Liver transcriptome analysis of juvenile largemouth bass under lead exposure by RNA-seq
Ontology highlight
ABSTRACT:
ORGANISM(S): Micropterus salmoides
PROVIDER: GSE124986 | GEO | 2019/01/12
REPOSITORIES: GEO
Similar Datasets
Project description:A novel custom microarray for largemouth bass (Micropterus salmoides) was designed from sequences obtained from a normalized cDNA library using the 454 Life Sciences GS-20 pyrosequencer. The GS-20 yielded in excess of 58 million bases of high-quality sequence. The sequence information was combined with 2,616 reads obtained by traditional suppressive subtractive hybridizations to derive a total of 31,391 unique sequences. Annotation and coding sequences were predicted for these transcripts where possible. 16,350 annotated transcripts were selected as target sequences for the design of the custom largemouth bass oligonucleotide microarray. The microarray was validated by examining the transcriptomic response in male largemouth bass exposed to 17 -oestradiol. Transcriptomic responses were assessed in liver and gonad, and indicated gene expression profiles typical of exposure to oestradiol. The results demonstrate the potential to rapidly create the tools necessary to assess large scale transcriptional responses in non-model species, paving the way for expanded impact of toxicogenomics in ecotoxicology. Keywords: E2 exposure, array validation This experiment tested two organs - liver and gonad from either E2-exposed or control fish, 4 fish (biological replicates) per treament (control and E2).
2010-05-25 | E-GEOD-10693 | biostudies-arrayexpress
Project description:A novel custom microarray for largemouth bass (Micropterus salmoides) was designed from sequences obtained from a normalized cDNA library using the 454 Life Sciences GS-20 pyrosequencer. The GS-20 yielded in excess of 58 million bases of high-quality sequence. The sequence information was combined with 2,616 reads obtained by traditional suppressive subtractive hybridizations to derive a total of 31,391 unique sequences. Annotation and coding sequences were predicted for these transcripts where possible. 16,350 annotated transcripts were selected as target sequences for the design of the custom largemouth bass oligonucleotide microarray. The microarray was validated by examining the transcriptomic response in male largemouth bass exposed to 17 -oestradiol. Transcriptomic responses were assessed in liver and gonad, and indicated gene expression profiles typical of exposure to oestradiol. The results demonstrate the potential to rapidly create the tools necessary to assess large scale transcriptional responses in non-model species, paving the way for expanded impact of toxicogenomics in ecotoxicology. Keywords: E2 exposure, array validation
2008-08-01 | GSE10693 | GEO
Project description:In the present study, we used NGST to characterize mRNA-seq of control-, moderate hypoxia-treated and severe hypoxia-treated Micropterus salmoides livers to elucidate the molecular mechanisms of hypoxia adaptation. This is the first report on integrated analysis of the tissue specific and temporal changes in gene expression in largemouth bass (Micropterus salmoides) exposed to hypoxia could reveal mechanisms of hypoxia adaptation. We provide a good case study with which to analyse mRNA expression and profile non-model fish species using NGST.
2020-07-22 | GSE134616 | GEO
Project description:Intensive aquaculture and environmental changes will inevitably lead to hypoxic stress for largemouth bass (Micropterus salmoides). To better understand the hypoxia responds mechanisms of largemouth bass, we compared the miRNA profile in liver under different environmental DO to determine which miRNAs are most affected during hypoxia. A total of 266 miRNAs were identified, and 84 miRNAs were differentially expressed compared with in control group. GO and KEGG analysis indicated that the miRNAs may play important roles in environment information processing. Specifically, we considered the VEGF signaling pathway, Phosphatidylinositol signaling system and MAPK signaling pathway, the results show that, the 13 miRNAs (miR-15b-5p, miR-30a-3p, miR-133a-3p, miR-19d-5p, miR-1288-3p, miR456, miR-96-5p, miR-23a-3p, miR-23b, miR-214, miR-24, miR-20a-3p and miR-2188-5p) involved in these three pathways are significantly down-regulated during hypoxia stress. And 12 target genes of these miRNAs were showed a higher degree of expression. We found the obvious negative correlation between miRNA and their target mRNAs, providing several miRNA-mRNA interaction networks in largemouth bass in response to hypoxia. Although relatively little information is currently available concerning the biological function of miRNAs identified to date, we strongly suggest that miRNAs play an important role in modulating gene expression involved in the physiological response to hypoxic stress in the fish liver.
2021-01-20 | GSE143641 | GEO
Project description:In this study, both male and female sexually regressed largemouth bass (Micropterus salmoides) (LMB) were fed a nominal concentration of 3.0 mg dieldrin/kg in feed for 60 days. A third group of male LMB was fed both 3.0 mg dieldrin/kg dieldrin and 0.7 mg E2/kg in feed. E2 was used as a model compound to elicit estrogenic effects via ER signaling.
2011-04-17 | GSE27963 | GEO
Project description:White bass (Morone chrysops) are a popular sportfish throughout the southern United States, and one parent of the commercially successful hybrid striped bass (M. chrysops x M. saxatilis). Currently, white bass are cultured using diets formulated for other carnivorous fish, such as largemouth bass (Micropterus salmoides) or hybrid striped bass and contain a significant percentage of marine fish meal. Since there are no studies regarding the utilization of alternative proteins in this species, we evaluated global gene expression of white bass fed diets in which fish meal was partially or totally replaced by various combinations of soybean meal, poultry by-product meal, canola meal, soy protein concentrate, wheat gluten, or a commercial protein blend (Pro-Cision). Significant differential expressed genes and gene ontology of pairwise comparisons between control diet and each test diet are presented and discussed.
2024-02-14 | GSE220235 | GEO
Project description:In this study, both male and female sexually regressed largemouth bass (Micropterus salmoides) (LMB) were fed a nominal concentration of 3.0 mg dieldrin/kg in feed for 60 days. A third group of male LMB was fed both 3.0 mg dieldrin/kg dieldrin and 0.7 mg E2/kg in feed. E2 was used as a model compound to elicit estrogenic effects via ER signaling. There were four samples analyzed for 1) control males 2) control females 3) males fed 3 mg/kg dieldrin 4) females fed 3.0 mg/kg dieldrin, and 5) males fed 3.0 mg/kg dieldrin + 0.7 mg/kg E2. There was a total of 20 microarrays and sample processed.
2011-04-17 | E-GEOD-27963 | biostudies-arrayexpress
Project description:This study used an emerging analytical technology (cDNA microarrays) to assess the potential effects of PFC exposure on largemouth bass in TCMA lakes. Microarrays simultaneously measure the expression of thousands of genes in various tissues from organisms exposed to different environmental conditions. From this large data set, biomarkers (i.e., genes that are expressed in response to an exposure to known stressors) and bioindicators (e.g., suites of genes that correspond to changes in organism health) can be simultaneously measured to clarify the relationship between contaminant exposure and organism health. Based on current scientific literature, we hypothesized that gene expression patterns would be altered in fish exposed to PFCs (as compared with fish from reference lakes), and that the magnitude of these changes would correspond to the concentrations of PFCs present throughout TCMA lakes. Patterns of gene expression in largemouth bass observed across the TCMA lakes corresponded closely with PFC concentration. Concentrations of PFCs in largemouth bass varied significantly across the sampled lakes, where the lowest concentrations were found in Steiger and Upper Prior Lakes and the highest concentrations were found in Calhoun and Twin Lakes. Patterns of gene expression were most different (relative to controls) in fish with the highest PFC tissue concentrations, where fish from Twin and Calhoun Lakes were observed to have between 5437 and 5936 differentially expressed genes in liver and gonad tissues. Although gene expression patterns demonstrated a high degree of correlation with PFC concentrations, microarray data also suggest there are likely additional factors influencing gene expression patterns in largemouth bass in TCMA lakes.
2014-07-31 | GSE57684 | GEO
Project description:Female largemouth bass were injected with 10mg/kg dieldrin and sacrificed after 7 days. Hypothalami were dissected and total RNA extracted for microarray analysis. Exposure to dieldrin induces neurotoxic effects in the vertebrate CNS and disrupts reproductive processes in teleost fish. Reproductive impairment observed in fish is likely the result of multiple mechanisms of action along the hypothalamic-pituitary-gonadal axis. To better elucidate the mode of action of dieldrin in the hypothalamus, we measured neurotransmitter levels and examined the transcriptomic response of female largemouth bass (LMB) to an acute treatment of dieldrin. Female LMB were injected with either vehicle or 10 mg/kg dieldrin and sacrificed after seven days. The neurotransmitter γ-aminobutyric acid was significantly elevated by approximately 25-30% in the hypothalamus and cerebellum but there was no change in dopamine levels in the hypothalamus, telencephalon, or cerebellum. We identified 270 transcripts (p<0.001) as being differentially regulated by dieldrin. Functional enrichment analysis identified transcription, DNA repair, ubiquitin pathway, cell communication, and phosphorylation as biological processes over-represented in the microarray analysis. Pathway analysis identified DNA damage, inflammation, regeneration, and Alzheimerâs disease as major cell processes and diseases affected by dieldrin. Using multiple bioinformatics approaches, this study demonstrates that the teleostean hypothalamus is a target for dieldrin-induced neurotoxicity and provides mechanistic evidence that dieldrin activates similar cell pathways and biological processes that are involved in the etiology of human neurological disorders. Key words: ubiquitin-proteasome pathway, mutagenicity, neurodegeneration, apoptosis, DNA damage Largemouth bass injected with single i.p. with 10 mg/kg diedrin; sacrificed 7 days later, hypothalamic tissue studied
2010-06-19 | E-GEOD-12698 | biostudies-arrayexpress
Project description:Male largemouth bass were injected with 25 mg/kg MXC and sacrificed after 48 hours; liver dissected and used for total RNA extraction Keywords: Methoxychlor injection; single injection and time point The organochlorine pesticide methoxychlor (MXC) (1,1,1-trichloro-2,2-bis(p-methoxyphenyl)ethane) has been used increasingly as an insecticide since the banning of DDT, the primary advantage being that MXC is rapidly metabolized and does not show high levels of bioaccumulation in non-target organisms. However, studies have shown that MXC can be metabolized into additional metabolites, such as mono-demethylated 2-(p-hydroxyphenyl)-2-(p-methoxyphenyl)-1,1,1-trichloroethane (OH-MXC) and bis-demethylated 2,2-bis(p-hydroxyphenyl)-1,1,1-trichloroethane (HPTE), both of which are estrogenic in mammals. In addition, there is increased potential for disruptions to normal hepatic physiology (Schlenk et al., 1998; Stuchal et al., 2006). The objectives of the present study were to study the hepatic genomic response in male largemouth bass to an i.p. injection of MXC. We performed a microarray analysis on 25 mg/kg MXC 48 hour injection because there was a significant induction of ERα and ERβb mRNA in the liver which was comparable to a 48 hour 1 mg/kg injection of E2 (previous work done by Blum et al., 2008; Aquat Toxicol. 86(4), 459-469). We chose the liver because of the significant role this tissue plays in detoxification of contaminants and due to the high capacity to produce vitellogenin in response to estrogenic chemicals. We were also interested in comparing the genomic response of MXC to estradiol alone to identify putative candidate genes and pathways that may be specific to MXC and not due to direct estrogenic effects mediated via E2 receptors. Largemouth bass injected with single i.p. with 25 mg/kg methoxychlor; sacrificed 48 days later,liver tissue studied. 4 individual liver samples (control and treatment)
2010-06-19 | E-GEOD-12700 | biostudies-arrayexpress