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Gene expression of rat cerebellum in a new animal model of hepatic encephalopathy (HE)

ABSTRACT: Identify differentially expressed genes related to the neurodegenerative process in a new animal model of hepatic encephalopathy (HE). The animal model consists on the simulation of several bouts of HE in PCA rats, being the precipitant factors of the episodes ammonia (NH3) and/or lipopolisaccharide (LPS) or saline.

ORGANISM(S): Rattus norvegicus

PROVIDER: GSE71425 | GEO | 2015/07/29

SECONDARY ACCESSION(S): PRJNA291186

REPOSITORIES: GEO

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Gene expression of rat cerebellum in a new animal model of hepatic encephalopathy (HE)

Project description:Identify differentially expressed genes related to the neurodegenerative process in a new animal model of hepatic encephalopathy (HE). The animal model consists on the simulation of several bouts of HE in PCA rats, being the precipitant factors of the episodes ammonia (NH3) and/or lipopolisaccharide (LPS) or saline. Regular administration (one every two weeks up to 10 infussion) of NH3 (20 μl/min along 3h) and/or LPS (5mg/kg) or in PCA rats. Sham rats were used as a surgery control.

2015-07-29 | E-GEOD-71425 | biostudies-arrayexpress

Experimental hepatic encephalopathy causes early but sustained glial transcriptional changes

Project description:Hepatic encephalopathy (HE) is a common complication of liver cirrhosis, associated with high morbidity and mortality, for which no brain-targeted therapies exist at present. The interplay between hyperammonemia and inflammation is thought to drive HE development. As such, astrocytes, the most important ammonia-metabolizing cells in the brain, and microglia, the main immunomodulatory cells in the brain, have been heavily implicated in HE development. As insight into cellular perturbations driving brain pathology remains largely elusive, we aimed to investigate cell-type specific transcriptomic changes in the HE brain. In the recently established mouse bile duct ligation (BDL) model of HE, we performed RNA-Seq of sorted astrocytes and microglia at 14 and 28 days after induction. This revealed a marked transcriptional response in both cell types which was most pronounced in microglia. In both cell types, pathways related to inflammation and hypoxia, mechanisms commonly implicated in HE, were enriched. Additionally, astrocytes exhibited increased corticoid receptor and oxidative stress signaling, whereas microglial transcriptome changes were linked to immune cell attraction. Accordingly, both monocytes and neutrophils accumulated in the BDL mouse brain. Time-dependent changes were limited in both cell types, suggesting early establishment of a pathological phenotype. While HE is often considered a unique form of encephalopathy, astrocytic and microglial transcriptomes showed significant overlap with previously established gene expression signatures in other neuroinflammatory diseases like septic encephalopathy and stroke, suggesting common pathophysiological mechanisms. Our dataset identifies key molecular mechanisms involved in preclinical HE and provides a valuable resource for development of novel glial-directed therapeutic strategies.

2023-05-30 | GSE230287 | GEO

Steady state growth under inorganic carbon limitation increases energy consumption for maintenance and enhances nitrous oxide production in Nitrosomonas europaea

Project description:Nitrosomonas europaea is a chemolithoautotrophic bacterium that oxidizes ammonia (NH3) to obtain energy for growth on carbon dioxide (CO2), and can also produce nitrous oxide (N2O), a greenhouse gas. We interrogated the growth, physiological, and transcriptome responses of N. europaea to replete (> 5.2 mM) and limited inorganic carbon (IC) provided by either 1.0 mM or 0.2 mM sodium carbonate (Na2CO3) supplemented with atmospheric CO2. IC-limited cultures oxidized 25 to 58% of available NH3 to nitrite, depending on dilution rate and Na2CO3 concentration. IC limitation resulted in a 1.5-fold increase in cellular maintenance energy requirements compared to NH3-limited cultures. Rates of N2O production increased 2- and 6.3 fold under the two IC-limited conditions increasing the percentage of oxidized NH3-N being transformed to N2O-N from 0.5% (replete) to 4.4% (0.25 mM Na2CO3). Transcriptome analysis showed differential expression (p ≤ 0.05) of 488 genes (20% of inventory) between replete and IC-limited conditions, but few differences were detected between the two IC-limiting treatments. IC-limited conditions resulted in decreased expression of ammonium/ammonia transporter and ammonia monooxygenase subunits, and increased expression of genes involved in C1 metabolism including RuBisCO (cbb gene cluster), carbonic anhydrase, folate-linked metabolism of C1 moieties, and putative C salvage due to oxygenase activity of RuBisCO. Increased expression of nitrite reductase (gene cluster NE0924-0927) correlated with increased production of N2O. Together, these data suggest that N. europaea adapts physiologically during IC-limited steady state growth, which leads to uncoupling of NH3 oxidation from growth and increased N2O production.

2016-03-28 | GSE70988 | GEO

Epileptic Encephalopathy

Project description:A novel null homozygous mutation confirms CACNA2D2 as a gene mutated in epileptic encephalopathy

| PRJEB4676 | ENA

Identification of miRNA, lncRNA and mRNA-associated ceRNA networks and potential biomarker for MELAS with mitochondrial DNA A3243G mutation [array]

Project description:To elucidate the regulating networks of dysregulated ncRNAs in Mitochondrial myopathy, Encephalopathy, Lactic Acidosis, and Stroke-like episodes (MELAS) with m.A3243G mutation.

2016-10-23 | GSE89059 | GEO

Identification of miRNA, lncRNA and mRNA-associated ceRNA networks and potential biomarker for MELAS with mitochondrial DNA A3243G mutation [sequencing]

2016-10-23 | GSE89065 | GEO

Steady state growth under inorganic carbon limitation increases energy consumption for maintenance and enhances nitrous oxide production in Nitrosomonas europaea

Project description:Nitrosomonas europaeais a chemolithoautotrophic bacterium that oxidizes ammonia (NH3) to obtain energy for growth on carbon dioxide (CO2), and can also produce nitrous oxide (N2O), a greenhouse gas. We interrogated the growth, physiological, and transcriptome responses ofN. europaeato replete (> 5.2 mM) and limited inorganic carbon (IC) provided by either 1.0 mM or 0.2 mM sodium carbonate (Na2CO3) supplemented with atmospheric CO2 IC-limited cultures oxidized 25 to 58% of available NH3to nitrite, depending on dilution rate and Na2CO3concentration. IC limitation resulted in a 2.3-fold increase in cellular maintenance energy requirements compared to NH3-limited cultures. Rates of N2O production increased 2.5- and 6.3-fold under the two IC-limited conditions increasing the percentage of oxidized NH3-N being transformed to N2O-N from 0.5% (replete) up to 4.4% (0.2 mM Na2CO3). Transcriptome analysis showed differential expression (pâ¤ 0.05) of 488 genes (20% of inventory) between replete and IC-limited conditions, but few differences were detected between the two IC-limiting treatments. IC-limited conditions resulted in decreased expression of ammonium/ammonia transporter and ammonia monooxygenase subunits, and increased expression of genes involved in C1 metabolism including RuBisCO (cbbgene cluster), carbonic anhydrase, folate-linked metabolism of C1 moieties, and putative C salvage due to oxygenase activity of RuBisCO. Increased expression of nitrite reductase (gene cluster NE0924-0927) correlated with increased production of N2O. Together, these data suggest thatN. europaeaadapts physiologically during IC-limited steady state growth, which leads to uncoupling of NH3oxidation from growth and increased N2O production. Transcriptome responses of N.Â europaea in 60Â mM NH4+ to suboptimum levels of carbonate (1.0 mM and 0.2 mM) in continuous steady-state culture in a bioreactor.

2016-03-28 | E-GEOD-70988 | biostudies-arrayexpress

Identification of hyperammonemia-induced changes in the cerebral transcriptome and proteome

Project description:In this study we applyed transcriptomics and proteomics to brains of mice with systemic hyperammonemia resulting from knockout of hepatic glutamine synthetase to identify new molecular players relevant for ammonia toxicity and hepatic encephalopathy.

2022-01-15 | GSE159625 | GEO

aquatic animal

Project description:aquatic animal Assembly

| PRJNA835981 | ENA

Quantitative metaproteomics highlight the metabolic contributions of uncultured phylotypes in a thermophilic anaerobic digester

Project description:In this study, we used multiple meta-omic approaches to characterize the microbial community and the active metabolic pathways of a stable industrial biogas reactor operating at thermophilic temperatures (60°C) and elevated levels of free ammonia (367 mg NH3-N/L).

2017-06-30 | PXD004538 | Pride

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