A Comparison of Computational Models for Eukaryotic Cell Shape and Motility

PLoS Computational Biology

Volumn 8, Issue 12, 2012, Pages

  Holmes, William R ^a,b   Edelstein Keshet, Leah ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELL SIGNALING; CELLS; COMPUTATION THEORY; COMPUTATIONAL METHODS; CYTOLOGY; FLOW OF FLUIDS; VISCOELASTICITY;

CELL MECHANICS; CELL MOTILITY; CELL SHAPES; COMPUTATIONAL MODELLING; CYTOSKELETONS; EUKARYOTIC CELLS; EXTERNAL STIMULUS; SHAPE CHANGE; SIGNALING MOLECULES; SPACE AND TIME;

MACHINERY;

ACTIN FILAMENT; ARTICLE; CELL ADHESION; CELL ASSAY; CELL MOTILITY; CELL SHAPE; CELL TYPE; CORNEA CELL; CYTOSOL; DICTYOSTELIUM DISCOIDEUM; EUKARYOTIC CELL; FIBROBLAST; FISH; GEOMETRY; INTERMETHOD COMPARISON; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; MEDICAL DECISION MAKING; MOLECULAR DYNAMICS; NEMATODE; NEUTROPHIL; NONHUMAN; POLARIZATION; SACCHAROMYCES CEREVISIAE; SIGNAL TRANSDUCTION; SPERM;

EUKARYOTA;

EID: 84872032983     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002793     Document Type: Article

References (82)

1. Lee J, Ishihara A, Theriot J, Jacobson K, (1993) Principles of locomotion for simple-shaped cells. Nature 362: 167-171.
2. Jilkine A, Edelstein-Keshet L, (2011) A comparison of mathematical models for polarization of single eukaryotic cells in response to guided cues. PLoS Comput Biol 7: e1001121 doi:10.1371/journal.pcbi.1001121.
3. Goryachev A, Pokhilko A, (2008) Dynamics of Cdc42 network embodies a Turing-type mechanism of yeast cell polarity. FEBS Letters 582: 1437-1443.
4. Savage N, Layton A, Lew D, (2012) Mechanistic mathematical model of polarity in yeast. Mol Biol Cell 23: 1998-2013.
5. Sambeth R, Baumgaertner A, (2001) Locomotion of a two dimensional keratocyte model. J Biol Sys 9: 201-220.
6. Grimm H, Verkhovsky A, Mogilner A, Meister J, (2003) Analysis of actin dynamics at the leading edge of crawling cells: implications for the shape of keratocyte lamellipodia. Eur Biophys J 32: 563-577.
7. Rubinstein B, Jacobson K, Mogilner A, (2005) Multiscale two-dimensional modeling of a motile simple-shaped cell. Multiscale Model Sim 3: 413-439.
8. Mareé AF, Jilkine A, Dawes A, Grieneisen VA, Edelstein-Keshet L, (2006) Polarization and movement of keratocytes: a multiscale modelling approach. Bull Math Biol 68 (5) (): 1169-1211.
9. Rubinstein B, Fournier M, Jacobson K, Verkhovsky A, Mogilner A, (2009) Actin-myosin viscoelastic flow in the keratocyte lamellipod. Biophys J 97: 1853-1863.
10. Herant M, Dembo M, (2010) Form and function in cell motility: from fibroblasts to keratocytes. Biophys J 98: 1408-1417.
11. Shao D, Levine H, Rappel W, (2012) Coupling actin flow, adhesion, and morphology in a computational cell motility model. Proc Natl Acad Sci 109: 6851-6856.
12. Marée A, Grieneisen V, Edelstein-Keshet L, (2012) How cells integrate complex stimuli: the effect of feedback from phosphoinositides and cell shape on cell polarization and motility. PLoS Comput Biol 8: e1002402 doi:10.1371/journal.pcbi.1002402.
13. Wolgemuth C, Stajic J, Mogilner A, (2010) Redundant mechanisms for stable cell locomotion revealed by minimal models. Biophys J 98: 160.
14. Mogilner A, Edelstein-Keshet L, (2002) Regulation of actin dynamics in rapidly moving cells: a quantitative analysis. Biophys J 83: 1237-1258.
15. Meinhardt H, (1999) Orientation of chemotactic cells and growth cones: models and mechanisms. J Cell Sci 112: 2867-2874.
16. Neilson M, Mackenzie J, Webb S, Insall R, (2011) Modelling cell movement and chemotaxis pseudopod based feedback. SIAM J Sci Comput 33: 1035-1057.
17. Neilson M, Veltman D, van Haastert P, Webb S, Mackenzie J, et al. (2011) Chemotaxis: a feedback based computational model robustly predicts multiple aspects of real cell behaviour. PLoS Biol 9: e1000618 doi:10.1371/journal.pbio.1000618.
18. Hecht I, Skoge M, Charest P, Ben-Jacob E, Firtel R, et al. (2011) Activated membrane patches guide chemotactic cell motility. PLoS Comput Biol 7: e1002044 doi:10.1371/journal.pcbi.1002044.
19. Hecht I, Levine H, Rappel W, Ben-Jacob E, (2011) "Self-assisted" amoeboid navigation in complex environments. PLoS ONE 6: e21955 doi:10.1371/journal.pone.0021955.
20. Insall R, (2010) Understanding eukaryotic chemotaxis: a pseudopod-centred view. Nat Rev Mol Cell Biol 11: 453-458.
21. Levchenko A, Iglesias P, (2002) Models of eukaryotic gradient sensing: application to chemotaxis of amoebae and neutrophils. Biophys J 82: 50-63.
22. Ma L, Janetopoulos C, Yang L, Devreotes P, Iglesias P, (2004) Two complementary, local excitation, global inhibition mechanisms acting in parallel can explain the chemoattractant-induced regulation of PI (3, 4, 5) P3 response in Dictyostelium cells. Biophys J 87: 3764-3774.
23. Janetopoulos C, Ma L, Devreotes P, Iglesias P, (2004) Chemoattractant-induced phosphatidylinositol 3, 4, 5-trisphosphate accumulation is spatially amplified and adapts, independent of the actin cytoskeleton. Proc Natl Acad Sci U S A 101: 8951-8956.
24. Xiong Y, Huang C, Iglesias P, Devreotes P, (2010) Cells navigate with a local-excitation, global-inhibition-biased excitable network. Proc Natl Acad Sci 107: 17079-17086.
25. Xu J, Wang F, Van Keymeulen A, Herzmark P, Straight A, et al. (2003) Divergent signals and cytoskeletal assemblies regulate self-organizing polarity in neutrophils. Cell 114: 201-214.
26. Wong K, Pertz O, Hahn K, Bourne H, (2006) Neutrophil polarization: spatiotemporal dynamics of RhoA activity support a self-organizing mechanism. Proc Natl Acad Sci 103: 3639-3644.
27. Strychalski W, Adalsteinsson D, Elston T, (2010) Simulating biochemical signaling networks in complex moving geometries. SIAM J Sci Comput 32: 3039-3070.
28. Vanderlei B, Feng J, Edelstein-Keshet L, (2011) A computational model of cell polarization and motility coupling mechanics and biochemistry. Multiscale Model Simul 9: 1420-1443.
29. Jilkine A, Marée AFM, Edelstein-Keshet L, (2007) Mathematical model for spatial segregation of the Rho-family GTPases based on inhibitory crosstalk. Bull Math Biol 69: 1943-1978.
30. Herant M, Marganski W, Dembo M, (2003) The mechanics of neutrophils: synthetic modeling of three experiments. Biophys J 84: 3389-3413.
31. Herant M, Heinrich V, Dembo M, (2005) Mechanics of neutrophil phagocytosis: behavior of the cortical tension. J Cell Sci 118: 1789-1797.
32. Herant M, Heinrich V, Dembo M, (2006) Mechanics of neutrophil phagocytosis: experiments and qualitative models. J Cell Sci 119: 1903-1913.
33. Stéphanou A, Mylona E, Chaplain M, Tracqui P, (2008) A computational model of cell migration coupling the growth of focal adhesions with oscillatory cell protrusions. J Theor Biol 253: 701-716.
34. Bottino D, Mogilner A, Roberts T, Stewart M, Oster G, (2002) How nematode sperm crawl. J Cell Sci 115: 367-384.
35. Wolgemuth C, Miao L, Vanderlinde O, Roberts T, Oster G, (2005) MSP dynamics drives nematode sperm locomotion. Biophys J 88: 2462-2471.
36. Zajac M, Dacanay B, Mohler W, Wolgemuth C, (2008) Depolymerization-driven flow in nematode spermatozoa relates crawling speed to size and shape. Biophys J 94: 3810-3823.
37. Nishimura S, Sasai M, (2007) Modulation of the reaction rate of regulating protein induces large morphological and motional change of amoebic cell. J Theor Biol 245: 230-237.
38. Mitchison T, Cramer L, (1996) Actin-based cell motility and cell locomotion. Cell 84: 371-379.
39. Pollard T, Blanchoin L, Mullins R, (2000) Molecular mechanisms controlling actin filament dynamics in nonmuscle cells. Ann Rev Bioph Biom 29: 545-576.
40. Lacayo C, Pincus Z, VanDuijn M, Wilson C, Fletcher D, et al. (2007) Emergence of large-scale cell morphology and movement from local actin filament growth dynamics. PLoS Biol 5: e233 doi:10.1371/journal.pbio.0050233.
41. Gracheva M, Othmer H, (2004) A continuum model of motility in ameboid cells. Bull Math Biol 66: 167-193.
42. Larripa K, Mogilner A, (2006) Transport of a 1D viscoelastic actin-myosin strip of gel as a model of a crawling cell. Physica A 372: 113-123.
43. Kabaso D, Shlomovitz R, Schloen K, Stradal T, Gov N, (2011) Theoretical model for cellular shapes driven by protrusive and adhesive forces. PLoS Comput Biol 7: e1001127 doi:10.1371/journal.pcbi.1001127.
44. Gierer A, Meinhardt H, (1972) A theory of biological pattern formation. Kybernetik 12: 30-39.
45. Meinhardt H, Gierer A, (1974) Application of a theory of biological pattern formation based on lateral inhibition. J Cell Sci 15: 321-346.
46. Satulovsky J, Lui R, Wang Y, (2008) Exploring the control circuit of cell migration by mathematical modeling. Biophys J 94: 3671-3683.
47. Osher S, Sethian JA, (1988) Fronts propagating with curvature-dependent speed: algorithms based on Hamilton-Jacobi formulations. J Comp Phys 79: 12-49.
48. Wolgemuth C, Zajac M, (2010) The moving boundary node method: a level set-based, finite volume algorithm with applications to cell motility. J Comp Phys 229 (19) (): 7287-7308.
49. Kockelkoren J, Levine H, Rappel W, (2003) Computational approach for modeling intra-and extracellular dynamics. Phys Rev E 68: 037702.
50. Li X, Lowengrub J, Ratz A, Voigt A, (2009) Solving PDEs in complex geometries: a diffuse domain approach. Commun Math Sci 7: 81-107.
51. Bueno-Orovio A, Pérez-García V, Fenton F, (2004) Spectral methods for partial differential equations in irregular domains: the spectral smoothed boundary method. Arxiv preprint math/0406327.
52. Shao D, Rappel WJ, Levine H, (2010) Computational model for cell morphodynamics. Phys Rev Lett 105: 108104.
53. Odell G, Oster G, Burnside B, Alberch P, (1980) A mechanical model for epithelial morphogenesis. J Math Biol 9: 291-295.
54. Odell G, Oster G, Alberch P, Burnside B, (1981) The mechanical basis of morphogenesis: I. epithelial folding and invagination. Dev Biol 85: 446-462.
55. Weliky M, Oster G, (1990) The mechanical basis of cell rearrangement. I. Epithelial morphogenesis during Fundulus epiboly. Development 109: 373-386.
56. Weliky M, Minsuk S, Keller R, Oster G, (1991) Notochord morphogenesis in Xenopus laevis: simulation of cell behavior underlying tissue convergence and extension. Development 113: 1231-1244.
57. Zhu C, Skalak R, (1988) A continuum model of protrusion of pseudopod in leukocytes. Biophys J 54: 1115-1137.
58. Mori Y, Jilkine A, Edelstein-Keshet L, (2008) Wave-pinning and cell polarity from a bistable reaction-diffusion system. Biophys J 94: 3684-3697.
59. Cogan N, Guy R, (2010) Multiphase flow models of biogels from crawling cells to bacterial biofilms. HFSP J 4: 11-25.
60. Dembo M, Harlow F, (1986) Cell motion, contractile networks, and the physics of interpenetrating reactive flow. Biophys J 50: 109-121.
61. He X, Dembo M, (1997) On the mechanics of the first cleavage division of the sea urchin egg. Exp Cell Res 233: 252-273.
62. Alt W, Dembo M, (1999) Cytoplasm dynamics and cell motion: two-phase flow models. Math Biosci 156: 207-228.
63. Kuusela E, Alt W, (2009) Continuum model of cell adhesion and migration. J Math Biol 58: 135-161.
64. Doubrovinski K, Kruse K, (2011) Cell motility resulting from spontaneous polymerization waves. Phys Rev Lett 107: 258103-258108.
65. Onsum MD, Wong K, Herzmark P, Bourne HR, Arkin AP, (2006) Morphology matters in immune cell chemotaxis: membrane asymmetry affects amplification. Phys Biol 3: 190-199.
66. Kholodenko BN, (2006) Cell-signalling dynamics in time and space. Nat Rev Mol Cell Biol 7: 165-176.
67. Meyers J, Craig J, Odde DJ, (2006) Potential for control of signaling pathways via cell size and shape. Curr Biol 16: 1685-1693.
68. Neves SR, Tsokas P, Sarkar A, Grace EA, Rangamani P, et al. (2008) Cell shape and negative links in regulatory motifs together control spatial information flow in signaling networks. Cell 133: 666-680.
69. Holmes W, Lin B, Levchenko A, Edelstein-Keshet L, (2012) Modelling cell polarization driven by synthetic spatially graded Rac activation. PLoS Comput Biol 8: e1002366 doi:10.1371/journal.pcbi.1002366.
70. Novak I, Slepchenko B, Mogilner A, (2008) Quantitative analysis of G-actin transport in motile cells. Biophys J 95: 1627-1638.
71. Loew L, Schaff J, (2001) The virtual cell: a software environment for computational cell biology. Trends Biotech 19: 401-406.
72. Ditlev J, Vacanti N, Novak I, Loew L, (2009) An open model of actin dendritic nucleation. Biophys J 96: 3529-3542.
73. Herant M, Dembo M, (2010) Cytopede: a three-dimensional tool for modeling cell motility on a flat surface. J Comput Biol 17: 1639-1677.
74. Keren K, Pincus Z, Allend GM, Barnhart EL, Marriott G, et al. (2008) Mechanism of shape determination in motile cells. Nature 453: 475-480.
75. Keren K, Yam P, Kinkhabwala A, Mogilner A, Theriot J, (2009) Intracellular fluid flow in rapidly moving cells. Nat Cell Biol 11: 1219-1224.
76. Prass M, Jacobson K, Mogilner A, Radmacher M, (2006) Direct measurement of the lamellipodial protrusive force in a migrating cell. J Cell Biol 174: 767-772.
77. Kim D, Wong P, Park J, Levchenko A, Sun Y, (2009) Microengineered platforms for cell mechanobiology. Ann Rev Biomed Eng 11: 203-233.
78. Smith K, Jasnow D, Balazs A, (2007) Designing synthetic vesicles that engulf nanoscopic particles. J Chem Phys 127: 084703.
79. Yalovsky S, Bloch D, Sorek N, Kost B, (2008) Regulation of membrane trafficking, cytoskeleton dynamics, and cell polarity by Rop/Rac GTPases. Plant Physiol 147: 1527-1543.
80. Goehring NW, Trong PK, Bois JS, Chowdhury D, Nicola EM, et al. (2011) Polarization of par proteins by advective triggering of a pattern-forming system. Science 334: 1137-1141.
81. Carlsson A, Sept D, (2008) Mathematical modeling of cell migration. Methods Cell Biol 84: 911-937.
82. Flaherty B, McGarry J, McHugh P, (2007) Mathematical models of cell motility. Cell Biochem Biophys 49: 14-28.