- Author:
- rcai987 <devnull@localhost>
- Date:
- 2015-02-05 13:15:09+13:00
- Desc:
- Added annotations to marhl_haberichter_brumen_heinrich_2000.cellml model
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/marhl_haberichter_brumen_heinrich_2000/rawfile/f53926c781c9fba3ca4214cfd236154576d1668c/marhl_haberichter_brumen_heinrich_2000.cellml
<?xml version='1.0'?>
<!-- FILE : marhl_model_2000.xml
CREATED : 4th April 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 Marhl et al's
2000 model of Ca2+ oscillations and the role of mitochondria and cytosolic proteins.
CHANGES:
18/07/2002 - CML - Added more metadata.
09/04/2003 - AAC - Added publication date information.
-->
<model cmeta:id="marhl_2000" name="marhl_2000" 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#">
<documentation xmlns="http://cellml.org/tmp-documentation">
<article>
<articleinfo>
<title>Complex Calcium Oscillations and the Role of Mitochondria and Cytosolic Proteins</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 are consistent.
</para>
</section>
<sect1 id="sec_structure">
<title>Model Structure</title>
<para>
ABSTRACT: Intracellular calcium oscillations, which are oscillatory changes of cytosolic calcium concentration in response to agonist stimulation, are experimentally well observed in various living cells. Simple calcium oscillations represent the most common pattern and many mathematical models have been published to describe this type of oscillation. On the other hand, relatively few theoretical studies have been proposed to give an explanation of complex intracellular calcium oscillations, such as bursting and chaos. In this paper, we develop a new possible mechanism for complex calcium oscillations based on the interplay between three calcium stores in the cell: the endoplasmic reticulum (ER), mitochondria and cytosolic proteins. The majority ( approximately 80%) of calcium released from the ER is first very quickly sequestered by mitochondria. Afterwards, a much slower release of calcium from the mitochondria serves as the calcium supply for the intermediate calcium exchanges between the ER and the cytosolic proteins causing bursting calcium oscillations. Depending on the permeability of the ER channels and on the kinetic properties of calcium binding to the cytosolic proteins, different patterns of complex calcium oscillations appear. With our model, we are able to explain simple calcium oscillations, bursting and chaos. Chaos is also observed for calcium oscillations in the bursting mode.
</para>
<para>
The original paper reference is cited below:
</para>
<para>
Complex calcium oscillations and the role of mitochondria and cytosolic proteins, Marko Marhl, Thomas Haberichter, Milan Brumen and Reinhart Heinrich, 2000, <emphasis>Biosystems</emphasis>, 57, 75-86. <ulink url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11004387&dopt=Abstract">PubMed ID: 11004387</ulink>
</para>
<informalfigure float="0" id="fig_cell_diagram">
<mediaobject>
<imageobject>
<objectinfo>
<title>cell schematic for the model</title>
</objectinfo>
<imagedata fileref="marhl_2000.png"/>
</imageobject>
</mediaobject>
<caption>Schematic diagram of the model sysytem.</caption>
</informalfigure>
</sect1>
</article>
</documentation>
<units name="micromolar">
<unit prefix="micro" units="mole"/>
<unit exponent="-1" units="litre"/>
</units>
<units name="flux">
<unit units="micromolar"/>
<unit exponent="-1" units="second"/>
</units>
<units name="first_order_rate_constant">
<unit exponent="-1" units="second"/>
</units>
<units name="second_order_rate_constant">
<unit exponent="-1" units="micromolar"/>
<unit exponent="-1" units="second"/>
</units>
<component name="environment">
<variable name="time" public_interface="out" units="second"/>
</component>
<component cmeta:id="id_000000001" name="total_calcium">
<variable cmeta:id="total_calcium_Ca_Pr" name="Ca_Pr" public_interface="out" units="micromolar"/>
<variable cmeta:id="id_000000002" initial_value="90.0" name="Ca_tot" units="micromolar"/>
<variable name="rho_ER" public_interface="in" units="dimensionless"/>
<variable name="beta_ER" public_interface="in" units="dimensionless"/>
<variable name="rho_m" public_interface="in" units="dimensionless"/>
<variable name="beta_m" public_interface="in" units="dimensionless"/>
<variable cmeta:id="id_000000003" name="Ca_cyt" public_interface="in" units="micromolar"/>
<variable cmeta:id="id_000000004" name="Ca_ER" public_interface="in" units="micromolar"/>
<variable cmeta:id="id_000000005" name="Ca_m" public_interface="in" units="micromolar"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="Ca_Pr_calculation">
<eq/>
<ci> Ca_Pr </ci>
<apply>
<minus/>
<ci> Ca_tot </ci>
<apply>
<plus/>
<ci> Ca_cyt </ci>
<apply>
<times/>
<apply>
<divide/>
<ci> rho_ER </ci>
<ci> beta_ER </ci>
</apply>
<ci> Ca_ER </ci>
</apply>
<apply>
<times/>
<apply>
<divide/>
<ci> rho_m </ci>
<ci> beta_m </ci>
</apply>
<ci> Ca_m </ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component cmeta:id="id_000000006" name="total_protein">
<variable cmeta:id="id_000000007" name="Pr" public_interface="out" units="micromolar"/>
<variable cmeta:id="id_000000008" initial_value="120.0" name="Pr_tot" units="micromolar"/>
<variable cmeta:id="id_000000009" name="Ca_Pr" public_interface="in" units="micromolar"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="Pr_calculation">
<eq/>
<ci> Pr </ci>
<apply>
<minus/>
<ci> Pr_tot </ci>
<ci> Ca_Pr </ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="id_000000010" name="cytosolic_calcium">
<variable initial_value="0.05" name="Ca_cyt" public_interface="out" units="micromolar"/>
<variable initial_value="0.1" name="k_plus" units="second_order_rate_constant"/>
<variable initial_value="0.01" name="k_minus" units="first_order_rate_constant"/>
<variable name="Pr" public_interface="in" units="micromolar"/>
<variable name="Ca_Pr" public_interface="in" units="micromolar"/>
<variable name="J_ch" public_interface="in" units="flux"/>
<variable cmeta:id="id_000000015" name="J_leak" public_interface="in" units="flux"/>
<variable cmeta:id="id_000000019" name="J_pump" public_interface="in" units="flux"/>
<variable name="J_out" public_interface="in" units="flux"/>
<variable name="J_in" public_interface="in" units="flux"/>
<variable name="time" public_interface="in" units="second"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="Ca_cyt_diff_eq">
<eq/>
<apply>
<diff/>
<bvar>
<ci> time </ci>
</bvar>
<ci> Ca_cyt </ci>
</apply>
<apply>
<minus/>
<apply>
<plus/>
<ci> J_ch </ci>
<ci> J_leak </ci>
<ci> J_out </ci>
<apply>
<times/>
<ci> k_minus </ci>
<ci> Ca_Pr </ci>
</apply>
</apply>
<apply>
<plus/>
<ci> J_pump </ci>
<ci> J_in </ci>
<apply>
<times/>
<ci> k_plus </ci>
<ci> Ca_cyt </ci>
<ci> Pr </ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component cmeta:id="id_000000011" name="ER_calcium">
<variable cmeta:id="id_000000012" initial_value="1.0" name="Ca_ER" public_interface="out" units="micromolar"/>
<variable cmeta:id="id_000000013" initial_value="0.01" name="rho_ER" public_interface="out" units="dimensionless"/>
<variable cmeta:id="id_000000014" initial_value="0.0025" name="beta_ER" public_interface="out" units="dimensionless"/>
<variable name="J_ch" public_interface="in" units="flux"/>
<variable cmeta:id="id_000000016" name="J_leak" public_interface="in" units="flux"/>
<variable cmeta:id="id_000000020" name="J_pump" public_interface="in" units="flux"/>
<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>
<times/>
<apply>
<divide/>
<ci> beta_ER </ci>
<ci> rho_ER </ci>
</apply>
<apply>
<minus/>
<ci> J_pump </ci>
<apply>
<plus/>
<ci> J_ch </ci>
<ci> J_leak </ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="mitochondrial_calcium">
<variable initial_value="0.4" name="Ca_m" public_interface="out" units="micromolar"/>
<variable initial_value="0.01" name="rho_m" public_interface="out" units="dimensionless"/>
<variable initial_value="0.0025" name="beta_m" public_interface="out" units="dimensionless"/>
<variable name="J_in" public_interface="in" units="flux"/>
<variable name="J_out" public_interface="in" units="flux"/>
<variable name="time" public_interface="in" units="second"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="Ca_m_diff_eq">
<eq/>
<apply>
<diff/>
<bvar>
<ci> time </ci>
</bvar>
<ci> Ca_m </ci>
</apply>
<apply>
<times/>
<apply>
<divide/>
<ci> beta_m </ci>
<ci> rho_m </ci>
</apply>
<apply>
<minus/>
<ci> J_in </ci>
<ci> J_out </ci>
</apply>
</apply>
</apply>
</math>
</component>
<component cmeta:id="id_000000022" name="ATP_dependent_Ca_uptake_into_the_ER">
<variable cmeta:id="ATP_dependent_Ca_uptake_into_the_ER_J_pump" name="J_pump" public_interface="out" units="flux"/>
<variable cmeta:id="id_000000021" initial_value="20.0" name="k_pump" units="first_order_rate_constant"/>
<variable name="Ca_cyt" public_interface="in" units="micromolar"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="J_pump_calculation">
<eq/>
<ci> J_pump </ci>
<apply>
<times/>
<ci> k_pump </ci>
<ci> Ca_cyt </ci>
</apply>
</apply>
</math>
</component>
<component cmeta:id="id_000000023" name="Ca_efflux_from_the_ER">
<variable cmeta:id="Ca_efflux_from_the_ER_J_ch" name="J_ch" public_interface="out" units="flux"/>
<variable cmeta:id="id_000000024" initial_value="4100.0" name="k_ch" units="first_order_rate_constant"/>
<variable initial_value="5.0" name="K1" units="micromolar"/>
<variable name="Ca_cyt" public_interface="in" units="micromolar"/>
<variable name="Ca_ER" public_interface="in" units="micromolar"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="J_ch_calculation">
<eq/>
<ci> J_ch </ci>
<apply>
<times/>
<ci> k_ch </ci>
<apply>
<divide/>
<apply>
<power/>
<ci> Ca_cyt </ci>
<cn cellml:units="dimensionless" xmlns:cellml="http://www.cellml.org/cellml/1.0#"> 2.0 </cn>
</apply>
<apply>
<plus/>
<apply>
<power/>
<ci> K1 </ci>
<cn cellml:units="dimensionless" xmlns:cellml="http://www.cellml.org/cellml/1.0#"> 2.0 </cn>
</apply>
<apply>
<power/>
<ci> Ca_cyt </ci>
<cn cellml:units="dimensionless" xmlns:cellml="http://www.cellml.org/cellml/1.0#"> 2.0 </cn>
</apply>
</apply>
</apply>
<apply>
<minus/>
<ci> Ca_ER </ci>
<ci> Ca_cyt </ci>
</apply>
</apply>
</apply>
</math>
</component>
<component cmeta:id="id_000000018" name="Ca_leak_flux_from_the_ER">
<variable cmeta:id="Ca_leak_flux_from_the_ER_J_leak" name="J_leak" public_interface="out" units="flux"/>
<variable cmeta:id="id_000000017" initial_value="0.05" name="k_leak" units="first_order_rate_constant"/>
<variable name="Ca_cyt" public_interface="in" units="micromolar"/>
<variable name="Ca_ER" public_interface="in" units="micromolar"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="J_leak_calculation">
<eq/>
<ci> J_leak </ci>
<apply>
<times/>
<ci> k_leak </ci>
<apply>
<minus/>
<ci> Ca_ER </ci>
<ci> Ca_cyt </ci>
</apply>
</apply>
</apply>
</math>
</component>
<component cmeta:id="id_000000025" name="mitochondrial_Ca_uptake">
<variable cmeta:id="mitochondrial_Ca_uptake_J_in" name="J_in" public_interface="out" units="flux"/>
<variable cmeta:id="id_000000026" initial_value="300.0" name="k_in" units="flux"/>
<variable initial_value="0.8" name="K2" units="micromolar"/>
<variable name="Ca_cyt" public_interface="in" units="micromolar"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="J_in_calculation">
<eq/>
<ci> J_in </ci>
<apply>
<times/>
<ci> k_in </ci>
<apply>
<divide/>
<apply>
<power/>
<ci> Ca_cyt </ci>
<cn cellml:units="dimensionless" xmlns:cellml="http://www.cellml.org/cellml/1.0#"> 8.0 </cn>
</apply>
<apply>
<plus/>
<apply>
<power/>
<ci> K2 </ci>
<cn cellml:units="dimensionless" xmlns:cellml="http://www.cellml.org/cellml/1.0#"> 8.0 </cn>
</apply>
<apply>
<power/>
<ci> Ca_cyt </ci>
<cn cellml:units="dimensionless" xmlns:cellml="http://www.cellml.org/cellml/1.0#"> 8.0 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component cmeta:id="id_000000027" name="mitochondrial_Ca_release">
<variable name="J_out" public_interface="out" units="flux"/>
<variable initial_value="125.0" name="k_out" units="first_order_rate_constant"/>
<variable initial_value="0.00625" name="k_m" units="first_order_rate_constant"/>
<variable initial_value="5.0" name="K3" units="micromolar"/>
<variable name="Ca_cyt" public_interface="in" units="micromolar"/>
<variable name="Ca_m" public_interface="in" units="micromolar"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply id="J_out_calculation">
<eq/>
<ci> J_out </ci>
<apply>
<times/>
<apply>
<plus/>
<apply>
<times/>
<ci> k_out </ci>
<apply>
<divide/>
<apply>
<power/>
<ci> Ca_cyt </ci>
<cn cellml:units="dimensionless" xmlns:cellml="http://www.cellml.org/cellml/1.0#"> 2.0 </cn>
</apply>
<apply>
<plus/>
<apply>
<power/>
<ci> K3 </ci>
<cn cellml:units="dimensionless" xmlns:cellml="http://www.cellml.org/cellml/1.0#"> 2.0 </cn>
</apply>
<apply>
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<ci> Ca_cyt </ci>
<cn cellml:units="dimensionless" xmlns:cellml="http://www.cellml.org/cellml/1.0#"> 2.0 </cn>
</apply>
</apply>
</apply>
</apply>
<ci> k_m </ci>
</apply>
<ci> Ca_m </ci>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_1="cytosolic_calcium" component_2="environment"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="ER_calcium" component_2="environment"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="mitochondrial_calcium" component_2="environment"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="total_calcium" component_2="ER_calcium"/>
<map_variables variable_1="rho_ER" variable_2="rho_ER"/>
<map_variables variable_1="beta_ER" variable_2="beta_ER"/>
<map_variables variable_1="Ca_ER" variable_2="Ca_ER"/>
</connection>
<connection>
<map_components component_1="total_calcium" component_2="mitochondrial_calcium"/>
<map_variables variable_1="rho_m" variable_2="rho_m"/>
<map_variables variable_1="beta_m" variable_2="beta_m"/>
<map_variables variable_1="Ca_m" variable_2="Ca_m"/>
</connection>
<connection>
<map_components component_1="total_calcium" component_2="cytosolic_calcium"/>
<map_variables variable_1="Ca_cyt" variable_2="Ca_cyt"/>
<map_variables variable_1="Ca_Pr" variable_2="Ca_Pr"/>
</connection>
<connection>
<map_components component_1="total_calcium" component_2="total_protein"/>
<map_variables variable_1="Ca_Pr" variable_2="Ca_Pr"/>
</connection>
<connection>
<map_components component_1="cytosolic_calcium" component_2="total_protein"/>
<map_variables variable_1="Pr" variable_2="Pr"/>
</connection>
<connection>
<map_components component_1="cytosolic_calcium" component_2="ATP_dependent_Ca_uptake_into_the_ER"/>
<map_variables variable_1="Ca_cyt" variable_2="Ca_cyt"/>
<map_variables variable_1="J_pump" variable_2="J_pump"/>
</connection>
<connection>
<map_components component_1="cytosolic_calcium" component_2="Ca_efflux_from_the_ER"/>
<map_variables variable_1="Ca_cyt" variable_2="Ca_cyt"/>
<map_variables variable_1="J_ch" variable_2="J_ch"/>
</connection>
<connection>
<map_components component_1="cytosolic_calcium" component_2="Ca_leak_flux_from_the_ER"/>
<map_variables variable_1="Ca_cyt" variable_2="Ca_cyt"/>
<map_variables variable_1="J_leak" variable_2="J_leak"/>
</connection>
<connection>
<map_components component_1="cytosolic_calcium" component_2="mitochondrial_Ca_release"/>
<map_variables variable_1="Ca_cyt" variable_2="Ca_cyt"/>
<map_variables variable_1="J_out" variable_2="J_out"/>
</connection>
<connection>
<map_components component_1="cytosolic_calcium" component_2="mitochondrial_Ca_uptake"/>
<map_variables variable_1="Ca_cyt" variable_2="Ca_cyt"/>
<map_variables variable_1="J_in" variable_2="J_in"/>
</connection>
<connection>
<map_components component_1="ER_calcium" component_2="ATP_dependent_Ca_uptake_into_the_ER"/>
<map_variables variable_1="J_pump" variable_2="J_pump"/>
</connection>
<connection>
<map_components component_1="ER_calcium" component_2="Ca_efflux_from_the_ER"/>
<map_variables variable_1="Ca_ER" variable_2="Ca_ER"/>
<map_variables variable_1="J_ch" variable_2="J_ch"/>
</connection>
<connection>
<map_components component_1="ER_calcium" component_2="Ca_leak_flux_from_the_ER"/>
<map_variables variable_1="Ca_ER" variable_2="Ca_ER"/>
<map_variables variable_1="J_leak" variable_2="J_leak"/>
</connection>
<connection>
<map_components component_1="mitochondrial_calcium" component_2="mitochondrial_Ca_release"/>
<map_variables variable_1="Ca_m" variable_2="Ca_m"/>
<map_variables variable_1="J_out" variable_2="J_out"/>
</connection>
<connection>
<map_components component_1="mitochondrial_calcium" component_2="mitochondrial_Ca_uptake"/>
<map_variables variable_1="J_in" variable_2="J_in"/>
</connection>
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<rdf:type>
<rdf:Description rdf:about="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
</rdf:type>
<rdf:_1 xml:lang="en">calcium dynamics</rdf:_1>
<rdf:_2 xml:lang="en">electrophysiology</rdf:_2>
<rdf:_3 xml:lang="en">mitochondria</rdf:_3>
<rdf:_4 xml:lang="en">oscillator</rdf:_4>
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A mathematical model of Ca2+ oscillations and the role of mitochondria
and cytosolic proteins.
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This is the CellML description of Marhl et al's 2000 model of Ca2+
oscillations and the role of mitochondria and cytosolic proteins.
With their model they are able to explain simple Ca2+ oscillations,
bursting and chaos.
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Complex calcium oscillations and the role of mitochondria and cytosolic proteins
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