Ontology highlight
ABSTRACT:
PROVIDER: PRJNA932979 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23378700_1.fastq.gz | Fastqsanger.gz | |||
| SRR23378700_2.fastq.gz | Fastqsanger.gz | |||
| SRR23378701_1.fastq.gz | Fastqsanger.gz | |||
| SRR23378701_2.fastq.gz | Fastqsanger.gz | |||
| SRR23378702_1.fastq.gz | Fastqsanger.gz |
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Project description:The effect of colonic pH on microbial activity and metabolite production using common prebiotics as substrates: an in vitro study
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Project description:Group 3 innate lymphoid cells (ILC3s) sense environmental signals that are critical for gut homeostasis and host defense. However, the metabolite-sensing G-protein-coupled receptors that regulate colonic ILC3s remain poorly understood. We found that colonic ILC3s expressed Ffar2, a microbial metabolite-sensing receptor, and that Ffar2 agonism promoted ILC3 expansion and function. Deletion of Ffar2 in ILC3s decreased their in situ proliferation and ILC3-derived IL-22 production. This led to impaired gut epithelial function characterized by altered mucus-associated proteins and antimicrobial peptides and increased susceptibility to colonic injury and bacterial infection. Ffar2 increased IL-22+ CCR6+ ILC3s and influenced ILC3 abundance in colonic lymphoid tissues. Ffar2 agonism differentially activated AKT or ERK signaling and increased ILC3-derived IL-22 via an AKT and STAT3 axis. Our findings demonstrate that Ffar2 regulates colonic ILC3 proliferation and function in a cell-intrinsic manner and identifies an ILC3-receptor signaling pathway regulating gut inflammatory tone and pathogen defense.
2019-09-16 | GSE137508 | GEO
Project description:Salmonella enteritidis is suggested to translocate in the small intestine. Previously we identified that prebiotics, fermented in the colon, increased Salmonella translocation in rats, suggesting involvement of the colon in translocation. Effects of Salmonella on colonic gene expression in vivo are largely unknown. The aim of this study was to characterize time dependent Salmonella induced changes of colonic mucosal gene expression in rats using whole genome microarrays. Rats were orally infected with Salmonella enteritidis to mimic a foodbore infection and colonic gene expression was determined at day 1, 3 and 6 post-infection (n=8 per timepoint). Agilent rat whole genome microarray (G4131A Agilent Technologies) were used. Results indicate that colon is clearly a target tissue for Salmonella considering the abundant changes in mucosal gene expression observed. Keywords: Time point infection study, colon mucosa, Rat
2007-10-18 | GSE7496 | GEO
Project description:Type I Protein Arginine Methyltransferases (PRMTs) catalyze asymmetric dimethylation of arginine (ADMA) residues on numerous protein substrates to modulate their activity. Type I PRMTs and many of their substrates have been implicated in human cancers, suggesting that inhibiting Type I PRMT activity offers a tractable approach for therapeutic intervention. The current report describes GSK3368715 (EPZ019997), a potent, reversible Type I PRMT inhibitor with anti-tumor activity against human cancer cells both in vitro and in vivo. GSK3368715 reduces ADMA on numerous substrates and concomitantly increases monomethyl (MMA) and symmetric dimethyl arginine (SDMA) levels. Inhibition of PRMT5, the major type II PRMT, attenuates this induction and produces synergistic antiproliferative effects in combination with GSK3368715 in cancer cells. PRMT5 activity is inhibited by 2-methylthioadenosine (MTA), a naturally occurring metabolite that accumulates in tumor cells deficient for the enzyme Methylthioadenosine Phosphorylase (MTAP). MTAP deletion in cancer cell lines correlates with sensitivity to GSK3368715, indicating a sufficient degree of PRMT5 inhibition from MTA accumulation to achieve a tumor cell-intrinsic combination. These data provide the rationale to explore MTAP status as a biomarker strategy for patient selection to maximize the anti-tumor activity of GSK3368715.
2019-08-15 | GSE126651 | GEO
Project description:Low pH-induced alterations in gene expression profiles and organic acids (OAs) and free amino acids (FAAs) abundances were investigated in Citrus sinensis leaves. We identified 503 downreg-ulated and 349 upregulated genes in low pH-treated leaves. Further analysis indicated that low pH impaired light reaction and carbon fixation in photosynthetic organisms, thereby lowering photosynthesis in leaves. Low pH reduced carbon and carbohydrate metabolisms, OAs biosyn-thesis and ATP production in leaves. Low pH downregulated the biosynthesis of nitrogen com-pounds, proteins and FAAs in leaves, which might be conducive to maintaining energy homeo-stasis during ATP deprivation. Low pH-treated leaves displayed some adaptive responses, in-cluding phosphate recycling, lipid remodeling and phosphate transport. Low pH upregulated the expression of some reactive oxygen species (ROS) and aldehyde detoxifying enzyme (peroxidase and superoxidase) genes and the concentrations of some antioxidants (L-tryptophan, L-proline, nicotinic acid, pantothenic acid and pyroglutamic acid), but it impaired pentose phosphate pathway, VE and secondary metabolite biosynthesis, downregulated the expression of some ROS and aldehyde detoxifying enzyme (ascorbate peroxidase, aldo-keto reductase and 2-alkenal re-ductase) genes and the concentrations of some antioxidants (pyridoxine and γ-aminobutyric acid), thus disturbing the balance between production and detoxification of ROS and aldehydes and causing oxidative damage to leaves.
2018-05-12 | GSE114369 | GEO
Project description:NLRX1 is a mitochondrial-associated NOD-like receptor that modulates antiviral immunity, cellular stress, autophagy, and reactive oxygen species (ROS) production. The role of NLRX1 in inflammatory bowel disease (IBD) remains largely unknown. This study aimed to characterize NLRX1-mediated mechanisms of protection from IBD. We investigated the ability of NLRX1 to modulate global colonic gene expression, gut pathology, inflammation and immunity by using loss-of-function approaches in dextran sodiu sulfate (DSS) and CD4+CD45RBhigh transfer colitis models. Colons, spleens, and mesenteric lymph nodes (MLN) were excised for characterizing immune cell subsets, histological analyses, cytokine, RNA sequencing analyses, and autophagy expression, NF-κB activity, and ROS production. The loss of NLRX1 increased severity of disease and colonic histopathology in both models of IBD. Colons of NLRX1-/- mice had significantly increased epithelial ulceration and leukocyte infiltration mostly in the form of neutrophils, lymphocytes, and macrophages in the DSS model, while recipients of NLRX1-/- CD4+ T cells had increased leukocytic infiltration, proliferation, fibrosis, and crypt abscessation in both colon and ileum. The loss of NLRX1 increased numbers of effector T helper (Th1), Th17, and regulatory T cells (Treg) cells in the colonic mucosa and spleen, increased colonic NF-κB activity, upregulation of IL-17, IFNγ and TNF-α production, and increased ROS production. Global transcriptomic analyses demonstrates that NLRX1 regulates immunity and lipid metabolism pathways. NLRX1 ameliorates intestinal pathology during IBD by acting as an internal thermostat that modulates the balance of effector versus regulatory CD4+ T cell responses, and suppressing colonic NF-κB activity, inflammatory cytokine expression, lipid metabolism gene expression, ROS production and autophagy.
2018-03-07 | GSE68419 | GEO
Project description:Trimethylamine N-oxide (TMAO), a metabolite derived from intestine microbial flora, enhances vascular inflammation in a variety of cardiovascular disease, and the bacterial communities associated with trimethylamine N-oxide (TMAO) metabolism is higher in pulmonary hypertension (PH) patients. The effects of TMAO on PH, however, has not been elucidated. In the present study, we found that circulating TMAO is elevated in intermediate to high-risk PH patients when compared to healthy control or low-risk PH patients. In monocrotaline-induced rat PH models, circulating TMAO is elevated; and reduction of TMAO using 3,3-dimethyl-1-butanol (DMB) significantly decreased right ventricle systolic pressure, pulmonary vascular muscularization in both monocrotaline-induced rat PH and hypoxia induced mice PH models. RNA sequencing of rat lungs on DMB revealed significant suppression of pathways involved in cytokine-cytokine receptor interaction, and cytokine and chemokine signaling. Protein-protein interaction analysis of the differentially expressed transcripts regulated by DMB showed 5 hub genes with a strong connectivity of proinflammatory cytokines and chemokines including Kng1, Cxcl1, Cxcl2, CxcL6 and Il6. In vivo, TMAO significantly increased the expression of Kng1, Cxcl1, Cxcl2, CxcL6 and Il6 in bone marrow derived macrophage. And TMAO-treated conditioned medium from macrophage increased the proliferation and migration of pulmonary artery smooth muscle cells; but TMAO treatment did not change the proliferation or migration of pulmonary artery smooth muscle cells. In conclusion, our study demonstrates that TMAO is increased in severe PH, and the reduction of TMAO using DMB reduces pulmonary vascular muscularization and alleviates PH via suppressing the macrophage production of chemokines and cytokines.
2022-06-07 | GSE190203 | GEO
Project description:Salmonella enteritidis is suggested to translocate in the small intestine. Previously we identified that prebiotics, fermented in the colon, increased Salmonella translocation in rats, suggesting involvement of the colon in translocation. Effects of Salmonella on colonic gene expression in vivo are largely unknown. The aim of this study was to characterize time dependent Salmonella induced changes of colonic mucosal gene expression in rats using whole genome microarrays. Rats were orally infected with Salmonella enteritidis to mimic a foodbore infection and colonic gene expression was determined at day 1, 3 and 6 post-infection (n=8 per timepoint). Agilent rat whole genome microarray (G4131A Agilent Technologies) were used. Results indicate that colon is clearly a target tissue for Salmonella considering the abundant changes in mucosal gene expression observed. Experiment Overall Design: In the present study, large-scale gene expression analysis was performed to reveal whether Salmonella induced changes of colonic mucosal gene expression in rats. Wistar rats were infected with Salmonella enteritidis. Non-infected control rats were sham-treated. Rats were sacrificed on day 1, 3 or 6 post infection or sham-treatment (n=8 rats per treatment and per time point). RNA was isolated from colonic mucosal scrapings. mRNA samples of 8 rats per group were pooled. Each pooled group-sample was hybridised in duplicate on Agilent rat whole genome microarrays containing 44290 60-mer spots. From the 12 arrays one duplicate array (Colon mucosa non-infected day6) did not pass quality control and was left out from further analysis.
2008-06-15 | E-GEOD-7496 | biostudies-arrayexpress
Project description:This a model from the article:
Fermentation pathway kinetics and metabolic flux control in suspended and immobilized Saccharomyces cerevisiae
Jorge L. Galazzo and James E. Bailey
Enzyme and Microbial TechnologyVolume 12, Issue 3, 1990, Pages 162-172.
DOI:10.1016/0141-0229(90)90033-M
Abstract:
Measurements of rates of glucose uptake and of glycerol and ethanol formation combined with knowledge of the metabolic pathways involved in S. cerevisiae were employed to obtain in vivo rates of reaction catalysed by pathway enzymes for suspended and alginate-entrapped cells at pH 4.5 and 5.5. Intracellular concentrations of substrates and effectors for most key pathway enzymes were estimated from in vivo phosphorus-31 nuclear magnetic resonance measurements. These data show the validity in vivo of kinetic models previously proposed for phosphofructokinase and pyruvate kinase based on in vitro studies. Kinetic representations of hexokinase, glycogen synthetase, and glyceraldehyde 3-phosphate dehydrogenase, which incorporate major regulatory properties of these enzymes, are all consistent with the in vivo data. This detailed model of pathway kinetics and these data on intracellular metabolite concentrations allow evaluation of flux-control coefficients for all key enzymes involved in glucose catabolism under the four different cell environments examined. This analysis indicates that alginate entrapment increases the glucose uptake rate and shifts the step most influencing ethanol production from glucose uptake to phosphofructokinase. The rate of ATP utilization in these nongrowing cells strongly limits ethanol production at pH 5.5 but is relatively insignificant at pH 4.5.
SBML level 2 code generated for the JWS Online project by Jacky Snoep using
PySCeS
Run this model online at
http://jjj.biochem.sun.ac.za
To cite JWS Online please refer to: Olivier, B.G. and Snoep, J.L. (2004)
Web-based
modelling using JWS Online, Bioinformatics, 20:2143-2144
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Biomodels Curation: The model reproduces Fig 2 of the paper. However, it appears that the figures are swapped, hence the plot for V/Vmax vs Glucose actually represnts V/Vmax vs ATP and the vice versa is true for the other figure. The rate of hexokinase reaction that is obtained upon simulation of the model is 17.24 mM/min, therefore V/Vmax has a value of 17.24/68.5=0.25. For steady state values of Glucose and ATP (0.038 and 1.213 mM respectively), the V/Vmax values correctly correspond to 0.25, if we were to assume that the figures are swapped.
BioModels Curation updated on 25th November 2010: Figure 3 of the reference publication has been reproduced and added as a curation figure for the model.
This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team.
For more information see the terms of use.
To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
2024-09-02 | BIOMD0000000063 | BioModels