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984 results for “Extracellular Vesicles”
Problems with nanoparticle tracking analysis (NTA) of urine extracellular vesicles (uEVs)
<p>Urinary extracellular vesicle (uEV) proteins may be used as specific markers of kidney damage in various pathophysiological conditions. The nanoparticle-tracking analysis (NTA) appears to be the most useful method for the analysis of uEVs due to its ability to analyze particles below 300 nm. The NTA method has been used to measure the size and concentration of uEVs and also allows for a deeper analysis of uEVs based on their protein composition using fluorescence measurements. However, despite much interest in the clinical application of uEVs, their analysis using the NTA method is poorly described and requires meticulous sample preparation, experimental adjustment of instrument settings, and above all, an understanding of the limitations of the method. We present the problems encountered during analysis with possible solutions: the choice of sample dilution, the method of the presentation and comparison of results, photobleaching, and the adjustment of instrument settings for a specific analysis.</p> <p> </p> <p>Figure 1. Expressions of specific markers CD63 in protein-standardized samples detected with Western blot analysis; anti-CD 63 (HPA010088, Sigma-Aldrich, Saint Louis, MO, USA, 1:1000); secondary antibodies conjugated to horseradish peroxidase (554021, BD Pharmingen (BD Biosciences, San Jose, CA, USA) 1:10000).</p> <p> </p> <p>Nanoparticle-Tracking Analysis of uEVs. A NanoSight NS300 instrument (Malvern Panalytical, Malvern, UK) was used to determine the concentrations and sizes of the uEVs in the samples. The total number of extracellular vesicles was measured during the continuous flow of samples delivered from a syringe pump.</p> <p>Figure 2. Determination of the size and concentration of uEVs: dilution factor—1:100; laser—405 nm.</p> <p>Figure 3. Effect of dilution on total number of particles per milliliter and size of uEVs in nanoparticle tracking analysis: sample dilutions—1:100, 1:500, and 1:1000; laser—488 nm.</p> <p>Figure 5. Fluorescence-based nanoparticle-tracking analysis of CD 63 expression in uEVs: without 500 nm long-pass filter; with 500 nm long-pass filter; comparison of sizes and concentrations of uEVs without and with 500 nm long-pass filter; dilution factor—1:100; laser—488 nm; anti-CD 63 (HPA010088, Sigma-Aldrich); secondary antibodies conjugated to Alexa Fluor 488 fluorescent dye (ab150073-500, Abcam, Cambridge, MA, USA).</p> <p>Figure 6. Fluorescence-based nanoparticle-tracking analysis of podocin expression in uEVs: without 500 nm long-pass filter; with 500 nm long-pass filter; comparison of sizes and concentrations of uEVs without and with 500 nm long-pass filter; dilution factor—1:100; laser—488 nm; anti-podocin (P0372, Sigma-Aldrich); secondary antibodies conjugated to Alexa Fluor 488 fluorescent dye (ab150073-500, Abcam, Cambridge, MA, USA).</p>
Ergolide Mediates Anti-Cancer Effects on Metastatic Uveal Melanoma Cells and Modulates their Cellular and Extracellular Vesicle proteomes
<p>Underlying dataset and extended dataset of the results described in the article "Ergolide Mediates Anti-Cancer Effects on Metastatic Uveal Melanoma Cells and Modulates their Cellular and Extracellular Vesicle proteomes".</p>
Fourier-transform Infrared (FT-IR) spectroscopy fingerprints subpopulations of extracellular vesicles of different sizes and cellular origin
<p>Atomic Force Microscopy images of Large (LEV), Medium (MEV) and Small (SEV) Extrzcellular vesicles (EVs) from murine cell line B16 (B16-F10, ATCC CRL-647; Mus musculus, mouse; tissue: melanoma skin). Image size 8.3 x 8.3 um. Analysis mode: Tapping mode in air as described in Paolini et al. https://doi.org/10.1080/20013078.2020.1741174</p>
Low dose rate radiation induced secretion of TGF-β3 together with an activator in small extracellular vesicles modifies low dose hyper-radiosensitivity through ALK1 binding
<p>This is a collection of results from all clonogenic assays on T-47D cells used in the manuscript "Low dose rate radiation induced secretion of TGF-β3 together with an activator in small extracellular vesicles modifies low dose hyper-radiosensitivity through ALK1 binding". </p> <p>T-47D cells were subjected to various pretreatments: low dose rate priming (0.1-0.3 Gy/h for 1 hour), small extracellular vesicles from irradiated or control cells, irradiated or control cell conditioned medium, MMP/ADAM inhibitor TAPI-2, recombinant TGF-B3, inhibitors of ALK1, ALK2, ALK5 or TGF-BRII, iNOS inhibitor 1400W, recombinant FKBP4, recombinant MMP14 and combinations of these. All pretreatments except low dose rate priming was administered for 24 hours. </p> <p>After pretreatments, cells were seeded to colonies and irradiated with 220 kV x-rays at a dose rate of 22.5 Gy/h or gamma rays from a Co-60 source at a dose rate of 20-25 Gy/h. </p> <p>Colonies were cultured for 2-3 weeks before fixation and manual counting. </p>
DATA: Diversity of extracellular vesicles derived from calli, cell culture and apoplastic fluid of tobacco
<p><span>The data includes .jpg files with fluorescence readings and .csv files with results of concentration and size measurements.</span></p>
Extracellular Vesicles Analysis in the COVID-19 Era: Insights on Serum Inactivation Protocols towards Downstream Isolation and Analysis
<p>Representative AFM images of the samples analyzed in the relative manuscript. Raw data just imported from the AFM multimode native format to the Gwyddion Open source data analysis software</p>
Small extracellular vesicles from malignant ascites of patients with advanced ovarian cancer provide insights into the dynamics of the extracellular matrix
<p>Representative Atomic Force Microscope images collected in liquid on Extracellular Vesicles from Ascite and Cell cultures. Data were collected by Broker Multimode VIII. Images like these were used in the paper to measure the contact angle and size distribution.</p>
Dataset related to article "Glia-to-neuron transfer of miRNAs via extracellular vesicles: a new mechanism underlying inflammation-induced synaptic alterations"
<p>This record contains raw data related to article "Glia-to-neuron transfer of miRNAs via extracellular vesicles: a new mechanism underlying inflammation-induced synaptic alterations"</p> <p>Recent evidence indicates synaptic dysfunction as an early mechanism affected in neuroinflammatory diseases, such as multiple sclerosis, which are characterized by chronic microglia activation. However, the mode(s) of action of reactive microglia in causing synaptic defects are not fully understood. In this study, we show that inflammatory microglia produce extracellular vesicles (EVs) which are enriched in a set of miRNAs that regulate the expression of key synaptic proteins. Among them, miR-146a-5p, a microglia-specific miRNA not present in hippocampal neurons, controls the expression of presynaptic synaptotagmin1 (Syt1) and postsynaptic neuroligin1 (Nlg1), an adhesion protein which play a crucial role in dendritic spine formation and synaptic stability. Using a Renilla-based sensor, we provide formal proof that inflammatory EVs transfer their miR-146a-5p cargo to neuron. By western blot and immunofluorescence analysis we show that vesicular miR-146a-5p suppresses Syt1 and Nlg1 expression in receiving neurons. Microglia-to-neuron miR-146a-5p transfer and Syt1 and Nlg1 downregulation do not occur when EV-neuron contact is inhibited by cloaking vesicular phosphatidylserine residues and when neurons are exposed to EVs either depleted of miR-146a-5p, produced by pro-regenerative microglia, or storing inactive miR-146a-5p, produced by cells transfected with an anti-miR-146a-5p. Morphological analysis reveals that prolonged exposure to inflammatory EVs leads to significant decrease in dendritic spine density in hippocampal neurons in vivo and in primary culture, which is rescued in vitro by transfection of a miR-insensitive Nlg1 form. Dendritic spine loss is accompanied by a decrease in the density and strength of excitatory synapses, as indicated by reduced mEPSC frequency and amplitude. These findings link inflammatory microglia and enhanced EV production to loss of excitatory synapses, uncovering a previously unrecognized role for microglia-enriched miRNAs, released in association to EVs, in silencing of key synaptic genes.</p>
Dataset related to article "Decoding distinctive features of plasma extracellular vesicles in amyotrophic lateral sclerosis"
<p>The mass spectrometry proteomics data have been deposited at the ProteomeXchange Consortium (<a href="http://proteomecentral.proteomexchange.org/cgi/GetDataset">http://proteomecentral.proteomexchange.org/cgi/GetDataset</a>) via the PRIDE partner repository with the data set identifier PXD020629.</p>
Extracellular vesicles from Fusarium graminearum contain protein effectors expressed during infection of corn
<p><em>Fusarium</em> <em>graminearum</em> (<em>Fgr</em>) is a devastating filamentous fungal pathogen that causes diseases in cereals, while producing mycotoxins that are toxic for humans and animals, and render grains unusable. Low efficiency in managing <em>Fgr</em> poses a constant need for identifying novel control mechanisms. Evidence that fungal extracellular vesicles (EVs) from pathogenic yeast have a role in human disease led us to question whether this is also true for fungal plant pathogens. We separated EVs from <em>Fgr</em> and performed a proteomic analysis to determine if EVs carry proteins with potential roles in pathogenesis. We revealed that protein effectors, which are crucial for fungal virulence, were detected in EV preparations and some of them did not contain predicted secretion signals. Furthermore, a transcriptomic analysis of corn (<em>Zea</em> <em>mays</em>) plants infected by <em>Fgr</em> revealed that the genes of some of the effectors were highly expressed in vivo, suggesting that the <em>Fgr</em> EVs are a mechanism for the unconventional secretion of effectors and virulence factors. Our results expand the knowledge on fungal EVs in plant pathogenesis and cross-kingdom communication, and may contribute to the discovery of new antifungals.</p> <p>The following are available online at www.mdpi.com/xxx/s1, Figure S1. Controls for the separation of EVs from <em>Fusarium</em> <em>graminearum</em> (<em>Fgr</em>) by SEC. Figure S2. The superoxide dismutase [Cu-Zn] (SOD1) from F. <em>graminearum</em> (<em>Fgr</em>) contains a diacidic amino acid motif implicated in unconventional secretion. Figure S3. Sequence alignment of the chitinase GH18 domain. Figure S4. Computational prediction of effector candidates detected in EV samples from <em>Fusarium</em> <em>graminearum</em> (<em>Fgr</em>). Table S1. List of proteins detected in EVs from <em>Fusarium</em> <em>graminearum</em> (<em>Fgr</em>). Table S2. List of proteins employed in the computational effector prediction analysis. Table S3. Proteins identified in the secretome from <em>Fusarium</em> <em>graminearum</em> (<em>Fgr</em>). Table S4. List of transcripts identified in corn (<em>Zea</em> <em>mays</em>) infected by <em>Fusarium</em> <em>graminearum</em> (<em>Fgr</em>). Table S5. Gene expression values per biological replicate.</p>
Raw Data for the article: Current Perspectives on Adult Mesenchymal Stromal Cell-Derived Extracellular Vesicles: Biological Features and Clinical Indications
<p>Extracellular vesicles (EVs) constitute one of the main mechanisms by which cells communicate with the surrounding tissue or at distance. Vesicle secretion is featured by most cell types, and adult mesenchymal stromal cells (MSCs) of different tissue origins have shown the ability to produce them. In recent years, several reports disclosed the molecular composition and suggested clinical indications for EVs derived from adult MSCs. The parental cells were already known for their roles in different disease settings in regulating inflammation, immune modulation, or transdifferentiation to promote cell repopulation. Interestingly, most reports also suggested that part of the properties of parental cells were maintained by isolated EV populations. This review analyzes the recent development in the field of cell-free therapies, focusing on several adult tissues as a source of MSC-derived EVs and the available clinical data from in vivo models.</p>
Fig. 1 in Secretion of extracellular vesicles during ontogeny of the tapeworm Schistocephalus solidus
Fig. 1. Evidence of secretion of extracellular vesicles (EVs) during the sexual maturation of Schistocephalus solidus (Müller, 1776). A – micrographs from the Cryo-TEM of EVs isolated by ultracentrifugation from the cultivation medium with adults; B, C – Nanosight-based measurements of abundance (B) and volume (C) of different EV subpopulations present in the isolated EVs.
Fig. 2 in Secretion of extracellular vesicles during ontogeny of the tapeworm Schistocephalus solidus
Fig. 2. Transmission electron microscopy of the egg and procercoid stages of Schistocephalus solidus (Müller, 1776). A – solid struc- ture of the egg shell; B – detail of an extracellular vesicle (EV)-like body in the underlying outer envelope; C – multivesicular bodies (MVB)-like structure with two distinct intraluminal vesicles (ILVs) of different sizes observed in the tissue of the developing embryo; D – EV-like bodies of the same structure and size as the observed ILVs in the lumen of the developing egg; E – procercoid of S. solidus in the infected copepod with a distinct layer of excretory-secretory products (ESP) surrounding the surface layer; F – detail of the EVlike bodies in the ESP-layer; G – vesicles/MVB-like structures in the underlying distal cytoplasm. Abbreviations: db – dense body; dc – distal cytoplasm; esp – excretory-secretory products; evl – extracellular vesicle-like body; ilv – intraluminal vesicle; mvb – multivesicular body; ft – filithrix; oe – outer envelope; sh – shell; v – vesicle.
Fig. 3 in Secretion of extracellular vesicles during ontogeny of the tapeworm Schistocephalus solidus
Fig. 3. Transmission electron microscopy of the plerocercoid and adult stages of Schistocephalus solidus (Müller, 1776). A, B – over- view of the internal structure of the syncitial tegument in plerocercoid (A) and adult (B); C, D – extracellular vesicles (EVs) of classical and elongated form (eEV) secreted on the surface of plerocercoids (C) and adults (D). Moreover, fusion of a dense body with the surface membrane is detected (arrow) (C); E, G – detail of multivesicular body (MVB)-like structures and their intraluminal vesicles (ILVs) in the syncitial tegument of plerocercoids (E) and adults (G); F – surface protuberances forming chains of EV-like structures that break (arrow) into separate EVs (F). Abbreviations: db – dense body; dc – distal cytoplasm; eEV – elongated extracellular vesicle; ev – extracellular vesicle; ft – filithrix; ilv – intraluminal vesicle; mvb – multivesicular body; sp – surface protuberance.
the supplemental data of 'It is the Frequency that Matters - Effects of Electromagnetic Fields on the Release and Content of Extracellular Vesicles.'
<p>This data set is the supplemental data of the manuscript ‘It is the Frequency that Matters - Effects of Electromagnetic Fields on the Release and Content of Extracellular Vesicles.’</p>
Hybrid nanoplasmonic porous biomaterial scaffold for liquid biopsy diagnostics using extracellular vesicles: data and media
<p>Raw datasets and media accompanying the manuscript: <strong>Hybrid nanoplasmonic porous biomaterial scaffold for liquid biopsy diagnostics using extracellular vesicles</strong>, published in ACS Sensors</p>
Extracellular Vesicles - Basics and Analysis
<p>On June 21, the 2nd IPANEMA Invited SOL on Extracellular Vesicles - Basics and Analysis was organized. The lecture has been given by Dr. Maja Kosanovic from the Institute for Application of Nuclear Energy, University of Belgrade.</p>
Extracellular Vesicles from Pneumocystis carinii-infected rats impair fungal viability but are dispensable for macrophage functions
<p><em>Pneumocystis</em> spp. are host obligate fungal pathogens that can cause severe pneumonia in mammals and rely heavily on their host for essential nutrients. The lack of a sustainable <em>in vitro</em> culture system poses challenges in understanding their metabolism and the acquisition of essential nutrients from host lungs remains unexplored.</p> <p>Transmission electron micrographs show Extracellular Vesicles (EVs) are found near <em>Pneumocystis</em>spp. within the lung. We hypothesized that EVs transport essential nutrients to the fungi during infection. To investigate this, EVs from <em>P. carinii</em>- and <em>P. murina-</em>infected rodents were biochemically and functionally characterized. These EVs contained host proteins involved in cellular, metabolic, and immune processes as well as proteins with homologs found in other fungal EV proteomes, indicating <em>Pneumocystis</em> may release EVs. Notably, EV uptake by<em> P. carinii</em> indicated their potential involvement in nutrient acquisition and indicated a possibility for using engineered EVs for efficient therapeutic delivery. However, EVs added to <em>P. carinii</em> <em>in vitro</em>, did not show increased growth or viability, implying that additional nutrients or factors are necessary to support their metabolic requirements. Exposure of macrophages to EVs increased proinflammatory cytokine levels but did not affect macrophages' ability to kill or phagocytose <em>P. carinii</em>. These findings provide vital insights into <em>P. carinii</em> and host EV interactions, yet the mechanisms underlying <em>P. carinii</em>'s survival in the lung remain uncertain. These studies are the first to isolate, characterize, and functionally assess EVs from <em>Pneumocystis</em>-infected rodents, promising to enhance our understanding of host-pathogen dynamics and therapeutic potential.</p>
Supplementary material Next-generation sequencing reveals that miR-16-5p, miR-19a-3p, miR-451a and miR-25-3p cargo in plasma extracellular vesicles differentiates sedentary young males from athletes.
<p>A sedentary lifestyle is a leading risk factor for global mortality. No objective molecular biomarker of sedentarism is available. Extracellular vesicles miRNAs have been described to respond to exercise. Our aim was to identify the extracellular vesicle miRNA profile of chronically trained young male athletes, endurance and resistance, compared to their sedentary counterparts. A descriptive case-control design with 16 sedentary young men, 16 Olympic male endurance athletes and 16 Olympic male resistance athletes. Next Generation Sequencing and RT-qPCR, external and internal validation, were performed in order to analysed extracellular vesicle miRNA profiles. miR-16-5p, miR-19a-3p and miR-451a were significantly upregulated in SED compared to END and RES. Besides, miR-25-3p was specifically down-regulated in END compared to SED. Extracellular vesicle miR-16-5p, miR-19a-3p, miR-451a provide an objective signature of sedentarism irrespective of the type of exercise and miR-25-3p as a specific responder to endurance training. Therefore, this study provides for the first time an objective measure to categorise individuals as sedentary or trained in young male population and moreover, it highlights a common epigenetic modulation between models of training.</p>
Human seminal extracellular vesicles enhance endometrial receptivity through leukemia inhibitory factor
<p>Seminal extracellular vesicles (EVs) contain different subgroups that have diverse effects on sperm function. However, the effect of seminal EVs—especially its subgroups, on the endometrial receptivity was largely unknown. Here, we found that the seminal EVs could be divided into high-density EV (EV-H), medium density EV (EV-M), and low-density EV (EV-L), after purification using iodixanol. Then we demonstrated that EV-H could promote the expression and secretion of leukemia inhibitor factor (LIF) in human endometrial cells. In EV-H-treated endometrial cells, we identified 1274 differentially expressed genes (DEGs). DEGs were enriched in cell adhesion and AKT, STAT3 pathways. Therefore, we illustrated that EV-H enhanced the adhesion of human choriocarcinoma JAr cell spheroids to endometrial cells through the LIF-STAT3 pathway. Collectively, our findings indicated that seminal EV-H could regulate endometrial receptivity through the LIF pathway, which would provide novel insights into male fertility.</p>
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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.