Steered MD simulations of the inactive-active transition
By onProtocol outlines simulations of PI3KC3-C1 complex transitioning from inactive to active state with RAB1A on a lipid membrane using steered molecular dynamics.
Molecular Dynamics Simulations of Active, Membrane-Engaged Complex
By onThe protocol describes molecular dynamics simulations of PI3KC3-C1 complex with RAB1A on a lipid membrane for studying protein interactions.
Image Processing and 3D Reconstruction
By onThis workflow was used to analyze a Krios dataset of the PI3KC3-C1/RAB1A Complex and generate a reconstruction of three distinct conformational states of the VPS34 lipid kinase domain.
Unbiased MD simulations of POPI entry into VPS34KD
By onThis protocol details molecular dynamics simulations of the kinase domain of VPS34 in a membrane containing 15% of POPI lipids and analysis of POPI entry into the catalytic site.
Costa Lab Nanoject Virus Injections
By onThis is the standard stereotaxic/Nanoject injection mouse surgery protocol for the Costa lab at Columbia University.
Open Field Behavior in Mice-Ding Lab
By onThe open field test is widely used to assess spontaneous locomotor activity, exploratory behavior, and anxiety-like responses in rodents.
Chronic Cranial Window and Micro-Optical Probe Implantation in Mice
By onMonitoring neuronal structure and activity in behaving animals helps understand movement control. Surgical procedures like chronic cranial window and micro-optical probe implantation allow optical monitoring of neural circuits.
Lewy body diseases and the gut
By onGI involvement in Lewy body diseases may start with ⍺-synuclein in the gut spreading to the brain. Gut microbiome, immune system, and toxins play roles. These connections could lead to new therapies targeting the gut-brain axis for disease treatment.
Tamoxifen Administration in Transgenic Mice-Ding Lab
By onThis protocol describes the procedure for inducing CreER-mediated recombination at loxP sites in transgenic mice through the administration of tamoxifen or 4-hydroxytamoxifen (4-OHT).
RNA In situ hybridization (ISH) using RNAscope®
By onThis protocol outlines the procedures for RNA in situ hybridization to simultaneously detect up to three targets using the RNAscope® Multiplex Fluorescent v2 assay (ACD).
Head-fixed Forelimb Reaching Task in Mice
By onThis protocol describes a head-fixed forelimb reaching task used to study motor learning and memory in mice suitable for recording neuronal activity concurrently.
α-Synuclein aggregates inhibit ESCRT-III through sequestration and collateral degradation
By onα-Synuclein aggregates deplete ESCRT-III by sequestration and "collateral degradation," impeding endolysosomal repair. This allows endocytosed fibrils to leak into the cytoplasm, triggering a toxic cycle of aggregation and endolysosomal dysfunction.
Measuring lysosomal exocytosis by Flow cytometry
By onFlow cytometry can be used to measure lysosomal exocytosis by analyzing changes in fluorescence intensity of lysosomal markers in cells, providing a protocol for studying this cellular process.
GPNMB is a biomarker for lysosomal dysfunction and is secreted via LRRK2-modulated lysosomal exocytosis
By on*GPNMB* is linked to Parkinson's Disease as a risk factor, affecting its transcription and protein levels in CSF. Macrophages secrete GPNMB in response to lysosomal stress through lysosomal exocytosis, with LRRK2 influencing its secretion.
Lysosomal Glucocerebrosidase is needed for ciliary Hedgehog signaling: A convergent pathway to Parkinson’s disease
By onMutations in LRRK2 and GBA1 are common in familial Parkinson’s disease. These mutations inhibit primary cilia formation, blocking Hedgehog signaling and reducing neuroprotective factors, contributing to PD pathogenesis.
A RAB7A Phosphoswitch Coordinates Rubicon Homology Protein Regulation of PINK1/Parkin-Dependent Mitophagy
By onPublished: Structural and functional data support a model in which the TBK1-dependent phosphorylation of RAB7A serves as a switch, promoting mitophagy by relieving Rubicon inhibition and favoring Pacer activation. View original preprint.
Adult-specific Reelin expression alters striatal neuronal organization: implications for neuropsychiatric disorders
By onReelin levels might modulate the numbers of striatal interneurons and the density of the nigrostriatal dopaminergic projections, suggesting that these changes may be involved in the protection of Reelin against neuropsychiatric disorders.
