Ontology highlight
ABSTRACT:
PROVIDER: PRJNA934718 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23477925_1.fastq.gz | Fastqsanger.gz | |||
| SRR23477925_2.fastq.gz | Fastqsanger.gz | |||
| SRR23477926_1.fastq.gz | Fastqsanger.gz | |||
| SRR23477926_2.fastq.gz | Fastqsanger.gz | |||
| SRR23477927_1.fastq.gz | Fastqsanger.gz |
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Project description:Transcriptional plasticity is a major driver of phenotypic differences between species. The lower temperature limit (LTL), namely the lower end of survival temperature, is an important trait delimiting the geographical distribution of a species, however, the genetic mechanisms are poorly understood. We investigated the inter-species transcriptional diversification in cold responses between zebrafish Danio rerio and tilapia Oreochromis niloticus, which were reared at a common temperature (28°C) but have distinct LTLs. We identified significant expressional divergence between the two species in the orthologous genes from gills when the temperature cooled to the LTL of tilapia (8°C). Five KEGG pathways were found sequentially over-represented in the zebrafish/tilapia divergently expressed genes in the duration (12 hour) of 8°C exposure, forming a signaling cascade from metabolic regulation to apoptosis via FoxO signaling. Consistently, we found differential progression of apoptosis in the gills of the two species in which zebrafish manifested a delayed and milder apoptotic phenotype than tilapia, corresponding with a lower LTL of zebrafish. We identified diverged expression in 25 apoptosis-related transcription factors between the two species which forms an interacting network with diverged factors involving the FoxO signaling and metabolic regulation. We propose a genetic network which regulates LTL in fishes. Examination of gene expressional divergence in gill between zebrafish and tilapia
2016-07-03 | E-GEOD-69965 | biostudies-arrayexpress
Project description:In fish, the sex determining mechanisms can broadly be classified as genotypic (GSD), temperature-dependent (TSD), or genotypic plus temperature effects (GSD+TE). For the fish species with TSD or GSD+TE, extremely high or low temperature can affect its sex determination and differentiation. For long time, the underlying changes in DNA methylation that occur during high or low temperature induced sex reversal have not been fully clarified. In this study, we used Nile tilapia as a model to perform a genome-wide survey of differences in DNA methylation in female and male gonads between control and high temperature induced groups using methylated DNA immunoprecipitation (MeDIP). We identified the high temperature induction-related differentially methylated regions (DMRs), and performed functional enrichment analysis for genes exhibiting DMR. These identified differentially methylated genes were potentially involved in the connection between environmental temperature and sex reversal in Nile tilapia. In this study, four samples (control females, CF; control males, CM; induced females, IF; induced males, IM) were analyzed.
2015-08-27 | E-GEOD-72386 | biostudies-arrayexpress
Project description:In their natural environments, microbes rarely exist in isolation; instead, they thrive in consortia where diverse interactions take place. In this study, a defined synthetic co-culture of the cyanobacterium S. elongatus cscB, which feeds the heterotrophic P. putida cscRABY with sucrose, was investigated to identify potential interactions. In initial experiments, a remarkable growth-promoting effect brought about by the presence of the heterotrophic partner on the cyanobacterium was observed, leading to a growth rate increase of up to 80% and increased photosynthetic capacity. Vice versa, the cyanobacterium had a neutral effect on P. putida cscRABY, highlighting the resilience against stress of Pseudomonads and their potential as co-culture partners. A suitable reference process reinforcing the growth-promoting effect was established in a parallel operating photobioreactor system, which sets the basis for the analysis of the co-culture at transcriptional, proteomic, and metabolomic level. This multi-OMICs approach revealed several moderate changes, including alterations in the metabolism, transportation, and stress response in both microbes, indicating multi-level interactions. These findings provide valuable insights into the complex dynamics within the co-culture system, suggesting the exchange of further molecules beyond the unidirectional feeding with sucrose.
2023-09-10 | PXD045253 |
Project description:GIFT is a type of freshwater farmed fish with high economic value and nutritional value. The liver is an important organ of fish metabolism. Once it is damaged or the disease occurs, it will lead to metabolic disorders and decreased disease resistance, and may cause other secondary diseases. In the high-density intensive culture of tilapia, the feed nutrition is not balanced, especially the addition of high-fat feed. High fat content can accelerate the growth of fish, but long-term feeding of high-fat diet can lead to metabolic disorders of fish, accumulation of fat in the body, easy to cause fatty liver, and ultimately death due to liver necrosis or hemorrhage, seriously affecting the breeding benefits. The main purpose of this study was to investigate the effects of apple peel added to feed on liver fat metabolism and fat deposition in tilapia tilapia; use transcriptomics to analyze related signal regulation pathways, focusing on fat metabolism and inflammatory response; and finally screening differentially expressed genes. The development of this study is helpful to understand the molecular mechanism of apple peel extract powder-mediated liver fat metabolism and inflammatory response in GIFT, and relieve liver stress. It also provides theoretical support for the application of apple peel extract powder as a feed additiion in aquatic products.
2019-12-04 | GSE127810 | GEO