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342 results for “Electron Microscopy”
Raw electron microscopy micrographs of the Nup84 subcomplex
<p>Raw electron microscopy micrographs of the Nup84 subcomplex of the <em>Saccharomyces cerevisiae </em>Nuclear Pore Complex.</p>
Modeling of the TFIIH complex using chemical cross-links and electron microscopy (EM) density maps
<p>TFIIH is essential for both RNA polymerase II transcription and DNA repair, and mutations in TFIIH can result in human disease. Here, we determine the molecular architecture of human and yeast TFIIH by an integrative approach using chemical crosslinking/mass spectrometry (CXMS) data, biochemical analyses, and previously published electron microscopy maps. We identified four new conserved "topological regions" that function as hubs for TFIIH assembly and more than 35 conserved topological features within TFIIH, illuminating a network of interactions involved in TFIIH assembly and regulation of its activities. We show that one of these conserved regions, the p62/Tfb1 Anchor region, directly interacts with the DNA helicase subunit XPD/Rad3 in native TFIIH and is required for the integrity and function of TFIIH. We also reveal the structural basis for defects in patients with xeroderma pigmentosum and trichothiodystrophy, with mutations found at the interface between the p62 Anchor region and the XPD subunit.</p> <p>For more information about how to reproduce this modeling, see https://salilab.org/tfiih or the README file.</p>
Figs 11–22 in Palp sensory structures in adult caddisflies of the suborder Annulipalpia (Trichoptera): a scanning electron microscopy study
Figs 11–22. Palp sensilla of caddisflies of the suborder Annulipalpia: 11 – N. bimaculata
Figs 7–10 in Palp sensory structures in adult caddisflies of the suborder Annulipalpia (Trichoptera): a scanning electron microscopy study
Figs 7–10. Labial palps of P. apicalis (7–8) and N. bimaculata (9–10) females. 7 – first
Figs 1–6 in Palp sensory structures in adult caddisflies of the suborder Annulipalpia (Trichoptera): a scanning electron microscopy study
Figs 1–6. Medial (1–5) and ventrolateral (6) surfaces of maxillary palp of D. robusta
Data accompanying the paper "Multi-wavelength Raman microscopy of nickel-based electron transport in cable bacteria"
<p>Data accompanying the paper "Resonance Raman microscopy of nickel-based electron transport in cable bacteria"</p>
Data from: Crustacean photoreceptor damage and recovery: Applying a novel scanning electronic microscopy protocol in artificial light at night studies
<p>As sources of artificial light at night (ALAN) expand worldwide, research on their impacts has also increased. Most of these studies, including those in coastal habitats, have focused on behavioral and ecological responses to ALAN, overlooking impacts on the photoreceptor, the basic functional structure of animals to absorb light. Examining structural changes in the photoreceptor is essential to understand the mechanisms by which ALAN may be impacting species, particularly those adapted to different light backgrounds. This study examined the photoreceptor (rhabdom) of two sandy beach crustaceans exhibiting different light tolerances at night: the amphipod <em>Orchestoidea tuberculata</em> and the isopod <em>Tylos spinulosus</em>. We developed a novel protocol to measure these species' photoreceptor areas and quantify the damage caused by ALAN using histological sections and scanning electron microscopy (SEM). Our results showed that in the isopod, a species naturally adapted to lower light intensities at night than the amphipod, the rhabdom surface was 20-times larger, and presented a tapetum, an adaptive feature found in species living in low light conditions. This confirmed that this species is potentially more sensitive to ALAN than the amphipod. Consistently, a brief period of exposure to ALAN (1 h, 20 lux) caused 3-6 times more damage in the isopod' rhabdom. In fact, ALAN caused structural damage in the isopod' but not in the amphipod' rhabdom, a damage that did not show signs of recovery from ALAN after 1 and 24 h. Thus, the damage caused by ALAN on an organism's photoreceptors is likely to be more severe and persistent in species naturally adapted to lower light levels at night. Installation of permanent ALAN sources nearby the burrowing area of these light sensitive species may have differential effects on their activity and interactions at night. ALAN may also become a new selection pressure on these species, a concern with wide implications given the ubiquity among animals of the photoreceptor structure and its response to light.</p>
Automated identification of small molecules in cryo-electron microscopy data with density- and energy-guided evaluation
<p>Data and turorials for ligand identification with EMERALD-ID. Each Zip file contains ligand models and data used to generate their respective figures in the EMERALD-ID manuscript. For specific details, consult the README file in each directory.</p>
Transmission electron microscopy (TEM) images of Silisyum dioxide nanoparticles.
<p>Transmission electron microscopy (TEM) images of Silisyum dioxide nanoparticles.</p>
Gold Nanoparticles Synthesized in the Presence of Peptides - UV-Vis Spectra, Fluorescence, USAXS, Electron Microscopy; pre-publication version
<p>Content Summary:</p> <ul> <li>Data from experiments in which gold nanoparticles were synthesized in the presence of peptides using a liquid-handling robot. Samples were analyzed using UV-Vis spectroscopy, fluorescence emission, USAXS, TEM, and SEM. </li> <li>Notebooks for loading and plotting data</li> <li>Code for synthesizing samples using an OT2 Opentrons liquid-handling robot.</li> </ul> <p>README:</p> <blockquote> <p><strong>/Data</strong></p> <p>Contains all UV-Vis, electron microscopy, fluorescence, and SAXS data for gold nanoparticles synthesized in the presence of peptides and HEPES.</p> <p><strong>/Data/2021_12_30_Prepared_UV_Vis_Data</strong></p> <p>The primary portion of the experimental dataset. UV-Vis spectroscopy data collected on a Biotek Epoch 2 microplate spectrophotometer 24 hours after samples were synthesized using a liquid handling robot (Opentrons OT2). The <strong>4x4x4_SI.csv </strong>file is the compilation of all sample information:</p> <ul> <li>Concentrations (M) of peptide, HAuCl4, and HEPES</li> <li>UID – unique ID based on date of synthesis, sample position, and peptide which was used to synthesize the sample.</li> <li>Peptide names: Z2: RMRMKMK; MZ2: myristoylated - RMRMKMK; MZ2R: myristoylated - KMKMRMR; PZ2: palmitoylated – RMRMKMK; Z2M6I: RMRMKIK; Z2M246I: RIRIKIK; AG3: AYSSGAPPMPPF.</li> </ul> <p>Each sample’s UID is a key to match with UV-Vis measurement result stored in the {<strong>UID}.txt </strong>files. Each of these files contains the wavelength, absorbance, and absorbance after subtraction of a water measurement.</p> <p><strong>/Data/ElectronMicroscopy</strong></p> <p>Scanning electron microscopy and transmission electron microscopy results of gold nanoparticles formed from the reduction of HAuCl4 in the presence or absence of different peptides.</p> <p>Fig A, B, C, D, E/F were prepared in the presence of Z2, Z2M6I, Z2M246I, no peptide, and MZ2R, respectively.</p> <p><strong>/Data/Fluorescence</strong></p> <p>Pyrene fluorescence data collected in the presence of different concentrations of lipidated peptides (MZ2, MZ2R, and PZ2) for estimation of the peptide critical micelle concentration.</p> <p><strong>/Data/SAXS</strong></p> <p>SAXS data of a high concentration of MZ2 which was fit using a cylindrical model form factor. The evaluated model is also shared in this directory.</p> <p><strong>/Data/USAXS</strong></p> <p>Similarly to the UV-Vis data directory, the <strong>USAXS_SI.csv</strong> file contains sample information for all of the USAXS measurements. The <strong>dsm_rg.csv</strong> file contains the output of AUTORG evaluated on the desmeared data after subtraction of a flat background at high-q. <strong>/DSM_Nexus, DSM_sub_AUTORG, </strong>and <strong>SMR_Nexus</strong> contain the desmeared, desmeared with background subtraction, and smeared versions of the USAXS data, respectively.</p> <p><strong>/Notebooks</strong></p> <p>Notebooks for plotting the shared data and estimating the CMC from the fluorescence data. See <strong>/Notebooks/environment.yml</strong> for packages necessary to execute the notebooks here and in <strong>/Synthesis_Protocol</strong>. Refer to <a href="https://github.com/SasView/sasmodels">https://github.com/SasView/sasmodels</a> for specific instructions on how to install the sasmodels module.</p> <p><strong>/Figures</strong></p> <p>Figures generated from <strong>/Notebooks</strong>.</p> <p><strong>/Synthesis_Protocol</strong></p> <p>Please read the instructions within <strong>/Synthesis_Procol/Example.ipynb</strong>. In short, this folder contains the code used to synthesize the samples in this dataset using an OT2 Opentrons liquid handling robot.</p> <p> </p> </blockquote>
Data of the protocol paper: Protein Structural Modeling for Electron Microscopy Maps Using VESPER and MAINMAST
<p>The archived file contains data of the test cases used used in the protocol paper. For each protocol, there's a folder containing input files the protocol takes, and a folder for the protocol output files.</p>
Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy – data set 03
<p>We developed a sedimentation method using desktop ultracentrifugation (see description below) to visualize SARS-CoV-2 particles in suspensions from oro- and/or nasopharyngeal swabs by thin section electron microscopy. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 03 is a stitched image montage recorded from an area of a thin section through the sediment obtained from a swab sample which was positive by quantitative PCR (delta variant). One infected ciliated cell is visible in the center of the recorded area. Virus particles are visible within membrane-bound compartments of the cytoplasm. Spike visibility is poor and some virus particles appear compressed.</p> <p>Related publication: Laue M, Hoffmann T, Michel J, Nitsche A. Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy. Virol J. 2023 Feb 6;20(1):21. doi: 10.1186/s12985-023-01981-9. PMID: 36747188; PMCID: PMC9901382.</p>
Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy – data set 04
<p>We developed a sedimentation method using desktop ultracentrifugation (see description below) to visualize SARS-CoV-2 particles in suspensions from oro- and/or nasopharyngeal swabs by thin section electron microscopy. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 04 is a stitched image montage recorded from an area of a thin section through the sediment obtained from a swab sample which was negative by quantitative PCR (negative control). The recorded area shows the profiles of four keratinocytes which are surrounded by heterogenous material (e.g. membrane lamella, needle-like crystals, round profiles with a fine-fibrous matrix). Virus partricles are not visible.</p> <p>Related publication: Laue M, Hoffmann T, Michel J, Nitsche A. Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy. Virol J. 2023 Feb 6;20(1):21. doi: 10.1186/s12985-023-01981-9. PMID: 36747188; PMCID: PMC9901382.</p>
Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy – data set 01
<p>We developed a sedimentation method using desktop ultracentrifugation (see description below) to visualize SARS-CoV-2 particles in suspensions from oro- and/or nasopharyngeal swabs by thin section electron microscopy. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 01 is a stitched image montage recorded from an area of a thin section through the sediment obtained from a swab sample which was positive by quantitative PCR (delta variant). Two, more or less, intact ciliated cells are visible and surrounded by other cells or cellular debris. The ciliated cell in the upper right corner is infected with SARS-CoV-2. Virus particles are visible within membrane-bound compartments of the cytoplasm. Several double-membrane vesicles, which are typical compartments of the coronavirus replication machinery, are also detectable.</p> <p>Related publication: Laue M, Hoffmann T, Michel J, Nitsche A. Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy. Virol J. 2023 Feb 6;20(1):21. doi: 10.1186/s12985-023-01981-9. PMID: 36747188; PMCID: PMC9901382.</p>
Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy – data set 02
<p>We developed a sedimentation method using desktop ultracentrifugation (see description below) to visualize SARS-CoV-2 particles in suspensions from oro- and/or nasopharyngeal swabs by thin section electron microscopy. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 02 is a stitched image montage recorded from an area of a thin section through the sediment obtained from a swab sample which was positive by quantitative PCR (delta variant). One ciliated cell is visible and surrounded by cellular debris. The ciliated cell is infected with SARS-CoV-2. Few virus particles are visible within membrane-bound compartments of the cytoplasm. Numerous virus particles are located at the cell surface intermingled between the cilia. The virus particles of this cell appear deformed and deviate from the oval/circular profile which is usually present.</p> <p>Related publication: Laue M, Hoffmann T, Michel J, Nitsche A. Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy. Virol J. 2023 Feb 6;20(1):21. doi: 10.1186/s12985-023-01981-9. PMID: 36747188; PMCID: PMC9901382.</p>
Correlative Raman Imaging and Scanning Electron Microscopy: The Role of Single Ga Islands in Surface-Enhanced Raman Spectroscopy of Graphene_experimental dataset
<p>This dataset contains the raw unprocessed data for Piastek et al., Correlative Raman Imaging and Scanning Electron Microscopy: The Role of Single Ga Islands in Surface-Enhanced Raman Spectroscopy of Graphene, <em>J. Phys. Chem. C</em> 2022, 126, 9, 4508–4514. </p>
Training Data for "DeepCLEM: automated registration for correlative light and electron microscopy using deep learning"
<p><strong>This folder contains the training dataset used for the paper</strong></p> <p>"DeepCLEM: automated registration for correlative light and electron microscopy using deep learning"</p> <p><em>Rick Seifert, Sebastian M. Markert, Sebastian Britz, Veronika Perschin, Christoph Erbacher, Christian Stigloher and Philip Kollmannsberger</em></p> <p>F1000Research 9:1275 (2020), https://f1000research.com/articles/9-1275</p> <p>------------------------------------------------------------</p> <p>These are 117+4 manually aligned CLEM images of C.elegans acquired by Sebastian M. Markert, Sebastian Britz and Rick Seifert in the Electron Microscopy Facility of the Biocenter of University of Wuerzburg, Germany. For details and experimental protocols, please see the paper linked above.</p> <p>Contents:</p> <ul> <li>"fluo_training": Fluorescence microscopic channel of the 117 training images </li> <li>"sem_training": Scanning electron microscopic channel of the 117 training images</li> <li>"fluo_validation": Fluorescence microscopic channel of the 4 validation images </li> <li>"sem_validation": Scanning electron microscopic channel of the 4 validation images</li> </ul> <p>License: CC-BY 4.0</p>
Supplemental Material to Journal Article "Determination of as-built properties of fiber reinforced polymers in a wind turbine blade using scanning electron and high-resolution X-ray microscopy"
<p>This set supplements the figure data to the article "Determination of as-built properties of fiber reinforced polymers in a wind turbine blade using scanning electron and high-resolution X-ray microscopy", DOI: <a href="https://doi.org/10.1016/j.jcomc.2022.100310">https://doi.org/10.1016/j.jcomc.2022.100310</a></p>
Soot particle images obtained by Environmental Transmission Electron Microscopy
<p>Transmission electron microscopy images used to generate frame sequences and calculate particle convexities, along with the associated script. The fractal soot particles were produced by combustion, lightly coated by sulfuric acid, deposited on SiN substrate, and then their response to humidification and drying was studied in a controlled microenvironment of a closed cell, using environmental transmission electron microscopy. </p>
Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy – data set 07
<p>We developed a sedimentation method using desktop ultracentrifugation (see description below) to visualize SARS-CoV-2 particles in suspensions from oro- and/or nasopharyngeal swabs by thin section electron microscopy. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 07 comprises three stitched image montages recorded from an area of a thin section through the sediment obtained from a swab sample which was negative by quantitative PCR (control). Ciliated cells and extracellular material, such as vesicles and needle-like crystals, are visible, but no coronavirus particles.</p> <p>Related publication: Laue M, Hoffmann T, Michel J, Nitsche A. Visualization of SARS-CoV-2 particles in naso/oropharyngeal swabs by thin section electron microscopy. Virol J. 2023 Feb 6;20(1):21. doi: 10.1186/s12985-023-01981-9. PMID: 36747188; PMCID: PMC9901382.</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.