O. volvulus and Wolbachia Stage-specifc proteomes
Ontology highlight
ABSTRACT:
INSTRUMENT(S):
ORGANISM(S): Wolbachia Endosymbiont Of Onchocerca Volvulus Str. Cameroon Onchocerca Volvulus
TISSUE(S): Whole Body
DISEASE(S): Onchocerciasis
SUBMITTER: 
Sasisekhar Bennuru
LAB HEAD: Thomas B Nutman
PROVIDER: PXD003585 | Pride | 2016-11-21
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Ov245.fasta | Fasta | |||
| OvAF.mgf | Mgf | |||
| OvAF.mzML | Mzml | |||
| OvAF_QE_T_hs-ovoc-volvulus.pepXML | Pepxml | |||
| OvAM.mgf | Mgf |
Items per page: 5 1 - 5 of 29 |
Similar Datasets
Project description:TGFβ1 is a profibrotic mediator that contributes to a broad spectrum of pathologies, including pulmonary fibrosis (PF). However, the secretome of TGFβ1-stimulated primary human normal lung (NL) fibroblasts has not been well characterized. Using fluorescent 2-dimensional gel electrophoresis (2D-PAGE) and differential gel electrophoresis (DIGE), we identified 37 differentially secreted proteins in the conditioned media of TGFβ1-activated NL fibroblasts and generated a protein-protein association network of the TGFβ1 secretome using STRING. Functional enrichment revealed that biological processes and pathways characteristics of PF were enriched. Using the DrugBank database, we determined that 32 of the secreted proteins are targets of known experimental, investigational and approved drugs. Additionally, by comparing the TGFβ1 secretome of NL fibroblasts to proteomic biomarkers from biological fluids of systemic sclerosis (SSc) patients, we identified 11 overlapping proteins. Together our data validate the TGFβ1-induced secretome of NL fibroblasts as a valid in vitro model that reflects SSc biomarkers and identifies potential therapeutic targets for SSc-PF.
2022-08-12 | PXD023862 | Pride
Project description:The cause of non-bacterial chronic prostatitis is unknown, yet its prevalence accounts for more than 90% of all prostatitis cases. Whole blood, plasma, and serum have been used to identify prostate cancer biomarkers; however, few studies have performed protein profiling to identify prostatitis biomarkers. The purpose of this study was to identify protein biomarkers altered by chronic prostatitis. To perform the study, we chemically induced chronic prostate inflammation in Sprague Dawley rats using estradiol benzoate (EB), testosterone (T), and estradiol (E), then examined protein levels in their plasma. Plasma was collected on postnatal days (PNDs) 90, 100, 145, and 200; plasma proteins were profiled using liquid chromatography-tandem mass spectrometry. Chronic inflammation was observed in rat prostate induced with EB on PNDs 1, 3, and 5. Rats then were dosed with T+E during PND 90-200 via subcutaneous implants. We identified time-specific expression for several proteins (i.e., CFB, MYH9, AZGP1). Some altered proteins that were expressed in the prostate (i.e., SERPINF1, CTR9) also were identified in rat plasma in the EB+T+E group on PNDs 145 and 200. These findings suggest that the identified proteins could be used as biomarkers of chronic prostatitis. Further studies are needed to verify the results in human samples.
2021-09-10 | PXD024422 | Pride
Project description:Personalized multi-peptide vaccines are currently being discussed intensively for tumor immunotherapy. In order to find epitopes - short, immunogenic peptides - suitable to elicit an immune response, human leukocyte antigen-presented peptides from cancer tissue samples are purified using immunoaffinity purification and analyzed by high performance liquid chromatography coupled to mass spectrometry. Here we report on a novel computational pipeline to identify peptides from large-scale immunopeptidomics raw data sets. In the conducted experiments we benchmarked our workflow to other existing mass spectrometry analysis software and achieved higher sensitivity. A dataset of 38 HLA immunopeptidomics raw files of peripheral blood mononuclear cells (PBMCs) from 10 healthy volunteers and 4 JY cell lines was used to assess the performance of the pipeline at each processing step. In addition, 66 isotope labeled known HLA-presented peptides were spiked into the JY cell extracts decreasing in concentration by log10 steps from 100 fmol to 0.1 fmol.
2019-10-14 | PXD011628 | Pride
Project description:Collectively classified as white-rot fungi, certain basidiomycetes efficiently degrade the major structural polymers of wood cell walls. A small subset of these Agaricomycetes, exemplified by Phlebiopsis gigantea, is capable of colonizing freshly exposed conifer sapwood despite its high pitch content, which retards the establishment of other fungal species. The mechanism(s) by which P. gigantea tolerates and metabolizes resinous compounds have not been explored. Here, we report the annotated P. gigantea genome and compare profiles of its transcriptome and secretome when cultured on fresh-cut versus solvent-extracted loblolly pine. The P. gigantea genome contains a conventional repertoire of hydrolase genes involved in cellulose/hemicellulose degradation, whose patterns of expression were relatively unperturbed by the absence of extractives. The expression of genes typically ascribed to lignin degradation was also largely unaffected. In contrast, genes likely involved in the transformation and detoxification of pitch were highly induced in its presence. Their products included an ABC transporter, lipases, cytochrome P450s, glutathione S-transferase and aldehyde dehydrogenase. Other regulated genes of unknown function and several constitutively expressed genes are also likely involved in P. gigantea’s pitch metabolism. These results contribute to our fundamental understanding of conifer colonization and carbon cycling processes. Phlebiopsis gigantea was cultivated in media containing one of three carbon sources: freshly harvested loblolly pine (3 replicates), acetone extracted lobollly pine (3 replicates), or glucose (2 replicates). RNA was extracted and processed for Illumina sequencing as described below.
2014-10-01 | E-GEOD-53112 | biostudies-arrayexpress
Project description:The eukaryotic microrchidia (MORC) protein family are DNA gyrase, Hsp90, histidine kinase, MutL (GHKL)-type ATPases involved in gene expression regulation and chromatin compaction. The molecular mechanisms underlying these activities are incompletely understood. Here, we studied the full-length human MORC2 protein biochemically. We identified a DNA binding site in the C-terminus of the protein, and we observe that this region is heavily phosphorylated in cells. Phosphorylation of MORC2 appears to reduce its affinity for DNA and exclude the protein from the nucleus. We observe that DNA binding by MORC2 reduces its ATPase activity and that MORC2 can topologically entrap multiple DNA substrates between its N-terminal GHKL and C-terminal coiled coil 3 dimerization domains. Finally, we observe that the MORC2 C-terminal DNA binding region is required for gene silencing in cells. Together, our data provide a model to understand how MORC2 engages with DNA substrates to mediate gene silencing.
2025-05-13 | PXD050648 | Pride
Project description:Synthetic peptides were spiked in at different levels in a digested cell lysate from Streptococcus pyogenes
2014-11-20 | PXD001091 | Pride
Project description:Two samples in submission PXD001091 were reanalysed 22 months later on the same instrument.
2015-04-20 | PXD002037 | Pride
Project description:Human brain tissue was obtained from the New Zealand Brain Bank from donors with Alzheimer's disease (AD) or age-matched controls (n=9/group). Mean post mortem delays were ~12h. Six distinct brain regions were dissected, Hippocampus, Cingulate Gyrus, Entorhinal Cortex (severely affected), Motor and Sensory Cortex (less affected) and Cerebellum (spared). Protein was extracted from each sample and, each region was analysed independently. For each region, samples were divided into 3 sets of 3 cases and 3 controls and assigned to an iTRAQ 8 plex, alongside two aliquots of a pooled QC sample. Samples were digested, iTRAQ labelled and analysed. For each region, between 3000 and 4200 proteins were compared between AD and control, identifying a series of known and novel protein expression changes associated with the progression of AD.
2019-02-15 | PXD008739 | Pride
Project description:Characterization of the reference epigenome in humans in a diverse panel of ES cells, tissue stem cells, reprogrammed stem cells, primary cells and tissues **************** For data usage terms and conditions, please refer to: http://www.nida.nih.gov/about/roadmap/epigenomics/data_access_policies.html **************** BI Human Reference Epigenome Mapping Project - samples and experiments will continue to be added to this study over the course of the project. EDACC Genboree Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSTUDY%2FEDACC.4057
2010-11-11 | E-GEOD-25248 | biostudies-arrayexpress
Project description:Mechanisms of infection and pathogenesis have predominantly been studied based on differential gene or protein expression. Less is known about posttranslational modifications, which are essential for protein functional diversity. We applied an innovative glycoproteomics method to study the systemic proteome-wide glycosylation in response to infection. The protein site-specific glycosylation was characterized in plasma derived from well-defined controls and patients. We found 3862 unique features, of which we identified 463 distinct intact glycopeptides, that could be mapped to more than 30 different proteins. Statistical analyses were used to derive a glycopeptide signature that enabled significant differentiation between patients with a bacterial or viral infection. Furthermore, supported by a machine learning algorithm, we demonstrated the ability to identify the causative pathogens based on the distinctive host blood plasma glycopeptide signatures. These results illustrate that glycoproteomics holds enormous potential as an innovative approach to improve the interpretation of relevant biological changes in response to infection.
2023-07-17 | PXD028437 | Pride