Modelling stripe formation in zebrafish: An agent-based approach

Journal of the Royal Society Interface

Volumn 12, Issue 112, 2015, Pages

  Volkening, Alexandria ^a   Sandstede, Björn ^a  

^a BROWN UNIVERSITY   (United States)

Author keywords

Agent based model; Growing domain; Pattern formation; Zebrafish

Indexed keywords

COMPUTATIONAL METHODS; LASER ABLATION;

AGENT-BASED APPROACH; AGENT-BASED MODEL; BLACK STRIPE; GROWING DOMAINS; LONG RANGE INTERACTIONS; PATTERN FORMATION; STRIPE PATTERN; ZEBRAFISH;

AUTONOMOUS AGENTS;

ANIMAL EXPERIMENT; MODEL; NONHUMAN; PIGMENT CELL; ZEBRA FISH; ANIMAL; BIOLOGICAL MODEL; MUTATION; PHYSIOLOGY; SKIN PIGMENTATION;

ANIMALS; MODELS, BIOLOGICAL; MUTATION; SKIN PIGMENTATION; ZEBRAFISH;

EID: 84948687017     PISSN: 17425689     EISSN: 17425662     Source Type: Journal    
DOI: 10.1098/rsif.2015.0812     Document Type: Article

References (40)

1. Dawid IB. 2004 Developmental biology of zebrafish. Ann. NY Acad. Sci. 1038, 88-93. (doi:10.1196/annals.1315.015)
2. Ceol CJ, Houvras Y, White RM, Zon LI. 2008 Melanoma biology and the promise of zebrafish. Zebrafish 5, 247-255. (doi:10.1089/zeb.2008.0544)
3. Howe K et al. 2013 The zebrafish reference genome sequence and its relationship to the human genome. Nature 496, 498-503. (doi:10.1038/nature12111)
4. Frohnhöfer HG, Krauss J, Maischein HM, Nüsslein-Volhard C. 2013 Iridophores and their interactions with other chromatophores are required for stripe formation in zebrafish. Development 140, 2997-3007. (doi:10.1242/dev.096719)
5. Nakamasu A, Takahashi G, Kanbe A, Kondo S. 2009 Interactions between zebrafish pigment cells responsible for the generation of Turing patterns. Proc. Natl Acad. Sci. USA 106, 8429-8434. (doi:10. 1073/pnas.0808622106)
6. Singh AP, Nüsslein-Volhard C. 2015 Zebrafish stripes as a model for vertebrate colour pattern formation. Curr. Biol. 25, R81-R92. (doi:10.1016/j.cub.2014. 11.013)
7. Hamada H, Watanabe M, Lau HE, Nishida T, Hasegawa T, Parichy DM, Kondo S. 2014 Involvement of Delta/Notch signaling in zebrafish adult pigment stripe patterning. Development 141, 318-324. (doi:10.1242/dev.099804)
8. Krauss J, Frohnhöfer HG, Walderich B, Maischein HM, Weiler C, Irion U, Nüsslein-Volhard C. 2014 Endothelin signalling in iridophore development and stripe pattern formation of zebrafish. Biol. Open 3, 503-509. (doi:10.1242/bio.20148441)
9. Oshima N, Kasai A. 2002 Iridophores involved in generation of skin color in the zebrafish, Brachydanio rerio. Forma-Tokyo 17, 91-101.
10. Singh AP, Schach U, Nüsslein-Volhard C. 2014 Proliferation, dispersal and patterned aggregation of iridophores in the skin prefigure striped colouration of zebrafish. Nat. Cell Biol. 16, 607-614. (doi:10. 1038/ncb2955)
11. Irion U, Frohnhöfer HG, Krauss J, Çolak Champollion T, Maischein HM, Geiger-Rudolph S, Weiler C, Nüsslein-Volhard C. 2014 Gap junctions composed of connexins 41.8 and 39.4 are essential for colour pattern formation in zebrafish. Elife 3, e05125. (doi:10.7554/eLife.05125)
12. McMenamin SK et al. 2014 Thyroid hormone-dependent adult pigment cell lineage and pattern in zebrafish. Science 345, 1358-1361. (doi:10. 1126/science.1256251)
13. Hirata M, Nakamura K, Kanemaru T, Shibata Y, Kondo S. 2003 Pigment cell organization in the hypodermis of zebrafish. Dev. Dyn. 227, 497-503. (doi:10.1002/dvdy.10334)
14. Parichy DM, Turner JM. 2003 Temporal and cellular requirements for Fms signaling during zebrafish adult pigment pattern development. Development 130, 817-833. (doi:10.1242/dev. 00307)
15. Mahalwar P, Walderich B, Singh AP, Nüsslein-Volhard C. 2014 Local reorganization of xanthophores fine-tunes and colors the striped pattern of zebrafish. Science 345, 1362-1364. (doi:10.1126/science.1254837)
16. Takahashi G, Kondo S. 2008 Melanophores in the stripes of adult zebrafish do not have the nature to gather, but disperse when they have the space to move. Pigment Cell Melanoma Res. 21, 677-686. (doi:10.1111/j.1755-148X.2008.00504.x)
17. Yamaguchi M, Yoshimoto E, Kondo S. 2007 Pattern regulation in the stripe of zebrafish suggests an underlying dynamic and autonomous mechanism. Proc. Natl Acad. Sci. USA 104, 4790-4793. (doi:10. 1073/pnas.0607790104)
18. Yamanaka H, Kondo S. 2014 In vitro analysis suggests that difference in cell movement during direct interaction can generate various pigment patterns in vivo. Proc. Natl Acad. Sci. USA 111, 1867-1872. (doi:10.1073/pnas.1315416111)
19. Inaba M, Yamanaka H, Kondo S. 2012 Pigment pattern formation by contact-dependent depolarization. Science 335, 677. (doi:10.1126/science.1212821)
20. Parichy DM, Ransom DG, Paw B, Zon LI, Johnson SL. 2000 An orthologue of the kit-related gene fms is required for development of neural crest-derived xanthophores and a subpopulation of adult melanocytes in the zebrafish, Danio rerio. Development 127, 3031-3044.
21. Maderspacher F, Nüsslein-Volhard C. 2003 Formation of the adult pigment pattern in zebrafish requires leopard and obelix dependent cell interactions. Development 130, 3447-3457. (doi:10.1242/dev.00519)
22. Parichy DM, Turner JM. 2003 Zebrafish puma mutant decouples pigment pattern and somatic metamorphosis. Dev. Biol. 256, 242-257. (doi:10. 1016/S0012-1606(03)00015-0)
23. Patterson LB, Bain EJ, Parichy DM. 2014 Pigment cell interactions and differential xanthophore recruitment underlying zebrafish stripe reiteration and Danio pattern evolution. Nat. Commun. 5, 5299. (doi:10.1038/ncomms6299)
24. Iwashita M, Watanabe M, Ishii M, Chen T, Johnson SL, Kurachi Y, Okada N, Kondo S. 2006 Pigment pattern in jaguar/obelix zebrafish is caused by a Kir7.1 mutation: implications for the regulation of melanosome movement. PLoS Genet. 2, e197. (doi:10.1371/journal.pgen.0020197)
25. Inoue S, Kondo S, Parichy DM, Watanabe M. 2014 Tetraspanin 3c requirement for pigment cell interactions and boundary formation in zebrafish adult pigment stripes. Pigment Cell Melanoma Res. 27, 190-200. (doi:10.1111/pcmr.12192)
26. Patterson LB, Parichy DM. 2013 Interactions with iridophores and the tissue environment required for patterning melanophores and xanthophores during zebrafish adult pigment stripe formation. PLoS Genet. 9, e1003561. (doi:10.1371/journal.pgen. 1003561)
27. Gaffney EA, Seirin Lee S. 2015 The sensitivity of Turing self-organization to biological feedback delays: 2D models of fish pigmentation. Math. Med. Biol. 32, 56-78. (doi:10.1093/imammb/dqt017)
28. Bullara D, De Decker Y. 2015 Pigment cell movement is not required for generation of Turing patterns in zebrafish skin. Nat. Commun. 6, 6971. (doi:10.1038/ncomms79710)
29. Moreira J, Deutsch A. 2005 Pigment pattern formation in zebrafish during late larval stages: a model based on local interactions. Dev. Dyn. 232, 33-42. (doi:10.1002/dvdy.20199)
30. Caicedo-Carvajal CE, Shinbrot T. 2008 In silico zebrafish pattern formation. Dev. Biol. 315, 397-403. (doi:10.1016/j.ydbio.2007.12.036)
31. Woolley TE, Maini PK, Gaffney EA. 2014 Is pigment cell pattern formation in zebrafish a game of cops and robbers? Pigment Cell Melanoma Res. 27, 686-687. (doi:10.1111/pcmr.12276)
32. Bloomfield JM, Painter KJ, Sherratt JA. 2011 How does cellular contact affect differentiation mediated pattern formation? Bull. Math. Biol. 73, 1529-1558. (doi:10.1007/s11538-010-9578-4)
33. Painter KJ, Bloomfield JM, Sherratt JA, Gerisch A. 2015 A nonlocal model for contact attraction and repulsion in heterogeneous cell populations. Bull. Math Biol. 77, 1132-1165. (doi:10.1007/s11538-015-0080-x)
34. Parichy DM, Elizondo MR, Mills MG, Gordon TN, Engeszer RE. 2009 Normal table of postembryonic zebrafish development: staging by externally visible anatomy of the living fish. Dev. Dyn. 238, 2975-3015. (doi:10.1002/dvdy.22113)
35. Kondo S. 2012 Turing pattern formation without diffusion. In How the world computes (eds SB Cooper, A Dawar, B Löwe), pp. 416-421. Berlin, Germany: Springer.
36. Budi EH, Patterson LB, Parichy DM. 2011 Postembryonic nerve-associated precursors to adult pigment cells: genetic requirements and dynamics of morphogenesis and differentiation. PLoS Genet. 7, e1002044. (doi:10.1371/journal.pgen.1002044)
37. Dooley CM, Mongera A,Walderich B, Nüsslein-Volhard C. 2013 On the embryonic origin of adult melanophores: the role of ErbB and Kit signalling in establishing melanophore stem cells in zebrafish. Development 140, 1003-1013. (doi:10.1242/dev.087007)
38. Parichy DM, Spiewak JE. 2015 Origins of adult pigmentation: diversity in pigment stem cell lineages and implications for pattern evolution. Pigment Cell Melanoma Res. 28, 31-50. (doi:10. 1111/pcmr.12332)
39. Gierer A, Meinhardt H. 1972 A theory of biological pattern formation. Kybernetik 12, 30-39. (doi:10. 1007/BF00289234)
40. Turing AM. 1952 The chemical basis of morphogenesis. Phil. Trans. R. Soc. Lond. B 237, 37-72. (doi:10.1098/rstb.1952.0012)