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1,218 results for “Vesicles”
Dataset for: Therapeutic potential of extracellular vesicles in preclinical stroke models: a systematic review and meta-analysis
<p>This upload contains the data extracted from studies included in our meta-analysis entitled "Therapeutic potential of extracellular vesicles in preclinical stroke models: a systematic review and meta-analysis". It also contains the code used to perform the meta-analysis and generate the figures in the publication in R. </p>
Dataset related to article "Intracerebral Injection of Extracellular Vesicles from Mesenchymal Stem Cells Exerts Reduced Aβ Plaque Burden in Early Stages of a Preclinical Model of Alzheimer's Disease."
<p>Bone marrow Mesenchymal Stem Cells (BM-MSCs), due to their strong protective and anti-inflammatory abilities, have been widely investigated in the context of several diseases for their possible therapeutic role, based on the release of a highly proactive secretome composed of soluble factors and Extracellular Vesicles (EVs). BM-MSC-EVs, in particular, convey many of the beneficial features of parental cells, including direct and indirect β-amyloid degrading-activities, immunoregulatory and neurotrophic abilities. Therefore, EVs represent an extremely attractive tool for therapeutic purposes in neurodegenerative diseases, including Alzheimer's disease (AD). We examined the therapeutic potential of BM-MSC-EVs injected intracerebrally into the neocortex of APPswe/PS1dE9 AD mice at 3 and 5 months of age, a time window in which the cognitive behavioral phenotype is not yet detectable or has just started to appear. We demonstrate that BM-MSC-EVs are effective at reducing the Aβ plaque burden and the amount of dystrophic neurites in both the cortex and hippocampus. The presence of Neprilysin on BM-MSC-EVs, opens the possibility of a direct β-amyloid degrading action. Our results indicate a potential role for BM-MSC-EVs already in the early stages of AD, suggesting the possibility of intervening before overt clinical manifestations.</p>
Data from: Profiling extracellular long RNA transcriptome in human plasma and extracellular vesicles for biomarker discovery
<p>The recent discovery of extracellular RNAs in blood, including RNAs in extracellular vesicles (EVs), combined with low-input RNA-sequencing advances have enabled scientists to investigate their role in human disease. To date, most studies have been focusing on small RNAs, and methodologies to optimize long RNAs measurement are lacking. We used plasma RNA to assess the performance of six long RNA sequencing methods, at two different sites, and we report their differences in reads (%) mapped to the genome/transcriptome, number of genes detected, long RNA transcript diversity, and reproducibility. Using the best performing method, we further compare the profile of long RNAs in the EV- and no-EV-enriched RNA plasma compartments. These results provide insights on the performance and reproducibility of commercially available kits in assessing the landscape of long RNAs in human plasma and different extracellular RNA carriers that may be exploited for biomarker discovery.</p>
Towards establishing extracellular vesicle-associated RNAs as biomarkers for HER2+ breast cancer
<p class="Abstract">Extracellular vesicles (EVs) are emerging as key players in breast cancer progression and hold immense promise as cancer biomarkers. However, difficulties in obtaining sufficient quantities of EVs for the identification of potential biomarkers hampers progress in this area. To circumvent this obstacle, we cultured BT-474 breast cancer cells in a two-chambered bioreactor with CDM-HD serum replacement to significantly improve the yield of cancer cell-associated EVs and eliminate bovine EV contamination. Cancer-relevant mRNAs <i>BIRC5 </i>(Survivin) and <i>YBX1</i>,<i> </i>as well as long-noncoding RNAs <i>HOTAIR</i>, <i>ZFAS1</i>, and <i>AGAP2-AS1 </i>were detected in BT-474 EVs by quantitative RT-PCR. Bioinformatics meta-analyses showed that <i>BIRC5 </i>and <i>HOTAIR </i>RNAs were substantially upregulated in breast tumours compared to non-tumour breast tissue, warranting further studies to explore their usefulness as biomarkers in patient EV samples. We envision this effective procedure for obtaining large amounts of cancer-specific EVs will accelerate discovery of EV-associated RNA biomarkers for cancers including HER2+ breast cancer.</p>
the supplemental data of 'The frequency-dependent effect of electrical fields on the mobility of intracellular vesicles in astrocytes'
<p>This data set is the supplemental data of the manuscript ‘The frequency-dependent effect of electrical fields on the mobility of intracellular vesicles in astrocytes’. Due to the size limitation of online storage, this data set contains partial data collected in this work, which consists of one experiment per condition. The full data that support the findings of this study are available from the corresponding author upon reasonable request.</p>
FIGURE 2. Dryinus tarraconensis Marshall, immature larva. A. Lateral view. B. Frontal view. C. Anterior region with cephalic vesicles, frontal view. D in Description of larval instars of Dryinus tarraconensis Marshall, 1868 and Gonatopus baeticus (Ceballos, 1927) (Hymenoptera: Chrysidoidea: Dryinidae), parasitoids of the genus Dictyophara Germar (Hemiptera: Auchenorrhyncha: Dictyopharidae)
FIGURE 2. Dryinus tarraconensis Marshall, immature larva. A. Lateral view. B. Frontal view. C. Anterior region with cephalic vesicles, frontal view. D. Anterior region with cephalic vesicles, lateral view.
AFM-Based High-Throughput Nanomechanical Screening of Single Extracellular Vesicles
<p>I the present study, a novel AFM-based high throughput mechanical characterization for extracellular vesicles is presented. The method relies on the analysis of vesicles morphometry following their adsorption on surfaces. The deformation extent of the vesicle, which is representative of the vesicle stiffness, is evaluated by the calculation of the so-called vesicle contact angle. The method was applied to different etracellular vesicles (EVs) samples from different natural sources and was employed for spotting the presence of non-vesicular contaminants.</p>
Development of a multivariable risk model integrating urinary peptide metabolites and Extracellular Vesicle RNA data to detect significant prostate cancer
<p>The aim of this study was to investigate whether the robust integration of expression data from urinary extracellular vesicle RNA (EV-RNA) with urine proteomic metabolites can accurately predict PCa biopsy outcome. Urine samples were analyzed by mass spectrometry and NanoString gene-expression analysis. As a result, four classifiers were generated: ‘MassSpec’ (CE-MS proteomics), ‘EV-RNA’, ‘SoC’ (standard of care) and ‘ExoSpec’. The best prediction for Gs³3+4 at initial biopsy (AUC=0.83, 95% CI:0.77-0.88) was achieved by applying ‘ExoSpec’ classifier and he outperformed other predictive classifiers. In addition, the results showed that the performance of ‘ExoSpec’ could reduce unnecessary biopsies by 30%.</p>
Cryo-EM structure of gas vesicles - supplementary data
<p>This deposition contains supplementary data from our preprint:</p><p>Huber, S. T., Terwiel, D., Evers, W. H., Maresca, D., & Jakobi, A. J. (2022). Cryo-EM structure of gas vesicles for buoyancy-controlled motility. <i>bioRxiv</i>, 2022-05.</p><p>(Update 26.04.2023), Now in:</p><p>Huber, S. T., Terwiel, D., Evers, W. H., Maresca, D., & Jakobi, A. J. (2023). Cryo-EM structure of gas vesicles for buoyancy-controlled motility. <i>Cell</i>, <i>186</i>(5), 975-986.</p><p> </p><p><strong>2Dclasses_AnaMega_SeamsEdgesWallTips.zip</strong></p><p>This folder contains 2D class averages of different features of <i>A.flos-aquae</i> and <i>B.megaterium</i> gas vesicles (GVs) such as the seams between both GV halves, GV wall edges, collapsed walls and tips. We use this data to inform our pseudo-atomic model of an entire gas vesicle, and derive a model for biogenesis and growth. Some 2D classes provide high-resolution views on the GV wall in projection with a resolution that show the α-helical pitch and large side-chain densities. We use those views to confirm the evolutionarily conserved fold of the gas vesicle wall protein.</p><p>The box size and pixel size of the 2D classes is contained in the file names. A selected and sharpened 2D class for display in the manuscript is included in .png format.</p><p><strong>AlphaFold2_Models_5merRib_DifferentOrganisms.zip</strong></p><p>This folder contains five AlphaFold2 predictions of a single rib of the gas vesicle wall for organisms that are evolutionarily only little related (GvpA1 and GvpA2 from <i>B.megaterium</i>, GvpA from <i>A.flos-aquae</i> and GvpA1 and GvpA2 from <i>H.salinarum</i>). AF2 predicts very similar structure for these organisms, further supporting the high conservation of the gas vesicle wall.</p><p><strong>AnaGvpA_GvpC_ComputationalDocking_HADDOCK.zip</strong></p><p>In the manuscript, we propose a binding mode of the secondary protein GvpC to <i>A.flos-aquae</i> gas vesicles using computational docking with HADDOCK. We present two possible solutions with opposite orientation. The cif-files of the docking solution is contained in this folder.</p><p><strong>GasPoreAnalysis.zip</strong></p><p>We analysed gas pores between α-helix 1 of adjacent GvpA monomers using MOLE2.5. The three resulting tunnels are in this folder. The respective pdb files contain the constriction in Ångstrom in each line. A Chimera 1.13.1 session is included for visualisation.</p>
Exploring the structural dynamics of the vesicle priming machinery
<p>Here are the pdb files for the simulations with only 6 central SNAREs and 6 central and 6 peripheral SNAREs with C2B of Syt1 and residue 51-75 of Cpx1 shown in figure 3.</p> <p>File for figure 3a: ic_6c_snares.pdb is the initial condition for simulations with only 6 central SNAREs, and the tcl file figure_3a.tcl is to show this initial condition.</p> <p>File for figure 3b: ic_6c6p_snares_c2b.pdb is the initial condition for simulations with 6 central and 6 peripheral SNAREs with a vesicle, and the tcl file figure_3b_top_view.tcl and figure_3b_side_view.tcl are to show this initial condition.</p> <p>File for figure 3c: ic_6c6p_snares_c2b_nd.pdb is the initial condition for simulations with 6 central and 6 peripheral SNAREs with a nanodisc and ic_6c6p_snares_c2b_nd.xtc file is the corresponding trajectory of this simulation. The tcl file movie_for_figure_3c.tcl is to show the movie of this simulation. If you want to look at all proteins in this simulation, the tcl file movie_for_figure_3c_all.tcl can do that.</p> <p>To view these snapshots by VMD, load the corresponding .tcl file or run "vmd -e name.tcl" in your terminal.</p>
FIGURES 6–9 in A new endoparasitic gregarine genus, Stomatocystis indica gen. nov., sp. nov. (Apicomplexa: Sporozoea: Stomatophorinae) from the seminal vesicles of an Indian earthworm (Annelida: Oligochaeta) Amynthas diffringens Baird
FIGURES 6–9. Camera lucida drawings of different stages in the life cycle of Stomatocystis indica gen. nov., sp. nov. from seminal vesicles of earthworm Amynthas diffringens Baird. 6. a mature gamont showing central mucron within the sucker; 7. syzygy; 8. gametocytes within a gametocyst; 9. oocyst. Abbreviation: prprotoplasmic ridges. Scale bars: Figs. 7–8 (50 µm), Fig. 9 (10 µm)
FIGURES 1–5 in A new endoparasitic gregarine genus, Stomatocystis indica gen. nov., sp. nov. (Apicomplexa: Sporozoea: Stomatophorinae) from the seminal vesicles of an Indian earthworm (Annelida: Oligochaeta) Amynthas diffringens Baird
FIGURES 1–5. Photomicrographs of different stages in the life cycle of Stomatocystis indica gen. nov, sp. nov. from seminal vesicles of earthworm Amynthas diffringens Baird. 1. a slightly curved trophozoite showing the sucker and epimeritelike structure; 2. enlarged view of the sucker showing protoplasmic ridgelike processes in its lateral margin; 3. syzygy; 4. gametocytes within a gametocyst; 5. navicular oocysts. Abbreviation: prprotoplasmic ridges. Scale bars: Figs. 1–4 (50 µm), Fig. 5 (10 µm)
Annual dynamics and metagenomics of marine vesicles: a layer of complexity in the dissolved organic fraction
<p>The dataset includes additional data for the same paper, <em>"Annual dynamics and metagenomics of marine vesicles: a layer of complexity in the dissolved organic fraction."</em> The data were uploaded separately due to the 50.00 GB limit on available upload space.</p> <p>The gene sequences contained within EVs were annotated using the DRAM program within the Kbase platform, enabling us to identify the specific types and functions of genes packaged within EV fractions. This annotation process provided a comprehensive overview of the genetic cargo potentially encapsulated in EV fractions 25% and 20%.</p> <p>The provided Excel files represent the output from DRAM annotation and contain the detected genes in EV fractions 25% and 20%. Although the gene names in the files are labeled as 30%, 25%, and 20%, this is a naming error. The file labeled "annotation for EVs 25%" contains genes detected in the 25% EV fraction, while the file labeled "annotation for EVs 20%" corresponds to genes from the 20% EV fraction.</p> <p>There are two replicates for the 20% EV fraction, denoted as rep1 and rep2, and both samples were analyzed. The gene abundance was calculated as the mean percentage of the two replicates, corrected with standard error.</p> <p> </p>
Figures for the publication ''The role of small extracellular vesicles and microRNA as their cargo in the spinal cord injury pathophysiology and therapy''
Open the record for dataset details and reuse information.
Long chain lipids facilitate insertion of large nanoparticles into membranes of small unilamellar vesicles
<p>DLS data and Cryo Images of SUVs-QDs</p>
How Can Giant Plasma Membrane Vesicles Serve as a Cellular Model for Controlled Transfer of Nanoparticles?
<p>Data underlying the figures in the publication “How Can Giant Plasma Membrane Vesicles Serve as a Cellular Model for Controlled Transfer of Nanoparticles?”, published in <em>Biomacromolecules</em>, <strong>2021</strong>, 22, 1, 106–115.</p> <p><a href="https://pubs.acs.org/doi/10.1021/acs.biomac.0c00624">https://pubs.acs.org/doi/10.1021/acs.biomac.0c00624</a></p> <p>Table of contents:</p> <p><strong>1. Figure 1</strong>; Zip file containing the data for <em>Figure 1</em>.</p> <p><strong>2. Figure 2</strong>; Zip file containing the TEM micrographs for <em>Figure 2</em>.</p> <p><strong>3. Figure 4</strong>; Zip file containing numerical data of the flow cytometry measurements and analysis for <em>Figure 4</em>.</p> <p><strong>4. Figure 5</strong>; Zip file containing the data for <em>Figure 5</em>.</p> <p><strong>5. Figure 6,7</strong>; Zip file containing numerical data for <em>Figures 6 </em>and <em>7</em>.</p>
Figure 5. Vesicles with silica-like granules within sponge cells. A in Recycling resources: silica of diatom frustules as a source for spicule building in Antarctic siliceous demosponges
Figure 5. Vesicles with silica-like granules within sponge cells. A, an amoeboid sponge cell (spc) in P. areolatus showing a cytoplasm packed with vesicles and an ingested diatom (di) within a large digestive vesicle. Note that three different granule types were identified by microanalysis in the section of this species: silica granules (si), and lead granules (Pb). B–C, highly vesiculated, amoeboid sponge cell in He. pilosus. Note the silica-like granules (si) first present within vesicles and later incorporated within the cytoplasm. D, amoeboid sponge cell in P. areolatus showing an ingested diatom (di) and silica-like granules (si).
Liquid chromatography tandem mass spectrometry of AMPA receptor containing vesicles
<p>Regulated delivery of AMPA receptors (AMPARs) to the postsynaptic membrane is an essential step in synaptic strength modification, and in particular, long-term potentiation (LTP). While LTP has been extensively studied using electrophysiology and light microscopy, several questions regarding the molecular mechanisms of AMPAR delivery via trafficking vesicles remain outstanding, including the gross molecular make up of AMPAR trafficking organelles and identification and location of calcium sensors required for SNARE complex-dependent membrane fusion of such trafficking vesicles with the plasma membrane. Here, we isolated AMPAR containing vesicles (ACVs) from whole mouse brains via immunoisolation and characterized them using immunoelectron microscopy, immunoblotting, and liquid chromatography tandem mass spectrometry (LC-MS/MS). We identified several proteins on ACVs that were previously found to play a role in AMPAR trafficking, including synaptobrevin-2, Rabs, the SM protein Munc18-1, the calcium-sensor synaptotagmin-1, as well as several new candidates, including synaptophysin and synaptogyrin on ACV membranes. Here, we present three biological replicates of liquid chromatography tandem mass spectrometry of AMPA receptor containing vesicles.</p>
Single vesicle fusion experiments illustrating the inhibition of the calcium triggered release by the inhibitory peptide SP9
<p>Synaptic neurotransmitter release is mediated by an orchestra of presynaptic proteins that precisely control and trigger fusion between synaptic vesicles and the neuron terminal at the active zone upon an action potential. Critical to this process are the neuronal SNAREs (Soluble N-ethylmaleimide sensitive factor Attachment protein REceptor), the Ca2+-sensor synaptotagmin, the activator/regulator complexin, and other factors. Here we present the data for single vesicle fusion experiments with synaptic vesicles in absence and presence of the inhibitory peptide SP9 that illustrate the inhibition of calcium-triggered release. </p>
Data set for: "Model atmospheric aerosols convert to vesicles upon entry into aqueous solution"
<p>This document compiles raw data used in the aerosol to vesicle transformation study carried out by <strong>Serge Nader <em>et al.</em></strong><br> For detailed information and context, refer to the main article and its supplementary material published in ACS Earth and Space Chemistry.</p> <p>The Excel file contains data relevant to each figure in the main article and supporting information. The additional compressed file contains raw Transmission Electron Microscopy (TEM) photographs.</p>
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