Methylation_CASES
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00010002368 | EGA |
REPOSITORIES: EGA
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Project description:Propolis is a resinous honeybee product, rich in polyphenolic compounds and with high economic value. Although extensive studies regarding the chemical composition of different propolis extracts have been carried out, the propolis proteome remained unknown. The present study aimed at characterizing the proteome of two geographically-distinct propolis originating from Belgium and Iran. Propolis extracts were analysed by SDS-PAGE followed by MALDI-TOFand LC/ESI- mass spectrometry (MS). Our in-depth proteomic analysis led to the identification of honeybee venom and royal jelly proteins, and numerous plant-defense proteins in propolis, extending our understanding on the antimicrobial properties of this complex natural substance. The proteome of both propolis was mainly made up of proteins belonging to the poplar tree. The poplar PR-2 (β-1,3-glucanases) and PR-8 (acidic endochitinases) proteins were found to be the major components of both propolis extracts, while bee venom (Api m 1) and royal jelly allergens (MJRP 1and 2) were only identified in the propolis from Belgium. Overall, our proteome analyses revealed that propolis extracts from Belgium and Iran shared a core protein composition originating from the poplar proteome. The majority of identified proteins are involved in the plant defense against pathogens, some belonging to well-known pathogenesis-related families.
2026-03-26 | PXD039653 | Pride
Project description:Filamentous algae (FA) have potential advantages over microalgae for wastewater treatment. However, their implementation at large-scale is hindered by an inability to predict performance. This study compared the cellular responses (photosynthesis and respiration) and composition (pigments and photosystem proteins) of FA Oedogonium acclimatised to average summer and winter conditions (Melbourne, Australia). After 7 days of acclimation the Chl a content of summer acclimated (SA) algae was about half that of the winter acclimated (WA) algae, which can be related to a strategy to reduce photodamage under high light intensities. No statistically significant changes were observed in any identified proteins associated with photosystem PSII and the reaction centre of PSI. Transmission electron microscopy images revealed more prominent lipid bodies within the SA filaments than in WA filaments, but no discernible difference in the abundance of starch granules. Photosynthetic irradiance curves were compared for the SA and WA algae. Consistent with the differences in chlorophyll, the specific gross photosynthetic rate (µP, gross) was generally higher for the WA algae. The relative difference increased from around 2-fold at 15°C to 3-fold at 25°C, and then decreased to less than 1.5-fold at 30 °C and 35 °C. At all the tested temperatures, saturation irradiance levels were in the range of 75 – 500 µmol/m2·s. Photoinhibition was observed at 30 °C (above ~300 µmol/m2·s) and was more severe at 35 °C (above ~500 µmol/m2·s), with WA algae showing greater inhibition. In contrast, the respiration response was similar for the SA and WA algae. The study emphasises the significance of accounting for seasonal variations and their effects on biomass productivity and utilisation. The data obtained will enable the incorporation of acclimation and its effect on biochemistry and photosynthetic response into predictive models of FA performance in outdoor cultures.
2026-01-12 | PXD040798 | Pride
Project description:The inflammatory functions of the cytokine tumor necrosis factor (TNF) rely on its ability to induce cytokine production and to induce cell death. Caspase dependent and independent pathways – apoptosis and necroptosis – respectively, regulate immunogenicity by the release of distinct sets of cellular proteins. To obtain an unbiased, systems-level understanding of this important process, we here applied mass spectrometry-based proteomics to dissect protein release during apoptosis and necroptosis. We report hundreds of proteins released from human myeloid cells in time-course experiments. Both cell death types induce receptor shedding, but only apoptotic cells released nucleosome components. Conversely, necroptotic cells release lysosomal components by activating lysosomal exocytosis at early stages of necroptosis- induced membrane permeabilisation and show reduced release of conventionally secreted cytokines.
2020-07-18 | PXD014966 | Pride
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study were to compare signals from competent and abnormal human embryos impacted differently on the expression of endometrial receptivity genes in mouse uteri using transcriptome profiling (RNA-seq). Methods: Immature female (25 d C57BL/6) mice were given a hormone treatment of a single dose 1 mg progesterone and 10 mg/kg/day ò-estradiol for a total of 3d to prime the uterus for embryo transfer. The uterine horns of control and study mice were injected with an equal volume (50 ül) of either unconditioned embryo culture medium (ECM), serving as controls, or pooled conditioned media from competent (n = 9) or arresting embryos (n = 18). Uterine mRNA profiles of 25-day-old wild-type (WT) were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000 platform. The sequence reads that passed quality filters were analyzed with the following methods: Bowtie Alignment followed by TopHat (splice juntions mapper) and Cufflinks (transcript abundance). qRTâÂÂPCR validation was performed using SYBR Green assays. Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm9) and identified 16,014 transcripts in the uteri WT and NrlâÂÂ/â mice with BWA workflow and 34,115 transcripts with TopHat workflow. RNA-seq data confirmed stable expression of 25 known housekeeping genes, and 12 of these were validated with qRTâÂÂPCR. RNA-seq data had a linear relationship with qRTâÂÂPCR for more than four orders of magnitude and a goodness of fit (R2) of 0.8798. Approximately 10% of the transcripts showed differential expression between the WT and NrlâÂÂ/â retina, with a fold change âÂÂ¥1.5 and p value <0.05. Altered expression of 25 genes was confirmed with qRTâÂÂPCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to retinal function. Data analysis with BWA and TopHat workflows revealed a significant overlap yet provided complementary insights in transcriptome profiling. Conclusions: Our study represents the first detailed analysis of maternal uterine reponse to signals from competent and abnormal human embryos, with biological replicates, generated by RNA-seq technology. Supernatant from competent and abnormal human embryos were flushed into the uterine horns of 25d old C57BL/6 female mice. Uterine mRNA profiles of 21-day old mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000 platform (HiSeq).
2014-02-11 | E-GEOD-47019 | biostudies-arrayexpress
Project description:CONTROL_SAMPLES using platform …..
| EGAD00010002367 | EGA
Project description:This single cell RNA-seq experiment was performed to quantify DLL3 expression in circulating tumor cells in small cell lung cancer patients to predict response to tarlatamab treatment. CTCs enriched from the blood of three SCLC patients prior or post tarlatamab treatment using the CTC-iChip followed by magnetic depletion of RBCs were processed with the 10x Genomics Chromium platform (Chromium GEM-X Single Cell 3' Kit v4) and sequenced on a NextSeq 2000 system. Corresponding EGA study number: EGAS50000001401, EGA dataset number: EGAD50000002035
2025-12-11 | E-MTAB-16413 | biostudies-arrayexpress
Project description:Spatial tissue proteomics integrating whole-slide imaging, laser microdissection and ultrasensitive mass spectrometry is a powerful approach to link cellular phenotypes to functional proteome states in (patho)physiology. To be applicable to large patient cohorts and low sample input amounts, including single-cell applications, loss-minimized and streamlined end-to-end workflows are key. We here introduce an automated sample preparation protocol for laser microdissected samples utilizing the cellenONE® robotic system, which has the capacity to process 192 samples in three hours. Following laser microdissection collection directly into the proteoCHIP LF 48 or EVO 96 chip, our optimized protocol facilitates lysis, formalin de-crosslinking and tryptic digest of low-input archival tissue samples. The seamless integration with the Evosep ONE LC system by centrifugation allows ‘on-the-fly’ sample clean-up, particularly pertinent for laser microdissected workflows. We validate our method in human tonsil archival tissue, where we profile proteomes of spatially-defined B-cell, T-cell and epithelial microregions of 4,000 µm2 to a depth of ~2,000 proteins and with high cell type specificity. We finally provide detailed equipment templates and experimental guidelines for broad accessibility.
2024-03-22 | PXD047762 | Pride
Project description:In the marine environment, surface-associated bacteria often produce an array of antimicrobial secondary metabolites (MSMs), which have predominantly been perceived as competition molecules. However, they may also affect other hallmarks of surface-associated living, such as motility and biofilm formation. Here, we investigate the ecological significance of an antibiotic secondary metabolite, tropodithietic acid (TDA), in the producing bacterium, Phaeobacter piscinae S26. We constructed a markerless in-frame deletion mutant deficient in TDA biosynthesis wherein TDA production was abolished. Molecular networking demonstrated that other chemical sulphur-containing features, likely related to TDA, were also altered in the secondary metabolome. We found dramatic changes in the physiology of the TDA-deficient mutant, S26�tdaB, compared to the wild type S26. Growth of the two strains were similar; however, S26�tdaB cells were shorter and more motile. Transcriptome and proteome profiling revealed an increase in expression of genes and relative abundance of proteins related to a type IV secretion system, a prophage, and a gene transfer agent (GTA) in S26�tdaB. All these systems may contribute to horizontal gene transfer (HGT), which may facilitate fast adaptation to novel niches. We speculate that, once a TDA-producing population has been established in a new niche, the accumulation of TDA acts as a signal of successful colonization, prompting a switch to a sessile lifestyle. This would lead to a decrease in motility and the rate of HGT, whilst filamentous cells could form the base of a biofilm. In addition, the antibiotic properties of TDA may inhibit invading competing microorganisms.
2023-01-01 | PXD035448 | Pride
Project description:Rheumatoid arthritis (RA) and periodontitis (PD) are chronic inflammatory diseases that appear to occur in tandem. Autoantibodies against citrullinated peptide antigens linked pathogeneses with PD preceding RA. However, the mutual impact PD exerts on RA and vice versa has not yet been defined. To address this issue, we set up an animal model and analyzed how the prime inducers of citrullination - Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans – differ in their pathogenic potential. Our experimental setup included collagen induced arthritis (CIA) in the mouse, oral inoculation with P. gingivalis or A. actinomycetemcomitans to induce alveolar bone loss and the combination of both diseases in inverted orders of events. Label-free quantitative proteome analysis revealed that P. gingivalis and A. actinomycetemcomitans led to differential expression patterns in the synovial membranes that were reminiscent of cellular and humoral immune responses, respectively. The P. gingivalis and A. actinomycetemcomitans specific signatures in the synovial proteomes suggest a role for oral pathogens in shaping disease subtypes and setting the stage for subsequent therapy response.
2020-12-04 | PXD020397 | Pride
Project description:Male mice on a homogenous C57BL6/J genetic background were sacrificed at 11 to 13 weeks of age by cervical dislocation. Brain, kidneys and liver were immediately harvested, flash frozen in liquid nitrogen and stored at -80°C until use. Animal handling was in accordance with guidelines approved by the European Molecular Biology Laboratory (EMBL). Organ sections (thickness 30 µm) were prepared in a Cryostat (Leica Biosystems, Leica CM3050 S) set to -20 °C and deposited onto SuperFrost glass slides (Carl Roth, H880); the glass slides were pre-cooled to -20°C in the cryostat. ~10 sections were placed on a glass slide, and a total of around 150 sections were prepared for each sample per mouse. Tissue sections on glass slides were then transferred onto metal plates placed on dry ice. The tissue sections were exposed or not to 1 J/cm2 of 254 nm UV light in a XL 1500 UV Spectrolinker (Spectronics Corporation) and subjected to eRIC to determine the RNA-bound proteome. eRIC eluates obtained from the respective organs of two mice were combined per independent experiment. The analyses were conducted in duplicate for each organ studied. For the no crosslink controls, organ sections from four mice were pooled to generate one unique no crosslink eRIC sample per organ studied.
2023-03-02 | PXD032113 | Pride