Theoretical basis of the community effect in development

BMC Systems Biology

Volumn 5, Issue , 2011, Pages

  Saka, Yasushi ^a   Lhoussaine, Cédric ^b,c   Kuttler, Celine ^b,c   Ullner, Ekkehard ^a,d   Thiel, Marco ^d  

^a UNIVERSITY OF ABERDEEN   (United Kingdom)

^b UNIV LILLE   (France)

^c CNRS   (France)

^d UNIVERSITY OF ABERDEEN   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMALIA; BACTERIA (MICROORGANISMS);

FGF4 PROTEIN, HUMAN; FIBROBLAST GROWTH FACTOR 4;

ANIMAL; ARTICLE; BIOLOGICAL MODEL; CELL COMMUNICATION; COMPUTER SIMULATION; DIFFUSION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HUMAN; METABOLISM; STATISTICAL MODEL; STATISTICS; SYSTEMS BIOLOGY; THEORETICAL MODEL; XENOPUS;

ANIMALS; CELL COMMUNICATION; COMPUTER SIMULATION; DIFFUSION; FIBROBLAST GROWTH FACTOR 4; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; MODELS, BIOLOGICAL; MODELS, STATISTICAL; MODELS, THEORETICAL; STOCHASTIC PROCESSES; SYSTEMS BIOLOGY; XENOPUS;

EID: 79955095033     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-5-54     Document Type: Article

References (46)

1. Gurdon JB, Lemaire P, Kato K. Community effects and related phenomena in development. Cell 1993, 75(5):831-4. 10.1016/0092-8674(93)90526-V, 8252618.
2. Gurdon JB. A community effect in animal development. Nature 1988, 336(6201):772-4. 10.1038/336772a0, 3205305.
3. Gurdon JB, Tiller E, Roberts J, Kato K. A community effect in muscle development. Current Biol 1993, 3:1-11.
4. Standley HJ, Zorn AM, Gurdon JB. eFGF and its mode of action in the community effect during Xenopus myogenesis. Development 2001, 128(8):1347-57.
5. Isaacs H, Slack J. eFGF regulates Xbra expression during Xenopus gastrulation. EMBO J 1994, 13:4469-4481. 395379, 7925289.
6. Casey ES, O'Reilly MA, Conlon FL, Smith JC. The T-box transcription factor Brachyury regulates expression of eFGF through binding to a non-palindromic response element. Development 1998, 125(19):3887-94.
7. Kroll KL, Amaya E. Transgenic Xenopus embryos from sperm nuclear transplantations reveal FGF signaling requirements during gastrulation. Development 1996, 122(10):3173-83.
8. Bolouri H, Davidson EH. The gene regulatory network basis of the "community effect," and analysis of a sea urchin embryo example. Dev Biol 2010, 340(2):170-8. 10.1016/j.ydbio.2009.06.007, 2854306, 19523466.
9. Duboc V, Lapraz F, Besnardeau L, Lepage T. Lefty acts as an essential modulator of Nodal activity during sea urchin oral-aboral axis formation. Dev Biol 2008, 320:49-59. 10.1016/j.ydbio.2008.04.012, 18582858.
10. Shahrezaei V, Swain PS. Analytical distributions for stochastic gene expression. Proc Natl Acad Sci USA 2008, 105(45):17256-61. 10.1073/pnas.0803850105, 2582303, 18988743.
11. Kaern M, Elston TC, Blake WJ, Collins JJ. Stochasticity in gene expression: from theories to phenotypes. Nat Rev Genet 2005, 6(6):451-64. 10.1038/nrg1615, 15883588.
12. Umbhauer M, Marshall CJ, Mason CS, Old RW, Smith JC. Mesoderm induction in Xenopus caused by activation of MAP kinase. Nature 1995, 376(6535):58-62. 10.1038/376058a0, 7541116.
13. Gotoh Y, Masuyama N, Suzuki A, Ueno N, Nishida E. Involvement of the MAP kinase cascade in Xenopus mesoderm induction. EMBO J 1995, 14:2491-2498. 398362, 7781601.
14. LaBonne C, Burke B, Whitman M. Role of MAP kinase in mesoderm induction and axial patterning during Xenopus development. Development 1995, 121(5):1475-86.
15. Nentwich O, Dingwell KS, Nordheim A, Smith JC. Downstream of FGF during mesoderm formation in Xenopus: the roles of Elk-1 and Egr-1. Dev Biol 2009, 336(2):313-26. 10.1016/j.ydbio.2009.09.039, 19799892.
16. Yu SR, Burkhardt M, Nowak M, Ries J, Petrasek Z, Scholpp S, Schwille P, Brand M. Fgf8 morphogen gradient forms by a source-sink mechanism with freely diffusing molecules. Nature 2009, 461(7263):533-6. 10.1038/nature08391, 19741606.
17. Standley HJ, Zorn AM, Gurdon JB. A dynamic requirement for community interactions during Xenopus myogenesis. Int J Dev Biol 2002, 46(3):279-83.
18. Saka Y, Smith JC. A mechanism for the sharp transition of morphogen gradient interpretation in Xenopus. BMC Dev Biol 2007, 7:47. 10.1186/1471-213X-7-47, 1885807, 17506890.
19. Dessaud E, Ribes V, Balaskas N, Yang LL, Pierani A, Kicheva A, Novitch BG, Briscoe J, Sasai N. Dynamic assignment and maintenance of positional identity in the ventral neural tube by the morphogen sonic hedgehog. PLoS Biol 2010, 8(6):e1000382. 10.1371/journal.pbio.1000382, 2879390, 20532235.
20. Hense BA, Kuttler C, Muller J, Rothballer M, Hartmann A, Kreft JU. Does efficiency sensing unify diffusion and quorum sensing?. Nat Rev Microbiol 2007, 5(3):230-9. 10.1038/nrmicro1600, 17304251.
21. Conlon I, Raff M. Size control in animal development. Cell 1999, 96(2):235-44. 10.1016/S0092-8674(00)80563-2, 9988218.
22. Cook DL, Gerber AN, Tapscott SJ. Modeling stochastic gene expression: implications for haploinsufficiency. Proc Natl Acad Sci USA 1998, 95(26):15641-6. 10.1073/pnas.95.26.15641, 28097, 9861023.
23. Bosl WJ, Li R. The role of noise and positive feedback in the onset of autosomal dominant diseases. BMC Syst Biol 2010, 4:93. 10.1186/1752-0509-4-93, 2902440, 20587063.
24. Smilenov LB. Tumor development: haploinsufficiency and local network assembly. Cancer Lett 2006, 240:17-28. 10.1016/j.canlet.2005.08.015, 16223564.
25. Agur Z, Kogan Y, Levi L, Harrison H, Lamb R, Kirnasovsky OU, Clarke RB. Disruption of a Quorum Sensing mechanism triggers tumorigenesis: a simple discrete model corroborated by experiments in mammary cancer stem cells. Biol Direct 2010, 5:20. 10.1186/1745-6150-5-20, 2874533, 20406437.
26. Ng WL, Bassler BL. Bacterial quorum-sensing network architectures. Annu Rev Genet 2009, 43:197-222. 10.1146/annurev-genet-102108-134304, 19686078.
27. Goryachev AB, Toh DJ, Lee T. Systems analysis of a quorum sensing network: design constraints imposed by the functional requirements, network topology and kinetic constants. Biosystems 2006, 83(2-3):178-87. 10.1016/j.biosystems.2005.04.006, 16174549.
28. Chen MT, Weiss R. Artificial cell-cell communication in yeast Saccharomyces cerevisiae using signaling elements from Arabidopsis thaliana. Nat Biotechnol 2005, 23(12):1551-5. 10.1038/nbt1162, 16299520.
29. Kobayashi H, Kaern M, Araki M, Chung K, Gardner TS, Cantor CR, Collins JJ. Programmable cells: interfacing natural and engineered gene networks. Proc Natl Acad Sci USA 2004, 101(22):8414-9. 10.1073/pnas.0402940101, 420408, 15159530.
30. Gillespie DT. Exact stochastic simulation of coupled chemical reactions. J Phys Chem 1977, 81(25):2340-2361.
31. Doob JL. Stochastic processes 1953, New York: Wiley.
32. Stochastic Pi Machine - Microsoft Research. , http://research.microsoft.com/en-us/projects/spim/
33. Phillips A, Cardelli L. Efficient, correct simulation of biological processes in the stochastic pi-calculus. Proceedings of the 2007 International Conference on Computational Methods in Systems Biology 2007, 184-199. CMSB'07, Berlin, Heidelberg: Springer-Verlag., http://portal.acm.org/citation.cfm?id=1780158.1780171
34. Priami C, Regev A, Shapiro E, Silverman W. Application of a stochastic name-passing calculus to representation and simulation of molecular processes. Inform Process Lett 2001, 80:25-31.
35. Regev A, Silverman W, Shapiro E. Representation and simulation of biochemical processes using the pi-calculus process algebra. Proceedings of the Pacific Symposium on Biocomputing 2001, 459-70., http://psb.stanford.edu/psb-online/proceedings/psb01/
36. Kuttler C, Niehren J. Gene regulation in the pi-calculus: Simulating cooperativity at the lambda switch. Transactions on Computational Systems Biology VII, Volume 4230 of Lecture Notes in Bioinformatics 2006, 24-55. Springer, Priami C, Ingólfsdóttir A, Mishra B, Nielson HR.
37. Blossey R, Cardelli L, Phillips A. Compositionality, stochasticity, and cooperativity in dynamic models of gene regulation. HFSP J 2008, 2:17-28. 10.2976/1.2804749, 2640994, 19404450.
38. Blossey R, Giuraniuc CV. Mean-field versus stochastic models for transcriptional regulation. Phys Rev E Stat Nonlin Soft Matter Phys 2008, 78(3 Pt 1):031909.
39. Arava Y, Wang Y, Storey JD, Liu CL, Brown PO, Herschlag D. Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 2003, 100(7):3889-94. 10.1073/pnas.0635171100, 153018, 12660367.
40. Belle A, Tanay A, Bitincka L, Shamir R, O'Shea EK. Quantification of protein half-lives in the budding yeast proteome. Proc Natl Acad Sci USA 2006, 103(35):13004-9. 10.1073/pnas.0605420103, 1550773, 16916930.
41. Beyer A, Hollunder J, Nasheuer HP, Wilhelm T. Post-transcriptional expression regulation in the yeast Saccharomyces cerevisiae on a genomic scale. Mol Cell Proteomics 2004, 3(11):1083-92. 10.1074/mcp.M400099-MCP200, 15326222.
42. Elf J, Li GW, Xie XS. Probing transcription factor dynamics at the single-molecule level in a living cell. Science 2007, 316(5828):1191-4. 10.1126/science.1141967, 2853898, 17525339.
43. Ghaemmaghami S, Huh WK, Bower K, Howson RW, Belle A, Dephoure N, O'Shea EK, Weissman JS. Global analysis of protein expression in yeast. Nature 2003, 425(6959):737-41. 10.1038/nature02046, 14562106.
44. Karpova TS, Kim MJ, Spriet C, Nalley K, Stasevich TJ, Kherrouche Z, Heliot L, McNally JG. Concurrent fast and slow cycling of a transcriptional activator at an endogenous promoter. Science 2008, 319(5862):466-9. 10.1126/science.1150559, 18218898.
45. Wen JD, Lancaster L, Hodges C, Zeri AC, Yoshimura SH, Noller HF, Bustamante C, Tinoco I. Following translation by single ribosomes one codon at a time. Nature 2008, 452(7187):598-603. 10.1038/nature06716, 2556548, 18327250.
46. Press W, Teukolsky S, Vetterling W, Flannery B. Numerical Recipes 3rd Edition: The Art of Scientific Computing 2007, Cambridge University Press.