Organelle isolation from mouse tissues expressing organelle tags
By savannah onThe organelles purified using this method are highly enriched, intact, largely contaminant-free and can be used for various downstream applications, including immunoblotting analysis and proteomic analysis (as described in dx.doi.org/10.17504/protocols.io.ewov1o627lr2/v1), but also lipidomic or metabolomic analysis (as described in dx.doi.org/10.17504/protocols.io.bybjpskn).
Proteomic data reported in doi.org/10.1073/pnas.2219953120 (Golgi-IP, a tool for multimodal analysis of Golgi molecular content)
By savannah onProteomic data associated with doi.org/10.1073/pnas.2219953120 deposited in ProteomeXchange PRIDE repository with PID: PXD038046.
twichma/Sequence-and-pattern-detection: Sequence and pattern detection code
By savannah onCode for sequence and pattern analyses.
Role of autophagy pathway in Parkinson’s disease and related genetic neurological disorders
By savannah onThe authors provide a comprehensive overview of the general importance of autophagy in Parkinson’s disease (PD) and related disorders of the central nervous system (CNS). This reveals a critical link between autophagy and neurodegenerative and neurodevelopmental disorders and suggests that strategies to modulate mitophagy may have greater relevance in the CNS beyond PD.
Targeting the GBA1 pathway to slow Parkinson’s disease: Insights into clinical aspects, pathogenic mechanisms, and new therapeutic avenues
By savannah onTreatments that target the GBA1 pathway could reverse these pathological processes and halt/slow the progression of PD. Ranges from augmentation of GCase activity via GBA1 gene therapy, restoration of normal intracellular GCase trafficking via molecular chaperones, and substrate reduction therapy. This review discusses the pathways associated with GBA1-PD and GBA1-targeted interventions for PD treatment.
LINE-1 retrotransposons drive human neuronal transcriptome complexity and functional diversification
By savannah onPublished: CRISPRi-silencing of LINC01876 results in reduced size of cerebral organoids and premature differentiation of neural progenitors, implicating L1s in human-specific developmental processes. In summary, the authors’ results demonstrate that L1-derived transcripts provide a previously undescribed layer of primate- and human-specific transcriptome complexity that contributes to the functional diversification of the human brain. View original preprint.
Immunoprecipitation (IP)
By savannah onThis protocol details about immunoprecipitation using anti-HA magnetic beads.
Nuclear isolation of post-mortem brain tissue for snRNAseq
By savannah onThis protocol details how to isolate nuclei from frozen brain tissue for single nuclear RNA sequencing using 10x Genomics GEM isolation using the Chromium accessory and Single Cell 3ʹ Reagent Kits.
Time to LiD GWAS dataset
By savannah onGWAS dataset derived on the study of LiD genetic determinants together with README. Code used to generate this GWAS file can be accessed at https://doi.org/10.5281/zenodo.7794491
Primary data associated with the manuscript “Genome wide screen reveals Rab12 GTPase as a critical activator of pathogenic LRRK2 kinase” (doi: 10.1101/2023.02.17.529028)
By savannah onPrimary data associated with the manuscript "Genome wide screen reveals Rab12 GTPase as a critical activator of pathogenic LRRK2 kinase." These include raw immunoblotting data (annotated .tiff exports of Image Studio Lite Licor scans) and their quantitation (.xlsx files) and graphs obtained using GraphPad Prism (.pzf files) for the indicated figures.
Splicing-accuracy-manuscript
By savannah onCode for the splicing-accuracy manuscript (pre-print DOI: doi.org/10.1101/2023.03.29.534370)
LiD genetic determinants study under CPH regression models
By savannah onCode to perform the study of LiD genetic determinants under CPH regression models and functional annotation analyses.
Splicing accuracy varies across human introns, tissues, and age
By savannah onThis in-depth characterization of mis-splicing can have important implications for our understanding of the role of splicing inaccuracies in human disease and the interpretation of long-read RNA-sequencing data.
Advances in AAV technology for delivering genetically encoded cargo to the nonhuman primate nervous system
By savannah onModern neuroscience approaches including optogenetics, calcium imaging, and other genetic manipulations have facilitated our ability to dissect specific circuits in rodent models to study their role in neurological disease. These approaches regularly use viral vectors to deliver genetic cargo (e.g., opsins) to specific tissues and genetically engineered rodents to achieve cell-type specificity.
PARK15/FBXO7 is dispensable for PINK1/Parkin-dependent mitophagy in iNeuron and HeLa cell systems
By savannah onThe protein kinase PINK1 and ubiquitin ligase Parkin promote removal of damaged mitochondria via a feed- forward mechanism involving ubiquitin (Ub) phosphorylation (pUb), Parkin activation, and ubiquitylation of mitochondrial outer membrane proteins to support recruitment of mitophagy receptors.
Collection of protocols of Team Deleidi used in the publication: “LRRK2 kinase activity regulates GCase level and enzymatic activity differently depending on cell type in Parkinson’s disease”
By savannah onCollection of protocols of Team Deleidi used in the publication: "LRRK2 kinase activity regulates GCase level and enzymatic activity differently depending on cell type in Parkinson’s disease."
Glucocerebrosidase, a Parkinson´s disease-associated protein, is imported into mitochondria and regulates complex I assembly and function
By savannah 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
Who is at risk of Parkinson’s disease? Refining the preclinical phase of GBA1 and LRRK2 variant carriers: a clinical, biochemical, and imaging approach
By savannah onGenetic variants in GBA1 and LRRK2 genes are the commonest genetic risk factor for Parkinson’s disease (PD); however, the preclinical profile of GBA1 and LRRK2 variant carriers who will develop PD is unclear. This review aims to highlight the more sensitive markers that can stratify PD risk in non-manifesting GBA1 and LRRK2 variant carriers.
LRRK2-G2019S synergizes with aging and low-grade inflammation to promote gut and peripheral immune cell activation that precede nigrostriatal degeneration
By savannah onOur study suggests an early role of the peripheral immune system and the gut in LRRK2 PD and provides a novel model to study early therapeutic immune targets and biomarkers.
