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opencc-by-4.0Dec 2020View details →

Extracellular vesicles from Fusarium graminearum contain protein effectors expressed during infection of corn

Fusarium graminearum (Fgr) 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 Fgr 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 Fgr 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 (Zea mays) plants infected by Fgr revealed that the genes of some of the effectors were highly expressed in vivo, suggesting that the Fgr 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. The following are available online at www.mdpi.com/xxx/s1, Figure S1. Controls for the separation of EVs from Fusarium graminearum (Fgr) by SEC. Figure S2. The superoxide dismutase [Cu-Zn] (SOD1) from F. graminearum (Fgr) 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 Fusarium graminearum (Fgr). Table S1. List of proteins detected in EVs from Fusarium graminearum (Fgr). Table S2. List of proteins employed in the computational effector prediction analysis. Table S3. Proteins identified in the secretome from Fusarium graminearum (Fgr). Table S4. List of transcripts identified in corn (Zea mays) infected by Fusarium graminearum (Fgr). Table S5. Gene expression values per biological replicate.

opencc-by-4.0Feb 2023View details →

Raw Data for the article: Current Perspectives on Adult Mesenchymal Stromal Cell-Derived Extracellular Vesicles: Biological Features and Clinical Indications

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.

opencc-by-4.0Mar 2023View details →

Dopamine transporter and synaptic vesicle sorting defects underlie auxilin-associated Parkinson's disease

Auxilin participates in clathrin uncoating to facilitate presynaptic endocytosis. Loss-of-function mutations of auxilin (PARK19) cause Parkinson’s disease. Using auxilin KO mice, Vidyadhara et al. (2023) show that synaptic vesicle sorting deficits, cytoplasmic dopamine accumulation, dopamine transporter mistrafficking, and synaptic autophagic overload may lead to pathogenesis of Parkinson’s disease in PARK19 patients. This file contains the data set used to generate all the main figures.

opencc-by-4.0Jan 2023View details →

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.

opencc-by-4.0Jan 2023View details →

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.

opencc-by-4.0Jan 2023View details →

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.

opencc-by-sa-4.0Jul 2023View details →

CELLOIDS: pH-responsive DOPC Giant Unilamellar Vesicles with and without Linoleic Acid

As part of the CELLOIDS project, one of our main research focuses is exploring the feasibility of making the microrobot's membrane responsive to a pH gradient. Specifically, we investigated the incorporation of linoleic acid into Giant unilamellar vesicles composed of DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine). The provided dataset compiles the diameters of liposomes prepared with DOPC (3.18 mM), DOPC:LA (linoleic acid) at a molar ratio of 100:1, and DOPC:LA at a molar ratio of 50:1. These liposomes were placed in buffers at both pH 6 and pH 7, simulating conditions similar to the tumor microenvironment. Our objective was to assess the stability of these liposomes under these conditions. In detail, we carefully prepared liposomes with varying molar ratios of DOPC and linoleic acid to determine the optimal amount of linoleic acid that induces membrane deformation while maintaining the structural integrity of the liposomes in acidic solutions. Subsequently, we subjected the liposomes to testing at the specified concentrations and compared their behavior under two different pH values. Finally, we observed the samples using a phase-contrast microscope immediately after the addition of the solutions and after a one-hour incubation period.

opencc-by-4.0Sep 2023View details →

the supplemental data of 'It is the Frequency that Matters - Effects of Electromagnetic Fields on the Release and Content of Extracellular Vesicles.'

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.’

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Data from: Kif1a and intact microtubules maintain synaptic-vesicle populations at ribbon synapses in zebrafish hair cells

Open the record for dataset details and reuse information.

publicOct 2024View details →

opencc-zeroAug 2020View details →

Hybrid nanoplasmonic porous biomaterial scaffold for liquid biopsy diagnostics using extracellular vesicles: data and media

Raw datasets and media accompanying the manuscript: Hybrid nanoplasmonic porous biomaterial scaffold for liquid biopsy diagnostics using extracellular vesicles, published in ACS Sensors

opencc-by-4.0Jun 2021View details →

Extracellular Vesicles - Basics and Analysis

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.

opencc-zeroDec 2023View details →

Data from: A maximum of two readily releasable vesicles per docking site at a cerebellar single active zone synapse

Recent research suggests that in central mammalian synapses, active zones contain several docking sites acting in parallel. Before release, one or several synaptic vesicles (SVs) are thought to bind to each docking site, forming the readily releasable pool (RRP). Determining the RRP size per docking site has important implications for short-term synaptic plasticity. Here, we take advantage of recently developed methods to count the number of released SVs at single glutamatergic synapses in response to trains of action potentials. In each recording, the number of docking sites was determined by fitting with a binomial model the number of released SVs in response to individual action potentials. After normalization with respect to the number of docking sites, the summed number of released SVs following a train of action potentials was used to estimate of the RRP size per docking site. To improve this estimate, various steps were taken to maximize the release probability of docked SVs, the occupancy of docking sites, as well as the extent of synaptic depression. Under these conditions, the RRP size reached a maximum value close to two SVs per docking site. The results indicate that each docking site contains two distinct SV binding sites that can simultaneously accommodate up to one SV each. They further suggest that under special experimental conditions, as both sites are close to full occupancy, a maximal RRP size of two SVs per docking site can be reached. More generally, the results validate a sequential two-step docking model previously proposed at this preparation.

opencc-zeroJan 2024View details →

Extracellular Vesicles from Pneumocystis carinii-infected rats impair fungal viability but are dispensable for macrophage functions

Pneumocystis 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 in vitro culture system poses challenges in understanding their metabolism and the acquisition of essential nutrients from host lungs remains unexplored. Transmission electron micrographs show Extracellular Vesicles (EVs) are found near Pneumocystisspp. within the lung. We hypothesized that EVs transport essential nutrients to the fungi during infection. To investigate this, EVs from P. carinii- and P. murina-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 Pneumocystis may release EVs. Notably, EV uptake by P. carinii indicated their potential involvement in nutrient acquisition and indicated a possibility for using engineered EVs for efficient therapeutic delivery. However, EVs added to P. carinii in vitro, 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 P. carinii. These findings provide vital insights into P. carinii and host EV interactions, yet the mechanisms underlying P. carinii's survival in the lung remain uncertain. These studies are the first to isolate, characterize, and functionally assess EVs from Pneumocystis-infected rodents, promising to enhance our understanding of host-pathogen dynamics and therapeutic potential.

opencc-by-4.0Jul 2023View details →

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.

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.

opencc-by-4.0Apr 2024View details →

Vesicle and reaction-diffusion hybrid modeling with STEPS

This repository, a snapshot from Github public repository <a href="https://github.com/CNS-OIST/STEPS_Validation/tree/main/vesicles">https://github.com/CNS-OIST/STEPS_Validation/vesicles</a>, contains all data and modeling scripts to reproduce the data presented in:  Iain Hepburn, Jules Lallouette, Weiliang Chen, Andrew R. Gallimore, Sarah Y. Nagasawa-Soeda, Erik De Schutter (2024) Vesicle and reaction-diffusion hybrid modeling with STEPS. Communications Biology 7(1):573. doi:10.1038/s42003-024-06276-5 The repository contains README files with instruction for how to run the model scripts and reproduce the figures. The work presented is based on the simulator STochastic Engine for Pathway Simulation (STEPS) version 5.0.1, which is publicly availble from: https://github.com/CNS-OIST/STEPS/releases/tag/5.0.1

opencc-zeroApr 2024View details →

Human seminal extracellular vesicles enhance endometrial receptivity through leukemia inhibitory factor

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.

opencc-zeroApr 2024View details →

Data from: Pharmacological HIF-1 activation upregulates extracellular vesicle production synergistically with adiponectin through transcriptional induction and protein stabilization of T-cadherin

Pharmacological activation of hypoxia-inducible factor 1alpha (HIF-1α), a hypoxia-responsive transcription factor, has attracted increasing attention due to its efficacy not only in renal anemia but also in various disease models. Our study demonstrated that a HIF-1 activator enhanced exosome production from cultured endothelial cells synergistically with adiponectin, an adipocyte-derived factor, through both transcriptional induction and posttranscriptional stabilization of an adiponectin binding partner, T-cadherin. Increased exosome levels were observed in wild-type mice but not in T-cadherin null mice after consecutive administration of roxadustat. Adiponectin- and T-cadherin-dependent increased exosome production may be involved in the pleiotropic effects of HIF-1 activators.

opencc-zeroApr 2024View details →

Synaptic vesicle glycoprotein 2C enhances vesicular storage of dopamine and counters dopaminergic toxicity

Dopaminergic neurons of the substantia nigra exist in a persistent state of vulnerability resulting from high baseline oxidative stress, high energy demand, and broad unmyelinated axonal arborizations. Impairments in the storage of dopamine compound this stress due to cytosolic reactions that transform the vital neurotransmitter into an endogenous neurotoxicant, and this toxicity is thought to contribute to the dopamine neuron degeneration that occurs Parkinson's disease. We have previously identified synaptic vesicle glycoprotein 2C (SV2C) as a modifier of vesicular dopamine function, demonstrating that genetic ablation of SV2C in mice results in decreased dopamine content and evoked dopamine release in the striatum. Here, we adapted a previously published in vitro assay utilizing false fluorescent neurotransmitter 206 (FFN206) to visualize how SV2C regulates vesicular dopamine dynamics and identified that SV2C promotes the uptake and retention of FFN206 within vesicles. In addition, we present data indicating that SV2C enhances the retention of dopamine in the vesicular compartment with radiolabeled dopamine in vesicles isolated from immortalized cells and from mouse brain. Further, we demonstrate that SV2C enhances the ability of vesicles to store the neurotoxicant 1-methyl-4-phenylpyridinium (MPP+) and that genetic ablation of SV2C results in enhanced 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced vulnerability in mice. Together, these findings establish that SV2C functions to enhance storage of dopamine and toxicants and helps maintain the integrity of dopaminergic neurons.

opencc-by-4.0Oct 2024View details →

Marine vesicles: one more layer of complexity in the dissolved organic fraction

These data include the genome of the Vibrio kanaloae strain, which was isolated in pure culture from a seawater sample collected on May 31, 2022, from Cape Huertas (Alicante, Spain). The genome was sequenced using PacBio HiFi long reads. Additionally,  reads sequences from the extracellular vesicles (EVs) in the 20% OptiPrep fraction were isolated from the Vibrio kanaloae culture incubated in dialysis tubing cellulose membranes (Sigma-Aldrich, ref: D9652-100FT, width: 33 mm, 14 kDa). These membranes were immersed in an aquarium filled with natural seawater collected on December 9, 2022, from Cape Huertas (Mediterranean Sea, Alicante) and incubated at room temperature (approximately 18–20°C) for 1 week. EVs_20_rep1_AQ_1C_culture_1 represents reads of the EVs 20% fraction isolated from the Vibrio kanaloae strain 1C aquarium culture, with rep1 and rep2 denoting the first and second replicates, respectively. The EV reads were analyzed to facilitate a comprehensive evaluation of the representation and distribution of the mapped reads across the Vibrio genome. This mapping approach enables the discernment of whether the mapped reads exhibit a uniform distribution, characteristic of a random DNA release process, or a non-uniform distribution, indicating a proclivity for alignment with specific genetic loci within the Vibrio genome. This distinction is crucial for unraveling the underlying intricacies governing DNA release and transfer in Vibrio kanaloae, thereby advancing our understanding of these complex processes.