint. 2005. Mobile genetic elements: The agents of open source evolution. Nat Rev Microbiol 3 (9):722-32.
Gamage, S. D., A. K. Patton, J. F. Hanson, and A. A. Weiss. 2004. Diversity and host range of Shiga toxin–encoding phage. Infect Immun 72 (12):7131-39.
Gamage, S. D., A. K. Patton, J. E. Strasser, C. L. Chalk, and A. A. Weiss. 2006. Commensal bacteria influence Escherichia coli O157:H
7 persistence and Shiga toxin production in the mouse intestine. Infect Immun 74 (3):1977-83.
Gamage, S. D., J. E. Strasser, C. L. Chalk, and A. A. Weiss. 2003. Nonpathogenic Escherichia coli can contribute to the production of Shiga toxin. Infect Immun 71 (6):3107-15.
Gardner, A., S. A. West, and A. Buckling. 2004. Bacteriocins, spite and virulence. Proc Biol Sci 271 (1547):1529-35.
Gardner, T. S., C. R. Cantor, and J. J. Collins. 2000. Construction of a genetic toggle switch in Escherichia coli. Nature 403 (6767):339-42.
Ge, F., L. S. Wang, and J. Kim. 2005. The cobweb of life revealed by genome-scale estimates of horizontal gene transfer. PLoS Biol 3 (10):e316.
Gelman, S.A. 2004. Psychological essentialism in children. Trends Cogn Sci 8 (9):404-9.
George, R. P., and A. Gomez-Lobo. 2005. The moral status of the human embryo. Perspect Biol Med 48 (2):201-10.
Gesteland, Raymond F., Thomas Cech, and John F. Atkins. 2006. The RNA world: The nature of modern RNA suggests a prebiotic RNA. 3rd ed. Cold Spring Harbor Monograph Series 43. Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press.
Ghannoum, Mahmoud A., and George A. O’Toole. 2004. Microbial biofilms. Washington, D.C.: ASM Press.
Gladman, B., L. Dones, H. F. Levison, and J.A. Burns. 2005. Impact seeding and reseeding in the inner solar system. Astrobiology 5 (4):483-96.
Goehring, N. W., and J. Beckwith. 2005. Diverse paths to midcell: Assembly of the bacterial cell division machinery. Curr Biol 15 (13):R514-26.
Gorvel, J.P. 2006. Microbiology: Bacterial bushwacking through a microtubule jungle. Science 314 (5801):931-32.
Gould, Stephen Jay. 1989. Wonderful life: The Burgess Shale and the nature of history. New York: W. W. Norton.
Graham, J. P., J. J. Boland, and E. Silbergeld. 2007. Growth-promoting antibiotics in food animal production: An economic analysis. Public Health Reports 122 (1):79-87.
Gray, C. H., and E. L. Tatum. 1944. X-ray induced growth factor requirements in bacteria. Proc Natl Acad Sci USA 30 (12):404-10.
Haldane, J.B.S. 1923. Daedalus; or, Science and the future: A paper read to the Heretics, Cambridge, on February 4th, 1923. http://www.cscs.umich.edu/~crshalizi/Daedalus.htm; accessed October 24, 2007.
Hall, Stephen S. 2002. Invisible frontiers: The race to synthesize a human gene. New York: Oxford University Press.
Harold, F. M. 2005. Molecules into cells: Specifying spatial architecture. Microbiol Mol Biol Rev 69 (4):544-64.
Hartwig, Mark. 2002. Whose comfortable myth? Focus on the Family, June 2002.
Heitkamp, M. A., J. F. Kane, P. J. Morris, M. Bianchini, M. D. Hale, and G. Bogosian. 1993. Fate in sewage of a recombinant Escherichia coli K-12 strain used in the commercial production of bovine somatotropin. J Ind Microbiol 11 (4): 243-52.
Hejnova, J., U. Dobrindt, R. Nemcova, C. Rusniok, A. Bomba, L. Frangeul, J. Hacker, P. Glaser, P. Sebo, and C. Buchrieser. 2005. Characterization of the flexible genome complement of the commensal Escherichia coli strain A0 34/86 (O83:K24:H31). Microbiology 151 (pt. 2):385-98.
Herring, C. D., A. Raghunathan, C. Honisch, T. Patel, M. K. Applebee, A. R. Joyce, T. J. Albert, F. R. Blattner, D. van den Boom, C. R. Cantor, and B. O. Palsson. 2006. Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale. Nat Genet 38 (12):1406-12.
Hershey, A. D., and M. Chase. 1952. Independent functions of viral protein and nucleic acid in growth of bacteriophage. J Gen Physiol 36 (1):39-56.
Higgins, Norman Patrick. 2005. The bacterial chromosome. Washington, D.C.: ASM Press.
Holmes, Frederick Lawrence. 2001. Meselson, Stahl, and the replication of DNA: A history of the “most beautiful experiment in biology.” New Haven: Yale University Press.
Hou, Shaobin, Jimmy H. Saw, Kit Shan Lee, Tracey A. Freitas, Claude Belisle, Yutaka Kawarabayasi, Stuart P. Donachie, Alla Pikina, Michael Y. Galperin, Eugene V. Koonin, Kira S. Makarova, Marina V. Omelchenko, Alexander Sorokin, Yuri I. Wolf, Qing X. Li, Young Soo Keum, Sonia Campbell, Judith Denery, Shin-Ichi Aizawa, Satoshi Shibata, Alexander Malahoff, and Maqsudul Alam. 2004. Genome sequence of the deep-sea ?-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy. Proc Natl Acad Sci USA 101 (52):18036-41.
Humes, Edward. 2007. Monkey girl: Evolution, education, religion, and the battle for America’s soul. New York: Ecco.
Inoue, T., R. Shingaki, S. Hirose, K. Waki, H. Mori, and K. Fukui. 2007. Genome-wide screening of genes required for swarming motility in Escherichia coli K-12. J Bacteriol 189(3):950-57.
Jackson, David Archer, and Stephen P. Stich. 1979. The recombinant DNA debate. Englewood Cliffs, N.J.: Prentice-Hall.
Jacob, François. 1995. The statue within: An autobiography. Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press.
Jennison, A. V., and N. K. Verma. 2004. Shigella flexneri infection: Pathogenesis and vaccine development. FEMS Microbiol Rev 28 (1):43-58.
Jones, Nancy. 2006. Round three—“mixing and matching” biological building blocks: Mouse-human chimeras are here! Center for Bioethics and Human Dignity. http://www.cbhd.org/resources/biotech/jones_2006-01-20.htm.
Jones, Shari A., F. A. Chowdhury, et al. 2007. Respiration of Escherichia coli in the mouse intestine. Infect Immun 75:4891-99.
Judson, Horace Freeland. 1996. The eighth day of creation: Makers of the revolution in biology. Expanded ed. Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press.
Jun, S., and B. Mulder. 2006. Entropy-driven spatial organization of highly confined polymers: Lessons for the bacterial chromosome. Proc Natl Acad Sci USA 103 (33):12388-93.
Kalir, S., S. Mangan, and U. Alon. 2005. A coherent feed-forward loop with a SUM input function prolongs flagella expression in Escherichia coli. Mol Syst Biol 1:2005.0006.
Kaper, J. B. 2005. Pathogenic Escherichia coli. Int J Med Microbiol 295 (6-7):355-56.
Karch, H., P. I. Tarr, and M. Bielaszewska. 2005. Enterohaemorrhagic Escherichia coli in human medicine. Int J Med Microbiol 295 (6-7):405-18.
Karp, P. D., I. M. Kessler, A. Shearer, et al. 2007. Multidimensional annotation of the Escherichia coli. K-12 genome. Nucleic Acids Res 35:7577-90.
Kass, Leon. 1997. National Bioethics Advisory Commission. Testimony of March 14. CyberCemetery. University of North Texas Libraries. http://govinfo.library.unt.edu/nbac/transcripts/1997/3-14-97.pdf.
Kass, Leon, and James Q. Wilson. 1998. The ethics of human cloning. Washington, D.C.: AEI Press.
Kerr, B., M.A. Riley, M.W. Feldman, and B.J. Bohannan. 2002. Local dispersal promotes biodiversity in a real-life game of rock-paper-scissors. Nature 418 (6894):171-74.
Kirkup, B. C., and M. A. Riley. 2004. Antibiotic-mediated antagonism leads to a bacterial game of rock-paper-scissors in vivo. Nature 428 (6981):412-14.
Kobayashi, I. 2001. Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution. Nucleic Acids Res 29 (18):3742-56.
Krawinkel, M.B. 2007. What we know and don’t know about Golden Rice. Nat Biotechnol 25 (6):623.
Krimsky, Sheldon. 1982. Genetic alchemy: The social history of the recombinant DNA controversy. Cambridge, Mass.: MIT Press.
Kropotkin, Petr Alekseevich. 1919. Mutual aid: A factor of evolution. New York: Alfred A. Knopf.
Kurata, H., H. El-Samad, R. Iwasaki, H. Ohtake, J. C. Doyle, I. Grigorova, C. A. Gross, and M. Khammash. 2006. Module-based analysis of robustness tradeoffs in the heat shock response system. PLoS Comput Biol 2 (7):e59.
Kussell, E., R. Kishony, N. Q. Balaban, and S. Leibler. 2005. Bacterial persistence: A model of survival in changing environments. Genetics 169 (4):1807-14.
La Duc, M. T., K. Venkateswaran, R. Sumner, and D. Pierson. 2004. Characterization and monitoring of microbes in the international space station drinking water. Beacon eSpace. Jet Propulsion Laboratory. http://hdl.handle.net/2014/37245.
Lamarck, Jean Baptiste Pierre Antoine de Monet de. 1984. Zoologi
cal philosophy: An exposition with regard to the natural history of animals. Chicago: University of Chicago Press.
Lambert, C., K. J. Evans, R. Till, L. Hobley, M. Capeness, S. Rendulic, S. C. Schuster, S. Aizawa, and R. E. Sockett. 2006. Characterizing the flagellar filament and the role of motility in bacterial prey-penetration by Bdellovibrio bacteriovorus. Mol Microbiol 60 (2):274-86.
Lawrence, J. G., and H. Ochman. 1998. Molecular archaeology of the Escherichia coli genome. Proc Natl Acad Sci USA 95 (16):9413-17.
Lawrence, S. 2007a. Agbiotech booms in emerging nations. Nat Biotechnol 25 (3):271.
———. 2007b. State of the biotech sector—2006. Nat Biotechol 25:706.
Lederberg, J. 1946. Bacterial genetics. Joshua Lederberg: Biomedical Science and the Public Interest. National Library of Medicine. http://profiles.nlm.nih.gov/hmd/lederberg/bacterial/html.
———. 1960. Exobiology: Approaches to life beyond the earth. Science 132 (3424):393-400.
———. 1963. Life beyond Earth. Stanford Today, Winter.
———. 1987. Genetic recombination in bacteria: A discovery account. Annu Rev Genet 21:23-46.
Lederberg, J., and E. M. Lederberg. 1952. Replica plating and indirect selection of bacterial mutants. J Bacteriol 63 (3):399-406.
Lenski, R. 2003. The ecology, genetics and evolution of bacteria in an experimental setting. Curr Biol 13 (12):R466-67.
Lerat, E., V. Daubin, H. Ochman, and N. A. Moran. 2005. Evolutionary origins of genomic repertoires in bacteria. PLoS Biol 3 (5):e130.
Levskaya, A., A. A. Chevalier, J. J. Tabor, Z. B. Simpson, L. A. Lavery, M. Levy, E. A. Davidson, A. Scouras, A. D. Ellington, E. M. Marcotte, and C. A. Voigt. 2005. Synthetic biology: Engineering Escherichia coli to see light. Nature 438 (7067):441-42.
Levy, Stuart B. 2002. The antibiotic paradox: How the misuse of antibiotics destroys their curative powers. 2nd ed. Cambridge, Mass.: Perseus.
Lewis, K. 2005. Persister cells and the riddle of biofilm survival. Biochemistry (Mosc) 70 (2):267-74.
———. 2007. Persister cells, dormancy, and infectious disease. Nat Rev Microbiol 5 (1):48-56.
Lim, H. N., and A. van Oudenaarden. 2007. A multistep epigenetic switch enables the stable inheritance of DNA methylation states. Nat Genet 39 (2):269-75.
