Location: Wolf, Heinrich, 2000 @ c2a8e06d7c39 / wolf_heinrich_2000.cellml

Author:
Catherine Lloyd <c.lloyd@auckland.ac.nz>
Date:
2010-06-04 01:55:35+12:00
Desc:
Removed xml:base="" from the model and also replaced wolf_2001 with wolf_2000 in both the model file and the session file.
Permanent Source URI:
https://models.physiomeproject.org/workspace/wolf_heinrich_2000/rawfile/c2a8e06d7c39dd24a502019fff1e95e744492cfc/wolf_heinrich_2000.cellml

<?xml version="1.0"?>
<!--  FILE :  wolf_2000.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: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:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" name="wolf_2000" cmeta:id="wolf_2000" xmlns="http://www.cellml.org/cellml/1.0#" xmlns:cellml="http://www.cellml.org/cellml/1.0#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#">

<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>
  

  
  
  
  <units name="minute">
    <unit multiplier="60.0" units="second"/>
  </units>
  
  <units name="millimolar">
    <unit prefix="milli" units="mole"/>
    <unit exponent="-1" units="litre"/>
  </units>

  <units name="flux">
    <unit units="millimolar"/>
    <unit exponent="-1" units="minute"/>
  </units>

  <units name="first_order_rate_constant">
    <unit exponent="-1" units="minute"/>
  </units>
  
  <units name="second_order_rate_constant">
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    <unit exponent="-1" units="minute"/>
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    <variable cmeta:id="S2_S2" initial_value="0.9" name="S2" public_interface="out" units="millimolar"/>
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    <variable name="v2" public_interface="in" units="flux"/>
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            <times/>
            <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless"> 2.0 </cn>
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    <variable cmeta:id="S4_S4" initial_value="0.2" name="S4" public_interface="out" units="millimolar"/>
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    <variable cmeta:id="S4_ex_S4_ex" initial_value="0.1" name="S4_ex" public_interface="out" units="millimolar"/>
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            <ci> phi </ci>
            <ci> J </ci>
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        </apply>
      </apply>
    </math>
  </component>
  
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    <variable cmeta:id="A3_A3" initial_value="2.4" name="A3" public_interface="out" units="millimolar"/>
    <variable name="v1" public_interface="in" units="flux"/>
    <variable name="v3" public_interface="in" units="flux"/>
    <variable name="v5" public_interface="in" units="flux"/>
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            <ci>v5</ci>
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    </math>
  </component>
  
  <component cmeta:id="A2" name="A2">
    
	<variable initial_value="4.0" name="A" units="millimolar"/>
    <variable cmeta:id="A2_A2" name="A2" public_interface="out" units="millimolar"/>
    <variable name="A3" public_interface="in" units="millimolar"/>
    
    <math xmlns="http://www.w3.org/1998/Math/MathML">
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  <component cmeta:id="N2" name="N2">
    
    <variable cmeta:id="N2_N2" initial_value="0.1" name="N2" public_interface="out" units="millimolar"/>
    <variable name="v2" public_interface="in" units="flux"/>
    <variable name="v4" public_interface="in" units="flux"/>
    <variable name="v6" public_interface="in" units="flux"/>
    <variable name="time" public_interface="in" units="minute"/>
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            <plus/>
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      </apply>
    </math>
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    <variable initial_value="1.0" name="N" units="millimolar"/>
    <variable cmeta:id="N1_N1" name="N1" public_interface="out" units="millimolar"/>
    <variable name="N2" public_interface="in" units="millimolar"/>
    <math xmlns="http://www.w3.org/1998/Math/MathML">
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  <component name="v1">
    <variable name="v1" public_interface="out" units="flux"/>

    <variable name="S1" public_interface="in" units="millimolar"/>
    <variable name="A3" public_interface="in" units="millimolar"/>
    
    <variable initial_value="0.52" name="K_I" units="millimolar"/>
    <variable initial_value="100.0" name="k_1" units="second_order_rate_constant"/>
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    <math xmlns="http://www.w3.org/1998/Math/MathML">
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          </apply>
          <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless"> -1.0 </cn>
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  <component name="v2">
    <variable name="v2" public_interface="out" units="flux"/>

    <variable name="S2" public_interface="in" units="millimolar"/>
    <variable name="N1" public_interface="in" units="millimolar"/>
    
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  <component name="v3">
    <variable name="v3" public_interface="out" units="flux"/>

    <variable name="S3" public_interface="in" units="millimolar"/>
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    </math>
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  <component name="v4">
    <variable name="v4" public_interface="out" units="flux"/>

    <variable name="S4" public_interface="in" units="millimolar"/>
    <variable name="N2" public_interface="in" units="millimolar"/>
    
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          <times/>
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  <component name="glucose_influx_rate">
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  <component name="S4_flux_rate_across_the_plasma_membrane">
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    <variable initial_value="13.0" name="kappa" units="first_order_rate_constant"/>
    
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    <map_components component_1="S1" component_2="environment"/>
    <map_variables variable_1="time" variable_2="time"/>
  </connection>
  
  <connection>
    <map_components component_1="S2" component_2="environment"/>
    <map_variables variable_1="time" variable_2="time"/>
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    <map_components component_1="S3" component_2="environment"/>
    <map_variables variable_1="time" variable_2="time"/>
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  <connection>
    <map_components component_1="S4" component_2="environment"/>
    <map_variables variable_1="time" variable_2="time"/>
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  <connection>
    <map_components component_1="S4_ex" component_2="environment"/>
    <map_variables variable_1="time" variable_2="time"/>
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  <connection>
    <map_components component_1="A3" component_2="environment"/>
    <map_variables variable_1="time" variable_2="time"/>
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  <connection>
    <map_components component_1="N2" component_2="environment"/>
    <map_variables variable_1="time" variable_2="time"/>
  </connection>
  
  <connection>
    <map_components component_1="S1" component_2="glucose_influx_rate"/>
    <map_variables variable_1="Jo" variable_2="Jo"/>
  </connection>
  
  <connection>
    <map_components component_1="S1" component_2="v1"/>
    <map_variables variable_1="S1" variable_2="S1"/>
    <map_variables variable_1="v1" variable_2="v1"/>
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  <connection>
    <map_components component_1="S2" component_2="v1"/>
    <map_variables variable_1="v1" variable_2="v1"/>
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  <connection>
    <map_components component_1="S2" component_2="v2"/>
    <map_variables variable_1="S2" variable_2="S2"/>
    <map_variables variable_1="v2" variable_2="v2"/>
  </connection>
  
  <connection>
    <map_components component_1="S2" component_2="v6"/>
    <map_variables variable_1="S2" variable_2="S2"/>
    <map_variables variable_1="v6" variable_2="v6"/>
  </connection>
  
  <connection>
    <map_components component_1="S3" component_2="v2"/>
    <map_variables variable_1="v2" variable_2="v2"/>
  </connection>
  
  <connection>
    <map_components component_1="S3" component_2="v3"/>
    <map_variables variable_1="S3" variable_2="S3"/>
    <map_variables variable_1="v3" variable_2="v3"/>
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  <connection>
    <map_components component_1="S4" component_2="v3"/>
    <map_variables variable_1="v3" variable_2="v3"/>
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  <connection>
    <map_components component_1="S4" component_2="v4"/>
    <map_variables variable_1="S4" variable_2="S4"/>
    <map_variables variable_1="v4" variable_2="v4"/>
  </connection>
  
  <connection>
    <map_components component_1="S4" component_2="S4_flux_rate_across_the_plasma_membrane"/>
    <map_variables variable_1="J" variable_2="J"/>
    <map_variables variable_1="S4" variable_2="S4"/>
  </connection>
  
  <connection>
    <map_components component_1="S4_ex" component_2="S4_flux_rate_across_the_plasma_membrane"/>
    <map_variables variable_1="J" variable_2="J"/>
    <map_variables variable_1="S4_ex" variable_2="S4_ex"/>
  </connection>
  
  <connection>
    <map_components component_1="S4_ex" component_2="v7"/>
    <map_variables variable_1="S4_ex" variable_2="S4_ex"/>
    <map_variables variable_1="v7" variable_2="v7"/>
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  <connection>
    <map_components component_1="A2" component_2="v3"/>
    <map_variables variable_1="A2" variable_2="A2"/>
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  <connection>
    <map_components component_1="A3" component_2="v1"/>
    <map_variables variable_1="A3" variable_2="A3"/>
    <map_variables variable_1="v1" variable_2="v1"/>
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  <connection>
    <map_components component_1="A3" component_2="v3"/>
    <map_variables variable_1="v3" variable_2="v3"/>
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  <connection>
    <map_components component_1="A3" component_2="v5"/>
    <map_variables variable_1="A3" variable_2="A3"/>
    <map_variables variable_1="v5" variable_2="v5"/>
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  <connection>
    <map_components component_1="A2" component_2="A3"/>
    <map_variables variable_1="A3" variable_2="A3"/>
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  <connection>
    <map_components component_1="N1" component_2="v2"/>
    <map_variables variable_1="N1" variable_2="N1"/>
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  <connection>
    <map_components component_1="N2" component_2="v2"/>
    <map_variables variable_1="v2" variable_2="v2"/>
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