pHAGE-FKBP-GFP-OPTN (2-119)
By savannah onPlasmid: Stably express GFP-tagged OPTN (2-119aa) for CID induced mitophagy.
Purification of NAP1 or GST-NAP1
By savannah onThis protocol describes purification of GST-NAP1 and unlabeled NAP1.
pGEX-4T1-MBP-TEV-NAP1_delta-NDP52 (S37K/A44E)
By savannah onPlasmid: For expression in E. coli of NAP1 (delta-NDP52).
pGEX-4T1-MBP-TEV-NAP1_delta-TBK1 (L226Q/L233Q)
By savannah onPlasmid: For expression in E. coli of NAP1 (delta-TBK1).
pFastBac_Dual-GST-TEV-SINTBAD-EGFP (codon optimized Sf9)
By savannah onPlasmid: Used for the expression and purification of EGFP labeled SINTBAD (SMC Internal No. 1613).
pFastBac-Dual-GST-TEV-SINTBAD-mCherry
By savannah onPlasmid: For expression in insect cells of SINTBAD-mCherry.
Control of mitophagy initiation and progression by the TBK1 adaptors NAP1 and SINTBAD
By savannah onMitophagy preserves overall mitochondrial fitness by selectively targeting damaged mitochondria for degradation. The regulatory mechanisms that prevent autophagy pathways from overreacting while ensuring swift progression once initiated are largely elusive. The authors shed light on a cellular strategy to prevent pathway hyperactivity while still ensuring efficient progression.
Identification of phosphorylation sites on NAP1/AZI2
By savannah onThe authors observed smearing for the TBK1-adaptor protein NAP1/AZI2 during mitophagy. To verify whether this smearing was due to phosphorylation by TBK1, the authors performed an in vitro kinase assay and complemented this with the immunoprecipitation of NAP1 from HAP1, whose genetic background (FIP200 knockout) results in hyperactivation of TBK1.
HeLa S3 AZI2 KO clone 32
By savannah onCell line from an African American Population. Knockout cell: Method=CRISPR/Cas9; HGNC; 24002; AZI2. Transformant: NCBI_TaxID; 333761; Human papillomavirus type 18 (HPV18). Miscellaneous: Cell line information from personal communication of Khuu G. Derived from site: In situ; Uterus, cervix; UBERON=UBERON_0000002.
Oxford Nanopore Technologies (ONT) library preparation and sequencing of DNA prepared using droplet Multiple Displacement Amplification (dMDA)
By savannah onDebranching of DNA generated by Multiple Displacement Amplification (MDA) is an essential step prior to nanopore sequencing. This protocol describes an optimized T7-based debranching protocol for genomic DNA amplified from single nuclei using droplet MDA (dMDA).
SoCal Kinesia and Incentivization for Parkinson’s Disease (SKIP)
By savannah onSKIP combines three task-based fMRI datasets and one resting-state fMRI dataset into a single, centralized repository, facilitating researchers across human sciences interested in human movement, the modulatory impact of incentivization, with specific reference to Parkinson’s disease (PD). The current version (1.0.1) contains healthy controls only.
Data sets related to “Kufor-Rakeb Syndrome-Associated Psychosis: A Novel Loss-of-Function ATP13A2 Variant and Response to Antipsychotic Therapy”
By savannah onData sets related to "Kufor-Rakeb Syndrome-Associated Psychosis: A Novel Loss-of-Function ATP13A2 Variant and Response to Antipsychotic Therapy."
Untargeted lipidomics of Tagless Lyso-IP
By Emma Sherrell onLysosomal biology is implicated in neurodegenerative diseases and health. It has traditionally been difficult to profile the lipidolomic homeostasis of the lysosome in disease states. To overcome this challenge, the authors have developed the Tagless Lyso-IP method to rapidly prepare lysosome-enriched samples from human peripheral blood.
Cathepsin D assay to verify the retention of lysosomal content
By Emma Sherrell onCathepsin D assay is a fluorescence-based assay that leverages the activity of cathepsin D to monitor the intactness of lysosomes in the cell. Here, the authors describe a method where the measurement of cathepsin D activity is used to verify the intactness of lysosomes.
Sample preparation protocol for proteomic analysis of isolated lysosomes and whole cell extracts
By Emma Sherrell onHere, the authors describe a step-wise protocol for proteomic sample preparation derived from cell line models or isolated human cells. The protocol has been optimized for organelle pulldown preps.
