A simplified cerebellar Purkinje neuron (the PPR model) (Brown et al. 2011)

 Download zip file   Auto-launch 
Help downloading and running models
Accession:126637
These models were implemented in NEURON by Sherry-Ann Brown in the laboratory of Leslie M. Loew. The files reproduce Figures 2c-f from Brown et al, 2011 "Virtual NEURON: a Strategy For Merged Biochemical and Electrophysiological Modeling".
Reference:
1 . Brown SA, Moraru II, Schaff JC, Loew LM (2011) Virtual NEURON: a strategy for merged biochemical and electrophysiological modeling. J Comput Neurosci 31(2):385-400 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell; Dendrite;
Brain Region(s)/Organism: Cerebellum;
Cell Type(s): Cerebellum purkinje cell;
Channel(s): I Na,p; I p,q; I A; I K; I M; I K,Ca; I Sodium; I Calcium; I Potassium;
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Dendritic Action Potentials; Simplified Models; Active Dendrites; Influence of Dendritic Geometry; Detailed Neuronal Models; Intrinsic plasticity; Methods; Synaptic Integration;
Implementer(s): Brown, Sherry-Ann [sabrown at student.uchc.edu];
Search NeuronDB for information about:  Cerebellum purkinje cell; I Na,p; I p,q; I A; I K; I M; I K,Ca; I Sodium; I Calcium; I Potassium;
These files reproduce Figures 2c-f from Brown et al, 2010 "Virtual
NEURON: a Strategy For Merged Biochemical and Electrophysiological
Modeling".

These models were implemented in NEURON by Sherry-Ann Brown in the
laboratory of Leslie M. Loew, to whom questions should be addressed.

Usage:
1. Unzip purkinje_ppr.zip into an empty directory.
2. Compile the mod files with mknrndll.
3. To reproduce results for the full model shown in Figures 2c and 2e,
double click on mosinit_spine and spine neck at spinydendrite133.hoc,
or execute nrngui mosinit_spine and spine neck at spinydendrite133.hoc
from the command line.
4. Panels will appear with labeled buttons that allow you to run the
simulation. Click on Init&Run to start the simulation. Voltage plots
will appear in the panels for the soma ("v."), spine, and a spiny
dendrite.
5. To reproduce results for the PPR model shown in Figures 2d and 2f,
double click on mosinit_reduced_PPR model.hoc, or execute nrngui
mosinit_reduced_PPR model.hoc from the command line.
6. Panels will appear with labeled buttons that allow you to run the
simulation. Click on Init&Run to start the simulation. Voltage plots
will appear in the panels for the soma ("v."), spine, and various
portions of dendrites.
7. To explore the PPR model using CVODE or other variable step
solvers, double click on mosinit_reduced_PPR model_cvode.hoc, or
execute nrngui mosinit_reduced_PPR model_cvode.hoc from the command
line.
8. Panels will appear with labeled buttons that allow you to run the
simulation. Click on Init&Run to start the simulation. Voltage plots
will appear in the pan els for the soma ("v."), spine, and various
portions of dendrites.

To reproduce Virtual Cell results for the PPR model shown in Figure 4
and some of the subsequent figures:

This model and all simulations can be accessed as a "Shared
BioModel" by logging in to VCell at http://www.vcell.org; the model
is entitled "Brown et al 2010 Purkinje MultiCompartmental Combined
Biochem and Electrophysiol" under the username Brown.

20111027 ModelDB Administrator: the two files KMcvode.mod Khhcvode.mod
had their integration methods changed from euler to cnexp.  See
http://www.neuron.yale.edu/phpBB/viewtopic.php?f=28&t=592
20120330 NaPcvode, NaFcvode, Khcvode, KDcvode, KC3cvode, KAcvode,
K23cvode, CaTcvode, CaP2cvode, CaEcvode were switched from euler to
cnexp and CalciumP.mod (with cad suffix) was switched from euler to
derivimplicit.  See above NEURON forum link.


Brown SA, Moraru II, Schaff JC, Loew LM (2011) Virtual NEURON: a strategy for merged biochemical and electrophysiological modeling. J Comput Neurosci 31(2):385-400[PubMed]

References and models cited by this paper

References and models that cite this paper

Berridge MJ, Lipp P, Bootman MD (2000) The versatility and universality of calcium signalling. Nat Rev Mol Cell Biol 1:11-21 [PubMed]

Bhalla US, Bilitch DH, Bower JM (1992) Rallpacks: a set of benchmarks for neuronal simulators. Trends Neurosci 15:453-8 [PubMed]

Booth V, Rinzel J, Kiehn O (1997) Compartmental model of vertebrate motoneurons for Ca2+-dependent spiking and plateau potentials under pharmacological treatment. J Neurophysiol 78:3371-85 [Journal] [PubMed]

Bower JM, Beeman D (2003) The book of GENESIS exploring realistic neural models with the GEneral NEural SImulation System (2nd ed) [Journal]

   Simulations of oscillations in piriform cortex (Wilson & Bower 1992) [Model]

Bower JM, Beeman D (2007) Constructing realistic neural simulations with GENESIS. Methods Mol Biol 401:103-25 [PubMed]

Brown SA, Morgan F, Watras J, Loew LM (2008) Analysis of phosphatidylinositol-4,5-bisphosphate signaling in cerebellar Purkinje spines. Biophys J 95:1795-812 [PubMed]

Burke RE, Fyffe RE, Moschovakis AK (1994) Electrotonic architecture of cat gamma motoneurons. J Neurophysiol 72:2302-16 [Journal] [PubMed]

   [24 reconstructed morphologies on NeuroMorpho.Org]

Bush PC, Sejnowski TJ (1993) Reduced compartmental models of neocortical pyramidal cells. J Neurosci Methods 46:159-66 [PubMed]

Clements JD, Redman SJ (1989) Cable properties of cat spinal motoneurones measured by combining voltage clamp, current clamp and intracellular staining. J Physiol 409:63-87 [PubMed]

De Schutter E, Bower JM (1994) An active membrane model of the cerebellar Purkinje cell. I. Simulation of current clamps in slice. J Neurophysiol 71:375-400 [Journal] [PubMed]

   Cerebellar purkinje cell (De Schutter and Bower 1994) [Model]

De Smedt H, Missiaen L, Parys JB, Henning RH, Sienaert I, Vanlingen S, Gijsens A, Himpens B, (1997) Isoform diversity of the inositol trisphosphate receptor in cell types of mouse origin. Biochem J 322 ( Pt 2):575-83

Destexhe A, Babloyantz A, Sejnowski TJ (1993) Ionic mechanisms for intrinsic slow oscillations in thalamic relay neurons. Biophys J 65:1538-52 [PubMed]

Di Gregorio E, Orsi L, Godani M, Vaula G, Jensen S, Salmon E, Ferrari G, Squadrone S, Abete M (2010) Two Italian families with ITPR1 gene deletion presenting a broader phenotype of SCA15. Cerebellum 9:115-23

Douglas R, Martin KAC (1992) Exploring cortical microcircuits: a combined anatomical, physiological, and computational approach Single Neuron Computation, Zometzer S:Davis :Mckenna T, ed. pp.381

Finch EA, Augustine GJ (2000) Local calcium signalling by inositol-1,4,5-trisphosphate in Purkinje cell dendrites. Nature 396:753-6 [PubMed]

Fleshman JW, Segev I, Burke RB (1988) Electrotonic architecture of type-identified alpha-motoneurons in the cat spinal cord. J Neurophysiol 60:60-85 [Journal] [PubMed]

Gilbert PF, Thach WT (1977) Purkinje cell activity during motor learning. Brain Res 128:309-28 [PubMed]

Hara K, Shiga A, Nozaki H, Mitsui J, Takahashi Y, Ishiguro H, Yomono H, Kurisaki H, Goto J, I (2008) Total deletion and a missense mutation of ITPR1 in Japanese SCA15 families. Neurology 71:547-51 [PubMed]

Harris KM, Stevens JK (1988) Dendritic spines of rat cerebellar Purkinje cells: serial electron microscopy with reference to their biophysical characteristics. J Neurosci 8:4455-69 [PubMed]

Hendrickson EB, Edgerton JR, Jaeger D (2011) The capabilities and limitations of conductance-based compartmental neuron models with reduced branched or unbranched morphologies and active dendrites. J. Comp. Neurosci. 30(2):301-321 [Journal] [PubMed]

   Comparison of full and reduced globus pallidus models (Hendrickson 2010) [Model]

Hernjak N, Slepchenko BM, Fernald K, Fink CC, Fortin D, Moraru II, Watras J, Loew LM (2005) Modeling and analysis of calcium signaling events leading to long-term depression in cerebellar Purkinje cells. Biophys J 89:3790-806 [PubMed]

Hines ML, Carnevale NT (1997) The NEURON simulation environment. Neural Comput 9:1179-209 [PubMed]

Hines ML, Carnevale NT (2001) NEURON: a tool for neuroscientists. Neuroscientist 7:123-35 [Journal] [PubMed]

   Spatial gridding and temporal accuracy in NEURON (Hines and Carnevale 2001) [Model]

Hodgkin AL, Huxley AF (1952) A quantitative description of membrane current and its application to conduction and excitation in nerve. J Physiol 117:500-44 [Journal] [PubMed]

   Squid axon (Hodgkin, Huxley 1952) (LabAXON) [Model]
   Squid axon (Hodgkin, Huxley 1952) (NEURON) [Model]
   Squid axon (Hodgkin, Huxley 1952) (SNNAP) [Model]
   Squid axon (Hodgkin, Huxley 1952) used in (Chen et al 2010) (R language) [Model]
   Squid axon (Hodgkin, Huxley 1952) (SBML, XPP, other) [Model]

Ito M, Kano M (1982) Long-lasting depression of parallel fiber-Purkinje cell transmission induced by conjunctive stimulation of parallel fibers and climbing fibers in the cerebellar cortex. Neurosci Lett 33:253-8 [PubMed]

Iwaki A, Kawano Y, Miura S, Shibata H, Matsuse D, Li W, Furuya H, Ohyagi Y, Taniwaki T, Kira (2008) Heterozygous deletion of ITPR1, but not SUMF1, in spinocerebellar ataxia type 16. J Med Genet 45:32-5 [PubMed]

Konnerth A, Dreessen J, Augustine GJ (1992) Brief dendritic calcium signals initiate long-lasting synaptic depression in cerebellar Purkinje cells. Proc Natl Acad Sci U S A 89:7051-5 [PubMed]

Loew LM, Schaff JC (2001) The Virtual Cell: a software environment for computational cell biology. Trends Biotechnol 19:401-6 [PubMed]

Major G, Larkman AU, Jonas P, Sakmann B, Jack JJ (1994) Detailed passive cable models of whole-cell recorded CA3 pyramidal neurons in rat hippocampal slices. J Neurosci 14:4613-38 [PubMed]

Manor Y, Gonczarowski J, Segev I (1991) Propagation of action potentials along complex axonal trees. Model and implementation. Biophys J 60:1411-23 [PubMed]

Matsumoto M, Nakagawa T, Inoue T, Nagata E, Tanaka K, Takano H, Minowa O, Kuno J, Sakakibara (1996) Ataxia and epileptic seizures in mice lacking type 1 inositol 1,4,5-trisphosphate receptor. Nature 379:168-71

McCormick DA, Huguenard JR (1992) A model of the electrophysiological properties of thalamocortical relay neurons. J Neurophysiol 68:1384-400 [Journal] [PubMed]

Miyasho T, Takagi H, Suzuki H, Watanabe S, Inoue M, Kudo Y, Miyakawa H (2001) Low-threshold potassium channels and a low-threshold calcium channel regulate Ca2+ spike firing in the dendrites of cerebellar Purkinje neurons: a modeling study. Brain Res 891:106-15 [Journal] [PubMed]

   Cerebellar purkinje cell: K and Ca channels regulate APs (Miyasho et al 2001) [Model]

Moraru II, Schaff JC, Slepchenko BM, Loew LM (2002) The virtual cell: an integrated modeling environment for experimental and computational cell biology. Ann N Y Acad Sci 971:595-6 [PubMed]

Napper RM, Harvey RJ (1988) Number of parallel fiber synapses on an individual Purkinje cell in the cerebellum of the rat. J Comp Neurol 274:168-77 [PubMed]

Napper RM, Harvey RJ (1988) Quantitative study of the Purkinje cell dendritic spines in the rat cerebellum. J Comp Neurol 274:158-67 [PubMed]

Ogura H, Matsumoto M, Mikoshiba K (2001) Motor discoordination in mutant mice heterozygous for the type 1 inositol 1,4,5-trisphosphate receptor. Behav Brain Res 122:215-9

Pinsky PF, Rinzel J (1994) Intrinsic and network rhythmogenesis in a reduced Traub model for CA3 neurons. J Comput Neurosci 1:39-60 [Journal] [PubMed]

   CA3 pyramidal cell: rhythmogenesis in a reduced Traub model (Pinsky, Rinzel 1994) [Model]

RALL W (1962) Electrophysiology of a dendritic neuron model. Biophys J 2(2)Pt 2:145-67 [PubMed]

Rall W (1969) Time constants and electrotonic length of membrane cylinders and neurons. Biophys J 9:1483-508 [PubMed]

Rall W, Agmon-snir H (1998) Cable theory for dendritic neurons Methods In Neuronal Modeling: From Ions To Networks, Koch C:Segev I, ed. pp.27

Rall W, Rinzel J (1973) Branch input resistance and steady attenuation for input to one branch of a dendritic neuron model. Biophys J 13:648-87 [PubMed]

Rapp M, Segev I, Yarom Y (1994) Physiology, morphology and detailed passive models of guinea-pig cerebellar Purkinje cells. J Physiol 474:101-18 [PubMed]

   [3 reconstructed morphologies on NeuroMorpho.Org]

Rapp M, Yarom Y, Segev I (1992) The impact of parallel fiber background activity on the cable properties of cerebellar Purkinje cells Neural Comput 4:518-533

Regehr WG, Mintz IM (1994) Participation of multiple calcium channel types in transmission at single climbing fiber to Purkinje cell synapses. Neuron 12:605-13 [PubMed]

Rinzel J, Rall W (1974) Transient response in a dendritic neuron model for current injected at one branch. Biophys J 14:759-90 [PubMed]

Sarkisov DV, Wang SS (2008) Order-dependent coincidence detection in cerebellar Purkinje neurons at the inositol trisphosphate receptor. J Neurosci 28:133-42 [PubMed]

Schaff J, Fink CC, Slepchenko B, Carson JH, Loew LM (1997) A general computational framework for modeling cellular structure and function. Biophys J 73:1135-46 [PubMed]

Shelton DP (1985) Membrane resistivity estimated for the Purkinje neuron by means of a passive computer model. Neuroscience 14:111-31 [PubMed]

Stratford KJ, Mason AJR, Larkman AU, Major G, Jack JJB (1989) The modelling of pyramidal neurones in the visual cortex The Computing Neuron, Durbin R:Miall C:Mitchison G, ed. pp.296

Street VA, Bosma MM, Demas VP, Regan MR, Lin DD, Robinson LC, Agnew WS, Tempel BL (1997) The type 1 inositol 1,4,5-trisphosphate receptor gene is altered in the opisthotonos mouse. J Neurosci 17:635-45

Takechi H, Eilers J, Konnerth A (2000) A new class of synaptic response involving calcium release in dendritic spines. Nature 396:757-60 [PubMed]

Traub RD, Wong RK, Miles R, Michelson H (1991) A model of a CA3 hippocampal pyramidal neuron incorporating voltage-clamp data on intrinsic conductances. J Neurophysiol 66:635-50 [Journal] [PubMed]

van de Leemput J, Chandran J, Knight MA, Holtzclaw LA, Scholz S, Cookson MR, Houlden H, Gwinn (2007) Deletion at ITPR1 underlies ataxia in mice and spinocerebellar ataxia 15 in humans. PLoS Genet 3:e108-6 [PubMed]

Wang SS, Denk W, Hausser M (2000) Coincidence detection in single dendritic spines mediated by calcium release. Nat Neurosci 3:1266-73 [PubMed]

Watanabe M (2008) Molecular mechanisms governing competitive synaptic wiring in cerebellar Purkinje cells. Tohoku J Exp Med 214:175-90 [PubMed]

Marasco A, Limongiello A, Migliore M (2012) Fast and accurate low-dimensional reduction of biophysically detailed neuron models Scientific Reports 2:928:1-7 [Journal] [PubMed]

   Ca1 pyramidal neuron: reduction model (Marasco et al. 2012) [Model]

Marasco A, Limongiello A, Migliore M (2013) Using Strahler`s analysis to reduce up to 200-fold the run time of realistic neuron model Sci. Rep. 3:2934 [Journal] [PubMed]

   Using Strahler`s analysis to reduce realistic models (Marasco et al, 2013) [Model]

McDougal RA, Bulanova AS, Lytton WW (2016) Reproducibility in computational neuroscience models and simulations IEEE Trans Biomed Eng 63(10):2021-2035 [Journal] [PubMed]

McDougal RA, Hines ML, Lytton WW (2013) Reaction-diffusion in the NEURON simulator. Front Neuroinform 7:28 [Journal] [PubMed]

   Reaction-diffusion in the NEURON simulator (McDougal et al 2013) [Model]

(60 refs)