Cortical oscillations and the basal ganglia (Fountas & Shanahan 2017)

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Accession:236306
"Although brain oscillations involving the basal ganglia (BG) have been the target of extensive research, the main focus lies disproportionally on oscillations generated within the BG circuit rather than other sources, such as cortical areas. We remedy this here by investigating the influence of various cortical frequency bands on the intrinsic effective connectivity of the BG, as well as the role of the latter in regulating cortical behaviour. To do this, we construct a detailed neural model of the complete BG circuit based on fine-tuned spiking neurons, with both electrical and chemical synapses as well as short-term plasticity between structures. As a measure of effective connectivity, we estimate information transfer between nuclei by means of transfer entropy. Our model successfully reproduces firing and oscillatory behaviour found in both the healthy and Parkinsonian BG. We found that, indeed, effective connectivity changes dramatically for different cortical frequency bands and phase offsets, which are able to modulate (or even block) information flow in the three major BG pathways. ..."
Reference:
1 . Fountas Z, Shanahan M (2017) The role of cortical oscillations in a spiking neural network model of the basal ganglia. PLoS One 12:e0189109 [PubMed]
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Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism: Subthalamic Nucleus; Basal ganglia;
Cell Type(s): Subthalamic nucleus principal GABA cell; Globus pallidus principal GABA cell; Substantia nigra pars reticulata principal GABA cell; Subthalamus nucleus projection neuron; Globus pallidus neuron;
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: Brian;
Model Concept(s): Short-term Synaptic Plasticity; Parkinson's; Information transfer; Pathophysiology; Synaptic Plasticity; Oscillations; Activity Patterns;
Implementer(s): Fountas, Zafeirios [zfountas at imperial.ac.uk];
Search NeuronDB for information about:  Substantia nigra pars reticulata principal GABA cell; Globus pallidus principal GABA cell; Subthalamic nucleus principal GABA cell;
from brian import mV, nS, ms

__author__ = "Zafeirios Fountas"
__credits__ = ["Murray Shanahan", "Mark Humphries",  "Rob Leech", "Jeanette Hellgren Kotaleski"]
__license__ = "GPLv3"
__version__ = "0.1"
__maintainer__ = "Zafeirios Fountas"
__email__ = "fountas@outlook.com"
__status__ = "Published"

data = dict()
data["MSN"] = dict()
data["MSN"]["tau"] = {
    "AMPA" :   { "value" : 6 * ms,    "source" : "Moyer etal 2007, Humphries 2014", "unit" : "ms"},
    "NMDA" :   { "value" : 160 * ms,  "source" : "Moyer etal 2007, Humphries 2014", "unit" : "ms"},
    "GABA" :   { "value" : 4 * ms,    "source" : "Moyer etal 2007, Humphries 2014", "unit" : "ms"}
}
data["MSN"]["E"] = {
    "AMPA" :   { "value" : 0 * mV,    "source" : "Moyer etal 2007, Humphries 2014", "unit" : "mV"},
    "NMDA" :   { "value" : 0 * mV,    "source" : "Moyer etal 2007, Humphries 2014", "unit" : "mV"},
    "GABA" :   { "value" : -60 * mV,  "source" : "Moyer etal 2007, Humphries 2014", "unit" : "mV"},
}
data["MSN"]["G"] = {
    "Ctx-MSN" : {
        "AMPA":   { "value" : 0.6,    "source" : "tuned to mach the FRs when only base cortical input is given","unit" : "nS"},
        "NMDA":   { "value" : 0.3,    "source" : "2:1 AMPA:NMDA ratio-Moyer 2007", "unit" : "nS"},
        "GABA":   { "value" : 0.0,    "source" : "None",  "unit" : "nS"},
    },
    "MSN-MSN" : {
        "AMPA":   { "value" : 0.0,    "source" : "None", "unit" : "nS"},
        "NMDA":   { "value" : 0.0,    "source" : "None", "unit" : "nS"},
        "GABA":   { "value" : 0.75,   "source" : "Koos etal 2004 - Humphries 2014",  "unit" : "nS"},
    },
    "FSI-MSN" : {
        "AMPA":   { "value" : 0.0,    "source" : "None", "unit" : "nS"},
        "NMDA":   { "value" : 0.0,    "source" : "None", "unit" : "nS"},
        "GABA":   { "value" : 3.75,   "source" : "Tuning in Humphries 2014", "unit" : "nS"},
    }
}

data["FSI"] = dict()
data["FSI"]["gap"] = {
    "tau" :   { "value" : 5 * ms,    "source" : "Humphries 2014", "unit" : "ms"},
    "g" :     { "value" : 5 * nS,    "source" : "Humphries 2014", "unit" : "nS"},
}
data["FSI"]["tau"] = {
    "AMPA" :   { "value" : 6 * ms,    "source" : "Moyer etal 2007, Humphries 2014", "unit" : "ms"},
    "GABA" :   { "value" : 4 * ms,    "source" : "Moyer etal 2007, Humphries 2014", "unit" : "ms"}
}
data["FSI"]["E"] = {
    "AMPA" :   { "value" : 0 * mV,    "source" : "Moyer etal 2007, Humphries 2014", "unit" : "mV"},
    "GABA" :   { "value" : -60 * mV,  "source" : "Moyer etal 2007, Humphries 2014", "unit" : "mV"},
}
data["FSI"]["G"] = {
    "Ctx-FSI" : {
        "AMPA":   { "value" : 0.55,    "source" : "My tuning (12.5-70Hz) with gap junctions", "unit" : "nS"},
    },
    "FSI-FSI" : {
        "GABA":   { "value" : 1.1,    "source" : "Gittis etal 2010 - used in Humphries 2014", "unit" : "nS"},
    }
}

data["STN"] = dict()
data["STN"]["tau"] = {
    "AMPA" :   { "value" : 2 * ms,    "source" : "Default value", "unit" : "ms"},
    "NMDA" :   { "value" : 100 * ms,  "source" : "Default value", "unit" : "ms"},
    "GABA" :   { "value" : 8 * ms,    "source" : "Lindahl 2013 from Baufreton 2005", "unit" : "ms"}
}
data["STN"]["E"] = {
    "AMPA" :   { "value" : 0 * mV,    "source" : "", "unit" : "mV"},
    "NMDA" :   { "value" : 0 * mV,    "source" : "", "unit" : "mV"},
    "GABA" :   { "value" : -84 * mV,  "source" : "Lindahl 2013 from Baufreton 2009", "unit" : "mV"},
}
data["STN"]["G"] = {
    "AMPA":      { "value" : 0.388,  "source" : "My tuning - Achieves 20 Hz (40Hz in high mode) FR when no GPe inhibition - works with different scales", "unit" : "nS"},
    "NMDA":      { "value" : 0.233,  "source" : "ampa*0.6 - Gotz:1997", "unit" : "nS"},
    "GABA":      { "value" : 0.518,  "source" : "My tuning - Achieves 10 Hz FR when GPe inhibition when C=300.", "unit" : "nS"}
}


data["GPe"] = dict()
data["GPe"]["tau"] = {
    "MSN-GPe" : {
        "GABA" :   { "value" : 6 * ms,    "source" : "Lindahl", "unit" : "ms"}
    },
    "GPe-GPe" : {
        "GABA" :   { "value" : 5 * ms,    "source" : "Lindahl", "unit" : "ms"}
    },
    "STN-GPe" : {
        "AMPA" :   { "value" : 2 * ms,    "source" : "General value, Abbott", "unit" : "ms"},
        "NMDA" :   { "value" : 100 * ms,  "source" : "General value, Abbott", "unit" : "ms"},
    }
}
data["GPe"]["E"] = {
    "AMPA" :   { "value" : 0 * mV,    "source" : "", "unit" : "mV"},
    "NMDA" :   { "value" : 0 * mV,    "source" : "", "unit" : "mV"},
    "GABA" :   { "value" : -65 * mV,  "source" : "RavAcha2005, Lindahl2013", "unit" : "mV"}
}
data["GPe"]["G"] = {
    "MSN-GPe" : {
        "GABA":      { "value" : 5.435, "source" : "c_GA_2-2", "unit" : "nS"}
    },
    "GPe-GPe" : {
        "GABA":      { "value" : 0.765, "source" : "c_GA_2-2", "unit" : "nS"}
    },
    "STN-GPe" : {
        "AMPA":      { "value" : 1.447, "source" : "Tuned to cause 30Hz in GPe when STN in 10Hz!", "unit" : "nS"},
        "NMDA":      { "value" : 0.518, "source" : "ampa*0.36 - Gotz:1997", "unit" : "nS"}
    } 
}

data["SNr"] = dict()
data["SNr"]["tau"] = {
    "GPe-SNr" : {
        "GABA" :   { "value" : 2.1 * ms,  "source" : "Lindahl 2013 from Conelly 2010", "unit" : "ms"}
    },
    "SNr-SNr" : {
        "GABA" :   { "value" : 3 * ms,    "source" : "General value", "unit" : "ms"}
    },
    "MSN-SNr" : {
        "GABA" :   { "value" : 5.2 * ms,  "source" : "Lindahl 2013 from Conelly 2010", "unit" : "ms"}
    },
    "STN-SNr" : {
        "AMPA" :   { "value" : 2 * ms,    "source" : "Default AMPA value", "unit" : "ms"},
        "NMDA" :   { "value" : 100 * ms,  "source" : "Default NMDA value", "unit" : "ms"},
    }

}
data["SNr"]["E"] = {
    "AMPA" :   { "value" : 0 * mV,    "source" : "Default AMPA value", "unit" : "mV"},
    "NMDA" :   { "value" : 0 * mV,    "source" : "Default NMDA value", "unit" : "mV"},
    "GABA" :   { "value" : -80 * mV,  "source" : "Default GABA value", "unit" : "mV"},
}
data["SNr"]["G"] = {
    "GPe-SNr" : {
        "GABA":      { "value" : 93.0,  "source" : "Manual tuning", "unit" : "nS"}
    },
    "SNr-SNr" : {
        "GABA":      { "value" : 0.2,  "source" : "Manual tuning", "unit" : "nS"}
    },
    "MSN-SNr" : {
        "GABA":      { "value" : 4.5,  "source" : "Manual tuning", "unit" : "nS"}
    },
    "STN-SNr" : {
        "AMPA":      { "value" : 14.0,"source" : "Local optimization", "unit" : "nS"},
        "NMDA":      { "value" : 5.88, "source" : "ampa*0.42 - Gotz:1997", "unit" : "nS"},
    }
}