Dataset Information

Larsen2004_CalciumSpiking_EnzymeBinding

ABSTRACT: This a model from the article: On the encoding and decoding of calcium signals in hepatocytes Ann Zahle Larsen, Lars Folke Olsen and Ursula Kummera Biophysical ChemistryVolume 107, Issue 1, 1 January 2004, Pages 83-99 14871603, Abstract: Many different agonists use calcium as a second messenger. Despite intensive research in intracellular calcium signalling it is an unsolved riddle how the different types of information represented by the different agonists, is encoded using the universal carrier calcium. It is also still not clear how the information encoded is decoded again into the intracellular specific information at the site of enzymes and genes. After the discovery of calcium oscillations, one likely mechanism is that information is encoded in the frequency, amplitude and waveform of the oscillations. This hypothesis has received some experimental support. However, the mechanism of decoding of oscillatory signals is still not known. Here, we study a mechanistic model of calcium oscillations, which is able to reproduce both spiking and bursting calcium oscillations. We use the model to study the decoding of calcium signals on the basis of co-operativity of calcium binding to various proteins. We show that this co-operativity offers a simple way to decode different calcium dynamics into different enzyme activities. Note: This model corresponds to the improved model eqn 1-7, as described by Larsen et al., 2004 implemented to investigate how the cell can decode different oscillations. This is done by introducing 2 more variables Enzyme and Product in addition to the 5 variables G-alpha, PLC, Ca_cyt, Ca_ER and Ca_mit receptor-operated model described in the first part of the paper. The receptor-operated model is itself a modified version of the model described in Kummer 2000 (PMID:10968983)

SUBMITTER: Vijayalakshmi Chelliah

PROVIDER: BIOMD0000000331 | BioModels | 2011-05-05

REPOSITORIES: BioModels

ACCESS DATA

Publications

On the encoding and decoding of calcium signals in hepatocytes.

Larsen Ann Zahle AZ Olsen Lars Folke LF Kummer Ursula U

Biophysical chemistry 20040101 1

Many different agonists use calcium as a second messenger. Despite intensive research in intracellular calcium signalling it is an unsolved riddle how the different types of information represented by the different agonists, is encoded using the universal carrier calcium. It is also still not clear how the information encoded is decoded again into the intracellular specific information at the site of enzymes and genes. After the discovery of calcium oscillations, one likely mechanism is that inf ...[more]

PMID: 14871603

Similar Datasets

Project description:This a model from the article: Effects of extracellular calcium on electrical bursting and intracellular and luminal calcium oscillations in insulin secreting pancreatic beta-cells. Chay TR Biophys J.1997 Sep;73(3):1673-88. 9284334, Abstract: The extracellular calcium concentration has interesting effects on bursting of pancreatic beta-cells. The mechanism underlying the extracellular Ca2+ effect is not well understood. By incorporating a low-threshold transient inward current to the store-operated bursting model of Chay, this paper elucidates the role of the extracellular Ca2+ concentration in influencing electrical activity, intracellular Ca2+ concentration, and the luminal Ca2+ concentration in the intracellular Ca2+ store. The possibility that this inward current is a carbachol-sensitive and TTX-insensitive Na+ current discovered by others is discussed. In addition, this paper explains how these three variables respond when various pharmacological agents are applied to the store-operated model. This model was taken from the CellML repository and automatically converted to SBML. The original model was: Chay TR (1997) - version05 The original CellML model was created by: Lloyd, Catherine, May c.lloyd@aukland.ac.nz The University of Auckland The Bioengineering Institute This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team. For more information see the terms of use. To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

Project description:Kummer2000 - Oscillations in Calcium Signalling Simplified (3-variable) calcium oscillation model Kummer et al. (2000) Biophys. J. 79, 1188-1195 This model is defined in a small compartment with low concentrations. You can run it first with the LSODA ODE solver and then with the Gillespie Monte Carlo method (in Time Course widget). This illustrates that at low particle numbers, as here, the stochastic simulation and the ODE approach produce different results (the stochastic approach is more correct in these circumstances). This file also demonstrates the use of several different plots to visualize results, including a histogram. This model is described in the article: Switching from simple to complex oscillations in calcium signaling. Kummer U, Olsen LF, Dixon CJ, Green AK, Bornberg-Bauer E, Baier G. Biophys. J. 2000 Sep; 79(3): 1188-1195 Abstract: We present a new model for calcium oscillations based on experiments in hepatocytes. The model considers feedback inhibition on the initial agonist receptor complex by calcium and activated phospholipase C, as well as receptor type-dependent self-enhanced behavior of the activated G(alpha) subunit. It is able to show simple periodic oscillations and periodic bursting, and it is the first model to display chaotic bursting in response to agonist stimulations. Moreover, our model offers a possible explanation for the differences in dynamic behavior observed in response to different agonists in hepatocytes. This model is hosted on BioModels Database and identified by: BIOMD0000000329. To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

Dataset Information

Larsen2004_CalciumSpiking_EnzymeBinding

Publications

On the encoding and decoding of calcium signals in hepatocytes.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure