Proteomics of iNeurons or HeLa cells with or without FBXO7
By onTMT proteomics datasets from FBXO7-/- hESC differentiation to iNeurons and HeLa cells.
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).
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.
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.
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.
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.
Immunoprecipitation (IP)
By onThis protocol details about immunoprecipitation using anti-HA magnetic beads.
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
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.
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.
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.
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.
HeLa ::TMEM192-HA YIPF3-/-
By onHeLa ::TMEM192-HA YIPF3-/- PubMed=37757899; Population: African American. Characteristics: Using CRISPR/Cas9 TMEM192 was C-terminally tagged on both alleles with a 3xHA epitope (from parent cell line). Knockout cell: Method=CRISPR/Cas9; HGNC; 21023; YIPF3. Transformant: NCBI_TaxID; 333761; Human papillomavirus type 18 (HPV18). Derived from site: In situ; Uterus, cervix; UBERON=UBERON_0000002. NCIt; C27677; Human papillomavirus-related cervical adenocarcinoma NCBI_TaxID=9606; ! Homo sapiens (Human) RRID:CVCL_D1KR ! HeLa::TMEM192-3xHA Female 30Y6M Cancer cell line
Glucocerebrosidase, a Parkinson´s disease-associated protein, is imported into mitochondria and regulates complex I assembly and function
By onRaw data files used for the manuscript "Glucocerebrosidase, a Parkinson´s disease-associated protein, is imported into mitochondria and regulates complex I assembly and function" https://www.researchsquare.com/article/rs-1521848/v1
Histology and Retention of Implanted Carbon Fiber Thread Electrodes in Fixed Tissue
By onMethods to cut and retain implanted carbon fiber electrodes in brain tissue.
PARK15/FBXO7 is dispensable for PINK1/Parkin mitophagy in iNeurons and HeLa cell systems
By onPINK1 and Parkin promote damaged mitochondria removal through Ub phosphorylation, Parkin activation. FBXO7 mutation in PD may not affect mitophagy in HeLa and neuron cells, suggesting it may not play a significant role in Parkin-dependent mitophagy.
Transcardiac Perfusion of Mouse for Brain Tissue
By onTranscardiac perfusion is a method used for clearing blood and preserving the mouse brain for immunostaining.
