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Marshall, R. E., C. T. Caskey, and M. Nirenberg. 1967. Fine structure of RNA codewords recognized by bacterial, amphibian, and mammalian transfer RNA.
Science
155 (764):820-26.

Matz, C., and S. Kjelleberg. 2005. Off the hook—how bacteria survive protozoan grazing.
Trends Microbiol
13 (7):302-7.

Matz, C., D. McDougald, A. M. Moreno, P. Y. Yung, F. H. Yildiz, and S. Kjelleberg. 2005. Biofilm formation and phenotypic variation enhance predation-driven persistence of
Vibrio cholerae. Proc Natl Acad Sci USA
102 (46):16819-24.

McElheny, Victor. 1976. Hunt for evidence of life on Mars is still a puzzle.
New York Times,
August 11, 1976.

Meltz Steinberg, K., and B. R. Levin. 2007. Grazing protozoa and the evolution of the
Escherichia coli
O157:H7 Shiga toxin–encoding prophage.
Proc Biol Sci
274 (1621):1924-29.

Meselson, M., and F.W. Stahl. 1958. The replication of DNA in
Escherichia coli. Proc Nat Acad Sci USA
44:671-82.

Mettetal, J. T., D. Muzzey, J. M. Pedraza, E. M. Ozbudak, and A. van Oudenaarden. 2006. Predicting stochastic gene expression dynamics in single cells.
Proc Natl Acad Sci USA
103 (19):7304-9.

Michaelian, K. 2005. Thermodynamic stability of ecosystems.
J Theor Biol
237 (3):323-35.

Michod, R. E. 2007. Evolution of individuality during the transition from unicellular to multicellular life.
Proc Natl Acad Sci USA
104 (1):S8613-18.

Milo, R., S. Shen-Orr, S. Itzkovitz, N. Kashtan, D. Chklovskii, and U. Alon. 2002. Network motifs: Simple building blocks of complex networks.
Science
298 (5594):824-27.

Mira, A., R. Pushker, and F. Rodriguez-Valera. 2006. The Neolithic revolution of bacterial genomes.
Trends Microbiol
14 (5):200-206.

Morbey, Y. E., C. E. Brassil, and A. P. Hendry. 2005. Rapid senescence in Pacific salmon.
Am Nat
166 (5):556-68.

Mrak, P., Z. Podlesek, J. P. van Putten, and D. Zgur-Bertok. 2007. Heterogeneity in expression of the
Escherichia coli
colicin K activity gene cka is controlled by the SOS system and stochastic factors.
Mol Genet Genomics
277 (4):391–401.

Mulec, J., Z. Podlesek, P. Mrak, A. Kopitar, A. Ihan, and D. Zgur-Bertok. 2003. A cka-gfp transcriptional fusion reveals that the colicin K activity gene is induced in only 3 percent of the population.
J Bacteriol
185 (2):654-59.

Müller-Hill, Benno. 1996.
The
lac
operon: A short history of a genetic paradigm.
New York: Walter de Gruyter.

Myllykangas, S., J. Himberg, T. Böhling, B. Nagy, J. Hollmén, and S. Knuutila. 2006. DNA copy number amplification profiling of human neoplasms.
Oncogene
25 (55):7324-32.

Napier, W. M. 2004. A mechanism for interstellar panspermia.
Monthly Notices of the Royal Astronomical Society
348 (1):46-51.

Nash, J. M. 2000. Grains of hope.
Time,
July 31, 2000, 38-46.

National Academy of Sciences. 1977.
Research with recombinant DNA: An Academy Forum, March 7
?
9, 1977.
Washington, D.C.: National Academy of Sciences.

Naylor, S. W., D. L. Gally, and J. C. Low. 2005. Enterohaemorrhagic
E. coli
in veterinary medicine.
Int J Med Microbiol
295 (6-7):419-41.

Neidhardt, Frederick C. 1996. Escherichia coli
and
Salmonella:
Cellular and molecular biology.
2nd ed. Washington, D.C.: ASM Press.

Nicholson, J. K., E. Holmes, and I. D. Wilson. 2005. Gut microorganisms, mammalian metabolism and personalized health care.
Nat Rev Microbiol
3 (5):431-38.

Nielsen, K. M., and J. P. Townsend. 2004. Monitoring and modeling horizontal gene transfer.
Nat Biotechnol
22 (9):1110-14.

Noireaux, V., R. Bar-Ziv, J. Godefroy, H. Salman, and A. Libchaber. 2005. Toward an artificial cell based on gene expression in vesicles.
Phys Biol
2 (3):P1-8.

Nordenberg, T. 1999. Maker of growth hormone feels long arm of law.
FDA Consum
33 (5):33.

Norris, V., T. den Blaauwen, A. Cabin-Flaman, R. H. Doi, R. Harshey, L. Janniere, A. Jimenez-Sanchez, D. J. Jin, P. A. Levin, E. Mileykovskaya, A. Minsky, M. Saier Jr., and K. Skarstad. 2007. Functional taxonomy of bacterial hyperstructures.
Microbiol Mol Biol Rev
71 (1):230-53.

Novick, A., and M. Weiner. 1957. Enzyme induction as an all-or-none phenomenon.
Proc Natl Acad Sci USA
43 (7):553-66.

Nystrom, T. 2004. Stationary-phase physiology.
Annu Rev Microbiol
58:161-81.

O’Donnell, M. 2006. Replisome architecture and dynamics in
Escherichia coli. J Biol Chem
281 (16):10653-56.

Ostrowski, E. A., D. E. Rozen, and R. E. Lenski. 2005. Pleiotropic effects of beneficial mutations in
Escherichia coli. Evolution Int J Org Evolution
59 (11):2343-52.

Ouzounis, C. A., V. Kunin, N. Darzentas, and L. Goldovsky. 2006. A minimal estimate for the gene content of the last universal common ancestor—exobiology from a terrestrial perspective.
Res Microbiol
157 (1):57-68.

Owen, M. D., and I. A. Zelaya. 2005. Herbicide-resistant crops and weed resistance to herbicides.
Pest Manag Sci
61 (3):301-11.

Ozbudak, E. M., M. Thattai, H. N. Lim, B. I. Shraiman, and A. Van Oudenaarden. 2004. Multistability in the lactose utilization network of
Escherichia coli. Nature
427 (6976):737-40.

Pallen, M. J., and N. J. Matzke. 2006. From
The Origin of Species
to the origin of bacterial flagella.
Nat Rev Microbiol
4 (10):784-90.

Park, H. K., S. S. Shim, S. Y. Kim, J. H. Park, S. E. Park, H. J. Kim, B. C. Kang, and C. M. Kim. 2005. Molecular analysis of colonized bacteria in a human newborn infant gut.
J Microbiol
43 (4):345-53.

Park, S., P. M. Wolanin, E. A. Yuzbashyan, P. Silberzan, J. B. Stock, and R. H. Austin. 2003. Motion to form a quorum.
Science
301 (5630): 188.

Patrick, W. M., E. M. Quandt, D. V. Swartzlander, and I. Matsumura. 2007. Multicopy suppression underpins metabolic evolvability.
Mol Bio Evo
24 (12):2716–22.

Pelosi, L., L. Kuhn, D. Guetta, J. Garin, J. Geiselmann, R. E. Lenski, and D. Schneider. 2006. Parallel changes in global protein profiles during long-term experimental evolution in
Escherichia coli. Genetics
173 (4): 1851-69.

Pennington, T. H. 2003.
When food kills: BSE,
E. coli,
and disaster science.
New York: Oxford University Press.

Perfeito, L., L. Fernandes, C. Mota, and I. Gordo. 2007. Adaptive mutations in bacteria: High rate and small effects.
Science
317:813-15.

Perna, N. T., G. Plunkett III, V. Burland, B. Mau, J. D. Glasner, D. J. Rose, G. F. Mayhew, P. S. Evans, J. Gregor, H. A. Kirkpatrick, G. Posfai, J. Hackett, S. Klink, A. Boutin, Y. Shao, L. Miller, E. J. Grotbeck, N. W. Davis, A. Lim, E. T. Dimalanta, K. D. Potamousis, J. Apodaca, T. S. Anantharaman, J. Lin, G. Yen, D. C. Schwartz, R. A. Welch, and F. R. Blattner. 2001. Genome sequence of enterohaemorrhagic
Escherichia coli
O157:H7.
Nature
409 (6819):529-33.

Perron, G. G., M. Zasloff, and G. Bell. 2006. Experimental evolution of resistance to an antimicrobial peptide.
Proc Biol Sci
273 (1583):251-56.

Peschel, A., and H. G. Sahl. 2006. The co-evolution of host cationic antimicrobial peptides and microbial resistance.
Nat Rev Microbiol
4 (7):529-36.

Ponder, R. G., N. C. Fonville, and S. M. Rosenberg. 2005. A switch from high-fidelity to error-prone DNA double-strand break repair underlies stress-induced mutation.
Mol Cell
19 (6):791-804.

Potrykus, I. 2001. Golden Rice and beyond.
Plant Physiol
125 (3):1157-61.

Power, M. L., J. Littlefield-Wyer, D. M. Gordon, D. A. Veal, and M. B. Slade. 2005. Phenotypic and genotypic characterization of encapsulated
Escherichia coli
isolated from blooms in two Australian lakes.
Environ Microbiol
7 (5):631-40.

Queitsch, C., T. A. Sangster, and S. Lindquist. 2002. Hsp90 as a capacitor of phenotypic variation.
Nature
417 (6889):618-24.

Raney, T. 2006. Economic impact of transgenic crops in developing countries.
Curr Opin Biotechnol
17 (2):174-78.

Rangel, J. M., P. H. Sparling, C. Crowe, P. M. Griffin, and D. L. Swerdlow. 2005. Epidemiology of
Escherichia coli
O157:H7 outbreaks, United States, 1982-2002.
Emerg Infect Dis
11 (4):603-9.

Raser, J. M., and E. K. O’Shea. 2005. Noise in gene expression: Origins, consequences, and control.
Science
309 (5743):2010-13.

Rasheed, J. K., C. Jay, B. Metchock, F. Berkowitz, L. Weigel, J. Crellin, C. Steward, B. Hill, A. A. Medeiros, and F. C. Tenover. 1997. Evolution of extended-spectrum betalactam resistance (SHV-8) in a strain of
Escherichia coli
during multiple episodes of bacteremia.
Antimicrob Agents Chemother
41 (3):647-53.

Raymond, J., and D. Segre. 2006. The effect of oxygen on biochemical networks and the evolution of complex life.
Science
311 (5768):1764-67.

Reinhold, Robert. 1969. Scientists isolate a gene: Steps in heredity control.
New York Times,
November 22, 1969.

Reisner, A., K. A. Krogfelt, B. M. Klein, E. L. Zechner, and S. Molin. 2006. In vitro biofilm formation of commensal and pathogenic
Escherichia coli
strains: Impact of environmental and genetic factors.
J Bacteriol
188 (10):3572-81.

Remold, S. K., and R. E. Lenski. 2004. Pervasive joint influence of epistasis and plasticity on mutational effects in
Escherichia coli. Nat Genet
36 (4):423-26.

Ren, C. P., S. A. Beatson, J. Parkhill, and M. J. Pallen. 2005. The Flag-2 locus, an ancestral gene cluster, is potentially associated with a novel flagellar system from
Escherichia coli. J Bacteriol
187 (4):1430-40.

Roberts, Richard B. 1955.
Studies of biosynthesis in
Escherichia coli. Washington, D.C.: Carnegie Institution.

Robicsek, A., J. Strahilevitz, G. A. Jacoby, M. Macielag, D. Abbanat, C. H. Park, K. Bush, and D. C. Hooper. 2006. Fluoroquinolone-modifying enzyme: A new adaptation of a common aminoglycoside acetyltransferase.
Nat Med
12 (1):83-88.

Rogers, Michael. 1977.
Biohazard.
New York: Alfred A. Knopf.

Roth, J. R., E. Kugelberg, A. B. Reams, E. Kofoid, and D. I. Andersson. 2006. Origin of mutations under selection: The adaptive mutation controversy.
Annu Rev Microbiol
60:477-501.

Rozen, D. E., D. Schneider, and R. E. Lenski. 2005. Long-term experimental evolution in
Escherichia coli.
XIII. Phylogenetic history of a balanced polymorphism.
J Mol Evol
61 (2):171-80.

Salyers, Abigail A., and Dixie D. Whitt. 2005.
Revenge of the microbes: How bacterial resistance is undermining the antibiotic miracle.
Washington, D.C.: ASM Press.

Sandermann, H. 2006. Plant biotechnology: Ecological case studies on herbicide resistance.
Trends Plant Sci
11 (7):324-28.

Sansonetti, P. J. 2006. Shigellosis: An old disease in new clothes?
PLoS Med
3 (9):e354.

Sapp, J. 1994.
Evolution by association: A history of symbiosis.
New York: Oxford University Press.

———. 2005. The prokaryote-eukaryote dichotomy: Meanings and mythology.
Microbiol Mol Biol Rev
69 (2):292-305.

Sauer, U. 2006. Metabolic networks in motion:
13
C-based flux analysis.
Mol Syst Biol
2:62.

Sauer, U., M. Heinemann, and N. Zamboni. 2007. Genetics: Getting closer to the whole picture.
Science
316 (5824):550-51.

Schaechter, Moselio, John L. Ingraham, and Frederick C. Neidhardt. 2006.
Microbe.
Washington, D.C.: ASM Press.

Schnapp, N., and Q. Schiermeier. 2001. Critics claim “sight-saving” rice is over-rated.
Nature
410 (6828):503.

Schneider, D., and R. E. Lenski. 2004. Dynamics of insertion sequence elements during experimental evolution of bacteria.
Res Microbiol
155 (5):319-27.

Scott, C. T. 2006. Chimeras in the crosshairs.
Nat Biotechnol
24 (5):487-90.

Segerstrale, Ullica. In press.
Nature’s oracle: A life of W. D. Hamilton.
Oxford: Oxford University Press.

Service, Robert F. 2003. Researchers create first autonomous synthetic life form.
Science
299 (5607): 640.

———. 2007. A growing threat down on the farm.
Science
316 (5828): 1114-17.

Shaikh, N., and P. I. Tarr. 2003.
Escherichia coli
O157: H7 Shiga toxin–encoding bacteriophages: Integrations, excisions, truncations, and evolutionary implications.
J Bacteriol
185 (12): 3596-605.

Shapiro, J., L. Machattie, L. Eron, G. Ihler, K. Ippen, and J. Beckwith. 1969. Isolation of pure
lac
operon DNA.
Nature
224 (5221):768-74.

Shi, W., and D. R. Zusman. 1993. Fatal attraction.
Nature
366 (6454):414-15.

Shin, T., D. Kraemer, J. Pryor, L. Liu, J. Rugila, L. Howe, S. Buck, K. Murphy, L. Lyons, and M. Westhusin. 2002. A cat cloned by nuclear transplantation.
Nature
415 (6874):859.

Shnayerson, Michael, and Mark J. Plotkin. 2002.
The killers within: The deadly rise of drug-resistant bacteria.
Boston: Little, Brown.

Silver, Lee M. 2006.
Challenging nature: The clash of science and spirituality at the frontiers of life.
New York: Ecco.

Sinervo, B. 2001. Runaway social games, genetic cycles driven by alternative male and female strategies, and the origin of morphs.
Genetica
112-13:417-34.

Singer, M. 2001. What did the Asilomar exercise accomplish, what did it leave undone?
Perspect Biol Med
44 (2):186-91.

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