Deep sequencing-based transcriptome profiling analysis of Oryzias melastigma exposed to PFOS

Long-term tralopyril exposure results in endocrinological and transgenerational toxicity: A two-generation study of marine medaka (Oryzias melastigma)

This study aims to investigate the impact of tralopyril, a newly developed marine antifouling agent, on the reproductive endocrine system and developmental toxicity of offspring in marine medaka. The results revealed that exposure to tralopyril (0, 1, 20 μg/L) for 42 days resulted in decreased reproductive capacity in marine medaka. Moreover, it disrupted the levels of sex hormones E2 and T, as well as the transcription levels of genes related to the HPG axis, such as cyp19b and star. Sex-dependent differences were observed, with females experiencing more pronounced effects. Furthermore, intergenerational toxicity was observed in F1 offspring, including increased heart rate, changes in retinal morphology and cartilage structure, decreased swimming activity, and downregulation of transcription levels of relevant genes (HPT axis, GH/IGF axis, cox, bmp4, bmp2, runx2, etc.). Notably, the disruption of the F1 endocrine system by tralopyril persisted into adulthood, indicating a transgenerational effect. Molecular docking analysis suggested that tralopyril's RA receptor activity might be one of the key factors contributing to the developmental toxicity observed in offspring. Overall, our study highlights the potential threat posed by tralopyril to the sustainability of fish populations, as it can disrupt the endocrine system and negatively impact aquatic organisms for multiple generations.

An integrated assessment of ecological and human health risks of per- and polyfluoroalkyl substances through toxicity prediction approaches

Per- and polyfluoroalkyl substances (PFAS) are also known as "forever chemicals" due to their persistence and ubiquitous environmental distribution. This review aims to summarize the global PFAS distribution in surface water and identify its ecological and human risks through integrated assessment. Moreover, it provides a holistic insight into the studies highlighting the human biomonitoring and toxicological screening of PFAS in freshwater and marine species using quantitative structure-activity relationship (QSAR) based models. Literature showed that PFOA and PFOS were the most prevalent chemicals found in surface water. The highest PFAS levels were reported in the US, China, and Australia. The TEST model showed relatively low LC50 of PFDA and PFOS for Pimephales promelas (0.36 and 0.91 mg/L) and high bioaccumulation factors (518 and 921), revealing an elevated associated toxicity. The risk quotients (RQs) values for P. promelas and Daphnia magna were found to be 269 and 23.7 for PFOS. Studies confirmed that long-chain PFAS such as PFOS and PFOA undergo bioaccumulation in aquatic organisms and induce toxicological effects such as oxidative stress, transgenerational epigenetic effects, disturbed genetic and enzymatic responses, perturbed immune system, hepatotoxicity, neurobehavioral toxicity, altered genetic and enzymatic responses, and metabolism abnormalities. Human biomonitoring studies found the highest PFOS, PFOA, and PFHxS levels in urine, cerebrospinal fluid, and serum samples. Further, long-chain PFOA and PFOS exposure create severe health implications such as hyperuricemia, reduced birth weight, and immunotoxicity in humans. Molecular docking analysis revealed that short-chain PFBS (-11.84 Kcal/mol) and long-chain PFUnDA (-10.53 Kcal/mol) displayed the strongest binding interactions with human serum albumin protein. Lastly, research challenges and future perspectives for PFAS toxicological implications were also discussed, which helps to mitigate associated pollution and ecological risks.

A new perspective on endocrine disrupting effects of triphenyltin on marine medaka: From brain transcriptome, gut content metabolome and behavior

Triphenyltin (TPT) is an endocrine contaminant that is often detected in the environment. However, the mechanism of the effects of TPT on biological systems is not fully understood. Here we exposed marine medaka (Oryzias melastigma) to TPT for 21 days. Brain transcriptome, intestinal content metabolism group, and behavior analysis were carried out. Through the comprehensive analysis of multiomics for the in-depth understanding of the ways related to health improvement, we determined that the glycine-serine-threonine metabolic axis was most perturbed by TPT. Through behavioral analysis, it was found that there was behavioral hyperactivity in the exposed group; behavioral hyperactivity may be caused by the interference of TPT with the neuroendocrine system. In order to gain a full understanding of the impacts of TPT on human health, transcriptomic screening of differential genes and an impartial attitude based on bioinformatics were used. Gene-disease interaction analysis using the Comparative Toxicogenomics Database (CTD) revealed the possible effects of TPT on human health. Finally, based on these findings, the relevant adverse outcome pathway (AOP), which is the "epigenetic modification of PPARG leading to adipogenesis," was identified from AOP Wiki. Further research is required to validate the potential AOP of TPT.

Next generation per- and poly-fluoroalkyl substances: Status and trends, aquatic toxicity, and risk assessment

Widespread application of poly- and per-fluoroalkyl substances (PFAS) has resulted in some substances being ubiquitous in environmental matrices. That and their resistance to degradation have allowed them to accumulate in wildlife and humans with potential for toxic effects. While specific substances of concern have been phased-out or banned, other PFAS that are emerging as alternative substances are still produced and are being released into the environment. This review focuses on describing three emerging, replacement PFAS: perfluoroethylcyclohexane sulphonate (PFECHS), 6:2 chlorinated polyfluoroalkyl ether sulfonate (6:2 Cl-PFAES), and hexafluoropropylene oxide dimer acid (HFPO-DA). By summarizing their physicochemical properties, environmental fate and transport, and toxic potencies in comparison to other PFAS compounds, this review offers insight into the viabilities of these chemicals as replacement substances. Using the chemical scoring and ranking assessment model, the relative hazards, uncertainties, and data gaps for each chemical were quantified and related to perfluorooctane sulfonic acid (PFOS) and perfluorooctanoic acid (PFOA) based on their chemical and uncertainty scores. The substances were ranked PFOS > 6:2 Cl-PFAES > PFOA > HFPO-DA > PFECHS according to their potential toxicity and PFECHS > HFPO-DA > 6:2 Cl-PFAES > PFOS > PFOA according to their need for future research. Since future uses of PFAS remain uncertain in the face of governmental regulations and production bans, replacement PFAS will continue to emerge on the world market and in the environment, raising concerns about their general lack of information on mechanisms and toxic potencies.

Size-dependent adverse effects of microplastics on intestinal microbiota and metabolic homeostasis in the marine medaka (Oryzias melastigma)

Microplastic (MP) is an emerging environmental pollutant and exposure to MPs has been associated with numerous adverse health outcomes in both wild and laboratory animals. The toxicity of MPs depends on concentration, exposure time, chemical composition and size distribution, but the impacts of particle size remain inconclusive yet. In this study, adult marine medaka (Oryzias melastigma) were exposed to different size of polystyrene MPs (PS-MPs) with concentration of 10 mg/L for 60 days and the growth performance, lipid metabolism, immune parameters and gut microbiome were determined. Results indicated that particle size is a dominant factor causing lipid metabolism disorders and hepatic toxicity in PS-MPs-exposed fish. The bodyweight, adipocyte size and hepatic lipid contents were significantly increased in 200 μm PS-MPs-exposed fish, while 2 and 10 μm PS-MPs-exposed fish exhibited liver injury principally manifested asthepresence oflittlefibrosis and inflammation. Given that larger particles could not enter the circulatory system, the impacts of PS-MPs on intestinal microbial biota homeostasis were further investigated. The results not only showed the characterization of gut microbial communities in Oryzias melastigma, but also indicated that microbial diversity and composition were altered in gut of fish exposed to PS-MPs, in particular 200 μm PS-MPs. The differentially abundant bacterial taxa in PS-MPs-exposed fish mainly belonged to the phylum Verrucomicrobia, Firmicutes and Fusobacteria. And furthermore, increased abundance of Verrucomicrobia and Firmicutes/Bacteroidetes ratio and decreased Fusobacteria were correlated with the increased bodyweight. Intestinal microbiome should play a critical role in regulating host lipid metabolism in fish exposed to lager size of PS-MPs.

Occurrence and toxicity of perfluoroalkyl acids along the estuarine and coastal regions under varied environmental factors

Due to the significant economic and ecological value, the increasing pollution threat to estuarine and coastal regions is of great concern. Perfluoroalkyl acids (PFAAs) are emerging pollutants which possess adverse ecological risk. In this review, we have compiled the data on the levels of PFAAs in environmental samples, mainly in estuarine and coastal zones. A worldwide map was generated to show the distribution of PFAAs. The experimental results have also been considered, which, together with those of environmental samples, has allowed us to infer about the factors that intervene in the behavior of PFAAs. The presence of PFAAs is determined primarily by the source of pollution. Salinity is as well shown as a significant condition, dependent too on the sampling environment. The analysis of PFAAs from environmental samples constitutes a fundamental tool for the surveillance of these pollutants, but the lack of homogeneity of protocols for sampling, as well as for the results presentation, limits the comparative capacity. Laboratory studies are also an essential tool in the analysis of particular aspects related to PFAAs, but many times the conditions tested are not environmentally significant. In this way, it would not be prudent to establish "paradigms" about the behavior of the PFAAs in certain areas or organisms, instead to suggest the points that can be considered fundamental for each issue addressed. The main variables that appear to intervene in estuarine and coastal regions are mainly the proximity to the source of pollution, salinity, pH, precipitation (rain) as well as types of PFAAs. All these can synergistically lead to different impacts on the ecosystem. Therefore, the particular risks of PFAAs in estuarine and coastal regions is a set of multiple variables, dependent on each sampling condition and according to the previously named parameters.

Assessing the Ecological Risks of Per- and Polyfluoroalkyl Substances: Current State-of-the Science and a Proposed Path Forward

Per- and poly-fluoroalkyl substances (PFAS) encompass a large, heterogenous group of chemicals of potential concern to human health and the environment. Based on information for a few relatively well-understood PFAS such as perfluorooctane sulfonate and perfluorooctanoate, there is ample basis to suspect that at least a subset can be considered persistent, bioaccumulative, and/or toxic. However, data suitable for determining risks in either prospective or retrospective assessments are lacking for the majority of PFAS. In August 2019, the Society of Environmental Toxicology and Chemistry sponsored a workshop that focused on the state-of-the-science supporting risk assessment of PFAS. The present review summarizes discussions concerning the ecotoxicology and ecological risks of PFAS. First, we summarize currently available information relevant to problem formulation/prioritization, exposure, and hazard/effects of PFAS in the context of regulatory and ecological risk assessment activities from around the world. We then describe critical gaps and uncertainties relative to ecological risk assessments for PFAS and propose approaches to address these needs. Recommendations include the development of more comprehensive monitoring programs to support exposure assessment, an emphasis on research to support the formulation of predictive models for bioaccumulation, and the development of in silico, in vitro, and in vivo methods to efficiently assess biological effects for potentially sensitive species/endpoints. Addressing needs associated with assessing the ecological risk of PFAS will require cross-disciplinary approaches that employ both conventional and new methods in an integrated, resource-effective manner. Environ Toxicol Chem 2021;40:564-605. © 2020 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC. This article has been contributed to by US Government employees and their work is in the public domain in the USA.

Transcriptomic analyses show that 24-epibrassinolide (EBR) promotes cold tolerance in cotton seedlings

In plants, brassinosteroids (BRs) are a class of steroidal hormones that are involved in numerous physiological responses. However, the function of BRs in cold tolerance in cotton has not been explored. In this study, cotton seedlings were treated with five concentrations (0, 0.05, 0.1, 0.2, 0.5 and 1.0 mg/L) of 24-Epibrassinolide (EBR) at 4°C. We measured the electrolyte leakage, malondialdehyde (MDA) content, proline content, and net photosynthesis rate (Pn) of the seedlings, which showed that EBR treatment increased cold tolerance in cotton in a dose-dependent manner, and that 0.2 mg/L is an optimum concentration for enhancing cold tolerance. The function of EBR in cotton cotyledons was investigated in the control 0 mg/L (Cold+water) and 0.2 mg/L (Cold+EBR) treatments using RNA-Seq. A total of 4,001 differentially expressed genes (DEGs), including 2,591 up-regulated genes and 1,409 down-regulated genes were identified. Gene Ontology (GO) and biochemical pathway enrichment analyses showed that EBR is involved in the genetic information process, secondary metabolism, and also inhibits abscisic acid (ABA) and ethylene (ETH) signal transduction. In this study, physiological experiments showed that EBR can increase cold tolerance in cotton seedlings, and the comprehensive RNA-seq data shed light on the mechanisms through which EBR increases cold tolerance in cotton seedlings.

Elevated bioaccumulation of PFAAs in Oryzias melastigma following the increase of salinity is associated with the up-regulated expression of PFAA-binding proteins

Perfluoroalkyl acids (PFAAs) are widely detected in the environment, especially in estuarine and coastal areas where fluctuation of salinity occurs. Salinity alteration affected the distribution of PFAAs and even the bioaccumulation in organisms. However, the inner mechanism is still unclear. In this study, the marine medaka (Oryzias melastigma), a euryhaline fish model, was exposed to four PFAAs congeners under three different salinities (0, 15 and 35 psu). Results showed that the bioaccumulation of PFAAs increased in fish as the water salinity increased. PFAAs with longer lengths of carbon‑fluorine bond showed higher bioaccumulation in the fish. Salinity did not alter the levels of PFAAs in water media, however, the uptake rate of PFAAs from gills did increase with the salinity. Further analysis of the mechanism showed that PFAA bound to branchial proteins as confirmed by fluorescence spectroscopy. Higher expressions of proteins binding to PFAAs including organic anion transporter 1 (OAT1) and fatty acid-binding protein (FABP) facilitated the uptake of PFAAs through gills in fish culturing under higher salinity. In all, our study showed that elevation of salinity can induce the expression of proteins binding to PFAAs in gills, thus facilitate the uptake of water PFAAs. Salinity fluctuation should be taken into consideration when assessing the chemical risk in the estuarine and coastal areas.

Transcriptome analysis of acute exposure of the Manila clam, Ruditapes philippinarum to perfluorooctane sulfonate (PFOS)

Perfluorooctane sulfonate (PFOS) is an increasingly important environmental pollutant, which has been detected almost everywhere in the environment. Despite the widespread presence of PFOS, much less notice is taken of its toxicology effects on marine bivalves. Thus, the transcriptome response to PFOS treatment (nominal concentration of 20 mg/L) in hepatopancreas of a sentinel organism, Ruditapes philippinarum was examined. Compared with the control group, 32,149 unigenes were up-regulated and 26,958 unigenes down-regulated. Notably, significant gene expression changes were found in carbohydrate metabolism, energy metabolism, amino acid metabolism, lipid metabolism and protein biosynthesis, indicating the metabolic disruptions caused by PFOS in R. philippinarum. Additionally, numerous other differentially expressed genes were involved in immune system, antioxidant defense system and detoxification metabolism. In summary, transcriptome profiling of R. philippinarum after exposure to PFOS provided molecular support for our current understanding of the detrimental toxicity of PFOS on marine bivalves.

Adverse effects of perfluoroalkyl acids on fish and other aquatic organisms: A review

Perfluoroalkyl acids (PFAAs) have been widely used in many industrial and consumer products. They have been detected ubiquitously in ambient water along with other environmental matrices, and their adverse effects on aquatic organisms have been a subject of active investigation. Here, we intended to summarize and synthesize the existing body of knowledge on PFAA toxicity through an extensive literature review, and shed light on areas where further research is warranted. PFAA toxicity appears to be influenced by the sex and developmental stages of aquatic organisms, but not significantly by exposure route. PFAA-induced aquatic toxicity could be classified as metabolism disturbance, reproduction disruption, oxidative stress, developmental toxicity, thyroid disruption, etc. At the molecular level, these responses can be initiated by key events, such as nuclear receptor activation, reactive oxygen species induction, or interaction with a membrane, followed by a cascade of downstream responses. PFAA-induced toxicity involves diverse metabolic processes, and therefore elucidating crosstalk or interactions among diverse metabolic pathways is a challenging task. In the presence of other chemicals, PFAAs can function as agonists or antagonists, resulting in different directions of combined toxicity. Therefore, mixture toxicity with other groups of chemicals is another research opportunity. Experimental evidence supports the trans-generational toxicity of PFAAs, suggesting that their long-term consequences for aquatic ecosystems should become of concern. A recent global ban of several PFAAs resulted in an increasing dependence on PFAA alternatives. The lack of sufficient toxicological information on this emerging group of chemicals warrant caution and rigorous toxicological assessments.

Transcriptomic Changes in Liver of Juvenile Cynoglossus semilaevis following Perfluorooctane Sulfonate Exposure

Perfluorooctane sulfonate (PFOS) is an increasingly important environmental pollutant that is pervasive in the environment. A number of studies have focused on the toxicological effects of PFOS on model fish species (zebrafish and medaka), but little is known about the impact of PFOS on commercially important marine fish. Thus, the present study examined transcriptome responses to PFOS exposure in the liver of juvenile Cynoglossus semilaevis, an important farmed flatfish in China. Then, in response to PFOS challenges, 1695 and 5244 genes were identified as significantly increased and depressed, respectively. Significant expression changes were observed in immune-related genes (cytokine-cytokine receptor interaction, T-helper [Th]17 cell differentiation, and the chemokine nuclear factor-kappa B and T-cell receptor signaling pathways), indicating that immunotoxicity is a key aspect of the effects of PFOS on C. semilaevis. Exposure to PFOS also altered the gene expression levels of hormones (inhibin, insulin, somatostatin, and glucagon), which could lead to severe metabolic and endocrine dysfunction. As expected from previous studies, several phase I and phase II detoxification enzymes were significantly up-regulated, which could facilitate the biotransformation and detoxification of PFOS in C. semilaevis. The present study provides new insights into the molecular toxicology of PFOS in a commercially important fish species. Environ Toxicol Chem 2020;39:556-564. © 2019 SETAC.

Sperm quality and oxidative stress in chub Squalius orientalis and Padanian barbel Barbus plebejus (Teleostei: Cyprinidae) after in vitro exposure to low doses of bisphenol A

In an aquatic environment, the presence of Bisphenol A (BPA) adversely affects reproduction, biology, behavior, gonads, and early larval development of fish due to being endocrine-disrupting compound. In addition, the detected concentration of BPA in water bodies is reported to be higher than 0.41 μg/L. As an alternative tool, sperm cells are used in toxicological assays for the reliable and practical assessment. For these reasons, we examined the effects of in vitro exposure of BPA on sperm quality of chub Squalius oriantalis and Padanian barbel Barbus plebejus. Spermatozoa were exposed to lower concentrations (0, 0.5, 1.25, 2.5, and 5 µg/L) of BPA for 2 h. The enzymatic activities [glutathione peroxidase (GSH-Px), catalase (CAT), and superoxide dismutase (SOD)] and lipid peroxidation (MDA) were evaluated in spermatozoa. The results demonstrated that BPA exposure significantly decreased activities of SOD and GSH-Px but increased CAT activity and lipid peroxidation (MDA). Compared to control, the percentage and duration of sperm motility significantly decreased. Overall, spermatozoa clearly showed the sensitivity to lower concentrations of BPA.

Digital gene expression analysis in the gills of Ruditapes philippinarum after nitrite exposure

Due to the overload of pollutants from highly intensive anthropic activities, nitrite accumulates in offshore seawater and has been a long-lasting pollutant to the healthy aquaculture of the mollusk. In the present study, Ruditapes philippinarum was used as the target bivalve to receive nitrite exposure at environmental concentration for 1 and 7 days. Differentially expressed genes (DEGs) were detected and analyzed by a digital gene expression (DGE) approach to describe the toxicity of nitrite on the bivalve at the gene level. In the N1 group, 185 DEGs were generated and enriched in six Gene Ontology (GO) terms, including oxidoreductase activity, heme binding, tetrapyrrole binding, iron ion binding, metal binding and cation binding. The DEGs in the N1 group were also enriched in two Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, e.g., arachidonic acid metabolism and ovarian steroidogenesis. In the N7 group, 81 DEGs were generated without any GO enrichment but were enriched in five KEGG pathways, including protein processing in the endoplasmic reticulum, protein export, prion diseases, thyroid hormone synthesis and arachidonic acid metabolism. This suggested that nitrite exposure might cause adverse effects to the clams in several aspects, including oxidative damage, depressed immunity, and disorders in cell proliferation, hormone metabolism and tissue regeneration. Evaluation of oxidative stress indicated that nitrite exposure actually induced redox state imbalance by enhancing the contents of thiobarbituric acid reactive substances (TBARSs) and glutathione (GSH), and the activity of glutathione peroxidase (GSH-PX) but not superoxide dismutase (SOD). These results will provide valuable gene references for further study on the toxicology mechanism of bivalves under environmental nitrite stress.

Blood Transcriptomics Analysis of Fish Exposed to Perfluoro Alkyls Substances: Assessment of a Non-Lethal Sampling Technique for Advancing Aquatic Toxicology Research

In contrast to mammals, the blood from other vertebrates such as fish contains nucleated red cells. Using a fathead minnow ( Pimephales promelas) oligonucleotide microarray, we compared altered transcripts in the liver and whole blood after exposure to environmentally relevant concentrations of perfluorooctanesulfonic acid (PFOS) and a mixture of seven types of perfluoro alkyl substances (PFAS), including perfluorooctanoic acid (PFOA). We used quantitative polymerase chain reactions and cell-based assays to confirm the main effects and found that blood responded with a greater number of altered genes than the liver. The exposure to PFAS altered similar genes with central roles in a cellular pathway in both tissues, including estrogen receptor α and peroxisome proliferator activator β and γ, indicating that the genes previously associated with PFAS exposure are differentially expressed in blood and liver. The altered transcripts are involved with cholesterol metabolism and mitochondrial function. Our data confirmed that PFAS are weak xenoestrogens and exert effects on DNA integrity. Gene expression profiling from blood samples not related with the immune system, including very-low-density lipoprotein, vitellogenin, estrogen receptor, and thyroid hormone receptor, demonstrated that blood is a useful tissue for assessing endocrine disruption in non-mammalian vertebrates. We conclude that the use of blood for non-lethal sampling in genomics studies is informative and particularly useful for assessing the effects of pollution in endangered species. Further, using blood will reduce animal use and widen the experimental design options for studying the effects of contaminant exposure on wildlife.

Detoxification and Immune Transcriptomic Response of the Gill Tissue of Bay Scallop (Argopecten irradians) Following Exposure to the Algicide Palmitoleic Acid

Palmitoleic acid (PA) is an effective algicide against Alexandrium tamarense. However, the toxicological mechanism of PA exposure is unclear. The transcript abundance and differentially expressed genes (DEGs) in gills of bay scallop were investigated following 80 mg/L PA exposure up to 48 h using the Illumina HiSeq 4000 deep-sequencing platform with the recommended read length of 100 bp. De novo assembly of paired-end reads yielded 62,099 unigenes; 5414 genes were identified as being significantly increased, and 4452 were decreased. Based on gene ontology classification and enrichment analysis, the ‘cellular process’, ‘metabolic process’, ‘response to stimulus’, and ‘catalytic process’ with particularly high functional enrichment were revealed. The DEGs, which are related to detoxification and immune responses, revealed that acid phosphatase, fibrinogen C domain-containing protein, cyclic AMP-responsive element-binding protein, glutathione reductase, ATP-binding cassette, nuclear factor erythroid 2-related factor, NADPH2:quinone reductase, and cytochrome P450 4F22, 4B1, and 2C8-related gene expression decreased. In contrast, some genes related to glutathione S-transferase, C-type lectin, superoxide dismutase, toll-like receptors, and cytochrome P450 2C14, 2U1, 3A24 and 4A2 increased. The results of current research will be a valuable resource for the investigation of gene expression stimulated by PA, and will help understanding of the molecular mechanisms underlying the scallops’ response to PA exposure.

New insights into the metabolism and toxicity of bisphenol A on marine fish under long-term exposure

Bisphenol A (BPA) exposure receives great ecotoxicological concern. However, gaps in knowledge, such as metabolism of BPA and inconsistent reports on reproductive toxicity, still exist. In this study, a marine fish model (Oryzias melastigma) was exposed to serial concentrations of BPA throughout its whole life cycle. The level of BPA-glucuronide (BPAG) dramatically increased throughout the embryonic stage since 4 dpf. Accordingly, the mRNA level and enzymatic activity of UDP-glucuronosyltransferases (UGTs) increased across the embryonic stage. The mRNA level of UGT2 subtype rather than UGT1 or UGT5 showed a concentration dependent response to BPA exposure. BPA exposure led to the morphological disruption of the chorion and villi as shown by scanning electron microscopy; however, the hatchability was not significantly influenced after exposure. Newly hatching larvae were continuously exposed to BPA for 120 days. Lower mRNA levels of hormone metabolism-related genes, decreased ratio of E2/T, slower ovary development and decreased egg production confirmed the inhibitory effect of BPA on reproduction. Overall, our results showed the conjugation of BPA into BPAG by UGT2 at the embryonic stage and convinced the reproductive toxicity from multiple levels after whole life exposure to BPA.

Characterization of transcriptional responses mediated by benzo[a]pyrene stress in a new marine fish model of goby, Mugilogobius chulae

Benzo[a]pyrene (BaP) is one of the most studied targets among polycyclic aromatic hydrocarbons (PAHs). Because of the complexity of the toxicity mechanism in BaP, little is known about the molecular mechanism at the level of transcription of BaP in marine fishes. The primary objective of this study was to investigate the molecular basis of the effects of BaP on marine fish, using Mugilogobius chulae (Smith 1932) as the model. A closed colony of M. chulae was used for the BaP toxicity test. Two fish liver samples per replicate from each group were excised and blended into one sample by pooling an equal amount of liver tissue. Total RNA of all samples was extracted separately. Equal quantities of total RNA from the three replicates of the two groups were pooled for sequencing. The sequencing cDNA libraries were sequenced using Illumina HiSeq 2000 system. Differentially expressed genes were detected with the DEGSeq R package. In total, 52,364,032 and 53,771,748 clean nucleotide reads were obtained in the control and BaP-exposed libraries, respectively, with N50 lengths of 1277 and 1288 bp, respectively. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed a significant enrichment of genes related to detoxification, transportation, and lipid metabolism. We also identified, for the first time, an association between endoplasmic reticulum dysfunction and lipid metabolism resulting from BaP exposure. Using quantitative real-time PCR, some effective molecular biomarkers for monitoring of BaP-polluted seawater were identified. The results demonstrate that BaP enhanced the expression of genes involved in detoxification in M. chulae and inhibited that of genes related to lipid metabolism, possibly by suppressing the expression of numerous ER-related genes involved in fat digestion and absorption.

Development and Characterization of High-Throughput EST-Based SSR Markers for Pogostemon cablin Using Transcriptome Sequencing

Simple sequence repeats (SSRs) or microsatellite markers derived from expressed sequence tags (ESTs) are routinely used for molecular assisted-selection breeding, comparative genomic analysis, and genetic diversity studies. In this study, we investigated 54,546 ESTs for the identification and development of SSR markers in Pogostemon cablin (Patchouli). In total, 1219 SSRs were identified from 1144 SSR-containing ESTs. Trinucleotides (80.8%) were the most abundant SSRs, followed by di- (10.8%), mono- (7.1%), and hexa-nucleotides (1.3%). The top six motifs were CCG/CGG (15.3%), AAG/CTT (15.0%), ACC/GGT (13.5%), AGG/CCT (12.4%), ATC/ATG (9.9%), and AG/CT (9.8%). On the basis of these SSR-containing ESTs, a total of 192 primer pairs were randomly designed and used for polymorphism analysis in 38 accessions collected from different geographical regions of Guangdong, China. Of the SSR markers, 45 were polymorphic and had allele variations from two to four. Furthermore, a transferability analysis of these primer pairs revealed a 10⁻40% cross-species transferability in 10 related species. This report is the first comprehensive study on the development and analysis of a large set of SSR markers in P. cablin. These markers have the potential to be used in quantitative trait loci mapping, genetic diversity studies, and the fingerprinting of cultivars of P. cablin.

Detoxification- and Immune-Related Transcriptomic Analysis of Gills from Bay Scallops (Argopectenirradians) in Response to Algal Toxin Okadaic Acid

To reveal the molecular mechanisms triggered by okadaic acid (OA)-exposure in the detoxification and immune system of bay scallops, we studied differentially-expressed genes (DEGs) and the transcriptomic profile in bay scallop gill tissue after 48 h exposure to 500 nM of OA using the Illumina HiSeq 4000 deep-sequencing platform. De novo assembly of paired-end reads yielded 55,876 unigenes, of which 3204 and 2620 genes were found to be significantly up- or down-regulated, respectively. Gene ontology classification and enrichment analysis of the DEGs detected in bay scallops exposed to OA revealed four ontologies with particularly high functional enrichment, which were ‘cellular process’ (cellular component), ‘metabolic process’ (biological process), ‘immune system process’ (biological process), and ‘catalytic process’ (molecular function). The DEGs revealed that cyclic AMP-responsive element-binding proteins, acid phosphatase, toll-like receptors, nuclear erythroid 2-related factor, and the NADPH2 quinone reductase-related gene were upregulated. In contrast, the expression of some genes related to glutathione S-transferase 1, C-type lectin, complement C1q tumor necrosis factor-related protein, Superoxide dismutase 2 and fibrinogen C domain-containing protein, decreased. The outcomes of this study will be a valuable resource for the study of gene expression induced by marine toxins, and will help understanding of the molecular mechanisms underlying the scallops’ response to OA exposure.

Differential gene expression revealed with RNA-Seq and parallel genotype selection of the ornithine decarboxylase gene in fish inhabiting polluted areas

How organisms adapt to unfavorable environmental conditions by means of plasticity or selection of favorable genetic variants is a central issue in evolutionary biology. In the Maipo River basin, the fish Basilichthys microlepidotus inhabits polluted and non-polluted areas. Previous studies have suggested that directional selection drives genomic divergence between these areas in 4% of Amplified Fragment Length Polymorphism (AFLP) loci, but the underlying genes and functions remain unknown. We hypothesized that B. microlepidotus in this basin has plastic and/or genetic responses to these conditions. Using RNA-Seq, we identified differentially expressed genes in individuals from two polluted sites compared with fish inhabiting non-polluted sites. In one polluted site, the main upregulated genes were related to cellular proliferation as well as suppression and progression of tumors, while biological processes and molecular functions involved in apoptotic processes were overrepresented in the upregulated genes of the second polluted site. The ornithine decarboxylase gene (related to tumor promotion and progression), which was overexpressed in both polluted sites, was sequenced, and a parallel pattern of a heterozygote deficiency and increase of the same homozygote genotype in both polluted sites compared with fish inhabiting the non-polluted sites was detected. These results suggest the occurrence of both a plastic response in gene expression and an interplay between phenotypic change and genotypic selection in the face of anthropogenic pollution.

The genome of the marine medaka Oryzias melastigma

Marine medaka (Oryzias melastigma) is considered to be a useful fish model for marine and estuarine ecotoxicology studies and has good potential for field-based population genomics because of its geographical distribution in Asian estuarine and coastal areas. In this study, we present the first whole-genome draft of O. melastigma. The genome assembly consists of 8,602 scaffolds (N50 = 23.737 Mb) and a total genome length of 779.4 Mb. A total of 23,528 genes were predicted, and 12,670 gene families shared with three teleost species (Japanese medaka, mangrove killifish and zebrafish) were identified. Genome analyses revealed that the O. melastigma genome is highly heterozygous and contains a large number of repeat sequences. This assembly represents a useful genomic resource for fish scientists.

Hepatic transcriptome analysis of juvenile GIFT tilapia (Oreochromis niloticus), fed diets supplemented with different concentrations of resveratrol

The GIFT (Genetically Improved Farmed Tilapia) tilapia, Oreochromis niloticus, is cultured widely for the production of freshwater fish in China. Streptococcosis, which is related to pathogenic infections, occurs frequently in juvenile and adult female GIFT individuals. Resveratrol (RES) has been used in feed to control these infections in freshwater tilapia. To address the effects of RES on tilapia, we used high-throughput RNA sequencing technology (RNA-Seq, HiSeq. 2500) to explore the global transcriptomic response and specific involvement of hepatic mRNA of juvenile O. niloticus fed with diets containing different concentrations of (0, 0.025, 0.05, and 0.1g/kg) RES. A total of > 24,513,018 clean reads were generated and then assembled into 23,244 unigenes. The unigenes were annotated by comparing them against non-redundant protein sequence (Nr), non-redundant nucleotide (Nt), Swiss-Prot, Pfam, Gene Ontology database (GO), Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, and 12,578 unigenes were annotated to the GO database. A total of 1444 (0.025g/kg RES), 1526 (0.05g/kg RES), and 3135 (0.1g/kg RES) genes were detected as significant differentially expressed genes (DEGs), when compared with the controls. A total of 6 (0.025 vs 0.05g/kg RES), 19 (0.025 vs 0.1g/kg RES), and 124 (0.05 vs 0.1g/kg RES) genes were detected as significant DEGs. Six genes, including dnah7x1, sox4, fam46a, hsp90a, ddit4, and nmrk2, were associated with an immune response. These findings provide information on the innate immunity of GIFT and might contribute to the development of strategies for the effective management of diseases and long-term sustainability of O. niloticus culture.

Digital gene expression analysis in the gills of Ruditapes philippinarum exposed to short- and long-term exposures of ammonia nitrogen

Previous study revealed severe toxic effects of ammonia nitrogen on Ruditapes philippinarum including lysosomal instability, disturbed metabolic profiles, gill tissues with damaged structure, and variation of neurotransmitter concentrations. However, the underlying molecular mechanism was not fully understood yet. In the present study, digital gene expression technology (DGE) was applied to globally screen the key genes and pathways involved in the responses to short- and long-term exposures of ammonia nitrogen. Results of DGE analysis indicated that short-term duration of ammonia exposure affected pathways in Dorso-ventral axis formation, Notch signaling, thyroid hormone signaling and protein processing in endoplasmic reticulum. The long-term exposure led to DEGs significantly enriched in gap junction, immunity, signal and hormone transduction, as well as key substance metabolism pathways. Functional research of significantly changed DEGs suggested that the immunity of R. philippinarum was weakened heavily by toxic effects of ammonia nitrogen, as well as neuro-transduction and metabolism of important substances. Taken together, the present study provides a molecular support for the previous results of the detrimental toxicity of ammonia exposure in R. philippinarum, further work will be performed to investigate the specific genes and their certain functions involved in ammonia toxicity to molluscs.

Toxic Effects and Molecular Mechanism of Different Types of Silver Nanoparticles to the Aquatic Crustacean Daphnia magna

Silver nanoparticles (AgNPs) have been assessed to have a high exposure risk for humans and aquatic organisms. Toxicity varies considerably between different types of AgNPs. This study aimed to investigate the toxic effects of AgNPs with different particle sizes (40 and 110 nm) and different surface coatings (sodium citrate and polyvinylpyrrolidone, PVP) on Daphnia magna and their mechanisms of action. The results revealed that the citrate-coated AgNPs were more toxic than PVP-coated AgNPs and that the 40 nm AgNPs were more toxic than the 110 nm AgNPs. Transcriptome analysis further revealed that the toxic effects of AgNPs on D. magna were related to the mechanisms of ion binding and several metabolic pathways, such as the "RNA polymerase" pathway and the "protein digestion and absorption" pathway. Moreover, the principal component analysis (PAC) results found that surface coating was the major factor that determines the toxicities compared to particle size. These results could help us better understand the possible mechanism of AgNP toxicity in aquatic invertebrates at the transcriptome level and establish an important foundation for revealing the broad impacts of nanoparticles on aquatic environments.

Transcriptomic analysis of the differentiating ovary of the protogynous ricefield eel Monopterus albus

BACKGROUND

The ricefield eel is a protogynous hermaphroditic Synbranchiform species that changes sex naturally from female to male, which offers an interesting model for studying gonadal (particularly ovarian) differentiation in vertebrates. In the present study, transcriptome sequencing of the gonad of ricefield eel larvae was performed to explore the molecular mechanisms underlying the ovarian differentiation and development.

RESULTS

A total of 301,267,988 clean reads were generated from cDNA libraries of gonadal tissues of ricefield eel larvae at 6, 9, 12, and 20 days post hatching (dph), which contained undifferentiated gonads, differentiating ovaries, ovaries with oogonia, and ovaries with meiotic oocytes, respectively. De-novo assembly of all the clean reads generated a total of 265,896 unigenes with a mean size of 720 bp and a N50 of 1107 bp. RT-qPCR analysis of the developmental expression of 13 gonadal development-related functional genes indicated that RNA-seq data are reliable. Transcriptome data suggest that high expression of female development-related genes and low expression of male development-related genes in the early gonads of ricefield eel larvae participate in the cascade of sex differentiation leading to the final female phenotype. The contrasting expression patterns of genes involved in retinoid acid (RA) synthesis and degradation might result in peak production of RA at 12 dph in the gonad of ricefield eel larvae, and induce molecular events responsible for the initiation of meiosis before the meiotic signs could be observed at 20 dph. In addition, only stra6 but not stra8 could be identified in gonadal transcriptome data of ricefield eel larvae, and the expression pattern of stra6 paralleled those of genes involved in RA synthesis, suggesting that stra6 may be a downstream target of RA and play a role in RA metabolism and/or meiotic initiation in the gonad of ricefield eel larvae.

CONCLUSIONS

The present study depicted the first large-scale RNA sequencing of the gonad of ricefield eel larvae, and identified many important functional genes, GO terms and KEGG pathways involved in gonadal development and germ cell meiosis. Results of the present study will facilitate future study on the ovarian differentiation of ricefield eels and other teleosts as well.

Organ-specific effects of low-dose zinc pre-exposure on high-dose zinc induced mitochondrial dysfunction in large yellow croaker Pseudosciaena crocea

The study was carried out to evaluate the effects of low-dose zinc (Zn) pre-exposure on survival rate, new Zn accumulation, and mitochondrial bioenergetics in the liver and spleen of large yellow croaker exposed to high-dose Zn. To the end, fish were pre-exposed to 0 and 2 mg L^-1 Zn for 48 h and post-exposed to 0 and 12 mg L^-1 Zn for 48 h. Twelve milligrams Zn per liter exposure alone reduced survival rate, but the effect did not appear in the 2 mg L^-1 Zn pre-exposure groups. Two milligrams per liter Zn pre-exposure also ameliorated 12 mg Zn L^-1 induced new Zn accumulation, reactive oxygen species (ROS) levels, and mitochondrial swelling in the liver. However, these effects did not appear in the spleen. In the liver, 2 mg L^-1 Zn pre-exposure apparently relieved 12 mg L^-1 Zn induced down-regulation of activities of ATP synthase (F-ATPase), succinate dehydrogenase (SDH), and malate dehydrogenase (MDH). The mRNA levels of these genes remained relatively stable in fish exposed to 12 mg L^-1 Zn alone, but increased in fish exposed to 12 mg L^-1 Zn with 2 mg L^-1 Zn pre-treatment. In the spleen, 2 mg Zn L^-1 pre-exposure did not mitigate the down-regulation of mRNA levels of genes and activities of relative enzymes induced by 12 mg L^-1 Zn. In conclusion, our study demonstrated low-dose zinc pre-exposure ameliorated high-dose zinc induced mitochondrial dysfunction in the liver but not in the spleen of large yellow croaker, indicating an organ-specific effect.

Gene Expression Profiling in Fish Toxicology: A Review

In this review, we present an overview of transcriptomic responses to chemical exposures in a variety of fish species. We have discussed the use of several molecular approaches such as northern blotting, differential display reverse transcription-polymerase chain reaction (DDRT-PCR), suppression subtractive hybridization (SSH), real time quantitative PCR (RT-qPCR), microarrays, and next-generation sequencing (NGS) for measuring gene expression. These techniques have been mainly used to measure the toxic effects of single compounds or simple mixtures in laboratory conditions. In addition, only few studies have been conducted to examine the biological significance of differentially expressed gene sets following chemical exposure. Therefore, future studies should focus more under field conditions using a multidisciplinary approach (genomics, proteomics and metabolomics) to understand the synergetic effects of multiple environmental stressors and to determine the functional significance of differentially expressed genes. Nevertheless, recent developments in NGS technologies and decreasing costs of sequencing holds the promise to uncover the complexity of anthropogenic impacts and biological effects in wild fish populations.

De novo characterization of the liver transcriptome of javelin goby Synechogobius hasta and analysis of its transcriptomic profile following waterborne copper exposure

Previous studies have investigated the physiological responses to chronic copper (Cu) exposure in the liver of Synechogobius hasta; however, little information is available on the underlying molecular mechanisms. In an effort to better understand the mechanisms of Cu toxicity and to illuminate global gene expression patterns modulated by Cu exposure, we obtained the liver transcriptome information of S. hasta by RNA sequencing (RNA-seq) technology and also investigated the differential expression of genes following waterborne Cu exposure. Using the Illumina sequencing platform, as many as 60,217 unigenes were generated, with 815 bp of average length and 1298 bp of unigene N50 after filtering and assembly. For functional annotation analysis, 34,860, 31,526, 31,576, 25,808, 11,542, and 21,721 unigenes were annotated to the NR, NT, Swiss-Prot, KEGG, COG, and GO databases, respectively, and total annotation unigenes were 37,764. After 30 days of exposure to 55 μg Cu/l, a total of 292 and 1076 genes were significantly up- and down-regulated, respectively. By KEGG analysis, 660 had a specific pathway annotation. Subsequent bioinformatics analysis revealed that the differentially expressed genes were mainly related to lipid metabolism, immune system, apoptosis, and signal transduction, suggesting that these signaling pathways may be regulated by Cu exposure. The present study provides comprehensive sequence information for subsequent gene expression studies regarding S. hasta, and the transcriptome profiling after Cu exposure is also expected to improve our understanding of the molecular toxicology of Cu.

Transcriptomic response to water accommodated fraction of crude oil exposure in the gill of Japanese flounder, Paralichthys olivaceus

Illumina-based RNA-seq was used to determine the short-term transcriptomic responses of Paralichthys olivaceus gill to an environmentally relevant level of water accommodated fraction (WAF) of crude oil. 213,979 transcripts and 128,482 unigenes were obtained. Differential expression analysis revealed that 1641 and 2142 genes were significantly up- and down-regulated. Enrichment analysis identified a set of GO terms and putative pathways involved in the response of P. olivaceus to WAF exposure. Analysis of the transcripts revealed the effective protective mechanisms of P. olivaceus to reduce the toxic effects of WAF. Moreover, WAF exposure induced the metabolism of energy substrates, and downstream pathway genes were modified to provide protection against toxic damage. Transcripts analysis demonstrated that the genes involved in circadian rhythm signaling were regulated in gills of P. olivaceus exposed to WAF. These results provide insights into the mechanisms of WAF-induced toxicity in fishes and into the WAF-sensitive biomarkers in P. olivaceus.

Identification of Immune-Related Genes and Development of SSR/SNP Markers from the Spleen Transcriptome of Schizothorax prenanti

Schizothorax prenanti (S. prenanti) is mainly distributed in the upstream regions of the Yangtze River and its tributaries in China. This species is indigenous and commercially important. However, in recent years, wild populations and aquacultures have faced the serious challenges of germplasm variation loss and an increased susceptibility to a range of pathogens. Currently, the genetics and immune mechanisms of S. prenanti are unknown, partly due to a lack of genome and transcriptome information. Here, we sought to identify genes related to immune functions and to identify molecular markers to study the function of these genes and for trait mapping. To this end, the transcriptome from spleen tissues of S. prenanti was analyzed and sequenced. Using paired-end reads from the Illumina Hiseq2500 platform, 48,517 transcripts were isolated from the spleen transcriptome. These transcripts could be clustered into 37,785 unigenes with an N50 length of 2,539 bp. The majority of the unigenes (35,653, 94.4%) were successfully annotated using non-redundant nucleotide sequence analysis (nt), and the non-redundant protein (nr), Swiss-Prot, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. KEGG pathway assignment identified more than 500 immune-related genes. Furthermore, 7,545 putative simple sequence repeats (SSRs), 857,535 single nucleotide polymorphisms (SNPs), and 53,481 insertion/deletion (InDels) were detected from the transcriptome. This is the first reported high-throughput transcriptome analysis of S. prenanti, and it provides valuable genetic resources for the investigation of immune mechanisms, conservation of germplasm, and molecular marker-assisted breeding of S. prenanti.

Molecular impacts of perfluorinated chemicals (PFASs) in the liver and testis of male largemouth bass (Micropterus salmoides) in Minnesota Lakes

Perfluorinated chemicals (PFASs) stem from a wide range of sources and have been detected in aquatic ecosystems worldwide, including the upper Midwest and the state of Minnesota in the USA. This study investigated whether fish with high body burden levels of PFASs in the Twin Cities Metro Areas showed any evidence of adverse effects at the level of the transcriptome. We hypothesized that fish with higher body burden levels of PFASs would exhibit molecular responses in the liver and testis that were suggestive of oxidative and general stress, as well as impaired reproduction. Concentrations of PFASs in largemouth bass varied significantly across the sampled lakes, with the lowest concentrations of PFASs found in fish from Steiger and Upper Prior Lakes and the highest concentrations found in fish from Calhoun and Twin Lakes. Largemouth bass with high PFAS concentrations exhibited changes in the expression of genes related to lipid metabolism, energy production, RNA processing, protein production/degradation and contaminant detoxification, all of which are consistent with biomarker responses observed in other studies with PFASs. However, given the wide range of genes that were differentially expressed across the lakes and the variability observed in the mechanisms through which biological processes were affected, it is unlikely that PFASs are the only stressors affecting largemouth bass in the Twin Cities Metro Areas lakes. Indeed, Twin Lake is affected by the Joslyn superfund site which contains polycyclic aromatic hydrocarbons, pentachlorophenol, polychlorinated biphenyls, and dioxins. These compounds are also expected to drive the transcriptomics responses observed, but to what degree is difficult to ascertain at this time.

Omics of the marine medaka (Oryzias melastigma) and its relevance to marine environmental research

In recent years, the marine medaka (Oryzias melastigma), also known as the Indian medaka or brackish medaka, has been recognized as a model fish species for ecotoxicology and environmental research in the Asian region. O. melastigma has several promising features for research, which include a short generation period (3-4 months), daily spawning, small size (3-4 cm), transparent embryos, sexual dimorphism, and ease of mass culture in the laboratory. There have been extensive transcriptome and genome studies on the marine medaka in the past decade. Such omics data can be useful in understanding the signal transduction pathways of small teleosts in response to environmental stressors. An omics-integrated approach in the study of the marine medaka is important for strengthening its role as a small fish model for marine environmental studies. In this review, we present current omics information about the marine medaka and discuss its potential applications in the study of various molecular pathways that can be targets of marine environmental stressors, such as chemical pollutants. We believe that this review will encourage the use of this small fish as a model species in marine environmental research.

Co-transcriptomic Analysis by RNA Sequencing to Simultaneously Measure Regulated Gene Expression in Host and Bacterial Pathogen

Intramacrophage pathogens subvert antimicrobial defence pathways using various mechanisms, including the targeting of host TLR-mediated transcriptional responses. Conversely, TLR-inducible host defence mechanisms subject intramacrophage pathogens to stress, thus altering pathogen gene expression programs. Important biological insights can thus be gained through the analysis of gene expression changes in both the host and the pathogen during an infection. Traditionally, research methods have involved the use of qPCR, microarrays and/or RNA sequencing to identify transcriptional changes in either the host or the pathogen. Here we describe the application of RNA sequencing using samples obtained from in vitro infection assays to simultaneously quantify both host and bacterial pathogen gene expression changes, as well as general approaches that can be undertaken to interpret the RNA sequencing data that is generated. These methods can be used to provide insights into host TLR-regulated transcriptional responses to microbial challenge, as well as pathogen subversion mechanisms against such responses.

Transciptomic and histological analysis of hepatopancreas, muscle and gill tissues of oriental river prawn (Macrobrachium nipponense) in response to chronic hypoxia

Background

Oriental river prawn, Macrobrachium nipponense, is a commercially important species found in brackish and fresh waters throughout China. Chronic hypoxia is a major physiological challenge for prawns in culture, and the hepatopancreas, muscle and gill tissues play important roles in adaptive processes. However, the effects of dissolved oxygen availability on gene expression and physiological functions of those tissues of prawns are unknown. Adaptation to hypoxia is a complex process, to help us understand stress-sensing mechanism and ultimately permit selection for hypoxia- tolerant prawns, we performed transcriptomic analysis of juvenile M. nipponense hepatopancreas, gill and muscle tissues by RNA-Seq.

Results

Approximately 46,472,741; 52,773,612 and 58,195,908 raw sequence reads were generated from hepatopancreas, muscle and gill tissues, respectively. A total of 62,722 unigenes were generated, of the assembled unigenes, we identified 8,892 genes that were significantly up-regulated, while 5,760 genes were significantly down-regulated in response to chronic hypoxia. Genes from well known functional categories and signaling pathways associated with stress responses and adaptation to extreme environments were significantly enriched, including genes in the functional categories “response to stimulus”, “transferase activity” and “oxidoreductase activity”, and the signaling pathways “oxidative phosphorylation”, “glycolysis/gluconeogenesis” and “MAPK signaling”. The expression patterns of 18 DEGs involved in hypoxic regulation of M. nipponense were validated by quantitative real-time reverse-transcriptase polymerase chain reactions (qRT-PCR; average correlation coefficient = 0.94). In addition, the hepatopancreas and gills exhibited histological differences between hypoxia and normoxia groups. These structural alterations could affect the vital physiological functions of prawns in response to chronic hypoxia, which could adversely affect growth and survival of M. nipponense.

Conclusions

Gene expression changes in tissues from the oriental river prawn provide a preliminary basis to better understand the molecular responses of M. nipponense to chronic hypoxia. The differentially expressed genes (DEGs) identified in M. nipponense under hypoxia stress may be important for future genetic improvement of cultivated prawns or other crustaceans through transgenic approaches aimed at increasing hypoxia tolerance.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1701-3) contains supplementary material, which is available to authorized users.

The co-transcriptome of uropathogenic Escherichia coli-infected mouse macrophages reveals new insights into host-pathogen interactions

Urinary tract infections (UTI) are among the most common infections in humans. Uropathogenic Escherichia coli (UPEC) can invade and replicate within bladder epithelial cells, and some UPEC strains can also survive within macrophages. To understand the UPEC transcriptional programme associated with intramacrophage survival, we performed host–pathogen co‐transcriptome analyses using RNA sequencing. Mouse bone marrow‐derived macrophages (BMMs) were challenged over a 24 h time course with two UPEC reference strains that possess contrasting intramacrophage phenotypes: UTI89, which survives in BMMs, and 83972, which is killed by BMMs. Neither of these strains caused significant BMM cell death at the low multiplicity of infection that was used in this study. We developed an effective computational framework that simultaneously separated, annotated and quantified the mammalian and bacterial transcriptomes. Bone marrow‐derived macrophages responded to the two UPEC strains with a broadly similar gene expression programme. In contrast, the transcriptional responses of the UPEC strains diverged markedly from each other. We identified UTI89 genes up‐regulated at 24 h post‐infection, and hypothesized that some may contribute to intramacrophage survival. Indeed, we showed that deletion of one such gene (pspA) significantly reduced UTI89 survival within BMMs. Our study provides a technological framework for simultaneously capturing global changes at the transcriptional level in co‐cultures, and has generated new insights into the mechanisms that UPEC use to persist within the intramacrophage environment.

High-throughput RNA sequencing reveals the effects of 2,2',4,4' -tetrabromodiphenyl ether on retina and bone development of zebrafish larvae

Background

2,2′,4,4′-Tetrabromodiphenyl ether (BDE47) is a prevalent environmental pollutant and has been demonstrated to be a serious toxicant in both humans and animals, but little is known about the molecular mechanism underlying its toxic effect on the early development of vertebrates. BDE47-treated zebrafish larvae were found to present the light-related locomotion reduction in our previous study, therefore, we aimed to use high throughput sequencing to investigate the possible reasons from a transcriptomic perspective.

Results

By exposing zebrafish embryos/larvae to 5 μg/l and 500 μg/l BDE47, we measured the influence of BDE47 on the mRNA expression profiles of zebrafish larvae until 6 days post-fertilization, using Illumina HiSeq 2000 sequencing. Differential expression analysis and gene enrichment analysis respectively revealed that a great number of genes, and gene sets based on two popular terminologies, were affected by the treatment of 500 μg/l BDE47. Among them, BDE47 caused changes in the retinal metabolism and related biological processes involving eye morphogenesis and visual perception, as confirmed by disordered photoreceptor arrangement and thickened bipolar cell layer of larval retina from histological observations. Other altered genes such as pth1a and collaborative cathepsin family exhibited disrupted bone development, which was consistent with the body curvature phenotype. The transcriptome of larvae was not significantly affected by the treatment of 5 μg/l BDE47, as well as the treatment of DMSO vehicle.

Conclusions

Our results suggest that high BDE47 concentrations disrupt the eye and bone development of zebrafish larvae based on both transcriptomic and morphological evidences. The abnormal visual perception may result in the alteration of dark adaption, which was probably responsible for the abnormal larval locomotion. Body curvature arose from enhanced bone resorption because of the intensive up-regulation of related genes. We also proposed the larval retina as a novel potential target tissue for BDE47 exposure.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-014-1194-5) contains supplementary material, which is available to authorized users.

Digital gene expression analysis of reproductive toxicity of benzo[a]pyrene in male scallop chlamys farreri

Benzo[a]pyrene (BaP) is a representative polycyclic aromatic hydrocarbon (PAH) and is studied widely for its strong toxicity and wide distribution. Although BaP pollution in marine environment is increasing, molecular mechanisms underlying reproductive toxicity of BaP in marine mollusks have been seldom systematically studied, especially in males. In this study, genes that regulated reproductive responses of Chlamys farreri under BaP stress were analyzed through digital gene expression (DGE) sequencing with testis tissues. A total of 12,485,055 and 14,454,127 clean reads were generated from control and BaP exposure DGE libraries, respectively. After comparing two libraries, 1051 differentially expressed genes were detected, with 223 up-regulated and 828 down-regulated genes. Gene ontology (GO) annotation and kyoto encyclopedia of genes and genomes (KEGG) pathway analyses were performed on all genes to understand their biological functions and processes. The results showed that numerous enriched, differentially expressed genes related to aromatic compound catabolic processes, spermatid development, microtubule-based movement, energy production and immune response. Quantitative real-time PCR was performed to verify the expressed genes of DGE. The study generated data to show the overall reproductive transcription responses of male C. farreri under BaP stress, and it also can serve as the reference for future study of organic pollutions in aquatic mollusks.

Deep sequencing of the scallop Chlamys farreri transcriptome response to tetrabromobisphenol A (TBBPA) stress

Tetrabromobisphenol-A (TBBPA) is currently the most widely used brominated flame retardant (BFR) and has been proven to have a very high toxicity to aquatic organisms including bivalves. However, molecular responses to TBBPA in bivalve remain largely unknown. Novel high-throughput deep sequencing technology has been a powerful tool for looking at molecular responses to toxicological stressors in organisms. Using Illumina's digital gene expression (DGE) system, we investigated TBBPA-induced transcriptome response in the digestive gland tissue of scallop Chlamys farreri. In total, 173 and 266 genes were identified as significantly up- or down-regulated, respectively. Functional analysis based on gene ontology (GO) classification system and Kyoto Encyclopedia of Genes and Genomes (KEGG) database revealed that TBBPA significantly altered the expression of genes involved in stress response, detoxification, antioxidation, and innate immunity which were extensively discussed. In particular, evidence for the endocrine disrupting effect of TBBPA on bivalve was first obtained in this study. Quantitative real-time PCR was performed to ascertain the mRNA expression of several genes identified by the DGE analysis. The results of this study may serve as a basis for future research on molecular mechanism of toxic effects of TBBPA on marine bivalves.

Tissue-specific gene expression and functional regulation of uncoupling protein 2 (UCP2) by hypoxia and nutrient availability in gilthead sea bream (Sparus aurata): implications on the physiological significance of UCP1-3 variants

The aim of this study was to assess in an integrative manner the physiological regulation of uncoupling protein 2 (UCP2) in gilthead sea bream. A contig of 1,325 nucleotides in length with an open reading frame of 307 amino acids was recognized as UCP2 after searches in our transcriptome reference database ( http://www.nutrigroup-iats.org/seabreamdb ). Gene expression mapping by quantitative real-time PCR revealed a ubiquitous profile that clearly differs from that of UCP1 and UCP3 variants with the greatest abundance in liver and white skeletal muscle, respectively. The greatest abundance of UCP2 transcripts was found in the heart, with a relatively high expression level in blood cells, where UCP1 and UCP3 transcripts were practically undetectable. Functional studies revealed that UCP2 mRNA expression remains either unaltered or up-regulated upon feed restriction in glycolytic (white skeletal muscle) and highly oxidative muscle tissues (heart and red skeletal muscle), respectively. In contrast, exposure to hypoxic conditions (18-19% oxygen saturation) markedly down-regulated the UCP2 mRNA expression in blood cells in a cellular environment with increased haematocrit, blood haemoglobin content, and circulating levels of glucose and lactate, and total plasma antioxidant activity. These findings demonstrated that UCP2 expression is highly regulated at the transcriptional level, arising this UCP variant as an important piece of the complex trade-off between metabolic and redox sensors. This feature would avoid the activation of futile cycles of energy wastage if changes in tissue oxidative and antioxidant metabolic capabilities are able to maintain the production of reactive oxygen species at a low regulated level.

Using combined bio-omics methods to evaluate the complicated toxic effects of mixed chemical wastewater and its treated effluent

Mixed chemical wastewaters (MCWW) from industrial park contain complex mixtures of trace contaminants, which cannot be effectively removed by wastewater treatment plants (WWTP) and have become an unignored threat to ambient environment. However, limited information is available to evaluate the complicated toxic effects of MCWW and its effluent from wastewater treatment plant (WTPE) from the perspective of bio-omics. In this study, mice were exposed to the MCWW and WTPE for 90 days and distinct differences in the hepatic transcriptome and serum metabolome were analyzed by digital gene expression (DGE) and proton nuclear magnetic resonance ((1)H-NMR) spectra, respectively. Our results indicated that disruption of lipid metabolism in liver and hepatotoxicity were induced by both MCWW and WTPE exposure. WTPE is still a health risk to the environment, which is in need of more attention. Furthermore, we demonstrated the potential ability of bio-omics approaches for evaluating toxic effects of MCWW and WTPE.

Development of a promising fish model (Oryzias melastigma) for assessing multiple responses to stresses in the marine environment

With the increasing number of contaminants in the marine environment, various experimental organisms have been “taken into labs” by investigators to find the most suitable environmentally relevant models for toxicity testing. The marine medaka, Oryzias melastigma, has a number of advantages that make it a prime candidate for these tests. Recently, many studies have been conducted on marine medaka, especially in terms of their physiological, biochemical, and molecular responses after exposure to contaminants and other environmental stressors. This review provides a literature survey highlighting the steady increase of ecotoxicological research on marine medaka, summarizes the advantages of using O. melastigma as a tool for toxicological research, and promotes the utilization of this organism in future studies.

Exposure to DEHP and MEHP from hatching to adulthood causes reproductive dysfunction and endocrine disruption in marine medaka (Oryzias melastigma)

Concern has increased regarding the adverse effects of di-(2-ethylhexyl)-phthalate (DEHP) on reproduction. However, limited information is available on the effects of DEHP in marine organisms. The aim of the present study was to examine whether long-term exposure to DEHP and its active metabolite mono-(2-ethylhexyl)-phthalate (MEHP) disrupts endocrine function in marine medaka (Oryzias melastigma). Marine medaka larvae were exposed to either DEHP (0.1 and 0.5mg/L) or MEHP (0.1 and 0.5mg/L) for 6 months, and the effects on reproduction, sex steroid hormones, liver vitellogenin (VTG), gonad histology and the expression of genes involved in the hypothalamic-pituitary-gonad (HPG) axis were investigated. Exposure to DEHP, but not MEHP, from hatching to adulthood accelerated the start of spawning and decreased the egg production of exposed females. Moreover, exposure to both DEHP and MEHP resulted in a reduction in the fertilization rate of oocytes spawned by untreated females paired with treated males. A significant increase in plasma 17β-estradiol (E2) along with a significant decrease in testosterone (T)/E2 ratios was observed in males, which was accompanied by the upregulation of ldlr, star, cyp17a1, 17βhsd, and cyp19a transcription in the testis. Increased concentrations of T and E2 were observed in females, which was consistent with the upregulation of ldlr. The expression of brain gnrhr2, fshβ, cyp19b and steroid hormone receptor genes also corresponded well with hormonal and reproductive changes. The liver VTG level was significantly increased after DEHP and MEHP exposure in males. DEHP induced histological changes in the testes and ovaries: the testes displayed a reduced number of spermatozoa, and the ovaries displayed an increased number of atretic follicles. In addition, the tissue concentrations of MEHP, MEHHP and MEOHP in DEHP-exposed groups were much higher than those in MEHP-exposed groups, and there were no dose- or sex-specific effects. Thus, DEHP exerts more obvious toxic effects compared with MEHP. There were some commonalities in the toxic effects and molecular mechanisms of DEHP and MEHP, suggesting that some of the toxic effects of DEHP may be induced by both DEHP itself and DEHP metabolites (including MEHP). Taken together, these results indicate that exposure to DEHP and MEHP from hatching to adulthood causes endocrine disruption with sex-specific effects in marine medaka, with males being more sensitive than females.

RNA-Seq technology and its application in fish transcriptomics

High-throughput sequencing technologies, also known as next-generation sequencing (NGS) technologies, have revolutionized the way that genomic research is advancing. In addition to the static genome, these state-of-art technologies have been recently exploited to analyze the dynamic transcriptome, and the resulting technology is termed RNA sequencing (RNA-seq). RNA-seq is free from many limitations of other transcriptomic approaches, such as microarray and tag-based sequencing method. Although RNA-seq has only been available for a short time, studies using this method have completely changed our perspective of the breadth and depth of eukaryotic transcriptomes. In terms of the transcriptomics of teleost fishes, both model and non-model species have benefited from the RNA-seq approach and have undergone tremendous advances in the past several years. RNA-seq has helped not only in mapping and annotating fish transcriptome but also in our understanding of many biological processes in fish, such as development, adaptive evolution, host immune response, and stress response. In this review, we first provide an overview of each step of RNA-seq from library construction to the bioinformatic analysis of the data. We then summarize and discuss the recent biological insights obtained from the RNA-seq studies in a variety of fish species.

Trascriptome analysis of the Pacific white shrimp Litopenaeus vannamei exposed to nitrite by RNA-seq

In the present study, transcriptome of nitrite-exposed Litopenaeus vannamei was performed using a newly developed high-throughput sequencing technology (Illumina RNA-seq). As many as 42,336 unigenes were generated with 561 bp of average length and 736 bp of unigene N50 after filtering and assembly. These unigenes from the de novo assembly were further annotated using BLAST and BLAST2GO softwares. A total of 23,532 unigenes were unambiguous alignments to the reference when BLAST against non-redundant protein sequence (Nr), non-redundant nucleotide (Nt), Swiss-Prot, Gene Ontology database (GO), Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases available at NCBI. Numerous candidate genes associated with immune response, detoxification, apoptosis pathway were identified. Ten candidate genes related to immune responses and apoptosis were selected for validating the results of assembly and annotation by real-time quantitative PCR. Results revealed that the expressions of all these ten genes were up-regulated after nitrite exposure. Combining to our previous study, we speculate that all these selected genes may be involved in the response to nitrite stress. The study shows a systematic overview of the transcriptome analysis in L. vannamei, and provides valuable gene information for studying molecular mechanisms under nitrite exposure.

Effect of sexual maturation on muscle gene expression of rainbow trout: RNA-Seq approach

Muscle degradation occurs as a response to various physiological states that are regulated by specific molecular mechanisms. Previously, we characterized the metabolic changes of muscle deterioration of the female rainbow trout at full sexual maturity and spawning (Salem et al., Physiol. Genomics 2006;28:33–45; J. Proteomics 2010;73:778–789). Muscle deterioration in this model represents nutrient mobilization as a response to the energetic overdemands of the egg/ovarian growth phase. Our recent studies showed that most of the changes in muscle growth and quality start 2–3 months before spawning. Gravid fish exhibited reduced intramuscular fat that is lower in saturated and monounsaturated fatty acids and higher in polyunsaturated fatty acids compared to sterile fish. In this study, RNA-Seq was used to explain the mechanisms underlying changes during this phase of sexual maturity. Furthermore, to minimize changes due to nutrient deficits, fish were fed on a high-plane of nutrition. The RNA-Seq technique identified a gene expression signature that is consistent with metabolic changes of gravid fish. Gravid fish exhibited increased abundance of transcripts in metabolic pathways of fatty acid degradation and up-regulated expression of genes involved in biosynthesis of unsaturated fatty acids. In addition, increased expression of genes involved in the citric acid cycle and oxidative phosphorylation was observed for gravid fish. This muscle transcriptomic signature of fish fed on a high nutritional plane is quite distinct from that previously described for fish at terminal stages of maturity and suggest that female rainbow trout approaching spawning, on high nutritional planes, likely mobilize intramuscular fat rather than protein to support gonadal maturation.

De novo assembly and characterization of the transcriptome, and development of SSR markers in wax gourd (Benicasa hispida)

BACKGROUND

Wax gourd is a widely used vegetable of Cucuribtaceae, and also has important medicinal and health values. However, the genomic resources of wax gourd were scarcity, and only a few nucleotide sequences could be obtained in public databases.

METHODOLOGY/PRINCIPAL FINDINGS

In this study, we examined transcriptome in wax gourd. More than 44 million of high quality reads were generated from five different tissues of wax gourd using Illumina paired-end sequencing technology. Approximately 4 Gbp data were generated, and de novo assembled into 65,059 unigenes, with an N50 of 1,132 bp. Based on sequence similarity search with known protein database, 36,070 (55.4%) showed significant similarity to known proteins in Nr database, and 24,969 (38.4%) had BLAST hits in Swiss-Prot database. Among the annotated unigenes, 14,994 of wax gourd unigenes were assigned to GO term annotation, and 23,977 were found to have COG classifications. In addition, a total of 18,713 unigenes were assigned to 281 KEGG pathways. Furthermore, 6,242 microsatellites (simple sequence repeats) were detected as potential molecular markers in wax gourd. Two hundred primer pairs for SSRs were designed for validation of the amplification and polymorphism. The result showed that 170 of the 200 primer pairs were successfully amplified and 49 (28.8%) of them exhibited polymorphisms.

CONCLUSION/SIGNIFICANCE

Our study enriches the genomic resources of wax gourd and provides powerful information for future studies. The availability of this ample amount of information about the transcriptome and SSRs in wax gourd could serve as valuable basis for studies on the physiology, biochemistry, molecular genetics and molecular breeding of this important vegetable crop.