Confinement regulates complex biochemical networks: Initiation of blood clotting by "diffusion acting"

Biophysical Journal

Volumn 97, Issue 8, 2009, Pages 2137-2145

  Feng, Shen ^a   Pompano, Rebecca R ^a   Kastrup, Christian J ^a   Ismagilov, Rustem F ^a  

^a UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

THROMBOPLASTIN;

ARTICLE; BLOOD CLOTTING; DIFFUSION CHAMBER; ENZYME REGULATION; MICROFLUIDIC ANALYSIS; OUTCOME ASSESSMENT; PLATELET MICROPARTICLE; SIMULATION;

BACILLUS CEREUS; BACTERIA (MICROORGANISMS);

EID: 70449091917     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2009.08.004     Document Type: Article

References (48)

1. Han, W. Q., S. S. Fan, Q. Q. Li, and Y. D. Hu. 1997. Synthesis of gallium nitride nanorods through a carbon nanotube-confined reaction. Science. 277:1287-1289.
2. Ajami, D., and J. Rebek. 2007. Adaptations of guest and host in expanded self-assembled capsules. Proc. Natl. Acad. Sci. USA. 104: 16000-16003.
3. Kreft, O., M. Prevot, H. Mohwald, and G. B. Sukhorukov. 2007. Shellin- shell microcapsules: a novel tool for integrated, spatially confined enzymatic reactions. Angew. Chem. Int. Ed. 46:5605-5608.
4. Nicholson, C. 2005. Factors governing diffusing molecular signals in brain extracellular space. J. Neural Transm. 112:29-44. (Pubitemid 40104715)
5. Verkman, A. S. 2002. Solute and macromolecule diffusion in cellular aqueous compartments. Trends Biochem. Sci. 27:27-33.
6. Brinker, A., G. Pfeifer, M. J. Kerner, D. J. Naylor, F. U. Hartl, et al. 2001. Dual function of protein confinement in chaperonin-assisted protein folding. Cell. 107:223-233. (Pubitemid 33035948)
7. Yu, H. M., I. Meyvantsson, I. A. Shkel, and D. J. Beebe. 2005. Diffusion dependent cell behavior in microenvironments. Lab Chip. 5:1089-1095.
8. Yu, H. M., C. M. Alexander, and D. J. Beebe. 2007. Understanding microchannel culture: parameters involved in soluble factor signaling. Lab Chip. 7:726-730.
9. Park, S., P. M. Wolanin, E. A. Yuzbashyan, H. Lin, N. C. Darnton, et al. 2003. Influence of topology on bacterial social interaction. Proc. Natl. Acad. Sci. USA. 100:13910-13915.
10. Redfield, R. J. 2002. Is quorum sensing a side effect of diffusion sensing? Trends Microbiol. 10:365-370.
11. Hense, B. A., C. Kuttler, J. Mueller, M. Rothballer, A. Hartmann, et al. 2007. Opinion - does efficiency sensing unify diffusion and quorum sensing? Nat. Rev. Microbiol. 5:230-239.
12. Horswill, A. R., P. Stoodley, P. S. Stewart, and M. R. Parsek. 2007. The effect of the chemical, biological, and physical environment on quorum sensing in structured microbial communities. Anal. Bioanal. Chem. 387:371-380.
13. Dulla, G., and S. E. Lindow. 2008. Quorum size of Pseudomonas syringae is small and dictated by water availability on the leaf surface. Proc. Natl. Acad. Sci. USA. 105:3082-3087.
14. Boedicker, J. Q., M. E. Vincent, and R. F. Ismagilov. 2009. Microfluidic confinement of single cells of bacteria in small volumes initiates high-density behavior of quorum sensing and growth and reveals its variability. Angew. Chem. 48:5908-5911.
15. Kastrup, C. J., M. K. Runyon, F. Shen, and R. F. Ismagilov. 2006. Modular chemical mechanism predicts spatiotemporal dynamics of initiation in the complex network of hemostasis. Proc. Natl. Acad. Sci. USA. 103:15747-15752.
16. Kastrup, C. J., J. Q. Boedicker, A. P. Pomerantsev, M. Moayeri, Y. Bian, et al. 2008. Spatial localization of bacteria controls coagulation of human blood by "quorum acting". Nat. Chem. Biol. 4:742-750.
17. Shen, F., C. J. Kastrup, and R. F. Ismagilov. 2008. Using microfluidics to understand the effect of spatial distribution of tissue factor on blood coagulation. Thromb. Res. 122:S27-S30.
18. Basmadjian, D. 1990. The effect of flow and mass-transport in thrombogenesis. Ann. Biomed. Eng. 18:685-709.
19. Basmadjian, D., M. V. Sefton, and S. A. Baldwin. 1997. Coagulation on biomaterials in flowing blood: some theoretical considerations. Biomaterials. 18:1511-1522. (Pubitemid 27518548)
20. Okorie, U. M., W. S. Denney, M. S. Chatterjee, K. B. Neeves, and S. L. Diamond. 2008. Determination of surface tissue factor thresholds that trigger coagulation at venous and arterial shear rates: amplification of 100 fM circulating tissue factor requires flow. Blood. 111:3507-3513.
21. Shen, F., C. J. Kastrup, Y. Liu, and R. F. Ismagilov. 2008. Threshold response of initiation of blood coagulation by tissue factor in patterned microfluidic capillaries is controlled by shear rate. Arterioscler. Thromb. Vasc. Biol. 28:2035-2041.
22. Runyon, M. K., B. L. Johnson-Kerner, C. J. Kastrup, T. G. Van Ha, and R. F. Ismagilov. 2007. Propagation of blood clotting in the complex biochemical network of hemostasis is described by a simple mechanism. J. Am. Chem. Soc. 129:7014-7015.
23. Jesty, J., and E. Beltrami. 2005. Positive feedbacks of coagulation-their role in threshold regulation. Arterioscler. Thromb. Vasc. Biol. 25:2463-2469.
24. Pompano, R. R., H. W. Li, and R. F. Ismagilov. 2008. Rate of mixing controls rate and outcome of autocatalytic processes: theory and micro- fluidic experiments with chemical reactions and blood coagulation. Biophys. J. 95:1531-1543.
25. Morrissey, J. H. 2001. Tissue factor: an enzyme cofactor and a true receptor. Thromb. Haemost. 86:66-74.
26. Mackman, N., R. E. Tilley, and N. S. Key. 2007. Role of the extrinsic pathway of blood coagulation in hemostasis and thrombosis. Arterioscler. Thromb. Vasc. Biol. 27:1687-1693.
27. Hockin, M. F., K. C. Jones, S. J. Everse, and K. G. Mann. 2002. A model for the stoichiometric regulation of blood coagulation. J. Biol. Chem. 277:18322-18333.
28. Kogan, A. E., D. V. Kardakov, and M. A. Khanin. 2001. Analysis of the activated partial thromboplastin time test using mathematical modeling. Thromb. Res. 101:299-310.
29. Jones, K. C., and K. G. Mann. 1994. A model for the tissue factor pathway to thrombin. 2. A mathematical simulation. J. Biol. Chem. 269:23367-23373.
30. Kockmann, N. 2008. Transport Phenomena in Micro Process Engineering. Springer, Berlin/Heidelberg.
31. Epstein, I. R. 1995. The consequences of imperfect mixing in autocatalytic chemical and biological systems. Nature. 374:321-327.
32. Aroesty, J., and J. F. Gross. 1970. Convection and diffusion in the micro circulation. Microvasc. Res. 2:247-267.
33. Hinshaw, L. B. 1996. Sepsis/septic shock: participation of the microcirculation: an abbreviated review. Crit. Care Med. 24:1072-1078.
34. Zeerleder, S., C. E. Hack, and W. A. Wuillemin. 2005. Disseminated intravascular coagulation in sepsis. Chest. 128:2864-2875.
35. Bogdanov, V. Y., V. Balasubramanian, J. Hathcock, O. Vele, M. Lieb, et al. 2003. Alternatively spliced human tissue factor: a circulating, soluble, thrombogenic protein. Nat. Med. 9:458-462.
36. Esmon, C. T. 1989. The roles of protein-C and thrombomodulin in the regulation of blood-coagulation. J. Biol. Chem. 264:4743-4746.
37. Dittrich, P. S., M. Jahnz, and P. Schwille. 2005. A new embedded process for compartmentalized cell-free protein expression and on-line detection in microfluidic devices. ChemBioChem. 6:811-814.
38. He, M. Y., J. S. Edgar, G. D. M. Jeffries, R. M. Lorenz, J. P. Shelby, et al. 2005. Selective encapsulation of single cells and subcellular organelles into picoliter- and femtoliter-volume droplets. Anal. Chem. 77:1539-1544.
39. Um, E., D. S. Lee, H. B. Pyo, and J. K. Park. 2008. Continuous generation of hydrogel beads and encapsulation of biological materials using a microfluidic droplet-merging channel. Microfluid. Nanofluidics. 5:541-549.
40. Huebner, A., L. F. Olguin, D. Bratton, G. Whyte, W. T. S. Huck, et al. 2008. Development of quantitative cell-based enzyme assays in microdroplets. Anal. Chem. 80:3890-3896.
41. Koster, S., F. E. Angile, H. Duan, J. J. Agresti, A. Wintner, et al. 2008. Drop-based microfluidic devices for encapsulation of single cells. Lab Chip. 8:1110-1115.
42. Clausell-Tormos, J., D. Lieber, J. C. Baret, A. El-Harrak, O. J. Miller, et al. 2008. Droplet-based microfluidic platforms for the encapsulation and screening of mammalian cells and multicellular organisms. Chem. Biol. 15:427-437.
43. Boedicker, J. Q., L. Li, T. R. Kline, and R. F. Ismagilov. 2008. Detecting bacteria and determining their susceptibility to antibiotics by stochastic confinement in nanoliter droplets using plug-based microfluidics. Lab Chip. 8:1265-1272.
44. Wu, L. Y., D. Di Carlo, and L. P. Lee. 2008. Microfluidic self-assembly of tumor spheroids for anticancer drug discovery. Biomed. Microdevices. 10:197-202.
45. Bradshaw, E. M., S. C. Kent, V. Tripuraneni, T. Orban, H. L. Ploegh, et al. 2008. Concurrent detection of secreted products from human lymphocytes by microengraving: cytokines and antigen-reactive antibodies. Clin. Immunol. 129:10-18.
46. Ramunas, J., M. Illman, A. Kam, K. Farn, L. Kelly, et al. 2006. True monolayer cell culture in a confined 3D microenvironment enables lineage informatics. Cytometry A. 69A:1202-1211.
47. Mann, K. G., K. Brummel, and S. Butenas. 2003. What is all that thrombin for? J. Thromb. Haemost. 1:1504-1514.
48. Grossman, Z., and W. E. Paul. 1992. Adaptive cellular interactions in the immune-system - the tunable activation threshold and the signifi- cance of subthreshold responses. Proc. Natl. Acad. Sci. USA. 89:10365-10369.