Tao Xu Similar Datasets
Project description:To further investigate the molecular mechanisms by which EVs mediated the abnormal localization of tight junction proteins and adherence junction protein, we performed miRNA microarray analysis of extracellular vesicles isolated from breast cancer cells. miRNA expression in extracellular vesicles was collected from MDA-MB-231-D3H1, MDA-MB-231-D3H2LN, BMD2a and BMD2b breast cancer cell lines.
2015-04-02 | E-GEOD-63445 | biostudies-arrayexpress
Project description:Synaptic vesicles (SVs) perform neurotransmitter uptake inside the presynaptic neuron and their delivery to the synaptic cleft. The molecular composition of SVs was investigated, largely by proteomic analysis and fluorescent microscopy, and a model of an average SV was proposed. However, structural heterogeneity and molecular architecture of individual SVs are not yet well described. Here we used cryo-electron tomography (cryo-ET) to visualize morphological and molecular details of SVs isolated from native sources and inside synapses of cultured neurons. Surprisingly, a large fraction of the SV’s membrane did not show visible proteins. We describe several classes of small proteins on SVs' surface and long proteinaceous densities inside SVs. We identified large V-ATPases and determined their structure using subtomogram average (StA), and showed that it forms a complex with another membrane-embedded protein. Interestingly, V-ATPases were randomly distributed among the SVs irrespective of their sizes. We observed clathrin coats on a subpopulation of the SVs and partially assembled clathrin cages on isolated SVs and SVs inside cells. Finally, we describe non-vesicle-containing clathrin baskets, both from extracted SV preparations and within hippocampal neurons. Our analysis contributes to the understanding of the diversity of SVs and their molecular architecture.
2025-03-17 | PXD045356 | Pride
Project description:current synapse proteomics are restricted to “average” composition of abundant synaptic proteins. Here we performed a subcellular proteomic workflow that could identify and quantify the deep proteome of synaptic vesicles purified from rat whole brain, including previously missing proteins present in a small percentage of central synapses. This synaptic vesicle proteome newly detected many proteins of physiological and pathological relevance particularly in low abundance range, thus providing a resource for future investigations on diversified synaptic functions and neuronal dysfunctions.
Raw data from 3 replicates of synaptosomes (P2') and 3 replicates of SV are deposited here. Each replicate coming from 24 fractions from a peptide fractionation step in the workflow.
2020-12-31 | PXD021549 | JPOST Repository
Project description:Differences in the levels of miRNAs in extracellular vesicles (EVs) between multiple sclerosis (MS) patients and healthy individuals were detected by means of microarray analysis.
2017-11-18 | GSE86863 | GEO
Project description:Synapses are the key structural units of information transmission between nerve cells, and synaptic vesicles play a central role in the release of neurotransmitters. The study of the mouse synaptic vesicles' proteome is helpful for in-depth understanding of mammalian neurophysiological and pathological mechanisms. However, there are relatively few studies on intestinal synapses and synaptic vesicles' content proteins. This study aims to fill this gap and explore the molecular characteristics and functional significance of their proteome.
2025-04-03 | PXD062546 |
Project description:To further investigate the molecular mechanisms by which EVs mediated the abnormal localization of tight junction proteins and adherence junction protein, we performed miRNA microarray analysis of extracellular vesicles isolated from breast cancer cells.
2015-04-02 | GSE63445 | GEO
Project description:Neurotransmitter release occurs through exocytosis of synaptic vesicles. α-Synuclein’s function and dysfunction in Parkinson’s disease and other synucleinopathies is tightly linked to synaptic vesicle binding. Age is the biggest risk factor for synucleinopathy, and ~15% of synaptic vesicle proteins are linked to diseases of the central nervous system. Yet, age- and disease-induced changes in synaptic vesicles remain unexplored. For an unbiased analysis of the synaptic vesicle proteome, we applied quantitative mass spectrometry to crude synaptic vesicles isolated at three time points (1 month, 3 months, and 10 months of age) from wild-type mice, alpha-synuclein knockout mice, and alpha-synuclein BAC mice, which express human wild-type alpha-synuclein under all human regulatory elements in absence of mouse alpha-synuclein, providing human-like spatiotemporal expression of alpha-synuclein and recapitulating motor and pathological features of Parkinson’s disease. We identified specific changes in synaptic vesicle proteins that capture aging and synucleinopathies. These findings not only provide new insights into synaptic vesicle biology and mechanisms of synucleinopathy, but also offer a baseline for further mechanistic exploration of age- and disease-related alterations in synaptic vesicles.
2025-05-02 | PXD048771 | Pride
Project description:Synaptic vesicles are organelles with a precisely defined protein and lipid composition, yet the molecular mechanisms for the biogenesis of synaptic vesicles are mainly unknown. Here, we discovered a well-defined interface between the synaptic vesicle V-ATPase and synaptophysin by in situ cryo-electron tomography and single particle cryo-electron microscopy of functional synaptic vesicles isolated from mouse brains. The synaptic vesicle V-ATPase is an ATP-dependent proton pump that establishes the protein gradient across the synaptic vesicle, which in turn drives the uptake of neurotransmitters. Synaptophysin and its paralogs synaptoporin and synaptogyrin belong to a family of abundant synaptic vesicle proteins whose function is still unclear. We performed structural and functional studies of synaptophysin knockout mice, confirming the identity of synaptophysin as an interaction partner with the V-ATPase. Although there is little change in the conformation of the V-ATPase upon interaction with synaptophysin, the presence of synaptophysin in synaptic vesicles profoundly affects the copy number of V-ATPases. This effect on the topography of synaptic vesicles suggests that synaptophysin assists in their biogenesis. In support of this model, we observed that synaptophysin knockout mice exhibit severe seizure susceptibility, suggesting an imbalance of neurotransmitter release as a physiological consequence of the absence of synaptophysin.
2024-06-04 | PXD052814 |
Project description:We have used a combined transcriptome-proteome approach to describe how EPS affected the cargo of extracellular vesicles derived from myotubes from morbidly obese patients with T2D, and revealed several new factors, both miRs and proteins, that might act as exercise factors. During exercise, skeletal muscles release signaling factors that communicate with other organs and mediate beneficial effects of exercise. These factors include myokines, metabolites, and extracellular vesicles (EVs). In the present study, we have examined how electrical pulse stimulation (EPS) of myotubes, a model of exercise, affects the cargo of released EVs. Chronic low frequency EPS was applied for 24 h to human myotubes isolated and differentiated from biopsy samples from 6 morbidly obese females with T2D, and EVs, both exosomes and microvesicles (MV), were isolated from cell media 24 h thereafter.Protein content was assessed by high-resolution proteomic analysis (LC-MS/MS), non-coding RNA was quantified by Affymetrix GeneChip Multispecies miRNA-4_0 Array and Flash Tag TM Biotin RNA labelling, Thermo Fisher), and selected microRNAs (miRs) validated by real time RT-qPCR. We found that human myotubes secrete both exosomes and MV. EPS treatment of the myotubes, clearly changed the protein content of both exosomes and MV, whereas the miR content was changed only in exosomes. We suggest that skeletal muscle derived EVs can contribute to circulatory EVs and mediate beneficial effects of exercise in metabolically active organs.
2023-04-19 | GSE227887 | GEO
Project description:Exosomes/microvesicles (hereafter referred to as extracellular vesicles) were isolated from the ULF of day 14 cyclic and pregnant ewes using ExoQuick-TC. Extracellular vesicle RNA was pooled (n=4 per status) and analyzed for small RNAs by sequencing on the Ion Torrent PGM platform and analysis with CLC Genomics Workbench small RNA workflow based on the miRBase (Release 19) Bos taurus database. Small RNA analysis of day 14 uterine luminal fluid extracellular vesicles isolated from pregnant and cyclic ewes.
2014-01-11 | E-GEOD-53974 | biostudies-arrayexpress