Pyramidal tract neurons and Parkinson’s disease in simulated mouse primary motor cortex

Pyramidal tract neurons are the most direct output to muscles from the primary motor cortex (M1). Liqiang Chu et al (2021) have shown that layer 5 pyramidal tract neurons (PT5B) decrease in excitability in parkinsonian as compared with control M1 in mice treated with 6-OHDA. We built this simulation, based on a detailed motor cortex implementation in NetPyNE, to see how the changed PT5B neuron excitability changes M1 spiking dynamics.

NetPyNE is a Python package for creating biological neural networks using the NEURON simulator.

The data that support the findings of this study are openly available on the DANDI Archive (RRID:SCR_017571) at https://doi.org/10.48324/dandi.001444/0.250805.2002

View and analyze our data in DANDI Archive through remote streaming, as demonstrated in the Jupyter notebooks Control_Quiet_Wakefulness.ipynb, Parkinsonian_Quiet_Wakefulness.ipynb, Control_Movement.ipynb, Parkinsonian_Movement.ipynb.

Read the paper Donald W. Doherty et al. (2025).

Cite the code:

Acknowlegements

This research was funded by Aligning Science Across Parkinson's [ASAP-020572] through the Michael J. Fox Foundation for Parkinson's Research (MJFF).

Parameter settings

Control rest

cfg.ihGbar = 0.75

gbar = 0.0055 # nap # all secs

gpeak = 7.251280172010002e-05 # kBK # soma only

cfg.gnafbar = 0.00086 # NaT # all secs

cfg.ratesLong = {'TPO': [0,5], 'TVL': [0,2.5], 'S1': [0,5], 'S2': [0,5], 'cM1': [0,2.5], 'M2': [0,2.5], 'OC': [0,5]}

Parkinsonian rest

cfg.ihGbar = 0.75

gbar = 0.0055 # nap # all secs

gpeak = 7.251280172010002e-04 # kBK # soma only

cfg.gnafbar = 0.0172 # NaT # all secs

cfg.ratesLong = {'TPO': [0,5], 'TVL': [0,2.5], 'S1': [0,5], 'S2': [0,5], 'cM1': [0,2.5], 'M2': [0,2.5], 'OC': [0,5]}

Control activated (movement)

cfg.ihGbar = 0.25

gbar = 0.0055 # nap # all secs

gpeak = 7.251280172010002e-05 # kBK # soma only

cfg.gnafbar = 0.00086 # NaT # all secs

cfg.ratesLong = {'TPO': [0,10], 'TVL': [0,10], 'S1': [0,5], 'S2': [0,5], 'cM1': [0,2.5], 'M2': [0,2.5], 'OC': [0,5]}

Parkinsonian activated (movement)

cfg.ihGbar = 0.25

gbar = 0.0055 # nap # all secs

gpeak = 7.251280172010002e-04 # kBK # soma only

cfg.gnafbar = 0.0172 # NaT # all secs

cfg.ratesLong = {'TPO': [0,10], 'TVL': [0,10], 'S1': [0,5], 'S2': [0,5], 'cM1': [0,2.5], 'M2': [0,2.5], 'OC': [0,5]}