Modelling Circadian Rhythms in Drosophila and Investigation of VRI and PDP1 Feedback Loops Using a New Mathematical Model

D. Kulasiri; Z. Xie

Mathematical Modelling of Natural Phenomena (2008)

  • Volume: 3, Issue: 2, page 1-26
  • ISSN: 0973-5348

Abstract

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We present a brief review of molecular biological basis and mathematical modelling of circadian rhythms in Drosophila. We discuss pertinent aspects of a new model that incorporates the transcriptional feedback loops revealed so far in the network of the circadian clock (PER/TIM and VRI/PDP1 loops). Conventional Hill functions are not used to describe the regulation of genes, instead the explicit reactions of binding and unbinding processes of transcription factors to promoters are probabilistically modelled. The model is described by a set of ordinary differential equations, and the parameters are estimated from the in vitro experimental data of the clocks' components. The model is robust over a wide range of parameter variations. Through the sensitivity analysis of the model, roles of VRI and PDP1 feedback loops are investigated, and it is proposed that they increase the robustness of the clock.

How to cite

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Kulasiri, D., and Xie, Z.. "Modelling Circadian Rhythms in Drosophila and Investigation of VRI and PDP1 Feedback Loops Using a New Mathematical Model." Mathematical Modelling of Natural Phenomena 3.2 (2008): 1-26. <http://eudml.org/doc/222419>.

@article{Kulasiri2008,
abstract = { We present a brief review of molecular biological basis and mathematical modelling of circadian rhythms in Drosophila. We discuss pertinent aspects of a new model that incorporates the transcriptional feedback loops revealed so far in the network of the circadian clock (PER/TIM and VRI/PDP1 loops). Conventional Hill functions are not used to describe the regulation of genes, instead the explicit reactions of binding and unbinding processes of transcription factors to promoters are probabilistically modelled. The model is described by a set of ordinary differential equations, and the parameters are estimated from the in vitro experimental data of the clocks' components. The model is robust over a wide range of parameter variations. Through the sensitivity analysis of the model, roles of VRI and PDP1 feedback loops are investigated, and it is proposed that they increase the robustness of the clock. },
author = {Kulasiri, D., Xie, Z.},
journal = {Mathematical Modelling of Natural Phenomena},
keywords = {circadian rhythms; Drosophila; gene expression; transcription; translation; robustness; Drosophila; robustness},
language = {eng},
month = {10},
number = {2},
pages = {1-26},
publisher = {EDP Sciences},
title = {Modelling Circadian Rhythms in Drosophila and Investigation of VRI and PDP1 Feedback Loops Using a New Mathematical Model},
url = {http://eudml.org/doc/222419},
volume = {3},
year = {2008},
}

TY - JOUR
AU - Kulasiri, D.
AU - Xie, Z.
TI - Modelling Circadian Rhythms in Drosophila and Investigation of VRI and PDP1 Feedback Loops Using a New Mathematical Model
JO - Mathematical Modelling of Natural Phenomena
DA - 2008/10//
PB - EDP Sciences
VL - 3
IS - 2
SP - 1
EP - 26
AB - We present a brief review of molecular biological basis and mathematical modelling of circadian rhythms in Drosophila. We discuss pertinent aspects of a new model that incorporates the transcriptional feedback loops revealed so far in the network of the circadian clock (PER/TIM and VRI/PDP1 loops). Conventional Hill functions are not used to describe the regulation of genes, instead the explicit reactions of binding and unbinding processes of transcription factors to promoters are probabilistically modelled. The model is described by a set of ordinary differential equations, and the parameters are estimated from the in vitro experimental data of the clocks' components. The model is robust over a wide range of parameter variations. Through the sensitivity analysis of the model, roles of VRI and PDP1 feedback loops are investigated, and it is proposed that they increase the robustness of the clock.
LA - eng
KW - circadian rhythms; Drosophila; gene expression; transcription; translation; robustness; Drosophila; robustness
UR - http://eudml.org/doc/222419
ER -

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