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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.
Dataset
ICC confocal images: Protein aggregation and calcium dysregulation are the earliest hallmarks of familial Parkinson’s disease in human midbrain dopaminergic neurons
Our 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.
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Article
RASP: Optimal single fluorescent puncta detection in complex cellular backgrounds
Preprint: 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.
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Protocol
Live-cell imaging; mitochondrial reactive oxygen species
This protocol presents instructions for assessing mitochondrial souced reactive oxygen species using MitoTracker® Red CM-H2XRos dye (Thermo Fisher Scientific), a reduced non-fluorescent version of Mitotracker red that is fluorescent upon oxidation within mitochondria, which accumulates in mitochondria upon oxidation.
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Article
Protein aggregation and calcium dysregulation are the earliest hallmarks of synucleinopathy in human midbrain dopaminergic neurons
Preprint: Mutations in the SNCA gene causes PD and aggregates of alpha-synuclein are well known to be present in PD pathology. However, understanding the cellular sequence of events that occurs from mutation to pathology is unresolved. The authors find the temporal sequence of pathophysiological events that occur during neuronal differentiation that likely cause synucleopathies.
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Article
Pseudogenes limit the identification of novel common transcripts generated by their parent genes
Preprint: Genetic analyses are often complicated by genomic sequences with high sequence similarity. Here, the authors examined the role of pseudogenes on transcriptomic analyses using GB1 and GBAP1 as examples.
Themes
Article
Regulation of mitophagy by the NSL complex underlies genetic risk for Parkinson’s disease at 16q11.2 and MAPT H1 loci
These results enrich our understanding of physiological events regulating mitophagy and establish a novel pathway for drug targeting in neurodegeneration.
Themes
Article
Splicing accuracy varies across human introns, tissues, and age
This in-depth characterization of mis-splicing can have important implications for our understanding of the role of splicing inaccuracies in human disease and the interpretation of long-read RNA-sequencing data.
Themes
Article
Protein aggregation and calcium dysregulation are hallmarks of familial Parkinson’s disease in midbrain dopaminergic neurons
Our 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.
Teams
Themes
Protocol
SoRA microscopy protocol for imaging oligomers in human brain tissue
This protocol gives a step-by-step guide to imaging oligomers in human brain tissue using a spinning disk confocal microscope. The microscope used for this protocol was a commercial set up produced by 3i; however the techniques described can be used as general guidelines with alternative microscopes.
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Dataset
Pseudogenes limit the identification of novel common transcripts generated by their parent genes
Genomic sequences with high sequence similarity, such as parent-pseudogene pairs, cause short sequencing reads to align to multiple locations, thus complicating genomic analyses. However, their impact on transcriptomic analyses, including the estimation of gene expression and transcript annotation, has been less studied. The authors investigated the impact of pseudogenes on transcriptomic analyses.
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Code
Long-read RNA seq analysis using Talon
This is a snakemake pipeline that takes Oxford Nanopore Sequencing (ONT) data (fastq) as input, generates fastq stats using nanostat, performs fastq processing and filtering using pychopper, maps the reads to the genome using minimap2, and uses talon to assemble and quantify transcripts. It is forked from ANNSeq. The link includes the dag of the pipeline.
Themes
Protocol
Free-floating mouse brain immunohistochemistry
This protocol enables immunohistochemical staining of murine tissue with superior penetration of the tissue by the reagents due to the free-floating approach. Watch an interview about this protocol with Jonathan Breiter, MSc.
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Code
TX2P – Transcript to protein
TX2P 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.
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Article
ggtranscript: an R package for the visualization and interpretation of transcript isoforms using ggplot2
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.
Themes