- Author:
- rcai987 <devnull@localhost>
- Date:
- 2015-01-06 14:39:24+13:00
- Desc:
- Added annotations to albrecht_colegrove_hongpaisan...
- Permanent Source URI:
- https://models.cellml.org/workspace/albrecht_colegrove_hongpaisan_pivovarova_andrews_friel_2001/rawfile/7fb33358bf25c4f067170946631842807b267ea2/albrecht_colegrove_hongpaisan_pivovarova_andrews_friel_2001.cellml
<?xml version="1.0"?>
<!-- FILE : albrecht_model_2001.xml
CREATED : 25th March 2002
LAST MODIFIED : 9th April 2003
AUTHOR : Catherine Lloyd
Bioengineering Institute
The University of Auckland
MODEL STATUS : This model conforms to the CellML 1.0 Specification released on
10th August 2001, and the 16/1/02 CellML Metadata 1.0 Specification.
DESCRIPTION : This file contains a CellML description of Albrecht et al's
2001 model of calcium-induced calcium release in sympathetic neurons.
CHANGES:
18/07/2002 - CML - Added more metadata.
09/04/2003 - AAC - Added publication date information.
--><model xmlns="http://www.cellml.org/cellml/1.0#" xmlns:bqs="http://www.cellml.org/bqs/1.0#" xmlns:cellml="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:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xml:base="file:///H:/Summer Research/Ray's 2nd/albrecht_colegrove_hongpaisan_pivovarova_andrews_friel_2001.cellml" cmeta:id="albrecht_colegrove_hongpaisan_pivovarova_andrews_friel_2001_version01" name="albrecht_colegrove_hongpaisan_pivovarova_andrews_friel_2001_version01">
<documentation xmlns="http://cellml.org/tmp-documentation">
<article>
<articleinfo>
<title>Multiple Modes of Calcium-induced Calcium Release in Sympathetic Neurons</title>
<author>
<firstname>Catherine</firstname>
<surname>Lloyd</surname>
<affiliation>
<shortaffil>Bioengineering Institute, University of Auckland</shortaffil>
</affiliation>
</author>
</articleinfo>
<section id="sec_status">
<title>Model Status</title>
<para>
This model is consistently represented within the CellML but contains sets of algebraic equations that prevent the model from being solved in currently available software - 03/08.
</para>
</section>
<sect1 id="sec_structure">
<title>Model Structure</title>
<para>
Calcium is an important signalling ion, and changes in Ca<superscript>2+</superscript> concentration ([Ca<superscript>2+</superscript>]) regulate diverse processes in many cellular compartments. In excitable cells, depolarisation-induced Ca<superscript>2+</superscript> entry increases [Ca<superscript>2+</superscript>]<subscript>i</subscript>, leading to secondary changes in [Ca<superscript>2+</superscript>] within organelles such as mitochondria and ER that regulate specific Ca<superscript>2+</superscript>-sensitive targets within these organelles. Although mitochondria accumulate Ca<superscript>2+</superscript> in response to depolarisation-evoked [Ca<superscript>2+</superscript>]<subscript>i</subscript> elevations (see <ulink url="${HTML_EXMPL_COLEGROVE_MODEL}">The Colegrove <emphasis>et al</emphasis> Model Of Mitochondrial Ca<superscript>2+</superscript> Uptake And Release, 2000</ulink>), the ER has been described as either a Ca<superscript>2+</superscript> source or sink. Different modes of net ER Ca<superscript>2+</superscript> transport are expected to have very different effects on cytoplasmic and intraluminal Ca<superscript>2+</superscript> signals and on the processes they regulate.
</para>
<para>
In their 2001 model, Meredith A. Albrecht, Stephen L. Colegrove, Jarin Hongpaisan, Natalia B. Pivovarova, S. Brian Andrews and David D. Friel have examined the relationship between changes in [Ca<superscript>2+</superscript>]<subscript>i</subscript> and [Ca<superscript>2+</superscript>]<subscript>ER</subscript> during weak depolarisation in sympathetic neurons. The total Ca<superscript>2+</superscript> flux during the recovery phase following membrane depolarisation was divided into four components (see <xref linkend="fig_cell_diagram"/> below). One representing net Ca<superscript>2+</superscript> extrusion across the plasma membrane (J<subscript>extru</subscript>), one representing Ca<superscript>2+</superscript> entry through voltage-gated Ca<superscript>2+</superscript> channels (J<subscript>ICa</subscript>), one representing ER Ca<superscript>2+</superscript> uptake via a Ca<superscript>2+</superscript> ATPase (J<subscript>SERCA</subscript>) and one representing passive ER Ca<superscript>2+</superscript> release. This mathematical model has been translated into a CellML description which can be downloaded in various formats as described in <xref linkend="sec_download_this_model"/>.
</para>
<para>
The complete original paper reference is cited below:
</para>
<para>
<ulink url="http://www.jgp.org/cgi/content/abstract/118/1/83">Multiple Modes of Calcium-induced Calcium Release in Sympathetic Neurons I: Attenuation of Endoplasmic Reticulum Ca<superscript>2+</superscript> Accumulation at Low [Ca<superscript>2+</superscript>]<subscript>i</subscript> during Weak Depolarisation</ulink>, Meredith A. Albrecht, Stephen L. Colegrove, Jarin Hongpaisan, Natalia B. Pivovarova, S. Brian Andrews and David D. Friel, 2001, <ulink url="http://www.jgp.org/">
<emphasis>The Journal Of General Physiology</emphasis>
</ulink>, 118, 83-100. (<ulink url="http://www.jgp.org/cgi/content/full/118/1/83">Full text</ulink> and <ulink url="http://www.jgp.org/cgi/reprint/118/1/83.pdf">PDF</ulink> versions of the article are available for Journal Members on the JGP website.) <ulink url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11429446&dopt=Abstract">PubMed ID: 11429446</ulink>
</para>
<informalfigure float="0" id="fig_cell_diagram">
<mediaobject>
<imageobject>
<objectinfo>
<title>cell schematic for the model</title>
</objectinfo>
<imagedata fileref="albrecht_2001.png"/>
</imageobject>
</mediaobject>
<caption>Schematic of the model indicating Ca<superscript>2+</superscript> compartmentation in the extracellular matrix, cytosol and the ER and pathways for Ca<superscript>2+</superscript> ion movement between the compartments.</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="per_second">
<unit exponent="-1" units="second"/>
</units>
<units name="millivolt">
<unit prefix="milli" units="volt"/>
</units>
<units name="millimolar">
<unit prefix="milli" units="mole"/>
<unit exponent="-1" units="litre"/>
</units>
<units name="micromolar">
<unit prefix="micro" units="mole"/>
<unit exponent="-1" units="litre"/>
</units>
<units name="nanomolar">
<unit prefix="nano" units="mole"/>
<unit exponent="-1" units="litre"/>
</units>
<units name="nanomolar_per_second">
<unit units="nanomolar"/>
<unit exponent="-1" units="second"/>
</units>
<units name="micromolar_per_second">
<unit units="micromolar"/>
<unit exponent="-1" units="second"/>
</units>
<units name="micro_litre">
<unit prefix="micro" units="litre"/>
</units>
<units name="coulomb_per_millimole">
<unit units="coulomb"/>
<unit exponent="-1" prefix="milli" units="mole"/>
</units>
<units name="picoA">
<unit prefix="pico" units="ampere"/>
</units>
<!--
The "environment" component is used to declare variables that are used by
all or most of the other components, in this case just "time".
-->
<component name="environment">
<variable name="time" public_interface="out" units="second"/>
</component>
<component cmeta:id="id_00001" name="total_cytoplasmic_Ca_flux">
<variable cmeta:id="id_00007" name="J_ICa" public_interface="out" units="nanomolar_per_second"/>
<variable name="v_i" public_interface="out" units="micro_litre"/>
<variable name="k_i" public_interface="out" units="dimensionless"/>
<variable initial_value="96.5" name="F" units="coulomb_per_millimole"/>
<variable cmeta:id="id_00008" name="I_Ca" units="picoA"/>
<variable name="time" public_interface="in" units="second"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="J_ICa_calculation">
<eq/>
<ci> J_ICa </ci>
<apply>
<divide/>
<ci> I_Ca </ci>
<apply>
<times/>
<cn cellml:units="dimensionless"> 2.0 </cn>
<ci> F </ci>
<ci> v_i </ci>
<ci> k_i </ci>
</apply>
</apply>
</apply>
</math>
</component>
<component cmeta:id="id_00002" name="Ca_extrusion_across_the_plasma_membrane">
<variable cmeta:id="id_00017" name="J_pm" public_interface="out" units="nanomolar_per_second"/>
<variable name="J_extru" units="nanomolar_per_second"/>
<variable cmeta:id="id_00018" initial_value="0.00000015" name="k_leak" units="per_second"/>
<variable initial_value="25.0" name="Vmax_extru" units="nanomolar_per_second"/>
<variable initial_value="386.0" name="EC50_extru" units="nanomolar"/>
<variable initial_value="2.4" name="n_extru" units="dimensionless"/>
<variable cmeta:id="id_00010" initial_value="2.0" name="Ca_o" units="millimolar"/>
<variable cmeta:id="id_00019" name="J_ICa" public_interface="in" units="nanomolar_per_second"/>
<variable cmeta:id="id_00009" name="Ca_i" public_interface="in" units="nanomolar"/>
<variable name="time" public_interface="in" units="second"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="J_pm_calculation">
<eq/>
<ci> J_pm </ci>
<apply>
<plus/>
<ci> J_extru </ci>
<ci> J_ICa </ci>
</apply>
</apply>
<apply id="J_extru_calculation">
<eq/>
<ci> J_extru </ci>
<apply>
<plus/>
<apply>
<times/>
<ci> k_leak </ci>
<apply>
<minus/>
<ci> Ca_i </ci>
<ci> Ca_o </ci>
</apply>
</apply>
<apply>
<divide/>
<ci> Vmax_extru </ci>
<apply>
<plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply>
<power/>
<apply>
<divide/>
<ci> EC50_extru </ci>
<ci> Ca_i </ci>
</apply>
<ci> n_extru </ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component cmeta:id="id_00003" name="Ca_uptake_by_SR_Ca_ATPase">
<variable cmeta:id="id_00020" name="J_SERCA" public_interface="out" units="nanomolar_per_second"/>
<variable cmeta:id="id_00021" initial_value="70.0" name="Vmax_SERCA" units="nanomolar_per_second"/>
<variable cmeta:id="id_00022" initial_value="700.0" name="EC50_SERCA" units="nanomolar"/>
<variable cmeta:id="id_00023" initial_value="1.0" name="n_SERCA" units="dimensionless"/>
<variable cmeta:id="id_00011" name="Ca_i" public_interface="in" units="nanomolar"/>
<variable name="time" public_interface="in" units="second"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="J_SERCA_calculation">
<eq/>
<ci> J_SERCA </ci>
<apply>
<divide/>
<ci> Vmax_SERCA </ci>
<apply>
<plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply>
<power/>
<apply>
<divide/>
<ci> EC50_SERCA </ci>
<ci> Ca_i </ci>
</apply>
<ci> n_SERCA </ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component cmeta:id="id_00004" name="ER_Ca_release">
<variable cmeta:id="id_00024" name="J_ER" public_interface="out" units="nanomolar_per_second"/>
<variable cmeta:id="id_00025" name="P_ER" units="per_second"/>
<variable initial_value="0.0000178" name="P_basal" units="per_second"/>
<variable cmeta:id="id_00036" initial_value="0.0009" name="Pmax_RyR" units="per_second"/>
<variable cmeta:id="id_00035" initial_value="1.0" name="EC50_RyR" units="micromolar"/>
<variable cmeta:id="id_00034" initial_value="1.0" name="n_RyR" units="dimensionless"/>
<variable name="J_release" units="nanomolar_per_second"/>
<variable cmeta:id="id_00031" name="J_SERCA" public_interface="in" units="nanomolar_per_second"/>
<variable cmeta:id="id_00012" name="Ca_i" public_interface="in" units="nanomolar"/>
<variable cmeta:id="id_00013" name="Ca_ER" public_interface="in" units="nanomolar"/>
<variable name="time" public_interface="in" units="second"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="J_release_calculation">
<eq/>
<ci> J_release </ci>
<apply>
<times/>
<ci> P_ER </ci>
<apply>
<minus/>
<ci> Ca_i </ci>
<ci> Ca_ER </ci>
</apply>
</apply>
</apply>
<apply id="J_ER_calculation">
<eq/>
<ci> J_ER </ci>
<apply>
<plus/>
<ci> J_SERCA </ci>
<ci> J_release </ci>
</apply>
</apply>
<apply id="P_ER_calculation">
<eq/>
<ci> P_ER </ci>
<apply>
<plus/>
<ci> P_basal </ci>
<apply>
<divide/>
<ci> Pmax_RyR </ci>
<apply>
<plus/>
<cn cellml:units="dimensionless"> 1.0 </cn>
<apply>
<power/>
<apply>
<divide/>
<ci> EC50_RyR </ci>
<ci> Ca_i </ci>
</apply>
<ci> n_RyR </ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component cmeta:id="id_00005" name="cytoplasmic_calcium">
<variable cmeta:id="id_00014" name="Ca_i" public_interface="out" units="nanomolar"/>
<variable name="J_i" units="nanomolar_per_second"/>
<variable cmeta:id="id_00026" name="J_ER" public_interface="in" units="nanomolar_per_second"/>
<variable cmeta:id="id_00033" name="J_pm" public_interface="in" units="nanomolar_per_second"/>
<variable name="time" public_interface="in" units="second"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="Ca_i_diff_eq">
<eq/>
<apply>
<diff/>
<bvar>
<ci> time </ci>
</bvar>
<ci> Ca_i </ci>
</apply>
<apply>
<minus/>
<ci> J_i </ci>
</apply>
</apply>
<apply id="J_i_calculation">
<eq/>
<ci> J_i </ci>
<apply>
<plus/>
<ci> J_pm </ci>
<ci> J_ER </ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="id_00006" name="intraluminal_calcium">
<variable cmeta:id="id_00015" name="Ca_ER" public_interface="out" units="nanomolar"/>
<variable cmeta:id="id_00027" name="v_ER" units="micro_litre"/>
<variable cmeta:id="id_00028" name="k_ER" units="dimensionless"/>
<variable cmeta:id="id_00029" initial_value="0.01" name="gamma_ER" units="dimensionless"/>
<variable cmeta:id="id_00016" name="Ca_i" public_interface="in" units="nanomolar"/>
<variable name="v_i" public_interface="in" units="micro_litre"/>
<variable name="k_i" public_interface="in" units="dimensionless"/>
<variable cmeta:id="id_00030" name="J_ER" public_interface="in" units="nanomolar_per_second"/>
<variable cmeta:id="id_00032" name="J_SERCA" public_interface="in" units="nanomolar_per_second"/>
<variable name="time" public_interface="in" units="second"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="Ca_ER_diff_eq">
<eq/>
<apply>
<diff/>
<bvar>
<ci> time </ci>
</bvar>
<ci> Ca_ER </ci>
</apply>
<apply>
<divide/>
<ci> J_ER </ci>
<ci> gamma_ER </ci>
</apply>
</apply>
<apply id="gamma_ER_calculation">
<eq/>
<ci> gamma_ER </ci>
<apply>
<divide/>
<apply>
<times/>
<ci> v_ER </ci>
<ci> k_ER </ci>
</apply>
<apply>
<times/>
<ci> v_i </ci>
<ci> k_i </ci>
</apply>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_1="total_cytoplasmic_Ca_flux" component_2="environment"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="Ca_extrusion_across_the_plasma_membrane" component_2="environment"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="Ca_uptake_by_SR_Ca_ATPase" component_2="environment"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="ER_Ca_release" component_2="environment"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="cytoplasmic_calcium" component_2="environment"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="intraluminal_calcium" component_2="environment"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="total_cytoplasmic_Ca_flux" component_2="Ca_extrusion_across_the_plasma_membrane"/>
<map_variables variable_1="J_ICa" variable_2="J_ICa"/>
</connection>
<connection>
<map_components component_1="total_cytoplasmic_Ca_flux" component_2="intraluminal_calcium"/>
<map_variables variable_1="v_i" variable_2="v_i"/>
<map_variables variable_1="k_i" variable_2="k_i"/>
</connection>
<connection>
<map_components component_1="Ca_extrusion_across_the_plasma_membrane" component_2="cytoplasmic_calcium"/>
<map_variables variable_1="Ca_i" variable_2="Ca_i"/>
<map_variables variable_1="J_pm" variable_2="J_pm"/>
</connection>
<connection>
<map_components component_1="Ca_uptake_by_SR_Ca_ATPase" component_2="cytoplasmic_calcium"/>
<map_variables variable_1="Ca_i" variable_2="Ca_i"/>
</connection>
<connection>
<map_components component_1="Ca_uptake_by_SR_Ca_ATPase" component_2="ER_Ca_release"/>
<map_variables variable_1="J_SERCA" variable_2="J_SERCA"/>
</connection>
<connection>
<map_components component_1="Ca_uptake_by_SR_Ca_ATPase" component_2="intraluminal_calcium"/>
<map_variables variable_1="J_SERCA" variable_2="J_SERCA"/>
</connection>
<connection>
<map_components component_1="ER_Ca_release" component_2="cytoplasmic_calcium"/>
<map_variables variable_1="J_ER" variable_2="J_ER"/>
<map_variables variable_1="Ca_i" variable_2="Ca_i"/>
</connection>
<connection>
<map_components component_1="ER_Ca_release" component_2="intraluminal_calcium"/>
<map_variables variable_1="J_ER" variable_2="J_ER"/>
<map_variables variable_1="Ca_ER" variable_2="Ca_ER"/>
</connection>
<connection>
<map_components component_1="cytoplasmic_calcium" component_2="intraluminal_calcium"/>
<map_variables variable_1="Ca_i" variable_2="Ca_i"/>
</connection>
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