Mediks International Hospital E11/2 Islamabad Pakistan,26000
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA565272 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Hospital environmental samples from Pakistan Metagenome
| PRJNA782966 | ENA
Project description:Women are twice as likely to have Alzheimer’s disease (AD) than men and multiparity has been suggested to be a risk factor for dementia. The present study evaluated whether the lack of certain nutrients during pregnancy influences cognition while pregnant and in old age in mouse model. Non-targeted NMR analysis revealed significantly lower levels of numerous plasma nutrients and metabolites including choline and its derivatives on gestation day 7 compared to day 1. Novel object recognition and Morris Water Maze tests revealed impaired cognition in pregnant mice compared to nonpregnant controls. Choline deprivation worsened the cognitive impairment during pregnancy and choline supplementation alleviated it. Furthermore, choline availability during pregnancy affected cognition and general health in old age, with mice given a choline-deficient diet during pregnancy performed more poorly. RNA-Seq analysis indicates lasting effect of choline intake during pregnancy on hippocampal gene signatures in old age. Choline deprivation was associated with more upregulation of proinflammatory genes, whereas choline supplementation showed upregulation of neuroprotective genes such as Prl, Gh, and hemoglobin (Hba and Hbb subunits). Together the study shows that choline supplement benefits women’s cognitive health during pregnancy and at the old age.
2025-09-04 | GSE293570 | GEO
Project description:Next-generation sequencing facilitates quantitative analysis of the transcriptomes of FOXG1 100% dosage GABA interneurons, FOXG1 60% dosage GABA interneurons, FOXG1 30% dosage GABA interneurons, and FOXG1 0% dosage GABA interneurons derived from human embryonic stem cells. We report a genetic manipulation system that enable precise dosage control of FOXG1 protein in human pluripotent stem cells (hPSCs). Using this system, we explored how the various reduced dosage affect human ventrol GABA interneuron development. We employed RNA seq on hPSC-derived GABA interneurons (day 60) to invest the expression pattern under different FOXG1 dosage conditions. RNA-Seq on GABA interneurons (Day 60) indicates that compared to the FOXG1 100% group, variable insufficiency of FOXG1 produces more than 1000 differently expressed genes (DEGs), and more DEGs in the group with less FOXG1 dosage. Heat map on Pearson Correlation indicates that groups with more discriminated FOXG1 exhibit much weaker correlation. Venn diagram reveals that each group has a set of distinct DEGs, suggesting that each FOXG1 protein dosage could results in different expression pattern during differentiation. The DEGs can be divided into two clusters, with one showing dosage-dependent regulation by FOXG1 and the other one typical binary. Key regulatory genes for GABA interneuron induction (NKX2-1, NKX6-2, GAD1, etc.) and for functional GABAergic-specific synapse formation (GABBR1, GABRA1, GABRB1, GABRG1, GABRQ, SHANK1, etc.) are down regulated along with reduction of FOXG1 protein.
2018-09-18 | GSE120079 | GEO
Project description:Dysregulated choline metabolism is a well-known feature of breast cancer, but the underlying mechanisms are not fully understood. In this study, the metabolomic and transcriptomic characteristics of a large panel of human breast cancer xenograft models were mapped, with focus on choline metabolism. Methods: Tumor specimens from 34 patient-derived xenograft models were collected and divided in two. One part was examined using high-resolution magic angle spinning (HR-MAS) MR spectroscopy while another part was analysed using gene expression microarrays. Expression data of genes encoding proteins in the choline metabolism pathway were analysed and correlated to the levels of choline (Cho), phosphocholine (PCho) and glycerophosphocholine (GPC) using Pearson’s correlation analysis. For comparison purposes, metabolic and gene expression data were collected from human breast tumors belonging to corresponding molecular subgroups. Results: Most of the xenograft models were classified as basal-like (N=19) or luminal B (N=7). These two subgroups showed significantly different choline metabolic and gene expression profiles. The luminal B xenografts were characterized by a high PCho/GPC ratio while the basal-like xenografts were characterized by highly variable PCho/GPC ratio. Also, Cho, PCho and GPC levels were correlated to expression of several genes encoding proteins in the choline metabolism pathway, including choline kinase alpha (CHKA) and glycerophosphodiester phosphodiesterase domain containing 5 (GDPD5). These characteristics were similar to those found in human tumor samples. Discussion: The higher PCho/GPC ratio found in luminal B compared with most basal-like breast cancer xenograft models and human tissue samples do not correspond to results observed from in vitro studies. It is likely that microenvironmental factors play a role in the in vivo regulation of choline metabolism. Cho, PCho and GPC were correlated to different choline pathway-encoding genes in luminal B compared with basal-like xenografts, suggesting that regulation of choline metabolism may vary between different breast cancer subgroups. The concordance between the metabolic and gene expression profiles from xenograft models with breast cancer tissue samples from patients indicates that these xenografts are representative models of human breast cancer and represent relevant models to study tumor metabolism in vivo. Gene expression was measured in 30 human breast cancer xenografts, one sample from each model
2014-01-16 | E-GEOD-44666 | biostudies-arrayexpress
Project description:Exposure of the preimplantation bovine embryo to choline programs development to alter postnatal phenotype of the resultant calves. To understand potential mechanisms, actions of choline on gene expression and DNA methylation of the bovine blastocyst were characterized. Embryos produced in vitro using oocytes collected by oocyte pickup procedures were cultured for 7 days with either 1.8 mM choline chloride or vehicle (consisting of 1.8 mM additional NaCl). Using an adjusted p of 0.05, the total number of differentially expressed genes (DEG) was 263 with 208 downregulated by choline. Analysis of gene ontologies of differentially expressed genes indicated choline causes reduced protein synthesis. DNA methylation was determined from another set of bovine blastocysts using whole genome enzymatic methyl sequencing. A total of 7,983 differentially methylated regions (DMR) were identified, with 6,174 hypermethylated (choline>vehicle) and 1,809 hypomethylated. Thus, as expected given its role as a methyl donor, the major action of choline was to promote methylation. The correlation coefficient between DNA methylation percent in promoters and gene expression was -0.21 for both vehicle and choline groups. Comparison of a DNA methylation data set of blood cells from heifers derived from choline- or vehicle-treated embryos identified 13 overlapping DMRs for the blastocyst and blood datasets where direction of methylation (hyper- or hypomethylated) was the same for blastocysts and blood. It was concluded that choline alters blastocyst gene expression in a manner consistent with reduced protein synthesis and causes small changes in DNA methylation. Moreover, a small number of DMR are retained into the postnatal period. Keywords: blastocyst, cattle, DNA methylation, gene expression, nutrient
2026-03-31 | GSE320000 | GEO
Project description: Not available
| S-EPMC11263194 | biostudies-literature
Project description: Not available
| S-EPMC8495393 | biostudies-literature
Project description:Plant response to waterlogging is well studied, but the understanding of plant responses during post-waterlogging recovery remains limited. In this study, we show that the waterlogging-sensitive (Z4847) and waterlogging-tolerant (ZM9001) cotton varieties have different rates of post-waterlogging recovery that correlate with waterlogging tolerance. The performance of a comparative transcriptome and metabolome analysis of the roots from two cotton varieties during recovery processes indicated the significant inhibition of the abundance of genes and metabolites related to energy metabolism in both varieties during post-waterlogging. The results also showed that the waterlogging tolerant ZM9001 plants maintained the higher carbon flows from glycolysis to the first reaction of the TCA cycle, leading to more energy production and restoring root activity during recovery processes. The interaction analysis of KEGG pathways in ZM9001 vs. Z4847 comparison during post-waterlogging displayed an extremely significant correlation between GABA metabolism and the glycolysis-citrate cycle. Therefore, we combined both multi-omics and physiological approaches and showed that the induced elevation of the GABA levels in the ZM9001 plants during recovery processes is essential in restoring its root function by generating more energy through the activation of the GABA shunt pathway. Consistent with this, the loss of GABA synthesis showed increased sensitivity to post-waterlogging, which was partially rescued by the exogenous application of GABA. Subsequently, elevated GABA levels could also provide better redox homeostasis by enhancing the antioxidant enzyme system during post-waterlogging recovery. Therefore, these findings indicate that the energy metabolism reconfiguration via re-activating GABA shunt participates in seedling survival after waterlogging stress, shedding light
2025-12-31 | GSE284486 | GEO
Project description: Not available
| S-EPMC11742144 | biostudies-literature
Project description:Prenatal alcohol exposure (PAE) is linked to elevated risk for systemic adult-onset diseases like hypertension, impaired glucose and immune regulation, and in animal models, to impaired recovery from acute onset diseases like cerebrovascular ischemic stroke. Recent evidence suggests that the gastrointestinal system rapidly becomes dysbiotic following cerebrovascular stroke, resulting in systemic inflammation. We hypothesized that a history of PAE would modify the systemic effects of stroke, and transduce exposure-dependent transcriptomic changes in downstream sentinel tissues of the enteric portal circulation that have previously been linked to biobehavioral outcomes in rodent PAE models. Pregnant Sprague Dawley rats were exposed to repeated episodes of vaporized ethanol or room air from gestational day 8 to 19. At 5 months, progeny from each treatment condition were subjected to unilateral endothelin-1 induced occlusion of the middle cerebral artery and outcomes evaluated after 2 days while other progeny stayed stroke-naïve. Stroke induced disabilities were assessed by behavioral assays (adhesive removal, Vibrissae evoked fore-limb placement, circling) and infarct size. The mesenteric adipose tissue and liver transcriptomes were assessed by sequencing, from age-matched stroke-exposed and stroke-naïve offspring. In stroke-naïve animals, pathway analysis identified rRNA processing as downregulated and citric acid cycle as upregulated in mesenteric adipose. Weighted gene correlation network analysis (WGCNA) identified, in the liver of stoke-naïve animals, a moderate but significant correlation between PAE status and necroptosis, a proinflammatory form of programmed cell death (Pearson’s r=0.554, p<0.05). Two days after a stroke, PAE rats exhibited worse neurological scores compared to controls (p<0.05). WGCNA after stroke identified an adipose gene network associated with B cell differentiation and NF-kappa B signaling as moderately correlated with post-stroke neurological function (Pearson's r=0.52, p=0.05). Post-stroke WGCNA also identified a liver proinflammatory gene network strongly correlated with post-stroke neurological function (Pearson's r=-0.63, p<0.01). PAE persistently alters the transcriptome of afferent tissue targets of enteric circulation in adult rat offspring. Moreover, PAE-linked enteric inflammation is correlated to worse outcomes following cerebrovascular ischemic stroke in adulthood. Enteric disturbances may mediate adverse brain health outcomes due to PAE in adulthood.
2023-08-29 | GSE217173 | GEO