Mathematical approaches in studying bicoid gene
Zara Ghodsi, Hossein Hassani, Kevin McGhee
Mathematical approaches in studying bicoid gene
It is widely believed that in Drosophila melanogaster the pattern of Bicoid protein gradient plays a crucial role in the segmentation stage of embryo development. As a result of its fundamental role, modelling the Bicoid gradient has become increasingly popular for researchers from many different areas of study. The aim of this paper is to bring together the most prominent studies on this maternal gene and discuss how existing techniques for modelling this gradient have evolved over the years.
bicoid / Drosophila melanogaster / model / segmentation gene
[1] |
Driesch,H. (1908). The science and philosophy of the organism. Aberdeen: Aberdeen University
|
[2] |
Driever,W. and Nusslein-Volhard, C. (1988) The bicoid protein determines position in the Drosophila embryo in a concentration-dependent manner. Cell, 54, 95104
|
[3] |
Frohnhöfer,H. G. and Nüsslein-Volhard,C. (1986) Organization of anterior pattern in the Drosophila embryo by the maternal gene bicoid. Nature, 324, 120–125
CrossRef
Google scholar
|
[4] |
Berleth,T., Burri, M., Thoma,G., Bopp,D., Richstein, S., Frigerio,G., Noll,M., Nüsslein-Volhard, C. (1988) The role of localization of bicoid RNA in organizing the anterior pattern of the Drosophila embryo. EMBO J., 7, 1749
|
[5] |
Embryos receiving different doses of Bcd have differently sized anterior structures.
|
[6] |
Grimm,O., Coppey, M. and Wieschaus,E. (2010) Modelling the Bicoid gradient. Development, 137, 2253–2264
CrossRef
Google scholar
|
[7] |
Grimm,O. and Wieschaus, E. (2010) The Bicoid gradient is shaped independently of nuclei. Development, 137, 2857–2862
CrossRef
Google scholar
|
[8] |
Houchmandzadeh,B., Wieschaus, E. and Leibler,S. (2002) Establishment of developmental precision and proportions in the early Drosophila embryo. Nature, 415, 798–802
CrossRef
Google scholar
|
[9] |
Gregor,T., Bialek, W., de Ruyter van Steveninck, R. R. and Tank,D. W.,Wieschaus. E.F.(2005). Diffusion and scaling during early embryonic pattern formation. Proc. Natl. Acad. Sci. USA., 102, 18402–18407
|
[10] |
Wartlick,O., Kicheva, A. and Gonzlez-Gaitn,M. (2009) Morphogen gradient formation. Cold Spring Harb. Perspect. Biol., 1, a001255
CrossRef
Google scholar
|
[11] |
Liu,W. (2013). Machine learning approaches to modelling bicoid morphogen in Drosophila melanogaster. Ph. D. Thesis, University of Southampton.
|
[12] |
Morgan,T. H. (1901). Regeneration. New York: The Macmillan Company
|
[13] |
Spemann,H. and Mangold, H. (1924) Introduction of embryonic primordia by implantation of organizers from a different species. Rouxs Arch. Entw. Mech, 100, 599638
|
[14] |
Child,C. M. (1941). Patterns and Problems of Development. Chicago: The university of chicago press
|
[15] |
Turing,A. M. (1952) The chemical basis of morphogenesis. Philos. Trans. R. Soc. Lond. B Biol. Sci., 237, 37–72
CrossRef
Google scholar
|
[16] |
Wolpert,L. (1969) Positional information and the spatial pattern of cellular differentiation. J. Theor. Biol., 25, 1–47
CrossRef
Google scholar
|
[17] |
Crick,F. (1970) Diffusion in embryogenesis. Nature, 225, 420–422
CrossRef
Google scholar
|
[18] |
Bergmann,S., Sandler, O., Sberro,H., Shnider,S., Schejter, E., Shilo,B. Z. and Barkai,N. (2007) Pre-steady-state decoding of the Bicoid morphogen gradient. PLoS Biol., 5, e46
CrossRef
Google scholar
|
[19] |
Gregor,T., Tank, D. W., Wieschaus,E. F. and Bialek,W. (2007) Stability and nuclear dynamics of the bicoid morphogen gradient. Cell, 130, 153–164
CrossRef
Google scholar
|
[20] |
Coppey,M., Berezhkovskii, A. M., Kim,Y., Boettiger,A.N. and Shvartsman,S. Y. (2007) Modeling the bicoid gradient: diffusion and reversible nuclear trapping of a stable protein. Dev. Biol., 312, 623– 630
CrossRef
Google scholar
|
[21] |
St Johnston,D., Driever, W., Berleth,T., Richstein,S. and Nusslein-Volhard,C. (1989) Multiple steps in the localization of bicoid RNA to the anterior pole of the Drosophila oocyte. Development, 107, 13
|
[22] |
Ephrussi,A. and Johnston, D. S. (2004) Seeing is believing: the bicoid morphogen gradient matures. Cell, 116, 143–152
CrossRef
Google scholar
|
[23] |
Surdej,P. and Jacobs-Lorena, M. (1989) Developmental regulation of bicoid mRNA stability is mediated by the first 43 nucleotides of the 3 untranslated region. Mol. Cell. Biol., 18, 28922900
|
[24] |
Dilão,R. and Muraro, D. (2010) mRNA diffusion explains protein gradients in Drosophila early development. J. Theor. Biol., 264, 847–853
CrossRef
Google scholar
|
[25] |
Little,S. C., Tkačik, G.Kneeland,T. B.Wieschaus,E. F., and GregorT. (2011) The formation of the bicoid morphogen gradient requires protein movement from anteriorly localized mRNA. PLoS Biol., 9, e1000596
CrossRef
Google scholar
|
[26] |
Gregor,T., Tank, D. W., Wieschaus,E. F. and Bialek,W. (2007) Probing the limits to positional information. Cell, 130, 153–164
CrossRef
Google scholar
|
[27] |
Wang,Y., Liu, F. and Wang,W. (2012) Dynamic mechanism for the tran-scription apparatus orchestrating reliable responses to activators. Sci. Rep., 2422,
|
[28] |
Crauk,O. and Dostatni, N. (2005) Bicoid determines sharp and precise target gene expression in the Drosophila embryo. Curr. Biol., 15, 1888–1898
CrossRef
Google scholar
|
[29] |
Lewis,J. (2008) From signals to patterns: space, time, and mathematics in developmental biology. Science, 322, 399–403
CrossRef
Google scholar
|
[30] |
Gibson,M. A. and Bruck,J. (2009) Efficient exact stochastic simulation of chemical systems with many species and many channels. J. Phys. Chem., 104, 18761889
|
[31] |
Andrews,S. S. and Bray,D. (2004) Stochastic simulation of chemical reactions with spatial resolution and single molecule detail. Phys. Biol.,1, 137–151
CrossRef
Google scholar
|
[32] |
Hattne,J., Fange, D. and Elf,J. (2005) Stochastic reaction-diffusion simulation with MesoRD. Bioinformatics, 21, 2923–2924
CrossRef
Google scholar
|
[33] |
Erban,R. and Chapman, S. J. (2009) Stochastic modelling of reaction diffusion processes: Algorithms for bimolecular reactions. Phys. Biol., 6, 046001
CrossRef
Google scholar
|
[34] |
Wu,Y. F., Myasnikova, E. and Reinitz,J. (2007) Master equation simulation analysis of immune stained Bicoid morphogen gradient. BMC Syst. Biol., 1, 52
CrossRef
Google scholar
|
[35] |
Hattne,J., Fange, D. and Elf,D. (2005) Stochastic reaction-diffusion simulation with MesoRD. Bioinformatics, 21, 2923–2924
CrossRef
Google scholar
|
[36] |
Dewar,M. A., Kadirkamanathan, V., Opper,M. and Sanguinetti,G. (2010) Parameter estimation and inference for stochastic reaction-diffusion systems: application to morphogenesis in D. melanogaster BMC Syst. Biol., 4, 21
CrossRef
Google scholar
|
[37] |
Okabe-Oho,Y., Murakami, H., Oho,S. and Sasai,M. (2009) Stable, precise, and reproducible patterning of bicoid and hunchback molecules in the early Drosophila embryo. PLoS Comput. Biol., 5, e1000486
CrossRef
Google scholar
|
[38] |
Deng,J., Wang, W., Lu,L. J. and Ma,J. (2010) A two-dimensional simulation model of the Bicoid gradient in Drosophila. PLoS One, 5, e10275
CrossRef
Google scholar
|
[39] |
Pisarev,A., Poustelnikova, E., Samsonova,M. and Reinitz,J. (2009) FlyEx, the quantitative atlas on segmentation gene expression at cellular resolution. Nucleic Acids Res., 37, D560–D566
CrossRef
Google scholar
|
[40] |
Myasnikova,E., Samsonova, M., Kosman,D. and R einitz,J. (2005) Removal of background signal from in situ data on the expression of segmentation genes in drosophila. Dev. Genes Evol., 215, 320–326
CrossRef
Google scholar
|
[41] |
Hassani,H. (2007) Singular spectrum analysis: Methodology and comparison. J. Data Sci., 5, 239–257
|
[42] |
Holloway, D. M., Harrison, L. G., Kosman,D., Vanario-Alonso,C. E. and Spirov,A. V. (2006) Analysis of pattern precision shows that Drosophila segmentation develops substantial independence from gradients of maternal gene products. Dev. Dyn., 235, 2949–2960
CrossRef
Google scholar
|
[43] |
Alexandrov,T., Golyandina, N. and Spirov,A. (2008) Singular spectrum analysis of gene expression profiles of early Drosophila embryo: Exponential-in-distance patterns. Res. Lett. Signal Process., 2008, 825758
CrossRef
Google scholar
|
[44] |
Alexandrov,T. (2009) A method for trend extraction using Singular Spectrum Analysis. Rev. Stat., 7, 1–22
|
[45] |
Golyandina, N. E., Holloway, D. M., Lopesc,F. J. P., Spirov,A. V., Spirova, E. N., and Usevich, K. D. (2012). Measuring gene expression noise in early Drosophila embryos: nucleus-to-nucleus variability. Procedia. Comput. Sci.9, 373–382
|
[46] |
Spirov,A. V., Golyandina, N. E., Holloway,D. M., Alexandrov,T., Spirova,E. N., Lope,F. (2012) Measuring gene expression noise in early Drosophila embryos: The highly dynamic Compartmentalized Micro-environment of the blastoderm is one of the main sources of noise. Evol. Comp. Mach. Learning and Data Mining in Bioinformatics, 7246, 177–188
|
[47] |
Holloway,D. M., Lopes, F. J. P., da Fontoura Costa, L., Travençolo,B. A. N., Golyandina,N., Usevich,K. and Spirov,A. V. (2011) Gene expression noise in spatial patterning: hunchback promoter structure affects noise amplitude and distribution in Drosophila segmentation. PLoS Comput. Biol., 7, e1001069
CrossRef
Google scholar
|
[48] |
Ghodsi,Z., Silva, E. S. and Hassani,H. (2015) Bicoid signal extraction with a selection of parametric and nonparametric signal processing techniques. Genomics Proteomics Bioinformatics, 13, 183–191
CrossRef
Google scholar
|
[49] |
Holloway,D. M., Lopes, F. J. P., da Fontoura Costa, L., Travençolo,B. A. N., Golyandina,N., Usevich,K. and Spirov,A. V. (2011) Gene expression noise in spatial patterning: hunchback promoter structure affects noise amplitude and distribution in Drosophila segmentation. PLoS Comput. Biol., 7, e1001069
CrossRef
Google scholar
|
[50] |
Golyandina,N. E., Holloway, D. M. and Lopes,F. J. P., Spirov,A. V., Spirova, E. N. and Usevich,K. D. (2012) Measuring gene expression noise in early Drosophila embryos: nucleus-to-nucleus variability. Procedia Comput. Sci., 9, 373–382
CrossRef
Google scholar
|
[51] |
Hassani,H. and Ghodsi, Z. (2014) Pattern recognition of gene expression with singular spectrum analysis. Med. Sci., 2, 127–139
|
[52] |
Tweedie S., Ashburner M.,FallsK.,LeylandP.,McQuilton P.,MarygoldS.,MillburnG.,Osumi-Sutherland D.,SchroederA.,SealR.,ZhangH., FlyBaseConsortium.(2009). FlyBase: Enhancing Drosophila gene ontology annotations. Nucleic Acids Res., 37, D555–D559
|
[53] |
Gelbart,W., Bayraktaroglu, L., Bettencourt,B. and Campbell,K. (2003) The FlyBase database of the Drosophila genome projects and community literature. Nucleic Acids Res., 31, 172–175
|
[54] |
Weigmann,K., Klapper, R., Strasser,T., Rickert,C., Technau, G., Jackle,H., Janning,W. and Klambt,C. (2003) FlyMove a new way to look at development of Drosophila. Trends Genet., 19, 310–311
CrossRef
Google scholar
|
[55] |
Poustelnikova,E., Pisarev, A., Blagov,M., Samsonova,M. and Reinitz,J. (2004) A database for management of gene expression data in situ. Bioinformatics, 20, 2212–2221
CrossRef
Google scholar
|
[56] |
BDGP Database.
|
[57] |
The Comprehensive Drosophila Interactions Database.
|
[58] |
FlyTF Database.
|
[59] |
FlyMine Database.
|
[60] |
FlyAtlas Database.
|
[61] |
FlyCircuit Database.
|
[62] |
|
[63] |
Kosman,D., Reinitz, J. and Sharp,D. H. (1998). Automated assay of gene expression at cellular resolution. In Proc. 1998 P SB, 617
|
[64] |
Janssens,H., Kosman, D., Vanario-Alonso,C. E., Jaeger,J., Samsonova, M. and Reinitz,J. (2005) A high-throughput method for quantifying gene expression data from early drosophila embryos. Dev. Genes Evol., 215, 374–381
CrossRef
Google scholar
|
[65] |
Myasnikova,E., Samsonova, A., Kozlov,K., Samsonova,M. and Reinitz,J. (2001) Registration of the expression patterns of Drosophila segmentation genes by two independent methods. Bioinformatics, 17, 3–12
CrossRef
Google scholar
|
[66] |
Kozlov,K., Myasnikova, E., Pisarev,A., Samsonova,M. and Reinitz,J. (2002) A method for two-dimensional registration and constrution of the two-dimensional atlas of gene expression patterns in situ. In Silio Biology, 2, 125–141
|
/
〈 | 〉 |