The vertebrate limb: An evolving complex of self-organizing systems

Progress in Biophysics and Molecular Biology - Tập 137 - Trang 12-24 - 2018
Stuart A. Newman1, Tilmann Glimm2, Ramray Bhat3
1Department of Cell Biology and Anatomy, New York Medical College, Valhalla, NY 10595, USA
2Department of Mathematics, Western Washington University Bellingham, WA, 98229, USA
3Department of Molecular Reproduction, Development and Genetics, Biological Sciences Division, Indian Institute of Science, Bangalore, 560012, India

Tài liệu tham khảo

Akam, 1989, Making stripes inelegantly, Nature, 341, 282, 10.1038/341282a0 Alber, 2005, Existence of solutions to a new model of biological pattern formation, J. Math. Anal. Appl., 308, 175, 10.1016/j.jmaa.2004.11.026 Alber, 2008, The morphostatic limit for a model of skeletal pattern formation in the vertebrate limb, Bull. Math. Biol., 70, 460, 10.1007/s11538-007-9264-3 Badugu, 2012, Digit patterning during limb development as a result of the BMP-receptor interaction, Sci. Rep., 2, 991, 10.1038/srep00991 Barna, 2007, Visualization of cartilage formation: insight into cellular properties of skeletal progenitors and chondrodysplasia syndromes, Dev. Cell, 12, 931, 10.1016/j.devcel.2007.04.016 Bhat, 2011, A regulatory network of two galectins mediates the earliest steps of avian limb skeletal morphogenesis, BMC Dev. Biol., 11, 6, 10.1186/1471-213X-11-6 Bhat, 2014, Structural divergence in vertebrate phylogeny of a duplicated prototype galectin, Genome Biol Evol., 6, 2721, 10.1093/gbe/evu215 Bhat, 2016, Deep phylogenomics of a tandem-repeat galectin regulating appendicular skeletal pattern formation, BMC Evol. Biol., 16, 162, 10.1186/s12862-016-0729-6 Brena, 2013, An analysis of segmentation dynamics throughout embryogenesis in the centipede Strigamia maritima, BMC Biol., 11, 112, 10.1186/1741-7007-11-112 Chaturvedi, 2005, On multiscale approaches to three-dimensional modelling of morphogenesis, J. R. Soc. Interface, 2, 237, 10.1098/rsif.2005.0033 Cickovski, 2005, A framework for three-dimensional simulation of morphogenesis, IEEE ACM Trans. Comput. Biol. Bioinf, 2, 273, 10.1109/TCBB.2005.46 Clack, 2012 Clyde, 2003, A self-organizing system of repressor gradients establishes segmental complexity in Drosophila, Nature, 426, 849, 10.1038/nature02189 Correia, 1997 Cuervo, 2012, Full regeneration of the tribasal Polypterus fin, Proc Natl Acad Sci U S A, 109, 3838, 10.1073/pnas.1006619109 Darwin, 1859 Davis, 2004, Pectoral fin and girdle development in the basal actinopterygians Polyodon spathula and Acipenser transmontanus, J Morphologie, 262, 608, 10.1002/jmor.10264 de Crombrugghe, 2000, Transcriptional mechanisms of chondrocyte differentiation, Matrix Biol., 19, 389, 10.1016/S0945-053X(00)00094-9 Dequéant, 2008, Segmental patterning of the vertebrate embryonic axis, Nat. Rev. Genet., 9, 370, 10.1038/nrg2320 Ede, 1977, The development of precartilage condensations in limb bud mesenchyme in vivo and in vitro, 161 Franssen, 2005, Limb chondrogenesis of the seepage salamander, Desmognathus aeneus (Amphibia: plethodontidae), J. Morphol., 265, 87, 10.1002/jmor.10339 Frenz, 1989, Latex beads as probes of cell surface-extracellular matrix interactions during chondrogenesis: evidence for a role for amino-terminal heparin-binding domain of fibronectin, Dev. Biol., 136, 87, 10.1016/0012-1606(89)90132-2 Frenz, 1989, The mechanism of precartilage mesenchymal condensation: a major role for interaction of the cell surface with the amino-terminal heparin-binding domain of fibronectin, Dev. Biol., 136, 97, 10.1016/0012-1606(89)90133-4 Gehrke, 2015, Deep conservation of wrist and digit enhancers in fish, Proc Natl Acad Sci U S A, 112, 10.1073/pnas.1420208112 Gierer, 1972, A theory of biological pattern formation, Kybernetik, 12, 30, 10.1007/BF00289234 Glimm, 2012, Reaction-diffusion systems and external morphogen gradients: the two-dimensional case, with an application to skeletal pattern formation, Bull. Math. Biol., 74, 666, 10.1007/s11538-011-9689-6 Glimm, 2014, Modeling the morphodynamic galectin patterning network of the developing avian limb skeleton, J. Theor. Biol., 346, 86, 10.1016/j.jtbi.2013.12.004 Glover, 2017, Hierarchical patterning modes orchestrate hair follicle morphogenesis, PLoS Biol., 15, 10.1371/journal.pbio.2002117 Hall, 2000, All for one and one for all: condensations and the initiation of skeletal development, Bioessays, 22, 138, 10.1002/(SICI)1521-1878(200002)22:2<138::AID-BIES5>3.0.CO;2-4 Hentschel, 2004, Dynamical mechanisms for skeletal pattern formation in the vertebrate limb, Proc R Soc Lond B Biol Sci., 271, 1713, 10.1098/rspb.2004.2772 Houzelstein, 2004, Phylogenetic analysis of the vertebrate galectin family, Mol. Biol. Evol., 21, 1177, 10.1093/molbev/msh082 Hudak, 2013, Pref-1, a gatekeeper of adipogenesis, Front. Endocrinol., 4, 79, 10.3389/fendo.2013.00079 Inaba, 2012, Pigment pattern formation by contact-dependent depolarization, Science, 335, 677, 10.1126/science.1212821 Izaguirre, 2004, CompuCell, a multi-model framework for simulation of morphogenesis, Bioinformatics, 20, 1129, 10.1093/bioinformatics/bth050 Kaltner, 2012, A toolbox of lectins for translating the sugar code: the galectin network in phylogenesis and tumors, Histol. Histopathol., 27, 397 Kauffman, 1978, Control of sequential compartment formation in Drosophila, Science, 199, 259, 10.1126/science.413193 Kerney, 2008, Gene expression reveals unique skeletal patterning in the limb of the direct-developing frog, Eleutherodactylus coqui, Evol. Dev., 10, 439, 10.1111/j.1525-142X.2008.00255.x Kosher, 1979, In vitro studies on the morphogenesis and differentiation of the mesoderm subjacent to the apical ectodermal ridge of the embryonic chick limb-bud, J. Embryol. Exp. Morphol., 50, 75 Kyttä, 2007, Complex turing patterns in non-linearly coupled systems, Physica, 385, 105, 10.1016/j.physa.2007.06.034 Leonard, 1991, Role of transforming growth factor-β in chondrogenic pattern formation in the embryonic limb: stimulation of mesenchymal condensation and fibronectin gene expression by exogenous TGF-β and evidence for endogenous TGF-β-like activity, Dev. Biol., 145, 99, 10.1016/0012-1606(91)90216-P Lettice, 2017, The conserved sonic hedgehog limb enhancer consists of discrete functional elements that regulate precise spatial expression, Cell Rep, 20, 1396, 10.1016/j.celrep.2017.07.037 Li, 2013, Mesenchymal stem cells exploit extracellular matrix as mechanotransducer, Sci. Rep., 3, 2425, 10.1038/srep02425 Lian, 2006, Networks and hubs for the transcriptional control of osteoblastogenesis, Rev. Endocr. Metab. Disord., 7, 1, 10.1007/s11154-006-9001-5 Lim, 2014, Induction of galectin-1 by TGF-β1 accelerates fibrosis through enhancing nuclear retention of Smad2, Exp. Cell Res., 326, 125, 10.1016/j.yexcr.2014.06.001 Lim, 2015, BMP-Smad4 signaling is required for precartilaginous mesenchymal condensation independent of Sox9 in the mouse, Dev. Biol., 400, 132, 10.1016/j.ydbio.2015.01.022 Litingtung, 2002, Shh and Gli3 are dispensable for limb skeleton formation but regulate digit number and identity, Nature, 418, 979, 10.1038/nature01033 Lorda-Diez, 2011, Defining the earliest transcriptional steps of chondrogenic progenitor specification during the formation of the digits in the embryonic limb, PLoS One, 6, 10.1371/journal.pone.0024546 Love, 2017, Perspectives on integrating genetic and physical explanations of evolution and development: an introduction to the symposium, Integr. Comp. Biol., 57, 1258, 10.1093/icb/icx121 Mabee, 2004, Development of the paired fins in the paddlefish, Polyodon spathula, J. Morphol., 261, 334, 10.1002/jmor.10253 Madzvamuse, 2015, Cross-diffusion-driven instability for reaction-diffusion systems: analysis and simulations, J. Math. Biol., 70, 709, 10.1007/s00285-014-0779-6 Mariani, 2003, Deciphering skeletal patterning: clues from the limb, Nature, 423, 319, 10.1038/nature01655 Meinhardt, 2006, Gierer-Meinhardt model, 1418 Mezentseva, 2008, The brown adipocyte differentiation pathway in birds: an evolutionary road not taken, BMC Biol., 6, 17, 10.1186/1741-7007-6-17 Moftah, 2002, Ectodermal FGFs induce perinodular inhibition of limb chondrogenesis in vitro and in vivo via FGF receptor 2, Dev. Biol., 249, 270, 10.1006/dbio.2002.0766 Montero, 2008, Activin/TGFb and BMP crosstalk determines digit chondrogenesis, Dev. Biol., 321, 343, 10.1016/j.ydbio.2008.06.022 Montero, 2017, Sox9 expression in amniotes: species-specific differences in the formation of digits, Front Cell Dev Biol., 5, 23, 10.3389/fcell.2017.00023 Moon, 2000, Fgf8 is required for outgrowth and patterning of the limbs, Nat. Genet., 26, 455, 10.1038/82601 Nakamura, 2016, Digits and fin rays share common developmental histories, Nature, 537, 225, 10.1038/nature19322 Nesterenko, 2017, Morphogene adsorption as a Turing instability regulator: theoretical analysis and possible applications in multicellular embryonic systems, PLoS One, 12, 10.1371/journal.pone.0171212 Newman, 1988, Lineage and pattern in the developing vertebrate limb, Trends Genet., 4, 329, 10.1016/0168-9525(88)90051-0 Newman, 1996, Sticky fingers: Hox genes and cell adhesion in vertebrate limb development, Bioessays, 18, 171, 10.1002/bies.950180302 Newman, 2007, Activator-inhibitor dynamics of vertebrate limb pattern formation, Birth Defects Res C Embryo Today, 81, 305, 10.1002/bdrc.20112 Newman, 1979, Dynamics of skeletal pattern formation in developing chick limb, Science, 205, 662, 10.1126/science.462174 Newman, 1988, On the stationary state analysis of reaction-diffusion mechanisms for biological pattern formation [published erratum appears in J Theor Biol 1988 Nov 8;135(1):137], J. Theor. Biol., 134, 183, 10.1016/S0022-5193(88)80201-7 Newman, 2008, Multiscale models for vertebrate limb development, Curr. Top. Dev. Biol., 81, 311, 10.1016/S0070-2153(07)81011-8 Onimaru, 2016, The fin-to-limb transition as the re-organization of a Turing pattern, Nat. Commun., 7, 11582, 10.1038/ncomms11582 Peters, 1993, Unique expression pattern of the FGF receptor 3 gene during mouse organogenesis, Dev. Biol., 155, 423, 10.1006/dbio.1993.1040 Raspopovic, 2014, Modeling digits. Digit patterning is controlled by a Bmp-Sox9-Wnt Turing network modulated by morphogen gradients, Science, 345, 566, 10.1126/science.1252960 Riddle, 1993, Sonic hedgehog mediates the polarizing activity of the ZPA, Cell, 75, 1401, 10.1016/0092-8674(93)90626-2 Riley, 2017, Similarity of morphological composition and developmental patterning in paired fins of the elephant shark, Sci. Rep., 7, 9985, 10.1038/s41598-017-10538-0 Roberts, 1988, Transforming growth factor beta stimulates the expression of fibronectin and of both subunits of the human fibronectin receptor by cultured human lung fibroblasts, J. Biol. Chem., 263, 4586, 10.1016/S0021-9258(18)68822-2 Salazar-Ciudad, 2010, A computational model of teeth and the developmental origins of morphological variation, Nature, 464, 583, 10.1038/nature08838 Salazar-Ciudad, 2001, Phenotypic and dynamical transitions in model genetic networks. II. Application to the evolution of segmentation mechanisms, Evol. Dev., 3, 95, 10.1046/j.1525-142x.2001.003002095.x Salazar-Ciudad, 2003, Mechanisms of pattern formation in development and evolution, Development, 130, 2027, 10.1242/dev.00425 Sampson, 2016, Galectin-8 promotes regulatory T-cell differentiation by modulating IL-2 and TGFβ signaling, Immunol. Cell Biol., 94, 213, 10.1038/icb.2015.72 Sansom, 2013, Unusual anal fin in a Devonian jawless vertebrate reveals complex origins of paired appendages, Biol. Lett., 9, 20130002, 10.1098/rsbl.2013.0002 Saunders, 1948, The proximo-distal sequence of origin of the parts of the chick wing and the role of the ectoderm, J. Exp. Zool., 108, 363, 10.1002/jez.1401080304 Sheth, 2012, Hox genes regulate digit patterning by controlling the wavelength of a Turing-type mechanism, Science, 338, 1476, 10.1126/science.1226804 Shyer, 2017, Emergent cellular self-organization and mechanosensation initiate follicle pattern in the avian skin, Science, 357, 811, 10.1126/science.aai7868 Silva, 2015, Systematics and morphology of potamotrygon orbignyi (Castelnau, 1855) and allied forms (Chondrichthyes: myliobatiformes: potamotrygonidae), Zootaxa, 3982, 1, 10.11646/zootaxa.3982.1.1 Silver, 1981, Distribution of fibronectin and collagen during mouse limb and palate development, Differentiation, 18, 141, 10.1111/j.1432-0436.1981.tb01115.x Manu, 2009, Canalization of gene expression in the Drosophila blastoderm by gap gene cross regulation, PLoS Biol., 7, 10.1371/journal.pbio.1000049 Stewart, 2017, The evolutionary origin of digit patterning, EvoDevo, 8, 21, 10.1186/s13227-017-0084-8 Stollewerk, 2003, Involvement of Notch and Delta genes in spider segmentation, Nature, 423, 863, 10.1038/nature01682 Szebenyi, 1995, Changes in the expression of fibroblast growth factor receptors mark distinct stages of chondrogenesis in vitro and during chick limb skeletal patterning, Dev. Dynam., 204, 446, 10.1002/aja.1002040410 Thorogood, 1975, An analysis of the condensation process during chondrogenesis in the embyronic hind limb, J. Embryol. Exp. Morphol., 33, 581 Tickle, 2017, Sonic hedgehog signaling in limb development, Front Cell Dev Biol., 5, 14, 10.3389/fcell.2017.00014 Tomasek, 1982, Nonuniform distribution of fibronectin during avian limb development, Dev. Biol., 90, 118, 10.1016/0012-1606(82)90217-2 Towers, 2008, Integration of growth and specification in chick wing digit-patterning, Nature, 452, 882, 10.1038/nature06718 Turing, 1952, The chemical basis of morphogenesis, Phil. Trans. Roy. Soc. Lond. B, 237, 37, 10.1098/rstb.1952.0012 Van Obberghen-Schilling, 1988, Transforming growth factor b1 positively regulates its own expression in normal and transformed cells, J. Biol. Chem., 263, 7741, 10.1016/S0021-9258(18)68561-8 Wang, 2010, Pref-1 interacts with fibronectin to inhibit adipocyte differentiation, Mol. Cell Biol., 30, 3480, 10.1128/MCB.00057-10 Wiener, 1961 Wolpert, 1989, Positional information revisited, Development, 107, 3, 10.1242/dev.107.Supplement.3 Yokouchi, 1995, Misexpression of Hoxa-13 induces cartilage homeotic transformation and changes cell adhesiveness in chick limb buds, Gene Dev., 9, 2509, 10.1101/gad.9.20.2509 Yu, 2007, FGF signaling regulates mesenchymal differentiation and skeletal patterning along the limb bud proximodistal axis, Development Zhang, 2013, Mathematical modeling of vertebrate limb development, Math. Biosci., 243, 1, 10.1016/j.mbs.2012.11.003 Zhu, 2009, Stem sarcopterygians have primitive polybasal fin articulation, Biol. Lett., 5, 372, 10.1098/rsbl.2008.0784 Zhu, 2009, Application of discontinuous Galerkin methods for reaction-diffusion systems in developmental biology, J. Sci. Comput., 40, 391, 10.1007/s10915-008-9218-4 Zhu, 2010, Bare bones pattern formation: a core regulatory network in varying geometries reproduces major features of vertebrate limb development and evolution, PLoS One, 5, 10.1371/journal.pone.0010892