The effect of reactions on the formation and readout of the gradient of Bicoid
During early development, the establishment of gradients of transcriptional factors determines the patterning of cell fates. The case of Bicoid (Bcd) in Drosophila melanogaster embryos is well documented and studied. There are still controversies as to whether SDD models in which Bcd is Synthesized...
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| Acceso en línea: | http://hdl.handle.net/20.500.12110/paper_14783967_v14_n1_p_Ipina |
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todo:paper_14783967_v14_n1_p_Ipina2023-10-03T16:19:25Z The effect of reactions on the formation and readout of the gradient of Bicoid Ipiña, E.P. Dawson, S.P. Bicoid fluorescence mathematical modeling reactions SDD model bicoid protein, Drosophila homeodomain protein transactivator protein animal biological model computer simulation diffusion Drosophila melanogaster embryology metabolism Animals Computer Simulation Diffusion Drosophila melanogaster Homeodomain Proteins Models, Biological Trans-Activators During early development, the establishment of gradients of transcriptional factors determines the patterning of cell fates. The case of Bicoid (Bcd) in Drosophila melanogaster embryos is well documented and studied. There are still controversies as to whether SDD models in which Bcd is Synthesized at one end, then Diffuses and is Degraded can explain the gradient formation within the timescale observed experimentally. The Bcd gradient is observed in embryos that express a Bicoid-eGFP fusion protein (Bcd-GFP) which cannot differentiate if Bcd is freely diffusing or bound to immobile sites. In this work we analyze an SDID model that includes the Interaction of Bcd with binding sites. We simulate numerically the resulting full reaction-diffusion system in a cylindrical domain using previously determined biophysical parameters and a simplified version of the Bcd source. In this way we obtain solutions that depend on the spatial location approximately as observed experimentally and that reach such dependence at a time that is also compatible with the experimental observations. Analyzing the differences between the free and bound Bcd distributions we observe that the latter spans over a longer lengthscale. We conclude that deriving the lengthscale from the distribution of Bcd-GFP can lead to an overestimation of the gradient lengthscale and of the Hill coefficient that relates the concentrations of Bcd and of the protein, Hunchback, whose production is regulated by Bcd. © 2017 IOP Publishing Ltd. JOUR info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar http://hdl.handle.net/20.500.12110/paper_14783967_v14_n1_p_Ipina |
| institution |
Universidad de Buenos Aires |
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I-28 |
| repository_str |
R-134 |
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Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) |
| topic |
Bicoid fluorescence mathematical modeling reactions SDD model bicoid protein, Drosophila homeodomain protein transactivator protein animal biological model computer simulation diffusion Drosophila melanogaster embryology metabolism Animals Computer Simulation Diffusion Drosophila melanogaster Homeodomain Proteins Models, Biological Trans-Activators |
| spellingShingle |
Bicoid fluorescence mathematical modeling reactions SDD model bicoid protein, Drosophila homeodomain protein transactivator protein animal biological model computer simulation diffusion Drosophila melanogaster embryology metabolism Animals Computer Simulation Diffusion Drosophila melanogaster Homeodomain Proteins Models, Biological Trans-Activators Ipiña, E.P. Dawson, S.P. The effect of reactions on the formation and readout of the gradient of Bicoid |
| topic_facet |
Bicoid fluorescence mathematical modeling reactions SDD model bicoid protein, Drosophila homeodomain protein transactivator protein animal biological model computer simulation diffusion Drosophila melanogaster embryology metabolism Animals Computer Simulation Diffusion Drosophila melanogaster Homeodomain Proteins Models, Biological Trans-Activators |
| description |
During early development, the establishment of gradients of transcriptional factors determines the patterning of cell fates. The case of Bicoid (Bcd) in Drosophila melanogaster embryos is well documented and studied. There are still controversies as to whether SDD models in which Bcd is Synthesized at one end, then Diffuses and is Degraded can explain the gradient formation within the timescale observed experimentally. The Bcd gradient is observed in embryos that express a Bicoid-eGFP fusion protein (Bcd-GFP) which cannot differentiate if Bcd is freely diffusing or bound to immobile sites. In this work we analyze an SDID model that includes the Interaction of Bcd with binding sites. We simulate numerically the resulting full reaction-diffusion system in a cylindrical domain using previously determined biophysical parameters and a simplified version of the Bcd source. In this way we obtain solutions that depend on the spatial location approximately as observed experimentally and that reach such dependence at a time that is also compatible with the experimental observations. Analyzing the differences between the free and bound Bcd distributions we observe that the latter spans over a longer lengthscale. We conclude that deriving the lengthscale from the distribution of Bcd-GFP can lead to an overestimation of the gradient lengthscale and of the Hill coefficient that relates the concentrations of Bcd and of the protein, Hunchback, whose production is regulated by Bcd. © 2017 IOP Publishing Ltd. |
| format |
JOUR |
| author |
Ipiña, E.P. Dawson, S.P. |
| author_facet |
Ipiña, E.P. Dawson, S.P. |
| author_sort |
Ipiña, E.P. |
| title |
The effect of reactions on the formation and readout of the gradient of Bicoid |
| title_short |
The effect of reactions on the formation and readout of the gradient of Bicoid |
| title_full |
The effect of reactions on the formation and readout of the gradient of Bicoid |
| title_fullStr |
The effect of reactions on the formation and readout of the gradient of Bicoid |
| title_full_unstemmed |
The effect of reactions on the formation and readout of the gradient of Bicoid |
| title_sort |
effect of reactions on the formation and readout of the gradient of bicoid |
| url |
http://hdl.handle.net/20.500.12110/paper_14783967_v14_n1_p_Ipina |
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1807319187497943040 |