Thu, 21 Aug 2008 00:02:07 BST CiteULike: Tag morphogenesis http://www.citeulike.org/tag/morphogenesis CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/xixibio/article/257709 <i>In Vitro Cellular and Development Biology - Plant, Vol. 41, No. 3. (June 2005), pp. 240-243.</i> THIDIAZURON-INDUCED MORPHOGENESIS IN TAMARIND SEEDLINGS Sulekha Hazra Urmil Mehta N Sahasrabudhe doi:10.1079/IVP2004611 In Vitro Cellular and Development Biology - Plant, Vol. 41, No. 3. (June 2005), pp. 240-243. 2005-07-16T11:24:35-00:00 2005 In Vitro Cellular and Development Biology - Plant 1054-5476 41 3 240 243 CABI Publishing in morphogenesis seedlings tamarind thidiazuron-induced http://www.citeulike.org/user/xico/article/447259 <i>Int J Biol Sci, Vol. 1, No. 2. (2005), pp. 87-95.</i><br /><br />The epidermis is the outermost layer in the skin, and it is the first line of defence against the environment. The epidermis also provides a barrier against loss of fluids and electrolytes, which is crucial for life. Essential in the maintenance of this tissue is its ability to continually self-renew and regenerate after injury. These two characteristics are critically dependent on the ability of the principal epidermal cell type, the keratinocyte, to proliferate and to respond to differentiation cues. Indeed, the epidermis is a multilayered tissue composed of keratinocyte stem cells and their differentiated progeny. Central for the control of cell proliferation is the E2F transcription factor regulatory network. This signaling network also includes cyclins, cdk, cdk inhibitors and the retinoblastoma (pRb) family of proteins. The biological importance of the E2F/pRb pathway is emphasized by the fact that a majority of human tumours exhibit alterations that disrupt the ability of pRb proteins to inhibit E2F, leading to permanent activation of the latter. Further, E2F is essential for normal epidermal regeneration after injury. Other member of the E2F signaling pathway are also involved in epidermal development and pathophysiology. Thus, whereas the pRb family of proteins is essential for epidermal morphogenesis, abnormal regulation of cyclins and E2F proteins results in tumorgenesis in this tissue. In this review, we discuss the role of each member of this important growth regulatory network in epidermal formation, homeostasis and carcinogenesis. Signalling In The Epidermis: The E2f Cell Cycle Regulatory Pathway In Epidermal Morphogenesis, Regeneration And Transformation. Iordanka A Ivanova Sudhir J A D'Souza Lina Dagnino Int J Biol Sci, Vol. 1, No. 2. (2005), pp. 87-95. 2005-12-22T16:52:02-00:00 2005 Int J Biol Sci 1449-2288 1 2 87 95 cdk cell cycle development e2f morphogenesis transcription http://www.citeulike.org/user/stajich/article/652300 <i>Proc Natl Acad Sci U S A, Vol. 78, No. 7. (July 1981), pp. 4596-4600.</i><br /><br />Three stages can be distinguished in the temperature-induced mycelial-to-yeast phase transition of Histoplasma capsulatum. Stage one is characterized by a progressive decrease in the respiration rate and in the intracellular concentrations of cysteine and other amino acids. By stage two, respiration has ceased completely and free cysteine has fallen to low levels. Exogenous cysteine is required during the second stage for activation of mitochondrial respiration (stage three) and completion of the morphological transition. Mitochondria isolated from cells in the second stage show no respiration with NADH, succinate, or other substrates unless they are first incubated with cysteine. In addition, a novel, cytosolic cysteine oxidase appears during the latter part of the second stage. In stage three, the respiration rate rises, intracellular concentrations of free cysteine and other amino acids increase to levels characteristic of yeast, and the morphological transition is completed. The results support the idea that alterations in cysteine metabolism play a key role in this differentiation process. Role of cysteine in regulating morphogenesis and mitochondrial activity in the dimorphic fungus Histoplasma capsulatum. B Maresca AM Lambowitz VB Kumar GA Grant GS Kobayashi G Medoff Proc Natl Acad Sci U S A, Vol. 78, No. 7. (July 1981), pp. 4596-4600. 2006-05-18T17:40:41-00:00 1981 Proc Natl Acad Sci U S A 0027-8424 78 7 4596 4600 dimorphism fungi histoplasma morphogenesis http://www.citeulike.org/user/samal/article/506455 <i>Nature, Vol. 439, No. 7078. (16 February 2006), pp. 856-860.</i> A bottom-up approach to gene regulation Nicholas Guido Xiao Wang David Adalsteinsson David Mcmillen Jeff Hasty Charles Cantor Timothy Elston JJ Collins doi:10.1038/nature04473 Nature, Vol. 439, No. 7078. (16 February 2006), pp. 856-860. 2006-02-15T18:22:28-00:00 2006 Nature 439 7078 856 860 collins collins_lab development evolution expression gene gene_expression gene-expression molecular-signaling morphogenesis networks noise regulation regulatory-cascades transcription transcriptional_regulation http://www.citeulike.org/user/madhadron/article/957573 <i>Microbiol Rev, Vol. 54, No. 4. (December 1990), pp. 381-431.</i><br /><br />We recognize organisms first and foremost by their forms, but how they grow and shape themselves still largely passes understanding. The objective of this article is to survey what has been learned of morphogenesis of walled eucaryotic microorganisms as a set of problems in cellular heredity, biochemistry, physiology, and organization. Despite the diversity of microbial forms and habits, some common principles can be discerned. (i) That the form of each organism represents the expression of a genetic program is almost universally taken for granted. However, reflection on the findings with morphologically aberrant mutants suggests that the metaphor of a genetic program is misleading. Cellular form is generated by a web of interacting chemical and physical processes, whose every strand is woven of multiple gene products. The relationship between genes and form is indirect and cumulative; therefore, morphogenesis must be addressed as a problem not of molecular genetics but of cellular physiology. (ii) The shape of walled cells is determined by the manner in which the wall is laid down during growth and development. Turgor pressure commonly, perhaps always, supplies the driving force for surface enlargement. Cells yield to this scalar force by localized, controlled wall synthesis; their forms represent variations on the theme of local compliance with global force. (iii) Growth and division in bacteria display most immediately the interplay of hydrostatic pressure, localized wall synthesis, and structural constraints. Koch's surface stress theory provides a comprehensive and quantitative framework for understanding bacterial shapes. (iv) In the larger and more versatile eucaryotic cells, expansion is mediated by the secretion of vesicles. Secretion and ancillary processes, such as cytoplasmic transport, are spatially organized on the micrometer scale. The diversity of vectorial physiology and of the forms it generates is illustrated by examples: apical growth of fungal hyphae, bud formation in yeasts, germination of fucoid zygotes, and development of cells of Nitella, Closterium, and other unicellular algae. (v) Unicellular organisms, no less than embryos, have a remarkable capacity to impose spatial order upon themselves with or without the help of directional cues. Self-organization is reviewed here from two perspectives: the theoretical exploration of morphogens, gradients, and fields, and experimental study of polarization in Fucus cells, extension of hyphal tips, and pattern formation in ciliates. Here is the heart of the matter, yet self-organization remains nearly as mysterious as it was a century ago, a subject in search of a paradigm. To shape a cell: an inquiry into the causes of morphogenesis of microorganisms. FM Harold Microbiol Rev, Vol. 54, No. 4. (December 1990), pp. 381-431. 2006-11-22T15:45:28-00:00 1990 Microbiol Rev 0146-0749 54 4 381 431 bacteria morphogenesis http://www.citeulike.org/user/madhadron/article/1414142 <i>(25 Jun 2007)</i><br /><br />A distinguishing feature of a multicellular living system is that it operates at various scales, from the intracellular to organismal. Very little is known at present on how tissue level properties are related to cell and subcellular properties. Modern measurement techniques provide quantitative results at both the intracellular and tissue level, but not on the connection between these. In the present work we outline a framework to address this connection. We specifically concentrate on the morphogenetic process of tissue fusion, by following the coalescence of two contiguous multicellular aggregates. The time evolution of this process can accurately be described by the theory of viscous liquids. We also study fusion by Monte Carlo simulations and a novel Cellular Particle Dynamics (CPD) model, which is similar to the earlier introduced Subcellular Element Model (Newman, 2005). Using the combination of experiments, theory and modeling we are able to relate the measured tissue level biophysical quantities to subcellular parameters. Our approach has validity beyond the particular morphogenetic process considered here and provides a general way to relate biophysical properties across scales. Relating Biophysical Properties Across Scales Elijah Flenner Francoise Marga Adrian Neagu Ioan Kosztin Gabor Forgacs (25 Jun 2007) 2007-06-26T15:09:39-00:00 2007 cellbiology morphogenesis http://www.citeulike.org/user/madhadron/article/2755692 <i>Current opinion in microbiology, Vol. 10, No. 6. (December 2007), pp. 591-595.</i><br /><br />Bacteria furnish tractable models for complex biological processes, and morphogenesis is now taking its turn. We can already explain in general terms how such elementary forms as rods and cocci are produced, and the shapes of several individual organisms are coming into focus. In most bacteria shape is maintained by the cell wall, specifically the peptidoglycan layer, which has the attributes of a strong stiff fabric. Compliance of that fabric with turgor pressure is an important aspect of morphogenesis. The shape of the wall sacculus is determined by the way it is deposited, which is controlled by a cytoskeleton made up of two molecular families. One, related to the eukaryotic tubulins, is responsible for the construction of the septum and the poles. The other, related to eukaryotic actins, localizes peptidoglycan synthesis in the lateral walls of rod-shaped cells. Just how the cytoskeleton itself is organized remains to be discovered, but it seems likely that, as in eukaryotes, the cytoskeleton is produced by self-organized assembly, guided by the fabric of the cell. Bacterial morphogenesis: learning how cells make cells. FM Harold doi:10.1016/j.mib.2007.07.003 Current opinion in microbiology, Vol. 10, No. 6. (December 2007), pp. 591-595. 2008-05-05T08:24:54-00:00 2007 Current opinion in microbiology 1369-5274 10 6 591 595 bacteria cellwall morphogenesis http://www.citeulike.org/user/ltabourier/article/1211983 <i>Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 72, No. 5. (2005)</i><br /><br />We investigate the clustering coefficient in bipartite networks where cycles of size three are absent and therefore the standard definition of clustering coefficient cannot be used. Instead, we use another coefficient given by the fraction of cycles with size four, showing that both coefficients yield the same clustering properties. The new coefficient is computed for two networks of sexual contacts, one bipartite and another where no distinction between the nodes is made (monopartite). In both cases the clustering coefficient is similar. Furthermore, combining both clustering coefficients we deduce an expression for estimating cycles of larger size, which improves previous estimations and is suitable for either monopartite and multipartite networks, and discuss the applicability of such analytical estimations. Cycles and clustering in bipartite networks Pedro Lind Marta Gonzalez Hans Herrmann doi:10.1103/PhysRevE.72.056127 Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 72, No. 5. (2005) 2007-04-06T15:01:29-00:00 2005 Physical Review E (Statistical, Nonlinear, and Soft Matter Physics) 72 5 APS bipartite_graph clustering cycles morphogenesis http://www.citeulike.org/user/ltabourier/article/913666 <i>Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 70, No. 3. (2004)</i><br /><br />We study collaboration networks in terms of evolving, self-organizing bipartite graph models. We propose a model of a growing network, which combines preferential edge attachment with the bipartite structure, generic for collaboration networks. The model depends exclusively on basic properties of the network, such as the total number of collaborators and acts of collaboration, the mean size of collaborations, etc. The simplest model defined within this framework already allows us to describe many of the main topological characteristics (degree distribution, clustering coefficient, etc.) of one-mode projections of several real collaboration networks, without parameter fitting. We explain the observed dependence of the local clustering on degree and the degree–degree correlations in terms of the "aging" of collaborators and their physical impossibility to participate in an unlimited number of collaborations. Self-organization of collaboration networks Jose Ramasco SN Dorogovtsev Romualdo Satorras doi:10.1103/PhysRevE.70.036106 Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 70, No. 3. (2004) 2006-10-26T15:14:01-00:00 2004 Physical Review E (Statistical, Nonlinear, and Soft Matter Physics) 70 3 APS bipartite_graph collaboration_networks morphogenesis http://www.citeulike.org/user/ltabourier/article/1211966 <i>(24 Nov 2006)</i><br /><br />Many real networks have cliques as their constitutional units. Here we present a family of scale-free network model consist of cliques, which is established by a simple recursive algorithm. We investigate the networks both analytically and numerically. The obtained analytical solution shows that the networks follow a power-law degree distribution, with degree exponent continuously tuned between 2 and 3, coinciding with the empirically found results. The exact expression of clustering coefficient is also provided for the networks. Furthermore, the investigation of the average path length reveals that the networks possess small-world feature. Evolving networks consist of cliques Zhongzhi Zhang Shuigeng Zhou (24 Nov 2006) 2007-04-06T14:43:55-00:00 2006 clique morphogenesis http://www.citeulike.org/user/ltabourier/article/1211964 <i>ArXiv Condensed Matter e-prints (December 2006)</i><br /><br />We consider the rewiring of a bipartite graph using a mixture of random and preferential attachment. The full mean field equations for the degree distribution and its generating function are given. The exact solution of these equations for all finite parameter values at any time is found in terms of standard functions. It is demonstrated that these solutions are an excellent fit to numerical simulations of the model. We discuss the relationship between our model and several others in the literature including examples of Urn, Backgammon, and Balls-in-Boxes models, the Watts and Strogatz rewiring problem and some models of zero range processes. Our model is also equivalent to those used in various applications including cultural transmission, family name and gene frequencies, glasses, wealth distributions. Finally some Voter models and an example of a Minority game also show features described by our model. Exact Solution for the Time Evolution of Network Rewiring Models TS Evans ADK Plato ArXiv Condensed Matter e-prints (December 2006) 2007-04-06T14:39:16-00:00 2006 ArXiv Condensed Matter e-prints bipartite_graph morphogenesis preferential_attachment http://www.citeulike.org/user/ltabourier/article/1388326 <i>Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 72, No. 6. (2005)</i><br /><br />In this paper, we present a method to project co-authorship networks, that accounts in detail for the geometrical structure of scientists' collaborations. By restricting the scope to three-body interactions, we focus on the number of triangles in the system, and show the importance of multi-scientist (more than two) collaborations in the social network. This motivates the introduction of generalized networks, where basic connections are not binary, but involve arbitrary number of components. We focus on the three-body case and study numerically the percolation transition. N-body decomposition of bipartite author networks R Lambiotte M Ausloos doi:10.1103/PhysRevE.72.066117 Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 72, No. 6. (2005) 2007-06-13T21:02:22-00:00 2005 Physical Review E (Statistical, Nonlinear, and Soft Matter Physics) 72 6 APS bipartite_graph clustering morphogenesis http://www.citeulike.org/user/ltabourier/article/1007017 <i>Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 70, No. 3. (2004)</i><br /><br />In this Brief Report we present a version of a network growth model, generalized in order to describe the behavior of social networks. The case of study considered is the preprint archive at cul.arxiv.org. Each node corresponds to a scientist, and a link is present whenever two authors wrote a paper together. This graph is a nice example of degree-assortative network, that is, to say a network where sites with similar degree are connected to each other. The model presented is one of the few able to reproduce such behavior, giving some insight on the microscopic dynamics at the basis of the graph structure. Assortative model for social networks Michele Catanzaro Guido Caldarelli Luciano Pietronero doi:10.1103/PhysRevE.70.037101 Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 70, No. 3. (2004) 2006-12-22T10:03:11-00:00 2004 Physical Review E (Statistical, Nonlinear, and Soft Matter Physics) 70 3 APS degree_assortative morphogenesis preferential_attachment http://www.citeulike.org/user/ltabourier/article/90545 <i>Phys Rev Lett, Vol. 89, No. 25. (16 December 2002)</i><br /><br />A new mechanism leading to scale-free networks is proposed in this Letter. It is shown that, in many cases of interest, the connectivity power-law behavior is neither related to dynamical properties nor to preferential attachment. Assigning a quenched fitness value x(i) to every vertex, and drawing links among vertices with a probability depending on the fitnesses of the two involved sites, gives rise to what we call a good-get-richer mechanism, in which sites with larger fitness are more likely to become hubs (i.e., to be highly connected). Scale-free networks from varying vertex intrinsic fitness. G Caldarelli A Capocci P De Los Rios MA Muñoz Phys Rev Lett, Vol. 89, No. 25. (16 December 2002) 2005-02-09T19:13:41-00:00 2002 Phys Rev Lett 0031-9007 89 25 fitness morphogenesis preferential_attachment http://www.citeulike.org/user/ltabourier/article/713345 <i>Inf. Process. Lett., Vol. 90, No. 5. (June 2004), pp. 215-221.</i> Bipartite structure of all complex networks Jean-Loup Guillaume Matthieu Latapy doi:10.1016/j.ipl.2004.03.007 Inf. Process. Lett., Vol. 90, No. 5. (June 2004), pp. 215-221. 2006-06-28T07:00:54-00:00 2004 Inf. Process. Lett. 0020-0190 90 5 215 221 Elsevier North-Holland, Inc. bipartite_graph morphogenesis http://www.citeulike.org/user/ltabourier/article/1250712 <i>Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 73, No. 1. (2006)</i><br /><br />This work is a study of the properties of collaboration networks employing the formalism of weighted graphs to represent their one-mode projection. The weight of the edges is directly the number of times that a partnership has been repeated. This representation allows us to define the concept of social inertia that measures the tendency of authors to keep on collaborating with previous partners. We use a collection of empirical datasets to analyze several aspects of the social inertia: (1) its probability distribution, (2) its correlation with other properties, and (3) the correlations of the inertia between neighbors in the network. We also contrast these empirical results with the predictions of a recently proposed theoretical model for the growth of collaboration networks. Social inertia in collaboration networks Jose Ramasco Steven Morris doi:10.1103/PhysRevE.73.016122 Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 73, No. 1. (2006) 2007-04-25T16:04:39-00:00 2006 Physical Review E (Statistical, Nonlinear, and Soft Matter Physics) 73 1 APS bipartite_graph collaboration_networks morphogenesis weighted_networks http://www.citeulike.org/user/livingthingdan/article/307517 <i>Biosystems, Vol. 64, No. 1-3. (January 2002), pp. 97-109.</i><br /><br />The importance of interactions between processes at diverse space and time scales in biological information processing is a recurrent theme in the work of Michael Conrad (BioSystems, 1995: 35, 157-160; BioSystems, 1999: 52, 99-100). In this paper I present some results of explicit computational models that aim to capture and exploit some of the essential features of such multi-level processes. In the model formulation, I try to minimize the explicit definition of inter-level interactions, while providing the possibility of such interactions to develop. As often argued by Conrad inter-level interactions limit programmability. Indeed, we use an evolutionary process to derive the specific models. We study morphogenesis. We show that the interplay between cell adhesion and cell differentiation provides interesting mechanisms for morphogenesis. We also show that the interplay can both reduce and enhance small random fluctuations. We show that unequal cell cleavage in the early embryo-genesis reduces inter-individual variation of the morphemes developed from the same 'genome'. Our results suggest that, during evolution, the interplay between levels is exploited while it is at the same time reduced so as to give a certain primacy to inherited information. Computing an organism: on the interface between informatic and dynamic processes. P Hogeweg Biosystems, Vol. 64, No. 1-3. (January 2002), pp. 97-109. 2005-08-30T19:58:46-00:00 2002 Biosystems 0303-2647 64 1-3 97 109 dynamicalsystems hierarchy informationtheory morphogenesis scaling simulation teachmyself upload http://www.citeulike.org/user/kaur/article/452302 <i>Phys Rev Lett, Vol. 90, No. 25 Pt 1. (27 June 2003)</i><br /><br />Self-organized pattern formation is observed in bacterial colony growth. The recently reported knotted-branching pattern of the Bacillus circulans colony consists of the trajectories of aggregates which grow, move, and reproduce simultaneously. We modeled these processes by combining a reaction diffusion system of nutrient dynamics, nucleation theory for aggregate generation, and individual based dynamics of motion and growth of aggregates. The branching pattern produced by computer simulation shows great similarity with experiments. Response to the initial nutrient concentration is also consistent with the experiments. Self-organized pattern formation of a bacteria colony modeled by a reaction diffusion system and nucleation theory. JY Wakano S Maenosono A Komoto N Eiha Y Yamaguchi Phys Rev Lett, Vol. 90, No. 25 Pt 1. (27 June 2003) 2005-12-28T22:22:59-00:00 2003 Phys Rev Lett 0031-9007 90 25 Pt 1 bacteria behavior biological-inspired-modeling evolution learning-and-memory modeling-and-simulation morphogenesis networks http://www.citeulike.org/user/jxavier/article/2262118 <i>Math Med Biol, Vol. 24, No. 2. (1 June 2007), pp. 209-224.</i><br /><br />Lung branching morphogenesis has been widely studied in the field of developmental biology. Lung airway trees consist of relatively regular-sized distal branches, but how this regular branched pattern is formed is not well understood. In the present study, we undertake a detailed mathematical analysis of the model proposed in (Hartmann & Miura (2006), which numerically captures branching morphogenesis of the simplest possible experimental system in vitro. We investigate analytically the stability of 1D travelling waves with respect to periodic perturbations in two dimensions. This linear stability analysis leads to the so-called dispersion relations, predicting that a certain representative length dominates in this model. As the analytical analysis is restricted to travelling waves, we generalize the linear analysis to any 1D solution by numerical simulations. Both results predict how the representative lengths will change by experimentally changing specific parameters. Finally, we discuss the importance of the analytical results from a biological point of view and propose an experimental scheme for a quantitative comparison between experiments and theory. 10.1093/imammb/dql029 Mathematical analysis of a free-boundary model for lung branching morphogenesis Dirk Hartmann Takashi Miura doi:10.1093/imammb/dql029 Math Med Biol, Vol. 24, No. 2. (1 June 2007), pp. 209-224. 2008-01-20T13:57:44-00:00 2007 Math Med Biol 24 2 209 224 branching mathematical model morphogenesis http://www.citeulike.org/user/jxavier/article/2262109 <i>Journal of Theoretical Biology, Vol. 242, No. 4. (21 October 2006), pp. 862-872.</i><br /><br />It has been shown experimentally that lung epithelial explants have an ability to undergo branching morphogenesis without mesenchyme. However, the mechanisms of this phenomenon remain to be elucidated. In the present study, we construct a mathematical model that can reproduce the dynamics of in vitro branching morphogenesis. We show that the system is essentially governed by three variables--c0 which is the initial fibroblast growth factor (FGF) concentration, D which is the diffusion coefficient of FGF, and [beta] which describes the mechanical strength of the cytoskeleton. It is confirmed by numerical simulations that this model can reproduce the experimentally obtained patterns qualitatively. Finally, we experimentally verify two predictions from the model: effects of very high FGF concentration and effects of small mechanical contributions of the cytoskeleton. The theoretical predictions match well with the experimental results. Modelling in vitro lung branching morphogenesis during development Dirk Hartmann Takashi Miura doi:10.1016/j.jtbi.2006.05.009 Journal of Theoretical Biology, Vol. 242, No. 4. (21 October 2006), pp. 862-872. 2008-01-20T13:56:10-00:00 2006 Journal of Theoretical Biology 242 4 862 872 branching mathematical model morphogenesis http://www.citeulike.org/user/jxavier/article/2262101 <i>Physical Review E, Vol. 61, No. 4. (April 2000), 4156.</i><br /><br />I show that a class of reaction-diffusion models of vasculature growth developed in the mid 1970s is in fact a class of dendritic growth models. I then comment on the relevance of these models. Branching morphogenesis in a reaction-diffusion model Vincent Fleury doi:10.1103/PhysRevE.61.4156 Physical Review E, Vol. 61, No. 4. (April 2000), 4156. 2008-01-20T13:53:56-00:00 2000 Physical Review E 61 4 4156 American Physical Society branching mathematical model morphogenesis http://www.citeulike.org/user/jxavier/article/2262074 <i>Annu Rev Physiol, Vol. 62 (2000), pp. 595-620.</i><br /><br />Epithelial tissues such as kidney, lung, and breast arise through branching morphogenesis of a pre-existing epithelial structure. They share common morphological stages and a need for regulation of a similar set of developmental decisions--where to start; when, where, and in which direction to branch; and how many times to branch--decisions requiring regulation of cell proliferation, apoptosis, invasiveness, and cell motility. It is likely that similar molecular mechanisms exist for the epithelial branching program. Here we focus on the development of the collecting system of the kidney, where, from recent data using embryonic organ culture, cell culture models of branching morphogenesis, and targeted gene deletion experiments, the outlines of a working model for branching morphogenesis begin to emerge. Key branching morphogenetic molecules in this model include growth factors, transcription factors, distal effector molecules (such as extracellular matrix proteins, integrins, proteinases and their inhibitors), and genes regulating apoptosis and cell proliferation. Branching morphogenesis during kidney development. M Pohl RO Stuart H Sakurai SK Nigam doi:10.1146/annurev.physiol.62.1.595 Annu Rev Physiol, Vol. 62 (2000), pp. 595-620. 2008-01-20T13:45:51-00:00 2000 Annu Rev Physiol 0066-4278 62 595 620 branching morphogenesis http://www.citeulike.org/user/josepe/article/1061014 <i>EXS, No. 94. (2005), pp. 115-125.</i><br /><br />Pericytes are solitary, smooth muscle-like mural cells that invest the wall of microvessels. For a long time, the functional significance of the presence and distribution of pericytes in the microvasculature was unclear. However, in recent years, the application of experimental genetics to the PDGF-B/PDGFRbeta signaling pathway in mice has provided a range of mutants with primary defects in pericytes, allowing for studies of the physiological consequences of pericyte deficiency in developmental angiogenesis and adult physiology. Interestingly, some of the phenotypic consequences of these mutations resemble human diseases, such as diabetic retinopathy. The studies have also led to the discovery of critical mechanisms involved in pericyte recruitment and differentiation. The present review focuses on genetic data suggesting that pericytes take active part in developmental angiogenic processes. Role of pericytes in vascular morphogenesis. C Betsholtz P Lindblom H Gerhardt EXS, No. 94. (2005), pp. 115-125. 2007-01-22T22:17:56-00:00 2005 EXS 1023-294X 94 115 125 morphogenesis pericytes http://www.citeulike.org/user/jonathanjacobs/article/2642545 <i>Nucl. Acids Res., Vol. 28, No. 5. (1 March 2000), pp. 1078-1084.</i><br /><br />People afflicted with certain rheumatological auto-immune diseases produce autoantibodies directed against a select group of proteins such as the La auto-antigen. Biochemical studies have revealed La to be a promiscuous RNA-binding protein that appears to play a role in a variety of intracellular activities such as processing and/or transport of RNA polymerase III precursor transcripts and translational regulation from internal ribosome entry sites (IRES). We have previously identified an RNA-binding protein that is a Drosophila melanogaster homolog of La (D-La) and shown that early transcript accumulation throughout the embryo is later refined to be most prevalent in the visceral mesoderm, gut, gonads and salivary glands. Here we report the first in vivo genetic characterization of a La homolog in a multicellular eukaryote. Lethality was observed in homozygous larvae harboring a small chromosomal deletion that removed the D-La gene, which was rescued by an inducible D-La cDNA transgene. This implies that D-La confers essential functions for larval development. In addition, loss of D-La function gives rise to defects in embryonic midgut morphogenesis; one of the midgut defects correlates with loss of Ultrabithorax (Ubx) expression along the second midgut constriction. Finally, genetic interactions between chromosomal deficiencies that remove D-La and certain Ubx alleles were demonstrated in adults. Our results support the hypothesis that D-La provides essential functions for proper Drosophila development and imply that the conserved La family of proteins may perform critical developmental functions in higher eukaryotes. 10.1093/nar/28.5.1078 Genetic analysis of a La homolog in Drosophila melanogaster Chunyang Bai Peter Tolias doi:10.1093/nar/28.5.1078 Nucl. Acids Res., Vol. 28, No. 5. (1 March 2000), pp. 1078-1084. 2008-04-08T18:50:15-00:00 2000 Nucl. Acids Res. 28 5 1078 1084 conserved development drosophila embryo embryonic eukaryote gene genetic homolog hypothesis ires la larvae melanogaster morphogenesis polymerase protein ribosome rna translational vivo http://www.citeulike.org/user/jnemecek/article/679542 <i>Proc Natl Acad Sci U S A, Vol. 93, No. 9. (30 April 1996), pp. 3870-3875.</i><br /><br />Addition of a saturated fatty acid (SFA) induced a strong increase in heat shock (HS) mRNA transcription when cells were heat-shocked at 37 degrees C, whereas treatment with an unsaturated fatty acid (UFA) reduced or eliminated the level of HS gene transcription at 37 degrees C. Transcription of the delta 9-desaturase gene (Ole1) of Histoplasma capsulatum, whose gene product is responsible for the synthesis of UFA, is up-regulated in a temperature-sensitive strain. We show that when the L8-14C mutant of Saccharomyces cerevisiae, which has a disrupted Ole1 gene, is complemented with its own Ole1 coding region under control of its own promoter or Ole1 promoters of H. capsulatum, the level of HS gene transcription depends on the activity of the promoters. Fluorescence anisotropy of mitochondrial membranes of completed strains corresponded to the different activity of the Ole1 promoter used. We propose that the SFA/UFA ratio and perturbation of membrane lipoprotein complexes are involved in the perception of rapid temperature changes and under HS conditions disturbance of the preexisting membrane physical state causes transduction of a signal that induces transcription of HS genes. Membrane lipid perturbation modifies the set point of the temperature of heat shock response in yeast. L Carratù S Franceschelli CL Pardini GS Kobayashi I Horvath L Vigh B Maresca Proc Natl Acad Sci U S A, Vol. 93, No. 9. (30 April 1996), pp. 3870-3875. 2006-06-01T15:14:48-00:00 1996 Proc Natl Acad Sci U S A 0027-8424 93 9 3870 3875 histoplasma membrane morphogenesis http://www.citeulike.org/user/jnemecek/article/651937 <i>J Biol Chem, Vol. 258, No. 13. (10 July 1983), pp. 8223-8230.</i><br /><br />When the mycelial to yeast transition of the dimorphic fungus Histoplasma capsulatum is induced by a temperature shift from 25 to 37 degrees C, the activities of the cytochrome system and the alternate oxidase decrease in parallel over the first 24 to 40 h (stage 1 of the transition). The decrease in activity of the cytochrome system is correlated with extensive decreases in the amounts of cytochromes b, c, and aa3, assayed spectrophotometrically. After 40 h, the cells enter a dormant phase (stage 2 of the transition) and cysteine or other sulfhydryl-containing compounds are required to reactivate mitochondrial respiration. This reactivation is due to the establishment of shunt pathways which bypass blocked segments of the electron transport system. The "shunt" pathways operate normally in mycelia grown at 25 degrees C, but are shut down during the transition, possibly because of depletion of intracellular cysteine. The longstanding observation that cysteine is required to progress beyond the initial stages of the morphological transition may be due, at least in part, to the reactivation of these "shunt" pathways. Sulfhydryl induced respiratory "shunt" pathways and their role in morphogenesis in the fungus, Histoplasma capsulatum. M Sacco G Medoff AM Lambowitz BV Kumar GS Kobayashi A Painter J Biol Chem, Vol. 258, No. 13. (10 July 1983), pp. 8223-8230. 2006-05-18T17:28:14-00:00 1983 J Biol Chem 0021-9258 258 13 8223 8230 histoplasma morphogenesis sulfhydryl http://www.citeulike.org/user/jnemecek/article/279448 <i>Sabouraudia, Vol. 18, No. 4. (December 1980), pp. 249-253.</i><br /><br />The highly variable mycelial phase cultures of Histoplasma capsulatum are generally described as brown to albino colonies with the albino type overtaking the brown in a unidirectional and mainly irreversible process. In this study it was found that cultures could be reversed from albino to brown type by manipulation of substrates. As the cultural morphology and stability were shown to be essentially substrate-dependent, the mycelial status of this organism was reassessed. It is proposed that albino and intermediate variants are usually artificially induced by conventional refined carbohydrate media, while crude guano substrates tend to promote cultures of a brown wild type. The mycelial status and reversibility in Histoplasma capsulatum. R Borok Sabouraudia, Vol. 18, No. 4. (December 1980), pp. 249-253. 2005-08-11T18:04:49-00:00 1980 Sabouraudia 0036-2174 18 4 249 253 histoplasma morphogenesis http://www.citeulike.org/user/jgoodwin/article/466389 <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, Vol. 237, No. 641. (1952), pp. 37-72.</i><br /><br />It is suggested that a system of chemical substances, called morphogens, reacting together and diffusing through a tissue, is adequate to account for the main phenomena of morphogenesis. Such a system, although it may originally be quite homogeneous, may later develop a pattern or structure due to an instability of the homogeneous equilibrium, which is triggered off by random disturbances. Such reaction-diffusion systems are considered in some detail in the case of an isolated ring of cells, a mathematically convenient, though biologically unusual system. The investigation is chiefly concerned with the onset of instability. It is found that there are six essentially different forms which this may take. In the most interesting form stationary waves appear on the ring. It is suggested that this might account, for instance, for the tentacle patterns on Hydra and for whorled leaves. A system of reactions and diffusion on a sphere is also considered. Such a system appears to account for gastrulation. Another reaction system in two dimensions gives rise to patterns reminiscent of dappling. It is also suggested that stationary waves in two dimensions could account for the phenomena of phyllotaxis. The purpose of this paper is to discuss a possible mechanism by which the genes of a zygote may determine the anatomical structure of the resulting organism. The theory does not make any new hypotheses; it merely suggests that certain well-known physical laws are sufficient to account for many of the facts. The full understanding of the paper requires a good knowledge of mathematics, some biology, and some elementary chemistry. Since readers cannot be expected to be experts in all of these subjects, a number of elementary facts are explained, which can be found in text-books, but whose omission would make the paper difficult reading. The Chemical Basis of Morphogenesis AM Turing Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, Vol. 237, No. 641. (1952), pp. 37-72. 2006-01-16T21:25:52-00:00 1952 Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 237 641 37 72 evolution morphogenesis http://www.citeulike.org/user/jgoodwin/article/511484 <i>Trends in Genetics, Vol. 15, No. 9. (1 September 1999), pp. 371-377.</i><br /><br />Pax 6 genes from various animal phyla are capable of inducing ectopic eye development, indicating that Pax 6 is a master control gene for eye morphogenesis. It is proposed that the various eye-types found in metazoa are derived from a common prototype, monophyletically, by a mechanism called intercalary evolution. Pax 6: mastering eye morphogenesis and eye evolution Walter Gehring Kazuho Ikeo doi:10.1016/S0168-9525(99)01776-X Trends in Genetics, Vol. 15, No. 9. (1 September 1999), pp. 371-377. 2006-02-19T05:19:26-00:00 1999 Trends in Genetics 15 9 371 377 evolution eye morphogenesis http://www.citeulike.org/group/916/article/306343 <i>Dev Neurosci, Vol. 27, No. 2-4. (g 2005), pp. 93-99.</i><br /><br />The dentate gyrus is one of two locations with continuing neurogenesis in adult mammals. While the function of adult neurogenesis is unknown, it is believed that it is involved in learning and memory. For adult neurogenesis to occur, the dentate gyrus must maintain the appropriate precursor cell niche in the subgranular zone, which is likely to be dependent on the developmental mechanisms at play in forming the dentate gyrus. In this review, we graft a molecular framework onto the known neuroanatomic developmental plan by considering the phenotypes of several mouse mutants that have well characterized dentate gyrus developmental abnormalities. This effort reveals that there are at least six distinct developmental steps that need to occur in the formation of the dentate gyrus, which can be associated with specific gene defects: (1) defining the dentate neuroepithelium; (2) forming the primary radial glial scaffolding; (3) radial migration of granule neurons to form the primordial granule cell layer; (4) establishing the precursor pool in the hilus; (5) radial transformation of the tertiary matrix, and (6) differentiation of dentate granule cells. From this analysis, it is clear that some molecular pathways control multiple steps in the development of the dentate gyrus. For example the Wnt pathway (steps 1, 2, 4) and the chemokine receptor CXCR4 (steps 3, 4) are involved in multiple developmental steps, while the neuronal differentiation gene NeuroD (step 6) and the integrin signaling pathway (step 5) are involved only in discrete stages of the dentate gyrus morphogenesis. Morphogenesis of the dentate gyrus: what we are learning from mouse mutants. G Li SJ Pleasure doi:10.1159/000085980 Dev Neurosci, Vol. 27, No. 2-4. (g 2005), pp. 93-99. 2005-08-29T19:15:14-00:00 2005 Dev Neurosci 0378-5866 27 2-4 93 99 development disorder morphogenesis neurogenesis http://www.citeulike.org/user/fluomouse/article/1572391 <i>J Neurobiol, Vol. 64, No. 1. (July 2005), pp. 47-57.</i><br /><br />Dendritic spines are small protrusions off the dendrite that receive excitatory synaptic input. Spines vary in size, likely correlating with the strength of the synapses they form. In the developing brain, spines show highly dynamic behavior thought to facilitate the formation of new synaptic contacts. Recent studies have illuminated the numerous molecules regulating spine development, many of which converge on the regulation of actin filaments. In addition, interactions with glial cells are emerging as important regulators of spine morphology. In many cases, spine morphogenesis, plasticity, and maintenance also depend on synaptic activity, as shown by recent studies demonstrating changes in spine dynamics and maintenance with altered sensory experience. Dendritic spine morphogenesis and plasticity. J Lippman A Dunaevsky doi:10.1002/neu.20149 J Neurobiol, Vol. 64, No. 1. (July 2005), pp. 47-57. 2007-08-17T11:31:12-00:00 2005 J Neurobiol 0022-3034 64 1 47 57 development morphogenesis plasticity review spine http://www.citeulike.org/user/fluomouse/article/2056758 <i>Neurochem Int, Vol. 51, No. 2-4. (p 2007), pp. 92-104.</i><br /><br />Dendritic spines are the postsynaptic receptive regions of most excitatory synapses, and their morphological plasticity play a pivotal role in higher brain functions, such as learning and memory. The dynamics of spine morphology is due to the actin cytoskeleton concentrated highly in spines. Filopodia, which are thin and headless protrusions, are thought to be precursors of dendritic spines. Drebrin, a spine-resident side-binding protein of filamentous actin (F-actin), is responsible for recruiting F-actin and PSD-95 into filopodia, and is suggested to govern spine morphogenesis. Interestingly, some recent studies on neurological disorders accompanied by cognitive deficits suggested that the loss of drebrin from dendritic spines is a common pathognomonic feature of synaptic dysfunction. In this review, to understand the importance of actin-binding proteins in spine morphogenesis, we first outline the well-established knowledge pertaining to the actin cytoskeleton in non-neuronal cells, such as the mechanism of regulation by small GTPases, the equilibrium between globular actin (G-actin) and F-actin, and the distinct roles of various actin-binding proteins. Then, we review the dynamic changes in the localization of drebrin during synaptogenesis and in response to glutamate receptor activation. Because side-binding proteins are located upstream of the regulatory pathway for actin organization via other actin-binding proteins, we discuss the significance of drebrin in the regulatory mechanism of spine morphology through the reorganization of the actin cytoskeleton. In addition, we discuss the possible involvement of an actin-myosin interaction in the morphological plasticity of spines. Role of actin cytoskeleton in dendritic spine morphogenesis. Y Sekino N Kojima T Shirao doi:10.1016/j.neuint.2007.04.029 Neurochem Int, Vol. 51, No. 2-4. (p 2007), pp. 92-104. 2007-12-04T11:35:43-00:00 2007 Neurochem Int 0197-0186 51 2-4 92 104 actin morphogenesis review spine http://www.citeulike.org/user/dibenedette/article/3136979 <i>Medical Mycology, Vol. 40, No. 3. (2002), pp. 225-242.</i><br /><br /><i>Paracoccidioides brasiliensis</i> is an amenable model to study the molecular and biochemical events that lead to morphological transition in fungi, because temperature seems to be the only factor regulating this process. It is the causative agent of paracoccidioidomycosis, a systemic mycosis that affects humans and that is geographically confined to Latin America, where it constitutes one of the most prevalent deep mycoses. With the help of molecular tools, events leading to the morphological transition have been traced to genes that control cell wall glucan and chitin syntheses, and other metabolic processes such as production of heat shock proteins and ornithine decarboxylase activity. Molecular diagnosis and epidemiology of paracoccidioidomycosis are also the focus of intensive research, with several primers being proposed as specific probes for clinical and field uses. Although <i>P. brasiliensis</i> is refractory to cytogenetic analysis, electrophoretic methods have allowed an approximation of its genomic organization and ploidy. Finally, the recognition of <i>P. brasiliensis</i> as an anamorph in the phylum Ascomycota, order <i>Onygenales</i>, family <i>Onygenaceae</i>, has been accomplished by means of molecular tools. This phylogenetic placement has revised the taxonomic position of this fungus, which was traditionally included within now-abandoned higher anamorph taxa, the phylum Deuteromycota and the class Hyphomycetes. <i>Paracoccidioides brasiliensis</i> and paracoccidioidomycosis: Molecular approaches to morphogenesis, diagnosis, epidemiology, taxonomy and genetics Gioconda San-Blas Gustavo Niño-Vega Teresa Iturriaga doi:10.1080/714031110 Medical Mycology, Vol. 40, No. 3. (2002), pp. 225-242. 2008-08-19T15:46:49-00:00 2002 Medical Mycology 40 3 225 242 Informa Healthcare and brasiliensis diagnosis epidemiology genetics morphogenesis paracoccidioides pb taxonomy http://www.citeulike.org/user/davidcsterratt/article/3111693 <i>Current topics in developmental biology, Vol. 81 (2008), pp. 291-310.</i><br /><br />Vertebrate lung has tree-like structure which facilitates gas exchange. After discovery of the involvement of several key toolkit genes--FGF10, BMP4, and Shh, huge amount of molecular information on lung development is now available. However, how their interactions result in a branched structure has not been elucidated. Recently, some studies have utilized mathematical models to understand the mechanism of branching morphogenesis, and we now have some models which are reliable enough to make experimental predictions in the in vitro system. In addition, a different type of modeling, which generates tree-like branching pattern by repeatedly applying a set of simple rules iteratively, is also utilized to model lung function. In this review, I focus on how these models can contribute to understand pattern formation phenomena from experimental biologist's point of view. Modeling lung branching morphogenesis. T Miura doi:10.1016/S0070-2153(07)81010-6 Current topics in developmental biology, Vol. 81 (2008), pp. 291-310. 2008-08-12T11:21:15-00:00 2008 Current topics in developmental biology 0070-2153 81 291 310 branching development morphogenesis http://www.citeulike.org/user/cwr/article/1552670 <i>pp. 389-416.</i><br /><br />This paper presents a simulation framework and computational testbed for studying multicellular pattern formation. The approach combines several developmental mechanisms (chemical, mechanical, genetic and electrical) known to be important for biological pattern formation. The mechanisms are present in an environment containing discrete cells which are capable of independent movement (cell migration). Experience with the testbed indicates that the interactions between the developmental... A Simulation Testbed for the Study of Multicellular Development: The Multiple Mechanisms of Morphogenesis Kurt Fleischer Alan Barr pp. 389-416. 2007-08-10T23:03:17-00:00 389 416 cellular morphogenesis http://www.citeulike.org/user/cwr/article/1552637 <i>pp. 229-236.</i><br /><br />this paper are best viewed in color. Color versions of some of the figures are available at the web page Investigations with a Multicellular Developmental Model Kurt Fleischer pp. 229-236. 2007-08-10T22:59:24-00:00 229 236 cellular morphogenesis http://www.citeulike.org/user/cwr/article/1070201 <i>Journal of Differential Equations, Vol. 191, No. 1. (10 June 2003), pp. 143-174.</i><br /><br />Several models have been proposed for describing the formation of animal coat patterns. We consider reaction-diffusion models due to Murray, which rely on a Turing instability for the pattern selection. In this paper, we describe the early stages of the pattern formation process for large domain sizes. This includes the selection mechanism and the geometry of the patterns generated by the nonlinear system on one-, two-, and three-dimensional base domains. These results are obtained by an adaptation of results explaining the occurrence of spinodal decomposition in materials science as modeled by the Cahn-Hilliard equation. We use techniques of dynamical systems, viewing solutions of the reaction-diffusion model in terms of nonlinear semiflows. Our results are applicable to any parabolic system exhibiting a Turing instability. Pattern formation in a nonlinear model for animal coats Evelyn Sander Thomas Wanner doi:10.1016/S0022-0396(02)00156-0 Journal of Differential Equations, Vol. 191, No. 1. (10 June 2003), pp. 143-174. 2007-01-27T03:02:02-00:00 2003 Journal of Differential Equations 191 1 143 174 morphogenesis pattern reaction-diffusion texture_synthesis http://www.citeulike.org/user/cwr/article/1552627 <i>Computer Graphics, Vol. 29, No. Annual Conference Series. (1995), pp. 239-248.</i><br /><br />We proposean approach for modeling surface details such as scales, feathers, or thorns. These types of cellular textures require a representation with more detail than texture-mapping but are inconvenient to model with hand-crafted geometry. We generate patterns of geometric elements using a biologically -motivated cellular development simulation together with a constraint to keep the cells on a surface. The surface may be defined by an implicit function, a volume dataset, or a polygonal mesh.... Cellular Texture Generation Kurt Fleischer David Laidlaw Bena Currin Alan Barr Computer Graphics, Vol. 29, No. Annual Conference Series. (1995), pp. 239-248. 2007-08-10T22:53:07-00:00 1995 Computer Graphics 29 Annual Conference Series 239 248 cellular morphogenesis http://www.citeulike.org/user/cwr/article/1512072 <i>Genetic Programming and Evolvable Machines, Vol. 8, No. 2. (June 2007), pp. 131-162.</i> Compositional pattern producing networks: A novel abstraction of development Stanley Kenneth doi:10.1007/s10710-007-9028-8 Genetic Programming and Evolvable Machines, Vol. 8, No. 2. (June 2007), pp. 131-162. 2007-07-29T23:54:19-00:00 2007 Genetic Programming and Evolvable Machines 1389-2576 8 2 131 162 Springer evolution humanfitnessfunction morphogenesis texture_synthesis http://www.citeulike.org/user/cwr/article/2820880 <i>(07 January 1999)</i><br /><br />The patterns of nature have fascinated humans for millennia. From spirals carved into rock during Neolithic times to the sand patterns of "executive" toys, we respond to and often replicate the underlying "order" of nature. The mathematical regularity of logarithmic spiral patterns in plant growth, such as seen in the florets of sunflowers and cauliflowers, was first characterised in 1202 by the Italian, Leonardo of Pisa, nicknamed Fibonacci. Since then technological and mathematical advances have allowed us to see patterning on all scales from spiral galaxies to vortices, waves and turbulence in the atmosphere and oceans and down into the packing of atoms and Mandelbrot fractal patterns of growth in all sorts of materials. So close do the worlds of the organic and inorganic become that they can be hard to tell apart. As Philip Ball asks: "Surely we can...tell a crystal from a living creature, an insect from a rock?" British science writer Philip Ball joins an illustrious band of scientists and writers who have been stimulated to try and make sense of all this patterning which surrounds us. He particularly follows in the footsteps of D'Arcy Wentworth Thompson, whose 1917 book _On Growth and Form_ has been enormously influential. Generations of scientists have been inspired to look more closely at the relationships between organisms and the way they use materials for constructing their skeletons and homes from individual shells to whole cities. Equally, artists have been reminded to look again at nature, just as their Renaissance forbears, such as Leonardo Da Vinci, did. Modern architects looked again at the logarithmic spiral and the Golden Section derived from it, as did the superlative architects of classical Greece, to proportion their buildings. Thompson's classic work is a particularly hard "act" to follow but Ball acquits himself very well. From his position as an editor at premier science journal _Nature_, Ball is particularly well placed to survey the enormous range of contemporary scientific investigation which reveals the extraordinary extent of nature's patterning. Using a wealth of illustration, Ball attempts to go beyond the niceties of a host of attractive examples, in order to "map many of nature's tapestries into some universal blueprints, in which the specifics cease to matter". The physics, mathematics and chemistry are well handled for the lay reader. A good bibliography, index and "home experiments" (not for the uninitiated) help those who want to explore further. After reading this book you will find yourself looking anew at cracked windows, fingerprints, dissolving coffee grains, boiling water, leaf veins... --_Douglas Palmer_ The Self-Made Tapestry: Pattern Formation in Nature Philip Ball (07 January 1999) 2008-05-21T17:00:50-00:00 1999 Oxford University Press, USA emergence insects morphogenesis pattern self_organizing texture_analysis texture_synthesis http://www.citeulike.org/user/cwr/article/1470075 <i>Computer Graphics, Vol. 25, No. 3. (July 1991), pp. 299-308.</i><br /><br />We present amethod for texture synthesisbased on the simulation of a process of local nonlinear interaction, called reaction-diffusion, which has been proposed as a model of biological pattern formation. We extend traditional reaction-diffusion systems by allowing anisotropic and spatially non-uniform diffusion, as well as multiple competing directions of diffusion. We adapt reaction-diffusion systems to the needs of computer graphics by presenting a method to synthesize patterns which compensate for the effects of non-uniform surface parameterization. Finally, we develop efficient algorithms for simulating reactiondiffusion systems and display a collection of resulting textures using standard texture- and displacement-mapping techniques. Reaction-diffusion textures Andrew Witkin Michael Kass doi:10.1145/122718.122750 Computer Graphics, Vol. 25, No. 3. (July 1991), pp. 299-308. 2007-07-20T17:49:07-00:00 1991 Computer Graphics 0097-8930 25 3 299 308 ACM Press morphogenesis reaction-diffusion texture_synthesis http://www.citeulike.org/user/cwr/article/2673804 <i>PLoS computational biology, Vol. 4, No. 4. (April 2008)</i><br /><br />We explore the possible role of elastic mismatch between epidermis and mesophyll as a driving force for the development of leaf venation. The current prevalent 'canalization' hypothesis for the formation of veins claims that the transport of the hormone auxin out of the leaves triggers cell differentiation to form veins. Although there is evidence that auxin plays a fundamental role in vein formation, the simple canalization mechanism may not be enough to explain some features observed in the vascular system of leaves, in particular, the abundance of vein loops. We present a model based on the existence of mechanical instabilities that leads very naturally to hierarchical patterns with a large number of closed loops. When applied to the structure of high-order veins, the numerical results show the same qualitative features as actual venation patterns and, furthermore, have the same statistical properties. We argue that the agreement between actual and simulated patterns provides strong evidence for the role of mechanical effects on venation development. The role of elastic stresses on leaf venation morphogenesis. MF Laguna S Bohn EA Jagla doi:10.1371/journal.pcbi.1000055 PLoS computational biology, Vol. 4, No. 4. (April 2008) 2008-04-15T15:44:14-00:00 2008 PLoS computational biology 1553-7358 4 4 morphogenesis self_organizing http://www.citeulike.org/user/cwr/article/2184060 <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, Vol. 295, No. 1078. (1981), pp. 473-496.</i><br /><br />The patterns on wings of Lepidoptera can be generated with a few pattern elements, but no mechanism has been suggested for producing them. I consider two of the basic patterns, namely, central symmetry and dependent patterns. A biochemically plausible model mechanism is proposed for generating major aspects of these patterns, based on a diffusing morphogen that activates a gene or colour-specific enzyme in a threshold manner to generate a stable heterogeneous spatial pattern. The model is applied to the determination stream hypothesis of Kühn & von Engelhardt (Wilhelm Roux Arch. Entw Mech. Org. 130, 660 (1933)), and results from the model compared with their microcautery experiments on the pupal wing of Ephestia kühniella. In the case of dependent patterns, results are compared with patterns on specific Papilionidae. For the same mechanism and a fixed set of parameters I demonstrate the important roles of geometry and scale on the spatial patterns obtained. The results and evidence presented here suggest the existence of diffusion fields of the order of several millimetres, which are very much larger than most embryonic fields. The existence of zones of polarizing activity is also indicated. Colour patterns on animals are considered to be genetically determined, but the mechanism is not known. I have previously suggested that a single mechanism that can exhibit an infinite variety of patterns is a candidate for that mechanism, and proposed that a reaction-diffusion system that can be diffusively driven unstable could be responsible for the laying down of the spacing patterns that generates the prepattern for animal coat markings. For illustrative purposes I consider a practical reaction mechanism, which exhibits substrate inhibition, and show that the geometry and scale of the domain (part of the epidermis) play a crucial role in the structural patterns that result. Patterns are obtained for a selection of geometries, and general features are related to the coat colour distribution in the spotted Felidae, giraffe, zebra and other animals. The patterns depend on the initial conditions, but for a given geometry and scale are qualitatively similar, a positive feature of the model and a necessary model attribute in view of the pattern individuality on animals of the same species. On Pattern Formation Mechanisms for Lepidopteran Wing Patterns and Mammalian Coat Markings JD Murray Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, Vol. 295, No. 1078. (1981), pp. 473-496. 2007-12-31T21:39:13-00:00 1981 Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 295 1078 473 496 morphogenesis reaction-diffusion texture_synthesis http://www.citeulike.org/user/cwr/article/363090 <i></i><br /><br />An extremely large body of theoretical work exists on pattern formation, but very few experimental results have confirmed the relevance of theoretical models. It is argued in this article that the notion of agent-based pattern formation, which is introduced and exemplified, can serve as a basis to study pattern formation in nature, especially because pattern-forming systems based on agents are (relatively) more easily amenable to experimental observations. Moreover, understanding... From classical models of morphogenesis to agent-based models of pattern formation E Bonabeau 2005-10-23T15:22:01-00:00 morphogenesis stigmergy swarm_intelligence http://www.citeulike.org/user/cwr/article/3134588 <i>ACM Trans. Graph., Vol. 27, No. 3. (August 2008), pp. 1-8.</i><br /><br />Programmable graphics hardware makes it possible to generate procedural noise textures on the fly for interactive rendering. However, filtering and antialiasing procedural noise involves a tradeoff between aliasing artifacts and loss of detail. In this paper we present a technique, targeted at interactive applications, that provides high-quality anisotropic filtering for noise textures. We generate noise tiles directly in the frequency domain by partitioning the frequency domain into oriented subbands. We then compute weighted sums of the subband textures to accurately approximate noise with a desired spectrum. This allows us to achieve high-quality anisotropic filtering. Our approach is based solely on 2D textures, avoiding the memory overhead of techniques based on 3D noise tiles. We devise a technique to compensate for texture distortions to generate uniform noise on arbitrary meshes. We develop a GPU-based implementation of our technique that achieves similar rendering performance as state-of-the-art algorithms for procedural noise. In addition, it provides anisotropic filtering and achieves superior image quality. Anisotropic noise Alexander Goldberg Matthias Zwicker Frédo Durand doi:10.1145/1360612.1360653 ACM Trans. Graph., Vol. 27, No. 3. (August 2008), pp. 1-8. 2008-08-19T00:18:02-00:00 2008 ACM Trans. Graph. 0730-0301 27 3 1 8 ACM morphogenesis pattern texture_synthesis http://www.citeulike.org/user/cwr/article/759570 <i>EMBO Reports, Vol. aop, No. current. (25 August 2006)</i> Spot pattern of leopard Danio is caused by mutation in the zebrafish connexin41.8 gene Masakatsu Watanabe Motoko Iwashita Masaru Ishii Yoshihisa Kurachi Atsushi Kawakami Shigeru Kondo Norihiro Okada doi:10.1038/sj.embor.7400757 EMBO Reports, Vol. aop, No. current. (25 August 2006) 2006-07-15T02:15:02-00:00 2006 EMBO Reports 1469-221X aop current Nature Publishing Group fish morphogenesis reaction-diffusion http://www.citeulike.org/user/chrn/article/461425 <i>Bioinformatics, Vol. 20, No. 7. (1 May 2004), pp. 1129-1137.</i><br /><br />MOTIVATION: CompuCell is a multi-model software framework for simulation of the development of multicellular organisms known as morphogenesis. It models the interaction of the gene regulatory network with generic cellular mechanisms, such as cell adhesion, division, haptotaxis and chemotaxis. A combination of a state automaton with stochastic local rules and a set of differential equations, including subcellular ordinary differential equations and extracellular reaction-diffusion partial differential equations, model gene regulation. This automaton in turn controls the differentiation of the cells, and cell-cell and cell-extracellular matrix interactions that give rise to cell rearrangements and pattern formation, e.g. mesenchymal condensation. The cellular Potts model, a stochastic model that accurately reproduces cell movement and rearrangement, models cell dynamics. All these models couple in a controllable way, resulting in a powerful and flexible computational environment for morphogenesis, which allows for simultaneous incorporation of growth and spatial patterning. RESULTS: We use CompuCell to simulate the formation of the skeletal architecture in the avian limb bud. AVAILABILITY: Binaries and source code for Microsoft Windows, Linux and Solaris are available for download from http://sourceforge.net/projects/compucell/ CompuCell, a multi-model framework for simulation of morphogenesis. JA Izaguirre R Chaturvedi C Huang T Cickovski J Coffland G Thomas G Forgacs M Alber G Hentschel SA Newman JA Glazier Bioinformatics, Vol. 20, No. 7. (1 May 2004), pp. 1129-1137. 2006-01-11T04:22:11-00:00 2004 Bioinformatics 1367-4803 20 7 1129 1137 ch3 compucell morphogenesis refs_ox simulation software http://www.citeulike.org/user/blobbybirdman/article/1390790 <i>Proc Natl Acad Sci U S A, Vol. 104 Suppl 1 (15 May 2007), pp. 8605-8612.</i><br /><br />Understanding the genetic and molecular mechanisms governing the evolution of morphology is a major challenge in biology. Because most animals share a conserved repertoire of body-building and -patterning genes, morphological diversity appears to evolve primarily through changes in the deployment of these genes during development. The complex expression patterns of developmentally regulated genes are typically controlled by numerous independent cis-regulatory elements (CREs). It has been proposed that morphological evolution relies predominantly on changes in the architecture of gene regulatory networks and in particular on functional changes within CREs. Here, we discuss recent experimental studies that support this hypothesis and reveal some unanticipated features of how regulatory evolution occurs. From this growing body of evidence, we identify three key operating principles underlying regulatory evolution, that is, how regulatory evolution: (i) uses available genetic components in the form of preexisting and active transcription factors and CREs to generate novelty; (ii) minimizes the penalty to overall fitness by introducing discrete changes in gene expression; and (iii) allows interactions to arise among any transcription factor and downstream CRE. These principles endow regulatory evolution with a vast creative potential that accounts for both relatively modest morphological differences among closely related species and more profound anatomical divergences among groups at higher taxonomical levels. Colloquium Papers: Emerging principles of regulatory evolution. B Prud'homme N Gompel SB Carroll doi:10.1073/pnas.0700488104 Proc Natl Acad Sci U S A, Vol. 104 Suppl 1 (15 May 2007), pp. 8605-8612. 2007-06-14T22:46:27-00:00 2007 Proc Natl Acad Sci U S A 0027-8424 104 Suppl 1 8605 8612 cis-regulatory-elements development evolution gene-regulation gene-regulatory-networks morphogenesis http://www.citeulike.org/user/balicea/article/332150 <i>Science, Vol. 309, No. 5740. (2 September 2005), pp. 1559-1563.</i><br /><br />This study describes comprehensive polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome. We identify the 5' and 3' boundaries of 181,047 transcripts with extensive variation in transcripts arising from alternative promoter usage, splicing, and polyadenylation. There are 16,247 new mouse protein-coding transcripts, including 5154 encoding previously unidentified proteins. Genomic mapping of the transcriptome reveals transcriptional forests, with overlapping transcription on both strands, separated by deserts in which few transcripts are observed. The data provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development. The transcriptional landscape of the mammalian genome. 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