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50 results for “virus particle”
Supplementary Material: Fluorescent Protein‐Tagged Sindbis Virus E2 Glycoprotein Allows Single Particle Analysis of Virus Budding from Live Cells
<p>Supplementary Videos for <em>Viruses</em> <strong>2015</strong>, <em>7</em>(12), 6182-6199; doi:10.3390/v7122926, http://www.mdpi.com/1999-4915/7/12/2926:</p> <p><strong>Video S1A</strong> BHK cells infected with mCherry-E2 virus at 3 h p.i. Glycoprotein containing vesicles are transported to the PM from where individual virions bud out. White arrow point to budding virions. Overall amount of glycoproteins present on the PM and the number of virus particles budding out are relatively reduced compared to the late stage of infection. Images were acquired at a rate of 0.99 fps and 75 frames were acquired. Video was generated using these images and played at a rate of 5 fps. Image acquisition time is shown as Time: hour: minute: second: millisecond (h:min:sec:msec ) and the scale bar represents 10 μm.</p> <p><strong>Video S1B </strong>Enlarged area of video S1A showing budding virus particles from PM. White arrow indicates single particle post-budding moving away from the cell. Images were acquired at a rate of 0.99 fps and 75 frames were acquired. Video was generated using these images and played at a rate of 5 fps. Image acquisition time is shown as Time: hour: minute: second: millisecond (h:min:sec:msec ) and the scale bar represents 10 μm.</p> <p><strong>Video S2A</strong> Virus budding and single particle movement associated with filopodial extensions observed from mCherry-E2 virus-infected BHK cells at 6 h p.i. Glycoprotein containing vesicle transport to the PM is also observed. Budded virions travel along the periphery of filopodia and are released from filopodial extensions to the surrounding media. Image acquisition was at a rate of 1 fps and 285 frames were acquired. Movie was generated using these images and played at a rate of 7 fps. Image acquisition time is shown as Time: h:min:sec:msec and the scale bar represents 10 μm.</p> <p><strong>Video S2B</strong> Enlarged area of video S2A showing budding virus particles from filopodia. White arrow indicates virus budding from filopodial extensions. Images were acquired at a rate of 1 fps and the acquired 285 frames were used to generate the video at a rate of 7 fps. Image acquisition time is shown as Time: h:min:sec:msec and the scale bar represents 10 μm.</p> <p><strong>Video S3</strong> BHK cells transfected with RNA from a non-budding cdE2 mutant <sub>416</sub>CC<sub>417</sub>/A2 mCherry-E2 virus. This non-budding mutant is unable to release fluorescent virus particles from the infected cells. The video shows the absence of fluorescent virus particle budding from the PM at 6 h post transfection even though the PM and filopodial extensions contain mCherry-E2. Despite the transport of glycoproteins to the PM, no fluorescent particles were released into the media. Yellow arrows point toward filopodial extensions. For the video, 304 images were acquired at a rate of 0.98 fps and the video was generated using the acquired images at a rate of 7 fps. Image acquisition time is shown as Time: h:min:sec:msec and the scale bar represents 10 μm.</p> <p><strong>Video S4</strong> BHK cells transfected with RNA from an E1 Fusion loop (G91D) mutant of mCherry-E2 virus at 6 h post transfection. This non-fusing mutant produces fluorescent virus particles at a slower rate compared to WT that are unable to fuse after entering a new cell. White arrow points to fluorescent particles that are releasing into the media from filopodial extensions. Yellow arrow represents a fluorescent particle that had entered an adjacent un-transfected cell. A total of 149 images were acquired at a rate of 0.98 fps. Video was generated using these images at a rate of 7 fps. Image acquisition time is shown as Time: h:min:sec:msec and the scale bar represents 10 μm.</p> <p> </p> <p><strong>Video S5A</strong> Glycoprotein E2 (mCherry-E2; red) colocalizing with Golgi stain (green) in BHK cells infected with mCherry-E2 virus and stained with BODIPY FL C5 ceramide at 5 h p.i. and imaged at 6 h p.i. Glycoprotein-containing red vesicles originate from Golgi as evidenced from the colocalization of red and green and these vesicles display anterograde transport to the PM and the virus particles are released by budding from the PM. Fluorescent particles are also seen budding from filopodial extensions (white arrows). Images were acquired at a rate of 0.13 fps for 295 seconds. Video was generated using these acquired images at a rate of 5 fps. Image acquisition time is shown as Time: h:min:sec:msec and the scale bar represents 10 μm.</p> <p><strong>Video S5B</strong> An enlarged area of the video S5A near the white arrow showing movement of particles on filopodial extensions between two cells. Movie was played at a rate of 5 fps. Image acquisition time is shown as Time: h:min:sec:msec and the scale bar represents 10 μm.</p> <p> </p> <p> </p>
CryoVirusDB: An Expert Labelled Cryo-EM Image Dataset for AI-Driven Virus Particle recognition and Extraction
<p><span>With the advancements in instrumentation, image processing algorithms, and computational capabilities, single-particle electron cryo-microscopy (cryo-EM) has achieved nearly atomic resolutions in the 3D reconstruction of viruses. These detailed structures play a crucial role in comprehending the biological functions and advancing the development of more precise vaccines and antiviral treatments. Despite the effectiveness of deep learning in analyzing microscopic images, its potential in identifying and extracting virus particles from cryo-EM micrographs has been hindered by the limited availability of diverse and high-quality datasets. In this study, we introduce 'CryoVirusDB,' a labeled dataset containing coordinates of accurately selected virus particles in cryo-EM micrographs. CryoVirusDB comprises 9,941 micrographs featuring 9 different viruses along with the coordinates of 0.2 million virus particles in total. We anticipate that CryoVirusDB will enhance the capabilities of deep learning in accurately identifying virus particles in cryo-EM micrographs, thereby facilitating the subsequent 2D-3D reconstruction process.</span></p> <p><span>Instructions to download and use dataset: https://github.com/BioinfoMachineLearning/CryoVirusDB</span></p>
"Palmitoylation Mediates Membrane Association of Hepatitis E Virus ORF3 Protein and is Required for Infectious Particle Secretion"
<p><strong>Hepatitis E virus (HEV) is a positive-strand RNA virus encoding 3 open reading frames (ORF). HEV ORF3 protein is a small, hitherto poorly characterized protein involved in viral particle secretion and possibly other functions. Here, we show that HEV ORF3 protein forms membrane-associated oligomers. Immunoblot analyses of ORF3 protein expressed in cell-free <em>vs</em>. cellular systems suggested a posttranslational modification. Further analyses revealed that HEV ORF3 protein is palmitoylated at cysteine residues in its N-terminal region, as corroborated by <sup>3</sup>H-palmitate labeling, the investigation of cysteine-to-alanine substitution mutants and treatment with the palmitoylation inhibitor 2-bromopalmitate (2-BP). Abrogation of palmitoylation by site-directed mutagenesis or 2-BP treatment altered the subcellular localization of ORF3 protein, reduced the stability of the protein and strongly impaired the secretion of infectious particles. </strong><strong>Moreover, selective membrane permeabilization coupled with immunofluorescence microscopy revealed that HEV ORF3 protein is entirely exposed to the cytosolic side of the membrane, allowing to propose a model for its membrane topology and interactions required in the viral life cycle. </strong><strong>In conclusion, palmitoylation determines the subcellular localization, membrane topology and function of HEV ORF3 protein in the HEV life cycle. </strong></p>
Supplementary Material: HIV-1-Induced Small T Cell Syncytia Can Transfer Virus Particles to Target Cells through Transient Contacts
<p>Videos supplementary to <em>Viruses</em> <strong>2015</strong>, <em>7</em>(12), 6590-6603; doi:10.3390/v7122959</p> <p><strong>Captions:</strong></p> <p><strong>Movie S1.</strong> <strong>HIV-1-infected cells in the lymph node of humanized mice.</strong></p> <p>Humanized BLT mice were injected in the footpad with HIV-nGFP, where GFP is highly enriched in cellular nuclei, and the draining popliteal lymph node prepared for MP-IVM at day 2. Representative infected cells (GFP+; green) that display one, two or three discernible nuclei are shown (<strong>top</strong>). In the bottom panels, green fluorescence signals above 80% of the intensity maximum were used to define cell nuclei, which are shown in white. The syncytium with two discernible nuclei remains elongated throughout the recording, while the syncytium with three discernible nuclei switches between coordinated and uncoordinated motility. Each individual frame is a maximum intensity projection of 11 <em>z</em>-stacks spaced 4 μm apart (for a total volume of 40 μm). Time is shown in minutes and seconds. Scale bar = 20 μm. See also Figure 1A.</p> <p><strong>Movie S2.</strong> <strong>Syncytia in the lymph node contact uninfected T cells without undergoing cell-cell fusion</strong>.</p> <p><em>In vitro</em>-generated central memory CD4+ T cells, either infected with HIV-GFP (GFP+; green) or uninfected (labeled with CellTracker Orange; red), were adoptively transferred by footpad injection into BLT mice pretreated with antiretroviral drugs (100 mg/kg FTC, 150 mg/kg TDF). After 12 h, the draining popliteal lymph node was prepared for MP-IVM. Two representative movies of T cell migration prior to (yellow circle) and during<br /> (blue circle) transient interactions with syncytia are shown, demonstrating cellular interactions without fusion. Each individual frame is a maximum intensity projection of 11 <em>z</em>-stacks spaced 4 μm apart (for a total volume of 40 μm). Time is shown in minutes and seconds. Scale bar = 40 μm. See also Figure 1F,G.</p> <p><strong>Movie S3.</strong> <strong>CD4</strong><strong>+ T cells in 3D culture form small syncytia with elongated morphology</strong>.</p> <p>Primary human CD4+ T cells isolated from a healthy donor were infected with VSV-G-pseudotyped NL4-3<sup>Gag-iGFP</sup> virus. The next day, cells were embedded in a 3D collagen gel as described in the Experimental Section, and 12 h later imaged live at 37 °C using a 20× objective on a DeltaVision widefield microscope. Six 3 µm-spaced Z-slices were taken every 20 s, and were subsequently projected into one image. The syncytium seen here in green has two nuclei located at opposite ends, and a central bulged region with high amounts of viral Gag. The diffuse fluorescence is a result of this syncytium being located at a higher part of the gel, where the limitations of widefield imaging become more prominent. See also Figure 2A.</p> <p><strong>Movie S4.</strong> <strong>Small CEM-SS syncytia in 3D culture can dynamically change their morphology</strong>.</p> <p>CEM-SS cells were infected with VSV-G-pseudotyped NL4-3<sup>Gag-iGFP</sup> virus. The next day, cells were embedded in a 3D Matrigel gel as described in the Experimental Section, and 24 h later imaged live at 37 °C using a<br /> 40× objective on a DeltaVision widefield microscope. Seven 2 μm-spaced Z-slices were taken every 5 min, and were subsequently projected into one image. A syncytium with two nuclei (dark areas within the cell in the GFP channel) begins with two lobes, which merge into a coordinated round morphology as the cell begins to migrate through the gel and leaves the plane of focus. See also Figure 2B.</p> <p><strong>Movie S5.</strong> <strong>CD4</strong><strong>+ T cells in 3D culture exhibit </strong><strong><em>in vivo</em>-like migratory behavior</strong>.</p> <p>Primary human CD4<sup>+</sup> T cells were infected, embedded in collagen, and imaged as in Movie S3 (though with a<br /> 10 s time lapse). The uninucleated infected cell migrating across the field moves by 108 μm over 560 s, for a mean velocity of 11.58 μm/min. Such fast directed amoeboid motility is not typically observed in classical 2D culture and requires the presence of a 3D ECM. See also Figure 2C.</p> <p><strong>Movie S6.</strong> <strong>Uninucleated infected cells and syncytia can transfer virus to target cells without fusion.</strong></p> <p>CEM-SS cells were infected, embedded in Matrigel, and imaged as in Movie S4. Virus transfer from a uninucleated infected cell (top) and a syncytium (bottom left) to a number of target cells (denoted by T) can be seen here.<br /> The uninucleated infected cell transfers virus to target cells T1–T5, and the syncytium transfers virus to target cells T6–T7. Images shown represent brightfield in gray (bottom right), or Gag-iGFP in green, shown either with normal scaling (bottom left, and merged with brightfield at top right), or with a 0.6 gamma correction applied and enhanced scaling to better show appearance of Gag-iGFP puncta on target cells (top left). Scale bar = 30 μm. A yellow arrow indicates the moment where the uninucleated infected cell begins transferring virus to target cells T1–T3, and all of the other transfer events in this field are happening at roughly the same time. At this time, Gag-iGFP puncta appear to distribute between cells T1–T3 in a progressive fashion, beginning from the point of contact with the infected cell (see also Figure 3A, middle panel). Cells T4 and T5 also receive virus particles from this infected cell, and T4 can be seen migrating away at the end. Also note a trail of released virus left behind by the uninucleated infected cell as it migrates from left to right from 08:00:00 to 09:10:00 (see also Movies S7 and S9, Figure 4 for similar events in syncytia). The syncytium’s targets, T6 and T7, are already in intimate contact with it at the start of the movie, and are obscured by lobes of the syncytium. At the 10:45:00 mark, cell T6 breaks free from the syncytium, now harboring a large amount of virus particles on its surface, as the syncytium slowly migrates away, and cell T7 also appears to harbor virus particles on its surface by the final time point.</p> <p><strong>Movie S7.</strong> <strong>A virus transfer event between a syncytium and two uninfected target cells.</strong></p> <p>CEM-SS cells were infected, embedded in Matrigel, and imaged as in Movies S4 and S6. The syncytium shown here initially has two nuclei, but soon fuses with an uninfected cell and now has three clearly visible nuclei. It remains stationary for several hours, before beginning to migrate towards a pair of uninfected target cells (top). Very soon after contact, virus particles can be seen covering the surface of both cells, one of which eventually migrates away. See also Figure 3A (left panel). Note also another instance of a dense accumulation of cell-free virus particles in what appears to be a pocket within the hydrogel that the syncytium moves one of its lobes out of, revealing the deposited free virus, before it moves back into the pocket. See also Figure 4A.</p> <p><strong>Movie S8.</strong> <strong>Cell-to-cell transfer of virus can take place while cells are migrating.</strong></p> <p>CEM-SS cells were infected, later mixed with CMAC-labeled uninfected CEM-SS cells (shown in blue), embedded in collagen, and imaged as above. A syncytium with two nuclei (one of which bears CMAC signal, indicating that it formed recently and not before the infected culture was mixed with the labeled uninfected cells) migrates across the field. Its trailing edge contacts an uninfected CMAC-labeled cell, which is then dragged along with it, and finally dropped in the corner of the field. The target cell now bears virus particles on its surface, and is no longer in contact with the syncytium, which has moved into a different focal plane and stopped migrating (not shown). The image was refocused at the 10:30:00 mark to better show the target cell and the virus particles on its surface. Note that this movie also shows an instance of newly synthesized Gag-iGFP appearing in a previously uninfected cell (not the target cell contacted by the syncytium). This non-CMAC labeled uninfected cell appears in the bottom left of the field at 07:20:00 and exhibits steadily increasing diffuse intracellular signal, as documented in Figure 3A (right) and Figure 3B,C (green traces).</p> <p><strong>Movie S9.</strong> <strong>Migrating infected cells can deposit a trail of released virus particles</strong>.</p> <p>CEM-SS cells were infected, embedded in Matrigel, and imaged as in Movies S4, S6, and S7. A syncytium with 3 nuclei switches into a coordinated morphology and begins migrating across the field. Released virus particles can be seen in its wake (also shown enlarged and with increased brightness as an inset). Shortly after the end of the movie, the cell-free virus accumulation appeared to dissipate (not shown), but it could not be determined whether this was because of photobleaching or if they had in fact diffused away. See also Figure 4B.</p>
Efficacy, Safety, and Immunogenicity of a Plant-Derived Quadrivalent Virus-Like Particles (VLPs) Influenza Vaccine in Adults
ClinicalTrials.gov study NCT03301051. IPD Sharing: NO. Countries: 7. Publications: 1.
VRC 313: A Trivalent Virus-like Particle (VLP) Encephalitis Vaccine (WEVEE) in Healthy Adults
ClinicalTrials.gov study NCT03879603. IPD Sharing: NO. Countries: 1. Publications: 3.
Safety and Immunogenicity of Norovirus GI.1/GII.4 Bivalent Virus-Like Particle (VLP) Vaccine in Children
ClinicalTrials.gov study NCT02153112. IPD Sharing: YES. Countries: 3. Publications: 1.
Efficacy of a Plant-derived Quadrivalent Virus-like Particle (VLP) Vaccine in the Elderly
ClinicalTrials.gov study NCT03739112. IPD Sharing: Not stated. Countries: 5. Publications: 1.
Safety and Immunogenicity of Norovirus Bivalent Virus-Like Particle Vaccine in Healthy Adults
ClinicalTrials.gov study NCT02142504. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Serologic Assay Validation, Proficiency Testing, Safety and Immunogenicity of Norovirus GI.1/GII.4 Bivalent Virus-Like Particle Vaccine
ClinicalTrials.gov study NCT02475278. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Lot-to-lot Consistency of a Plant-Derived Quadrivalent Virus-Like Particles Influenza Vaccine in Healthy Adults
ClinicalTrials.gov study NCT03321968. IPD Sharing: NO. Countries: 1. Publications: 1.
Phase 2 Open-label Study of Alum-adjuvanted Chikungunya Virus-like Particle Vaccine (PXVX0317)
ClinicalTrials.gov study NCT03992872. IPD Sharing: NO. Countries: 1. Publications: 1.
Engineered virus-like particles for transient delivery of prime editor ribonucleoprotein complexes in vivo
Open the record for dataset details and reuse information.
Particle picks of HIV virus-like particles from cryo-electron tomography data
<p>Particle picks of HIV virus-like particles from cryo-electron tomography data in EMPIAR-10164. Modified from https://zenodo.org/doi/10.5281/zenodo.6504890 to add pixel size to the particle picks file.</p>
Datasets for: Inactivation mechanisms of Influenza A virus under pH conditions encountered in aerosol particles as revealed by whole-virus HDX-MS.
<p>Datasets associated with the publication '<strong>Inactivation mechanisms of Influenza A virus under pH conditions encountered in aerosol particles as revealed by whole-virus HDX-MS</strong>', published by mSphere [DOI: <a href="http://dx.doi.org/10.1128/msphere.00226-23">10.1128/msphere.00226-23</a>]</p> <p>Data included here encompasses infectivity (IAV and VSV), RT-qPCR , and HDX-MS datasets. </p> <p>The raw mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD037176.</p>
Safety Study of a Plant-based H5 Virus-Like Particles (VLP) Vaccine in Healthy Adults
ClinicalTrials.gov study NCT00984945. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Study of a Severe Acute Respiratory Syndrome CoV-2 (SARS-CoV-2) Virus-like Particle (VLP) Vaccine in Healthy Adults
ClinicalTrials.gov study NCT04818281. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Long-Term Immunogenicity of the Norovirus GI.1/GII.4 Bivalent Virus-like Particle (VLP) Vaccine (NoV Vaccine) in Adults
ClinicalTrials.gov study NCT03039790. IPD Sharing: YES. Countries: 2. Publications: 0.
Immunogenicity, Safety and Tolerability of a Plant-Derived Seasonal Virus-Like-Particle Quadrivalent Influenza Vaccine in Adults
ClinicalTrials.gov study NCT02233816. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Study of a Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) Virus-like Particle (VLP) Vaccine
ClinicalTrials.gov study NCT04962893. IPD Sharing: Not stated. Countries: 1. Publications: 1.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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)
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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.