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37 results for “Degradation pathway”
Amoxicillin degradation pathways and mass spectra raw data (using LC-MS orbitrap)
<p>The link provides five documents namely:</p> <p>File No.1 (Proposed Chemical Structures-tabulated)</p> <p>File No.2 (MS and MS2 images) support for File no.1</p> <p>File No.3 Transformation Products Pathway</p> <p>File No.4 Explanation + Justification of proposed chemical structures</p> <p>Raw Data obtained from compound discoverer</p>
Data from: Rotavirus NSP1 subverts the antiviral oligoadenylate synthetase-RNase L pathway by inducing RNase L degradation
<div>The interferon (IFN)-inducible 2′,5′-oligoadenylate synthetase (OAS)-RNase L pathway plays a critical role in antiviral immunity. Group A rotaviruses, including the simian SA11 strain, inhibit this pathway through two activities: an E3-ligase related activity of NSP1 that degrades proteins necessary for IFN signaling, and a phosphodiesterase (PDE) activity of VP3 that hydrolyzes the RNase L-activator 2′,5′-oligoadenylate. Unexpectedly, we found that a recombinant (r) SA11 double mutant virus deficient in both activities (rSA11-VP3H797R-NSP1ΔC17) retained the ability to prevent RNase L activation. Mass spectrometry led to the discovery that NSP1 interacts with RNase L in rSA11-infected HT29 cells. This interaction was confirmed through copulldown assay of cells transiently expressing NSP1 and RNase L. Immunoblot analysis showed that infection with wild-type rSA11 virus, rSA11-VP3H797R-NSP1ΔC17 double mutant virus, or single mutant forms of the latter virus all resulted in the depletion of endogenous RNase L. The loss of RNase L was reversed by addition of the neddylation inhibitor MLN4924, but not the proteasome inhibitor MG132. Analysis of additional mutant forms of rSA11 showed that RNase L degradation no longer occurred when either the N-terminal RING domain of NSP1 was mutated or the C-terminal 98 amino acids of NSP1 were deleted. The C-terminal RNase L degradation domain is positioned upstream and is functionally independent of the NSP1 domain necessary for inhibiting IFN expression. Our studies reveal a new role for NSP1 and its E3-ligase related activity as an antagonist of RNase L and uncover a novel virus-mediated strategy of inhibiting the OAS-RNase L pathway.</div>
Targeted protein degradation reveals BET bromodomains as the cellular target of Hedgehog Pathway Inhibitor-1
<p>Raw experimental data for the manuscript entitled 'Targeted protein degradation reveals BET bromodomains as the cellular target of Hedgehog Pathway Inhibitor-1'. This includes the data underlying all figures, DESeq2 files, modeling and MD simulations, and chemical compound characterization (NMR, LC-MS, HRMS). Also, the custom Matlab script to analyse cilium intensity from microscopy images is included (cilia-track_v4.0).</p>
Data from: Comparative genomic analysis of nine Sphingobium strains: insights into their evolution and Hexachlorocyclohexane (HCH) degradation pathways
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Data from: Rotavirus NSP1 subverts the antiviral oligoadenylate synthetase-RNase L pathway by inducing RNase L degradation
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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>
Carbon loss pathways in degraded peatlands: Repository dataset
<p>The data on the following sheets is associated with the paper:</p> <p> </p> <p>Evans, M.G., Alderson, D.M., Evans, C.D., Stimson, A., Goulsbra, C., Allott,T.E.H., Worrall, F., Crouch, T., Walker, J., Garnett, M.H., Rowson, J. (2022). Carbon Loss Pathways in Degraded Peatlands: New Insights from Radiocarbon Measurements of Peatland Waters. </p> <p> </p> <p>The data are organised according to the figures within the paper, with the data for each figure corresponding to an individual datasheet. The methods for data collection can be found in the associated manuscript.</p> <p> </p> <p>For further information please contact Martin Evans (martin.g.evans@manchester.ac.uk) or Danielle Alderson (danielle.alderson@manchester.ac.uk).</p> <p> </p> <p>Figures 1, 7 and 11 either do not contain data or are visual model outputs and are therefore not included. </p> <p> </p>
The midnolin-proteasome pathway catches proteins for ubiquitination-independent degradation
<p class="MsoNormal">Cells use ubiquitin to mark proteins for proteasomal degradation. While the proteasome also eliminates proteins that are not modified by ubiquitin, how this occurs mechanistically is unclear. We show here that midnolin promotes the destruction of many nuclear proteins including transcription factors encoded by the immediate-early-genes. Diverse environmental cues induce midnolin and its overexpression is sufficient to cause the degradation of its targets by a mechanism, which, remarkably, does not require ubiquitination. Instead, midnolin associates with the proteasome via <span>an alpha</span><span>-helix</span>, employs its Catch-domain to bind a region within substrates that adopts a beta-strand conformation, and uses a ubiquitin-like-domain to promote substrate destruction. Thus, midnolin contains three regions that function in concert to target a large set of nuclear proteins to the proteasome for degradation. </p>
Data from: Comparative genomic analysis of nine Sphingobium strains: insights into their evolution and hexachlorocyclohexane (HCH) degradation pathways
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The midnolin-proteasome pathway catches proteins for ubiquitination-independent degradation
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microRNA-22 Inhibition Stimulates Mitochondrial Homeostasis and Intracellular Degradation Pathways to Prevent Muscle Wasting
GEO Series GSE309212. Mus musculus. 10 samples. Type: Expression profiling by high throughput sequencing.
The conserved regulatory RNA RsaE down-regulates the arginine degradation pathway in Staphylococcus aureus [ssRNA-Seq]
GEO Series GSE106456. Staphylococcus aureus. 10 samples. Type: Expression profiling by high throughput sequencing.
The conserved regulatory RNA RsaE down-regulates the arginine degradation pathway in Staphylococcus aureus [Hybrid-Trap-seq]
GEO Series GSE106327. Staphylococcus aureus. 4 samples. Type: Expression profiling by high throughput sequencing; Other.
Development of an orally bioavailable CDK12/13 degrader and induction of synthetic lethality with AKT pathway inhibition [nascent]
GEO Series GSE262120. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
Development of an orally bioavailable CDK12/13 degrader and induction of synthetic lethality with AKT pathway inhibition [bulk]
GEO Series GSE262119. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
Polyomic elucidation of the 9,10-anthraquinone biodegradation pathway by a newly isolated oxy-PAH degrading specialist from PAH-contaminated soil
GEO Series GSE199781. Sphingobium sp. AntQ-1. 6 samples. Type: Expression profiling by high throughput sequencing.
Targeted protein degradation reveals BET bromodomains as the cellular target of Hedgehog Pathway Inhibitor-1
GEO Series GSE228015. Mus musculus. 12 samples. Type: Expression profiling by high throughput sequencing.
Comparing gene expression timing and amplitude to delineate the unique pathways of brown and white rot wood-degrading fungi
GEO Series GSE108189. Pleurotus ostreatus; Gloeophyllum trabeum; Trametes versicolor; Rhodonia placenta. 36 samples. Type: Expression profiling by high throughput sequencing.
Free glycans derived from O-mannosylated glycoproteins suggest the presence of an O-glycoprotein degradation pathway in yeast
GEO Series GSE130332. Saccharomyces cerevisiae. 6 samples. Type: Expression profiling by high throughput sequencing.
P53-P21-RB pathway promotes BRD4 degradation in liver cancer through decreasing USP1 transcription
GEO Series GSE243936. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing.
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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.