Catalog
ASAP is committed to accelerating the pace of discovery and informing a path to a cure for Parkinson’s disease through collaboration, research-enabling resources, and data sharing. We’ve created this catalog to showcase the research outputs and tools developed by ASAP-funded programs.
surmeierlab/EZT2022SA: EZTNotebooks
This repository contains five Jupyter Notebooks (Python 3.0) created or modified for specific use with action potential analysis for the Zampese, et.al. 2022 Science Advances paper.
Teams
Source data for Mendonça et al 2024
Source data and code from dopamine neuron activity encode the length of upcoming contralateral movement sequences by Mendonça et al 2024.
Source data for “α-Synuclein pathology disrupts mitochondrial function in dopaminergic and cholinergic neurons at-risk in Parkinson’s disease”
Images and raw data for the figures in the paper, “α-Synuclein pathology disrupts mitochondrial function in dopaminergic and cholinergic neurons at-risk in Parkinson’s disease.”
Tonic dendritic GABA release by substantia nigra dopaminergic neurons
Preprint: Recent studies have demonstrated the importance of extrastriatal dopamine release in motor deficits of Parkinson’s disease (PD). To characterize the actions of dopamine on substantia nigra pars reticulata (SNr) GABAergic neurons, optogenetic and electrophysiological tools were used in ex vivo mouse brain slices to monitor synaptic transmission arising from neurons.
Dopamine neuron activity encodes the length of upcoming contralateral movement sequences
Published: Dopamine neurons (DANs) in the substantia nigra pars compacta (SNc) have been related to movement vigor, and loss of these neurons leads to bradykinesia in Parkinson’s disease. Here the authors investigate whether DANs encode a general motivation signal or modulate movement kinematics. View original preprint.
RectiPy software package
Recurrent neural network training in Python (RectiPy) is a software package developed by Richard Gast that allows for lightweight implementations of recurrent neural networks (RNNs) based on ordinary or delayed differential equations. Here, the team provides a tool that allows for the implementation of biologically informed spiking neural networks and optimizes the parameters of these networks via gradient descent.
Teams
State-dependent GABAergic regulation of striatal spiny projection neuron excitability: NEURON + Python model of striatal projection neurons
This repository contains a NEURON + Python model of striatal projection neurons (or SPNs) designed to simulate the interaction between GABAergic and glutamatergic synaptic inputs.
Teams
Disrupted sleep-wake regulation in the MCI-Park mouse model of Parkinson’s disease
Published: To understand PD-associated sleep-wake abnormalities, a new progressive model of PD – the MCI-Park mouse – was studied. Near the transition to the parkinsonian state, these mice exhibited significantly altered sleep-wake regulation, including increased wakefulness, decreased non-rapid eye movement (NREM) sleep, increased sleep fragmentation, reduced rapid eye movement (REM) sleep, and altered EEG activity patterns. View original preprint.
Teams
Sleep-wake recording in Dan Lab
Surgery and setups for recording 24-hour natural sleep/wake cycles in mice.
Teams
Rethinking the network determinants of motor disability in Parkinson’s disease
While the basal ganglia circuit model underpinning the notion that striatal dopamine (DA) depletion was the critical determinant of network pathophysiology underlying the motor symptoms of Parkinson’s disease, the hypothesis itself has never been directly tested. It is time for a new model of the network determinants of motor disability in PD.
Teams
Gavage – food supplementation for stalled weight gain in mice
Feeding protocol for Ndufs2fl/fl mice,
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Macroscopic dynamics of neural networks with heterogeneous spiking thresholds
Published: The authors develop a new computational model to represent different neuron types and spiking dynamics. The model is comprised of biophysical state variables and parameters, incorporates realistic spike resetting conditions, and accounts for heterogeneity in neural spiking thresholds. These features allow for a broad applicability of the model as well as for a direct comparison to experimental data. View original preprint.
Teams
α-Synuclein pathology disrupts mitochondrial function in dopaminergic and cholinergic neurons at-risk in Parkinson’s disease
The mechanisms by which intracellular aSYN pathology contributes to dysfunction and degeneration of neurons in the brain are still unclear. Genetic and physiological methods were used to monitor mitochondrial function in substantia nigra pars compacta (SNc) dopaminergic and pedunculopontine nucleus (PPN) cholinergic neurons after stereotaxic injection of aSYN pre-formed fibrils (PFFs) into the mouse brain.
Teams
Motor learning selectively strengthens cortical and striatal synapses of motor engram neurons Dataset
This upload includes 1) ImageJ macros / scripts for minor automated cell counting for brain slides with immunostaining and 2) MATLAB functions / scripts for minor automated spine location cluster analysis (nearest neighbor distance / index).
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