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7,327 results for “Pathway”
Data from: TAPBPR bridges UDP-glucose:glycoprotein glucosyltransferase 1 onto MHC class I to provide quality control in the antigen presentation pathway
Recently we revealed that TAPBPR is a peptide exchange catalyst important for optimal peptide selection by MHC class I molecules. Here we asked if any other co-factors associate with TAPBPR which would explain its effect on peptide selection. We identify an interaction between TAPBPR and UDP-glucose:glycoprotein glucosyltransferase 1 (UGT1), a folding sensor in the calnexin/calreticulin quality control cycle known to regenerate the Glc1Man9GlcNAc2 moiety on glycoproteins. Our results suggest the formation of a multimeric complex, dependent on a conserved cysteine at position 94 in TAPBPR, in which TAPBPR promotes the association of UGT1 with peptide-receptive class I molecules. We reveal that the interaction between TAPBPR and UGT1 facilities the reglucosylation of the glycan on class I, promoting their recognition by calreticulin. Our results suggest that in addition to being a peptide-editor, TAPBPR improves peptide optimisation by promoting peptide-receptive MHC class I molecules to associate with the peptide-loading complex.
Data from: Litter movement pathways across terrestrial-aquatic ecosystem boundaries affect litter colonization and decomposition in streams
1. Streams and their riparian zones are connected by spatial flows of organic matter, and constitute a model example of a meta-ecosystem. Fluxes of leaf litter from the riparian zone to the stream are a major energy source in stream food webs. Leaf litter can enter the stream vertically, falling from the tree and into the stream, or laterally, washing into the stream after a period of exposure in the terrestrial ecosystem. The latter can contribute up to 23% to the total amount of litterfall entering streams. 2. To determine if decomposition, microbial and invertebrate colonization of lateral litter inputs are similar to those of vertical inputs, we assessed leaf decomposition of alder, poplar and a 1:1 mixture of the two species in three scenarios across a gradient of terrestrial:aquatic exposures. 3. Overall decomposition was explained by a negative exponential model and decreased with the increase in the period of terrestrial exposure in all cases. Invertebrate colonization tended to decrease with the increase in the period of terrestrial exposure, but total invertebrate richness and biomass were more affected by litter type than by the exposure scenario, attaining higher values in the mixture than in the species alone. 4. As the length of exposure in the terrestrial ecosystem increased, in-stream decomposition rates of leaf litter decreased. Comparing leaf species treatments, alder decomposition rates were faster than poplar and the alder-poplar mixture. 5. The richness of the aquatic hyphomycete community colonizing leaf litter after submergence decreased and sporulation rates were strongly inhibited with an increasing terrestrial exposure period. While fungi colonizing leaf litter exposed only in the stream invested in rapid reproduction, fungi colonizing litter with prior terrestrial exposure built up more biomass. 6. We conclude that the path taken by the litter fluxes has important effects on the functioning of the receiving ecosystem. Studies relying only on the fate of freshly abscissed leaf litter (vertical inputs) may not present a complete picture of the decomposition process in streams and may have been overestimating the overall richness and reproductive activity of the aquatic hyphomycetes colonizing leaf litter.
Data from: Novel adverse outcome pathways revealed by chemical genetics in a developing marine fish
Crude oil spills are a worldwide ocean conservation threat. Fish are particularly vulnerable to the oiling of spawning habitats, and crude oil causes severe abnormalities in embryos and larvae. However, the underlying mechanisms for these developmental defects are not well understood. Here, we explore the transcriptional basis for four discrete crude oil injury phenotypes in the early life stages of the commercially important Atlantic haddock (Melanogrammus aeglefinus). These include defects in (1) cardiac form and function, (2) craniofacial development, (3) ionoregulation and fluid balance, and (4) cholesterol synthesis and homeostasis. Our findings suggest a key role for intracellular calcium cycling and excitation-transcription coupling in the dysregulation of heart and jaw morphogenesis. Moreover, the disruption of ionoregulatory pathways sheds new light on buoyancy control in marine fish embryos. Overall, our chemical-genetic approach identifies initiating events for distinct adverse outcome pathways and novel roles for individual genes in fundamental developmental processes.
Data from: Deconstruction of archaeal genome depict strategic consensus in core pathways coding sequence assembly
A comprehensive in silico analysis of 71 species representing the different taxonomic classes and physiological genre of the domain Archaea was performed. These organisms differed in their physiological attributes, particularly oxygen tolerance and energy metabolism. We explored the diversity and similarity in the codon usage pattern in the genes and genomes of these organisms, emphasizing on their core cellular pathways. Our thrust was to figure out whether there is any underlying similarity in the design of core pathways within these organisms. Analyses of codon utilization pattern, construction of hierarchical linear models of codon usage, expression pattern and codon pair preference pointed to the fact that, in the archaea there is a trend towards biased use of synonymous codons in the core cellular pathways and the Nc-plots appeared to display the physiological variations present within the different species. Our analyses revealed that aerobic species of archaea possessed a larger degree of freedom in regulating expression levels than could be accounted for by codon usage bias alone. This feature might be a consequence of their enhanced metabolic activities as a result of their adaptation to the relatively O2-rich environment. Species of archaea, which are related from the taxonomical viewpoint, were found to have striking similarities in their ORF structuring pattern. In the anaerobic species of archaea, codon bias was found to be a major determinant of gene expression. We have also detected a significant difference in the codon pair usage pattern between the whole genome and the genes related to vital cellular pathways, and it was not only species-specific but pathway specific too. This hints towards the structuring of ORFs with better decoding accuracy during translation. Finally, a codon-pathway interaction in shaping the codon design of pathways was observed where the transcription pathway exhibited a significantly different coding frequency signature.
Data from: Identification of reactive intermediate formation and bioactivation pathways in Abemaciclib metabolism by LC–MS/MS: in vitro metabolic investigation
Abemaciclib (Verzenio®) is approved as tyrosine kinase inhibitor (TKI) for breast cancer treatment. In this study, in vitro phase I metabolic profiling of Abemaciclib (ABC) was done using rat liver microsomes (RLMs). We checked the formation of reactive intermediates in ABC metabolism using (RLMs) in the presence of potassium cyanide (KCN) that was used as capturing agent for iminium reactive intermediates forming a stable complex that can be characterized by LC-MS/MS. Nine in vitro phase I metabolites and three cyano adducts were identified. The metabolic reactions involved in formation of these metabolites and adducts are reduction, oxidation, hydroxylation and cyanide addition. The bioactivation pathway was also proposed. Knowing the electrodeficient bioactive centre in ABC structure helped in making targeted modifications to improve its safty and retain its efficacy. Blocking or isosteric replacement of α carbon to the tertiary nitrogen atoms of piperazine ring can aid in reducing toxic side effects of ABC. No previous articles were found about in vitro metabolic profiling for ABC or structural identification of the formed reactive metabolites for ABC.
Predicting Drug Synergy through Drug-Associated Pathways Using Deep Learning
<p>example input dataset for one cross-validation run</p>
Data from: In-situ recording of ionic currents in projection neurons and Kenyon cells in the olfactory pathway of the honeybee
The honeybee olfactory pathway comprises an intriguing pattern of convergence and divergence: ~60.000 olfactory sensory neurons (OSN) convey olfactory information on ~900 projection neurons (PN) in the antennal lobe (AL). To transmit this information reliably, PNs employ relatively high spiking frequencies with complex patterns. PNs project via a dual olfactory pathway to the mushroom bodies (MB). This pathway comprises the medial (m-ALT) and the lateral antennal lobe tract (l-ALT). PNs from both tracts transmit information from a wide range of similar odors, but with distinct differences in coding properties. In the MBs, PNs form synapses with many Kenyon cells (KC) that encode odors in a spatially and temporally sparse way. The transformation from complex information coding to sparse coding is a well-known phenomenon in insect olfactory coding. Intrinsic neuronal properties as well as GABAergic inhibition are thought to contribute to this change in odor representation. In the present study, we identified intrinsic neuronal properties promoting coding differences between PNs and KCs using in-situ patch-clamp recordings in the intact brain. We found very prominent K+ currents in KCs clearly differing from the PN currents. This suggests that odor coding differences between PNs and KCs may be caused by differences in their specific ion channel properties. Comparison of ionic currents of m- and l-ALT PNs did not reveal any differences at a qualitative level.
Modeling of the SEA complex, a modulator of the TORC1 pathway
<p>These scripts demonstrate the use of IMP, MODELLER, and PMI in the modeling of the SEA complex using 188 DSS chemical cross-links and 23 composites from affinity purification.</p> <p>First, MODELLER is used to generate initial structures for the individual components where reliable templates are available. Then, IMP / PMI are used to model these components using the DSS crosslinks and the affinity purification data for the entire SEA complex.</p> <p>For more information about how to reproduce this modeling, see https://salilab.org/sea or the README file.</p>
Enhancing Luminescent Solar Concentrator Efficiency via Lossless Propagation Pathways
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Fig. 7. A proposed pathway for compound 3 in Cytotoxic sesquiterpene lactones from Campuloclinium macrocephalum (=Eupatorium macrocephalum)
Fig. 7. A proposed pathway for compound 3.
EV71 induced skeletal muscle injury in BALB/c lactating mice through the Caspase-1/IL-1β signaling pathway
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Phylogeographic structure and putative migration pathway of Sogatella furcifera in China based on microsatellite markers
<p>Sequencing data of 12 microsatellite loci from 25 populations of in China.</p>
Supplementary material 2 from: Mayer K, Heger T, Kühn I, Nehring S, Gaertner M (2023) Germany's first Action plan on the pathways of invasive alien species to prevent their unintentional introduction and spread. NeoBiota 89: 209-227. https://doi.org/10.3897/neobiota.89.106323
List of some countries or regions that have already implemented action plans or similar documents
Supplementary material 1 from: Mayer K, Heger T, Kühn I, Nehring S, Gaertner M (2023) Germany's first Action plan on the pathways of invasive alien species to prevent their unintentional introduction and spread. NeoBiota 89: 209-227. https://doi.org/10.3897/neobiota.89.106323
19 sectors identified and assigned to the 14 prioritised pathways
supplementary materials of NMN supplement ameliorates psoriasis-associated inflammation, oxidative stress and mitochondrial dysfunction by activating SIRT1 pathway
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Test Anndata file for Decoupler Pathway Inference
<p>Test Anndata file, generated by Decoupler Pathway Inference script for Galaxy Wrapper </p>
Code for "Dynamic pathway linking Pakistan flooding to East Asian heatwaves"
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Figures for "A Strategic Pathway from Cell to Pack-Level Battery Lifetime Model Development"
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raw data - circNR3C2 promote chondrogenic differentiation and cartilage repair of human adipose-derived stem cells via hsa-miR-647/SOX9 pathway
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Wiki pathways (mirror https://wikipathways-data.wmcloud.org/20201010/)
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ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.