Ontology highlight
ABSTRACT:
PROVIDER: PRJNA609452 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11221364_1.fastq.gz | Fastqsanger.gz | |||
| SRR11221364_2.fastq.gz | Fastqsanger.gz | |||
| SRR11221365_1.fastq.gz | Fastqsanger.gz | |||
| SRR11221365_2.fastq.gz | Fastqsanger.gz | |||
| SRR11221366_1.fastq.gz | Fastqsanger.gz |
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Project description:The discus fish (Symphysodon aequifasciatus) is an ornamental fish, which occupies important position on the freshwater aquarium trade. We built two cDNA libraries from an adult male brain and an adult female brain, and performed RNA-sequencing for identifying sex-biased candidate genes , a total number of 40209 non-redundant genes (unigenes) were obtained, of which 250 unigenes were significant overexpressed in the male brain, and 436 unigenes were significant overexpressed in the female. A total of 439 miRNAs were identified, of which 60 miRNAs were differentially expressed between male brain and female brain. These results can provide important evidence for better understanding the molecular mechanisms of the brain's amphoteric dimorphism in discus fish
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Project description:The discus fish, Symphysodon spp., a South American cichlid, has a unique parental care behavior where fry bite on parental skin mucus after hatching. In this study, we used LC-MS/MS technique to compare the skin mucus proteome composition of male or female discus fish during parental and non-parental care periods. By multivariate statistical analysis, we found clear separations between different periods and between different sexes of mucus proteome. Compared with non-parental female fish, parental female fish had 283 up-regulated and 235 down-regulated expressed proteins. Compared with non-parental male fish, parental male fish had 169 up-regulated and 120 down-regulated expressed proteins. The differentially expressed proteins for male fish were enriched in sulfur relay system, mucin type O-glycan biosynthesis and antigen processing and presentation pathways, while those for female fish were enriched in sulfur relay system, steroid biosynthesis and complement and coagulation cascades pathways. During the parental care, both male and female discus showed an enhanced lipid metabolism, producing more phospholipids and cholesterol. The difference is that male discus had increased tricarboxylic acid cycle producing more energy during the parental care, while females produced more nucleotides especially guanylic acid. Our study could provide new insights into the understanding of the unique mucus supply behavior of discus fish based on proteomic change.
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Project description:This study aims to evaluate the transcriptome alterations, through cDNA libraries, associated with the effects of the combination of two PAHs, benzo[a]pyrene (0.5M-NM-<g/L) and phenanthrene (50M-NM-<g/L), present in crude oil, on specimens of Symphysodon aequifasciatus (discus fish) after 48h of exposure. The cDNA libraries were constructed according to the SOLiDTM SAGETM protocol for sequencing in the SOLiD v.3 Plus sequencer. The results were analyzed by bioinformatics and differentially expressed genes were categorized using the gene ontology program (AmiGO v.1.8). The functional categories (terms) found in the gene ontology and the gene network generated using STRING software were used to predict the adverse effects in the liver. In the present study, 27,127 genes (compared to Danio rerio database) were identified. Considering only those genes with a p-value less than or equal to 0.05 and a greater than or equal to two-fold change in expression across libraries, we found 804 genes, 438 down-regulated (54%) and 366 up-regulated genes (46%), in the experimental group compared to the control group. Out of this total, 327 genes were successfully categorized, 174 down-regulated and 153 up-regulated genes, using gene ontology tool. The final confidence gene network, analyzed in STRING, was composed by 199 nodes of proteins, 124 of them resulted in 274 interactions. The results showed that even an acute exposure of 48 h caused metabolic change in response to environmental contaminants, resulting in changes of cell integrity, changes in oxidation-reduction processes, disturbances of intracellular signaling and changes in the immune response of discus fish. Also the gene network interactions have showed no central interplay cluster, exhibiting interconnected clusters interactions and sparsely connected sub-networks. These findings highlight that even an acute and sublethal exposure of PAHs can cause metabolism changes that may affect this fish species survival rates. Our findings using the SAGE-method and the SOLiD sequencer showed that this is a powerful tool for gene expression analysis in discus fish, a non-model organism. Transcriptome analysis of differentially expressed genes in liver in benzo[a]pyrene and phenanthrene-exposed and non-exposed fish (N=6 per treatment)
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Project description:Small intestinal bacterial overgrowth (SIBO) has been implicated in symptoms associated with functional gastrointestinal disorders (FGIDs), though mechanisms remain poorly defined and treatment involves non-specific antibiotics. Here we show that SIBO based on duodenal aspirate. culture reflects an overgrowth of anaerobes, does not correspond with patient symptoms, and may be a result of dietary preferences. Small intestinal microbial composition, on the other hand, is significantly altered in symptomatic patients and does not correspond with aspirate culture results. In a pilot interventional study we found that switching from a high fiber diet to a low fiber, high simple sugar diet triggered FGID-related symptoms and decreased small-intestinal microbial diversity and small-intestinal permeability. Our findings demonstrate that characterizing small intestinal microbiomes in patients with gastrointestinal symptoms may allow a more targeted antibacterial or a diet-based approach to treatment.
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