Enteric immunity simulator: A tool for in silico study of gastroenteric infections

IEEE Transactions on Nanobioscience

Volumn 11, Issue 3, 2012, Pages 273-288

  Wendelsdorf, Katherine V ^a   Alam, Maksudul ^a   Bassaganya Riera, Josep ^b   Bisset, Keith ^a   Eubank, Stephen ^a   Hontecillas, Raquel ^b   Hoops, Stefan ^a   Marathe, Madhav ^a  

^a VIRGINIA BIOINFORMATICS INSTITUTE   (United States)

^b VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY   (United States)

Author keywords

Biological systems; computational biology; multiagent systems

Indexed keywords

ANTI-INFLAMMATORIES; CLINICAL SYMPTOMS; COMPUTATIONAL BIOLOGY; GASTROINTESTINAL TRACT; IMMUNE CELLS; IMMUNE MECHANISM; IN-SILICO; IN-VITRO; IN-VIVO; MICROBIAL INFECTIONS; PATHOGEN REMOVAL; TISSUE DAMAGE;

BIOINFORMATICS; BIOLOGICAL SYSTEMS; MULTI AGENT SYSTEMS; PATHOGENS; SIMULATORS; TISSUE;

PATHOLOGY;

BACTERIA (MICROORGANISMS);

ANIMAL; ARTICLE; BIOLOGICAL MODEL; BIOLOGY; COMPUTER SIMULATION; DENDRITIC CELL; DYSENTERY; EPITHELIUM CELL; GASTROINTESTINAL DISEASE; GASTROINTESTINAL TRACT; HOST PATHOGEN INTERACTION; IMMUNOLOGY; METHODOLOGY; MICROBIOLOGY; MUCOSAL IMMUNITY; SWINE; T LYMPHOCYTE;

ANIMALS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DENDRITIC CELLS; DYSENTERY; EPITHELIAL CELLS; GASTROINTESTINAL DISEASES; GASTROINTESTINAL TRACT; HOST-PATHOGEN INTERACTIONS; IMMUNITY, MUCOSAL; MODELS, BIOLOGICAL; SWINE; T-LYMPHOCYTES;

EID: 84866510577     PISSN: 15361241     EISSN: None     Source Type: Journal    
DOI: 10.1109/TNB.2012.2211891     Document Type: Article

References (54)

1. S. Gordon and P. R. Taylor, "Monocyte and macrophage heterogeneity," Nat. Rev. Immunol., vol. 5, no. 12, pp. 953-964, 2005. (Pubitemid 41746764)
2. A. Iwasaki, "Mucosal dendritic cells," Annu. Rev. Immunol., vol. 25, pp. 381-418, 2007. (Pubitemid 46697912)
3. D. A. Hill and D. Artis, "Intestinal bacteria and the regulation of immune cell homeostasis," Annu. Rev. Immunol., vol. 28, pp. 623-667, 2010.
4. Y. Onishi, Z. Fehervari, T. Yamaguchi, and S. Sakaguchi, "Foxp3(+) natural regulatory t cells preferentially form aggregates on dendritic cells in vitro and actively inhibit their maturation," Proc. Natl. Acad. Sci. USA, vol. 105, no. 29, pp. 10 113-10 118, 2008.
5. S. C. Ng,M. A. Kamm, A. J. Stagg, and S. C. Knight, "Intestinal dendritic cells: Their role in bacterial recognition, lymphocyte homing, and intestinal inflammation," Inflamm. Bowel Dis., vol. 16, no. 10, pp. 1787-1807, 2010.
6. J. C.Arciero, G.B. Ermentrout, J. S. Upperman, Y. Vodovotz, and J. E. Rubin, "Using a mathematical model to analyze the role of probiotics and inflammation in necrotizing enterocolitis," PLoS One, vol. 5, no. 4, p. e10066, 2010.
7. J. E. Wigginton and D. Kirschner, "A model to predict cell-mediated immune regulatory mechanisms during human infection with mycobacterium tuberculosis," J. Immunol., vol. 166, no. 3, pp. 1951-1967, 2001. (Pubitemid 32114683)
8. M. J. Blaser and D. Kirschner, "Dynamics of helicobacter pylori colonization in relation to the host response," Proc. Natl. Acad. Sci. USA, vol. 96, no. 15, pp. 8359-8364, 1999. (Pubitemid 29354796)
9. M. Blaser and D. Kirschner, "The equilibria that allow bacterial persistence in human hosts," Nature, vol. 449, no. 7164, pp. 843-849, 2007. (Pubitemid 47598613)
10. H. Y. Lee, D. J. Topham, S. Y. Park, J. Hollenbaugh, J. Treanor, T. R. Mosmann, X. Jin, B. M. Ward, H. Miao, J. Holden-Wiltse, A. S. Perelson, M. Zand, and H. Wu, "Simulation and prediction of the adaptive immune response to influenza a virus infection," J. Virol. vol. 83, no. 14, pp. 7151-7165, Jul. 2009 [Online]. Available: http://dx.doi. org/10.1128/JVI.00098-09
11. G. Shahaf, K. Johnson, and R. Mehr, "B cell development in aging mice: Lessons from mathematical modeling," Int. Immunol. vol. 18, no. 1, pp. 31-39, Jan. 2006 [Online]. Available: http://dx.doi.org/10. 1093/intimm/dxh346 (Pubitemid 43057034)
12. N. Burroughs, B. M. P. M. de Oliveira, and A. A. Pinto, "Regulatory t cell adjustment of quorum growth thresholds and the control of local immune responses," J. Theor. Biol. vol. 241, no. 1, pp. 134-141, 2006 . Available: http://www.sciencedirect.com/science/article/pii/S0022519305004959 (Pubitemid 43817990)
13. J. Carneiro, T. Paixão, D. Milutinovic, J. Sousa, K. Leon, R. Gardner, and J. Faro, "Immunological self-tolerance: Lessons from mathematical modeling," J. Comput. Appl.Math. vol. 184, pp. 77-100,Dec. 2005 . Available: http://dx.doi.org/10.1016/j.cam.2004.10.025 (Pubitemid 41100714)
14. D. Fouchet and R. Regoes, "A population dynamics analysis of the interaction between adaptive regulatory t cells and antigen presenting cells," PLoS ONE vol. 3, no. 5, p. e2306, 2008 [Online]. Available: http://dx.plos.org/10.1371
15. R. Antia, C. T. Bergstrom, S. S. Pilyugin, S.M. Kaech, and R. Ahmed, "Models of cd8+ responses: 1. What is the antigen-independent proliferation program," J. Theor. Biol. vol. 221, no. 4, pp. 585-598, 2003. Available: http://www.sciencedirect.com/science/article/pii/S0022519303932085 (Pubitemid 36444527)
16. D.Wodarz and A. R. Thomsen, "Effect of the ctl proliferation program on virus dynamics," Int. Immunol. vol. 17, no. 9, pp. 1269-1276, 2005. Available: http://www.ingentaconnect.com/content/oup/intimm/2005/00000017/ 00000009/art01269 (Pubitemid 41236082)
17. P. S. Kim, P. P. Lee, and D. Levy, "Modeling regulation mechanisms in the immune system," J. Theor. Biol. vol. 246, no. 1, pp. 33-69, 2007. Available: http://www.sciencedirect.com/science/article/pii/S0022519306005625 (Pubitemid 46550513)
18. C. Colijn andM. C.Mackey, "Amathematicalmodel of hematopoiesis: II. cyclical neutropenia," J. Theor. Biol. vol. 237, no. 2, pp. 133-146, 2005 [Online]. Available: http://www.ncbi.nlm.nih.gov/pubmed/15975606
19. M. Onsum and C. V. Rao, "A mathematical model for neutrophil gradient sensing and polarization," PLoS Comput. Biol. vol. 3, no. 3, p. e36 [Online]. Available: http://dx.plos.org/10.1371, 03 2007
20. M. T. Figge, "Optimization of immunoglobulin substitution therapy by a stochastic immune response model," PLoS ONE vol. 4, no. 5, p. e5685 [Online]. Available: http://dx.doi.org/10.1371, 05 2009
21. A. L. Bauer, C.A. Beauchemin, and A. S. Perelson, "Agent- basedmodeling of host-pathogen systems: The successes and challenges," Inf. Sci. vol. 179, no. 10, pp. 1379-1389, 2009 [Online]. Available: http://www.sciencedirect.com/science/article/pii/S0020025508004726
22. N. Fachada, V. V. Lopes, and A. Rosa, "Agent based modelling and simulation of the immune system: A review," Systems and Robotics Institute, Instituto Superior Tecnico, Lisboa, Portugal, Tech. Rep., Feb. 2000.
23. A. Grilo, A. Caetano, and A. Rosa, "Agent-based artificial immune system," in Proc. 2001 Genet. Evol. Comput. Conf. Late Breaking Papers, San Francisco, CA.
24. J. C. Tay and A. Jhavar, "Cafiss: A complex adaptive framework for immune system simulation," in Proc. 2005 ACM Symp. Appl. Comput., New York, 2005, pp. 158-164 [Online]. Available: http://doi.acm.org/10.1145/1066677. 1066716
25. F. Celada and P. E. Seiden, "A computer model of cellular interactions in the immune system," Immunol. Today vol. 13, no. 2, pp. 56-62, Feb. 1992 [Online]. Available: http://view.ncbi.nlm.nih.gov/pubmed/ 1575893
26. F. Castiglione, K. Duca, A. Jarrah, R. Laubenbacher, D. Hochberg, and D. Thorley-Lawson, "Simulating epstein-barr virus infection with c-immsim," Bioinformatics vol. 23, pp. 1371-1377 Jun. 2007 [Online]. Available: http://dl.acm.org/citation.cfm?id=1346089.1346095 (Pubitemid 47050519)
27. M. Bernaschi and F. Castiglione, "Design and implementation of an immune system simulator," Comput. Biol. Med., vol. 31, no. 5, pp. 303-331, 2001. (Pubitemid 32787012)
28. E. A. and R. E. , "Immunogrid-The virtual human immune system project," Stud. Health Technol. Inf., pp. 56-62, 2007.
29. M. Meier-Schellersheim and G.Mack, "Simmune, a tool for simulating and analyzing immune system behavior," CoRR, vol. cs.MA/9903017, 1999.
30. J. Mata and M. Cohn, "Cellular automata-based modeling program: Synthetic immune system," Immunol. Rev. vol. 216, no. 1, pp. 198-212, Apr. 2007 [Online]. Available: http://dx.doi.org/10.1111/j. 1600-065X.2007.00511.x (Pubitemid 46426523)
31. F. Pappalardo, P. Zhang, M. Halling-Brown, K. Basford, A. Scalia, A. J. Shepherd, D. Moss, S. Motta, and V. Brusic, "Computational simulations of the immune system for personalized medicine: State of the art and challenges," System pp. 1-36, 2008 [Online]. Available: http://dx.doi.org/10.2174/187569208786733839
32. S. C. I. Efroni and D. Harel, "Reactive animation: Realistic modeling of complex dynamic systems," Computer, pp. 38-47, 2005. (Pubitemid 40583541)
33. N. Swerdlin, I. R.Cohen, andD.Harel, "The lymph node b cell immune response: Dynamic analysis in-silico," Proc. IEEE, vol. 96, no. 8, pp. 1421-1443, 2008.
34. M. W. Sneddon, J. R. Faeder, and T. Emonet, "Efficient modeling, simulation and coarse-graining of biological complexity with nfsim," Nat. Methods, vol. 8, no. 2, p. 177-U112, 2011.
35. T. Sutterlin, S. Huber, H. Dickhaus, and N. Grabe, "Modeling multicellular behavior in epidermal tissue homeostasis via finite state machines in multi-agent systems," Bioinformatics, vol. 25, no. 16, pp. 2057-2063, 2009.
36. C. Jacob, J. Litorco, and L. Lee, Immunity Through Swarms: Agent-Based Simulations of the Human Immune System. New York: Springer, 2004, pp. 400-412 [Online]. Available: http://www. springeronline.com/sgw/cda/frontpage/0,11855,4- 40109-22-3444 8379-0,00.html, LNCS 3239
37. C. L. Barrett, K. Bisset, J. Chen, S. Eubank, B. Lewis, V. S. A. Kumar, M. V. Marathe, and H. S. Mortveit, "Interactions among human behavior, social networks, and societal infrastructures: A case study in computational epidemiology," in Fundamental Problems in Computing, S. S. Ravi and S. K. Shukla, Eds. Dordrecht, The Netherlands: Springer Netherlands, 2009, pp. 477-507.
38. K. Wendelsdorf, J. Bassaganya-Riera, K. Bisset, S. Eubank, R. Hontecillas, and M. Marathe, "ENteric Immunity SImulator: A tool for in silico study of gut immunopathologies," NDSSL, TR-11-072, 2011 [Online]. Available: http://modelingimmunity.vbi.vt.edu/modeling/enisi/, vol.
39. D. T. Gillespie, "Exact stochastic simulation of coupled chemical reactions," J. Phys. Chem., vol. 81, no. 25, pp. 2340-2361, 1977.
40. D. Kelly, J. I. Campbell, T. P. King, G. Grant, E. A. Jansson, A. G. Coutts, S. Pettersson, and S. Conway, "Commensal anaerobic gut bacteria attenuate inflammation by regulating nuclear-cytoplasmic shuttling of ppar-gamma and rela," Nat. Immunol., vol. 5, no. 1, pp. 104-112, 2004. (Pubitemid 38081475)
41. D. Gery and E. Harel, "Executable object modeling with statecharts," Computer, vol. 30, no. 7, pp. 31-42, 1997.
42. D. Artis, "Epithelial-cell recognition of commensal bacteria and maintenance of immune homeostasis in the gut," Nat. Rev. Immunol., vol. 8, no. 6, pp. 411-420, 2008. (Pubitemid 351733416)
43. A. Lanzavecchia and F. Sallusto, "Regulation of t cell immunity by dendritic cells," Cell, vol. 106, no. 3, pp. 263-266, 2001. (Pubitemid 32772609)
44. D. R. Littman and A. Y. Rudensky, "Th17 and regulatory t cells in mediating and restraining inflammation," Cell, vol. 140, no. 6, pp. 845-858, 2010.
45. S. Stoll, J. Delon, T. M. Brotz, and R. N. Germain, "Dynamic imaging of t cell-dendritic cell interactions in lymph nodes," Science, vol. 296, no. 5574, pp. 1873-1876, 2002. (Pubitemid 34596274)
46. C. Janeway, P. Travers, M. Walport, and M. Shlomchik, Immunobiology: The Immune System in Health and Disease, 5th ed. New York: Garland Science, 2001.
47. A. L. Marzo, K. D. Klonowski, A. Le Bon, P. Borrow, D. F. Tough, and L. Lefrancois, "Initial t cell frequency dictates memory cd8+ t cell lineage commitment," Nat. Immunol., vol. 6, no. 8, pp. 793-799, 2005. (Pubitemid 43090465)
48. E. M. Shevach, R. A. DiPaolo, J. Andersson, D. M. Zhao, G. L. Stephens, and A. M. Thornton, "The lifestyle of naturally occurring cd4+ cd25+ foxp3+ regulatory t cells," Immunol. Rev., vol. 212, pp. 60-73, 2006. (Pubitemid 44116700)
49. F. Sallusto, J. Geginat, and A. Lanzavecchia, "Central memory and effector memory t cell subsets: Function, generation, and maintenance," Annu. Rev. Immunol., vol. 22, pp. 745-763, 2004. (Pubitemid 38680440)
50. S.M. Kaech and R. Ahmed, "Immunology: CD8 T cells remember with a little help," Science, vol. 300, no. 5617, pp. 263-265, 2003. (Pubitemid 36433703)
51. R. Naresh, Y. Song, and D. J. Hampson, "The intestinal spirochete brachyspira pilosicoli attaches to cultured caco-2 cells and induces pathological changes," PLoS One, vol. 4, no. 12, p. e8352, 2009.
52. R. Hontecillas and J. Bassaganya-Riera, "Peroxisome proliferator-activated receptor gamma is required for regulatory cd4+ t cell-mediated protection against colitis," J Immunol., vol. 178, no. 5, pp. 2940-2949, 2007. (Pubitemid 46333173)
53. R. Jonasson, M. Andersson, T. Rasback, A. Johannisson, and M. Jensen-Waern, "Immunological alterations during the clinical and recovery phases of experimental swine dysentery," J. Med. Microbiol., vol. 55, pt. 7, pp. 845-855, 2006. (Pubitemid 43974689)
54. A. T.Haase, "Population biology ofHIV-1 infection: Viral and CD4(+) t cell demographics and dynamics in lymphatic tissues," Annu. Rev. Immunol., vol. 17, pp. 625-656, 1999.