- Author:
- Catherine Lloyd <c.lloyd@auckland.ac.nz>
- Date:
- 2010-04-07 09:26:37+12:00
- Desc:
- Added initial conditions, rearranged the conservation equations, fixed broken RDF and documentation and added a curation status comment.
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/wolf_heinrich_2000/rawfile/9717c8699a94bee91495b74b3445425eeacaf969/wolf_heinrich_2000.cellml
<?xml version='1.0' encoding='utf-8'?>
<!-- FILE : wolf_2001.xml
CREATED : 1st June 2007
LAST MODIFIED : 1st June 2007
AUTHOR : Catherine Lloyd
Bioengineering Institute
The University of Auckland
MODEL STATUS : This model conforms to the CellML 1.1 Specification.
DESCRIPTION : This file contains a CellML description of Wolf and Heinrich's 2000 model of the effect of cellular interaction on glycolytic oscillations in yeast.
CHANGES:
--><model xmlns="http://www.cellml.org/cellml/1.0#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqs="http://www.cellml.org/bqs/1.0#" xmlns:cellml="http://www.cellml.org/cellml/1.0#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" cmeta:id="wolf_2001" name="wolf_2001">
<documentation xmlns="http://cellml.org/tmp-documentation">
<article>
<articleinfo>
<title>Effect of Cellular Interaction on Glycolytic Oscillations in Yeast</title>
<author>
<firstname>Catherine</firstname>
<surname>Lloyd</surname>
<affiliation>
<shortaffil>Auckland Bioengineering Institute, The University of Auckland</shortaffil>
</affiliation>
</author>
</articleinfo>
<section id="sec_status">
<title>Model Status</title>
<para>
This CellML model runs in both OpenCell and COR to recreate the published results. The units have been checked and they are consistent. Note that the CellML model represents a single cell (N=1).
</para>
</section>
<sect1 id="sec_structure">
<title>Model Structure</title>
<para>
ABSTRACT: On the basis of a detailed model of yeast glycolysis, the effect of intercellular dynamics is analysed theoretically. The model includes the main steps of anaerobic glycolysis, and the production of ethanol and glycerol. Transmembrane diffusion of acetaldehyde is included, since it has been hypothesized that this substance mediates the interaction. Depending on the kinetic parameter, the single-cell model shows both stationary and oscillatory behaviour. This agrees with experimental data with respect to metabolite concentrations and phase shifts. The inclusion of intercellular coupling leads to a variety of dynamical modes, such as synchronous oscillations, and different kinds of asynchronous behavior. These oscillations can co-exist, leading to bi- and tri-rhythmicity. The corresponding parameter regions have been identified by a bifurcation analysis. The oscillatory dynamics of synchronized cell populations are investigated by calculating the phase responses to acetaldehyde pulses. Simulations are performed with respect to the synchronization of two subpopulations that are oscillating out of phase before mixing. The effect of the various process on synchronization is characterized quantitatively. While continuous exchange of acetaldehyde might synchronize the oscillations for appropriate sets of parameter values, the calculated synchronization time is longer than that observed experimentally. It is concluded either that addition to the transmembrane exchange of acetaldehyde, other processes may contribute to intercellular coupling, or that intracellular regulator feedback plays a role in the acceleration of the synchronization. for appropriate sets of parameter values, the calculated synchronization time is longer than that observed experimentally. It is concluded either that addition to the transmembrane exchange of acetaldehyde, other processes may contribute to intercellular coupling, or that intracellular regulator feedback plays a role in the acceleration of the synchronization.
</para>
<para>
The original paper reference is cited below:
</para>
<para>
Effect of cellular interaction on glycolytic oscillations in yeast: a theoretical investigation, Jana Wolf and Reinhart Heinrich, 2000, <emphasis>Biochemical Journal</emphasis>, 345, 321-334. <ulink url="http://www.ncbi.nlm.nih.gov/pubmed/10702114">PubMed ID: 10702114</ulink>
</para>
<informalfigure float="0" id="fig_reaction_diagram">
<mediaobject>
<imageobject>
<objectinfo>
<title>schematic diagram</title>
</objectinfo>
<imagedata fileref="wolf_heinrich_2000.png"/>
</imageobject>
</mediaobject>
<caption>The scheme shows the main reactions of anaerobic glycolysis in yeast, in addition to transmembrane transport of glucose and the coupling substance (S4,ex). For further explanation of the symbols used, see the text.</caption>
</informalfigure>
</sect1>
</article>
</documentation>
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sum of the concentrations of ATP and ADP
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pool of glyceraldehyde 3-phosphate and dihydroxyacetone phosphate
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pool of cytosolic pyruvate and acetaldehyde
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coupling substance in the external solution
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<vCard:Orgname>The University of Auckland</vCard:Orgname>
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<rdf:value>The new version of this model has been re-coded to remove the reaction element and replace it with a simple MathML description of the model reaction kinetics. This is thought to be truer to the original publication, and information regarding the enzyme kinetics etc will later be added to the metadata through use of an ontology.
The model runs in the PCEnv simulator but gives a flat output.</rdf:value>
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<dc:title>Biochemical Journal</dc:title>
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<vCard:FN>Catherine Lloyd</vCard:FN>
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<dc:title>Effect of cellular interaction on glycolytic oscillations in yeast: a theoretical investigation</dc:title>
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<bqs:first_page>321</bqs:first_page>
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<vCard:Given>Reinhart</vCard:Given>
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