- Author:
- pmr2.import <nobody@models.cellml.org>
- Date:
- 2007-05-18 02:59:06+12:00
- Desc:
- committing version02 of chay_lee_fan_1995
- Permanent Source URI:
- https://models.fieldml.org/workspace/chay_lee_fan_1995/rawfile/901c4114ef233b7afb0d4c13d2cebc434ed8b6e6/chay_lee_fan_1995.cellml
<?xml version='1.0' encoding='utf-8'?>
<!-- FILE : chay_model_1995.xml
CREATED : 18th May 2007
LAST MODIFIED : 18th May 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 Chay et al's
1995 mathematical model of intracellular calcium spikes in non-excitable cells.
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="chay_model_1995_version02" name="chay_model_1995_version02">
<documentation xmlns="http://cellml.org/tmp-documentation">
<article>
<articleinfo>
<title>Intracellular Ca2+ Spikes in Non-excitable Cell Models</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>
Intracellular Ca<superscript>2+</superscript> ions are essential for the initiation of cellular events such as the fertilisation of eggs, muscle contraction and hormone and peptide secretion. In excitable cells such as neurons, an increase in intracellular Ca<superscript>2+</superscript> is brought about by the Ca<superscript>2+</superscript> channels in the plasma membrane when these channels open during depolarisation, permitting extracellular Ca<superscript>2+</superscript> to enter the cell. By contrast, in non-excitable cells Ca<superscript>2+</superscript> is supplied mainly by internal stores. These stores release Ca<superscript>2+</superscript> when neurotransmitters and hormones engage in the phospholinositide signalling pathway.
</para>
<para>
Oscillatory signals in [Ca<superscript>2+</superscript>]<subscript>i</subscript> in non-excitable cells are frequency encoded. These patterns are similar to action potential responses observed in excitable cells upon stimulation. A model exclusively studied in this paper is based on the receptor-operated model of Cuthberson and Chay (1991) (see <xref linkend="fig_schematic_diagram"/> below). The essence of this model is that the resting period between the Ca<superscript>2+</superscript> spikes are timed by the build up of GTP-binding proteins combined with positive feedback effects and co-operation, leading to the sudden activation of phospholipase C (PLC). Activated PLC converts phosphatidylinositol 4,5-bisphosphate (PIP<subscript>2</subscript>) into two second messengers, diacylglycerol (DAG) and inositol 1,4,5-triphosphate (IP<subscript>3</subscript>), which releases Ca<superscript>2+</superscript> from intracellular stores (see <xref linkend="fig_signaling_pathway"/> below).
</para>
<para>
The complete original paper reference is cited below:
</para>
<para>
<ulink url="http://www.idealibrary.com/links/doi/10.1006/jtbi.1995.0077">Appearance of phase-locked wenckebach-like rhythms, devil's staircase and universality in intracellular calcium spikes in non-excitable cell models</ulink>, Teresa Ree Chay, Young Seek Lee and Yin Shui Fan, 1995, <ulink url="http:www.academicpress.com/jtb">
<emphasis>Journal Of Theoretical Biology</emphasis>
</ulink>, 174, 21-44. (A <ulink url="http://www.idealibrary.com/links/doi/10.1006/jtbi.1995.0077/pdf">PDF</ulink> of the article is available to subscribers on the IDEAL website.) <ulink url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=7643604&dopt=Abstract">PubMed ID: 7643604</ulink>
</para>
<para>
The raw CellML description of the intracellular Ca<superscript>2+</superscript> spikes in non-excitable cells model can be downloaded in various formats as described in <xref linkend="sec_download_this_model"/>.
</para>
<informalfigure float="0" id="fig_schematic_diagram">
<mediaobject>
<imageobject>
<objectinfo>
<title>A schematic diagram of the G-protein pathway</title>
</objectinfo>
<imagedata fileref="chay_1995a.png"/>
</imageobject>
</mediaobject>
<caption>A schematic diagram of the Bourne-Stryer mechanism, PLC acts as a protein activating G-alpha-GTP. PLC is an effector which is activated when bound to G-alpha-GTP. The exchange of GTP for bound GDP is catalysed by the hormone-receptor complex R*, with the help of the G-beta-gamma subunit. Hydrolysis of the bound GTP brings the G-protein back to the inactive state. GTP hydrolysis by the G-alpha_GTP complexed with PLC is much faster than that of G-alpha-GTP alone. The model is based on these four reaction steps.</caption>
</informalfigure>
<informalfigure float="0" id="fig_signaling_pathway">
<mediaobject>
<imageobject>
<objectinfo>
<title>A diagram of the G-protein signaling pathway</title>
</objectinfo>
<imagedata fileref="chay_1995b.png"/>
</imageobject>
</mediaobject>
<caption>The Ca<superscript>2+</superscript>-phosphatidylinositol signalling pathway plays a major role in transmembrane signalling in a large number of different cell types. In this pathway hormonal stimuli lead to the activation of G-proteins as an effector system. This initiates PLC activation and the subsequent formation of DAG and IP<subscript>3</subscript> which triggers the generation of repetitive [Ca<superscript>2+</superscript>]<subscript>i</subscript> spikes varying in frequency, amplitude and duration depending on the strength and the type of the extracellular agonist.</caption>
</informalfigure>
</sect1>
</article>
</documentation>
<!--
Below, we define some additional units for association with variables and
constants within the model. The identifiers are fairly self-explanatory.
-->
<units name="nanomolar">
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<unit units="litre" exponent="-1"/>
</units>
<units name="fifth_order_rate_constant">
<unit units="nanomolar" exponent="-4"/>
<unit units="second" exponent="-1"/>
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</units>
<units name="second_order_rate_constant">
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<unit units="second" exponent="-1"/>
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<!--
The "environment" component is used to declare variables that are used by
all or most of the other components, in this case just "time".
-->
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</component>
<!--
The following components describe all the reactants and products involved in
reactions.
-->
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<variable units="first_order_rate_constant" name="kg" initial_value="0.005"/>
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<variable units="first_order_rate_constant" name="kd"/>
<variable units="first_order_rate_constant" name="kd_" initial_value="700.0"/>
<variable units="first_order_rate_constant" name="hd" initial_value="100.0"/>
<variable units="second_order_rate_constant" name="ld" initial_value="250.0"/>
<variable units="nanomolar" public_interface="in" name="KD"/>
<variable units="nanomolar" public_interface="in" name="PLC_active"/>
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<apply>
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<ci>hd</ci>
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<ci> ld </ci>
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<apply id="kd_calculation">
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<cn cellml:units="dimensionless"> 2.0 </cn>
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<component name="Ca_i">
<variable units="nanomolar" name="Ca_i"/>
<variable units="second_order_rate_constant" name="rho_kc" initial_value="90000.0"/>
<variable units="first_order_rate_constant" name="rho_hc" initial_value="1.0"/>
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<ci> rho_lc </ci>
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<apply>
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<variable units="nanomolar" public_interface="in" name="G_alpha_GTP"/>
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<variable units="nanomolar" public_interface="in" name="DAG"/>
<variable units="second" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
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<ci> hp </ci>
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<ci> hp_ </ci>
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<apply>
<power/>
<ci> DAG </ci>
<cn cellml:units="dimensionless"> 2.0 </cn>
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<apply>
<power/>
<ci> KD </ci>
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<apply>
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<ci> DAG </ci>
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<variable units="nanomolar" name="PLC_total" initial_value="10.0"/>
<variable units="nanomolar" public_interface="in" name="PLC_active"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
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<variable units="nanomolar" public_interface="in" name="G_alpha_GTP"/>
<variable units="nanomolar" public_interface="in" name="PLC_active"/>
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<vCard:Given>Young</vCard:Given>
<vCard:Family>Lee</vCard:Family>
<vCard:Other>Seek</vCard:Other>
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<dc:publisher>The University of Auckland, Bioengineering Institute</dc:publisher>
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<dc:title>Journal of theoretical Biology</dc:title>
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<vCard:Given>Teresa</vCard:Given>
<vCard:Family>Chay</vCard:Family>
<vCard:Other>Ree</vCard:Other>
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<rdf:Description rdf:about="#chay_model_1995_version02">
<dc:title>
The Chay et al 1995 mathematical model of intracellular calcium spikes
in non-excitable cells.
</dc:title>
<cmeta:bio_entity>non-excitable cell</cmeta:bio_entity>
<cmeta:comment rdf:resource="rdf:#22cd0a2b-7582-4508-a8ed-b68f1799ab33"/>
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</rdf:Description>
<rdf:Description rdf:about="rdf:#de37b0b1-9bc5-4ecc-b94a-e70c1a5fecae">
<dcterms:W3CDTF>1995-05-07</dcterms:W3CDTF>
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<bqs:subject_type>keyword</bqs:subject_type>
<rdf:value>calcium dynamics</rdf:value>
</rdf:Description>
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<rdf:value>This is the CellML description of Chay et al's 1995 mathematical model of intracellular calcium spikes in non-excitable cells.</rdf:value>
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<dcterms:W3CDTF>2007-05-18</dcterms:W3CDTF>
</rdf:Description>
<rdf:Description rdf:about="rdf:#acb67b01-fab9-42d4-9129-cc8c417e1fad">
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<vCard:Given>Catherine</vCard:Given>
<vCard:Family>Lloyd</vCard:Family>
<vCard:Other>May</vCard:Other>
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<vCard:ORG rdf:resource="rdf:#f150f5ad-f3e0-423d-ba94-75772b53467a"/>
<vCard:EMAIL rdf:resource="rdf:#21a57c64-6cb8-4733-a229-d9876ef0e53c"/>
<vCard:N rdf:resource="rdf:#f5a97e68-6c76-432a-8b28-280f70da70e6"/>
</rdf:Description>
<rdf:Description rdf:about="rdf:#484eed33-f532-43b7-b8f9-40ceccba97b3">
<vCard:FN>Catherine Lloyd</vCard:FN>
</rdf:Description>
<rdf:Description rdf:about="rdf:#11479da2-670a-4d12-a806-3f55089056a0">
<dc:creator rdf:resource="rdf:#fcdc5155-ea6f-4fff-88b0-d9188dffb2e8"/>
</rdf:Description>
<rdf:Description rdf:about="rdf:#21a57c64-6cb8-4733-a229-d9876ef0e53c">
<rdf:type rdf:resource="http://imc.org/vCard/3.0#internet"/>
<rdf:value>c.lloyd@auckland.ac.nz</rdf:value>
</rdf:Description>
<rdf:Description rdf:about="rdf:#4298c2d3-dc33-4533-b813-1b03f16230ec">
<dcterms:W3CDTF>2007-06-05T09:21:48+12:00</dcterms:W3CDTF>
</rdf:Description>
<rdf:Description rdf:about="rdf:#9d4cec15-9de6-4b8d-adc8-061c0e4b56b1">
<dcterms:modified rdf:resource="rdf:#4298c2d3-dc33-4533-b813-1b03f16230ec"/>
<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 and gives a nice curved output. However it does not provide the spiked output which has been published in the original paper.</rdf:value>
<cmeta:modifier rdf:resource="rdf:#fb072cd9-6083-4a61-ab5c-e7658fbb3f92"/>
</rdf:Description>
<rdf:Description rdf:about="rdf:#f5a97e68-6c76-432a-8b28-280f70da70e6">
<vCard:Given>Catherine</vCard:Given>
<vCard:Family>Lloyd</vCard:Family>
<vCard:Other>May</vCard:Other>
</rdf:Description>
<rdf:Description rdf:about="rdf:#f150f5ad-f3e0-423d-ba94-75772b53467a">
<vCard:Orgname>The University of Auckland</vCard:Orgname>
<vCard:Orgunit>The Bioengineering Institute</vCard:Orgunit>
</rdf:Description>
<rdf:Description rdf:about="rdf:#c7dce5a0-61ad-4c73-8c26-2ba86f3f5668">
<dc:creator rdf:resource="rdf:#b2fc8c4b-a4b7-4d1b-b9df-e029efbd282c"/>
<dc:title>Appearance of Phase-locked Wenchbach-like Rhythms, Devil's Staircase and Universality in Intracellular Calcium Spikes in Non-excitable Cell Models</dc:title>
<bqs:volume>174</bqs:volume>
<bqs:first_page>21</bqs:first_page>
<bqs:Journal rdf:resource="rdf:#ae700e9e-fc3a-435a-b0c6-9b24a9e30c92"/>
<dcterms:issued rdf:resource="rdf:#de37b0b1-9bc5-4ecc-b94a-e70c1a5fecae"/>
<bqs:last_page>44</bqs:last_page>
</rdf:Description>
<rdf:Description rdf:about="rdf:#daf33780-afb4-4886-a9c5-293b364430fa">
<vCard:Given>Yin</vCard:Given>
<vCard:Family>Fan</vCard:Family>
<vCard:Other>Shui</vCard:Other>
</rdf:Description>
</rdf:RDF>
</model>
