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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
“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.
Teams
Themes
Protocol
3′ mRNA-sequencing
Protocol for 3′ mRNA sequencing of mouse gastrointestinal tract tissues.
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
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.
Teams
Themes
Code
3D printed MR-compatible stereotaxic frame for NHPs
A compact MRI-compatible stereotaxis suitable for a variety of NHP species (Macaca mulatta, Macaca fascicularis, and Cebus apella) that allows multimodal alignment through technique-specific fiducial markers.
Teams
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.
Teams
Themes
Teams
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.
Teams
Themes
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.
Teams
Themes
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.
Teams
Protocol
A human development-based protocol for the differentiation of human ESCs into midbrain dopaminergic neurons
Protocol for the differentiation of human embryonic stem cells into midbrain dopaminergic neurons. This protocol recapitulates the activation of developmental pathways known to be important for mDA neuron development and mimics key sequences of events taking place in human midbrain development.
Teams
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.
Teams
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.
Teams
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.
Teams
Themes