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17 results for “membrane-bound”
Data from: Sorting states of environmental DNA: Effects of isolation method and water matrix on recovery of membrane-bound, dissolved, and adsorbed states of eDNA
<p>Environmental DNA (eDNA) once shed can exist in numerous states with varying behaviors including degradation rates and transport potential. In this study we consider three states of eDNA: 1) a membrane-bound state referring to DNA enveloped in a cellular or organellar membrane, 2) a dissolved state defined as the extracellular DNA molecule in the environment without any interaction with other particles, and 3) an adsorbed state defined as extracellular DNA adsorbed to a particle surface in the environment. Capturing, isolating, and analyzing a target state of eDNA provides utility for better interpretation of eDNA degradation rates and transport potential. While methods for separating different states of DNA have been developed, they remain poorly evaluated due to the lack of state-controlled experimentation. We evaluated the methods for separating states of eDNA from a single sample by spiking DNA from three different species to represent the three states of eDNA as state-specific controls. We used chicken DNA to represent the dissolved state, cultured mouse cells for the membrane-bound state, and salmon DNA adsorbed to clay particles as the adsorbed state. We performed the separation in three water matrices, two environmental and one synthetic, spiked with the three eDNA states. The membrane-bound state was the only state that was isolated with minimal contamination from non-target states. The membrane-bound state also had the highest recovery (54.11 ± 19.24 %), followed by the adsorbed state (5.08 ± 2.28 %), and the dissolved state had the lowest total recovery (2.21 ± 2.36 %). This study highlights the potential to sort the states of eDNA from a single sample and independently analyze them for more informed biodiversity assessments. However, further method development is needed to improve recovery and reduce cross-contamination.</p>
Data from: Sorting states of environmental DNA: Effects of isolation method and water matrix on recovery of membrane-bound, dissolved, and adsorbed states of eDNA
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Mechanistic principles of hydrogen evolution in the membrane-bound hydrogenase
<p>Optimized coordinates of DFT models of the [NiFe] active-site from the membrane-bound hydrogenase</p> <p>Table of contents<br>1. Ni-SIa state<br>2. Ni-L and Ni-C state<br>3. Ni-R state<br>4. Ni-SIa state (with His75+)<br>5. Ni-L and Ni-C state (with His75+)<br>6. Ni-R state (with His75+)<br>7. [NiFe] active-site from DvMF in the Ni-R state (Geometries optimized using various DFT functional)</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>
Data from: Conformational dynamics and asymmetry in multimodal inhibition of membrane-bound pyrophosphatases
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Molecular Dynamics Trajectories of Membrane-bound Influenza Hemagglutinin (A/duck/Alberta/35/76) in Complex with 0-3 Copies of FISW84 Fab Fragments
<p>MD simulation trajectories of influenza hemagglutinin (A/duck/Alberta/35/76) in a bilayer mimicking the viral membrane, with 0-3 copies of FISW84 antibody's Fab domains bound.</p> <p>Files are named as (copy number of Fab).(simulation replica ID).(file type extension). The systems were constructed in CHARMM format PSF files and the trajectories were recorded in DCD format.</p> <p>Simulations were performed with NAMD3. The trajectories were re-centered and re-wrapped about the periodic boundary from the raw trajectories, in order to keep the HA-Fab complex and the lipid bilayer appearing as a single continuous entity instead of isolated molecules at the opposite side of the periodic boundary. Water molecules in the simulation were removed in these trajectories due to file size limitations.</p>
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>
Active nematic order and dynamic lane formation of microtubules driven by membrane-bound diffusing motors
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Hippocampal neurons’ cytosolic and membrane-bound ribosomal transcript profiles are differentially regulated by learning and subsequent sleep
GEO Series GSE216163. Mus musculus. 180 samples. Type: Expression profiling by high throughput sequencing.
Regulatory B cells suppress GVHD and prolong survival of GVHD via membrane-bound IL-35 and secretion of exosomes with membrane-bound IL-35
GEO Series GSE263242. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
Vaccination with an mRNA-encoded membrane-bound HIV envelope trimer induces neutralizing antibodies in animal models
GEO Series GSE298795. Macaca mulatta. 36 samples. Type: Expression profiling by high throughput sequencing.
A novel membrane-bound IL-2 for NK cell immunotherapy
GEO Series GSE199391. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
Comparative transcriptomics between species attributes reactogenicity pathways induced by the capsular group B meningococcal vaccine, 4CMenB, to the membrane-bound endotoxin of its outer membrane vesi
GEO Series GSE131914. Mus musculus. 59 samples. Type: Expression profiling by high throughput sequencing.
Identifying membrane-bound transcriptional regulatory proteins from rare but evolutionarily conserved domain combinations
GEO Series GSE309766. Mus musculus. 18 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Interaction between tumor cell TNFR2 and monocyte membrane-bound TNFα triggers tumorigenic inflammation in neuroblastoma
GEO Series GSE218915. Homo sapiens/Mus musculus xenograft. 10 samples. Type: Expression profiling by high throughput sequencing.
Transcriptional profiling of bladder carcinoma T24 cells following CD40 activation by membrane-bound CD40L (mCD40L) compared to soluble CD40L (sCD40L)
GEO Series GSE98891. Homo sapiens. 12 samples. Type: Expression profiling by array.
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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.