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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.
Code
FIJI Syn_Bot Macro
At a neuronal synapse, presynaptic and postsynaptic terminals are ~50nm apart, and thus immunohistochemical staining of a protein from each compartment will give a colocalized signal due to the resolution limits of traditional fluorescence microscopy. This macro counts the number of colocalized synaptic puncta in fluorescence microscopy images.
Teams
Article
Astrocytic LRRK2 controls synaptic connectivity through ERM phosphorylation
This work reveals a causal link between the astrocytic and synaptic dysfunction induced by the PD-linked mutation, LRRK2 G2019S, providing a non-cell autonomous mechanism for rescuing aberrant cortical wiring
Teams
Article
The integrated stress response in brain diseases: A double-edged sword for proteostasis and synapses
The integrated stress response (ISR) is a conserved biochemical pathway that regulates protein synthesis. As such, the ISR is implicated in a wide range of diseases, including brain disorders. In this review, the authors consider the ISR’s contribution to brain disorders through the lens of its potential effects on synaptic plasticity.
Teams
Code
Installing FIJI and SynBot (Windows version)
Video instructions for installing FIJI and SynBot and a simple SynBot run for Windows operating system.
Teams
Code
ilastik install and run for Syn Bot (Mac version)
Video instructions for installing ilastik, training an ilastik project, and using the ilastik project for simple SynBot run for Mac operating system.
Teams
Code
ilastik install and run for Syn Bot (Windows version)
Video instructions for installing ilastik, training an ilastik project, and using the ilastik project for simple SynBot run for Windows operating system.
Teams
Code
Synapse quantification with Puncta Analyzer
Protocol for installing Puncta Analyzer and using it to analyze synapse images.
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Article
SynBot: An open-source image analysis software for automated quantification of synapses
Quantifying the number of synapses from light microscopy images enables screening the impacts of experimental manipulations on synapse development. This approach utilizes low-throughput analysis methods that are challenging to learn and results are variable between experimenters. The authors developed SynBot, which automates imaging analysis.
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Article
Selective dopaminergic neurotoxicity modulated by inherent cell-type specific neurobiology
This review focuses on the inherent neurobiology of nigral DAergic neurons and how such neurobiology impacts the primary mechanism of neurotoxicity.
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Protocol
Designing sgRNA oligos and inserting guides into the GEARBOCS vector
Protocol for designing sgRNAs for genes using GEARBOCS vector backbone enabling astrocyte-specific genetic manipulation in CRISPR/Cas9 mice for in vivo assays.
Teams
Dataset
An open source head-fixation and implant-protection system for mice – Dataset
The authors present a suite of open source, customizable head fixation designs with standard variants including head-fix hardware as well as implant protection systems.
Teams
Article
GEARBOCS: An adeno associated virus tool for in vivo gene editing in astrocytes
GEARBOCS is a non-invasive method for precise gene editing in astrocytes using CRISPR/Cas9. It allows knockout, tagging, and reporter knock-in strategies, revealing the roles of Sparcl1 and Vamp2 in synapse maintenance in the mouse visual cortex.
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Protocol
Culturing 3T3 cells for validating GEARBOCS constructs
This protocol is for culturing Cas9 NIH/3T3 cells for the validation of GEARBOCS 2.0 and similar constructs for use in in vivo assays.
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