Output 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 created this catalog to showcase the research outputs and tools developed by ASAP-funded programs.
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Output Type
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Program
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CRN Team Name
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Theme
An ImageJ/FIJI Preprocessing Workflow for Multi-Series Confocal Microscopy Datasets Prior To CellProfiler Analysis
A workflow using ImageJ/FIJI aims to create three-slice MIPs from multi-series .czi files to capture weak signals. It involves extracting datasets, creating projections, and saving images for efficient analysis in CellProfiler.
State-dependent modulation of spiny projection neurons controls levodopa-induced dyskinesia in a mouse model of Parkinson’s disease
LID is poorly understood, our research on dyskinetic mice show SPNs' properties oscillate during LID and are influenced by dopamine and acetylcholine signaling. Targeting M1 receptors in iSPNs reduced LID severity and improved levodopa effects.
Excitatory synaptic structural abnormalities produced by templated aggregation of α-syn in the basolateral amygdala
PD and DLB involve α-syn inclusions in the amygdala affecting cognition and emotions. Cortico-amygdala synapses with α-syn aggregates show increased volume of synapses, potentially contributing to behavioral impairments.
Striatal dopamine signals internal states related to behavioral performance over prolonged timescales in monkeys
Dopamine plays dual roles in behavior: fast reward prediction errors and slow motivational states. Dopamine release in monkeys' brain regions tracks performance changes, suggesting a single signal for both functions.
Single cell eQTL mapping reveals convergent glial–neuronal risk architecture in Parkinson’s disease
Population-scale, disease-context aware meta single-nucleus eQTLs mapping (N = 1,197) in nine cell types from cortex and substantia nigra identifies 125 risk genes and cell types for PD GWAS signals.
MANUAL CELL COUNTING
MANUAL CELL COUNTING
CREsted: modeling genomic and synthetic cell-type-specific enhancers across tissues and species
CREsted, a sequence-based deep learning model, analyzes genomic regulatory code, decodes enhancer grammar, and designs synthetic enhancers. It preprocesses single-cell data, models chromatin accessibility, and compares cell states across tissues.
EnvA-N2c-deltaG-H2B-HA-FlpO
Generated for anatomical anterograde tracing experiments by Columbia University Zuckerman Institute Molecular Tools Core Facility (RRID:SCR_026201).
pAAVDJ-Ef1a-FDOI-mScarlet
Generated for anatomical tracing experiments by Columbia University Zuckerman Institute Molecular Tools Core Facility (RRID:SCR_026201).
FushikiA_etal_2024: PD Model Mice Study – v1.0 Code
Repository offers tools for processing, analyzing, and visualizing data related to PD and dopaminergic neurons.
A druggable ATP13A3–antizyme switch controls adaptive polyamine uptake in cancer
Cellular polyamine depletion for cancer treatment is hindered by compensatory uptake. ATP13A3, not ATP13A2, is the key polyamine importer affected by DFMO. Antizyme inhibits uptake by ATP13A3, suggesting a targetable strategy for cancer therapy.
A single Citrobacter rodentium infection in Pink1 knockout and wild type mice leads to regional blood-brain-barrier perturbation and limited microglial activation without dopamine neuron axon terminal loss
Research suggests immune system activation may contribute to Parkinson’s disease development. Mild infections can increase BBB permeability, triggering brain inflammation in genetically susceptible individuals, potentially leading to PD pathology.
Dataset for “A single Citrobacter rodentium infection in Pink1 knockout and wild-type mice leads to regional blood-brain-barrier perturbation and limited microglial activation without dopamine neuron axon terminal loss”
Immune system activation may contribute to PD development. Infection increases BBB permeability in mice, leading to brain inflammation. This suggests infections could trigger PD in genetically susceptible individuals.
Generation of DATcrePink1 Knockout Mice Expressing tdTomato in Dopaminergic Neurons
Protocol details generation of DATcrePink1 mice expressing tdTomato in dopaminergic neurons. Covers Pink1 KO, HET, WT variants, animal housing, breeding, and genotyping procedures.
Semi-automated quantification of microglial CD68 and Iba1 immunohistochemistry signal in mouse brain slices
A standardized method for semi-automated detection and quantification of CD68 and Iba1 in brain sections using image acquisition, AI segmentation, and data analysis.
