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39 results for “Degradation mechanism”
Dataset of "PEMFC performance decay during real-world automotive operation: evincing degradation mechanisms and heterogeneity of ageing"
<p>This is the underlying dataset of "PEMFC performance decay during real-world automotive operation: evincing degradation mechanisms and heterogeneity of ageing"</p>
Supplementary Data for "Substrate-Assisted Mechanism for the Degradation of N-glycans by a Gut Bacterial Mannoside Phosphorylase"
<p>This dataset contains atomic coordinates of the molecular dynamics simulations described in "Substrate-Assisted Mechanism for the Degradation of N-glycans by a Gut Bacterial Mannoside Phosphorylase" by M. Alfonso-Prieto, I. Cuxart, G. Potocki-Véronèse, I. André and C. Rovira, published in ACS Catalysis (https://doi.org/10.1021/acscatal.3c00451). Further details on the setup of the simulations can be found in the Supplementary Information of the article. </p> <p>If you use this dataset, please cite this zenodo upload (https://doi.org/10.5281/zenodo.7704778), as well as the the original journal article (https://doi.org/10.1021/acscatal.3c00451). </p> <p>This dataset is organized in the following folders:</p> <p><strong>Snapshots_Figures_Main_Text.zip</strong>, that contains a README.txt file and:</p> <p><strong>- Figure_3</strong> contains representative structures (atomic coordinates) of the hexameric form of UhgbMP in complex with 3 different disaccharide molecules, Man-b-(1,4)-GlcNAc, Man-b-(1,4)-Glc and Man-b-(1,4)-Man.</p> <p><strong>- Figure_4</strong> contains representative structures (atomic coordinates) of the hexameric form of UhgbMP at the three minima observed along the reaction coordinate corresponding to phosphorolysis of the disaccharide Man-b-(1,4)-GlcNAc: Michaelis complex (MC), transition state (TS) and product (P) complex.</p> <p>Files in this dataset are in PDB format. For all structures, the solvation box (water and ions) has been stripped to reduce file size. See README.txt inside <a href="https://zenodo.org/api/files/f3836540-b7b6-4820-87b3-7fa5dff7840c/Snapshots_Figures_Main_Text.zip">Snapshots_Figures_Main_Text.zip </a>for more information.</p>
Metagenomic analysis of gut microbiome illuminates the mechanisms and evolution of lignocellulose degradation in mangrove herbivorous crabs
<p><strong>Background:</strong></p> <p>Sesarmid crabs dominate mangrove habitat as the major primary consumers, which facilitates the trophic link and nutrient recycling in the ecosystem. Therefore, the adaptations and mechanisms of sesarmid crabs to herbivory is not only crucial to terrestrialization and its evolutionary success, but also to the healthy functioning of mangrove forest ecosystems. Although endogenous cellulases expressions were reported in crab species, it remains unknown if the endogenous enzymes alone can complete the whole lignocellulolytic pathway, or they also depend on the contribution from their intestinal microbiome. We attempt to investigate the role of gut symbiotic microbes of mangrove-feeding sesarmid crabs in plant digestion using a comparative metagenomic approach.</p> <p><strong>Results:</strong></p> <p>Metagenomics analyses on 43 crab gut samples from 23 species of mangrove crabs revealed a wide coverage of 127 CAZy families and nine KOs targeting lignocellulose and their derivatives in all species analyzed, including predominantly carnivorous species, suggesting the crab species gut microbiome have lignocellulolytic capacity regardless of dietary preference. Microbial cellulase, hemicellulase and pectinase genes in herbivorous and detritivorous crabs were differentially more abundant when compared to omnivorous and carnivorous crabs, indicating the importance of gut symbionts in lignocellulose degradation in mangrove crabs and the enrichment of lignocellulolytic microbes in response to diet with higher lignocellulose content. The herbivorous and detritivorous crabs showed highly similar CAZyme composition compared to dissimilarities observed in taxonomic profiles observed in both groups, suggesting a stronger selection force to gut microbiota by its functional capacity than by taxonomy. The gut microbiota in herbivorous sesarmid crabs were also enriched with nitrogen reduction and fixation genes, implying possible roles of the gut microbiota in supplementing nitrogen that is deficient in plant diet.</p> <p><strong>Conclusions:</strong></p> <p>Endosymbiotic cellulolytic microbes play an important role in lignocellulose degradation in most crab species but their abundance is strongly correlated with dietary preference, and they are highly enriched in herbivorous sesarmids, thus enhancing their capacity for digestion of mangrove leaves. Dietary preference is a stronger driver in determining the microbial CAZyme composition and taxonomic profile in mangrove crab microbiome, resulting in functional redundancy of endosymbiotic microbes. Our results showed that crabs implement a mixed mode of digestion utilizing both endogenous and microbial enzymes in lignocellulose degradation, as observed in most of the more advanced herbivorous invertebrate species.</p>
A Tungsten Deep Neural-Network Potential for Simulating Mechanical Property Degradation Under Fusion Service Environment
<p>The DP-HYB and DP-SE2potential and the W training database.</p>
Reaction Mechanism of the PET Degrading Enzyme PETase Studied with DFT/MM Molecular Dynamics Simulations
<p>Raw simulations of the acylation step by PETase on a PET dimer model substrate, ran with CP2K 6.1 software at the PBE:AMBER level. Details can be found in the original manuscript (<a href="https://doi.org/10.1021/acscatal.1c03700">https://doi.org/10.1021/acscatal.1c03700</a>): Molecular topology in AMBER Parameter Topology format and Trajectories in CHARMM binary coordinate format DCD.</p> <p>RESIDUE LIST:<br> GLY57<br> TYR58<br> SER131<br> MET132<br> TRP156<br> ASP177<br> SER178<br> ILE179<br> ALA180<br> HID208<br> MOL262</p> <p>VMD selection:<br> (name CA C O HA2 HA3 and resname GLY and resid 57) or (name N CA CB H HA HB2 HB3 and resname TYR and resid 58) or (name CA C O OG CB HA HB2 HB3 HG and resname SER and resid 131) or (name N CA SD CE CB CG H HA HB2 HB3 HG2 HG3 HE1 HE2 HE3 and resname MET and resid 132) or (name CB CG CD1 CD2 CE2 CE3 NE1 CZ2 CZ3 CH2 HB2 HB3 HD1 HE1 HE3 HZ2 HZ3 HH2 and resname TRP and resid 156) or (name CG OD1 OD2 CB HB2 HB3 and resname ASP and resid 177) or (name C O and resname SER and resid 178) or (name N CA C O CG2 CD1 CB CG1 H HA HB HG12 HG13 HG21 HG22 HG23 HD11 HD12 HD13 and resname ILE and resid 179) or (name N CA H HA and resname ALA and resid 180) or (name CB CG CD2 ND1 CE1 NE2 HB2 HB3 HD1 HD2 HE1 and resname HID and resid 208) or (name C1 C10 C11 C12 C13 C14 C15 C16 C17 C18 C19 C2 C20 C3 C4 C5 C6 C7 C8 C9 H1 H10 H11 H12 H13 H14 H15 H16 H17 H2 H3 H4 H5 H6 H7 H8 H9 O1 O2 O3 O4 O5 O6 O7 O8 O9 and resname MOL and resid 262)</p> <p>PYMOL selection:<br> (name CA+C+O+HA2+HA3 & resn GLY & resi 57) | (name N+CA+CB+H+HA+HB2+HB3 & resn TYR & resi 58) | (name CA+C+O+OG+CB+HA+HB2+HB3+HG & resn SER & resi 131) | (name N+CA+SD+CE+CB+CG+H+HA+HB2+HB3+HG2+HG3+HE1+HE2+HE3 & resn MET & resi 132) | (name CB+CG+CD1+CD2+CE2+CE3+NE1+CZ2+CZ3+CH2+HB2+HB3+HD1+HE1+HE3+HZ2+HZ3+HH2 & resn TRP & resi 156) | (name CG+OD1+OD2+CB+HB2+HB3 & resn ASP & resi 177) | (name C+O & resn SER & resi 178) | (name N+CA+C+O+CG2+CD1+CB+CG1+H+HA+HB+HG12+HG13+HG21+HG22+HG23+HD11+HD12+HD13 & resn ILE & resi 179) | (name N+CA+H+HA & resn ALA & resi 180) | (name CB+CG+CD2+ND1+CE1+NE2+HB2+HB3+HD1+HD2+HE1 & resn HID & resi 208) | (name C1+C10+C11+C12+C13+C14+C15+C16+C17+C18+C19+C2+C20+C3+C4+C5+C6+C7+C8+C9+H1+H10+H11+H12+H13+H14+H15+H16+H17+H2+H3+H4+H5+H6+H7+H8+H9+O1+O2+O3+O4+O5+O6+O7+O8+O9 & resn MOL & resi 262)</p>
Data for "Structure and mechanism of oxalate transporter OxlT in an oxalate-degrading bacterium in the gut microbiota"
<p>MD simulation data of OxlT. Trajectory data and NAMD input files are included. The first 500 ns trajectory that starts from the occluded conformation with a transition to the outward-open conformation is in the OxlT-occ directory. The 200 ns trajectories that start from the outward-open conformation with different protonation states of K355 are in the OxlT-out directory. </p>
The reaction mechanism for glycolysis side product degradation by Parkinson's disease-linked DJ-1
Open the record for dataset details and reuse information.
Metagenomic analysis of gut microbiome illuminates the mechanisms and evolution of lignocellulose degradation in mangrove herbivorous crabs
Open the record for dataset details and reuse information.
A singlet oxygen non-radical pathway for Rhodamine B dye degradation: Study on its stability, mechanism of degradation, and detoxification
<p><span>This study examined the degradation pathway of used face mask-derived carbon (UFMC) as a catalyst to activate peroxymonosulfate (PMS) without light sources and metal for Rhodamine B (RhB) dye degradation.</span><span> </span><span>The structural changes in the UFMC catalyst resulting from RhB degradation reduced its oxygen functionality and so reduced the rate of RhB dye degradation with each usage. </span><span>The structural changes of UFMC catalysts were confirmed by Fourier transform infrared, Raman, and X-ray photoelectron spectroscopy. The oxygen functionalities were involved in the generation of reactive oxygen species (ROS), in terms of singlet oxygen (<sup>1</sup>O<sub>2</sub>), which are involved in the RhB dye degradation mechanism. This was confirmed using paramagnetic resonance (EPR) spectroscopy and scavenging analyses. </span><span>Re-useability and stability investigations revealed the UFMC catalyst reached a minimum degradation percentage (38.8%) in the 5<sup>th</sup> cycle, confirming the complete utilization of UFMC functional groups for RhB dye degradation. </span><span>Finally, the ability to detoxify the RhB dye water was assessed using zebrafish (<em>Danio rerio) </em>with different RhB dye concentrations (2 to 6 mg/L), and 0 to 72 h of incubation at 26 °C and the<em> </em>yeast<em> </em>cells<em> (Saccharomyces cerevisiaetests)</em> harvested about 10<sup>7</sup> cells per mL for 24 h under shaking at 160 rpm at 30 °C. </span><span>Based on these results, the animal models were exposed to the RhB dye water, the significant changes in their growth were evident. However, treated with the RhB degraded water as a control, no developmental deformity was observed. This research employed the </span><span>UFM</span><span> derived carbon conveniently supported with PMS for dye removal application.</span></p>
Extra Throughput versus Days Lost in V2G services: Influence of dominant degradation mechanism
<div> <div>This code reads the simulated data generated by Pybamm, calculates the LLI due to each mechanism, and plots the results.</div> </div>
Supplementary Tables: The symbiotic lignocellulose degradation in termite guts: Novel insights into main bacterial players and mechanisms, with focus on the phylum Fibrobacterota
<p>This repo contains the Supplementary Tables for the thesis entitled "The symbiotic lignocellulose degradation in termite guts: Novel insights into main bacterial players and mechanisms, with focus on the phylum <em>Fibrobacterota</em>" by João Salgado.</p>
Dataset for publication "Comparative Analysis of the Pharmacokinetics of a New Migliol-Based Antiviral Agent Campecin and Investigation of Degradation Mechanisms"
Open the record for dataset details and reuse information.
Reaction Mechanism of the PET Degrading Enzyme PETase Studied with DFT/MM Molecular Dynamics Simulations
<p>Raw simulations of the deacylation step by PETase on a PET dimer model substrate, ran with CP2K 6.1 software at the PBE:AMBER level. Details can be found in the original manuscript (<a href="https://doi.org/10.1021/acscatal.1c03700">https://doi.org/10.1021/acscatal.1c03700</a>): Molecular topology in AMBER Parameter Topology format and Trajectories in CHARMM binary coordinate format DCD.</p> <p>QM RESIDUE LIST:<br> GLY57<br> TYR58<br> SEP131<br> MET132<br> TRP156<br> ASP177<br> SER178<br> ILE179<br> ALA180<br> HID208<br> WAT6290<br> WAT6318<br> WAT7630</p> <p>VMD selection:<br> (name CA C O HA2 HA3 and resname GLY and resid 57) or (name N CA CB H HA HB2 HB3 and resname TYR and resid 58) or (name O2 C3 O3 C4 O4 C5 O5 O6 C7 O7 C8 C9 C10 C11 C12 C13 C14 C15 C16 H5 H6 H7 H12 H13 H14 H15 H16 H17 H18 H19 H20 and resname SEP and resid 131) or (name N CA SD CE CB CG H HA HB2 HB3 HG2 HG3 HE1 HE2 HE3 and resname MET and resid 132) or (name CB CG CD1 CD2 CE2 CE3 NE1 CZ2 CZ3 CH2 HB2 HB3 HD1 HE1 HE3 HZ2 HZ3 HH2 and resname TRP and resid 156) or (name CG OD1 OD2 CB HB2 HB3 and resname ASP and resid 177) or (name C O and resname SER and resid 178) or (name N CA C O CG2 CD1 CB CG1 H HA HB HG12 HG13 HG21 HG22 HG23 HD11 HD12 HD13 and resname ILE and resid 179) or (name N CA CB H HA HB1 HB2 HB3 and resname ALA and resid 180) or (name CB CG CD2 ND1 CE1 NE2 HB2 HB3 HD1 HD2 HE1 and resname HID and resid 208) or (name O H1 H2 and resname WAT and resid 6290) or (name O H1 H2 and resname WAT and resid 6318) or (name O H1 H2 and resname WAT and resid 7630)</p> <p>PYMOL selection:<br> (name CA+C+O+HA2+HA3 & resn GLY & resi 57) | (name N+CA+CB+H+HA+HB2+HB3 & resn TYR & resi 58) | (name O2+C3+O3+C4+O4+C5+O5+O6+C7+O7+C8+C9+C10+C11+C12+C13+C14+C15+C16+H5+H6+H7+H12+H13+H14+H15+H16+H17+H18+H19+H20 & resn SEP & resi 131) | (name N+CA+SD+CE+CB+CG+H+HA+HB2+HB3+HG2+HG3+HE1+HE2+HE3 & resn MET & resi 132) | (name CB+CG+CD1+CD2+CE2+CE3+NE1+CZ2+CZ3+CH2+HB2+HB3+HD1+HE1+HE3+HZ2+HZ3+HH2 & resn TRP & resi 156) | (name CG+OD1+OD2+CB+HB2+HB3 & resn ASP & resi 177) | (name C+O & resn SER & resi 178) | (name N+CA+C+O+CG2+CD1+CB+CG1+H+HA+HB+HG12+HG13+HG21+HG22+HG23+HD11+HD12+HD13 & resn ILE & resi 179) | (name N+CA+CB+H+HA+HB1+HB2+HB3 & resn ALA & resi 180) | (name CB+CG+CD2+ND1+CE1+NE2+HB2+HB3+HD1+HD2+HE1 & resn HID & resi 208) | (name O+H1+H2 & resn WAT & resi 6290) | (name O+H1+H2 & resn WAT & resi 6318) | (name O+H1+H2 & resn WAT & resi 7630)</p>
Morphological and genetic screens reveal mechanisms of BiDAC-induced plasma membrane protein degradation
GEO Series GSE291219. Homo sapiens. 4 samples. Type: Other.
Functional E3 ligase hotspots and resistance mechanisms to small-molecule degraders [Saturating mutagenesis]
GEO Series GSE198278. Homo sapiens. 38 samples. Type: Other.
Functional E3 ligase hotspots and resistance mechanisms to small-molecule degraders via chemical genetics [Hybrid capture]
GEO Series GSE198279. Homo sapiens. 7 samples. Type: Other.
Development of an orally bioavailable SWI/SNF ATPase degrader and acquired mechanisms of resistance [RNA-seq]
GEO Series GSE250326. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing.
CEG1 DEPLETION REVEALS MECHANISMS GOVERNING DEGRADATION OF NON-CAPPED RNAs
GEO Series GSE213942. Saccharomyces cerevisiae. 8 samples. Type: Expression profiling by high throughput sequencing.
Deciphering regulatory mechanisms associated with hemicellulose degradation in Neurospora crassa
GEO Series GSE34098. Neurospora crassa. 23 samples. Type: Expression profiling by array.
Functional E3 ligase hotspots and resistance mechanisms to small-molecule degraders via chemical genetics
GEO Series GSE198280. Homo sapiens. 45 samples. Type: Other.
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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.