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2018 | OriginalPaper | Chapter

Bacterial Chemotaxis: A Classic Example of Multiscale Modeling in Biology

Author : Chuan Xue

Published in: Cell Movement

Publisher: Springer International Publishing

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Abstract

Both individual-based models and PDE models have been developed to describe the active movement of cell populations in various contexts. Individual-based models can faithfully replicate the detailed mechanisms of cell signaling and movement but are computationally intensive. PDE models are amenable for fast computation and mathematical analysis but are often based on phenomenological descriptions of macroscopic cell fluxes. Multiscale methods must be developed to elucidate the connections between individual-based models and PDE models in order to combine the strengths of these approaches. This chapter summarizes recent progress in connecting individual-based models and PDE models for chemotaxis of bacterial populations, which is a classic example for multiscale modeling in biology. The application scope and limitations of the Keller-Segel chemotaxis equation are also discussed.

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Literature
1.
go back to reference Sean P Cook, Charles J Brokaw, Charles H Muller, and Donner F Babcock. Sperm chemotaxis: egg peptides control cytosolic calcium to regulate flagellar responses. Developmental biology, 165(1):10–19, 1994.CrossRef Sean P Cook, Charles J Brokaw, Charles H Muller, and Donner F Babcock. Sperm chemotaxis: egg peptides control cytosolic calcium to regulate flagellar responses. Developmental biology, 165(1):10–19, 1994.CrossRef
2.
go back to reference Robert F Diegelmann, Melissa C Evans, et al. Wound healing: an overview of acute, fibrotic and delayed healing. Front Biosci, 9(1):283–289, 2004.CrossRef Robert F Diegelmann, Melissa C Evans, et al. Wound healing: an overview of acute, fibrotic and delayed healing. Front Biosci, 9(1):283–289, 2004.CrossRef
3.
go back to reference P. Friedl and D. Gilmour. Collective cell migration in morphogenesis, regeneration and cancer. Nat Rev Mol Cell Biol, 10(7):445–457, Jul 2009.CrossRef P. Friedl and D. Gilmour. Collective cell migration in morphogenesis, regeneration and cancer. Nat Rev Mol Cell Biol, 10(7):445–457, Jul 2009.CrossRef
4.
go back to reference G. Pandey and R. K. Jain. Bacterial chemotaxis toward environmental pollutants: role in bioremediation. Appl Environ Microbiol, 68(12):5789–5795, Dec 2002.CrossRef G. Pandey and R. K. Jain. Bacterial chemotaxis toward environmental pollutants: role in bioremediation. Appl Environ Microbiol, 68(12):5789–5795, Dec 2002.CrossRef
5.
go back to reference J. P. Armitage, T. P. Pitta, M. A. Vigeant, H. L. Packer, and R. M. Ford. Transformations in flagellar structure of rhodobacter sphaeroides and possible relationship to changes in swimming speed. J Bacteriol, 181(16):4825–4833, Aug 1999. J. P. Armitage, T. P. Pitta, M. A. Vigeant, H. L. Packer, and R. M. Ford. Transformations in flagellar structure of rhodobacter sphaeroides and possible relationship to changes in swimming speed. J Bacteriol, 181(16):4825–4833, Aug 1999.
6.
go back to reference K. J. Duffy and R. M. Ford. Turn angle and run time distributions characterize swimming behavior for pseudomonas putida. J Bacteriol, 179(4):1428–1430, Feb 1997.CrossRef K. J. Duffy and R. M. Ford. Turn angle and run time distributions characterize swimming behavior for pseudomonas putida. J Bacteriol, 179(4):1428–1430, Feb 1997.CrossRef
7.
go back to reference C. V. Rao, J. R. Kirby, and A. P. Arkin. Design and diversity in bacterial chemotaxis: a comparative study in Escherichia coli and Bacillus subtilis. PLoS Biol, 2(2):E49, Feb 2004.CrossRef C. V. Rao, J. R. Kirby, and A. P. Arkin. Design and diversity in bacterial chemotaxis: a comparative study in Escherichia coli and Bacillus subtilis. PLoS Biol, 2(2):E49, Feb 2004.CrossRef
8.
go back to reference G. L. Hazelbauer. Bacterial chemotaxis: the early years of molecular studies. Annu Rev Microbiol, 66:285–303, Oct 2012.CrossRef G. L. Hazelbauer. Bacterial chemotaxis: the early years of molecular studies. Annu Rev Microbiol, 66:285–303, Oct 2012.CrossRef
9.
go back to reference D. E. Koshland. Bacterial Chemotaxis as a Model Behavioral System. Raven Press, New York, 1980. D. E. Koshland. Bacterial Chemotaxis as a Model Behavioral System. Raven Press, New York, 1980.
10.
go back to reference H. C. Berg. Random Walks in Biology. Princeton University Press, 1983. H. C. Berg. Random Walks in Biology. Princeton University Press, 1983.
11.
go back to reference X. Xin and H. G. Othmer. A “trimer of dimers”-based model for the chemotactic signal transduction network in bacterial chemotaxis. Bull Math Biol, 74(10):2339–2382, Oct 2012.MathSciNetCrossRef X. Xin and H. G. Othmer. A “trimer of dimers”-based model for the chemotactic signal transduction network in bacterial chemotaxis. Bull Math Biol, 74(10):2339–2382, Oct 2012.MathSciNetCrossRef
12.
13.
go back to reference Julius Adler. Effect of amino acids and oxygen on chemotaxis in escherichia coli. Journal of bacteriology, 92(1):121–129, 1966. Julius Adler. Effect of amino acids and oxygen on chemotaxis in escherichia coli. Journal of bacteriology, 92(1):121–129, 1966.
14.
go back to reference Julius Adler. Chemotaxis in bacteria. Annual review of biochemistry, 44(1):341–356, 1975.CrossRef Julius Adler. Chemotaxis in bacteria. Annual review of biochemistry, 44(1):341–356, 1975.CrossRef
15.
go back to reference E. O. Budrene and H. C. Berg. Complex patterns formed by motile cells of Escherichia coli. Nature, 349(6310):630–633, February 1991.CrossRef E. O. Budrene and H. C. Berg. Complex patterns formed by motile cells of Escherichia coli. Nature, 349(6310):630–633, February 1991.CrossRef
16.
go back to reference E. O. Budrene and H. C. Berg. Dynamics of formation of symmetrical patterns by chemotactic bacteria. Nature, 376(6535):49–53, 1995.CrossRef E. O. Budrene and H. C. Berg. Dynamics of formation of symmetrical patterns by chemotactic bacteria. Nature, 376(6535):49–53, 1995.CrossRef
17.
go back to reference C. Xue, E. O. Budrene, and H. G. Othmer. Radial and spiral stream formation in Proteus mirabilis colonies. PLoS Comput Biol, 7(12):e1002332, 12 2011.CrossRef C. Xue, E. O. Budrene, and H. G. Othmer. Radial and spiral stream formation in Proteus mirabilis colonies. PLoS Comput Biol, 7(12):e1002332, 12 2011.CrossRef
18.
go back to reference B. Franz, C. Xue, K. J. Painter, and R. Erban. Travelling waves in hybrid chemotaxis models. Bull Math Biol, 76(2):377–400, Feb 2014.MathSciNetCrossRef B. Franz, C. Xue, K. J. Painter, and R. Erban. Travelling waves in hybrid chemotaxis models. Bull Math Biol, 76(2):377–400, Feb 2014.MathSciNetCrossRef
19.
go back to reference X. Xue, C. Xue, and M. Tang. The role of intracellular signaling in the stripe formation in engineered E. coli populations. submitted, 2017. X. Xue, C. Xue, and M. Tang. The role of intracellular signaling in the stripe formation in engineered E. coli populations. submitted, 2017.
20.
go back to reference A Decoene, A Lorz, S Martin, B Maury, and M Tang. Simulation of self-propelled chemotactic bacteria in a stokes flow. In ESAIM: proceedings, volume 30, pages 104–123. EDP Sciences, 2010. A Decoene, A Lorz, S Martin, B Maury, and M Tang. Simulation of self-propelled chemotactic bacteria in a stokes flow. In ESAIM: proceedings, volume 30, pages 104–123. EDP Sciences, 2010.
21.
go back to reference A. Decoene, S. Martin, and B. Maury. Microscopic modelling of active bacterial suspensions. Mathematical Modelling of Natural Phenomena, 6:98–129, 2011.MathSciNetCrossRef A. Decoene, S. Martin, and B. Maury. Microscopic modelling of active bacterial suspensions. Mathematical Modelling of Natural Phenomena, 6:98–129, 2011.MathSciNetCrossRef
22.
go back to reference Robert Dillon, Lisa Fauci, and III Donald Gaver. A microscale model of bacterial swimming, chemotaxis and substrate transport. Journal of Theoretical Biology, 177(4):325–340, 1995. Robert Dillon, Lisa Fauci, and III Donald Gaver. A microscale model of bacterial swimming, chemotaxis and substrate transport. Journal of Theoretical Biology, 177(4):325–340, 1995.
23.
go back to reference Heather Flores, Edgar Lobaton, Stefan Méndez-Diez, Svetlana Tlupova, and Ricardo Cortez. A study of bacterial flagellar bundling. Bulletin of Mathematical Biology, 67(1):137–168, 2005.MathSciNetCrossRef Heather Flores, Edgar Lobaton, Stefan Méndez-Diez, Svetlana Tlupova, and Ricardo Cortez. A study of bacterial flagellar bundling. Bulletin of Mathematical Biology, 67(1):137–168, 2005.MathSciNetCrossRef
24.
go back to reference J. P. Hernández-Ortiz, Ch. G. Stoltz, and M. D. Graham. Transport and collective dynamics in suspensions of confined swimming particles. Physical Review Letters, 95:204501, 2005. (doi:10.1103/PhysRevLett.95.204501). J. P. Hernández-Ortiz, Ch. G. Stoltz, and M. D. Graham. Transport and collective dynamics in suspensions of confined swimming particles. Physical Review Letters, 95:204501, 2005. (doi:10.1103/PhysRevLett.95.204501).
25.
go back to reference J. P. Hernández-Ortiz, P. T. Underhill, and M. D. Graham. Dynamics of confined suspensions of swimming particles. J. Phys.: Condens. Matter, 21(20):204107, 2009. J. P. Hernández-Ortiz, P. T. Underhill, and M. D. Graham. Dynamics of confined suspensions of swimming particles. J. Phys.: Condens. Matter, 21(20):204107, 2009.
26.
go back to reference S. D. Ryan, B. M. Haines, L. Berlyand, F. Ziebert, and I. S. Aranson. Viscosity of bacterial suspensions: Hydrodynamic interactions and self-induced noise. Physical Review E, 83(050904(R)), 2011. S. D. Ryan, B. M. Haines, L. Berlyand, F. Ziebert, and I. S. Aranson. Viscosity of bacterial suspensions: Hydrodynamic interactions and self-induced noise. Physical Review E, 83(050904(R)), 2011.
27.
go back to reference S. D. Ryan, A. Sokolov, L. Berlyand, and I. S. Aranson. Correlation properties of collective motion in bacterial suspensions. New Journal of Physics, 15:105021, 2013.CrossRef S. D. Ryan, A. Sokolov, L. Berlyand, and I. S. Aranson. Correlation properties of collective motion in bacterial suspensions. New Journal of Physics, 15:105021, 2013.CrossRef
28.
go back to reference H. G. Othmer, S. R. Dunbar, and W. Alt. Models of dispersal in biological systems. J. Math. Biol., 26(3):263–298, 1988.MathSciNetCrossRef H. G. Othmer, S. R. Dunbar, and W. Alt. Models of dispersal in biological systems. J. Math. Biol., 26(3):263–298, 1988.MathSciNetCrossRef
29.
go back to reference H. Othmer and C. Xue. The mathematical analysis of biological aggregation and dispersal: progress, problems and perspectives. In M. Lewis, P. Maini, and S. Petrovskii, editors, Dispersal, individual movement and spatial ecology: A mathematical perspective. Springer, 2013. H. Othmer and C. Xue. The mathematical analysis of biological aggregation and dispersal: progress, problems and perspectives. In M. Lewis, P. Maini, and S. Petrovskii, editors, Dispersal, individual movement and spatial ecology: A mathematical perspective. Springer, 2013.
30.
go back to reference H. C. Berg and D. Brown. Chemotaxis in Escherichia Coli analyzed by three-dimensional tracking. Nature, 239:502–507, 1972.CrossRef H. C. Berg and D. Brown. Chemotaxis in Escherichia Coli analyzed by three-dimensional tracking. Nature, 239:502–507, 1972.CrossRef
31.
go back to reference R. M. Macnab. Sensing the environment: Bacterial chemotaxis. In R. Goldberg, editor, Biological Regulation and Development, pages 377–412, New York, 1980. Plenum Press.CrossRef R. M. Macnab. Sensing the environment: Bacterial chemotaxis. In R. Goldberg, editor, Biological Regulation and Development, pages 377–412, New York, 1980. Plenum Press.CrossRef
32.
go back to reference P. Cluzel, M. Surette, and S. Leibler. An ultrasensitive bacterial motor revealed by monitoring signaling proteins in single cells. Science, 287:1652–1655, 2000.CrossRef P. Cluzel, M. Surette, and S. Leibler. An ultrasensitive bacterial motor revealed by monitoring signaling proteins in single cells. Science, 287:1652–1655, 2000.CrossRef
33.
go back to reference Clinton H Durney. A two-component model for bacterial chemotaxis, 2013. Clinton H Durney. A two-component model for bacterial chemotaxis, 2013.
34.
go back to reference H. G. Othmer, X. Xin, and C. Xue. Excitation and adaptation in bacteria-a model signal transduction system that controls taxis and spatial pattern formation. Int J Mol Sci, 14(5):9205–9248, 2013.CrossRef H. G. Othmer, X. Xin, and C. Xue. Excitation and adaptation in bacteria-a model signal transduction system that controls taxis and spatial pattern formation. Int J Mol Sci, 14(5):9205–9248, 2013.CrossRef
35.
go back to reference M. J. Tindall, S. L. Porter, P. K. Maini, G. Gaglia, and J. P. Armitage. Overview of mathematical approaches used to model bacterial chemotaxis I: the single cell. Bull Math Biol, 70(6):1525–1569, Aug 2008.MathSciNetCrossRef M. J. Tindall, S. L. Porter, P. K. Maini, G. Gaglia, and J. P. Armitage. Overview of mathematical approaches used to model bacterial chemotaxis I: the single cell. Bull Math Biol, 70(6):1525–1569, Aug 2008.MathSciNetCrossRef
36.
go back to reference R. Erban and H. G. Othmer. From individual to collective behavior in bacterial chemotaxis. SIAM J. Appl. Math., 65(2):361–391, 2004.MathSciNetCrossRef R. Erban and H. G. Othmer. From individual to collective behavior in bacterial chemotaxis. SIAM J. Appl. Math., 65(2):361–391, 2004.MathSciNetCrossRef
37.
go back to reference R. Erban and H. Othmer. From signal transduction to spatial pattern formation in E. coli: A paradigm for multiscale modeling in biology. Multiscale Modeling & Simulation 3(2):362–394, 2005.MathSciNetCrossRef R. Erban and H. Othmer. From signal transduction to spatial pattern formation in E. coli: A paradigm for multiscale modeling in biology. Multiscale Modeling & Simulation 3(2):362–394, 2005.MathSciNetCrossRef
38.
go back to reference C. Xue. Macroscopic equations for bacterial chemotaxis: integration of detailed biochemistry of cell signaling. J Math Biol, 70(1–2):1–44, Jan 2015.MathSciNetCrossRef C. Xue. Macroscopic equations for bacterial chemotaxis: integration of detailed biochemistry of cell signaling. J Math Biol, 70(1–2):1–44, Jan 2015.MathSciNetCrossRef
40.
41.
go back to reference E. F. Keller and L. A. Segel. Initiation of slime mold aggregation viewed as an instability. J. Theor. Biol., 26:399–415, 1970.CrossRef E. F. Keller and L. A. Segel. Initiation of slime mold aggregation viewed as an instability. J. Theor. Biol., 26:399–415, 1970.CrossRef
42.
go back to reference E. F. Keller and L. A. Segel. Model for chemotaxis. J. Theor. Biol., 30:225–234, 1971.CrossRef E. F. Keller and L. A. Segel. Model for chemotaxis. J. Theor. Biol., 30:225–234, 1971.CrossRef
43.
go back to reference E. F. Keller and L. A. Segel. Traveling bands of chemotactic bacteria: A theoretical analysis. J. Theor. Biol., 30:235–248, 1971.CrossRef E. F. Keller and L. A. Segel. Traveling bands of chemotactic bacteria: A theoretical analysis. J. Theor. Biol., 30:235–248, 1971.CrossRef
44.
go back to reference Benoit Perthame. Pde models for chemotactic movements: parabolic, hyperbolic and kinetic. Applications of Mathematics, 49(6):539–564, 2004.MathSciNetCrossRef Benoit Perthame. Pde models for chemotactic movements: parabolic, hyperbolic and kinetic. Applications of Mathematics, 49(6):539–564, 2004.MathSciNetCrossRef
45.
go back to reference M. J. Tindall, P. K. Maini, S. L. Porter, and J. P. Armitage. Overview of mathematical approaches used to model bacterial chemotaxis II: bacterial populations. Bull Math Biol, 70(6):1570–1607, Aug 2008.MathSciNetCrossRef M. J. Tindall, P. K. Maini, S. L. Porter, and J. P. Armitage. Overview of mathematical approaches used to model bacterial chemotaxis II: bacterial populations. Bull Math Biol, 70(6):1570–1607, Aug 2008.MathSciNetCrossRef
46.
go back to reference Mercedes A Rivero, Robert T Tranquillo, Helen M Buettner, and Douglas A Lauffenburger. Transport models for chemotactic cell populations based on individual cell behavior. Chemical engineering science, 44(12):2881–2897, 1989.CrossRef Mercedes A Rivero, Robert T Tranquillo, Helen M Buettner, and Douglas A Lauffenburger. Transport models for chemotactic cell populations based on individual cell behavior. Chemical engineering science, 44(12):2881–2897, 1989.CrossRef
47.
go back to reference T. Hillen and H. G. Othmer. The diffusion limit of transport equations derived from velocity-jump processes. SIAM J. Appl. Math., 61(3):751–775, 2000.MathSciNetCrossRef T. Hillen and H. G. Othmer. The diffusion limit of transport equations derived from velocity-jump processes. SIAM J. Appl. Math., 61(3):751–775, 2000.MathSciNetCrossRef
48.
go back to reference H. G. Othmer and T. Hillen. The diffusion limit of transport equations II: chemotaxis equations. SIAM J. Appl. Math., 62:1222–1250, 2002.MathSciNetCrossRef H. G. Othmer and T. Hillen. The diffusion limit of transport equations II: chemotaxis equations. SIAM J. Appl. Math., 62:1222–1250, 2002.MathSciNetCrossRef
49.
go back to reference F. A. C. C. Chalub, P. A. Markowich, B. Perthame, and C. Schmeiser. Kinetic models for chemotaxis and their drift-diffusion limits. Monatshefte für Mathematik, 142(1):123–141, 2004.MathSciNetCrossRef F. A. C. C. Chalub, P. A. Markowich, B. Perthame, and C. Schmeiser. Kinetic models for chemotaxis and their drift-diffusion limits. Monatshefte für Mathematik, 142(1):123–141, 2004.MathSciNetCrossRef
50.
go back to reference C. Xue and H. G. Othmer. Multiscale models of taxis-driven patterning in bacterial populations. SIAM J. Appl. Math., 70(1):133–167, 2009.MathSciNetCrossRef C. Xue and H. G. Othmer. Multiscale models of taxis-driven patterning in bacterial populations. SIAM J. Appl. Math., 70(1):133–167, 2009.MathSciNetCrossRef
51.
go back to reference Yevgeniy V. Kalinin, Lili Jiang, Yuhai Tu, and Mingming Wu. Logarithmic sensing in Escherichia coli bacterial chemotaxis. Biophys J, 96(6):2439–2448, Mar 2009.CrossRef Yevgeniy V. Kalinin, Lili Jiang, Yuhai Tu, and Mingming Wu. Logarithmic sensing in Escherichia coli bacterial chemotaxis. Biophys J, 96(6):2439–2448, Mar 2009.CrossRef
52.
go back to reference C. Xue and X. Yang. Moment-flux models for bacterial chemotaxis in large signal gradients. J Math Biol, 73(4):977–1000, 2016.MathSciNetCrossRef C. Xue and X. Yang. Moment-flux models for bacterial chemotaxis in large signal gradients. J Math Biol, 73(4):977–1000, 2016.MathSciNetCrossRef
53.
go back to reference J. E. Simons and P. A. Milewski. The volcano effect in bacterial chemotaxis. Mathematical and Computer Modelling, 53(7–8):1374–1388, 2011.MathSciNetCrossRef J. E. Simons and P. A. Milewski. The volcano effect in bacterial chemotaxis. Mathematical and Computer Modelling, 53(7–8):1374–1388, 2011.MathSciNetCrossRef
54.
go back to reference B. Franz, C. Xue, K. Painter, and R. Erban. Travelling waves in hybrid chemotaxis models. Bull. Math. Biol., 2014. B. Franz, C. Xue, K. Painter, and R. Erban. Travelling waves in hybrid chemotaxis models. Bull. Math. Biol., 2014.
Metadata
Title
Bacterial Chemotaxis: A Classic Example of Multiscale Modeling in Biology
Author
Chuan Xue
Copyright Year
2018
DOI
https://doi.org/10.1007/978-3-319-96842-1_6

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