- Author:
- Tommy Yu <tommy.yu@auckland.ac.nz>
- Date:
- 2015-02-12 19:28:32+13:00
- Desc:
- Merging to remove the extra head
- Since the title is changed and in the interest of maintaining the
current structure we keep it as is.
- Permanent Source URI:
- https://staging.physiomeproject.org/w/matthiaskoenig/MetabolicComponentLibrary/rawfile/e0e2c28e2dfdfe37ea2cae3390a6ae26c28a3393/examples/wolf_heinrich_2000 _MCL.cellml
<?xml version="1.0"?>
<!--
This CellML file was generated on 4/18/2013 at 9:41:47 at PM using:
COR (0.9.31.1409)
Copyright 2002-2013 Dr Alan Garny
http://cor.physiol.ox.ac.uk/ - cor@physiol.ox.ac.uk
CellML 1.0 was used to generate this model
http://www.cellml.org/
--><model xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cmeta="http://www.cellml.org/metadata/1.1#" cmeta:id="wolf_2000_MCL" name="heinrich_wolf_2000_MCL">
<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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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"><rdf:Description rdf:nodeID="n1"><endingValue xmlns="http://www.cellml.org/metadata/simulation/1.0#" xml:lang="en">100</endingValue></rdf:Description><rdf:Description rdf:about="rdf:#ba93e525-4591-434f-9857-5cfad929ad9c"><rdf:type><rdf:Description rdf:about="http://www.w3.org/1999/02/22-rdf-syntax-ns#Seq"/></rdf:type><rdf:_2><rdf:Description rdf:about="rdf:#fc9d817c-976f-46f5-b0e0-1661811932f2"/></rdf:_2><rdf:_1><rdf:Description rdf:about="rdf:#038e034e-132f-42b9-8b69-3b8ee69484dc"/></rdf:_1></rdf:Description><rdf:Description rdf:about="rdf:#d6fdbc8b-3bc5-4d15-8a8c-e2774ded14dc"><W3CDTF xmlns="http://purl.org/dc/terms/" xml:lang="en">2007-06-01T00:00:00+00:00</W3CDTF></rdf:Description><rdf:Description rdf:about="rdf:#c7b55376-e027-402a-a185-b040e7a5ee45"><FN xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en">Catherine Lloyd</FN></rdf:Description><rdf:Description rdf:nodeID="n2"><rdf:type><rdf:Description rdf:about="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/></rdf:type><rdf:_5 xml:lang="en">yeast</rdf:_5><rdf:_4 xml:lang="en">glycolysis</rdf:_4><rdf:_3 xml:lang="en">metabolism</rdf:_3><rdf:_2 xml:lang="en">oscillator</rdf:_2><rdf:_1 xml:lang="en">cellular interactions</rdf:_1></rdf:Description><rdf:Description rdf:about="rdf:#fc9d817c-976f-46f5-b0e0-1661811932f2"><rdf:type><rdf:Description rdf:about="http://www.cellml.org/bqs/1.0#Person"/></rdf:type><N xmlns="http://www.w3.org/2001/vcard-rdf/3.0#"><rdf:Description rdf:about="rdf:#d5f122ef-7d07-4331-85d1-cb40e1a9192a"/></N></rdf:Description><rdf:Description rdf:about="rdf:#90e0fba7-56c4-4f05-9554-60bbbf65e3ce"><last_page xmlns="http://www.cellml.org/bqs/1.0#" xml:lang="en">334</last_page><Journal xmlns="http://www.cellml.org/bqs/1.0#"><rdf:Description rdf:about="rdf:#676b0ef9-95d3-4328-80fb-a60515ebaab4"/></Journal><first_page xmlns="http://www.cellml.org/bqs/1.0#" xml:lang="en">321</first_page><volume xmlns="http://www.cellml.org/bqs/1.0#" xml:lang="en">345</volume><issued xmlns="http://purl.org/dc/terms/"><rdf:Description rdf:about="rdf:#153e7b1c-7b89-4c8a-896b-5905fb890a9a"/></issued><creator xmlns="http://purl.org/dc/elements/1.1/"><rdf:Description rdf:about="rdf:#ba93e525-4591-434f-9857-5cfad929ad9c"/></creator><title xmlns="http://purl.org/dc/elements/1.1/" xml:lang="en">Effect of cellular interaction on glycolytic oscillations in yeast: a theoretical investigation</title></rdf:Description><rdf:Description rdf:about="rdf:#0928b755-a3ad-458f-93f9-44ef02482471"><Other xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en">May</Other><Family xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en">Lloyd</Family><Given xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en">Catherine</Given></rdf:Description><rdf:Description rdf:about="rdf:#be72be56-df0e-43cd-a1d2-6543ec8f1de6"><subject xmlns="http://purl.org/dc/elements/1.1/"><rdf:Description rdf:about="rdf:#c2a0092c-68ce-4be5-83c7-3487e872e6b1"/></subject></rdf:Description><rdf:Description rdf:about=""><cmeta:modification><rdf:Description rdf:about="rdf:#539a8e46-ded7-4251-adce-a92885f98d3c"/></cmeta:modification><creator xmlns="http://purl.org/dc/elements/1.1/"><rdf:Description rdf:about="rdf:#302fb0bd-0d97-4779-a69a-6979c72c31a1"/></creator><created xmlns="http://purl.org/dc/terms/"><rdf:Description rdf:about="rdf:#d6fdbc8b-3bc5-4d15-8a8c-e2774ded14dc"/></created><cmeta:comment><rdf:Description rdf:about="rdf:#9204ac25-9bd7-40d7-a617-559493a9442c"/></cmeta:comment><publisher xmlns="http://purl.org/dc/elements/1.1/" xml:lang="en">The University of Auckland, Auckland Bioengineering Institute</publisher></rdf:Description><rdf:Description rdf:about="rdf:#8b0c1cff-3351-4eff-a84a-b306ef2ee7d0"><N xmlns="http://www.w3.org/2001/vcard-rdf/3.0#"><rdf:Description rdf:about="rdf:#69ff35bc-0359-4d9e-a68c-3d8bb7d676ce"/></N></rdf:Description><rdf:Description rdf:about="rdf:#539a8e46-ded7-4251-adce-a92885f98d3c"><cmeta:modifier><rdf:Description rdf:about="rdf:#8b0c1cff-3351-4eff-a84a-b306ef2ee7d0"/></cmeta:modifier><modified xmlns="http://purl.org/dc/terms/"><rdf:Description rdf:about="rdf:#84461ddf-c803-4c6a-84c8-c48ba71fd0b9"/></modified><rdf:value xml:lang="en">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></rdf:Description><rdf:Description rdf:about="#N2"><title xmlns="http://purl.org/dc/elements/1.1/" xml:lang="en">N2</title><alternative xmlns="http://purl.org/dc/terms/" xml:lang="en">NADH</alternative></rdf:Description><rdf:Description rdf:about="#A3"><title xmlns="http://purl.org/dc/elements/1.1/" xml:lang="en">A3</title><alternative xmlns="http://purl.org/dc/terms/" xml:lang="en">ATP</alternative></rdf:Description><rdf:Description rdf:about="#S2"><title xmlns="http://purl.org/dc/elements/1.1/" xml:lang="en">S2</title><alternative xmlns="http://purl.org/dc/terms/" xml:lang="en">
pool of glyceraldehyde 3-phosphate and dihydroxyacetone phosphate
</alternative></rdf:Description><rdf:Description rdf:about="rdf:#676b0ef9-95d3-4328-80fb-a60515ebaab4"><title xmlns="http://purl.org/dc/elements/1.1/" xml:lang="en">Biochemical Journal</title></rdf:Description><rdf:Description rdf:about="rdf:#153e7b1c-7b89-4c8a-896b-5905fb890a9a"><W3CDTF xmlns="http://purl.org/dc/terms/" xml:lang="en">2000-01-15</W3CDTF></rdf:Description><rdf:Description rdf:about="rdf:#69ff35bc-0359-4d9e-a68c-3d8bb7d676ce"><Other xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en">May</Other><Family xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en">Lloyd</Family><Given xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en">Catherine</Given></rdf:Description><rdf:Description rdf:about="rdf:#b97e3054-fdfc-4e7f-ac4d-2fb8a4803b2f"><Orgunit xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en">Auckland Bioengineering Institute</Orgunit><Orgname xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en">The University of Auckland</Orgname></rdf:Description><rdf:Description rdf:about="rdf:#6a9f1bec-c537-447a-82e2-44ef5c704106"><JournalArticle xmlns="http://www.cellml.org/bqs/1.0#"><rdf:Description rdf:about="rdf:#90e0fba7-56c4-4f05-9554-60bbbf65e3ce"/></JournalArticle><Pubmed_id xmlns="http://www.cellml.org/bqs/1.0#" xml:lang="en">10702114</Pubmed_id></rdf:Description><rdf:Description rdf:about="rdf:#038e034e-132f-42b9-8b69-3b8ee69484dc"><rdf:type><rdf:Description rdf:about="http://www.cellml.org/bqs/1.0#Person"/></rdf:type><N xmlns="http://www.w3.org/2001/vcard-rdf/3.0#"><rdf:Description rdf:about="rdf:#c3853548-6b92-4a8e-8f36-74f9a0097a9e"/></N></rdf:Description><rdf:Description rdf:nodeID="n3"><rdf:rest><rdf:Description rdf:about="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/></rdf:rest><rdf:first><rdf:Description rdf:nodeID="n1"/></rdf:first></rdf:Description><rdf:Description rdf:about="rdf:#c3853548-6b92-4a8e-8f36-74f9a0097a9e"><Family xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en">Wolf</Family><Given xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en">Jana</Given></rdf:Description><rdf:Description rdf:about="#S4"><title xmlns="http://purl.org/dc/elements/1.1/" xml:lang="en">S4</title><alternative xmlns="http://purl.org/dc/terms/" xml:lang="en">
pool of cytosolic pyruvate and acetaldehyde
</alternative></rdf:Description><rdf:Description rdf:about="rdf:#cd71dded-482f-4780-85c7-7563c81d6507"><rdf:type><rdf:Description rdf:about="http://imc.org/vCard/3.0#internet"/></rdf:type><rdf:value xml:lang="en">c.lloyd@auckland.ac.nz</rdf:value></rdf:Description><rdf:Description rdf:about="#wolf_2000_MCL"><simulation xmlns="http://www.cellml.org/metadata/simulation/1.0#"><rdf:Description rdf:nodeID="n4"/></simulation></rdf:Description><rdf:Description rdf:about="#S3"><title xmlns="http://purl.org/dc/elements/1.1/" xml:lang="en">S3</title><alternative xmlns="http://purl.org/dc/terms/" xml:lang="en">1,3-bisphosphoglycerate</alternative></rdf:Description><rdf:Description rdf:about="rdf:#c2a0092c-68ce-4be5-83c7-3487e872e6b1"><subject_type xmlns="http://www.cellml.org/bqs/1.0#" xml:lang="en">keyword</subject_type><rdf:value><rdf:Description rdf:nodeID="n2"/></rdf:value></rdf:Description><rdf:Description rdf:about="#S4_ex"><title xmlns="http://purl.org/dc/elements/1.1/" xml:lang="en">S4_ex</title><alternative xmlns="http://purl.org/dc/terms/" xml:lang="en">
coupling substance in the external solution
</alternative></rdf:Description><rdf:Description rdf:about="rdf:#d5f122ef-7d07-4331-85d1-cb40e1a9192a"><Family xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en">Heinrich</Family><Given xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en">Reinhart</Given></rdf:Description><rdf:Description rdf:nodeID="n4"><boundIntervals xmlns="http://www.cellml.org/metadata/simulation/1.0#"><rdf:Description rdf:nodeID="n3"/></boundIntervals></rdf:Description><rdf:Description rdf:about="#wolf_2000"><reference xmlns="http://www.cellml.org/bqs/1.0#"><rdf:Description rdf:about="rdf:#6a9f1bec-c537-447a-82e2-44ef5c704106"/></reference><reference xmlns="http://www.cellml.org/bqs/1.0#"><rdf:Description rdf:about="rdf:#be72be56-df0e-43cd-a1d2-6543ec8f1de6"/></reference><cmeta:bio_entity xml:lang="en">yeast</cmeta:bio_entity><cmeta:comment><rdf:Description rdf:about="rdf:#70edc128-875b-4f6e-9764-f1ae389d8696"/></cmeta:comment><title xmlns="http://purl.org/dc/elements/1.1/" xml:lang="en">A dynamic model of glycolytic oscillations in yeast</title></rdf:Description><rdf:Description rdf:about="rdf:#84461ddf-c803-4c6a-84c8-c48ba71fd0b9"><W3CDTF xmlns="http://purl.org/dc/terms/" xml:lang="en">2007-06-05T10:49:34+12:00</W3CDTF></rdf:Description><rdf:Description rdf:about="rdf:#302fb0bd-0d97-4779-a69a-6979c72c31a1"><EMAIL xmlns="http://www.w3.org/2001/vcard-rdf/3.0#"><rdf:Description rdf:about="rdf:#cd71dded-482f-4780-85c7-7563c81d6507"/></EMAIL><ORG xmlns="http://www.w3.org/2001/vcard-rdf/3.0#"><rdf:Description rdf:about="rdf:#b97e3054-fdfc-4e7f-ac4d-2fb8a4803b2f"/></ORG><N xmlns="http://www.w3.org/2001/vcard-rdf/3.0#"><rdf:Description rdf:about="rdf:#0928b755-a3ad-458f-93f9-44ef02482471"/></N></rdf:Description><rdf:Description rdf:about="rdf:#9204ac25-9bd7-40d7-a617-559493a9442c"><creator xmlns="http://purl.org/dc/elements/1.1/"><rdf:Description rdf:about="rdf:#fda76ec7-9ea2-448e-bfa6-992f056919b2"/></creator></rdf:Description><rdf:Description rdf:about="#N"><title xmlns="http://purl.org/dc/elements/1.1/" xml:lang="en">N</title><alternative xmlns="http://purl.org/dc/terms/" xml:lang="en">
sum of the concentrations of NAD+ and NADH
</alternative></rdf:Description><rdf:Description rdf:about="#S1"><title xmlns="http://purl.org/dc/elements/1.1/" xml:lang="en">S1</title><alternative xmlns="http://purl.org/dc/terms/" xml:lang="en">glucose</alternative></rdf:Description><rdf:Description rdf:about="rdf:#70edc128-875b-4f6e-9764-f1ae389d8696"><rdf:value xml:lang="en">This is the CellML description of Wolf and Heinrich's 2000 mathematical model of the effect of glycolytic oscillations in yeast.</rdf:value><creator xmlns="http://purl.org/dc/elements/1.1/"><rdf:Description rdf:about="rdf:#c7b55376-e027-402a-a185-b040e7a5ee45"/></creator></rdf:Description><rdf:Description rdf:about="#A"><title xmlns="http://purl.org/dc/elements/1.1/" xml:lang="en">A</title><alternative xmlns="http://purl.org/dc/terms/" xml:lang="en">
sum of the concentrations of ATP and ADP
</alternative></rdf:Description></rdf:RDF></model>
