pCAG- WIPI2dK128E- cs-TEV -STREP
By onPlasmid: Mammalian expression of human WIPI2d K128E with C-terminal Strep.
Preparation and imaging of enriched Golgi from GolgiTAG-IP using Transmission Electron Microscopy
By onA protocol where Golgi, isolated from cells by GolgiTAG immunoprecipitation (IP) can be prepared and imaged using TEM. This protocol can also be used to image any organelles isolated using various organelle-IP protocols that are available.
pCMV-pOTC-3H-GFP
By onExpression of GFP fused with pOTC-3H, a leader peptide from mitochondrial matrix enzyme ornithine transcarbamylase and a thermostable three helix-bundle
Single-cell spatial transcriptomic and translatomic profiling of dopaminergic neurons in health, aging, and disease
By onThis study used two complementary approaches in a Parkinson's disease mouse model and revealed insights into dopaminergic neuron characteristics, aging markers, and potential disease genes like CASR.
Generation of CRISPR constructs
By onThis protocol details the procedure of generation of CRISPR constructs.
pU6-pegRNA-LRRK2-G2019S-3b
By onIt can be used to introduce LRRK2-G2019S mutation using prime editing.
Photometry Analysis Code
By onThis set of functions extracts GCaMP Fiber Photometry data obtained with a TDT system, performs isosbestic and exponential correction, and computes the number and amplitude of transients over time. The code was originally used for the following experiment: MFB-lesioned 6-OHDA D1-cre or A2A-cre mice were injected with a cre-dependent GCaMP6f in dorsolateral striatum and implanted with 400um optical fibers. Mice were placed in an open field arena and recorded for 30 minutes before levodopa injection, and 120 minutes after levodopa injection. The experiment includes video from 2 cameras and a TTL pulse from an Arduino indicating the time when levodopa was injected.
Image processing and 3D reconstruction
By onProtocol describing image processing and 3D reconstruction.
Sample Collection and Measurement of Serum Neurofilament Light (NfL)
By onThis protocol details the steps for the preparation of serum from human blood samples and the measurement of NfL concentration using the NF-Light Advantage kit on the HD-X Analyzer (Quanterix, Billerica, MA).
Expression and purification GST-tagged ATG13:ATG101 constructs
By onExpression and purification of GST-tagged ATG13/ATG101 constructs.
pCAG-TSF-ATG13 (363-517)
By onPlasmid: Mammalian expression of TwinStrep-Flag tagged ATG13 (363-517).
Pseudogenes limit the identification of novel common transcripts generated by their parent genes
By onGenomic sequences with high sequence similarity cause short sequencing reads to align to multiple locations, thus complicating genomic analyses. The authors investigated the impact of pseudogenes on transcriptomic analyses.
AAV injection in the nodose ganglia of mouse
By onThe gut-brain axis links the visceral organs to the medulla oblongata via the vagus nerve. Accessing to the afferent vagal pathway is important to dissect the role of cell populations in the bidirectional communication between brain and body. The jugular-nodose ganglion (JNG) complex contains the cell bodies of many heterogenous neural subpopulations responsible for sensing the physiological and pathological conditions of the thoracic and abdominal organs. However, the study of these ganglia is challenging in small animals due to size and location. Hence, in this protocol we describe a practical surgical approach to the vagal trunk, and the JNG complex in mice.
Incentivized Vigor Task
By onCode for an fMRI task in which human participants use a joystick to make speeded reaches to cued targets. This task examines incentive effects on movement, part of the Socal Kinesia and Incentivization for Parkinson's Disease (SKIP) dataset.
pCAG-mcherry- WIPI2dC93E-cs- TEV -STREP
By onPlasmid for mammalian expression of human WIPI2d C93E with N-terminal mCherry and C-terminal Strep.
Single-cell dissociation of brain organoids
By onThis protocol details single cell dissociation of brain organoids. This protocol is part of a Collection of protocols (dx.doi.org/10.17504/protocols.io.8epv593dng1b/v1) for the paper "Glucocerebrosidase, a Parkinson´s disease-associated protein, is imported into mitochondria and regulates complex I assembly and function" (https://doi.org/10.21203/rs.3.rs-1521848/v1)
RNA extraction and quantitative PCR to assay inflammatory gene expression
By onProtocol for RT-qPCR to test levels of NF-kB response genes in a cell model transiently over-expressing Parkin. We found upregulation of key pro-inflammatory genes normalized to housekeeping gene, Gapdh.
Open Field Test to assess motor coordination in a mouse parkinsonian model
By onThe Open Field task is a simple sensorimotor test used to determine general activity levels, gross locomotor activity, and exploration habits in rodent models of CNS disorders. Open Field Test
Detection of Tau ubiquitylation
By onThis protocol is associated with the following preprint, published on February 19th 2022: The AAA+ chaperone VCP disaggregates Tau fibrils and generates aggregate seeds Itika Saha, Patricia Yuste-Checa, Miguel Da Silva Padilha, Qiang Guo, Roman Körner, Hauke Holthusen, Victoria A. Trinkaus, Irina Dudanova, Rubén Fernández-Busnadiego, Wolfgang Baumeister, David W. Sanders, Saurabh Gautam, Marc I. Diamond, F. Ulrich Hartl, Mark S. Hipp bioRxiv 2022.02.18.481043; doi: https://doi.org/10.1101/2022.02.18.481043
