Evaluation of an adapted semi-automated DNA extraction for human salivary shotgun metagenomics
By savannah onPublished: This study demonstrates that the authors’ semi-automated protocol is suitable for shotgun metagenomic analysis, while allowing for a better sample treatment logistic with reduced technical variability and without compromising the structure of the oral microbiome. View original preprint.
Western blot – alpha-synuclein
By savannah onThis protocol describes how to detect alpha-synuclein in protein derived from STC-1 cells by western blot using DAB/peroxidase or ECL to visualize the bands.
α-Synuclein expression in response to bacterial ligands and metabolites in gut enteroendocrine cells – an in vitro proof of concept study
By savannah onPublished: Elevated intracellular α-synuclein increases the likelihood of aggregation and conversion to toxic forms. Factors derived from bacteria induce α-synuclein accumulation in STC-1 cells. Provided support for a mechanism by which exposure of enteroendocrine cells to specific bacterial factors found in PD gut dysbiosis might facilitate accumulation, transmission of α-synuclein pathology from the gut to the brain. View original preprint.
circRNA custom code
By savannah onCustom code associated with (Dong et al., Nature Communications, in press) is publicly available at https://github.com/sterding/circRNA.
circRNA dataset
By savannah onNew data set on circRNA in laser-captured neuron samples from 190 human brains of healthy controls, prodromal PD, and clinical PD (Dong et al., Nature Communications, in press). The RNA-seq raw FASTQ data and normalized expression matrix of all circRNAs in this study have been deposited in GEO under accession number GSE218203.
FM1-43 endocytic uptake assay in HIPSC derived neurons
By savannah onWhen the cells undergo another stimulation (through KCL or electrical), the FM1-43 dye containing vesicles will be released through exocytosis, thus, resulting in a decrease in the FM1-43 fluorescence intensity.
Nuclei isolation and sorting from frozen human temporal cortex
By savannah onThis protocol is about nuclei isolation and sorting from frozen human temporal cortex.
Transferrin uptake assay to measure Clathrin-mediated endocytosis in HIPCS derived neurons
By savannah onThis protocol is used to measure Transferrin uptake as a way to investigate Clathrin-mediated endocytosis in HIPCS derived neurons, or other cell types.
α-synuclein promotes neuronal dysfunction and death by disrupting the binding of ankyrin to ß-spectrin
By savannah onPublished: The authors’ findings define a specific molecular mechanism by which elevated levels of α-synuclein in Parkinson’s disease and related α-synucleinopathies leads to neuronal dysfunction and death. View original preprint.
The Parkinson’s disease protein alpha-synuclein is a modulator of processing bodies and mRNA stability
By savannah onGenetic modulation of P-body components alters αS toxicity, and human genetic analysis lends support to the disease-relevance of these interactions. Beyond revealing an unexpected aspect of αS function and pathology, the authors’ data highlight the versatility of conformationally plastic proteins with high intrinsic disorder.
Incentivized vigor task
By savannah onA python program for a task in human participants using a joystick to make speeded reaches to cued targets. Also includes scripts for extracting behavioral variables, including kinematics.
Fluorescence in situ hybridization (FISH)
By savannah onFluorescence in situ hybridization (FISH) in Conserved and cell type-specific transcriptional responses to IFN-γ in the ventral midbrain.
Immunohistochemistry (IHC)
By savannah onImmunohistochemistry for Conserved and cell type-specific transcriptional responses to IFN-γ in the ventral midbrain.
Interaction of an α-synuclein epitope with HLA-DRB1*15:01 triggers enteric features in mice reminiscent of prodromal Parkinson’s disease
By savannah onPublished: Interaction of α-syn32-46 and HLA-DRB1*15:0 is critical for gut inflammation and CD4+ T cell-mediated loss of enteric neurons in humanized mice, suggesting potential mechanisms of prodromal enteric PD.
Stereotaxic injections
By savannah onStereotaxic injections for Conserved and cell type-specific transcriptional responses to IFN-γ in the ventral midbrain.
Cellular lipid uptake with flow cytometry readout
By savannah onThis protocol describes cellular lipid uptake with flow cytometry readout.
Immunofluorescent staining with anti-GFP and anti-CD63 antibodies
By savannah onThis protocol describes immunofluorescent staining with anti-GFP and anti-CD63 antibodies.
Regular maintenance of human pluripotent stem cells
By savannah onThis protocol describes the regular maintenance and passaging human iPSCs.
