Synthetic biology: a new approach to study biological pattern formation

The principles and molecular mechanisms underlying biological pattern formation are difficult to elucidate in most cases due to the overwhelming physiologic complexity associated with the natural context. The understanding of a particular mechanism, not to speak of underlying universal principles, is difficult due to the diversity and uncertainty of the biological systems. Although current genetic and biochemical approaches have greatly advanced our understanding of pattern formation, the progress mainly relies on experimental phenotypes obtained from time-consuming studies of gain or loss of function mutants. It is prevailingly considered that synthetic biology will come to the application age, but more importantly synthetic biology can be used to understand the life. Using periodic stripe pattern formation as a paradigm, we discuss how to apply synthetic biology in understanding biological pattern formation and hereafter foster the applications like tissue engineering.

[1]  Lewis Wolpert,et al.  Chapter 6 Positional Information and Pattern Formation , 1971 .

[2]  Michael T. Laub,et al.  Rewiring the Specificity of Two-Component Signal Transduction Systems , 2008, Cell.

[3]  L. Held,et al.  Models for embryonic periodicity. , 1992, Monographs in developmental biology.

[4]  O. Pourquié The Segmentation Clock: Converting Embryonic Time into Spatial Pattern , 2003, Science.

[5]  Karen M Polizzi What is synthetic biology? , 2013, Methods in molecular biology.

[6]  E. C. Zeeman,et al.  A clock and wavefront model for control of the number of repeated structures during animal morphogenesis. , 1976, Journal of theoretical biology.

[7]  T.W.Sadler Langman's Medical Embryology , 1969 .

[8]  Andrew Hodges,et al.  Alan Turing: The Enigma , 1983 .

[9]  Drew N. Robson,et al.  Supplementary Materials for Differential Diffusivity of Nodal and Lefty Underlies a Reaction-Diffusion Patterning System , 2012 .

[10]  Shigeru Kondo,et al.  Reaction-Diffusion Model as a Framework for Understanding Biological Pattern Formation , 2010, Science.

[11]  M E Cates,et al.  Arrested phase separation in reproducing bacteria creates a generic route to pattern formation , 2010, Proceedings of the National Academy of Sciences.

[12]  K. Müller Synthetic Gene Networks , 2012, Methods in Molecular Biology.

[13]  Robert M. May,et al.  Simple mathematical models with very complicated dynamics , 1976, Nature.

[14]  G. Church,et al.  Synthetic Gene Networks That Count , 2009, Science.

[15]  S. Basu,et al.  A synthetic multicellular system for programmed pattern formation , 2005, Nature.

[16]  L. Tsimring,et al.  A synchronized quorum of genetic clocks , 2009, Nature.

[17]  Gary Ruvkun,et al.  The unc-86 gene product couples cell lineage and cell identity in C. elegans , 1990, Cell.

[18]  G F Oster,et al.  A mechanical model for mesenchymal morphogenesis , 1983, Journal of mathematical biology.

[19]  I. Sussex Developmental programming of the shoot meristem , 1989, Cell.

[20]  C. Nüsslein-Volhard,et al.  Mutations affecting segment number and polarity in Drosophila , 1980, Nature.

[21]  R. FitzHugh Impulses and Physiological States in Theoretical Models of Nerve Membrane. , 1961, Biophysical journal.

[22]  L. Wolpert Positional information and the spatial pattern of cellular differentiation. , 1969, Journal of theoretical biology.

[23]  J. Cooke,et al.  Control of somite number during morphogenesis of a vertebrate, Xenopus laevis , 1975, Nature.

[24]  T. Hwa,et al.  Stripe formation in bacterial systems with density-suppressed motility. , 2012, Physical review letters.

[25]  P. Lawrence Drosophila Unfolded. (Book Reviews: The Making of a Fly. The Genetics of Animal Design.) , 1992 .

[26]  M. Elowitz,et al.  Build life to understand it , 2010, Nature.

[27]  Paul Houston,et al.  Models for pattern formation in somitogenesis: a marriage of cellular and molecular biology. , 2002, Comptes rendus biologies.

[28]  Ariel D. Chipman,et al.  Arthropod Segmentation: beyond the Drosophila paradigm , 2005, Nature Reviews Genetics.

[29]  Mat E. Barnet,et al.  A synthetic Escherichia coli predator–prey ecosystem , 2008, Molecular systems biology.

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

[31]  Ahmad S. Khalil,et al.  Synthetic biology: applications come of age , 2010, Nature Reviews Genetics.

[32]  N. Swindale A model for the formation of ocular dominance stripes , 1980, Proceedings of the Royal Society of London. Series B. Biological Sciences.

[33]  J. Collins,et al.  Programmable cells: interfacing natural and engineered gene networks. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[34]  H. Meinhardt,et al.  Applications of a theory of biological pattern formation based on lateral inhibition. , 1974, Journal of cell science.

[35]  Olivier Pourquié,et al.  FGF Signaling Controls Somite Boundary Position and Regulates Segmentation Clock Control of Spatiotemporal Hox Gene Activation , 2001, Cell.

[36]  R. Weiss,et al.  Programmed population control by cell–cell communication and regulated killing , 2004, Nature.

[37]  T. Hwa,et al.  Sequential Establishment of Stripe Patterns in an Expanding Cell Population , 2011, Science.

[38]  A. Spradling,et al.  bag-of-marbles: a Drosophila gene required to initiate both male and female gametogenesis. , 1990, Genes & development.

[39]  Christopher A. Voigt,et al.  A Synthetic Genetic Edge Detection Program , 2009, Cell.

[40]  J. Collins,et al.  Bacterial charity work leads to population-wide resistance , 2010, Nature.

[41]  P K Maini,et al.  Bifurcating spatially heterogeneous solutions in a chemotaxis model for biological pattern generation. , 1991, Bulletin of mathematical biology.

[42]  Olivier Pourquié,et al.  Segmental patterning of the vertebrate embryonic axis , 2008, Nature Reviews Genetics.

[43]  M. Elowitz,et al.  A synthetic oscillatory network of transcriptional regulators , 2000, Nature.

[44]  Christopher A. Voigt,et al.  Synthetic biology: Engineering Escherichia coli to see light , 2005, Nature.

[45]  James D. Murray,et al.  Spatial models and biomedical applications , 2003 .

[46]  Shankar Mukherji,et al.  Synthetic biology: understanding biological design from synthetic circuits , 2009, Nature Reviews Genetics.