Tuna microbiome
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ABSTRACT:
PROVIDER: PRJNA679546 | ENA |
REPOSITORIES: ENA
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Project description:Globel gene expression was analyzed by RNA-seq to study the role of lincRNA TUNA in pluripotent mouse embryonic stem cells. mRNA profiles of CCE mES cells with shRNA-mediated depletion of lincRNA TUNA on days 2, 4, and 6, compared to a control shRNA.
2014-02-03 | E-GEOD-46730 | biostudies-arrayexpress
Project description:Cadmium (Cd) is a toxic heavy metal found throughout the environment and one of the top ten toxicants of major public health concern identified by the World Health Organization.InuteroCd exposure causes fetal growth restriction, malformation, and spontaneous abortion; however, the mechanisms by which Cd impacts these outcomes are poorly understood. Cd accumulates in the placenta, suggesting that these negative outcomes may be a consequence of disrupted placental function and placental insufficiency. To understand the impact of Cd on gene expression within the placenta, we developed a mouse model of Cd-induced fetal growth restriction through maternal consumption of CdCl2 and performed RNA-seq on control and CdCl2 exposed placentae. The top differentially expressed transcript was the Tcl1Upstream Neuron-Associated (Tuna) long non-coding RNA, which was up-regulated over 25-fold in CdCl2 exposed placentae. Tuna has been shown to be critical for neural stem cell differentiation. However, within the placenta, there is no evidence that Tuna is normally expressed or functional at any developmental stage. To determine the spatial expression of Cd-activated Tuna within the placenta, we used in situ hybridization as well as placental layer-specific RNA isolation and analysis. Both methods confirmed the absence of Tuna expression in control samples and determined that Cd-induced Tuna expression is specific to the junctional zone. Since many lncRNAs regulate gene expression, we hypothesized that Tunaforms part of the mechanism of Cd-induced transcriptomic changes. To test this, we over-expressed Tuna in cultured choriocarcinoma cells and compared gene expression profiles to those of control and CdCl2 exposed cells. We demonstrate significant overlap between genes activated byTunaoverexpression and genes activated by CdCl2 exposure, with enrichment in the NRF2-mediated oxidative stress response. Herein we analyze the NRF2 pathway and show that Tuna increases NRF2/NRF2 both at the transcript and protein levels. Tuna drives increased NRF2 target gene expression, a result that is abrogated with the use of an NRF2 inhibitor, confirming that Tuna activates oxidative stress response genes through this pathway. This work identifies the lncRNA Tuna as a potential novel player in Cd-induced placental insufficiency.
2023-05-31 | GSE233252 | GEO
Project description:Cadmium (Cd) is a toxic heavy metal found throughout the environment and one of the top ten toxicants of major public health concern identified by the World Health Organization.InuteroCd exposure causes fetal growth restriction, malformation, and spontaneous abortion; however, the mechanisms by which Cd impacts these outcomes are poorly understood. Cd accumulates in the placenta, suggesting that these negative outcomes may be a consequence of disrupted placental function and placental insufficiency. To understand the impact of Cd on gene expression within the placenta, we developed a mouse model of Cd-induced fetal growth restriction through maternal consumption of CdCl2 and performed RNA-seq on control and CdCl2 exposed placentae. The top differentially expressed transcript was the Tcl1Upstream Neuron-Associated (Tuna) long non-coding RNA, which was up-regulated over 25-fold in CdCl2 exposed placentae. Tuna has been shown to be critical for neural stem cell differentiation. However, within the placenta, there is no evidence that Tuna is normally expressed or functional at any developmental stage. To determine the spatial expression of Cd-activated Tuna within the placenta, we used in situ hybridization as well as placental layer-specific RNA isolation and analysis. Both methods confirmed the absence of Tuna expression in control samples and determined that Cd-induced Tuna expression is specific to the junctional zone. Since many lncRNAs regulate gene expression, we hypothesized that Tunaforms part of the mechanism of Cd-induced transcriptomic changes. To test this, we over-expressed Tuna in cultured choriocarcinoma cells and compared gene expression profiles to those of control and CdCl2 exposed cells. We demonstrate significant overlap between genes activated byTunaoverexpression and genes activated by CdCl2 exposure, with enrichment in the NRF2-mediated oxidative stress response. Herein we analyze the NRF2 pathway and show that Tuna increases NRF2/NRF2 both at the transcript and protein levels. Tuna drives increased NRF2 target gene expression, a result that is abrogated with the use of an NRF2 inhibitor, confirming that Tuna activates oxidative stress response genes through this pathway. This work identifies the lncRNA Tuna as a potential novel player in Cd-induced placental insufficiency.
2023-05-31 | GSE233281 | GEO
Project description:Globel gene expression was analyzed by RNA-seq to study the role of lincRNA TUNA in pluripotent mouse embryonic stem cells.
2014-02-03 | GSE46730 | GEO
Project description:This study elucidated the role of DHA-modulated genes in the development and growth of bluefin tuna (Thunnus thynnus) larvae ingesting increasing levels of DHA in their rotifer prey. The effect of feeding low, medium, and high rotifer (Brachionus rotundiformis) DHA levels (2.0, 3.6 and 10.9 mg DHA g-1 DW, respectively) was tested on 2-15 days post hatching (dph) bluefin tuna larvae. Larval DHA content markedly (P < 0.05) increased in a DHA dose-dependent manner (1.5, 3.9, 6.1 mg DHA g-1 DW larva, respectively), that was positively correlated with larval prey consumption, and growth (P < 0.05). Gene ontology enrichment analyses of DEGs demonstrated dietary DHA significantly (P < 0.05) affected different genes and biological processes at different developmental ages. The number of DHA up-regulated DEGs was highest in 10 dph larvae (408), compared to 5 (11) and 15 dph fish (34), and were mainly involved in neural and synaptic development in the brain and spinal cord. In contrast, DHA in older 15 dph larvae elicited fewer DEGs but played critical roles over a wider range of developing organs. The emerging picture underscores the importance of DHA-modulated gene expression as a driving force in bluefin tuna larval development and growth.
2024-10-09 | GSE263473 | GEO
Project description:The largest of the tuna species, Atlantic bluefin tuna, Thunnus thynnus (Linnaeus, 1758), inhabits the North Atlantic Ocean and the Mediterranean Sea and is considered to be an endangered species, largely through overfishing. Thus, the development of aquaculture practices independent of wild resources can provide an important contribution towards ensuring security and sustainability of this species in the longer-term. In order to provide a resource for ongoing studies, we have used 454 pyrosequencing technology to sequence a mixed-tissue normalized cDNA library, derived from adult individuals. Transcript sequences were used to develop a novel 15K Agilent oligo microarray for T. thynnus and comparative tissue gene expression profiles were inferred for gill, heart, liver, ovaries and testes.
2015-08-10 | E-MTAB-3412 | biostudies-arrayexpress
Project description:In this study, we examined the transcriptomic responses to temperature acclimation (14oC, 20oC, and 25oC) in atrial and ventricular tissues of Pacific bluefin tuna (PBFT). A global gene expression analysis using a bluefin tuna-specific microarray indicated profound changes in expression of genes associated with energy metabolism, protein turnover, cellular stress response, oxidative stress and apoptosis. A principal component analysis revealed tissue-specific transcriptomic responses to temperature, with atrium at 25oC showing the greatest variation. Overall transcriptomic data suggests that PBFT can optimize cardiac function in the cold by acclimating to 14oC. Capacity to acclimate to colder temperatures potentially underlies this species ability to expand its vertical and horizontal thermal niche and migrate to colder oceans at high latitudes. In contrast, the cardiac phenotype of 25oC acclimated fish infers that PBFT hearts struggle to maintain cellular homeostasis and are subjected to programmed cell death. The goal of this study was to compare transcriptomic response to cold and warm temperature acclimations across cardiac tissues in Pacific bluefin tuna. Fish (n=4) were acclimated to 14C, 20C and 25C, and RNA was extracted from atrial, ventricular compact and spongy tissues. Experimental samples were hybridyzed against a reference pool that contained a mix of RNA from every sample.
2012-03-31 | E-GEOD-36886 | biostudies-arrayexpress
Project description:Aging is associated with declining immunity and inflammation as well as alterations in the gut microbiome with a decrease of beneficial microbes and increase in pathogenic ones. The aim of this study was to investigate aging associated gut microbiome in relation to immunologic and metabolic profile in a non-human primate (NHP) model. 12 old (age>18 years) and 4 young (age 3-6 years) Rhesus macaques were included in this study. Immune cell subsets were characterized in PBMC by flow cytometry and plasma cytokines levels were determined by bead based multiplex cytokine analysis. Stool samples were collected by ileal loop and investigated for microbiome analysis by shotgun metagenomics. Serum, gut microbial lysate and microbe-free fecal extract were subjected to metabolomic analysis by mass-spectrometry. Our results showed that the old animals exhibited higher inflammatory biomarkers in plasma and lower CD4 T cells with altered distribution of naïve and memory T cell maturation subsets. The gut microbiome in old animals had higher abundance of Archaeal and Proteobacterial species and lower Firmicutes than the young. Significant enrichment of metabolites that contribute to inflammatory and cytotoxic pathways was observed in serum and feces of old animals compared to the young. We conclude that aging NHP undergo immunosenescence and age associated alterations in the gut microbiome that has a distinct metabolic profile.
2022-02-01 | E-MTAB-10160 | biostudies-arrayexpress
Project description:In this study, we examined the transcriptomic responses to temperature acclimation (14oC, 20oC, and 25oC) in atrial and ventricular tissues of Pacific bluefin tuna (PBFT). A global gene expression analysis using a bluefin tuna-specific microarray indicated profound changes in expression of genes associated with energy metabolism, protein turnover, cellular stress response, oxidative stress and apoptosis. A principal component analysis revealed tissue-specific transcriptomic responses to temperature, with atrium at 25oC showing the greatest variation. Overall transcriptomic data suggests that PBFT can optimize cardiac function in the cold by acclimating to 14oC. Capacity to acclimate to colder temperatures potentially underlies this species ability to expand its vertical and horizontal thermal niche and migrate to colder oceans at high latitudes. In contrast, the cardiac phenotype of 25oC acclimated fish infers that PBFT hearts struggle to maintain cellular homeostasis and are subjected to programmed cell death.
2012-04-01 | GSE36886 | GEO
Project description:Development and validation of a mixed-tissue oligonucleotide DNA microarray for Atlantic bluefin tuna, Thunnus thynnus (Linnaeus, 1758).
| PRJEB7253 | ENA