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56 results for “Neurites”
Data for: Dysregulation of mTOR signaling mediates common neurite and migration defects in both idiopathic and 16p11.2 deletion autism neural precursor cells
<p>Autism spectrum disorder (ASD) is defined by common behavioral characteristics, raising the possibility of shared pathogenic mechanisms. Yet, vast clinical and etiological heterogeneity suggests personalized phenotypes. Surprisingly, our iPSC studies find that six individuals from two distinct ASD subtypes, idiopathic and 16p11.2 deletion, have common reductions in neural precursor cell (NPC) neurite outgrowth and migration even though whole genome sequencing demonstrates no genetic overlap between the datasets. To identify signaling differences that may contribute to these developmental defects, an unbiased phospho-(p)-proteome screen was performed. Surprisingly, despite the genetic heterogeneity, hundreds of shared p-peptides were identified between autism subtypes including the mTOR pathway. mTOR signaling alterations were confirmed in all NPCs across both ASD subtypes and mTOR modulation rescued ASD phenotypes and reproduced autism NPC-associated phenotypes in control NPCs. Thus, our studies demonstrate that genetically distinct ASD subtypes have common defects in neurite outgrowth and migration which are driven by the shared pathogenic mechanism of mTOR signaling dysregulation.</p>
Data on: Impact of neurite alignment on organelle motion
<p><strong>Impact of neurite alignment on organelle motion.</strong></p> <p>Maria Mytiliniou, Joeri A. J. Wondergem, Thomas Schmidt, Doris Heinrich.<br>J. R. Soc. Interface <strong>19</strong>:20210617.<br>doi: https://doi.org/10.1098/rsif.2021.0617</p> <p><strong>Abstract</strong></p> <p>Intracellular transport is pivotal for cell growth and survival. Malfunctions in this process have been associated with devastating neurodegenerative diseases, posing a need for deeper understanding of the involved mechanisms. Here, we used an experimental methodology that lead neurites of differentiated PC12 cells in either of two configurations: an one-dimensional, where the neurites align along lines, or a two-dimensional configuration, where the neurites adopt a random orientation and shape on a flat substrate. We subsequently monitored the motion of functional organelles, the lysosomes, inside the neurites. Implementing a time-resolved analysis of the mean-squared displacement, we quantitatively characterized distinct motion modes of the lysosomes. Our results indicate that neurite alignment gives rise to faster diiffusive and super-diiffusive lysosomal motion in comparison to the situation where the neurites are randomly oriented. After inducing lysosome swelling through an osmotic challenge by sucrose, we confirmed the predicted slowdown in diffusive mobility. Surprisingly we found that the swelling-induced mobility change affected each of the (sub- /super-) diiffusive motion modes differently and depended on the alignment configuration of the neurites. Our findings imply that intracellular transport is significantly and robustly dependent on cell morphology, which might be in part controlled by the extracellular matrix.</p>
Data for: Dysregulation of mTOR signaling mediates common neurite and migration defects in both idiopathic and 16p11.2 deletion autism neural precursor cells
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Uncovering kinesin dynamics in neurites with MINFLUX - Repository
<p><strong>Data repository for the publication Uncovering kinesin dynamics in neurites with MINFLUX and corresponding matlab scripts to evaluate the data</strong>. </p> <p>.zip file contains:</p> <ol> <li>Data repository</li> <li>Matlab scripts</li> </ol> <p>Please do not change the contained folders or rename them, otherwise the matlab scripts will stop working.</p> <p>Matlab scripts were prepared in matlab 2022b.</p>
Microscopy images - " Particulate matter constituents trigger the formation of extracellular amyloid β and Tau -containing plaques and neurite shortening in vitro"
<p>This repository contains microscopy data from the manuscript "Particulate matter constituents trigger the formation of extracellular amyloid β and Tau -containing plaques and neurite shortening in vitro" by Aleksandar Sebastijanović, Laura Maria Azzurra Camassa, Vilhelm Malmborg, Slavko Kralj, Joakim Pagels, Ulla Vogel, Shan Zienolddiny-Narui, Iztok Urbančič, Tilen Koklič, and Janez Štrancar (published in Nanotoxicology, 18(4), 335–353. https://doi.org/10.1080/17435390.2024.2362367).</p> <p>Raw data are organized in folders named by image number, containing a subfolder with the date (year-day-month) of image acquisition. Followed by a subfolder named by a nanomaterial to which neurons were exposed. Each folder contains images from individual multi-channel, multi-position time-lapse experiments with different combinations of cells exposed to one nanomaterial. Files are named as: IMGxxxx_[ExperimentCode]_ROIxx_[Channel].tif, where each of the varying elements in [..] denotes the following:<br>• [ExperimentCode]: a short name of the experiment<br>• [Channel]: membrane (MEM), cytoplasm neuronal cells (NEU), nanomaterial (NANO), amyloid beta (AMY)</p>
Re-Read Study to Compare the Brain Uptake of [18F]Flutemetamol With Brain Neuritic Plaque Density Determined Postmortem
ClinicalTrials.gov study NCT02090855. IPD Sharing: Not stated. Countries: 1. Publications: 5.
Data for Machine Learning Guided Design of Nerve-on-A-Chip Platforms with Promoted Neurite Outgrowth
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DeepCAD-RT dataset: mouse neurites
<p>DeepCAD-RT dataset: mouse neurites</p>
SNEMI3D: 3D Segmentation of neurites in EM images
<p>In this challenge, a full stack of electron microscopy (EM) slices will be used to train <strong>machine-learning algorithms</strong> for the purpose of <strong>automatic</strong> <strong>segmentation of neurites in 3D</strong>. This imaging technique visualizes the resulting volumes in a highly anisotropic way, i.e., the x- and y-directions have a high resolution, whereas the z-direction has a low resolution, primarily dependent on the precision of serial cutting. EM produces the images as a projection of the whole section, so some of the neural membranes that are not orthogonal to a cutting plane can appear very blurred. None of these problems led to major difficulties in the manual labeling of each neurite in the image stack by an expert human neuro-anatomist.</p> <p>In order to gauge the current state-of-the-art in automated neurite segmentation on EM and compare between different methods, we are organizing a 3D Segmentation of neurites in EM images (SNEMI3D) challenge in conjunction with the<a href="http://www.biomedicalimaging.org/2013/program/isbi-challenges/"> ISBI 2013 conference</a>. For this purpose, we are making available a large training dataset of mouse cortex in which the neurites have been manually delineated. In addition, we also provide a test dataset where the 3D labels are not available. The aim of the challenge is to compare and rank the different competing methods based on their<strong> object classification accuracy</strong> in three dimensions.</p> <p>The <strong>image data</strong> used in the challenge was produced by <a href="http://lichtmanlab.fas.harvard.edu/">Lichtman Lab at Harvard University</a> (Daniel R. Berger, Richard Schalek, Narayanan "Bobby" Kasthuri, Juan-Carlos Tapia, Kenneth Hayworth, Jeff W. Lichtman) and manually annotated by <a href="http://lichtmanlab.fas.harvard.edu/people/daniel-berger">Daniel R. Berger</a>. Their corresponding biological findings were published in <a href="http://www.ncbi.nlm.nih.gov/pubmed/26232230">Cell (2015)</a>.</p>
Directional control of neurite outgrowth: emerging technologies for Parkinson's Disease using magnetic nanoparticles and magnetic field gradients
<p>Data set for publication '<strong>Directional control of neurite outgrowth: emerging technologies for Parkinson’s Disease using magnetic nanoparticles and magnetic field gradients'</strong></p> <p><strong>Journal of The Royal Society Interface</strong></p> <p><strong>2022</strong></p>
Effect of G4C2 Repeat Expansions on the Motion of1 Lysosomes Inside Neurites.
<p>Data concerning the above-mentioned paper.</p> <p> </p> <p><strong>Abstract</strong></p> <p>The G4C2 hexanucleotide repeat expansion (HRE) in the c9orf72 locus is a mutation associated with amyotrophic lateral sclerosis, and recent evidence suggests a link with disrupted axonal trafficking in neurons. <br> Here, using a neuron-like cell line without, or transfected with, G4C2 repeats, we characterize the motion of lysosomes inside neurites which were either aligned or oriented randomly on the substrate, implementing time-resolved (local) mean squared displacement (l)MSD analysis and differentiation among sub-diffusive, diffusive, and super-diffusive trajectory parts. <br> Our results suggest that in the presence of the G4C2 repeats, lysosome motility is hampered, exhibiting overall decreased MSD and speed, more prominently inside aligned neurites. <br> Moreover, a more prominent effect in the super-diffusive drift velocity and diffusive motion diffusion coefficient was evident when the motion occurred inside aligned neurites. <br> Trajectories which included super-diffusive motion, exhibited a varied ratio of anterograde/retrograde/neutral for both neurite geometries in the presence of G4C2 repeats but a similar instantaneous velocity decrease for both directions in each neurite geometry.<br> Our findings support the hypothesis that impaired axonal trafficking emerges in the presence of the G4C2 HRE, and demonstrate that this effect is more prominent when the neurites are aligned.</p>
Generation of human induced pluripotent stem cells-derived cortical neurons for high throughput imaging of neurite morphology and neuron maturation
<p>Figure 5: Whole cell patch clamping showed the differentiated neurons are functional.</p>
Generation of human induced pluripotent stem cells-derived cortical neurons for high throughput imaging of neurite morphology and neuron maturation
<p>Figure 3 - Neurite outgrowth dataset. Comparing neurite outgrowth at Day1 and 15 post-seeding cortical neural progenitors. </p>
The MR1/MAIT cell axis reduces dystrophic neurite development in Alzheimer’s disease
GEO Series GSE273139. Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing.
Functional Recovery from Human Pluripotent Stem-Derived Dopamine Neuron Grafts is Dependent on Neurite Outgrowth
GEO Series GSE186243. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
Axon guidance signal ensures neurite growth pace while sensitizing repulsive cues through induction of a dual function facilitator
GEO Series GSE196558. Mus musculus. 8 samples. Type: Expression profiling by high throughput sequencing.
Peripheral nerve derived fibroblasts promote neurite outgrowth in adult dorsal root ganglion neurons more effectively than skin-derived fibroblasts
GEO Series GSE211427. Rattus norvegicus. 9 samples. Type: Expression profiling by high throughput sequencing.
Typical western diet exacerbates dystrophic neurite pathology in APP/PS1 and APP/PS1/Tau mouse models by reducing the clustering of microglia around β-amyloid plaques
GEO Series GSE144746. Mus musculus. 45 samples. Type: Expression profiling by high throughput sequencing.
The histone deacetylase complex MiDAC regulates a neurodevelopmental gene expression to control neurite outgrowth [RNA-Seq]
GEO Series GSE131060. Mus musculus. 10 samples. Type: Expression profiling by high throughput sequencing.
Profiling of soma and neurite transcriptomes
GEO Series GSE67828. Mus musculus. 48 samples. Type: Expression profiling by high throughput sequencing.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.