Manual Tracking/image_prep.ijm
By onA script to register 2-channel timelapse images using HyperStackReg, using only 1 of the channels to compute transformation. The script also enhances contrast and prepares the image for manual tracking.
Manual Tracking/measure_ECM.ijm
By onA script to generate circular ROIs in each frame of a timelapse, using a previously generated track as reference. Used to measure fluorescence intensity (i.e., extracellular matrix content) along a microglia track. .
Manual Tracking/tracking.ijm
By onA script to store in ImageJ’s ROImanager the tracks generated using Manual Tracking plugin, for later use (drawing tracks, frame-by-frame analysis). To be used as a continuation of 1_image_prep.ijm.
Preparation of unilamellar liposomes
By onA protocol for preparing liposomes that can be used to monitor binding of proteins to vesicles of various membrane curvatures.
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.
Genetic meta-analysis of levodopa induced dyskinesia in Parkinson’s disease
By onBased on a functional annotation analysis on chromosome 1, the authors determined that changes in DNAJB4 gene expression is an additional potential cause of increased susceptibility to LiD.
Detecting rhythmic spiking through the power spectra of point process model residuals
By onThe work highlighted in this manuscript improves the ability to characterize oscillatory activity and detect pathological changes at the level of individual neurons.
Standard Operating Procedure (SOP) for Combined ICA and Systemic Administration of MPTP: The Overlesioned (Bilateral Asymmetric) Non-human Primate Model
By onThis standard operating procedure (SOP) describes safe methods for the use of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) in non-human primates (adult macaque monkeys).
Mitochondrial degradation: Mitophagy and beyond
By onMitochondria are vital for cellular function. Degradation pathways like mitophagy regulate their quality and activity. Various mechanisms, such as mitophagy and mitochondrial extrusion, ensure cellular homeostasis by removing unwanted mitochondria.
Parkinson’s genes orchestrate pyroptosis through selective trafficking of mtDNA to leaky lysosomes
By onThese data place mitochondria-to-lysosome transport as a driver of pyroptosis and link multiple PD proteins along a common inflammatory pathway.
State-dependent GABAergic regulation of striatal spiny projection neuron excitability
By onSynaptic transmission mediated by GABAA receptors (GABAARs) in adult, principal striatal spiny projection neurons (SPNs) can suppress ongoing spiking, but its effect on synaptic integration at sub-threshold membrane potentials is less well characterized, particularly those near the resting down-state. To fill this gap, a combination of molecular, optogenetic, optical and electrophysiological approaches were used to study SPNs in mouse ex vivo brain slices, and computational tools were used to model somatodendritic synaptic integration. Activation of GABAARs, either by uncaging of GABA or by optogenetic stimulation of GABAergic synapses, evoked currents with a reversal potential near −60 mV in perforated patch recordings from both juvenile and adult SPNs. Molecular profiling of SPNs suggested that this relatively positive reversal potential was not attributable to NKCC1 expression, but rather to a dynamic equilibrium between KCC2 and Cl-/HCO3- cotransporters. Regardless, from down-state potentials, optogenetic activation of dendritic GABAergic synapses depolarized SPNs. This GABAAR-mediated depolarization summed with trailing ionotropic glutamate receptor (iGluR) stimulation, promoting dendritic spikes and increasing somatic depolarization. Simulations revealed that a diffuse dendritic GABAergic input to SPNs effectively enhanced the response to coincident glutamatergic input. Taken together, our results demonstrate that GABAARs can work in concert with iGluRs to excite adult SPNs when they are in the resting down-state, suggesting that their inhibitory role is limited to brief periods near spike threshold. This state-dependence calls for a reformulation of the role intrastriatal GABAergic circuits.
Video tutorials for Curtain and Curtain-PTM
By onVideo tutorials to assist users of Curtain and Curtain-PTM proteomic data analysis web tools (described in ).
A computational pipeline to quantify perinuclear lysosomes in fibroblasts using CellProfiler
By onHere we present a CellProfiler software pipeline to quantify the distribution of lysosomes in MEF cells. The lysosomes were stained using anti-LAMP1 antibody, and nuclei were labeled using DAPI. The images were acquired using a Zeiss laser scanning confocal microscope and were maximum intensity projected in FIJI.
Testing AAVrg-hSyn-mCherry in the Putamen of Rhesus Macaques
By onTwo rhesus macaques were tested with AAVrg-hSyn-mCherry in the putamen, showing numerous mCherry-positive neurons in motor cortical regions projecting to the putamen.
Circular RNA in the human brain are tailored to neuron identity and neuropsychiatric disease
By onLittle is known about circular RNAs (circRNAs) in specific brain cells and human neuropsychiatric disease. Here, we systematically identify over 11,039 circRNAs expressed in vulnerable dopamine and pyramidal neurons laser-captured from 190 human brains and non-neuronal cells using ultra-deep, total RNA sequencing. 1526 and 3308 circRNAs are custom-tailored to the cell identity of dopamine and pyramidal neurons and enriched in synapse pathways. 29% of Parkinson's and 12% of Alzheimer's disease-associated genes produced validated circRNAs. circDNAJC6, which is transcribed from a juvenile-onset Parkinson's gene, is already dysregulated during prodromal, onset stages of common Parkinson's disease neuropathology. Globally, addiction-associated genes preferentially produce circRNAs in dopamine neurons, autism-associated genes in pyramidal neurons, and cancers in non-neuronal cells. This study shows that circular RNAs in the human brain are tailored to neuron identity and implicate circRNA-regulated synaptic specialization in neuropsychiatric diseases.
Testing AAVrg-hSyn-mCherry in the Spinal Cord of Rhesus Macaques
By onViral Vector: Two rhesus macaque animals were tested for AAVrg-hSyn-mCherry in the spinal cord. The authors observed abundant mCherry-positive neurons in expected targets (i.e., motor cortical regions known to project to the spinal cord).
Generation of stable cell lines using viral infection
By onProtocol for generation and precipitation of retrovirus, and infection of HeLa cells to generate stable cell lines.
Mitophagy induction using Oligomycin/Antimycin A
By onMitophagy induction in HeLa cells using Oligomycin/Antimycin A.
Induction of starvation stress
By onProtocol describing the induction of starvation stress using EBSS in HeLa cells