- Author:
- pmr2.import <nobody@models.cellml.org>
- Date:
- 2009-06-17 16:25:18+12:00
- Desc:
- committing version02 of wolf_heinrich_2000
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/wolf_heinrich_2000/rawfile/d2b8190ae863434da8db1a3c2c2fa6e2b772fd72/wolf_heinrich_2000.cellml
<?xml version='1.0' encoding='utf-8'?>
<!-- FILE : wolf_heinrich_model_2000_version02.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:pathway_editor="http://www.physiome.com/pathway_editor/1.0#" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" cmeta:id="wolf_heinrich_model_2000_version02" name="wolf_heinrich_2000_version01">
<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>Bioengineering Institute, University of Auckland</shortaffil>
</affiliation>
</author>
</articleinfo>
<sect1 id="sec_structure">
<title>Model Structure</title>
<para>
Glycolytic oscillations are a well studied example of rhythmic behaviour on a cellular level. They occur in a diverse array of cells including muscle, heart and pancreatic beta-cells, however the oscillations have been studied most extensively in yeast cells. Theoretical models based on experimental observations have tried to accurately define the underlying oscillatory mechanism.
</para>
<para>
In 2000, Jana Wolf and Reinhart Heinrich published a mathematical model describing the effect of cellular interaction on glycolytic oscillations in yeast (see the figure below). Unlike earlier models of glycolytic oscillations which are restricted to single cells, Wolf and Heinrich consider the effects of intercellular interaction on glycolytic oscillations. Cells often communicate by exchanging metabolic intermediates via the external medium.
</para>
<para>
The model they present in their paper is a detailed model for anaerobic energy metabolism in yeast cells. The model includes the main steps of anaerobic glycolysis and the production of ethanol and glycerol. Transmembrane diffusion of acetaldehyde is included since it is hypothesized that this metabolite mediates the intercellular interaction.
</para>
<para>
The complete original paper reference is cited below:
</para>
<para>
<ulink url="http://www.biochemj.org/bj/345/bj3450321.htm">Effect of cellular interaction on glycolytic oscillations in yeast: a theoretical investigation</ulink>, Jana Wolf and Reinhart Heinrich, 2000, <ulink url="http://www.biochemj.org/">
<emphasis>Biochemical Journal</emphasis>
</ulink>, 345, 321-334. (The <ulink url="http://www.biochemj.org/bj/345/0321/3450321.pdf">PDF</ulink> and <ulink url="http://www.biochemj.org/bj/345/0321/bj3450321.htm">full text</ulink> versions of the article are available on the Biochemical Journal website.) <ulink url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10702114&dopt=Abstract">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"/>
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</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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pool of glyceraldehyde 3-phosphate and dihydroxyacetone phosphate
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<dcterms:alternative>
pool of cytosolic pyruvate and acetaldehyde
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<dcterms:alternative>
coupling substance in the external solution
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<vCard:Given>Jana</vCard:Given>
<vCard:Family>Wolf</vCard:Family>
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<dc:title>A dynamic model of glycolytic oscillations in yeast</dc:title>
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<rdf:li>cellular interactions</rdf:li>
<rdf:li>oscillator</rdf:li>
<rdf:li>metabolism</rdf:li>
<rdf:li>glycolysis</rdf:li>
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<rdf:value>This is the CellML description of Wolf and Heinrich's 2000
mathematical model of the effect of glycolytic oscillations in yeast.</rdf:value>
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<rdf:value>c.lloyd@auckland.ac.nz</rdf:value>
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<rdf:Description rdf:about="rdf:#b97e3054-fdfc-4e7f-ac4d-2fb8a4803b2f">
<vCard:Orgname>The University of Auckland</vCard:Orgname>
<vCard:Orgunit>The Bioengineering Institute</vCard:Orgunit>
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<bqs:Pubmed_id>10702114</bqs:Pubmed_id>
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<vCard:Given>Catherine</vCard:Given>
<vCard:Family>Lloyd</vCard:Family>
<vCard:Other>May</vCard:Other>
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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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<dcterms:W3CDTF>2000-01-15</dcterms:W3CDTF>
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<rdf:Description rdf:about="rdf:#676b0ef9-95d3-4328-80fb-a60515ebaab4">
<dc:title>Biochemical Journal</dc:title>
</rdf:Description>
<rdf:Description rdf:about="rdf:#c7b55376-e027-402a-a185-b040e7a5ee45">
<vCard:FN>Catherine Lloyd</vCard:FN>
</rdf:Description>
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<dc:creator rdf:resource="rdf:#ba93e525-4591-434f-9857-5cfad929ad9c"/>
<dc:title>Effect of cellular interaction on glycolytic oscillations in yeast: a theoretical investigation</dc:title>
<bqs:volume>345</bqs:volume>
<bqs:first_page>321</bqs:first_page>
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<bqs:last_page>334</bqs:last_page>
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<vCard:Given>Reinhart</vCard:Given>
<vCard:Family>Heinrich</vCard:Family>
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</model>
