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

“LRRK2 phosphorylation of Rab GTPases in Parkinson’s disease”

Review: This paper highlights new findings related to LRRK2-mediated phosphorylation of Rab GTPases and their consequences.

Article

17q21.31 sub-haplotypes underlying H1-associated risk for Parkinson’s disease are associated with LRRC37A/2 expression in astrocytes

Published: This paper examines the H1 haplotype of the MAPT 17q.21.31 locus to better understand its contribution to PD. The authors found three novel H1 sub-haplotype blocks across the 17q.21.31 locus that is associated with PD risk.

 

Protocol

3D FIBSEM CLEM

This protocol details the procedure of Correlative Light Microscopy and Electron Microscopy (CLEM) with 3D Focus Ion Beam Scanning Electron Microscopy (FIBSEM) technique in Zeiss Crossbeam 550 FIBSEM system.

Protocol

3D-correlative FIB-milling and Cryo-ET of Autophagic structures in Yeast Cells

This protocol describes how to plunge-freeze yeast on EM grids and how to target autophagic structures by combining cryo confocal fluorescence data to FIB-milling and tomogram acquisition.

Blog Post

A Blueprint for Training and Development in GP2

This blog written by Dr. Alastair Noyce and Dr. Sara Bandres-Ciga discusses GP2’s plan to train students and investigators and the new considerations as a result of the COVID-19 pandemic.

Protocol

A computational pipeline to quantify primary cilia in mouse embryonic fibroblasts with CellProfiler

This protocol works with .czi format images which are acquired using a Zeiss laser scanning confocal microscope and are maximum intensity projected.

Article

A feed-forward pathway drives LRRK2 kinase membrane recruitment and apparent activation

Published: Mutations in LRRK2 that cause PD activate its kinase activity. These activating mutations of LRRK2 phosphorylate Rab GTPases. The authors define two binding sites on LRRK2 that deliver it to the surfaces of specific intracellular membranes, and then retain it there after an initial phosphorylation event. View original preprint here.

Article

A fluid-walled microfluidic platform for human neuron microcircuits and directed axotomy

Preprint: Cortical axons in conduits are severed by a media jet; then, brain-derived neurotrophic factor and striatal neurons in distal chambers promote axon regeneration. As additional conduits and chambers are easily added, this opens up the possibility of mimicking complex neuronal networks and screening drugs for their effects on connectivity.

Protocol

A fluorescence-based in vitro scrambling assay for yeast MCP1 and human XK

Detailed procedure of purification, reconstitution, and scrambling assay for both MCP1 and XK.

Article

A leaky gut dysregulates gene networks in the brain associated with immune activation, oxidative stress, and myelination in a mouse model of colitis

Preprint: The team provides a comprehensive evaluation of multiple systems in a prevalent experimental model of intestinal permeability, which will inform future studies using this model and others, assist in the identification of druggable targets in the gut-brain axis, and contribute to our understanding of the concomitance of intestinal and neuropsychiatric dysfunction.

Blog Post

A letter to the patient community from Randy Schekman, ASAP Scientific Director

This blog written by Dr. Randy Schekman and Benjamin Stecher describes the motivation and beginnings of the ASAP initiative. It also includes a letter written to the PD comunity by Dr. Schekman.

Article

A Markov random field model-based approach for differentially expressed gene detection from single-cell RNA-seq data

The MARBLES, a Markov Random Field model-based approach for differentially expressed gene detection from scRNA-seq data can capture cell-type relationships and account for sample variation by modeling cell-type-specific pseudobulk data. The authors used simulation results to compare this approach to existing methods from two scRNA-seq datasets.

Article

A mono- and intralink filter (mi-filter) to reduce false identifications in cross-linking mass spectrometry data

The authors show that this simple and intuitive filter has a dramatic effect on different types of cross-linking data ranging from individual protein complexes over medium-complexity affinity enrichments to proteome-wide cell lysates and significantly reduces the number of false-positive identifications for inter-protein links in all these types of XL-MS data.