Single-cell Whole Genome Amplification (scWGA) of human post-mortem brain samples isolated by Laser Capture Microdissection (LCM)
By savannah onThis protocol uses Laser Capture Microdissection (LCM) technology on human post-mortem brain tissue slides with rapid Giemsa staining to isolate single nuclei for Single-cell Whole Genome Amplification (scWGA) in order to do low coverage (<1x) single-cell whole genome sequencing to detect mega-base somatic Copy Number Variations (CNVs).
ICC confocal images: Protein aggregation and calcium dysregulation are the earliest hallmarks of familial Parkinson’s disease in human midbrain dopaminergic neurons
By savannah onOur differentiation paradigm generates an efficient model for studying disease mechanisms in PD, and highlights that protein misfolding to generate intraneuronal oligomers is one of the earliest critical events driving disease in human neurons, rather than a late-stage hallmark of the disease.
RASP: Optimal single fluorescent puncta detection in complex cellular backgrounds
By savannah onPublished: This sensitive, computationally efficient approach enables fluorescent puncta and cellular features to be distinguished in cellular and tissue environments with a sensitivity down to the level of the single protein. View original preprint.
TX2P – Transcript to protein
By savannah onTX2P allows for automated integration of mass spectometry data in long-read RNA-sequencing workflow. It does so by predicting open reading frames for each transcripts within an input GTF/GFF file, translates it into peptide sequences and then searches for those predicted proteins in mass spec datasets using MetaMorpheus.
Gavage – food supplementation for stalled weight gain in mice
By Emma Sherrell onFeeding protocol for Ndufs2fl/fl mice,
Disrupted sleep-wake regulation in the MCI-Park mouse model of Parkinson’s disease
By Emma Sherrell onPublished: 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.
State-dependent GABAergic regulation of striatal spiny projection neuron excitability: NEURON + Python model of striatal projection neurons
By Emma Sherrell onThis repository contains a NEURON + Python model of striatal projection neurons (or SPNs) designed to simulate the interaction between GABAergic and glutamatergic synaptic inputs.
Preparation of tissue for Ribo-Tag/RNAseq analysis
By Emma Sherrell onThis protocols describes the RiboTag virus vectors injected into mouse brain, tissue dissection, immunoprecipitation and RNA extraction for RNAseq.
Sleep-wake recording in Dan Lab
By Emma Sherrell onSurgery and setups for recording 24-hour natural sleep/wake cycles in mice.
Rethinking the network determinants of motor disability in Parkinson’s disease
By Emma Sherrell onWhile 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.
RectiPy software package
By Emma Sherrell onRecurrent 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.
α-Synuclein pathology disrupts mitochondrial function in dopaminergic and cholinergic neurons at-risk in Parkinson’s disease
By Emma Sherrell onThe 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.
Motor learning selectively strengthens cortical and striatal synapses of motor engram neurons Dataset
By Emma Sherrell onThis 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).
surmeierlab/EZT2022SA: EZTNotebooks
By Emma Sherrell onThis 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.
Source data for “Ca2+ channels couple spiking to mitochondrial metabolism in substantia nigra dopaminergic neurons”
By Emma Sherrell onSource data for publication: "Ca2+ channels couple spiking to mitochondrial metabolism in substantia nigra dopaminergic neurons."
Dynamic behaviour restructuring mediates dopamine-dependent credit assignment
By Emma Sherrell onPublished: Reinforcement mechanism promotes not only reinforcement, but gradual refinement of the entire behavioral repertoire to assign credit to specific actions and action sequences that lead to dopamine release.
Day2023 dataset
By Emma Sherrell onDatasets for all figures 1-8 in: GABAergic regulation of striatal spiny projection neuron excitability depends upon their activity state Image is taken from Fig 1B inset and illustrates RiboTag-eGFP in SPNs of the striatum.
Day2023 supplementary dataset
By Emma Sherrell onDatasets for all supplementary figures S1-4 in GABAergic regulation of striatal spiny projection neuron excitability depends upon their activity state (2023).
Day2024 R code and analysis
By Emma Sherrell onThis script and accompanying folder containing *.csv files of data should reproduce figures 1-4 and supplementary figure S1 of the manuscript in GABAergic regulation of striatal spiny projection neuron excitability depends upon their activity state (2023).
Scalable, flexible carbon fiber electrode thread arrays for three-dimensional probing of neurochemical activity in deep brain structures of rodents
By Emma Sherrell onThe authors' CFET array has the potential to unlock a wide range of applications, from uncovering the role of neuromodulators in synaptic plasticity, to addressing critical safety barriers in clinical translation towards diagnostic and adaptive treatment in Parkinson’s disease and major mood disorders.
