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2,216 results for “membrane”
Coarse-grained simulations of a phase-separated membrane with different LINCS settings (part 1/3)
<p>systems with lincs_iter = 1. To be written.</p>
Coarse-grained simulations of a phase-separated membrane with different LINCS settings (part 3/3)
<p>Additional simulations with lincs_order 10 & 12</p>
Atomistic simulations of a POPC / POPC+cholesterol membrane with different simulation parameters
<p>Atomistic</p>
Data from: Phylogenomic analysis supports the ancestral presence of LPS-outer membranes in the Firmicutes
One of the major unanswered questions in evolutionary biology is when and how the transition between diderm (two membranes) and monoderm (one membrane) cell envelopes occurred in Bacteria. The Negativicutes and the Halanaerobiales belong to the classically monoderm Firmicutes, but possess outer membranes with lipopolysaccharide (LPS-OM). Here, we show that they form two phylogenetically distinct lineages, each close to different monoderm relatives. In contrast, their core LPS biosynthesis enzymes were inherited vertically, as in the majority of bacterial phyla. Finally, annotation of key OM systems in the Halanaerobiales and the Negativicutes shows a puzzling combination of monoderm and diderm features. Together, these results support the hypothesis that the LPS-OMs of Negativicutes and Halanaerobiales are remnants of an ancient diderm cell envelope that was present in the ancestor of the Firmicutes, and that the monoderm phenotype in this phylum is a derived character that arose multiple times independently through OM loss.
Data from: Membrane potential dynamics of spontaneous and visually evoked gamma activity in V1 of awake mice
Cortical gamma activity (30–80 Hz) is believed to play important functions in neural computation and arises from the interplay of parvalbumin-expressing interneurons (PV) and pyramidal cells (PYRs). However, the subthreshold dynamics underlying its emergence in the cortex of awake animals remain unclear. Here, we characterized the intracellular dynamics of PVs and PYRs during spontaneous and visually evoked gamma activity in layers 2/3 of V1 of awake mice using targeted patch-clamp recordings and synchronous local field potentials (LFPs). Strong gamma activity patterned in short bouts (one to three cycles), occurred when PVs and PYRs were depolarizing and entrained their membrane potential dynamics regardless of the presence of visual stimulation. PV firing phase locked unconditionally to gamma activity. However, PYRs only phase locked to visually evoked gamma bouts. Taken together, our results indicate that gamma activity corresponds to short pulses of correlated background synaptic activity synchronizing the output of cortical neurons depending on external sensory drive.
Data from: Halloysite nanotube-based electrospun ceramic nanofibre mat: a novel support for zeolite membranes
Some key parameters of supports such as porosity, pore shape and size are of great importance for fabrication and performance of zeolite membranes. In this study, we fabricated millimetre-thick, self-standing electrospun ceramic nanofibre mats and employed them as a novel support for zeolite membranes. The nanofibre mats were prepared by electrospinning a halloysite nanotubes/polyvinyl pyrrolidone composite followed by a programmed sintering process. The interwoven nanofibre mats possess up to 80% porosity, narrow pore size distribution, low pore tortuosity and highly interconnected pore structure. Compared with the commercial α-Al2O3 supports prepared by powder compaction and sintering, the halloysite nanotube-based mats (HNMs) show higher flux, better adsorption of zeolite seeds, adhesion of zeolite membranes and lower Al leaching. Four types of zeolite membranes supported on HNMs have been successfully synthesized with either in situ crystallization or a secondary growth method, demonstrating good universality of HNMs for supporting zeolite membranes.
Data from: Myelin basic protein induces neuron-specific toxicity by directly damaging the neuronal plasma membrane
The central nervous system (CNS) insults may cause massive demyelination and lead to the release of myelin-associated proteins including its major component myelin basic protein (MBP). MBP is reported to induce glial activation but its effect on neurons is still little known. Here we found that MBP specifically bound to the extracellular surface of the neuronal plasma membrane and induced neurotoxicity in vitro. This effect of MBP on neurons was basicity-dependent because the binding was blocked by acidic lipids and competed by other basic proteins. Further studies revealed that MBP induced damage to neuronal membrane integrity and function by depolarizing the resting membrane potential, increasing the permeability to cations and other molecules, and decreasing the membrane fluidity. At last, artificial liposome vesicle assay showed that MBP directly disturbed acidic lipid bilayer and resulted in increased membrane permeability. These results revealed that MBP induces neurotoxicity through its direct interaction with acidic components on the extracellular surface of neuronal membrane, which may suggest a possible contribution of MBP to the pathogenesis in the CNS disorders with myelin damage.
Data from: Evidence for amino acid snorkeling from a high-resolution, in vivo analysis of Fis1 tail anchor insertion at the mitochondrial outer membrane
Proteins localized to mitochondria by a carboxyl-terminal tail anchor (TA) play roles in apoptosis, mitochondrial dynamics, and mitochondrial protein import. To reveal characteristics of TAs that may be important for mitochondrial targeting, we focused our attention upon the TA of the Saccharomyces cerevisiae Fis1 protein. Specifically, we generated a library of Fis1p TA variants fused to the Gal4 transcription factor, then, using next-generation sequencing, revealed which Fis1p TA mutations inhibited membrane insertion and allowed Gal4p activity in the nucleus. Prompted by our global analysis, we subsequently analyzed the ability of individual Fis1p TA mutants to localize to mitochondria. Our findings suggest that the membrane-associated domain of the Fis1p TA may be bipartite in nature, and we encountered evidence that the positively charged patch at the carboxyl-terminus of Fis1p is required for both membrane insertion and organelle specificity. Furthermore, lengthening or shortening of the Fis1p TA by up to three amino acids did not inhibit mitochondrial targeting, arguing against a model in which TA length directs insertion of TAs to distinct organelles. Most importantly, positively charged residues were more acceptable at several positions within the membrane-associated domain of the Fis1p TA than negatively charged residues. These findings, emerging from the first high-resolution analysis of an organelle targeting sequence by deep mutational scanning, provide strong, in vivo evidence that lysine and arginine can "snorkel," or become stably incorporated within a lipid bilayer by placing terminal charges of their side chains at the membrane interface.
Data from: Enhanced virus filtration in hybrid membranes with MWCNT nanocomposite
Membrane separation is proved to be a powerful tool for several applications such as wastewater treatment or the elimination of various microorganisms from drinking water. In this study, the efficiency of inorganic composite based multi-walled carbon nanotube hybrid membranes was investigated in the removal of MS2 bacteriophages from contaminated water. With this object multi-walled carbon nanotubes were coated with copper(I) oxide, titanium(IV) oxide and iron(III) oxide nanoparticles, respectively, and their virus removal capability was tested in both batch and flow experiments. Considering the possible pH range of drinking water, the filtration tests were carried out at pH 5.0, 7.5 and 9.0 as well. The extent of MS2 removal strongly depended on the pH values for each composite, which can be due to electrostatic interactions between the membrane and the virus. The highest removal (≥99.99%) was obtained with the Cu2O-coated MWCNT water membrane in the whole pH range. The fabricated nanocomposites were characterized by X-ray diffraction, specific surface area measurement, dynamic light scattering, zeta potential measurement, Raman spectroscopy, transmission electron microscopy and scanning electron microscopy techniques. This study presents a simple route to design novel and effective nanocomposite-based hybrid membranes for virus removal.
Data from: Membrane-assisted extraction of monoterpenes: from in-silico solvent screening towards biotechnological process application
This work focuses on the process development of membrane-assisted solvent extraction of hydrophobic compounds such as monoterpenes. Beginning with the choice of suitable solvents, quantum chemical calculations with the simulation tool COSMO-RS were carried out to predict the partition coefficient (logP) of (S)-(+)-carvone and terpinen-4-ol in various solvent-water systems and validated afterwards with experimental data. COSMO-RS results show good prediction accuracy for nonpolar solvents like n-hexane, ethyl acetate and n-heptane even in the presence of salts and glycerol in aqueous medium. Based on the high logP value, n-heptane was chosen for the extraction of (S)-(+)-carvone in a lab-scale hollow-fiber membrane contactor. Two operation modes are investigated where experimental and theoretical mass transfer values, based on their related partition coefficients were compared. In addition, the process is evaluated in terms of extraction efficiency and overall product recovery, and its biotechnological application potential discussed. Our work demonstrates that the combination of in-silico prediction by COSMO-RS with membrane-assisted extraction is a promising approach for the recovery of hydrophobic compounds from aqueous solutions.
Data from: Recruitment dynamics of ESCRT-III and Vps4 to endosomes and implications for reverse membrane budding
The ESCRT machinery mediates reverse membrane scission. By quantitative fluorescence lattice light-sheet microscopy, we have shown that ESCRT-III subunits polymerize rapidly on yeast endosomes, together with the recruitment of at least two Vps4 hexamers. During their 3-45 second lifetimes, the ESCRT-III assemblies accumulated 75-200 Snf7 and 15-50 Vps24 molecules. Productive budding events required at least two additional Vps4 hexamers. Membrane budding was associated with continuous, stochastic exchange of Vps4 and ESCRT-III components, rather than steady growth of fixed assemblies, and depended on Vps4 ATPase activity. An all-or-none step led to final release of ESCRT-III and Vps4. Tomographic electron microscopy demonstrated that acute disruption of Vps4 recruitment stalled membrane budding. We propose a model in which multiple Vps4 hexamers (four or more) draw together several ESCRT-III filaments. This process induces cargo crowding and inward membrane buckling, followed by constriction of the nascent bud neck and ultimately ILV generation by vesicle fission.
Data from: Electrospinning preparation of oxygen-deficient nano TiO2-x/carbon fibre membrane as a self-standing high performance anode for Li-ion batteries
Improving the specific capacity and electronic conductivity of TiO2 can boost its practical application as a promising anode material for lithium ion batteries. In this work, a three-dimensional networking oxygen-deficient nano TiO2-x/carbon fibre membrane was achieved by combining the electrospinning process with a hot-press sintering method and directly used as a self-standing anode. With the synergistic effects of three-dimensional conductive networks, surface oxygen deficiency, high specific surface area and high porosity, binder-free and self-standing structure, etc., the nano TiO2-x/carbon fibre membrane electrode displays a high electrochemical reaction kinetics and a high specific capacity. The reversible capacity could be jointly generated from porous carbon, full-lithiation of TiO2 and interfacial lithium storage. At a current density of 100 mA g−1, the reversible discharge capacity can reach 464 mA h g−1. Even at 500 mA g−1, the discharge capacity still remains at 312 mA h g−1. Compared with pure carbon fibre and TiO2 powder, the TiO2-x/C fibre membrane electrode also exhibits an excellent cycle performance with a discharge capacity of 209 mA h g−1 after 700 cycles at the current density of 300 mA g−1, and the coulombic efficiency always remains at approximately 100%.
Membrane-Anchoring, Comb-Like Pseudopeptides for Efficient, pH-Mediated Membrane Destabilization and Intracellular Delivery
<p>The data used in this paper is uploaded</p>
Impact of chronic psychological stress on platelet membrane fatty acid composition in type 1 diabetes mellitus
Open the record for dataset details and reuse information.
How Do Xanthophylls Protect Lipid Membranes from Oxidative Damage?
<p><span>equatorial optical cross-sections of liposomes recorded with the FLIM technique<br></span></p>
Long-chain lipids facilitate insertion of large nanoparticles into membranes of small unilamellar vesicles
<div> <p>DLS data and Cryo Images of SUVs-QDs</p> <p> </p> </div>
Multiresolution molecular dynamics simulations reveal the interplay between conformational variability and functional interactions in membrane-bound cytochrome 2B4
<p>This dataset contains coordinate files, scripts and input parameters to run and analyse molecular dynamics simulations of membrane bound CYP 2B4.</p> <p> </p> <p>The associated study is described in: </p> <p>data - containes input data & last simulation frames for all of the described MD simulations and analyses described in the manuscript</p> <p>Structures_used_for_figures - contains .pdb and .pse files of all protein structures depicted in the manuscript</p>
3D localization AFM (3D-LAFM) density map of Annexin-V, membrane-bound in a p6 lattice
<p>3D localization AFM (3D-LAFM) density map of Annexin-V, membrane-bound in a p6 lattice, in <code>.afm</code> format and in <code>.mrc</code> format.</p> <p>Note: The <code>.afm</code> file encodes details for constructing 3D-LAFM density maps and includes experimental conditions in its header. Using <code>.afm</code> files requires the additional installation of the AFM file encoder (available from <a href="https://github.com/rafaeljiang23/3D-LAFM/tree/main/ChimeraX-AfmFormat_v2">GitHub</a>). Once the relevant installation is complete, <code>.afm</code> files can be opened in ChimeraX via drag-and-drop. In contrast, <code>.mrc</code> files, which encode only the density values equivalent to <code>.afm</code> files, can be directly opened in ChimeraX without requiring additional software installation.</p> <p>The deposited <code>.afm</code> file follows the 'AFM1' (metacode) format standard.</p>
Data Repository: Fast Single-Particle Tracking of Membrane Proteins Combined with Super-Resolution Imaging of Actin Nanodomains
<p>This repository contains a collection of correlated 2D super-resolution images obtained through single molecule localization microscopy and 3D time series of single particle tracking data of membrane proteins. By utilizing high-speed fluorescent microscopy, we tracked a transmembrane protein – the high-affinity IgE receptor – and an outer-leaflet protein – GPI-anchored protein – at the frame rate of 490 Hz. Subsequently, actin structures of the same cells were captured using a super-resolution microscopy (dSTORM technique). Additionally, this dataset includes Technical Validation to support the transition from live-cell imaging to fixed-cell imaging when adding fixation buffers. </p> <p>The data was classified as “Class I” and “Class II” describing two categories of RBL-2H3 cells. In "Class I", the cells were untransfected. In “Class II”, the cells were transfected to express GFP-GPI-anchored fusion protein. The zip folder names that include “IgE Untreated” include image time series of fluorescently labeled IgE receptors in untreated RBL-2H3 cells and image series of corresponding super-resolution imaging of fluorescently labeled actin filaments of the same cell in “SRImage” folder.</p> <p>The data with folder names including with “IgE Treated” are image time series of fluorescently labeled IgE receptors in either phalloidin- or PMA-treated RBL-2H3 cells and corresponding image series of super-resolution imaging of fluorescently labeled actin filaments in the same cell.</p> <p>Similarly, the data with folder names starting with “GPI Untreated” are image time series of fluorescently labeled GPI-anchored proteins in untreated RBL-2H3 cells and corresponding image series of super-resolution imaging of fluorescently labeled actin filaments in the same cell.</p> <p>The data with folder names starting with “GPI Treated” are image time series of fluorescently labeled GPI-anchored proteins in phalloidin treated RBL-2H3 cells and corresponding image series of super-resolution imaging of fluorescently labeled actin filaments in the same cell.</p> <p>The number within each folder name represents an individual experiment and the corresponding data collected under the same conditions.</p> <p>For all experiments an IR movie was added to monitor the cell morphology during live-cell image and adding initial fixation buffer and it was saved in the tracking file. </p> <p>The HDF5 files of all data are available in the second version of this repository. For each sample, there are two files: "Tracking.h5" and "SuperResolution_actin.h5". The "Tracking" files include two groups: single-particle tracking data and IR images during tracking. The "SuperResolution_actin" files contain two groups: super-resolution images of actin filaments and IR reference images for image registeration and drift correction during data collection. </p> <p> </p> <p> </p> <p> </p>
Photocleavable Fluorescent Membrane Tension Probes
<p>Original data</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.