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ABSTRACT: Comparative transcriptome analysis of swim bladder between sexes in Nibea coibor

PROVIDER: PRJNA763018 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15882882_1.fastq.gz	Fastqsanger.gz
	SRR15882882_2.fastq.gz	Fastqsanger.gz
	SRR15882883_1.fastq.gz	Fastqsanger.gz
	SRR15882883_2.fastq.gz	Fastqsanger.gz
	SRR15882884_1.fastq.gz	Fastqsanger.gz

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Transcriptome Analysis of Tra Catfish (Pangasianodon hypophthalmus) Early Development Provides Novel Insights for the Terrestrial Adaptation

Project description:Channel catfish (Ictalurus punctatus) and tra catfish (Pangasianodon hypophthalmus) both belong to the order Siluriformes. Channel catfish does not possess an air-breathing organ (ABO), and thus cannot breathe in the air, while tra catfish is a facultative air-breather and use the swim bladder as its air-breathing organ, which provides for aerial breathing in low oxygen conditions. Tra and channel catfish serve as a great comparative model for studying the transition of life from water to terrestrial living, as well as for understanding genes that are crucial for development of the swim bladder and the function of air-breathing in tra catfish. We selected seven developmental stages in tra catfish for RNA-Seq analysis based on their transition to a stage that could live at 0 ppm oxygen. More than 587 million sequencing clean reads were generated in tra catfish, and a total of 21, 448 unique genes were detected. A comparative genomic analysis was conducted between channel catfish and tra catfish. Gene expression analysis was performed for these tra catfish specific genes. Hypoxia challenge and microtomy experiments collectively suggested that there are critical timepoints for the development of the air-breathing function and swim bladder development stages in tra catfish. Key genes were identified to be the best candidates of genes related to the air-breathing ability in tra catfish. This study provides a large data resource for functional genomic studies in air-breathing function in tra catfish, and sheds light on the adaption of aquatic organisms to the terrestrial environment.

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Project description:Swim bladder of Takifugu rubripes Transcriptome or Gene expression

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Project description:Objective To investigate aging-related changes and their sex differences in in vivo and in vitro functions and gene expression in the bladder of mice. Materials and Methods Mature (12-month old) and aged (27–30-month old) mice of both sexes were studied. In in vivo experiments, frequency, volume, and conscious free-moving cystometry measurements were investigated. In in vitro experiments, organ bath studies using detrusor strips were performed to observe functional changes, and serum sex hormone levels and mRNA expression of muscarinic, purinergic, and β-adrenergic receptors in the bladder using a cDNA microarray were evaluated. Results Although few differences were detected in the frequency/volume measurements between the two groups in either sex, aged mice showed a lower mean flow rate and higher number of non-voiding contractions in both sexes and lower maximum pressure and smaller voided volume and bladder capacity was observed in males according to cystometry measurements. Detrusor strips from aged mice showed weaker contractile responses to carbachol and electrical field stimulation, particularly in the cholinergic component, and relaxant responses to isoproterenol, which were accompanied by a decreased mRNA expression of M3 muscarinic receptors in aged males and β2-adrenoceptors in aged females. This aging-related bladder dysfunction was more severe in males, and the serum testosterone level in aged males was significantly decreased. Gene expression changes in the bladder with aging were different between sexes: 469 and 544 genes in males, 392 and 75 in females, and 8 and 37 in both sexes were significantly upregulated and downregulated, respectively, with aging. Conclusions Aged mice of both sexes demonstrated both voiding and storage dysfunctions, which were more pronounced in males. Sex hormone and genomic changes associated with aging may contribute to this functional deterioration in mice.

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Adult mouse hippocampal transcriptome changes associated with long-term behavioral and metabolic effects of gestational air pollution toxicity

Project description:Gestational exposure to air pollution increases the risk of autism spectrum disorder and cognitive impairments with unresolved molecular mechanisms. This study exposed mice throughout gestation to urban derived nanosized particulate matter (nPM). Young adult male and female offspring were studied for behavioral and metabolic changes using forced swim test, fat gain, glucose tolerance, and hippocampal transcriptome. Gestational nPM exposure caused increased depressive behaviors, decreased neurogenesis in the dentate gyrus, and increased glucose tolerance in adult male offspring. Both sexes gained fat and body weight. Gestational nPM exposure induced 29 differentially expressed genes (DEGs) in adult hippocampus related to cytokine production, IL17a signaling, and dopamine degradation in both sexes. Stratification by sex showed 2-fold more DEGs in males than females (69 vs 37), as well as male-specific enrichment of DEGs mediating serotonin signaling, endocytosis, Gai, and cAMP signaling. Gene co-expression analysis (WCGNA) identified a module of 43 genes with divergent responses to nPM between the sexes. Chronic changes in 14 DEGs (e.g., miR9-1) were associated with depressive behaviors, adiposity and glucose intolerance. These genes enriched neuroimmune pathways such as HMGB1 and TLR4. Based on cerebral cortex transcriptome data of neonates, we traced the initial nPM responses of HMGB1 pathway. In vitro, mixed glia responded to 24 h nPM with lower HMGB1 protein and increased proinflammatory cytokines. This response was ameliorated by TLR4 knockdown. In sum, we identified transcriptional changes that could underlie air pollution mediated behavioral and phenotypic changes. These identified genes merit further studies for therapeutic intervention development.

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