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2,216 results for “membrane”
Characterizing multidimensional cellular physiological states with quantitative three-dimensional shape descriptors for cell membranes
<h3>Supplementary dataset and code for the article "<em>Characterizing Cellular Physiological States with Three-Dimensional Shape Descriptors for Cell Membranes</em>"</h3> <p>CShaper Dataset.zip: The 3D cell regions reused from the previously published article <a href="https://doi.org/10.1038/s41467-020-19863-x">https://doi.org/10.1038/s41467-020-19863-x</a>.</p> <p>Cell Shape Descriptors - Code & Data.zip: The code (exemplifed by embryo Sample04) and data (including embryo Sample04-Sample20) of 12 3D shape descriptors for all 3D cell regions in the <em>CShaper</em> dataset.</p> <p>GUI.zip: The user-friendly software <em>Shape Descriptor Tool</em> is a Graphical User Interface based on <em>Matlab</em> for calculating 12 shape descriptors for a 3D cell region (exemplified by embryo Sample20, time point 14, ABpl cell in the <em>CShaper</em> dataset). The instruction guidebook is included in the Supplementary Material of the article.</p>
Quantification of membrane fluidity in bacteriaTIR-FCS: Research data
<p>Dataset supporting the research paper:<sup><br></sup></p> <p><br>Barbotin A, Billaudeau C, Sezgin E, Carballido-López R, Quantification of membrane fluidity in bacteria using TIR-FCS, Biophysical Journal (2024), doi:<a href="https://doi.org/10.1016/"> <span>https://doi.org/10.1016/j.bpj.2024.06.012</span></a></p> <p> </p>
Supplementary Material 1: Phylogenetic tree from Unraveling an unknown diversity of archaeal and bacterial tetraether membrane lipid producers in a euxinic marine system
<p>Phylogenetic tree (Black Sea MAGs)</p>
Altered mitochondria-associated ER membranes (MAM) function shifts mitochondrial metabolism in amyotrophic lateral sclerosis (ALS)
<p><span>Mitochondrial function is modulated by its functional interaction with the endoplasmic reticulum.</span><span> Recent research indicates that these contacts are disrupted in familial models of amyotrophic lateral sclerosis. We report here this impairment in the crosstalk between mitochondria and the endoplasmic reticulum impedes the use of glucose-derived pyruvate as mitochondrial fuel, causing a shift to fatty acids to sustain energy production. Over time, this deficiency alters mitochondrial electron flow and the active/dormant status of complex I in spinal cord tissues, but not in the brain. These findings suggest MAM plays a crucial role in regulating cellular glucose metabolism and that its dysfunction may underlie the bioenergetic deficits observed in ALS. The dataset includes the lipid profiles of the total homogenates and motchondrial fractions from SOD1.</span></p>
SN2N's 3D dataset of outer mitochondrial membrane network of live COS-7 cells labeled with Tom20-mCherry on SD-SIM sysytem.
Open the record for dataset details and reuse information.
Can calmodulin bind to lipids of the cytosolic leaflet of plasma membranes? - additional data
<p>CaM_Data_Repository_Revision:<br>This folder contains the experimental raw data, analysis and source for the final figures reported in the paper after revision (Open Biology): "Can calmodulin bind to lipids of the cytosolic leaflet of plasma membranes?". It is divided into five (1-3) folders, named as the technique used to obtain the data. Each of them, where applicable, consists of three different subfolders (raw data, analysed data, final graph). Read below for more details. </p> <p>1) ConfocalMicroscopy</p> <p> 1a) Raw_Data: the raw images are reported as .dat and .bmp formats, divided into folders (according date first yymmdd, and within the same day according to composition). Each folder contains a .txt file reporting the experimental details </p> <p> 1b) Final_Graph<br> - Figure_1E.csv is the new source file x-y of the bar plot shown in figure 1E (% of GUVs which showed adsorption of CaM over the total amount of measured GUVs) in the revised version of the manuscript<br> <br>2) DLS</p> <p> 2a) Raw Data: <br> - DLS_lipid 0.4mM_1.7uM CaM_10mM CaCl2 contains all the data in .dts and in .xlsx formats for the experiments described in the Experimental details.txt file stored in the same folder <br> - DLS_lipid 0.4mM_10mM CaCl2_1.7uM CaM contains all the data in .dts and in .xlsx formats for the experiments described in the Experimental details.txt file stored in the same folder </p> <p> 2b) Final_Graph: <br> - Fig.S4B.xlsx contains the x-y source file for the figure S4B<br> - Fig.S5A.xlsx contains the x-y source file for the figure S5A </p> <p>3) Z-potential</p> <p> 3a) Raw Data: <br> - ZetaPotential_lipid 0.4mM_1.7uM CaM_10mM CaCl2 contains all the data in .dts and in .xlsx formats for the experiments described in the Experimental details.txt file stored in the same folder <br> - ZetaPotential_lipid 0.4mM_10mM CaCl2_1.7uM CaM contains all the data in .dts and in .xlsx formats for the experiments described in the Experimental details.txt file stored in the same folder </p> <p> 3b) Final_Graph: <br> - Fig.S4C.xlsx contains the x-y source file for the figure S4C<br> - Fig.S5B.xlsx contains the x-y source file for the figure S5B </p> <p> </p> <p> </p>
(TM3_D2A-CIS) Simulation POPC_512_TM3_D2A_10_5up_5down_NaCl_150mM_310K membrane (rep1)
<p><strong>Title</strong>: (TM3_D2A-CIS) Simulation POPC_512_TM3_D2A_10_5up_5down_NaCl_150mM_310K membrane (rep1)</p> <p><strong>Description</strong>: Simulation of a POPC membrane containing ten LAPTM4B-TM3_D2A peptides using charmm36 at 310K. (TM3_D2A peptides have cis peptides bonds by mistake)</p> <p><strong>MD engine</strong>: gromacs 2016.1</p> <p><strong>Force field</strong>: charmm36</p> <p><strong>Temperature</strong>: 310K</p> <p><strong>Simulation time</strong>: 1000ns</p> <p><strong>Saving frequency</strong>: 100ps</p> <p><strong>Molecular content</strong>:<br> TM3_D2A 10<br> POPC 512<br> SOL 20470<br> NA 55<br> CL 55</p> <p><strong>Other information</strong>:<br> * Membrane containing LAPTM4B TM3 peptides.<br> * The peptide presents the D202A mutation.<br> * 5 peptides pointing up/ 5 peptides pointing down.<br> <br> - Problems<br> * By mistake some peptides bonds in TM3 are in CIS configuration</p>
(TM3_D2A-CIS) Simulation POPC_512_TM3_D2A_10_5up_5down_NaCl_150mM_310K membrane (rep2)
<p>System description<br> -------------------<br> - Title: (TM3_D2A-CIS) Simulation POPC_512_TM3_D2A_10_5up_5down_NaCl_150mM_310K membrane (rep2)</p> <p>- Description: Simulation of a POPC membrane containing ten LAPTM4B-TM3_D2A peptides using charmm36 at 310K. (TM3_D2A peptides have cis peptides bonds by mistake)</p> <p>- MD engine: gromacs 2016.1</p> <p>- Force field: charmm36</p> <p>- Temperature: 310K</p> <p>- Simulation time: 1000ns</p> <p>- Saving frequency: 100ps</p> <p>- Molecular content:<br> TM3_D2A 10<br> POPC 512<br> SOL 20470<br> NA 55<br> CL 55</p> <p>- Other information:<br> * Membrane containing LAPTM4B TM3 peptides.<br> * The peptide presents the D202A mutation.<br> * 5 peptides pointing up/ 5 peptides pointing down.<br> <br> - Problems<br> * By mistake some peptides bonds in TM3 are in CIS configuration</p>
(TM3-CIS) Simulation POPC_512_TM3_10_5up_5down_NaCl_150mM_310K membrane
<p>System description<br> -------------------<br> - Title: (TM3-CIS) Simulation POPC_512_TM3_10_5up_5down_NaCl_150mM_310K membrane</p> <p>- Description: Simulation of a POPC membrane containing ten LAPTM4B-TM3 peptides using charmm36 at 310K. (TM3 peptides have cis peptides bonds by mistake)</p> <p>- MD engine: gromacs 5.0.4</p> <p>- Force field: charmm36</p> <p>- Temperature: 310K</p> <p>- Simulation time: 2000ns</p> <p>- Saving frequency: 100ps</p> <p>- Molecular content:<br> TM3 10<br> POPC 512<br> SOL 20470<br> NA 65<br> CL 55</p> <p>- Other information:<br> * Membrane containing LAPTM4B TM3 peptides.<br> * 5 peptides pointing up/ 5 peptides pointing down</p> <p>- Problems<br> * By mistake some peptides bonds in TM3 are in CIS configuration</p>
Dataset for journal JFS: "Near-wake characteristics of rigid and membrane wings in ground effect" 2018 by R.Bleischwitz, R.de Kat, B.Ganapathisubramani
<p>Complete Dataset for Journal of Fluids and Structures publication:</p> <p>"Near-wake characteristics of rigid and membrane wings in ground effect" (2018) by, R.Bleischwitz, R.de Kat, B.Ganapathisubramani<br> Written 01-04-2018<br> by Robert Bleischwitz (robert.bleischwitz@gmail.com)</p> <p>General Comments</p> <p>0.) This specific upload contains the full timeresolved dataset of the JFS-paper (~27GB of timeresolved MATLAB files)</p> <p>1.) The attached time-resolved-data relates to experimental windtunnel measurements on passive membrane wings for MAVs. The data was aquired between 2012-2016 at the University of Southampton, involving Robert Bleischwitz as PhD student, who was supervised by Roeland de Kat and Bharathram Ganapathisubramani.</p> <p>2.) The attached data is given time-resolved and time-synchronised at 800Hz over a imaging-period of 5000 images, involving load measurements via a 6-axis load-cell ATI Nano17 /25N, deformation measurements via Digitial Image Processing (high-speed DIC) and stereo flow measurements via two high-speed cameras (high-speed stereo PIV). </p> <p>3.) More setup and processing details can be found in the paper "Near-wake characteristics of rigid and membrane wings in ground effect" (2018) by the authors R. Bleischwitz, R. de Kat, B. Ganapathisubramani<br> Published in:</p> <p>-Journal of Fluids and Structures: <a href="https://doi.org/10.1016/j.jfluidstructs.2018.03.007">https://doi.org/10.1016/j.jfluidstructs.2018.03.007</a> </p> <p>- University of Southampton: <a href="http://doi.org/10.5258/SOTON/D0461">http://doi.org/10.5258/SOTON/D0461</a> </p> <p>4.) All load/deformation/flow folders contain a README.txt(Use 1st) and Instructions.m (Use 2nd) MATLAB-file, which give further supporting details how to illustrate the time-resolved-data</p> <p>5.) This specific upload contains the full time-resolved dataset, including:</p> <p>-Cases:</p> <p>a.) Rigid and Membrane wings</p> <p>b.) Height of ground(from trailing edge, in referecne to chord length): h/c=2, 0.25 and 0.1</p> <p>c.) Angle-of-attack: 10,15,25deg</p> <p>d.) DATA available (Timeresolved and time-synchronised):</p> <p>-Loads in high speed (10 kHz)</p> <p>-Membrane deformations in high speed(800Hz)</p> <p>-Stereo Flow velocities in wake at high-speed (800Hz)</p> <p><strong><em>Abstract of Journal-publication:</em><br> Wind tunnel measurements are conducted at a Reynolds numbers of Re = 56,000 to examine the characteristics of<br> near-wake vortices of rigid flat-plates and membrane wings from free-flight into ground–effect conditions. Synchronised<br> high-speed load cell measurements, digital image correlation and particle image velocimetry are performed to<br> resolve lift, drag and pitch oscillations simultaneously with membrane deformation and flow dynamics. Flow measurements<br> are acquired in a crossflow-plane, one chord downstream of the trailing-edge, allowing the examination of<br> time evolution of the wake and its relationship to the forces and membrane deformation. Membrane wings are found<br> to delay ground–effect or high angles-of-attack induced tip-vortex break-down and result in larger tip-vortex push-out<br> (beyond the wing span) compared to rigid flat-plate wings. The leading-edge vortex appears to shed with streamwise<br> vorticity close to the root of the wing and this frequency of this shedding is found to match with the dominant frequency<br> observed in membrane fluctuations. In specific resonance conditions, membrane and flow fluctuations are found to<br> correlate well to the fluctuations in loads and moments.</strong></p>
TGA data for the manuscript "Synergistic fire-retardancy properties of melamine coated ammonium poly(phosphate) in combination with rod-like mineral filler attapulgite for polymer-modified bitumen roofing membranes"
<p>The file "SynergisticFireRetardencyPaper_data" containns the raw data and data tretment used in the manuscript<br> "Synergistic fire-retardancy properties of melamine coated ammonium poly(phosphate) in combination with rod-like mineral filler attapulgite for polymer-modified bitumen roofing membranes" for the the TGA part of the work.<br> The file "TGA_Data_and_Data_treatment.xls" contains the TGA raw data used in the manuscript and the recaluclation to a common temperature scale. The file "TGA_plots_20180611.opju" caontian the contruction of the plots shown in the paper.</p> <p> </p>
New Azo-DMOF-1 MOF as a photo-responsive low-energy CO2 adsorbent and its exceptional CO2/N2 separation performance in mixed matrix membranes
<p>Data repository for manuscript, published in <em>ACS Applied Materials & Interfaces</em>, <strong>2018</strong>, <em>10</em> (40), pp 34291–34301, <a href="https://dx.doi.org/10.1021/acsami.8b12261">http://dx.doi.org/10.1021/acsami.8b12261</a></p> <p><strong>Abstract</strong></p> <p>A new generation-2 light-responsive metal–organic framework (MOF) has been successfully synthesized using Zn as the metal source and both 2-phenyldiazenyl terephthalic acid and 1,4-diazabicyclo[2.2.2]octane (DABCO) as the ligands. It was found that Zn-azo-dabco MOF (Azo-DMOF-1) exhibited a photoresponsive CO<sub>2</sub> adsorption both in static and dynamic condition because of the presence of azobenzene functionalities from the ligand. Further application of this MOF was evaluated by incorporating it as a filler in a mixed matrix membrane for CO<sub>2</sub>/N<sub>2</sub> gas separation. Matrimid and polymer of intrinsic microporosity-1 (PIM-1) were used as the polymer matrix. It was found that Azo-DMOF-1 could enhance both the CO<sub>2</sub> permeability and selectivity of the pristine polymer. In particular, the Azo-DMOF-1–PIM-1 composite membranes have shown a promising performance that surpassed the 2008 Robeson Upper Bound.</p>
Dataset Inhibition of membrane-bound BAFF by the anti-BAFF antibody belimumab
<p>This dataset is related to "Inhibition of membrane-bound BAFF by the anti-BAFF antibody belimumab" (Kowalczyk-Quintas C, Chevalley D, Willen L, Jandus C, Vigolo M, Schneider P).</p>
Nanoscale dipole dynamics of protein membranes studied by broadband dielectric microscopy
<p>Original data in support of our publication: Nanoscale dipole dynamics of protein membranes studied by broadband dielectric microscopy</p>
Drug-membrane transfer free energies for coarse-grained trimers and tetramers
<p>The databases contain drug-membrane transfer free energies for coarse-grained Martini trimers and tetramers inserted in a one-component DOPC membrane. We also provide a database of atomistic-resolution compounds mined from the GDB and that map to trimers.</p>
Simulation POPC_512_NaCl_150mM_310K membrane
<p><strong>Title publication: </strong><em>A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction</em></p> <p><strong>Year publication: </strong>2018</p> <p><strong>DOI publication: </strong>10.1021/acscentsci.7b00582</p> <p><strong>Description:</strong> Simulation POPC membrane using charmm36 at 310K.</p> <p><strong>MD engine:</strong> 2016.1<br> <br> </p> <p><strong>Force field</strong>: charmm36</p> <p><strong>Temperature</strong>: 310 K</p> <p><strong>Pressure:</strong> 1 bar</p> <p><strong>Simulation time</strong>: 4200 ns</p> <p><strong>Saving frequency</strong>: 100 ps</p> <p><strong>Molecular content</strong>:</p> <p>POPC 512<br> water 20480<br> Cl- 55<br> Na+ 55</p> <p><strong>Other information:</strong><br> * Center of mass motion removed independently for bilayer and water+ions<br> * 01-* are the merged files.<br> * 02-* are the original simulation files. So do not concatenate 02 and 01 files.</p>
Simulation POPC_512_TM3_D2A_10_5up_5down_NaCl_150mM_310K_rep2 membrane
<p><strong>Title publication: </strong><em>A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction</em></p> <p><strong><strong>Year publication:</strong></strong><strong> </strong>2018</p> <p><strong>DOI publication: </strong>10.1021/acscentsci.7b00582</p> <p><strong>Description:</strong> Simulation POPC membrane containing ten LAPTM4B-TM3 with D2A mutation in the water phase using charmm36 at 310K.</p> <p><strong>MD engine:</strong> gromacs 5.1.3-dev-20160627-f16daab</p> <p><strong>Force field</strong>: charmm36</p> <p><strong>Temperature</strong>: 310 K</p> <p><strong>Pressure:</strong> 1 bar</p> <p><strong>Simulation time</strong>: 800 ns</p> <p><strong>Saving frequency</strong>: 100 ps</p> <p><strong>Molecular content</strong>:</p> <p>TM3_D2A 10<br> POPC 512<br> SOL 29366<br> NA 79<br> CL 79</p> <p><strong>Additional </strong><strong>information</strong>:<br> * Membrane containing LAPTM3_D2A peptides (Ac-AWIIPFFCYQIFDFALNMLVAITVLIY-NH2). D to A muation.</p>
Simulation POPC_512_TM3_D2A_10_5up_5down_NaCl_150mM_310K_rep1 membrane
<p><strong>Title publication: </strong><em>A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction</em></p> <p><strong><strong>Year publication:</strong></strong><strong> </strong>2018</p> <p><strong>DOI publication: </strong>10.1021/acscentsci.7b00582</p> <p><strong>Description:</strong> Simulation POPC membrane containing ten LAPTM4B-TM3 with D2A mutation in the water phase using charmm36 at 310K.</p> <p><strong>MD engine:</strong> gromacs 2016.1</p> <p><strong>Force field</strong>: charmm36</p> <p><strong>Temperature</strong>: 310 K</p> <p><strong>Pressure:</strong> 1 bar</p> <p><strong>Simulation time</strong>: 800 ns</p> <p><strong>Saving frequency</strong>: 100 ps</p> <p><strong>Molecular content</strong>:</p> <p>TM3_D2A 10<br> POPC 512<br> SOL 29366<br> NA 79<br> CL 79</p> <p><strong>Additional </strong><strong>information</strong>:<br> * Membrane containing LAPTM3_D2A peptides (Ac-AWIIPFFCYQIFDFALNMLVAITVLIY-NH2). D to A muation.</p>
Simulation POPC_512_TM3_D2A_10_5up_5down_NaCl_150mM_310K_rep3 membrane
<p><strong>Title publication: </strong><em>A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction</em></p> <p><strong><strong>Year publication:</strong></strong><strong> </strong>2018</p> <p><strong>DOI publication: </strong>10.1021/acscentsci.7b00582</p> <p><strong>Description:</strong> Simulation POPC membrane containing ten LAPTM4B-TM3 with D2A mutation in the water phase using charmm36 at 310K.</p> <p><strong>MD engine:</strong> gromacs 2016.1</p> <p><strong>Force field</strong>: charmm36</p> <p><strong>Temperature</strong>: 310 K</p> <p><strong>Pressure:</strong> 1 bar</p> <p><strong>Simulation time</strong>: 2000 ns</p> <p><strong>Saving frequency</strong>: 100 ps</p> <p><strong>Molecular content</strong>:</p> <p>TM3_D2A 10<br> POPC 512<br> SOL 29366<br> NA 79<br> CL 79</p> <p><strong>Additional </strong><strong>information</strong>:<br> * Membrane containing LAPTM3_D2A peptides (Ac-AWIIPFFCYQIFDFALNMLVAITVLIY-NH2). D to A muation.</p>
Simulation CER160_128_POPC_512_TM3_10_5up_5down_NaCl_150mM_310K_rep2 membrane
<p><strong>Title publication:</strong> <em>A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction</em></p> <p><strong>Year publication:</strong> 2018</p> <p><strong>DOI publication: </strong>10.1021/acscentsci.7b00582</p> <p><strong>Description:</strong> Simulation of a membrane containing 512 POPC and 128 ceramide (CER160) together with ten LAPTM4B-TM3 peptides using charmm36 at 310K.</p> <p><strong>MD engine:</strong> 2016.2-dev-20170105-4feb0be</p> <p><strong>Force field</strong>: charmm36</p> <p><strong>Temperature</strong>: 310 K</p> <p><strong>Pressure:</strong> 1 bar</p> <p><strong>Simulation time</strong>: 4200 ns</p> <p><strong>Saving frequency</strong>: 100 ps</p> <p><strong>Molecular content</strong>:</p> <p>TM3 10<br> POPC 512<br> CER160 128<br> SOL 31990<br> NA 96<br> CL 86</p> <p><strong>Additional </strong><strong>information</strong>:<br> * Membrane containing LAPTM4B TM3 peptides (Ac-AWIIPFFCYQIFDFALNMLVAITVLIY-NH2).</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.