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Using microarrays to investigate differential gene expression in gills from smallmouth bass after various exposures.

ABSTRACT: The purpose of this study was to investigate differentially expressed genes in gill and liver tissue from smallmouth bass (Micropterus dolomieu) after exposure to various treatments, compared to controls. The treatments consisted of bacteria, estradiol, and a mixture of bacteria plus estradiol. Four-condition experiment with biological replicates: 4 control replicates, 4 of each treatment for liver and gill tissue.

ORGANISM(S): Micropterus salmoides

SUBMITTER: Barbara Carter

PROVIDER: E-GEOD-33959 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Using microarrays to investigate differential gene expression in gills from smallmouth bass after various exposures.

Project description:The purpose of this study was to investigate differentially expressed genes in gill and liver tissue from smallmouth bass (Micropterus dolomieu) after exposure to various treatments, compared to controls. The treatments consisted of bacteria, estradiol, and a mixture of bacteria plus estradiol.

2012-08-31 | GSE33959 | GEO

Liver transcriptome analysis of juvenile largemouth bass under lead exposure by RNA-seq

Project description:We sequenced mRNA from 9 liver samples of juvenile largemouth bass (Micropterus salmoides) taken from different lead concentration exposure treatment fish and control fish to investigate the transcriptome and comparative expression profiles of largemouth bass liver undergoing lead exposure.

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Largemouth Bass E2 exposure

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

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Largemouth Bass E2 exposure

2010-05-25 | E-GEOD-10693 | biostudies-arrayexpress

Gene expression profiling of white bass when fed fish meal or fish meal replacement diets

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

Acute hypoxia changes the utilization mode of glucose / lipid in the liver of the largemouth bass (Micropterus salmoides)

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.

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Sexually dimorphic transcriptomic responses in the largemouth bass to the neuroactive pesticide dieldrin

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Dataset of the proteome profiles of sea bass (Dicentrarchus labrax) skin-scale exposed to estradiol and fluoxetine

Project description:Contamination of aquatic ecosystems with anthropogenic pollutants, including pharmaceutical drugs, is a major concern worldwide. Fish are particularly at risk of exposure to pollutants but their impacts on mineralized fish tissues, particularly the scales that form a barrier between the fish and the environment, are poorly understood. The proteome data here presented support the findings reported in the associated research article “Disruption of the sea bass (Dicentrarchus labrax) skin-scale by estradiol and fluoxetine, an emerging pollutant”. Juvenile sea basses were exposed by intraperitoneal injections to: a) the antidepressant fluoxetine (FLX), a widely prescribed psychotropic drug and an emerging pollutant; b) the natural estrogen 17β-estradiol (E2) and c) coconut oil alone (control). The scale proteome profiles of fish exposed to these compounds for 5 days were analysed by the quantitative label-free proteomics technology SWATH-MS (Sequential Windowed data-independent Acquisition of the Total High-resolution-Mass Spectra). LC-MS data from pooled protein extracts from the scales of all experimental groups were acquired using information-dependent acquisition (IDA), which allowed the identification of 1,254 proteins through searches against the sea bass genome database. 715 proteins were confidently quantified by SWATH acquisition, from which 213 proteins had modified levels (p<0.05) between E2- or FLX-exposed fish and control. The main biological processes and KEGG pathways affected by E2 or FLX treatments were identified using Cytoscape/ClueGO enrichment analyses.

2022-01-11 | PXD020983 | Pride

Sexually dimorphic transcriptomic responses in the largemouth bass to the neuroactive pesticide dieldrin

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

Gene expression profiles of white bass (Morone chrysops) and hybrid striped bass (M. chrysops x M. saxatilis) gill tissue over time following Flavobacterium covae exposure

Project description:Columnaris disease is a prevalent disease in freshwater environments worldwide caused by the ubiquitous aquatic bacterium Flavobacterium species. Adhesion to the external mucosal surfaces of fishes is the initial stage of infection, and the gills specifically have been identified as both a primary target and release site for this pathogen. Previous research has indicated that a predominant US aquaculture product, the hybrid striped bass (Morone chrysops x M. saxatilis), is more susceptible to infection with Flavobacterium columnare (covae) than the maternal white bass (M. chrysops) parental species. Therefore, to further elucidate the differences between these fish we conducted a transcriptomic profiling study examining the differences of gene expression in gill mucosal tissue over time after exposure to F. covae isolate LSU-066-04. Combined with previous work, these data provide a greater understanding of host immune response to a common pathogen in moronids.

2024-05-09 | GSE246056 | GEO

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