Evolution of resistance to quorum quenching in digital organisms

Artificial Life

Volumn 18, Issue 3, 2012, Pages 291-310

  Beckmann, Benjamin E ^a   Knoester, David B ^b   Connelly, Brian D ^b   Waters, Christopher M ^c   Mckinley, Philip K ^b  

^a GE GLOBAL RESEARCH   (United States)

^b Michigan State University   (United States)

^c Michigan State University ^*  (United States)

Author keywords

Anti infective; Bacteria; Digital evolution; Quorum quenching; Quorum sensing; Resistance

Indexed keywords

ANTIBIOTICS; BACTERIA; ELECTRIC RESISTANCE; ENZYMES;

ANTI-INFECTIVE; BACTERIAL INFECTIONS; COLLECTIVE BEHAVIOR; DIGITAL EVOLUTION; EVOLVED RESISTANCES; PATHOGENIC ORGANISMS; QUORUM QUENCHING; QUORUM-SENSING;

QUENCHING;

ARTICLE; EVOLUTION; QUORUM SENSING;

BIOLOGICAL EVOLUTION; QUORUM SENSING;

EID: 84989304044     PISSN: 10645462     EISSN: 15309185     Source Type: Journal    
DOI: 10.1162/artl_a_00066     Document Type: Article

References (63)

1. André, J.-B., & Godelle, B. (2005). Multicellular organization in bacteria as a target for drug therapy. Ecology Letters, 8(8), 800-810. (Pubitemid 41009255)
2. Bassler, B. L., Wright, M., Showalter, R. E., & Silverman, M. R. (1993). Intercellular signalling in Vibrio harveyi: Sequence and function of genes regulating expression of luminescence. Molecular Microbiology, 9(4), 773-786. (Pubitemid 23253503)
3. Beckmann, B. E. (2010). Evolving cooperative, energy-conserving agent-based systems. Ph.D. thesis, Department of Computer Science and Engineering, Michigan State University, East Lansing, MI.
4. Beckmann, B. E., & McKinley, P. K. (2008). Evolution of adaptive population control in multi-agent systems. In Proceedings of the Second IEEE International Conference on Self-Adaptive and Self-Organizing Systems (pp. 181-190).
5. Beckmann, B. E., & McKinley, P. K. (2009). Evolving quorum sensing in digital organisms. In Proceedings of the ACM Genetic and Evolutionary Computation Conference (GECCO-2009) (pp. 97-104).
6. Beckmann, B. E., McKinley, P. K., Knoester, D. B., & Ofria, C. (2007). Evolution of cooperative information gathering in self-replicating digital organisms. In Proceedings of the First International Conference on Self-Adaptive and Self-Organizing Systems (SASO) (pp. 65-76).
7. Beckmann, B., McKinley, P. K., & Ofria, C. A. (2007). Evolution of adaptive sleep response in digital organisms. In Advances in Artificial Life, Proceedings of the 9th European Conference on Artificial Life (pp. 233-242).
8. Béjà, O., Spudich, E. N., Spudich, J. L., Leclerc, M., & DeLong, E. F. (2001). Proteorhodopsin phototrophy in the ocean. Nature, 411, 786-789. (Pubitemid 32588098)
9. Bernardini, F., Gheorghe, M., & Krasnogor, N. (2007). Quorum sensing P systems. Theoretical Computer Science, 371(1-2), 20-33. (Pubitemid 46215847)
10. Brown, S. P., & Johnstone, R. A. (2001). Cooperation in the dark: Signalling and collective action in quorum-sensing bacteria. Proceedings of the Royal Society of London B: Biological Sciences, 268(1470), 961-965. (Pubitemid 32453386)
11. Brown, S. P., West, S. A., Diggle, S. P., & Griffin, A. S. (2009). Social evolution in micro-organisms and a Trojan horse approach to medical intervention strategies. Philosophical Transactions of the Royal Society B: Biological Sciences, 364(1533), 3157-3168.
12. Chow, S., Wilke, C. O., Ofria, C., Lenski, R. E., & Adami, C. (2004). Adaptive radiation from resource competition in digital organisms. Science, 305(5680), 84-86. (Pubitemid 38869376)
13. Clatworthy, A. E., Pierson, E., & Hung, D. T. (2007). Targeting virulence: A new paradigm for antimicrobial therapy. Nature Chemical Biology, 3(6), 541-548. (Pubitemid 47294400)
14. Costerton, J. W., & Stewart, P. S. (2010). Battling biofilms. Scientific American, 285(7), 60-67.
15. Crespi, B. J. (2001). The evolution of social behavior in microorganisms. Trends in Ecology and Evolution, 16(4), 178-183. (Pubitemid 32197564)
16. Czárán, T., & Hoekstra, R. F. (2009). Microbial communication, cooperation and cheating: Quorum sensing drives the evolution of cooperation in bacteria. PLoS ONE, 4(8), e6655.
17. Davies, D. (2003). Understanding biofilm resistance to antibacterial agents. Nature Reviews Drug Discovery, 2(2), 114-122. (Pubitemid 37361643)
18. Defroirdt, T., Boon, N., & Bossier, P. (2010). Can bacteria evolve resistance to quorum sensing disruption? PLoS Pathogens, 6(7), 73-87.
19. Dickschat, J. S. (2010). Quorum sensing and bacterial biofilms. Natural Product Reports, 27(3), 343-369.
20. Diggle, S. P., Griffin, A. S., Campbell, G. S., & West, S. A. (2007). Cooperation and conflict in quorum-sensing bacterial populations. Nature, 450, 411-414. (Pubitemid 350126749)
21. de Kievit, T. R., & Iglewski, B. H. (2000). Bacterial quorum sensing in pathogenic relationships. Infection and Immunity, 68(9), 4839-4849.
22. Dockery, J., & Keener, J. (2001). A mathematical model for quorum sensing in Pseudomonas aeruginosa. Bulletin of Mathematical Biology, 63(1), 95-116. (Pubitemid 32577425)
23. Floreano, D., Mitri, S., Magnenat, S., & Keller, L. (2007). Evolutionary conditions for the emergence of communication in robots. Current Biology, 17(3), 514-519. (Pubitemid 46401376)
24. Fuqua, C., Winans, S., & Greenberg, E. (1996). Census and consensus in bacterial ecosystems: The LuxR-LuxI family of quorum-sensing transcriptional regulators. Annual Review of Microbiology, 50, 727-751. (Pubitemid 26337480)
25. Goings, S., Clune, J., Ofria, C., & Pennock, R. (2004). Kin selection: The rise and fall of kin-cheaters. In Proceedings of the Ninth International Conference on Artificial Life (pp. 303-308).
26. Hall-Stoodley, L., Costerton, J. W., & Stoodley, P. (2004). Bacterial biofilms: From the environment to infectious disease. Nature Reviews Microbiology, 2(2), 95-108. (Pubitemid 39490064)
27. Hamilton, W. D. (1963). The evolution of altruistic behavior. The American Naturalist, 97(896), 354-356.
28. Hammer, B. K., & Bassler, B. L. (2003). Quorum sensing controls biofilm formation in Vibrio cholerae. Molecular Microbiology, 50(1), 101-104.
29. Hansen, S. K., Rainey, P. B., Haagensen, J. A. J., & Molin, S. (2007). Evolution of species interactions in a biofilm community. Nature, 445, 533-536. (Pubitemid 46197632)
30. Hill, J. L. (2003). System architecture for wireless sensor networks. Ph.D. thesis, University of California at Berkeley.
31. Kambam, P. K. R., Henson, M. A., & Sun, L. (2008). Design and mathematical modelling of a synthetic symbiotic ecosystem. IET Systems Biology, 2(1), 33-38. (Pubitemid 351217540)
32. Kiran, M. D., Giacometti, A., Cirioni, O., & Balaban, N. (2008). Suppression of biofilm related, device-associated infections by staphylococcal quorum sensing inhibitors. International Journal of Artificial Organs, 31(9), 761-770.
33. Knoester, D. B., & McKinley, P. K. (2009). Evolution of probabilistic consensus in digital organisms. In Proceedings of the Third IEEE International Conference on Self-Adaptive and Self-Organizing Systems (pp. 223-232).
34. Knoester, D. B., & McKinley, P. K. (2011). Evolution of synchronization and desynchronization in digital organisms. Artificial Life, 17(1), 1-20.
35. Knoester, D. B., McKinley, P. K., & Ofria, C. (2008). Cooperative network construction using digital germlines. In Proceedings of the Genetic and Evolutionary Computation Conference (GECCO) (pp. 217-224).
36. Lenski, R. E., Ofria, C., Pennock, R. T., & Adami, C. (2003). The evolutionary origin of complex features. Nature, 423, 139-144. (Pubitemid 36569531)
37. Lewandowski, Z. (2000). Structure and function of biofilms. In L. Evans (Ed.), Biofilms: Recent advances in their study and control (pp. 1-17). Amsterdam, The Netherlands: Harwood Academic Publishers.
38. McKinley, P., Cheng, B., Ofria, C., Knoester, D., Beckmann, B., & Goldsby, H. (2008). Harnessing digital evolution. IEEE Computer, 41(1), 54-63.
39. Miller, M. B., & Bassler, B. L. (2001). Quorum sensing in bacteria. Annual Review of Microbiology, 55, 165-199. (Pubitemid 32978104)
40. Monds, R. D., & O'Toole, G. A. (2009). The developmental model of microbial biofilms: Ten years of a paradigm up for review. Trends in Microbiology, 17(2), 73-87.
41. Nadell, C. D., Foster, K. R., & Xavier, J. B. (2010). Emergence of spatial structure in cell groups and the evolution of cooperation. PLoS Computational Biology, 6(3), e1000716.
42. Nadell, C. D., Xavier, J. B., Levin, S. A., & Foster, K. R. (2008). The evolution of quorum sensing in bacterial biofilms. PLoS Biology, 6(January), 0171-0179. (Pubitemid 351226055)
43. Nealson, K., & Hastings, J. (1979). Bacterial bioluminescence: Its control and ecological significance. Microbiological Reviews, 43(4), 496-518. (Pubitemid 10125953)
44. Nealson, K. H., Platt, T., & Hastings, J. W. (1970). Cellular control of the synthesis and activity of the bacterial luminescent system. Journal of Bacteriology, 104(1), 313-322.
45. Njoroge, J., & Sperandio, V. (2009). Jamming bacterial communication: New approaches for the treatment of infectious diseases. EMBO Molecular Medicine, 1(4), 201-210.
46. Ofria, C., & Wilke, C. O. (2004). Avida: A software platform for research in computational evolutionary biology. Artificial Life, 10(2), 191-229.
47. Ostrowski, E., Ofria, C., & Lenski, R. E. (2007). Ecological specialization and adaptive decay in digital organisms. The American Naturalist, 169(1), E1-E20.
48. Pan, J., & Ren, D. (2009). Quorum sensing inhibitors: A patent overview. Expert Opinion on Therapeutic Patents, 19(11), 1581-1601.
49. Paun, G., & Rozenberg, G. (2002). A guide to membrane computing. Theoretical Computer Science, 287(1), 73-100. (Pubitemid 35019161)
50. Raina, S., De Vizio, D., Odell, M., Clements, M., Vanhulle, S., & Keshavarz, T. (2009). Microbial quorum sensing: A tool or a target for antimicrobial therapy? Biotechnology and Applied Biochemistry, 54(2), 65-84.
51. Romero-Campero, F. J., & Pérez-Jiménez, M. J. (2008). A model of the quorum sensing system in Vibrio fischeri using P systems. Artificial Life, 14(1), 95-109.
52. Rumbaugh, K. P., Diggle, S. P., Watters, C. M., Ross-Gillespie, A., Griffin, A. S., & West, S. A. (2009). Quorum sensing and the social evolution of bacterial virulence. Current Biology, 19(4), 341-345.
53. Sandoz, K. M., Mitzimberg, S. M., & Schuster, M. (2007). Social cheating in Pseudomonas aeruginosa quorum sensing. Proceedings of the National Academy of Sciences, 104(40), 15876-15881. (Pubitemid 350035392)
54. Schauder, S., Shokat, K., Surette, M., & Bassler, B. (2001). The LuxS family of bacterial autoinducers: Biosynthesis of a novel quorum-sensing signal molecule. Molecular Microbiology, 41(2), 463-476. (Pubitemid 32730544)
55. Terrazas, G., Krasnogor, N., Gheorghe, M., Bernardini, F., Diggle, S., & Cámara, M. (2005). An environment aware P-system model of quorum sensing. In S. B. Cooper, B. Löwe, & L. Torenvliet (Eds.), New Computational Paradigms, First Conference on Computability in Europe (CiE) (pp. 479-485). Berlin: Springer. (Pubitemid 41422241)
56. Waters, C. M., & Bassler, B. L. (2005). Quorum sensing: Cell-to-cell communication in bacteria. Annual Review of Cell and Developmental Biology, 21, 319-346. (Pubitemid 41740638)
57. Waters, C., Lu, W., Rabinowitz, J. D., & Bassler, B. L. (2008). Quorum sensing controls biofilm formation in Vibrio cholerae through modulation of cyclic di-GMP levels and repression of vpsT. Journal of Bacteriology, 190(7), 2527-2536. (Pubitemid 351466348)
58. Watnick, P., & Kolter, R. (2000). Biofilm, city of microbes. Journal of Bacteriology, 182(10), 2675-2679. (Pubitemid 30246894)
59. Whitley, W. D., Rana, S. B., & Heckendorn, R. B. (1997). Island model genetic algorithms and linearly separable problems. In Selected Papers from AISB Workshop on Evolutionary Computing (pp. 109-125). Berlin: Springer-Verlag.
60. Wilke, C. O., Wang, J., Ofria, C., Adami, C., & Lenski, R. E. (2001). Evolution of digital organisms at high mutation rate leads to survival of the flattest. Nature, 412, 331-333. (Pubitemid 32691846)
61. Xavier, K. B., & Bassler, B. L. (2005). Interference with AI-2-mediated bacterial cell-cell communication. Nature, 437, 750-753. (Pubitemid 41486545)
62. Xavier, J. B., & Foster, K. R. (2007). Cooperation and conflict in microbial biofilms. Proceedings of the National Academy of Sciences, 104(3), 876-881. (Pubitemid 46154704)
63. Zhu, J., & Mekalanos, J. J. (2003). Quorum sensing-dependent biofilms enhance colonization in Vibrio cholerae. Developmental Cell, 5(4), 647-656. (Pubitemid 37243052)