Using chemistry and microfluidics to understand the spatial dynamics of complex biological networks

Accounts of Chemical Research

Volumn 41, Issue 4, 2008, Pages 549-558

  Kastrup, Christian J ^a   Runyon, Matthew K ^a   Lucchetta, Elena M ^a   Price, Jessica M ^a   Ismagilov, Rustem F ^a  

^a UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; BIOCHEMISTRY; CHEMICAL MODEL; HEMOSTASIS; MICROFLUIDICS; REVIEW;

ANIMALS; BIOCHEMISTRY; HEMOSTASIS; MICROFLUIDICS; MODELS, CHEMICAL;

EID: 43649102021     PISSN: 00014842     EISSN: None     Source Type: Journal    
DOI: 10.1021/ar700174g     Document Type: Review

References (72)

1. Milo, R.; Shen-Orr, S.; Itzkovitz, S.; Kashtan, N.; Chklovskii, D.; Alon, U. Network motifs: Simple building blocks of complex networks. Science 2002, 298, 824-827.
2. Hartwell, L. H.; Hopfield, J. J.; Leibler, S.; Murray, A. W. From molecular to modular cell biology. Nature 1999, 402, C47-C52.
3. (a) Bertozzi, C. R.; Kiessling, L. L. Chemical glycobiology. Science 2001, 291, 2357-2364.
4. (b) Jessani, N.; Cravatt, B. F. The development and application of methods for activity-based protein profiling. Curr. Opin. Chem. Biol. 2004, 8, 54-59.
5. Kastrup, C. J.; Runyon, M. K.; Shen, F.; Ismagilov, R. F. Modular chemical mechanism predicts spatiotemporal dynamics of initiation in the complex network of hemostasis. Proc. Natl. Acad. Sci. USA. 2006, 103, 15747-15752.
6. Runyon, M. K.; Johnson-Kerner, B. L.; Ismagilov, R. F. Minimal functional model of hemostasis in a biomimetic microfluidic system. Angew. Chem., Int. Ed. 2004, 43, 1531-1536.
7. Runyon, M. K.; Johnson-Kerner, B. L.; Kastrup, C. J.; Van Ha, T. G.; Ismagilov, R. F. Propagation of blood clotting in the complex biochemical network of hemostasis is described by a simple mechanism. J. Am. Chem. Soc. 2007, 129, 7014-7015.
8. Lucchetta, E. M.; Lee, J. H.; Fu, L. A.; Patel, N. H.; Ismagilov, R. F. Dynamics of Drosophila embryonic patterning network perturbed in space and time using microfluidics. Nature 2005, 434, 1134-1138.
9. Ephrussi, A.; Johnston, D. Seeing is believing: The bicoid morphogen gradient matures. Cell 2004, 116, 143-152, and references cited therein.
10. Mann, K. G.; Butenas, S.; Brummel, K. The dynamics of thrombin formation. Arterioscler. Thromb. Vasc. Biol. 2003, 23, 17-25, and references cited therein.
11. Morrissey, J. H. Tissue factor: in at the start. . . and the finish. J. Thromb. Haemostasis 2003, 1, 878-880.
12. Beltrami, E.; Jesty, J. The role of membrane patch size and flow in regulating a proteolytic feedback threshold on a membrane: Possible application in blood coagulation. Math. Biosci. 2001, 172, 1-13.
13. (a) Butenas, S.; Mann, K. G. Active tissue factor in blood. Nat. Med. 2004, 10, 1155-1156.
14. (b) Bogdanov, V. Y.; Hathcock, J.; Nemerson, Y. Active tissue factor in blood? Reply. Nat. Med. 2004, 10, 1156.
15. Tyson, J. J.; Chen, K. C.; Novak, B. Sniffers, buzzers, toggles and blinkers: Dynamics of regulatory and signaling pathways in the cell. Curr. Opin. Cell Biol. 2003, 15, 221-231.
16. Witkowski, F. X.; Leon, L. J.; Penkoske, P. A.; Giles, W. R.; Spano, M. L.; Ditto, W. L.; Winfree, A. T. Spatiotemporal evolution of ventricular fibrillation. Nature 1998, 392, 78-82.
17. Frohnhofer, H. G.; Nusslein-Volhard, C. Organization of anterior pattern in the Drosophila embryo by the maternal gene bicoid. Nature 1986, 324, 120-125.
18. (a) Whitesides, G. M.; Ismagilov, R. F. Complexity in chemistry. Science 1999, 284, 89-92.
19. (b) Kastrup, C. J.; Ismagilov, R. F. A physical-organic mechanistic approach to understanding the complex reaction network of hemostasis (blood clotting). J. Phys. Org. Chem. 2007, 20, 711-715.
20. Houchmandzadeh, B.; Wieschaus, E.; Leibler, S. Establishment of developmental precision and proportions in the early Drosophila embryo. Nature 2002, 415, 798-802.
21. (a) McAdams, H. H.; Shapiro, L. A bacterial cell-cycle regulatory network operating in time and space. Science 2003, 301, 1874-1877.
22. (b) Stelling, J.; Sauer, U.; Szallasi, Z.; Doyle, F. J.; Doyle, J. Robustness of cellular functions. Cell 2004, 118, 675-685.
23. Bhattacharyya, R. P.; Remenyi, A.; Yeh, B. J.; Lim, W. A. Domains, motifs, and scaffolds: The role of modular interactions in the evolution and wiring of cell signaling circuits. Annu. Rev. Biochem. 2006, 75, 655-680.
24. Goldbeter, A.; Koshland, D. E. An amplified sensitivity arising from covalent modification in biological-systems. Proc. Natl. Acad. Sci. U.S.A. 1981, 78, 6840-6844.
25. Pomerening, J. R.; Kim, S. Y.; Ferrell, J. E. Systems-level dissection of the cell-cycle oscillator: Bypassing positive feedback produces damped oscillations. Cell 2005, 122, 565-578.
26. Ferrell, J. E. Self-perpetuating states in signal transduction: Positive feedback, double-negative feedback and bistability. Curr. Opin. Cell Biol. 2002, 14, 140-148.
27. 2. J. Am. Chem. Soc. 2001, 123, 7194-7195.
28. (b) Tshuva, E. Y.; Lippard, S. J. Synthetic models for non-heme carboxylate-bridged diiron metalloproteins: Strategies and tactics. Chem. Rev. 2004, 104, 987-1011.
29. Halpern, J.; Kim, S. H.; Leung, T. W. Cobalt carbon bond-dissociation energy of coenzyme-B12. J. Am. Chem. Soc. 1984, 106, 8317-8319.
30. Ross, J. New approaches to the deduction of complex reaction mechanisms. Acc. Chem. Res. 2003, 36, 839-847.
31. Sprinzak, D.; Elowitz, M. B. Reconstruction of genetic circuits. Nature 2005, 438, 443-448.
32. Isaacs, F. J.; Hasty, J.; Cantor, C. R.; Collins, J. J. Prediction and measurement of an autoregulatory genetic module. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 7714-7719.
33. Elowitz, M. B.; Leibler, S. A synthetic oscillatory network of transcriptional regulators. Nature 2000, 403, 335-338.
34. Basu, S.; Gerchman, Y.; Collins, C. H.; Arnold, F. H.; Weiss, R. A synthetic multicellular system for programmed pattern formation. Nature 2005, 434, 1130-1134.
35. (a) Cirak, F.; Cisternas, J. E.; Cuitino, A. M.; Ertl, G.; Holmes, P.; Kevrekidis, I. G.; Ortiz, M.; Rotermund, H. H.; Schunack, M.; Wolff, J. Oscillatory thermomechanical instability of an ultrathin catalyst. Science 2003, 300, 1932-1936.
36. (b) Mikhailov, A. S.; Showalter, K. Control of waves, patterns and turbulence in chemical systems. Phys. Rep.-Rev. Sec. Phys. Lett. 2006, 425, 79-194.
37. Gerdts, C. J.; Sharoyan, D. E.; Ismagilov, R. F. A synthetic reaction network: Chemical amplification using nonequilibrium autocatalytic reactions coupled in time. J. Am. Chem. Soc. 2004, 126, 6327-6331.
38. Kurin-Csorgei, K.; Epstein, I. R.; Orban, M. Systematic design of chemical oscillators using complexation and precipitation equilibria. Nature 2005, 433, 139-142.
39. (a) Song, H.; Chen, D. L.; Ismagilov, R. F. Reactions in droplets in microflulidic channels. Angew. Chem., Int. Ed. 2006, 45, 7336-7356.
40. (b) deMello, A. J. Control and detection of chemical reactions in microfluidic systems. Nature 2006, 442, 394-402.
41. (c) El-Ali, J.; Sorger, P. K.; Jensen, K. F. Cells on chips. Nature 2006, 442, 403-411.
42. (d) Squires, T. M.; Quake, S. R. Microfluidics: Fluid physics at the nanoliter scale. Rev. Mod. Phys. 2005, 77, 977-1026.
43. (e) Karlsson, M.; Davidson, M.; Karlsson, R.; Karlsson, A.; Bergenholtz, J.; Konkoli, Z.; Jesorka, A.; Lobovkina, T.; Hurtig, J.; Voinova, M.; Orwar, O. Biomimetic nanoscale reactors and networks. Annu. Rev. Phys. Chem. 2004, 55, 613-649.
44. (f) Whitesides, G. M. The origins and the future of microfluidics. Nature 2006, 442, 368-373.
45. (g) Mao, H. B.; Yang, T. L.; Cremer, P. S. A microfluidic device with a linear temperature gradient for parallel and combinatorial measurements. J. Am. Chem. Soc. 2002, 124, 4432-4435.
46. (h) Wheeler, A. R.; Throndset, W. R.; Whelan, R. J.; Leach, A. M.; Zare, R. N.; Liao, Y. H.; Farrell, K.; Manger, I. D.; Daridon, A. Microfluidic device for single-cell analysis. Anal. Chem. 2003, 75, 3581-3586.
47. (i) King, K. R.; Wang, S. H.; Irimia, D.; Jayaraman, A.; Toner, M.; Yarmush, M. L. A high-throughput microfluidic real-time gene expression living cell array. Lab Chip 2007, 7, 77-85.
48. Weibel, D. B.; DiLuzio, W. R.; Whitesides, G. M. Microfabrication meets microbiology. Nat. Rev. Microbiol. 2007, 5, 209-218.
49. (a) Takayama, S.; Ostuni, E.; LeDuc, P.; Naruse, K.; Ingber, D. E.; Whitesides, G. M. Laminar flows - Subcellular positioning of small molecules. Nature 2001, 411, 1016-1016.
50. (b) Jeon, N. L.; Baskaran, H.; Dertinger, S. K. W.; Whitesides, G. M.; Van de Water, L.; Toner, M. Neutrophil chemotaxis in linear and complex gradients of interleukin-8 formed in a microfabricated device. Nat. Biotechnol. 2002, 20, 826-830.
51. (c) Olofsson, J.; Bridle, H.; Sinclair, J.; Granfeldt, D.; Sahlin, E.; Orwar, O. A chemical waveform synthesizer. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 8097-8102.
52. (a) Chin, V. I.; Taupin, P.; Sanga, S.; Scheel, J.; Gage, F. H.; Bhatia, S. N. Microfabricated platform for studying stem cell fates. Biotechnol. Bioeng. 2004, 88, 399-415.
53. (b) Lee, P. J.; Hung, P. J.; Shaw, R.; Jan, L.; Lee, L. P. Microfluidic application-specific integrated device for monitoring direct cell-cell communication via gap junctions between individual cell pairs. Appl. Phys. Lett. 2005, 86, 223902.
54. (a) DiLuzio, W. R.; Turner, L.; Mayer, M.; Garstecki, P.; Weibel, D. B.; Berg, H. C.; Whitesides, G. M. Escherichia coli swim on the right-hand side. Nature 2005, 435, 1271-1274.
55. (b) Mao, H. B.; Cremer, P. S.; Manson, M. D. A sensitive, versatile microfluidic assay for bacterial chemotaxis. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 5449-5454.
56. (a) Keymer, J. E.; Galajda, P.; Muldoon, C.; Park, S.; Austin, R. H. Bacterial metapopulations in nanofabricated landscapes. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 17290-17295.
57. (b) Balagadde, F. K.; You, L. C.; Hansen, C. L.; Arnold, F. H.; Quake, S. R. Long-term monitoring of bacteria undergoing programmed population control in a microchemostat. Science 2005, 309, 137-140.
58. Groves, J. T.; Boxer, S. G. Micropattern formation in supported lipid membranes. Acc. Chem. Res. 2002, 35, 149-157.
59. Whitesides, G. M.; Ostuni, E.; Takayama, S.; Jiang, X. Y.; Ingber, D. E. Soft lithography in biology and biochemistry. Annu. Rev. Biomed. Eng. 2001, 3, 335-373.
60. (a) Mrksich, M. A surface chemistry approach to studying cell adhesion. Chem. Soc. Rev. 2000, 29, 267-273.
61. (b) Mossman, K. D.; Campi, G.; Groves, J. T.; Dustin, M. L. Altered TCR signaling from geometrically repatterned immunological synapses. Science 2005, 310, 1191-1193.
62. Langer, R.; Tirrell, D. A. Designing materials for biology and medicine. Nature 2004, 428, 487-492.
63. Nagypal, I.; Epstein, I. R. Systematic design of chemical oscillators. 37. Fluctuations and stirring rate effects in the chlorite thiosulfate reaction. J. Phys. Chem. 1986, 90, 6285-6292.
64. Kastrup, C.-J.; Shen, F.; Ismagilov, R. F. Response to shape emerges in a complex biochemical network and its simple chemical analogue. Angew. Chem., Int. Ed. 2007, 46, 3660-3662.
65. Kastrup, C. J.; Shen, F.; Runyon, M. K.; Ismagilov, R. F. Characterization of the threshold response of initiation of blood clotting to stimulus patch size. Biophys. J. 2007, 93, 2969-2977.
66. Lobanova, E. S.; Ataullakhanov, F. I. Unstable trigger waves induce various intricate dynamic regimes in a reaction-diffusion system of blood clotting. Phys. Rev. Lett. 2003, 91, 138301.
67. De Renzis, S.; Elemento, O.; Tavazoie, S.; Wieschaus, E. F. Unmasking activation of the zygotic genome using chromosomal deletions in the Drosophila embryo. PLoS Biol. 2007, 5, 1036-1051.
68. For definitions and illustrations, see http://www.flybase.org.
69. (a) Mehra, A.; Hong, C. I.; Shi, M.; Loras, J. J.; Dunlap, J. C.; Ruoff, P. Circadian rhythmicity by autocatalysis. PLoS Comput. Biol. 2006, 2, 816-823.
70. (b) Hong, C. I.; Conrad, E. D.; Tyson, J. J. A proposal for robust temperature compensation of circadian rhythms. Proc. Natl. Acad. Sci. USA. 2007, 104, 1195-1200.
71. French, V.; Feast, M.; Partridge, L. Body size and cell size in Drosophila. The developmental response to temperature. J. Insect Physiol. 1998, 44, 1081-1089.
72. Lucchetta, E. M.; Munson, M. S.; Ismagilov, R. F. Characterization of the local temperature in space and time around a developing Drosophila embryo in a microfluidic device. Lab Chip 2006, 6, 185-190.