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113 results for “Secreted proteins”
The Vibrio Type III Secretion System 2 is not restricted to the Vibrionaceae and encodes differentially distributed repertoires of effector proteins
<p>Supplementary Dataset for the work entitled "The Vibrio Type III Secretion System 2 is not restricted to the Vibrionaceae and encodes differentially distributed repertoires of effector proteins".</p> <p>This dataset includes files for the T3SS2 reconstructed phylogenetic tree (Newick tree and fasta file), hierarchical clustering data analysis file from MORPHEUS, Table S1 with genome accession numbers, and all the data of the absence/presence of T3SS2-related components, Table S2 with the prediction of novel effector proteins.</p>
"Palmitoylation Mediates Membrane Association of Hepatitis E Virus ORF3 Protein and is Required for Infectious Particle Secretion"
<p><strong>Hepatitis E virus (HEV) is a positive-strand RNA virus encoding 3 open reading frames (ORF). HEV ORF3 protein is a small, hitherto poorly characterized protein involved in viral particle secretion and possibly other functions. Here, we show that HEV ORF3 protein forms membrane-associated oligomers. Immunoblot analyses of ORF3 protein expressed in cell-free <em>vs</em>. cellular systems suggested a posttranslational modification. Further analyses revealed that HEV ORF3 protein is palmitoylated at cysteine residues in its N-terminal region, as corroborated by <sup>3</sup>H-palmitate labeling, the investigation of cysteine-to-alanine substitution mutants and treatment with the palmitoylation inhibitor 2-bromopalmitate (2-BP). Abrogation of palmitoylation by site-directed mutagenesis or 2-BP treatment altered the subcellular localization of ORF3 protein, reduced the stability of the protein and strongly impaired the secretion of infectious particles. </strong><strong>Moreover, selective membrane permeabilization coupled with immunofluorescence microscopy revealed that HEV ORF3 protein is entirely exposed to the cytosolic side of the membrane, allowing to propose a model for its membrane topology and interactions required in the viral life cycle. </strong><strong>In conclusion, palmitoylation determines the subcellular localization, membrane topology and function of HEV ORF3 protein in the HEV life cycle. </strong></p>
Protein structure model predictions for secreted fungal proteins
<p><strong>Dataset A - Alphafold2 prediction output data for 753 secreted proteins of <em>Rhizophagus irregularis </em>DAOM197198</strong>. Gene IDs are taken from the annotation by Yildirir et al. 2021, <a href="https://doi.org/10.1111/nph.17842">doi.org/10.1111/nph.17842</a></p> <p><strong>Dataset B - Alphafold2 prediction output data for 10 fungal effectors.</strong><strong> </strong>These are nine effectors from <em>Fusarium oxysporum</em> f. sp.<em> lycopersici</em> and RiSLM from <em>Rhizophagus irregularis</em> as well as their amino acid sequences. Signal peptides and sequences preceding a predicted Kex2 processing site were removed.</p> <p><strong>Dataset C - Alphafold2 prediction output data for 454 matches of a MycFOLD-HMM search</strong> across the Mycocosm genome database (<a href="https://mycocosm.jgi.doe.gov/mycocosm/home">https://mycocosm.jgi.doe.gov/mycocosm/home</a>) and 36 Glomeromycotina fungal genomes.</p>
Dataset for the Secreted frizzled-related protein 1 antibody screening study
<p><strong>This antibody characterization dataset is related to the F1000 research article openly available at F1000Research.</strong></p> <p><em>This project contains the following underlying data included in a study aiming at characterizing antibodies for the Secreted frizzled-related protein 1 protein, encoded by the SFRP1 gene. The original study is also available on Zenodo YCharOS community (<a href="https://doi.org/10.5281/zenodo.6370454">https://doi.org/10.5281/zenodo.6370454</a>).</em></p>
Data from: Innate and adaptive immune proteins in the preen gland secretions of male house sparrows
<p>Recent studies have demonstrated that preen oil acts to reduce or eliminate feather-associated bacteria. The mechanisms underlying this antibacterial activity, however, are incompletely understood. In addition to the activity of alcohols (i.e. 3,7-dimethyloctan-1-ol), recent research has suggested that antimicrobial peptides may underlie the antibacterial activity of preen oil. Here, we document the presence of innate and adaptive immune proteins, lysozyme and immunoglobulin Y (IgY), in the preen oil of house sparrows (<i>Passer domesticus</i>). We suggest lysozyme functions as an antimicrobial agent, with potentially important impacts against Gram-positive feather degrading bacteria. Furthermore, both lysozyme and IgY likely act in local immune defence of the preen gland, and may also play a role in regulating the local microbiome, with potentially important consequences for chemical communication and signalling. Our findings suggest that the preen gland and its secretions should be considered an integral part of the body's first line of defence against invading infections.</p>
Datasets of protein models from plasmids containing conjugative Type 4 Secretion Systems
<p>In the connected article, we have created a database of all modelled protein structures encoded on plasmids that contain conjugative type 4 secretion systems. In this deposition, you will find zip files of all structures modelled by AlphaFold, as well as the ones that were modelled using EMS fold. Further, there the csv file containing the DeepFRI output, as well as a fasta file containing the sequences of the plasmids.</p> <p>The AlphaFold and ESM databases contain the structural models of the curated/triaged proteins, as described in the paper.</p> <p> </p>
Discovery proteomics by mass spectrometry comparing secreted proteins from young and old mouse lung mesenchymal stromal cells
<p>Lung mesenchymal stromal cells (L-MSCs) were isolated from the young ( 3 months) and old (22-24 months) mice (N = 4 each) following collagenase digestion of the lungs and anchorage-dependent growth. Culture media was collected from young and old L-MSCs (10^6 cells) grown in culture for 24 hrs in serum-free condition. Culture media was then centrifuged to remove any cellular debris. Five (5) ml of supernatants were concentrated using 3kDa Molecular weight cut-off filters, and 10 micrograms of proteins were <span><span><span><span><span>run as multiple MW 1D PAGE fractions using a standard </span><span>GeLC</span><span> approach with a </span><span>nano</span><span>-HPLC in-line with a </span><span>Velos</span><span> Pro Orbitrap MS. </span></span></span></span></span><span><span><span><span><span>Individual data files were searched using </span><span>Sequest</span><span>, the results were then combined for each sample, followed by grouping, filtering, and quantifying by normalized spectral counts. </span></span></span></span></span></p> <p> </p>
Type III secretion system effector proteins are mechanically labile
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Data from: Innate and adaptive immune proteins in the preen gland secretions of male house sparrows
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Discovery proteomics by mass spectrometry comparing secreted proteins from young and old mouse lung mesenchymal stromal cells
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Predicted Secreted Proteins for the Citrus Stem-End Rot Fungal Pathogen Lasiodiplodia theobromae CITRA15
<p>Lasiodiplodia theobromae (L. theobromae) belongs to a diverse genus of fungal pathogens associated with perennial tropical fruit plants worldwide. In citrus, L. theobromae causes stem-end rot (SER), a damaging postharvest disease that is aggravated when trees are also infected with the citrus greening bacterium, a Candidatus Liberibacter asiaticus. Due to the latent infection of L. theobromae during the preharvest stage, it is also difficult to control by chemical and physical treatment. We sequenced and assembled the first genome of isolate CITRA15 of L. theobromae obtained from citrus, providing a resource for future research on postharvest and preharvest disease management of citrus and other fruit crops and diagnostics. Here we want to share a set of i) 10,496 predicted coding gene sequences (cds) and ii) 10,496 predicted proteins and ii) 1,016 predicted secreted proteins using SignalP v2.0 and TMHMM v2.0.</p> <p> </p>
Supplemental Material S2 for "Development of a highly sensitive luciferase-based reporter system to study two-step protein secretion in cyanobacteria"
<p>Table S1. Densitometric analysis of NLuc immunoblot in Fig. 2A.</p> <p>Figure S1. PilA1 quantification in the sheared pili fractions of WT, Δ<em>hfq</em> and Δ<em>pilT1</em> <em>Synechocystis</em> mutants.</p>
Protein, Calcium and Gut Hormone Secretion
ClinicalTrials.gov study NCT04659902. IPD Sharing: NO. Countries: 1. Publications: 1.
Modified White Blood Cells That Secrete IL-2 and Express a Protein That Targets the ESO-1tumor Protein for Metastatic Cancer
ClinicalTrials.gov study NCT01457131. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Protein, Amino Acids & Insulin & Glucagon Secretion in Humans
ClinicalTrials.gov study NCT01471509. IPD Sharing: Not stated. Countries: 1. Publications: 43.
Regulation of gastric acid secretion in situ by an endogenous activator protein: Studies with activator-specific antibody
Monospecific polyclonal antibody was raised against a homogenous preparation of endogenous activator protein (HAF) for the gastric H+,K+-ATPase system. Antibody was used to assess the regulatory role of the HAF in gastric acid secretion by isolated rabbit glands in situ. Immunohistochemical studies revealed aredistribution of theHAFtowards discrete intracellular zones following stimulation of the glands with histamine. The antibody, when inserted into the stimulated gastric glands by digitonin permeabilization, could effectively block the acid forming ability of the cells. The data offers, for the first time, some concrete in situ evidence for the role of the HAF as an intracellular regulator of gastric H+ transport .
Hepatocyte CCAAT/enhancer-binding protein alpha restricts liver fibrosis by inhibiting secreted phosphoprotein 1 expression (I)
GEO Series GSE212646. Mus musculus. 30 samples. Type: Expression profiling by high throughput sequencing.
Characterization and quantification of proteins secreted by single human embryos prior to implantation
GEO Series GSE72685. Homo sapiens. 20 samples. Type: Expression profiling by array; Genome variation profiling by array.
Chondroprotective functions of neutrophil-derived extracellular vesicles via promoting the production of secreted frizzled related protein 5 in cartilage [SFRP5]
GEO Series GSE271171. Mus musculus. 9 samples. Type: Expression profiling by high throughput sequencing.
High capacity of the endoplasmic reticulum to prevent secretion and aggregation of amyloidgenic proteins
GEO Series GSE98580. Homo sapiens. 6 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.