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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.
Article
3D bioprinting of human neural tissues with functional connectivity
Probing how human neural networks operate is hindered by the lack of reliable human neural tissues amenable to the dynamic functional assessment of neural circuits. Team Scherzer developed a 3D bioprinting platform to assemble tissues with defined human neural cell types in a desired dimension using a commercial bioprinter.
Teams
Themes
Report
README guide for code
The purpose of this document is to provide guidance on how to write README files for code.
Dataset
Human Postmortem-Derived Brain Sequencing Collection (Harmonized Collection)
The Human Postmortem-Derived Brain Sequencing Collection is a harmonized repository comprised of sequencing data contributed by ASAP CRN teams.
Article
The Parkinson’s disease protein alpha-synuclein is a modulator of Processing-bodies and mRNA stability
Publication: The paper describes a new function for alpha synuclein – an ability to bind to structures known as a “P-body”. P-body machinery in the cell regulates the expression of our genes through mRNAs. When alpha-synuclein abnormally accumulates, the physiologic structure and functions of the P-body are lost.
Themes
Article
The Parkinson’s disease protein alpha-synuclein is a modulator of processing bodies and mRNA stability
Genetic modulation of P-body components alters αS toxicity, and human genetic analysis lends support to the disease-relevance of these interactions. Beyond revealing an unexpected aspect of αS function and pathology, the authors’ data highlight the versatility of conformationally plastic proteins with high intrinsic disorder.
Themes
Article
Deep sequencing of proteotoxicity modifier genes uncovers a Presenilin-2/beta-amyloid-actin genetic risk module shared among alpha-synucleinopathies
Conventional genetic analyses are underpowered to address whether neurodegenerative diseases linked to misfolding of the same protein share genetic risk drivers or whether different protein-aggregation pathologies in neurodegeneration are mechanistically related. The authors study patients based on protein aggregation phenotype to detect variants in a targeted set of genes.
Themes
Protocol
Sample collection and processing for RNA analysis
This protocol delineates the steps taken to collect frozen postmortem human brain samples and process them for RNA extraction and analysis.
Teams
Themes
Protocol
Confirming circRNA expression by qPCR
This protocol delineates a qPCR method to confirm the expression of circRNAs extracted from brain samples.
Teams
Themes
Article
Detecting Full-Length EccDNA with FLED and long-reads sequencing
The authors’ method takes advantage of nanopore long reads and enables unbiased reconstruction of full-length eccDNA sequences. FLED is implemented using Python3 which is freely available on GitHub (https://github.com/FuyuLi/FLED).
Teams
Themes
Article
Targeting cellular senescence with senotherapeutics: senolytics and senomorphics
Review: This article reviews the current state of the development of senolytics and senomorphics for the treatment of age-related diseases and disorders and extension of healthy longevity. In addition, the challenges of documenting senolytic and senomorphic activity in pre-clinical models and the current state of the clinical application of the different senotherapeutics are discussed.
Teams
Themes
Article
Towards a phenome-wide view of Parkinson’s disease
Preprint: The authors examine that relationship between PD and the environment by holistically characterizing environmental, health, and pharmacological traits associated with PD patients. They found numerous traits that were positively and negatively associated with PD.
Teams
Themes
Article
Nicotine-mediated rescue of α-synuclein toxicity requires synaptic vesicle glycoprotein 2
Published: Parkinson’s disease likely reflects a complex interaction among genetic and environmental factors. Here, the role of nicotine, SV2 and the alpha-synuclein were examined. The study suggests that SV2 may be needed for the protection nicotine provides from Parkinson’s-related neurotoxicity. View original preprint.
Teams
Themes
Protocol
Transferrin uptake assay to measure Clathrin-mediated endocytosis in HIPCS derived neurons
This protocol is used to measure Transferrin uptake as a way to investigate Clathrin-mediated endocytosis in HIPCS derived neurons, or other cell types.
Teams
Themes
Code
powereQTL – An R shiny application for calculating sample size and power of bulk tissue and single-cell eQTL analysis
An R shiny application for calculating sample size and power of bulk tissue and single-cell eQTL analysis
Teams
Themes