Simulation study on effects of signaling network structure on the developmental increase in complexity

Journal of Theoretical Biology
Soile V E Keränen

Abstract

The developmental increase in structural complexity in multicellular lifeforms depends on local, often non-periodic differences in gene expression. These, in turn, depend on a network of gene-gene interactions coded within the organismal genome. To see what architectural features of a network (size, connectivity, etc.) affect the likelihood of patterns with multiple cell types (i.e. patterns where cells express > or = 3 different combinations of genes), developmental pattern formation was simulated in virtual blastoderm embryos with small artificial genomes. Several basic properties of these genomic signaling networks, such as the number of genes, the distributions of positive (inductive) and negative (repressive) interactions, and the strengths of gene-gene interactions were tested. The results show that the frequencies of complex and/or stable patterns depended not only on the existence of negative interactions, but also on the distribution of regulatory interactions: for example, coregulation of signals and their intracellular effectors increased the likelihood of pattern formation compared to differential regulation of signaling pathway components. Interestingly, neither quantitative differences in strengths of signaling in...Continue Reading

References

Aug 1, 1989·The Journal of Experimental Zoology·G F Oster, J D Murray
Apr 21, 1986·Journal of Theoretical Biology·E R JacksonW G Nash
Feb 1, 1972·Journal of Theoretical Biology·L Glass, S A Kauffman
Oct 1, 1993·Current Opinion in Cell Biology·M W Bosenberg, J Massagué
Feb 1, 1994·Scientific American·W McGinnis, M Kuziora
Oct 1, 1993·Current Opinion in Cell Biology·R L Juliano, J A Varner
Mar 21, 1993·Journal of Theoretical Biology·F A Bignone
Jun 1, 1997·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·D W StockZ Zhao
Jul 22, 1998·Proceedings of the National Academy of Sciences of the United States of America·M Kirschner, J Gerhart
Jul 31, 1998·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·L Wolpert
Dec 9, 1998·Nature·S L Rutherford, S Lindquist
Dec 16, 1998·Science·UNKNOWN C. elegans Sequencing Consortium
Aug 17, 1999·Current Opinion in Genetics & Development·R F Bachvarova
Nov 24, 1999·Mechanisms of Development·R AsaiS Kondo
Dec 22, 1999·Seminars in Cell & Developmental Biology·L G Lundin
Jan 27, 2000·Cell·T Hunter
May 29, 2000·Bulletin of Mathematical Biology·H J WearingJ A Sherratt
Jun 13, 2000·Nature·A Becskei, L Serrano
Jul 26, 2000·Nature·G von DassowG M Odell
Aug 10, 2000·Journal of Theoretical Biology·I Salazar-CiudadR V Solé
Apr 26, 2001·Journal of Theoretical Biology·C Furusawa, K Kaneko
Jun 23, 2001·Journal of Theoretical Biology·L Sánchez, D Thieffry
Oct 26, 2001·Nature·J B Gurdon, P Y Bourillot
Nov 22, 2001·Bio Systems·X Lu, Y Li
Mar 2, 2002·Science·Eric H DavidsonHamid Bolouri
Apr 23, 2002·Nature Genetics·Nabil GuelzimFrançois Képès
Apr 23, 2002·Nature Genetics·Shai S Shen-OrrUri Alon
May 4, 2002·Science·Sergei Maslov, Kim Sneppen
May 17, 2002·Current Biology : CB·Eli MeirGarrett M Odell
Jun 6, 2002·Proceedings of the National Academy of Sciences of the United States of America·Isaac Salazar-Ciudad, Jukka Jernvall
Jul 5, 2002·Nature·Gernot GlöcknerUNKNOWN Dictyostelium Genome Sequencing Consortium
Jul 23, 2002·Nature Genetics·Jan IhmelsNaama Barkai
Aug 17, 2002·Science·Michael B ElowitzPeter S Swain
Aug 31, 2002·Science·E RavaszA L Barabási
Nov 15, 2002·Nature·Jeff HastyJ J Collins
Dec 31, 2002·Current Opinion in Structural Biology·Frank Sobott, Carol V Robinson
Feb 13, 2003·Nucleic Acids Research·M Madan Babu, Sarah A Teichmann
Apr 2, 2003·Cell Biology Education·Bruce Alberts, UNKNOWN National Academies
Jun 17, 2003·Proceedings of the National Academy of Sciences of the United States of America·Tomoaki NishiyamaMitsuyasu Hasebe

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Citations

May 3, 2007·Proceedings. Biological Sciences·Rolf LohausRicardo B R Azevedo
May 21, 2008·Artificial Life·Nicholas Geard, Janet Wiles
Oct 15, 2011·PLoS Computational Biology·Kirsten H Ten Tusscher, Paulien Hogeweg
May 28, 2013·The European Physical Journal. E, Soft Matter·K H W J Ten Tusscher

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