Modelling the Drosophila embryo.

I provide a historical overview on the use of mathematical models to gain insight into pattern formation during early development of the fruit fly Drosophila melanogaster. It is my intention to illustrate how the aims and methodology of modelling have changed from the early beginnings of a theoretical developmental biology in the 1960s to modern-day systems biology. I show that even early modelling attempts addressed interesting and relevant questions, which were not tractable by experimental approaches. Unfortunately, their validation was severely hampered by a lack of specificity and appropriate experimental evidence. There is a simple lesson to be learned from this: we cannot deduce general rules for pattern formation from first principles or spurious reproduction of developmental phenomena. Instead, we must infer such rules (if any) from detailed and accurate studies of specific developmental systems. To achieve this, mathematical modelling must be closely integrated with experimental approaches. I report on progress that has been made in this direction in the past few years and illustrate the kind of novel insights that can be gained from such combined approaches. These insights demonstrate the great potential (and some pitfalls) of an integrative, systems-level investigation of pattern formation.

[1]  G. Odell,et al.  Design and constraints of the Drosophila segment polarity module: robust spatial patterning emerges from intertwined cell state switches. , 2002, The Journal of experimental zoology.

[2]  M. Levine,et al.  Computational Models for Neurogenic Gene Expression in the Drosophila Embryo , 2006, Current Biology.

[3]  H. Othmer,et al.  The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster. , 2003, Journal of theoretical biology.

[4]  B Bunow,et al.  Pattern formation by reaction-diffusion instabilities: application to morphogenesis in Drosophila. , 1980, Journal of theoretical biology.

[5]  Johannes Jaeger,et al.  Pattern formation and nuclear divisions are uncoupled in Drosophila segmentation: comparison of spatially discrete and continuous models , 2004 .

[6]  R. Tjian,et al.  Orchestrated response: a symphony of transcription factors for gene control. , 2000, Genes & development.

[7]  R. Thomas,et al.  Boolean formalization of genetic control circuits. , 1973, Journal of theoretical biology.

[8]  S. Salzberg,et al.  Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura , 2004, Genome Biology.

[9]  Diethard Tautz,et al.  A morphogenetic gradient of hunchback protein organizes the expression of the gap genes Krüppel and knirps in the early Drosophila embryo , 1990, Nature.

[10]  V. French,et al.  Distal regeneration and symmetry. , 1981, Science.

[11]  Rui Dilão,et al.  Modeling segmental patterning in Drosophila: Maternal and gap genes. , 2006, Journal of theoretical biology.

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

[13]  V. French,et al.  Pattern regulation in epimorphic fields. , 1976, Science.

[14]  John Reinitz,et al.  Bicoid cooperative DNA binding is critical for embryonic patterning in Drosophila. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[15]  T. Lacalli Modeling the Drosophila pair-rule pattern by reaction-diffusion: gap input and pattern control in a 4-morphogen system. , 1990, Journal of theoretical biology.

[16]  John Reinitz,et al.  FlyEx, the quantitative atlas on segmentation gene expression at cellular resolution , 2008, Nucleic Acids Res..

[17]  W. Bialek,et al.  Stability and Nuclear Dynamics of the Bicoid Morphogen Gradient , 2007, Cell.

[18]  Christopher R. Myers,et al.  Universally Sloppy Parameter Sensitivities in Systems Biology Models , 2007, PLoS Comput. Biol..

[19]  A. Simcox,et al.  When does determination occur in Drosophila embryos? , 1983, Developmental biology.

[20]  H. Meinhardt,et al.  A theory of biological pattern formation , 1972, Kybernetik.

[21]  Janet Wiles,et al.  Robustness and state-space structure of Boolean gene regulatory models. , 2007, Journal of theoretical biology.

[22]  P. Ingham The molecular genetics of embryonic pattern formation in Drosophila , 1988, Nature.

[23]  G. von Dassow,et al.  Modularity in animal development and evolution: elements of a conceptual framework for EvoDevo. , 1999, The Journal of experimental zoology.

[24]  L Wolpert,et al.  One hundred years of positional information. , 1996, Trends in genetics : TIG.

[25]  John Reinitz,et al.  A database for management of gene expression data in situ , 2004, Bioinform..

[26]  J. W. Bodnar Programming the Drosophila embryo. , 1997, Journal of theoretical biology.

[27]  L Wolpert,et al.  Positional information and pattern formation in development. , 1994, Developmental genetics.

[28]  S. Panchanathan,et al.  BEST: a novel computational approach for comparing gene expression patterns from early stages of Drosophila melanogaster development. , 2002, Genetics.

[29]  J. Helden,et al.  Establishement of the dorso-ventral pattern during embryonic development of drosophila melanogasater: a logical analysis , 1997, Journal of theoretical biology.

[30]  David H. Sharp,et al.  Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene , 2006, Nature Genetics.

[31]  Jingyuan Deng,et al.  Probing intrinsic properties of a robust morphogen gradient in Drosophila. , 2008, Developmental cell.

[32]  S. Leibler,et al.  Precise domain specification in the developing Drosophila embryo. , 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.

[33]  G. Odell,et al.  Ingeneue: a versatile tool for reconstituting genetic networks, with examples from the segment polarity network. , 2002, The Journal of experimental zoology.

[34]  Rustem F. Ismagilov,et al.  Dynamics of Drosophila embryonic patterning network perturbed in space and time using microfluidics , 2005, Nature.

[35]  R. Forman,et al.  Modeling the precision and robustness of Hunchback border during Drosophila embryonic development. , 2008, Journal of theoretical biology.

[36]  N. Monk Elegant hypothesis and inelegant fact in developmental biology. , 2000, Endeavour.

[37]  Michael Akam,et al.  Making stripes inelegantly , 1989, Nature.

[38]  Thomas Gregor,et al.  Shape and function of the Bicoid morphogen gradient in dipteran species with different sized embryos. , 2008, Developmental biology.

[39]  Yuefan Deng,et al.  Parallel Simulated Annealing by Mixing of States , 1999 .

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

[41]  Johannes Jaeger,et al.  Regulative feedback in pattern formation: towards a general relativistic theory of positional information , 2008, Development.

[42]  J. Reinitz,et al.  Cell divisions as a mechanism for selection in stable steady states of multi-stationary gene circuits , 2006 .

[43]  J. Stark,et al.  Network motifs: structure does not determine function , 2006, BMC Genomics.

[44]  B C Goodwin,et al.  Spatial harmonics and pattern specification in early Drosophila development. Part II. The four colour wheels model. , 1990, Journal of theoretical biology.

[45]  Dmitri Papatsenko,et al.  A self-organizing system of repressor gradients establishes segmental complexity in Drosophila , 2003, Nature.

[46]  Carlos E Vanario-Alonso,et al.  A kinetic mechanism for Drosophila bicoid cooperative binding. , 2005, Journal of theoretical biology.

[47]  Réka Albert,et al.  Studying the effect of cell division on expression patterns of the segment polarity genes , 2008, Journal of The Royal Society Interface.

[48]  B C Goodwin,et al.  Drosophila segmentation: supercomputer simulation of prepattern hierarchy. , 1990, Journal of theoretical biology.

[49]  R. Tjian,et al.  Transcription regulation and animal diversity , 2003, Nature.

[50]  Robert P Zinzen,et al.  A novel multifunctional factor involved in trans-splicing of chloroplast introns in Chlamydomonas , 2006, Nucleic acids research.

[51]  David M. Holloway,et al.  Spatial Bistability Generates hunchback Expression Sharpness in the Drosophila Embryo , 2008, PLoS Comput. Biol..

[52]  Michael J. Lyons,et al.  Stripe selection: An intrinsic property of some pattern‐forming models with nonlinear dynamics , 1992, Developmental dynamics : an official publication of the American Association of Anatomists.

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

[54]  T. Bisseling,et al.  Model for the robust establishment of precise proportions in the early Drosophila embryo. , 2004, Journal of theoretical biology.

[55]  Michael A. Russell,et al.  Positional information in insect segments , 1985 .

[56]  G. Rubin,et al.  Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[57]  René Thomas Regulatory networks seen as asynchronous automata: A logical description , 1991 .

[58]  Rustem F. Ismagilov,et al.  A Precise Bicoid Gradient Is Nonessential during Cycles 11–13 for Precise Patterning in the Drosophila Blastoderm , 2008, PloS one.

[59]  Denis Thieffry,et al.  Alternative Epigenetic States Understood in Terms of Specific Regulatory Structures , 2002, Annals of the New York Academy of Sciences.

[60]  B. Goodwin,et al.  A phase-shift model for the spatial and temporal organization of developing systems. , 1969, Journal of theoretical biology.

[61]  David H. Sharp,et al.  Canalization of Gene Expression in the Drosophila Blastoderm by Gap Gene Cross Regulation , 2009, PLoS biology.

[62]  Alexander Spirov,et al.  Formation of the bicoid morphogen gradient: an mRNA gradient dictates the protein gradient , 2009, Development.

[63]  Jaap A. Kaandorp,et al.  Efficient parameter estimation for spatio-temporal models of pattern formation: case study of Drosophila melanogaster , 2007, Bioinform..

[64]  A. Riggs,et al.  Determinator-inhibitor pairs as a mechanism for threshold setting in development: a possible function for pseudogenes. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[65]  P. R. ten Wolde,et al.  Finding the center reliably: robust patterns of developmental gene expression. , 2005, Physical review letters.

[66]  David H. Sharp,et al.  Known maternal gradients are not sufficient for the establishment of gap domains in Drosophila melanogaster , 2007, Mechanisms of Development.

[67]  S. Kauffman Pattern formation in the Drosophila embryo. , 1981, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[68]  Z Burstein A network model of developmental gene hierarchy. , 1995, Journal of theoretical biology.

[69]  J. Fak,et al.  Transcriptional Control in the Segmentation Gene Network of Drosophila , 2004, PLoS biology.

[70]  David H. Sharp,et al.  Dynamic control of positional information in the early Drosophila embryo , 2004, Nature.

[71]  M. Kreitman,et al.  Canalization of segmentation and its evolution in Drosophila , 2007, Proceedings of the National Academy of Sciences.

[72]  S. Leibler,et al.  Establishment of developmental precision and proportions in the early Drosophila embryo , 2002, Nature.

[73]  W. Bialek,et al.  Probing the Limits to Positional Information , 2007, Cell.

[74]  H. Berg,et al.  Physics of chemoreception. , 1977, Biophysical journal.

[75]  Stanislav Y Shvartsman,et al.  Modeling the bicoid gradient: diffusion and reversible nuclear trapping of a stable protein. , 2007, Developmental biology.

[76]  Leon Glass,et al.  Reverse Engineering the Gap Gene Network of Drosophila melanogaster , 2006, PLoS Comput. Biol..

[77]  C. Nüsslein-Volhard,et al.  A gradient of bicoid protein in Drosophila embryos , 1988, Cell.

[78]  David H. Sharp,et al.  Mechanism of eve stripe formation , 1995, Mechanisms of Development.

[79]  John Reinitz,et al.  Pipeline for acquisition of quantitative data on segmentation gene expression from confocal images , 2008, Fly.

[80]  Luhua Lai,et al.  Robustness and modular design of the Drosophila segment polarity network , 2006, Molecular systems biology.

[81]  M. Levine,et al.  Regulation of even‐skipped stripe 2 in the Drosophila embryo. , 1992, The EMBO journal.

[82]  R. Lehmann,et al.  Cross-regulatory interactions among the gap genes of Drosophila , 1986, Nature.

[83]  B. Alberts,et al.  Studies of nuclear and cytoplasmic behaviour during the five mitotic cycles that precede gastrulation in Drosophila embryogenesis. , 1983, Journal of cell science.

[84]  W. Bialek,et al.  Diffusion and scaling during early embryonic pattern formation. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[85]  L. Pick,et al.  Non-periodic cues generate seven ftz stripes in the Drosophila embryo , 1995, Mechanisms of Development.

[86]  J J Hopfield,et al.  Neurons with graded response have collective computational properties like those of two-state neurons. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[87]  David Kosman,et al.  Analysis of pattern precision shows that Drosophila segmentation develops substantial independence from gradients of maternal gene products , 2006, Developmental dynamics : an official publication of the American Association of Anatomists.

[88]  R. Tchuraev,et al.  A new method for the analysis of the dynamics of the molecular genetic control systems. II. Application of the method of generalized threshold models in the investigation of concrete genetic systems. , 1991, Journal of theoretical biology.

[89]  G. Odell,et al.  A genetic switch, based on negative regulation, sharpens stripes in Drosophila embryos. , 1989, Developmental genetics.

[90]  R. Tchuraev,et al.  A new method for the analysis of the dynamics of the molecular genetic control systems. I. Description of the method of generalized threshold models. , 1991, Journal of theoretical biology.

[91]  L Wolpert,et al.  Thresholds in development. , 1977, Journal of theoretical biology.

[92]  H. Meinhardt,et al.  Hierarchical Inductions of Cell States: A Model for Segmentation in Drosophila , 1986, Journal of Cell Science.

[93]  Madalena Chaves,et al.  Robustness and fragility of Boolean models for genetic regulatory networks. , 2005, Journal of theoretical biology.

[94]  M. Isalan,et al.  Engineering Gene Networks to Emulate Drosophila Embryonic Pattern Formation , 2005, PLoS biology.

[95]  Nicholas T Ingolia,et al.  Topology and Robustness in the Drosophila Segment Polarity Network , 2004, PLoS biology.

[96]  Wouter-Jan Rappel,et al.  Determining the scale of the Bicoid morphogen gradient , 2009, Proceedings of the National Academy of Sciences.

[97]  D. Thieffry,et al.  A logical analysis of the Drosophila gap-gene system. , 2001, Journal of theoretical biology.

[98]  John Reinitz,et al.  Developmental biology: A ten per cent solution , 2007, Nature.

[99]  J. Monod,et al.  Teleonomic mechanisms in cellular metabolism, growth, and differentiation. , 1961, Cold Spring Harbor symposia on quantitative biology.

[100]  H. Meinhardt,et al.  Space-dependent cell determination under the control of morphogen gradient. , 1978, Journal of theoretical biology.

[101]  G. Schubiger,et al.  Temporal regulation of gene expression in the blastoderm Drosophila embryo. , 1991, Genes & development.

[102]  R. Lehmann,et al.  Determination of anteroposterior polarity in Drosophila. , 1987, Science.

[103]  M. Levine,et al.  Transcriptional repression in the Drosophila embryo. , 1995, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[104]  R. Tchuraev,et al.  Modeling of Actual Eukaryotic Control Gene Subnetworks Based on the Method of Generalized Threshold Models , 2001, Molecular Biology.

[105]  J. Monod,et al.  Genetic regulatory mechanisms in the synthesis of proteins. , 1961, Journal of molecular biology.

[106]  K. G. Coleman,et al.  Expression of engrailed proteins in arthropods, annelids, and chordates , 1989, Cell.

[107]  Arthur D Lander,et al.  Morpheus Unbound: Reimagining the Morphogen Gradient , 2007, Cell.

[108]  N. Dostatni,et al.  Bicoid Determines Sharp and Precise Target Gene Expression in the Drosophila Embryo , 2005, Current Biology.

[109]  Alexander M. Samsonov,et al.  Model with asymptotically stable dynamics for Drosophila gap gene network , 2008 .

[110]  D. Sharp,et al.  Stripe forming architecture of the gap gene system. , 1998, Developmental genetics.

[111]  J. W. Bodnar,et al.  Programming the Drosophila embryo 2 , 2007, Cell Biochemistry and Biophysics.

[112]  S A Kauffman,et al.  Control of sequential compartment formation in Drosophila. , 1978, Science.

[113]  D. Thieffry,et al.  Segmenting the fly embryo: logical analysis of the role of the segment polarity cross-regulatory module. , 2008, The International journal of developmental biology.

[114]  David H. Sharp,et al.  Transcriptional Control in Drosophila , 2003, Complexus.

[115]  Johannes Jaeger,et al.  On the dynamic nature of positional information. , 2006, BioEssays : news and reviews in molecular, cellular and developmental biology.

[116]  S. Bergmann,et al.  Pre-Steady-State Decoding of the Bicoid Morphogen Gradient , 2007, PLoS biology.

[117]  B. Nagorcka A pattern formation mechanism to control spatial organization in the embryo of Drosophila melanogaster. , 1988, Journal of theoretical biology.

[118]  Nicolas E. Buchler,et al.  Molecular titration and ultrasensitivity in regulatory networks. , 2008, Journal of molecular biology.

[119]  C. Nüsslein-Volhard,et al.  The origin of pattern and polarity in the Drosophila embryo , 1992, Cell.

[120]  S. Kauffman,et al.  Spatial harmonics and pattern specification in early Drosophila development. Part I. Bifurcation sequences and gene expression. , 1990, Journal of theoretical biology.

[121]  Johannes Jaeger,et al.  Parameter estimation and determinability analysis applied to Drosophila gap gene circuits , 2008, BMC Systems Biology.

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

[123]  S. Shvartsman,et al.  Nuclear Trapping Shapes the Terminal Gradient in the Drosophila Embryo , 2008, Current Biology.

[124]  Mehmet M. Dalkilic,et al.  Data Pushing: A Fly-Centric Guide to Bioinformatics Tools , 2008, Fly.

[125]  David H. Sharp,et al.  Prediction of mutant expression patterns using gene circuits. , 1998, Bio Systems.

[126]  W. Rappel,et al.  Embryonic pattern scaling achieved by oppositely directed morphogen gradients , 2006, Physical biology.

[127]  J. Raven Astrobiology: Photosynthesis in watercolours , 2007, Nature.

[128]  Manu,et al.  Characterization of the Drosophila segment determination morphome. , 2008, Developmental biology.

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

[130]  David H. Sharp,et al.  Canalization of Gene Expression and Domain Shifts in the Drosophila Blastoderm by Dynamical Attractors , 2009, PLoS Comput. Biol..

[131]  E. Segal,et al.  Predicting expression patterns from regulatory sequence in Drosophila segmentation , 2008, Nature.

[132]  D. Papatsenko,et al.  Dual regulation by the Hunchback gradient in the Drosophila embryo , 2008, Proceedings of the National Academy of Sciences.

[133]  Denis Thieffry,et al.  Segmenting the fly embryo: a logical analysis of the pair-rule cross-regulatory module. , 2003, Journal of theoretical biology.

[134]  C. Nüsslein-Volhard,et al.  The bicoid protein determines position in the Drosophila embryo in a concentration-dependent manner , 1988, Cell.

[135]  Claude Desplan,et al.  Synergy between the hunchback and bicoid morphogens is required for anterior patterning in Drosophila , 1994, Cell.

[136]  David H. Sharp,et al.  Dynamical Analysis of Regulatory Interactions in the Gap Gene System of Drosophila melanogaster , 2004, Genetics.

[137]  Sadri Hassani,et al.  Nonlinear Dynamics and Chaos , 2000 .

[138]  David H. Sharp,et al.  Model for cooperative control of positional information in Drosophila by bicoid and maternal hunchback. , 1995, The Journal of experimental zoology.