Genetic meta-analysis of levodopa induced dyskinesia in Parkinson’s disease
By savannah onPublished: Based on a functional annotation analysis on chromosome 1, we determined that changes in DNAJB4 gene expression, close to LRP8, are an additional potential cause of increased susceptibility to LiD. Baseline anxiety status was significantly associated with LiD.
Mitochondrial degradation: Mitophagy and beyond
By savannah onPublished: The molecular signals driving varied pathways are discussed, including the cellular and physiological contexts under which the different degradation pathways are engaged.
A RAB7A phosphoswitch coordinates rubicon homology protein regulation of PINK1/Parkin-dependent mitophagy
By savannah onPreprint: Structural and functional data support a model in which the TBK1-dependent phosphorylation of RAB7A serves as a switch, promoting mitophagy by relieving Rubicon inhibition and favoring Pacer activation.
Therapeutic potential of PTB inhibition through converting glial cells to neurons in the brain
By savannah onPublished: Multiple lines of evidence suggest that Ptbp1 depletion can convert a selective subpopulation of glial cells into neurons and, via this and other mechanisms, reverse deficits in a Parkinson's disease model, emphasizing the importance of future efforts in exploring this therapeutic strategy.
Endosomal escape of RNA therapeutics: How do we solve this rate-limiting problem?
By savannah onPublished: Over 15 FDA approved drugs, numerous ongoing clinical trials, RNA therapeutics, such as small interfering RNAs (siRNAs) and antisense oligonucleotides (ASOs), have shown potential to treat human disease. RNA therapeutics can be used to treat widespread human disease, the rate-limiting delivery problem of endosomal escape must be solved in a nontoxic manner.
Feed-forward metabotropic signaling by Cav1 Ca2+ channels supports pacemaking in pedunculopontine cholinergic neurons
By savannah onPublished: Like a handful of other neuronal types in the brain, cholinergic neurons (CNs) in the pedunculopontine nucleus (PPN) are lost in the course of Parkinson’s disease (PD). PPN CNs have a distinctive physiological phenotype that shares some, but not all, of the features of other neurons that are selectively vulnerable in PD. View original preprint.
Functional characterization of ATP13A2 variants associated with distinct neurodegenerative disorders
By savannah onPreprint: Loss-of-function variants in ATP13A2 are causative for Kufor-Rakeb syndrome (KRS, a recessive juvenile-onset parkinsonism with dementia) and also identified in early-onset PD (EOPD) and hereditary spastic paraplegia (HSP). The ALS and MSA variants presented a subtle functional defect, questioning whether these heterozygous variants are pathogenic and ATP13A2 dysfunction may cause MSA or ALS.
Manual Tracking/measure_ECM.ijm
By savannah onA script to generate circular ROIs in each frame of a timelapse, using a previously generated track as reference. Used to measure fluorescence intensity (i.e., extracellular matrix content) along a microglia track. To be used as a continuation of 2_tracking.ijm.
Manual Tracking/tracking.ijm
By savannah onA script to store in ImageJ’s ROImanager the tracks generated using Manual Tracking plugin, for later use (drawing tracks, frame-by-frame analysis). To be used as a continuation of 1_image_prep.ijm.
Manual Tracking/image_prep.ijm
By savannah onA script to register 2-channel timelapse images using HyperStackReg, using only 1 of the channels to compute transformation. The script also enhances contrast and prepares the image for manual tracking.
Free-floating mouse brain immunohistochemistry
By savannah onThis 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.
Primary data associated with the manuscript “CURTAIN – A Unique Web-based tool for exploration and sharing of MS-based proteomics data” (doi: https://doi.org/10.1101/2023.07.25.550405)
By savannah onRaw immunoblotting data and their quantitation and graphs obtained using GraphPad Prism; PCR and sequencing data confirming that PPM1H-BromoTag clone E5 (used for all experiments in the manuscript) is a homozygous clone.
A computational pipeline to quantify primary cilia in mouse embryonic fibroblasts with CellProfiler
By savannah onThis protocol works with .czi format images which are acquired using a Zeiss laser scanning confocal microscope and are maximum intensity projected.
Preparation of unilamellar liposomes
By savannah onThe authors present here a protocol for preparing liposomes that can be used to monitor binding of proteins to vesicles of various membrane curvatures. The authors used this to study the association of the PPM1H phosphatase with highly curved membranes due to its N-terminal amphipathic helix.
Gibson Assembly Cloning
By savannah onGibson assembly requires a vector backbone and one or more inserts that have been PCR amplified. The inserts should have 15-20 base pairs of overlap at ligation sites, so primers used to amplify the inserts should contain a tail overhang with this homology. The vector backbone should be linear.
Lentivirus plasmid: pLV[Exp]-U6>PINK1_P1_Seq3-hPGK>mApple
By savannah onPlasmid vector encoding a sgRNA sequence which targets the human PINK1 promoter for CRISPRi, under a U6 promoter and a mApple fluorescent reporter. Generated by Vectorbuilder in the pLV backbone.
Fecal metagenomic sequencing data for PD patients and controls from the BioCollective
By savannah onFecal metagenomic sequencing data associated with Boktor et al., 2023. This dataset includes samples from the BioCollective cohort.