Remote ischemic conditioning–induced shift from a vulnerable to a tolerant penumbra: a proteomic perspective
Ontology highlight
ABSTRACT:
INSTRUMENT(S): LTQ Orbitrap Elite
ORGANISM(S): Rattus Norvegicus (rat)
TISSUE(S): Brain
DISEASE(S): Brain Ischemia
SUBMITTER: 
Maksym Danchenko
LAB HEAD: Peter Barath
PROVIDER: PXD061081 | Pride | 2025-05-18
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| 230812_RatBrainI11.raw | Raw | |||
| 230812_RatBrainI12.raw | Raw | |||
| 230812_RatBrainI13.raw | Raw | |||
| 230812_RatBrainI14.raw | Raw | |||
| 230812_RatBrainK1.raw | Raw |
Items per page: 5 1 - 5 of 19 |
Similar Datasets
Project description:Mesenchymal stem cells (MSCs) are an essential tool in cell-based therapies. One of the most crucial factors for efficacy in regenerative medicine is the source of MSCs. Tissue origin has long been suggested as a potential determinant of MSC properties. Human dermal fibroblasts share similar characteristics to MSCs, and the question of whether fibroblasts are functionally equivalent to MSCs is still debated. The present work used proteomic and phenotypic analyses to compare human dermal fibroblasts, dental pulp stem cells (DPSCs), and adipose-derived mesenchymal stem cells (AD-MSCs). We observed similarities and differences in morphology, cell surface markers, differentiation, and proteomic profile. Proteome was profiled by nano liquid chromatography and comprehensively quantified by ion mobility-enhanced mass spectrometry. Fibroblasts and MSCs shared similar surface markers, growth kinetics, and differentiation capacity. Proteomic analysis reproducibly identified and quantified 3051 proteins, 109 of them were differentially abundant according to strict statistic criteria. We showed that CD13, CD9, and CD105 could potentially distinguish MSCs of different origin and fibrobrasts. GO term and GSEA enrichment analysis of differentially accumulated proteins identified signaling pathways characteristic to individual cell types. Particularly, we highlighted signaling pathways involved in cell migration, adhesion, and Wnt signaling as downregulated in fibroblasts in comparison to DPSCs. Angiogenesis and vascularization were specifically associated with AD-MSCs.
2025-06-24 | PXD061092 | Pride
Project description:Euglena gracilis is a flagellate photosynthetic microalga that, thanks to its metabolic adaptability, can grow under both autotrophic and heterotrophic conditions. We focused on the proteome of E. gracilis cultivated in Cramer-Myers medium in dark and light conditions. Cultures grown in the light showed a characteristic green coloration, while cultures incubated in the dark were bright, almost colorless, and had 60% fewer cells per volume. When cultured in the dark, microalga showed reduced concentration of chlorophylls (a, b, and total) and carotenoids compared to cells cultured in the light. Conversely, there was an increase in proline content in the dark compared to light cultivation. Phenol-extracted proteins were digested and purified using the SP3 protocol. We revealed 162 proteins, classified into 12 functional groups, which differentially accumulated in light- and dark-grown cells. The most represented categories in the case of dark cultivation were defense mechanisms, metabolism, and energy. Of note, in the category metabolism of lipids and sterols, we detected 4 proteins involved in the β-oxidation of fatty acids more abundant in the dark. Accumulation os stress- and detoxification-related proteins in microalgal cells cultivated in darkness supported interpretation of such condition as challenging stress factor. Euglena gracilis cultured in the dark is useful for basic research, applied biotechnology, and environmental protection.
2025-03-06 | PXD058143 | Pride
Project description:Chronic ionizing radiation imposes direct and indirect damage on plants that could modify their morphology, biochemistry, physiology, as well as responses to biotic agents. Plants experience elevated levels of DNA damage and reactive oxygen species; thus, they adjust cellular homeostasis. Aquatic ecosystems in Chornobyl zone, a major radiological disaster site, are contaminated by harmful radionuclides. This study focused on changes in the proteome of leaves as well as carbonylated proteins, which might explain the biochemical mechanisms responsible for the susceptibility of a wild aquatic plant (common reed, Phragmites australis) grown in Chornobyl zone to biotic stress. The fungal infection assay indicated that life in a radionuclide-contaminated environment compromised plant immunity. The protein profiling identified 1,867 proteins; among them, 174 were differentially accumulated. We selected several dozen proteins with consistently higher and lower abundance in the samples from areas around the contaminated lakes by hierarchical clustering. Discordant expression of coding genes pointed to posttranscriptional regulation. Furthermore, the quantification of antioxidant enzyme activities (glutathione reductase, ascorbate peroxidase, catalase, and glutathione S-transferase) and carbonylated proteins rebutted the idea about substantial oxidative stress in chronically irradiated plants. We advocate the necessity to consider plausibly increased pathogen sensitivity while developing policies for the management of radionuclide-contaminated areas.
2025-05-07 | PXD060551 | Pride
Project description:Despite serving as a central experimental technique in epigenetics research, chromatin immunoprecipitation (ChIP) suffers from several serious drawbacks: it is a relative measurement untethered to any external scale that obviates fair comparison amongst experiments; it employs antibody reagents that have differing affinity and specificity for target epitopes, which are in turn variable in abundance; and it is frequently not reproducible. To address these problems, we developed internal standard calibrated ChIP (ICeChIP), a method of spiking a native chromatin sample with nucleosomes reconstituted from recombinant and semisynthetic histones on barcoded DNA prior to immunoprecipitation. ICeChIP measures local histone modification densities on a biologically meaningful scale, enabling unbiased trans-experimental comparisons and revealing a correlation between the apparent symmetry of H3K4me3 in promoter nucleosomes and gene expression. Direct in situ assessment of immunoprecipitation accommodates for a number of experimental pitfalls, and provides a critical examination of untested assumptions inherent in conventional ChIP. Examination of spiked-in semi-synthetic nucleosomes in ICeChIP-seq experiments performed for HEK293, mESC E14 and DM S2 cell line
2015-05-07 | E-GEOD-60378 | biostudies-arrayexpress
Project description:The experiment was carried out to examine the effect of Srrt knockdown on the U1 snRNP/pre-mRNA interaction pattern. A2Lox mouse embryonic stem cells were transfected with either an Srrt-specific or a non-targeting siRNA. 48 hours post transfection the cells were cross-linked using 2% formaldehyde and lysed. RNA was partially fragmented by sonication, hybridized with U1 snRNA-specific biotinilated probes and pulled down. U1-associated RNA sequences were then purified and RNA-seq libraries were generated using a NEBNext® rRNA Depletion Kit and NEBNext® Ultra8482 II Directional RNA Library Preparation kit. Paired-end sequencing was performed using a HiSeq4000 75bp platform.
2019-11-27 | E-MTAB-7635 | biostudies-arrayexpress
Project description:SOX6 CUT&RUN on HUDEP1 over expressing SOX6-Flag. The experiment is done using and anti Flag Ab to assist the genome wide binding profile of SOX6 in HUDEP1 (Human Umbilical cord blood-Derived Erythroid Progenitor-1).
2023-04-07 | E-MTAB-12800 | biostudies-arrayexpress
Project description:During germination and early seedling development plants rely entirely on their seed storage compounds to provide energy and precursors for the synthesis of macromolecular structures such as cell walls until the seedling has emerged from the soil and photosynthesis can be established. Lupin seeds use proteins as their major storage compounds, accounting for up to 40% of the seed dry weight. Lupins are therefore a valuable complement to soy as a source of plant protein for human and animal nutrition. However, knowledge on protein and amino acid metabolism during germination and seedling establishment in lupin plants is still limited. The aim of this study was to elucidate how storage protein metabolism is coordinated with other metabolic processes to meet the requirements of the growing seedling. In a quantitative approach, we analyzed seedling growth, as well as alterations in biomass composition, the proteome, and metabolite profiles during germination and seedling establishment in Lupinus albus. The reallocation of nitrogen resources from seed storage proteins to functional seed proteins was mapped based on a manually curated functional protein annotation database. Although classified as a protein crop, Lupinus albus does not use amino acids as a primary resource during germination. The predominant role of the stored proteins is to act as a nitrogen resource for vigorous post-germinative growth. The degradation of storage lipids and carbohydrates is sufficient to meet the energy requirements for early seedling establishment until the onset of photosynthesis. However, our results suggest that during germination fatty acid and amino acid metabolism may be integrated at the level of malate synthase to combine stored carbon from lipids and proteins into gluconeogenesis.
2024-07-26 | PXD046789 | Pride
Project description:Bordetella pertussis is the bacterial causative agent of whooping cough, a serious respiratory illness. An extensive knowledge on its virulence regulation and metabolism is a key factor to ensure pertussis vaccine manufacturing process robustness. The aim of this study was to refine our comprehension of B. pertussis physiology along the fermentation process. A longitudinal multi-omics analysis was carried out over a 26-hour small-scale fermentation of B. pertussis. Fermentations were performed in batch mode and under culture conditions intending to mimic industrial processes. Putative cysteine and proline starvations were respectively observed at the beginning of the exponential phase (from 4h to 8h) and during the exponential phase (18h45). As revealed by multi-omics analyses, the proline starvation induced major molecular changes, including a transient metabolism with internal stock consumption. In the meantime, growth and specific total PT, PRN and Fim2 antigen productions were negatively affected. Interestingly, the master virulence-regulating two-component system of B. pertussis (BvgASR) was not evidenced as the sole virulence regulator in this in vitro growth condition. Indeed, novel intermediate regulators were identified as putatively involved in the expression of some virulence-activated genes (vags). Such longitudinal multi-omics analysis applied to B. pertussis fermentation process emerges as a powerful tool for characterization and incremental optimization of vaccine antigen production.
2023-03-11 | PXD039615 | Pride
Project description:Metaproteomics is gaining momentum in microbiome research due to the multi-dimensional information it provides. However, current approaches have reached their detection limits. We present a highly-sensitive metaproteomic workflow using the extra information captured by Parallel Accumulation-Serial Fragmentation (PASEF) technology. The comparison of different acquisition modes and data analysis software packages showed that DIA-PASEF and DIA-NN doubled protein identifications in the mouse gut microbiota and, importantly, also in the host proteome compared to DDA-PASEF. DIA-PASEF significantly improved peptide detection reproducibility and quantification accuracy, which resulted in more than twofold identified taxa, reaching depths comparable to metagenomic studies. Consequently, DIA-PASEF exhibited improved coverage of functional networks revealing 131 additional pathways compared to DDA-PASEF. We applied our optimized workflow to a pre-clinical mouse model of chronic pain, in which we deciphered novel host-microbiome interactions. In summary, we present here a metaproteomic approach that paves the way for increasing the functional characterization of microbiome ecosystems and is applicable to diverse fields of biological research.
2023-05-04 | PXD040947 | Pride
Project description:The human gut microbiota plays a vital role in host health by acting as a barrier against pathogens, boosting the immune system, and metabolizing complex carbon sources into beneficial compounds such as short-chain fatty acids (SCFAs). However, external factors like diet and xenobiotics, including food colorants, can impact this microbial community. Brilliant blue FCF (E-133), a common food dye that is not absorbed or metabolized by the body, thus, leading to significant exposure of the gut microbiota, and its effects on it are not well-documented. This study investigated the impact of brilliant blue on the simplified human gut microbiota model (SIHUMIx) over a seven-day exposure period, followed by a four-day recovery phase. Using continuous culture bioreactors along with metaproteomic and metabolomic analyses, the research uncovered substantial structural and functional changes in the microbiota. Our findings showed alterations in the species abundance such as B. thetaiotaomicron, B. longum, and C. butyricum, reductions in energy metabolism by-products, particularly lactate and butyrate, and disruptions in metabolic pathways involved in the metabolism of xenobiotics and amino acids. The results indicate that brilliant blue exposure compromises microbiota stability and functionality, highlighting the need for further research on its long-term effects and recovery mechanisms. This study underscores the importance of assessing the impacts of food additives on gut microbiota as part of comprehensive health risk evaluations.
2025-05-07 | PXD055767 | Pride