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To determine and compare the toxic effects of Iranian heavy crude oil (IHCO) on the embryonic development of two fish species, we examined transcriptome profiles using RNA-seq. The assembled contigs were 66,070 unigenes in olive flounder embryos and 76,498 unigenes in spotted seabass embryos. In the differential gene expression (DEG) profiles, olive flounder embryos showed different up- and down-regulated patterns than spotted seabass embryos in response to fresh IHCO (FIHCO) and weathered IHCO (WIHCO). In this work, we categorized DEG profiles into six pathways: ribosome, oxidative phosphorylation, Parkinson's disease, Alzheimer's disease, Huntington's disease, and cardiac muscle contraction, validating the expression patterns of 13 DEGs using real-time quantitative RT-PCR. The expression of the CYP1A, CYP1B1, and CYP1C1 genes in spotted seabass embryos was higher than in olive flounder embryos, whereas genes related to cell processing, development, and the immune system showed the opposite trend. Orthologous gene cluster analysis showed that olive flounder embryos were sensitive (fold change of genes with cutoff P<0.05) to both FIHCO and WIHCO, but spotted seabass embryos exhibited higher sensitivity to WIHCO than FIHCO, indicating that species-specific differences are likely to be reflected in population levels after oil spills. Overall, our study provides new insight on the different embryonic susceptibilities of two marine fish species to FIHCO and WIHCO and a better understanding of the underlying molecular mechanisms via RNA-seq and DEGs.
After the Hebei Spirit oil spill (HSOS, Dec. 2007), many marine species were found dead on rocky shores and beaches and >8571ha of land-based fish aquaculture facilities were directly affected by the crude oil. The fish population in shallow water regions near the oil stranding shoreline exhibited reductions in the number of species and diversity for two years after the HSOS compared with the reference site (MLTM, 2011). Some winter spawning fish species populations decreased for up to four years in the coastal spill area (MLTM, 2012), because of an overlap between the timing of the embryonic periods of some species and the persistence of residual crude oil in nearshore areas (Jung et al., 2015a). A knowledge gap persists about the comparative susceptibility of embryonic stages in endemic fish species to oil pollution, as the embryonic stage is known to be sensitive to environmental change. After the Exxon Valdez oil spill in Alaska in 1989, Pacific herring (Clupea pallasii) larvae experienced significant morphological deformities and abnormalities due to polluted spawning sites (Brown et al., 1996, Hose et al., 1996, McGurk and Brown, 1996). Also, the early life stages of Pacific herring (C. pallasii), pink salmon (Oncorhynchus gorbuscha), zebrafish (Danio rerio), and Atlantic killifish (Fundulus heteroclitus) have been reported to experience developmental alteration from petroleum products (Marty et al., 1997, Carls et al., 1999, Heintz et al., 1999, Incardona et al., 2004, Incardona et al., 2013, Brown et al., 2016). In crude oil exposure conditions, fish developmental impairment was closely associated with malformations that caused slower heart rate, impaired swimming performance, and altered gene and protein expression (Marty et al., 1997, Carls et al., 1999, Heintz et al., 1999, Hicken et al., 2011, Incardona et al., 2011, Incardona et al., 2013, Jung et al., 2013, Jung et al., 2015a). However, the toxic mechanisms and molecular pathways that lead to polyaromatic hydrocarbon (PAH) composition–associated malformations and sublethal effects during fish development are not fully understood.
Verifying the effects of oil exposure in fish requires the validation of wild species-specific differences in oil spill areas. Cardiotoxicity was previously demonstrated in zebrafish (D. rerio), olive flounder (Paralichthys olivaceus), and spotted seabass (Lateolabrax maculatus) in response to Iranian heavy crude oil (IHCO; HSOS crude oil). Comparative studies between species-specific differences and weathering status in crude oil have not been conducted. To date, in olive flounder (P. olivaceus), spotted seabass (L. maculatus), Pacific herring (C. pallasii), and pink salmon, developmental toxic effects from crude oil exposure were determined by extrapolating zebrafish data (Hicken et al., 2011, Incardona et al., 2004, Jung et al., 2013).
Transcriptomic analysis (e.g., RNA-seq) using toxicant-exposed samples helps to identify potential biomarker genes that will uncover the underlying mode of action in response to environmental pollution in marine environments (Bougas et al., 2013, Cai et al., 2014, Jin et al., 2015, Mu et al., 2015). However, in marine fish, the accessibility of genomic resources (e.g., genomic DNA, RNA-seq) is limited, even though gene expression profiling has been widely applied to predict the toxicity of various chemical compounds and to unravel the underlying molecular mechanisms. Next-generation sequencing is a powerful technique in analyzing gene expression, with its relatively high sensitivity, specificity, and ability to sequence rare transcripts. In particular, Illumina Hi-Seq sequencing provides deep coverage of identified genes, allowing the quantification of gene expression over reference genomes.
In this study, we profiled the transcriptomes of olive flounder (P. olivaceus) and spotted seabass (L. maculatus) embryos in response to fresh IHCO (FIHCO) and weathered IHCO (WIHCO), as they are widely distributed in the northwest Pacific rim and Yellow Sea (Kim et al., 2007, Shao et al., 2009). Also they are the main species of artificial seedling production and juvenile release in spill area. They produce buoyant pelagic eggs that develop in the costal shallow water, rendering them susceptible to the exposure during the oil spill incident. The hatching periods (November–February) of both species coincided with the time of the HSOS in December 2008, leading to developmental impairment of the two species. Overall, our primary aim in this study was to determine and compare the developmental toxic effects of FIHCO and WIHCO on the embryonic development of two wild fish species using transcriptome profiling.
Fish embryos and exposure
Olive flounder (P. olivaceus) and spotted sea bass (L. maculatus) eggs were artificially fertilized at two hatcheries, Ihwasangrok, Jeju, South Korea, and Geunyang, Jeollabuk-do, South Korea. Both fish produce buoyant and pelagic eggs that develop in the upper water column and are vulnerable to oil spills. At 6h after fertilization, eggs were transported to the laboratory in Korea Institute of Ocean Science and Technology, Geoje, Korea. Eggs were acclimated for 24h in flowing seawater at 16°C.
Sequencing and unigene assembly
We sequenced a total of 185,266 million reads in the olive flounder and 182,956 million reads in the spotted seabass, with an average of 60.7–62.8 million clean reads per sample. In the olive flounder, 88,343 transcripts were identified and assembled into transcripts (N50=2148bp), and the spotted seabass had 98,148 transcripts (N50=1286bp) (Table 2). After clustering, we obtained 66,070 and 76,498 unigenes in the olive flounder and spotted seabass, respectively. A BLAST search against the
Water PAH concentrations were shown in a previous paper (Jung et al., 2015b): initially 12,100ngL−1 for FIHCO and 10,800ngL−1 for WIHCO, declining after 48h to 4340 and 6420ngL−1 for FIHCO and WIHCO, respectively. Those concentrations were 41–46 times higher than those in clean gravel (>300ngL−1). The relative compositions of PAH compounds in FIHCO and WIHCO effluents were similar, with a dominance of naphthalenes (C0 to C4) followed by dibenzothiophene and fluorene groups. However, the
This study was supported by research funds (‘Oil Spill Environmental Impact Assessment and Environmental Restoration’ and ‘Development of techniques for assessment and management of hazardous chemicals in the marine environment’) from the Ministry of Oceans and Fisheries, Korea.
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Morphological and transcriptional effects of crude oil and dispersant exposure on the marine sponge Cinachyrella alloclada
2023, Science of the Total Environment
Marine sponges play important roles in benthic ecosystems. More than providing shelter and food to other species, they help maintain water quality by regulating nitrogen and ammonium levels in the water, and bioaccumulate heavy metals. This system, however, is particularly sensitive to sudden environmental changes including catastrophic pollution event such as oil spills. Hundreds of oil platforms are currently actively extracting oil and gas in the Gulf of Mexico. To test the vulnerability of the benthic ecosystems to oil spills, we utilized the Caribbean reef sponge, Cinachyrella alloclada, as a novel experimental indicator. We have exposed organisms to crude oil and oil dispersant for up to 24h and measured resultant gene expression changes. Our findings indicate that 1-hour exposure to water accommodated fractions (WAF) was enough to elicit massive shifts in gene expression in sponges and host bacterial communities (8052 differentially expressed transcripts) with the up-regulation of stress related pathways, cancer related pathways, and cell integrity pathways. Genes that were upregulated included heat shock proteins, apoptosis, oncogenes (Rab/Ras, Src, CMYC), and several E3 ubiquitin ligases. 24-hour exposure of chemically enhanced WAF (CE-WAF) had the greatest impact to benthic communities, resulting in mostly downregulation of gene expression (4248 differentially expressed transcripts). Gene deregulation from 1-hour treatments follow this decreasing trend of toxicity: WAF>CE-WAF>Dispersant, while the 24-hour treatment showed a shift to CE-WAF>Dispersant>WAF in our experiments. Thus, this study supports the development of Cinachyrella alloclada as a research model organism and bioindicator species for Florida reefs and underscores the importance of developing more efficient and safer ways to remove oil in the event of a spill catastrophe.
Speciation-specific Cr bioaccumulation, morphologic and transcriptomic response in liver of Plectropomus leopardus exposed to dietary Cr(III) and Cr(VI)
2022, Ecotoxicology and Environmental Safety
Trivalent chromium (Cr(III)) and hexavalent chromium (Cr(VI)) are the two mainly stable oxidation states of Cr in aquatic environments, while the difference of their bioavailability and toxicity by dietary exposure has been rarely known in aquatic organisms. Using juvenile coral trout (Plectropomus leopardus), Cr(III) and Cr(VI) as model system, this study tested the hypothesis that the dietary Cr bioaccumulation and toxicity in fish were highly dependent on Cr speciation. The fish were chronically exposed to 200mgkg−1 of dietary Cr(III) and Cr(VI) for 8 weeks, and then the Cr bioaccumulation, morphologic change, and RNA-Seq in fish liver were determined. The results showed that dietary Cr(III) and Cr(VI) exposure significantly induced fish weight gain, while 1.17 folds and 1.26 folds increased in relation to Control group, respectively. Cr contents in liver was increased significantly in dietary Cr(VI) but not in Cr(III) groups. Both Cr treatment induced lipid deposition in liver tissue structure, moreover, pancreatic part was increased in dietary Cr(III) but its reduced in Cr(VI) exposure. RNA-Seq in fish liver were significantly different as well. Specifically, there were 138 differentially expressed genes (DEGs) in dietary Cr(III) group, including 76 up-regulated and 62 down-regulated, and these DEGs were mainly involved in lipid metabolism, while there were 175 DEGs in dietary Cr(VI) group, including 85 up-regulated and 90 down-regulated, and these DEGs were mainly involved in immune system. The qRT-PCR confirmed the RNA-seq data were reliable. Overall, these results supported our hypothesis that the chronic dietary Cr(III) and Cr(VI) exposure resulted in apparently different Cr bioaccumulation and toxicity in fish. Our findings here help us to fill in a big gap in our knowledge of speciation-specific Cr bioavailability and toxicity in aquatic organisms, which has been largely unclear previously.
Dietary Cr(III) increased lipid metabolism and dietary Cr(VI) activated immune system in liver of coral trout at transcription levels.
Comparative toxicity study of waterborne two booster biocides (CuPT and ZnPT) on embryonic flounder (Paralichthys olivaceus)
2022, Ecotoxicology and Environmental Safety
A new generation of booster biocides that include metal pyrithiones (PTs) such as copper pyrithione (CuPT) and zinc pyrithione (ZnPT) are being used as tributyltin alternatives. In the marine environment, ZnPT can easily transchelate Cu to form CuPT, and the environmental fate and persistence of these two metal pyrithiones are closely related. Although some data on the toxicity of biocides on marine fish are available, little is known about their toxicity and toxic pathway. We thus compared the toxic effects of CuPT and ZnPT on embryonic olive flounder (Paralichthys olivaceus) by investigating their adverse effects based on developmental morphogenesis and transcriptional variation. In our study, the toxic potency of CuPT was greater with respect to developmental malformation and mortality than ZnPT. Consistent with the developmental effects, the expression of genes related to tail fin malformation (including plod2, furin, and wnt3a) was higher in embryonic flounder exposed to CuPT than in those exposed to ZnPT. Genes related to muscle and nervous system development exhibited significant changes on differential gene expression profiles using RNA sequencing (cutoff value P< 0.05). Gene ontology analysis of embryos exposed to CuPT revealed affected cellular respiration and kidney development, whereas genes associated with cell development, nervous system development and heart development showed significant variation in embryonic flounder exposed to ZnPT. Overall, our study clarifies the common and unique developmental toxic effects of CuPT and ZnPT through transcriptomic analyses in embryonic flounder.
Sediment quality assessment combining chemical and biological (non)target analysis
2021, Aquatic Toxicology
Citation Excerpt :
Especially, cardiac formation was affected significantly in embryos exposed to SEY. After crude oil exposure, the main developmental dysfunction in zebrafish (D. rerio), pink salmon (O. gorbuscha), and olive flounder (P. olivaceus) was heart formation impairment (Incardona et al., 2004, 2005; Jung et al., 2017). In our previous study, it was also revealed that the cardiac impairment was highly related to crude oils exposure with high three- or four-ring PAH compositions (Jung et al., 2017).
Aquatic sediments act as a storage for diverse mixtures of organic and inorganic contaminants. Nevertheless, most evaluations of contaminated sediments have been limited to the assessment of concentrations of target compounds and lethal effects on some test species. To identify the organic contaminants causing sub-lethal effects of contaminated sediment, this study combined chemical and biological (non)target analysis involving comprehensive two-dimensional gas chromatography coupled with a time-of-flight Mass Spectrometer (GCxGC/ToF-MS) analysis, embryonic malformation and high-throughput sequencing (RNA-seq) analysis on developing flounder. Polycyclic aromatic hydrocarbons were more abundant in the sediment extract of Yeongil Bay (SEY), while Jinhae Bay (SEJ) was contaminated with a large amount of unidentified chemicals. The unidentified chemicals of SEJ included branched alkanes, oxygenated cycloalkanes, heterogeneous hydrocarbons, and other unknown compounds. Percentage of pericardial edema was the highest in embryonic flounder exposed to SEY. Consistent with the morphogenesis results, the expression level of genes related to heart formation including the nkx2.5 and robo1 was greater in embryonic flounder exposed to SEY. In the analyses of differential gene expression profiles (cutoff P < 0.05), by RNA-seq, embryos exposed to SEJ showed changes related to cell differentiation, cell part morphogenesis, neurogenesis, and neuron development. Genes related to neurogenesis and positive regulation of molecular functions variated significantly in embryos exposed to SEY. These results demonstrated the advantages of combining target and non-target analysis to accurately evaluate the major chemical groups causing sediment toxicity. Therefore, this work provided a useful approach to tracking and revealing the causes of toxic effects and identifying potential toxic mechanisms.
Phenotypic and transcriptomic consequences in zebrafish early-life stages following exposure to crude oil and chemical dispersant at sublethal concentrations
2021, Science of the Total Environment
Citation Excerpt :
Recent advancement in next-generation sequencing (NGS) technologies, like high-throughput transcriptome sequencing (RNA-Seq), facilitates identifying differentially expressed genes (DEGs) and significantly enriched pathways that will uncover the subcellular responses of fish in ELS following oil-derived hydrocarbons exposure (Chandhini and Rejish Kumar, 2019; Portnoy et al., 2020). Several studies have been recently published on exploring the changes in global gene expression that might elucidate the molecular initiating events (MIEs) preceding the observed phenotypic effects related to embryonic development exposed to oil-derived hydrocarbons (Jones et al., 2017; Jung et al., 2017; Sørhus et al., 2017; Xu et al., 2017a; Xu et al., 2017b; Greer et al., 2019). However, knowledge of the underlying mechanisms involved in the transcriptomic responses in developing fish following sublethal exposure to chemically dispersed crude oil at sublethal concentrations remains limited (Jones et al., 2017; Greer et al., 2019).
To further understand the underlying mechanisms involved in the developmental toxicity of crude oil and chemically dispersed crude oil on fish early-life stages (ELS), zebrafish (Danio rerio) embryos were exposed to GM-2 chemical dispersant (DISP), low-energy water-accommodated fractions (LEWAF), and chemically enhanced WAF (CEWAF) of Merey crude oil at sublethal concentrations for 120h. We employed the General Morphology Score (GMS) and General Teratogenic Score (GTS) systems in conjunction with high-throughput RNA-Seq analysis to evaluate the phenotypic and transcriptomic responses in zebrafish ELS. Results showed that ΣPAHs concentrations in LEWAF and CEWAF solutions were 507.63±80.95ng·L−1 and 4039.51±241.26ng·L−1, respectively. The GMS and GTS values indicated that CEWAF exposure caused more severe developmental delay and higher frequencies of teratogenic effects than LEWAF exposure. Moreover, no significant change in heart rate was observed in LEWAF treatment, while CEWAF exposure caused a significant reduction in heart rate. LEWAF and CEWAF exposure exhibited an overt change in eye area, with a reduction of 4.0% and 25.3% (relative to the control), respectively. Additionally, no obvious impact on phenotypic development was observed in zebrafish embryo-larvae following DISP exposure. Significant changes in gene expression were detected in LEWAF and CEWAF treatments, with a total of 957 and 2062 differentially expressed genes (DEGs), respectively, while DISP exposure altered only 91 DEGs. Functional enrichment analysis revealed that LEWAF and CEWAF exposure caused significant perturbations in the pathways associated with phototransduction, retinol metabolism, metabolism of xenobiotics by cytochrome P450, and immune response-related pathways. Our results provide more valid evidence to corroborate the previous suggestion that ocular impairment is an equal or possibly more sensitive biomarker than cardiotoxicity in fish ELS exposed to oil-derived PAHs. All these findings could gain further mechanistic insights into the effects of crude oil and chemical dispersant on fish ELS.
Is hull cleaning wastewater a potential source of developmental toxicity on coastal non-target organisms?
2020, Aquatic Toxicology
Chemical contaminants can be discharged by vessel hull cleaning processes, such as scraping, jet spraying, and painting, all of which produce readily transportable contaminants into the marine environment, where they are referred to as ‘hotspots’ of contamination in coastal areas. However, many countries have not yet established effective evaluation methods for disposal of waste mixtures or management guidelines for areas of hull cleaning. To define the toxic effects of wastewater from vessel hull cleaning in dry docks on resident non-target organisms, we investigated the chemical concentrations and developmental toxicity on embryonic flounder, which is an organism sensitive to chemical contamination. In this study, the dominant inorganic metal discharged was zinc when cleaning Ship A (300 tons) and copper for Ship B (5,000 tons). The wastewater from high-pressure water blasting (WHPB) of Ship A (300 tons) and Ship B (5,000 tons) produced a largely overlapping suite of developmental malformations including pericardial edema, spinal curvature, and tail fin defects. Forty-eight hours after exposure, the frequency percentage of malformation began to increase in embryos exposed to a 500-fold dilution of WHPB from Ships A and B. We performed transcriptome sequencing to characterize the toxicological developmental effects of WHPB exposure at the molecular level. The results of the analysis revealed significantly altered expression of genes associated with muscle cell differentiation, actin-mediated cell contraction, and nervous system development (cutoff P < 0.01) in embryonic flounder exposed to high-pressure cleaning effluent from Ship A. Genes associated with chromatin remodeling, cell cycling, and insulin receptor signaling pathways were significantly altered in embryonic flounder exposed to WHPB of Ship B (cutoff P < 0.01). These findings provide a greater understanding of the developmental toxicity and potential effects of WHPB effluent on coastal embryonic fish. Furthermore, our results could inform WHPB effluent management practices to reduce impacts on non-target coastal organisms.
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RNA-seq analysis of local tissue of Carassius auratus gibelio with pharyngeal myxobolosis: Insights into the pharyngeal mucosal immune response in a fish-parasite dialogue
Fish & Shellfish Immunology, Volume 94, 2019, pp. 99-112
The lack of practical control measures for pharyngeal myxobolosis is becoming an important limiting factor for the sustainable development of the gibel carp (Carassius auratus gibelio) culture industry in China. Myxobolus honghuensis has been identified as the causative agent of this pandemic disease, which exclusively infects the pharynx of gibel carp, a potential important mucosal lymphoid-associated tissue (MLAT). Myxozoa generally initiate invasion through the mucosal tissues of fish, where some of them also complete their sporogonial stages. However, the pharynx-associated immune responses of teleost against myxosporeans infection remain unknown. Here, a de novo transcriptome assembly of the pharynx of gibel carp naturally infected with M. honghuensis was performed for the first time, using RNA-seq. Comparative analysis of severely infected and mildly infected pharyngeal tissues (SI group and MI group) from the same fish individuals and control pharyngeal tissues (C group) from the uninfected fish was carried out to investigate the potential mucosal immune function of the fish pharynx, and characterize the panoramic picture of pharynx local mucosal immune responses of gibel carp against the M. honghuensis infection. A total of 242,341 unigenes were obtained and pairwise comparison resulted in 13,009 differentially-expressed genes (DEGs) in the SI/C group comparison, 6014 DEGs in the MI/C group comparison, and 9031 DEGs in the SI/MI group comparison. Comprehensive analysis showed that M. honghuensis infection elicited a significant parasite load-dependent alteration of the expression of numerous innate and adaptive immune-related genes in the local lesion tissue. Innate immune molecules, including mucins, toll-like receptors, C-type lectin, serum amyloid A, cathepsins and complement components were significantly up-regulated in the SI group compared with the C group. Up-regulation of genes involved in apoptosis signaling pathway and the IFN-mediated immune system were found in the SI group, suggesting these two pathways played a crucial role in innate immune response to M. honghuensis infection. Up-regulation of chemokines and chemokine receptors and the induction of the leukocyte trans-endothelial migration pathways in the severely and mildly infected pharynx suggested that many leucocytes were recruited to the local infected sites to mount a strong mucosal immune responses against the myxosporean infection. Up-regulation of CD3D, CD22, CD276, IL4/13A, GATA3, arginase 2, IgM, IgT and pIgR transcripts provided strong evidences for the presence of T/B cells and specific mucosal immune responses at local sites with M. honghuensis infection. Our results firstly demonstrated the mucosal function of the teleost pharynx and provided evidences of intensive local immune defense responses against this mucosa-infecting myxosporean in the gibel carp pharynx. Pharyngeal myxobolosis was shaped by a prevailing anti-inflammatory response pattern during the advanced infection stages. Further understanding of the functional roles of fish immune molecules involved in the initial invasion and/or final sporogony site may facilitate future development of control strategies for this myxobolosis.
Comparative transcriptome analysis reveals the gene expression profiling in bighead carp (Aristichthys nobilis) in response to acute nitrite toxicity
Fish & Shellfish Immunology, Volume 79, 2018, pp. 244-255
Nitrite exposure induces growth inhibition, metabolic disturbance, oxidative stress, organic damage, and infection-mediated mortality of aquatic organism. This study aimed to investigate the mechanism in responses to acute nitrite toxicity in bighead carp (Aristichthys nobilis, A. nobilis) by RNA-seq analysis.
Bighead carps were exposed to water with high nitrite content (48.63 mg/L) for 72 h, and fish livers and gills were separated for RNA-seq analysis. De novo assembly was performed, and differentially expressed genes (DEGs) between control and nitrite-exposed fishes were identified. Furthermore, enrichment analysis was performed for DEGs to annotate the molecular functions.
A total of 406,135 transcripts and 352,730 unigenes were tagged after de novo assembly. Accordingly, 4108 and 928 DEGs were respectively identified in gill and liver in responses to nitrite exposure. Most of these DEGs were up-regulated DEGs. Enrichment analysis showed these DEGs were mainly associated with immune responses and nitrogen metabolism.
We suggested that the nitrite toxicity-induced DEGs were probably related to dysregulation of nitrogen metabolism and immune responses in A. nobilis, particularly in gill.
RNA-Seq analysis of transcriptome responses in Atlantic cod (Gadus morhua) precision-cut liver slices exposed to benzo[a]pyrene and 17α-ethynylestradiol
Aquatic Toxicology, Volume 201, 2018, pp. 174-186
Polycyclic aromatic hydrocarbons such as benzo[a]pyrene (BaP) that activate the aryl hydrocarbon receptor (Ahr) pathway, and endocrine disruptors acting through the estrogen receptor pathway are among environmental pollutants of major concern. In this work, we exposed Atlantic cod (Gadus morhua) precision-cut liver slices (PCLS) to BaP (10 nM and 1000 nM), ethynylestradiol (EE2) (10 nM and 1000 nM), and equimolar mixtures of BaP and EE2 (10 nM and 1000 nM) for 48 h, and performed RNA-Seq based transcriptome mapping followed by systematic bioinformatics analyses. Our gene expression analysis showed that several genes were differentially expressed in response to BaP and EE2 treatments in PCLS. Strong up-regulation of genes coding for the cytochrome P450 1a (Cyp1a) enzyme and the Ahr repressor (Ahrrb) was observed in BaP treated PCLS. EE2 treatment of liver slices strongly up-regulated genes coding for precursors of vitellogenin (Vtg) and eggshell zona pellucida (Zp) proteins. As expected, pathway enrichment and network analysis showed that the Ahr and estrogen receptor pathways are among the top affected by BaP and EE2 treatments, respectively. Interestingly, two genes coding for fibroblast growth factor 3 (Fgf3) and fibroblast growth factor 4 (Fgf4) were up-regulated by EE2 in this study. To our knowledge, the fgf3 and fgf4 genes have not previously been described in relation to estrogen signaling in fish liver, and these results suggest the modulation of the FGF signaling pathway by estrogens in fish. The signature expression profiles of top differentially expressed genes in response to the single compound (BaP or EE2) treatment were generally maintained in the expression responses to the equimolar binary mixtures. However, in the mixture-treated groups, BaP appeared to have anti-estrogenic effects as observed by lower number of differentially expressed putative EE2 responsive genes. Our in-depth quantitative analysis of changes in liver transcriptome in response to BaP and EE2, using PCLS tissue culture provides further mechanistic insights into effects of the compounds. Moreover, the analyses demonstrate the usefulness of PCLS in cod for omics experiments.
RNA-Seq analysis of immune-relevant genes in Lateolabrax japonicus during Vibrio anguillarum infection
Fish & Shellfish Immunology, Volume 52, 2016, pp. 57-64
Lateolabrax japonicus is one of the main marine aquatic fish species, and is popularly cultured in East Asia due to its highly commercial value. In recent years, because of large-scale and intensive farming and seawater pollution, fish diseases keep breaking out. However, systematic study on L.japonicus immunogenetics is limited due to the deficiency of deep sequencing technologies and genome backgrounds. In this study, the widely analysis at the transcriptome level for L.japonicus that infected with Vibrio anguillarum was performed. In total, 334,388,688 high quality reads were obtained in six libraries (HK-VA, HK-PBS, LI-VA, LI-PBS, SP-VA and SP-PBS) and de novo assembled into 101,860 Unigenes with an average unigene length of 879 bp. Based on sequence similarity 30,142 unigenes (29.59%) were annotated in the public databases. Comparative analysis revealed, 1,202, 3034 and 3519 differentially expressed genes (DEGs) were identified in three comparisons (HK-PBS VS HK-VA, LI-PBS VS LI-VA and SP-PBS VS SP-VA). Enrichment and pathway analysis of the DEGs was also carried out to excavate the candidate genes related to immunity. In conclusion, this study identifies and evaluates dozen of potential immune related pathways and candidate genes, which are indispensable for padding genomic resources of L.japonicus, and would lay the foundation for further studying and illuminating the mechanism of host-pathogen interactions.
Identification of signal pathways for immunotoxicity in the spleen of common carp exposed to chlorpyrifos
Ecotoxicology and Environmental Safety, Volume 182, 2019, Article 109464
Chlorpyrifos (CPF) is an environmental pollutant due to its high toxicity to aquatic animals. Because CPF was detected in aquatic environments in many countries, it has been widely concerned by researchers. Although the immunotoxicity of CPF to fish had been reported, the immunotoxicity mechanism is still not clear. Recently, transcriptome analysis has become a major method to study the toxic mechanism of pollutants in environmental toxicology. However, the immunotoxicity identification of CPF on fish had not been reported by transcriptome analysis. In the present study, we examined the effects of CPF on organismal system in the spleen of common carp by transcriptome analysis. We have successfully constructed a database of transcriptome analysis of carp spleens under exposure to CPF and found 773 differentially expressed genes (DEGs) (including 498 up-regulated DEGs and 275 down-regulated DEGs) and 4 branches (containing 33 known KEGG pathways). Some genes associated with the 4 pathways (Complement and coagulation cascades, PPAR signaling pathway, Fat digestion and absorption, and Collecting duct acid secretion) contained in organismal system were validated by quantitative real-time PCR and showed significant improvement compared with the control group. Our results indicated that exposure to CPF caused a change in the signal pathways of organismal system in carp spleens. The present study provides new insights into the immunotoxicity mechanism and risk assessment of CPF, as well as references for comparative medicine.
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