The non-specific lethal complex regulates genes and pathways genetically linked to Parkinson’s disease
By onHere, the authors sought to identify whether the non-specific lethal complex has potential regulatory relationships with other genes associated with Parkinson's disease in human brain.
HyDrop-RNA v1.0
By onStep-by-step protocol for performing HyDrop-RNA. The duration of each step assumes an experienced protocol user. For a first-time user, we recommend doubling the expected time for each step.
pGST2-GST-TEV-NDP52
By onPlasmid: Plasmid for the expression and purification of GST-TEV-NDP52 in E. coli Rosetta pLysS. Internal reference: SMC1586
Localization of PPM1H phosphatase tunes Parkinson’s disease-linked LRRK2 kinase-mediated Rab GTPase phosphorylation and ciliogenesis
By onThe data support a model in which localization drives PPM1H substrate selection and centriolar PPM1H is critical for regulation of Rab GTPase-regulated ciliogenesis.
Investigation_of_mitophagy_in_Hippo_neurons
By onWe developed a method for assessing mitochondrial clearance in primary hippocampal neurons.
Halo assay to assess mitophagy
By onThis protocol describes how to assess mitophagy using Halo assay developed by Mizushima lab (DOI: 10.7554/eLife.78923).
Proteomics of iNeurons or HeLa cells with or without FBXO7
By onTMT proteomics datasets from FBXO7-/- hESC differentiation to iNeurons and HeLa cells.
Immunofluorescence imaging of cells expressing GolgiTAG (TMEM115-3HA) or HA-tagged non-Golgi annotated proteins
By onA method that can be used to verify the correct localisation of HA-tagged Golgi proteins by assessing their colocalization with known Golgi markers. olocalization with ACBD3.
Essential surgeries for the electrophysiological recording from a behaving non-human primate brain 1 (Head fixation post and recording chamber implantation)
By onProtocol for implanting head fixation post and recording chamber in non-human primates for electrophysiological recording.
Integrating protein networks and machine learning for disease stratification in the Hereditary Spastic Paraplegias
By onThe authors used validated human data to create a protein-protein interaction map using causative genes to identify core proteins and processes.
Mechanisms underlying ubiquitin-driven selective mitochondrial and bacterial autophagy
By onThe authors review efforts to understand the biochemical mechanisms and principles by which cargo are marked with ubiquitin and how ubiquitin-binding cargo receptors use conserved structural modules to recruit autophagosome initiation machinery
pCAG-TSF-ATG13 (450-517)-ULK1 (836-1050)
By onPlasmid for mammalian expression of ATG13 C-terminal and ULK1 MIT domain fusion complex.
Whole proteome copy number dataset in primary mouse cortical neurons
By onThe authors provide a proteomic reference dataset that has been generated to identify proteins and quantify their level of expression in primary mouse cortical neurons.
Quantification of Extracellular 𝜶-synuclein Assay
By onThis protocol uses a classical ELISA experimental design with sensitive electrochemical detection to provide measure of 𝜶-synuclein concentration in the conditioned media of cultured iPSC-derived human cells.
Highly efficient generation of isogenic pluripotent stem cell models using prime editing – Datasets
By onThis collection contains the following datasets related to the paper Highly efficient generation of isogenic pluripotent stem cell models using prime editing 1. AAVS1 knock-in genotyping 2. aCGH karyotyping 3. Tabular datasets for associated graphical figures
Immunoprecipitation (IP)
By onThis protocol details about immunoprecipitation using anti-HA magnetic beads.
ALS and FTD-associated missense mutations in TBK1 differentially disrupt mitophagy
By onTBK1 mutations are linked to neurodegenerative disorders. The authors explored TBK1 functions in PINK1/Parkin-dependent mitophagy and how mutations lead to disease.
Serine-129 phosphorylation of α-synuclein is an activity-dependent trigger for physiologic protein-protein interactions and synaptic function
By onPhosphorylation of α-synuclein at the serine-129 site (α-syn Ser129P) is an established pathologic hallmark of synucleinopathies and a therapeutic target. In physiologic states, only a fraction of α-syn is phosphorylated at this site, and most studies have focused on the pathologic roles of this post-translational modification. We found that unlike wild-type (WT) α-syn, which is widely expressed throughout the brain, the overall pattern of α-syn Ser129P is restricted, suggesting intrinsic regulation. Surprisingly, preventing Ser129P blocked activity-dependent synaptic attenuation by α-syn—thought to reflect its normal function. Exploring mechanisms, we found that neuronal activity augments Ser129P, which is a trigger for protein-protein interactions that are necessary for mediating α-syn function at the synapse. AlphaFold2-driven modeling and membrane-binding simulations suggest a scenario where Ser129P induces conformational changes that facilitate interactions with binding partners. Our experiments offer a new conceptual platform for investigating the role of Ser129 in synucleinopathies, with implications for drug development.
H9 ES AAVS1-NGN2 FAM134C/A-/-; PiggyBac-Keima-RAMP4
By onES cells were modified using CRISPR/Cas9 to express a Keima-RAMP4 ER-phagy flux reporter and lack the FAM134C ER-phagy receptor. The cells were derived from a female human blastocyst stage embryonic stem cell line.
