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175 results for “Single-molecule”
Data deposition for "Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins"
<p>The deposited data for the publication "Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins".</p> <p>Data contains folder and sub-folders for the raw data, Main excel sheet named as "MasterTable_FRET-Challenge-Protein-Dynamics_Nat_Meth_Agam et al" has most of the data used in the publication. Another excel sheets "Data List for FIgures for Agam et al_revised" and "Data List for Supplmentary FIgures for Agam et al_revised" have the information regarding the Figure-wise data description and where the respective data locates.</p>
Fibertools: fast and accurate m6A calling using single-molecule long-read sequencing (ML data)
<p>Fibertools is a convolutional neural network that permits the fast and accurate identification of endogenous and exogenous N6-methyladenine (m6A)-marked bases using single-molecule long-read sequencing.<strong> </strong>This dataset (ML data) provides training and validation data for training fibertools supervised and semi-supervised CNN models for three long-read chemistries.</p>
Label-free adaptive optics single-molecule localization microscopy for whole zebrafish
<p>The specimen-induced aberration has been a major factor limiting the imaging depth of single-molecule localization microscopy (SMLM). Here, we report the application of label-free wavefront sensing adaptive optics to SMLM for deep-tissue super-resolution imaging. The proposed system measures complex tissue aberrations from intrinsic reflectance rather than fluorescence emission and physically corrects the wavefront distortion more than three-fold stronger than the previous limit. This enables us to resolve sub-diffraction morphologies of cilia and oligodendrocytes in whole zebrafish as well as dendritic spines in thick mouse brain tissues at the depth of up to 102 μm with localization number enhancement by up to 37 times and localization precision comparable to aberration-free samples. The proposed approach can expand the application range of SMLM to whole zebrafish that cause the loss of localization points owing to severe tissue aberrations.</p>
High-temperature magnetic blocking in a monometallic dysprosium azafullerene single-molecule magnet
<p>Single-molecule magnets (SMMs) showing magnetic blocking near or above liquid nitrogen temperature have recently been achieved by inducing exceptionally strong and axial crystal fields via double decker ligands. However, further enhancing the performance at higher temperatures becomes a formidable task. Here we provide an alternative strategy to advance towards this goal by entrapping a single dysprosium(III) ion within a nitrogen-substituted carbon cage. In this structure of Dy@C<sub>81</sub>N, Dy<sup>III</sup> is asymmetrically coordinated by one side to a hexagonal carbon ring of the azafullerene, while lacking any coordination ligand on the other side. Despite the very weak crystal field resulting from this very unusual low-coordination environment, this compound exhibits a high blocking temperature (<em>T</em><sub>B</sub>, defined as <em>T</em>(t<sub>100s</sub>)) of 45 K. Its extraordinary magnetic behavior is attributed to the minimal number of vibrations that couple to its spin states, being also responsible for the unusual slow Raman relaxation mechanism observed at high temperatures.</p>
Single-molecule and bulk fluorescence and biolayer interferometry on the NAD-II riboswitch and its interactions with NMN
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Single-molecule analysis of the entire perfringolysin O pore formation pathway
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Single-molecule localization microscopy reveals the molecular organization of endogenous membrane receptors
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Data from: Quantitative single-molecule FLIM and PIE-FRET imaging of biomolecular systems
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Identification of distinct pH-and zeaxanthin-dependent quenching in LHCSR3 from C. reinhardtii - single-molecule photon stream
<p>Photon stream used in the article "Identification of distinct pH-and zeaxanthin-dependent quenching in LHCSR3 from <em>Chlamydomonas reinhardtii"</em> to analyze single-molecule fluorescence emission. Detected emission of WT LHCSR3 and stop-LHCSR3 at pH 7.5 and pH 5 along with associated instrument response function (IRF) and measurements of background fluorescence (BG). Each detected photon is described by its time within the collected photon stream and its time relative to the excitation laser.</p>
single-molecule chirality data
<p>single-molecule electrical data for chirality discrimination</p><p>all the data are zip file.</p><p>mono amino acid: Ala.zip, Arg.zip, Asn.zip, Asp.zip, Cys.zip, Gln.zip, Glu.zip, His.zip, Ile.zip, Leu.zip, Lys.zip, Met.zip, Phe.zip, Pro.zip, Ser.zip, Thr.zip, Trp.zip, Tyr.zip, Val.zip</p><p>mixed four kinds of amino acid data#1: D_Y_L_SHF.zip</p><p>mixed four kinds of solution#2: L_F_D_LPY.zip</p><p>video data: Single Molecule Electrical Measurement by MCBJ.zip</p>
Single-Molecule FRET-Resolved Protein Dynamics - from Plasmid to Data in Six Steps
<p>SmFRET trace files of 58 yeast Hsp90 molecules (in presence of AMP-PNP) containing raw intensity values through time of acceptor emission after acceptor excitation (r_r_*), donor emission after donor excitation (o_g_*), and acceptor emission after donor excitation (r_g_*).</p>
Data from "Single-molecule fluorescence multiplexing by multi-parameter spectroscopic detection of nanostructured FRET labels"
<p>Source data for all figures; full table of all nucleic acid sequences used; Supplementary Video 1 showing rotating view of Fig. 4e.</p>
Single-molecule analysis of specificity and multivalency in binding of short linear substrate motifs to the APC/C
<p>Robust regulatory signals in the cell often depend on interactions between short linear motifs (SLiMs) and globular proteins. Many of these interactions are poorly characterized because the binding proteins cannot be produced in the amounts needed for traditional methods. To address this problem, we developed a single-molecule off-rate (SMOR) assay based on microscopy of fluorescent ligand binding to immobilized protein partners. We used it to characterize substrate binding to the Anaphase-Promoting Complex/Cyclosome (APC/C), a ubiquitin ligase that triggers chromosome segregation. We find that SLiMs in APC/C substrates (the D box and KEN box) display distinct affinities and specificities for the substrate-binding subunits of the APC/C, and we show that multiple SLiMs in a substrate generate a high-affinity multivalent interaction. The remarkably adaptable substrate-binding mechanisms of the APC/C have the potential to govern the order of substrate destruction in mitosis.</p>
Correlating single-molecule rupture mechanics with cell population adhesion by yeast display
<p>Data underlying the figures in the publication “Correlating single-molecule rupture mechanics with cell population adhesion by yeast display”, published in <em>Biophysical Reports, </em><em><strong>2022</strong></em><em>, Volume 2, Issue 1, 100035, ISSN 2667-0747.</em></p> <p><em><a href="https://doi.org/10.1016/j.bpr.2021.100035">https://doi.org/10.1016/j.bpr.2021.100035</a></em></p> <p>Table of contents:</p> <p><strong>1. Fig2_SMFS.xlsx</strong>: Contour Length vs probability density values for <em>Figure 2D</em>. Rupture Force and Loading rate values for all SMFS curves analysed for <em>Figure 2E</em> and <em>2F</em>.</p> <p><strong>2. Fig3_SDA.xlsx</strong>: Shear Stress <em>vs</em> Cell Density values of all replicates and speeds for F<em>igures 3D</em> and <em>3E</em>.</p> <p><strong>3. FigS1_SPR curves.xlsx</strong>: SPR curves reported in Supplementary <em>Figure 1</em>.</p> <p><strong>4. FigS2_one step FLN.xlsx</strong>: Force <em>vs</em> Extension trace and Contour Length Histogram values for one step FLN unfolding shown in <em>Supplementary Figure 2</em>.</p> <p><strong>5. FigS3_SMFS_internal control.xlsx</strong>: Rupture Force and Loading rate values for N-S25H reported in <em>Supplementary Figure 3</em>.</p> <p><strong>6. FigS5_SDA_internal control.xlsx</strong>: Shear Stress <em>vs</em> Cell Density values of N-WT shown in <em>Supplementary figure 5B</em>.</p> <p><strong>7. FigS6_SDA_induction timepoints.xlsx</strong>: Shear Stress <em>vs</em> Cell Density values and median of expression detected by flow cytometry reported in <em>Supplementary Figure 6</em>.</p>
Raw single-molecule imaging data for "Tuning levels of low-complexity domain interactions to modulate endogenous oncogenic transcription"
<p><strong>Raw single-molecule imaging data for "Tuning levels of low-complexity domain interactions to modulate endogenous oncogenic transcription"</strong></p> <p>Shasha Chong<sup>1</sup>, Thomas G.W. Graham<sup>2</sup>, Claire Dugast-Darzacq<sup>2,5</sup>, Gina M. Dailey<sup>2</sup>, Xavier Darzacq<sup>2,5</sup>, Robert Tjian<sup>2,3,4,5</sup>*</p> <p><sup>1 </sup>Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA</p> <p><sup>2 </sup>Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.</p> <p><sup>3 </sup>Howard Hughes Medical Institute, University of California, Berkeley, CA, USA.</p> <p><sup>4</sup><sup> </sup>Li Ka Shing Center for Biomedical & Health Sciences, University of California, Berkeley, CA, USA.</p> <p><sup>5</sup><sup> </sup>CIRM Center of Excellence, University of California, Berkeley, CA. </p> <p>* Lead contact</p> <p><strong>Overview</strong></p> <p>This repository contains 1) movies of endogenously expressed EWS::FLI1-Halo in genome-edited A673 cells acquired using stroboscopic photo-activatable single particle tracking (spaSPT) and 2) images of exogenously expressed mNeonGreen-EWS-NPM1 fusion protein in the above cells before and after spaSPT movies were acquired. The uploaded files include data acquired from 80 live cells on 4 different days. The imaging data, after being processed, were used to generate Figure 4C-E of the manuscript in the title. </p> <p><strong>Method details</strong></p> <p>The genome-edited A673 cells (described in https://www.science.org/doi/10.1126/science.aar2555) with inducible expression of mNeonGreen-EWS-NPM1 were grown on 25 mm circular No. 1.5 cover glasses (Azer Scientific, 200251) that were plasma-cleaned prior to use. We induced the cells with 200 ng/ml of doxycycline for 96 hours, stained the cells with 20 nM PA-JF646 and 200 nM JFX549 HaloTag ligands, and performed single-molecule imaging of EWS::FLI1-Halo on a custom-built Nikon (Nikon Instruments Inc.) TI microscope described in (https://elifesciences.org/articles/25776). We took images with a 100x/NA 1.49 oil-immersion TIRF objective (Nikon apochromat CFI Apo TIRF 100x Oil) under highly inclined and laminated optical sheet (HILO) illumination (https://www.nature.com/articles/nmeth1171) using following laser lines: 488 nm for mNG; 561 nm for JFX549; 405 nm and 633 nm for photo-activation and excitation of PA-JF646, respectively. The incubation chamber maintained a humidified 37°C atmosphere with 5% CO<sub>2</sub> and the objective was similarly heated to 37°C for live-cell experiments. </p> <p>High-concentration JFX549 staining allows visualization of the intracellular distribution of EWS::FLI1-Halo. We chose cells with EWS::FLI1-Halo enriched in the nucleolus to perform spaSPT. The procedure of spaSPT largely follows what is described in (https://elifesciences.org/articles/25776). Both the excitation laser (633 nm) and the photo-activation laser (405 nm) for PA-JF646 were pulsed. Each frame consisted of a 7-ms camera exposure time followed by a ~500 μs camera ‘dead’ time. The excitation laser (633 nm) was pulsed for 1 ms starting at the beginning for the 7 ms camera exposure time. The photo-activation laser (405 nm) was pulsed during the ~500 μs camera ‘dead’ time, minimizing fluorescence background. Each cell was imaged for 20,000 frames corresponding to ~1.5 min. Images of mNeonGreen-EWS-NPM1 were collected with a camera exposure time of 500 ms before and after the acquisition of each spaSPT movie.</p>
Source data for "Single-molecule analysis of actin filament debranching by cofilin and GMF"
<p>Source data for "Single-molecule analysis of actin filament debranching by cofilin and GMF"</p>
Single-molecule tracking of Nodal and Lefty in live zebrafish embryos supports hindered diffusion model
<p><span>The hindered diffusion model postulates that the movement of a signaling molecule through an embryo is affected by tissue geometry and binding-mediated hindrance, but these effects have not been directly demonstrated <em>in vivo</em>. Here, we visualize extracellular movement and binding of individual molecules of the activator-inhibitor signaling pair Nodal and Lefty in live developing zebrafish embryos using reflected light-sheet microscopy. We observe that diffusion coefficients of molecules are high in extracellular cavities, whereas mobility is reduced and bound fractions are high within cell-cell interfaces. Counterintuitively, molecules nevertheless accumulate in cavities, which we attribute to the geometry of the extracellular space by agent-based simulations. We further find that Nodal has a larger bound fraction than Lefty and shows a binding time of tens of seconds. Together, our measurements and simulations provide direct support for the hindered diffusion model and yield insights into the nanometer-to-micrometer-scale mechanisms that lead to macroscopic signal dispersal.</span></p>
Structural dynamics of DNA strand break sensing by PARP-1 at a single-molecule level
<p><span>Single-stranded breaks (SSBs) are the most frequent DNA lesions threatening genomic integrity. A highly kinked DNA structure in complex with human PARP-1 domains led to the proposal that SSB sensing in Eukaryotes relies on dynamics of both the broken DNA double helix and PARP-1's multi-domain organization. Here, we directly probe this fundamental yet poorly understood process at the single-molecule level. Quantitative smFRET and structural ensemble calculations reveal how PARP-1's N-terminal zinc fingers convert DNA SSBs from a largely unperturbed conformation, via an intermediate state into the highly kinked DNA conformation. Our data suggest an induced fit mechanism via a multi-domain assembly cascade that drives SSB sensing and stimulates an interplay with the scaffold protein XRCC1 orchestrating subsequent DNA repair events. Interestingly, a clinically used PARP-1 inhibitor Niraparib shifts the equilibrium towards the unkinked DNA conformation, whereas the inhibitor EB47 stabilizes the kinked state. </span></p>
Supplemental information for "Single-Molecule Dynamics of Surface Lipoproteins in Bacteroides Indicate Similarities and Cooperativity"
<p>Supplemental Movies 1 - 3</p> <p><strong>SI Movie S1 - Representative movie of SusG-HT dynamics in <em>Bt</em> cells grown in amylopectin.</strong> The <em>Bt</em> cell outlines (white) are determined from the corresponding phase-contrast image. The single-molecule localization fits (circles) and corresponding trajectories (lines) are overlaid with the same colors as in Figure 1c. Below the scale bar is the date of the experiment, the movie number, the number of the photo-activation pulse that the sequence follows (in parentheses), and the frame number. These indicators are displayed in green during the imaging frames and in red during the photo-activation pulse. Scale bar: 1 µm; imaging rate: 20 ms/frame.</p> <p><strong>SI Movie S2 - Representative movie of SusG-HT dynamics in <em>Bt</em> cells grown in maltose.</strong> The <em>Bt</em> cell outlines (white) are determined from the corresponding phase-contrast image. The single-molecule localization fits (circles) and corresponding trajectories (lines) are overlaid with the same colors as in Figure 1c. Below the scale bar is the date of the experiment, the movie number, the number of the photo-activation pulse that the sequence follows (in parentheses), and the frame number. These indicators are displayed in green during the imaging frames and in red during the photo-activation pulse. Scale bar: 1 µm; imaging rate: 20 ms/frame.</p> <p><strong>SI Movie S3 - Representative movie of SusG-HT dynamics in <em>Bt</em> cells grown in glucose.</strong> The <em>Bt</em> cell outlines (white) are determined from the corresponding phase-contrast image. The single-molecule localization fits (circles) and corresponding trajectories (lines) are overlaid with the same colors as in Figure 1c. Below the scale bar is the date of the experiment, the movie number, the number of the photo-activation pulse that the sequence follows (in parentheses), and the frame number. These indicators are displayed in green during the imaging frames and in red during the photo-activation pulse. Scale bar: 1 µm; imaging rate: 20 ms/frame.</p>
Supplementary Videos for "Monitoring electrochemical dynamics through single-molecule imaging of hBN surface emitters in organic solvents"
<p><strong>Supplementary Video 1: Out-of-plane emitter control. </strong>The video included is a wide-field view of an hBN flake immersed in acetonitrile while an electrochemical potential of the ITO working electrode is cycled in the three-electrode out-of-plane configuration between +1.5 V and 0 V vs Ag/AgCl. The change in potential induces a change in density of emitters. This data corresponds to a flake used in spectral analysis (data presented in <strong>Fig. 3c–e</strong>). Continuous ~1.6 kW cm<sup>–2</sup> illumination with a 561 nm laser is used. The original images were acquired at a rate of 50.091 ms per frame but here we combined frames to present a lighter video with a lower sampling rate (1 s). The total experiment took 750 seconds, but we present the image stack at a rate of 10 frames per second to make the video only 75 seconds. The scale bar is 5 µm.</p> <p><strong><span>Supplementary Video 2: In-plane emitter control.</span></strong> Here we present a wide-field video of the hBN flake shown in <strong>Figure 4b-d</strong> in between two titanium electrodes. Continuous ~1 kW cm<sup>–2</sup> illumination is used with a 561 nm laser while the polarization of the electrodes is cycled in the two-electrode in-plane configuration, inducing a change in density of emitters correlated with potential. The high-density region follows the negatively charged electrode. The original images were acquired with a 50.091 ms rate, but here we combined frames to present a lighter video with a lower sampling rate (2.5 s). The total experiment took 540 seconds, but we display 5 of the stacked images per second, making make the video around 40 seconds. The scale bar is 5 µm.</p>
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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)
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.