Evaluation of a novel method for spectral analysis of neurophysiology data
By onThis code implements a novel method for correcting a distortion effect that is present in the power spectra of neuronal spike trains.
pCAG-MBP-ATG9 (801-839)
By onPlasmid: To make monomeric ATG9 C-terminal tail for expression in mammalian cells.
Damaged mitochondria recruit the effector NEMO to activate NF-κB signaling
By onThe connections between molecular mechanisms like mitophagy and tissue-wide features like neuro-inflammation remain unclear. Here, the authors characterize a novel link between these two hallmarks of neurodegeneration.
Mitochondrial isolation protocol
By onThis protocol describes how to isolate crude mitochondrial fractions from HeLa cells.
α-synuclein promotes neuronal dysfunction and death by disrupting the binding of ankyrin to ß-spectrin
By onα-synuclein plays a key role in the pathogenesis of Parkinson’s disease and related disorders, but critical interacting partners and molecular mechanisms mediating neurotoxicity are incompletely understood. We show that α-synuclein binds directly to ß-spectrin. Using males and females in a Drosophila model of α-synuclein-related disorders we demonstrate that ß-spectrin is critical for α-synuclein neurotoxicity. Further, the ankyrin binding domain of ß-spectrin is required for α-synuclein binding and neurotoxicity. A key plasma membrane target of ankyrin, Na+/K+ ATPase, is mislocalized when human α-synuclein is expressed in Drosophila. Accordingly, membrane potential is depolarized in α-synuclein transgenic fly brains. We examine the same pathway in human neurons and find that Parkinson’s disease patient-derived neurons with a triplication of the α-synuclein locus show disruption of the spectrin cytoskeleton, mislocalization of ankyrin and Na+/K+ ATPase, and membrane potential depolarization. Our findings define a specific molecular mechanism by which elevated levels of α-synuclein in Parkinson’s disease and related α-synucleinopathies leads to neuronal dysfunction and death.
GFP Immunoprecipitation and Sample Preparation for Tandem Mass Tag (TMT) Mass Spectrometry Analysis
By onWe describe a method to identify potential interactors of any Green Fluorescent Protein (GFP) tagged protein expressed in mammalian cells by GFP immunoprecipitation coupled to Tandem Mass Tag (TMT) mass spectrometry analysis. As an example, we used a GFP-tagged phosphoRab interactor protein (RILPL1-GFP), and its non-binding mutant (RILPL1 -GFP, which cannot interact with phosphorylated Rab proteins) as a control.
Three-step docking by WIPI2, ATG16L1 and ATG3 delivers LC3 to the phagophore
By onIn this manuscript, in a near-complete pathway from initial membrane recruitment to LC3 lipidation reaction, we show how a three-step targeting mechanism of the ATG12-ATG5-ATG16L1 machinery ensures a high level of regulatory control on autophagy.
ATP13A2 Regulates Cellular α-Synuclein Multimerization, Membrane Association, and Externalization
By onATP13A2 loss-of-function mutations are linked to Parkinson’s disease and alpha-synuclein pathology. The authors found that loss of ATP13A2 disrupts lysosomal membrane integrity and causes alpha-synuclein multimerization.
Constructs and generation of stable cell lines
By onProtocol used to generate stable Flp-In T-REx-HEK 293 cell lines expressing WT or mutant GCase (E326K or L444P) as a V5-FLAG-tagged protein using a tetracycline-inducible system.
pCAG-mcherry- WIPI2dR125E- cs-TEV -STREP
By onPlasmid for mammalian expression of human WIPI2d R125E with N-terminal mCherry and C-terminal Strep.
Local diffusion in the extracellular space of the brain
By onThe authors highlight emerging technological advances to respectively interrogate and model diffusion through the ECS, and point out how these may contribute in resolving the remaining enigmas of the ECS.
H9 ES AAVS1-NGN2 FAM134B-/-
By onCell Line: ES cells for making iNeurons lacking the ER-phagy receptor FAM134B.
Software for analyzing the expression of TEs at locus-specific resolution
By onWe enable the locus-specific analysis of transposable elements, with curated GTF files to improve detection of yound transposable elements, such as HERVs and young L1s. Parts of this software will be used for single-cell TE anlaysis protocols, which are under development
Immunofluorescence of RAB5 and FLAG-EEA1 puncta after Dynamin-1 and -2 inhibition with Dyngo4a
By onSelective purification of early endosomes can be achieved through affinity capture of the early endosome-associated protein EEA1 (termed Endo-IP) (Park et al. in submission). These purified endosomes can be used for proteomic and lipidomic studies to obtain snapshots of early endosomes. Here we present an immunofluorescence protocol to assess the extent of colocalization between FLAG-EEA1 and RAB5 with and without the Dynamin-1 and -2 (DNM1/2) inhibitor Dyngo4a.
Sex-Specific Microglial Responses to Glucocerebrosidase Inhibition: Relevance to GBA1-Linked Parkinson’s Disease
By onMicroglia are heterogenous cells characterized by distinct populations each contributing to specific biological processes in the nervous system, including neuroprotection. To elucidate the impact of sex-specific microglia heterogenicity to the susceptibility of neuronal stress, we video-recorded with time-lapse microscopy the changes in shape and motility occurring in primary cells derived from mice of both sexes in response to pro-inflammatory or neurotoxic stimulations. With this morpho-functional analysis, we documented distinct microglia subpopulations eliciting sex-specific responses to stimulation: male microglia tended to have a more pro-inflammatory phenotype, while female microglia showed increased sensitivity to conduritol-B-epoxide (CBE), a small molecule inhibitor of glucocerebrosidase, the enzyme encoded by the GBA1 gene, mutations of which are the major risk factor for Parkinson’s Disease (PD). Interestingly, glucocerebrosidase inhibition particularly impaired the ability of female microglia to enhance the Nrf2-dependent detoxification pathway in neurons, attenuating the sex differences observed in this neuroprotective function. This finding is consistent with the clinical impact of GBA1 mutations, in which the 1.5–2-fold reduced risk of developing idiopathic PD observed in female individuals is lost in the GBA1 carrier population, thus suggesting a sex-specific role for microglia in the etiopathogenesis of PD-GBA1
pCAG-OSF-ATG13 (2-197)-F16D
By onPlasmid for expression of human ATG13 HORMA F16D mutant in mammalian cells.
Toward a standard model for autophagosome biogenesis
By onHere, we discuss two papers focusing on autophagosome biogenesis in mammals: Olivas et al. confirming ATG9A as an autophagosome component using biochemistry, while Broadbent et al. showing autophagy protein dynamics using particle tracking.
A computational pipeline to quantify primary cilia in mouse embryonic fibroblasts with CellProfiler
By onThis protocol works with .czi format images which are acquired using a Zeiss laser scanning confocal microscope and are maximum intensity projected.
