Biological Development of Cell Patterns: Characterizing the Space of Cell Chemistry Genetic Regulatory Networks

Genetic regulatory networks (GRNs) control gene expression and are responsible for establishing the regular cellular patterns that constitute an organism. This paper introduces a model of biological development that generates cellular patterns via chemical interactions. GRNs for protein expression are generated and evaluated for their effectiveness in constructing 2D patterns of cells such as borders, patches, and mosaics. Three types of searches were performed: (a) a Monte Carlo search of the GRN space using a utility function based on spatial interestingness; (b) a hill climbing search to identify GRNs that solve specific pattern problems; (c) a search for combinatorial codes that solve difficult target patterns by running multiple disjoint GRNs in parallel. We show that simple biologically realistic GRNs can construct many complex cellular patterns. Our model provides an avenue to explore the evolution of complex GRNs that drive development.

[1]  A. Lindenmayer.  Mathematical models for cellular interactions in development. II. Simple and branching filaments with two-sided inputs. , 1968, Journal of theoretical biology.

[2]  David H. Sharp,et al.  A connectionist model of development. , 1991, Journal of theoretical biology.

[3]  Paulien Hogeweg,et al.  Computing an organism: on the interface between informatic and dynamic processes. , 2002, Bio Systems.

[4]  Douglas A Lauffenburger,et al.  Modeling and computational analysis of EGF receptor-mediated cell communication in Drosophila oogenesis. , 2002, Development.

[5]  Kunihiko Kaneko,et al.  Emergence of Multicellular Organisms with Dynamic Differentiation and Spatial Pattern , 1997, Artificial Life.

[6]  Howard J. Hamilton,et al.  Heuristic for Ranking the Interestigness of Discovered Knowledge , 1999, PAKDD.

[7]  Tim Taylor.  A Genetic Regulatory Network-Inspired Real-Time Controller for a Group of Underwater Robots , 2005 .

[8]  J. Skeath.  At the nexus between pattern formation and cell-type specification: the generation of individual neuroblast fates in the Drosophila embryonic central nervous system. , 1999, BioEssays : news and reviews in molecular, cellular and developmental biology.

[9]  P. Maini,et al.  Pattern formation by lateral inhibition with feedback: a mathematical model of delta-notch intercellular signalling. , 1996, Journal of theoretical biology.

[10]  Larry D. Pyeatt,et al.  A comparison between cellular encoding and direct encoding for genetic neural networks , 1996 .

[11]  Josh Bongard,et al.  Evolving modular genetic regulatory networks , 2002, Proceedings of the 2002 Congress on Evolutionary Computation. CEC'02 (Cat. No.02TH8600).

[12]  D. Federici.  Using Embryonic Stages to increase the evolvability of development , 2004 .

[13]  Risto Miikkulainen,et al.  A Taxonomy for Artificial Embryogeny , 2003, Artificial Life.

[14]  Daniel Roggen,et al.  Multi-cellular Development: Is There Scalability and Robustness to Gain? , 2004, PPSN.

[15]  Atsushi Mochizuki,et al.  Pattern formation of the cone mosaic in the zebrafish retina: a cell rearrangement model. , 2002, Journal of theoretical biology.

[16]  M. Gnegy,et al.  Retinal mosaics: new insights into an old concept , 2000 .

[17]  Christoph Adami,et al.  A Developmental Model for the Evolution of Artificial Neural Networks , 2000, Artificial Life.

[18]  T. Jessell.  Neuronal specification in the spinal cord: inductive signals and transcriptional codes , 2000, Nature Reviews Genetics.

[19]  Christopher G. Langton,et al.  Artificial Life III , 2000 .

[20]  P. Lawrence.  The making of a fly , 1992 .

[21]  A. M. Turing,et al.  The chemical basis of morphogenesis , 1952, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences.

[22]  HighWire Press.  Philosophical Transactions of the Royal Society of London , 1781, The London Medical Journal.

[23]  G. Odell,et al.  The segment polarity network is a robust developmental module , 2000, Nature.

[24]  A. Lindenmayer.  Mathematical models for cellular interactions in development. I. Filaments with one-sided inputs. , 1968, Journal of theoretical biology.

[25]  J. Clarke,et al.  Dorso-ventral ectodermal compartments and origin of apical ectodermal ridge in developing chick limb. , 1997, Development.

[26]  Jesús A. Izaguirre,et al.  COMPUCELL, a multi-model framework for simulation of morphogenesis , 2004, Bioinform..