Identifying health impacts of exposure to copper using transcriptomics and metabolomics in a fish model

Differences in the transcriptome response in the gills of sea lamprey acutely exposed to 3-trifluoromethyl-4-nitrophenol (TFM), niclosamide or a TFM:niclosamide mixture

Sea lamprey (Petromyzon marinus) control in the Laurentian Great Lakes of North America makes use of two pesticides: 3-trifluoromethyl-4-nitrophenol (TFM) and niclosamide, which are often co-applied. Sea lamprey appear to be vulnerable to these agents resulting from a lack of detoxification responses with evidence suggesting that lampricide mixtures produce a synergistic effect. However, there is a lack of information pertaining to the physiological responses of sea lamprey to niclosamide and TFM:niclosamide mixtures. Here, we characterized the transcriptomic responses of the sea lamprey to TFM, niclosamide, and a TFM:niclosamide (1.5 %) mixture in the gill. Along with a control, larval sea lamprey were exposed to each treatment for 6 h, after which gill tissues were extracted for measuring whole-transcriptome responses using RNA sequencing. Differential gene expression patterns were summarized, which included identifying the broad roles of genes and common expression patterns among the treatments. While niclosamide treatment resulted in no differentially expressed genes, TFM- and mixture-treated fish had several differentially expressed genes that were associated with the cell cycle, DNA damage, metabolism, immune function, and detoxification. However, there was no common differential expression among treatments. For the first time, we characterized the transcriptomic response of sea lamprey to niclosamide and a TFM:niclosamide mixture and identified that these agents impact mRNA transcript abundance of genes associated with the cell cycle and cellular death, and immune function, which are likely mediated through mitochondrial dysregulation. These results may help to inform the production of more targeted and effective lampricides in sea lamprey control efforts.

Genome-wide transcriptomics and microRNAomics analyses uncover multi-faceted mechanisms to cope with copper stress in ancient macrobenthos amphioxus

The mechanisms underlying the toxicity of environmental stress are unclear for marine macrobenthos. Copper/Cu has posed the most serious threats to amphioxus, an ancient and model benthic cephalochordate. Herein, a dynamic change in the physiological parameters (GR, SOD, ATP, and MDA) was detected with ROS accumulation in Branchiostoma belcheri exposed to 0.3 mg·L-1 Cu. Transcriptomes and microRNAomes of B. belcheri were generated to investigate the molecular mechanisms by which this amphioxus copes with Cu exposure. Time-specific genes identified at different time points after exposure were involved in the stimulus and immune response, detoxification and ionic homeostasis, aging and the nervous system, sequentially, with prolongation of exposure time, forming a dynamic process of molecular response to Cu stress. In total, 57 differentially expressed miRNAs were identified under Cu stress. Transcriptomics-miRNAomics analyses indicate that these miRNAs targeted genes associated with many key biological processes such as xenobiotics degradation, oxidative stress, and energy metabolism. The constructed miRNA-mRNA-pathway network uncovered a broad post-transcriptional regulatory mechanism in B. belcheri to cope with Cu stress. Overall, this integrated analyses show that enhanced defense response, accelerated ROS elimination, and repressed ATP production constitute a comprehensive strategy to cope with Cu toxicity in the ancient macrobenthos.

Integrated metabolomics, transcriptomics, and proteomics analyses reveal co-exposure effects of polycyclic aromatic hydrocarbons and cadmium on ryegrass (Lolium perenne L.)

Cadmium (Cd) and polycyclic aromatic hydrocarbons (PAHs) are prominent soil contaminants found in industrial sites, and their combined effects on plants are not yet fully understood. To investigate the mechanisms underlying the co-exposure of Cd and PAHs and identify key biomarkers for their co-effects, an integrated analysis of metabolomics, transcriptomics, and proteomics was conducted on ryegrass leaves cultivated in soil. In nontarget metabolomics analysis, nine differentially expressed metabolites that were specifically induced by the compound exposure were identified. When combined with the analysis of differentially expressed genes and proteins, it was determined that the major pathways involved in the response to the co-stress of Cd and PAHs were linoleic acid metabolism and phenylpropanoid biosynthesis. The upregulation of 12,13-dihydroxy-9Z-octadecenoic acid and the downregulation of sinapyl alcohol were identified as typical biomarkers, respectively. Compared to scenarios of single exposures, the compound exposure to Cd and PAHs disrupted the oxidation of linoleic acid, leading to alterations in the profiles of linoleate metabolites. Additionally, it intensified hydroxylation, carboxylation, and methylation processes, and interfered with reactions involving coenzyme A, thus inhibiting lignin production. As a result, oxidative stress was elevated, and the cell wall defense system in ryegrass was weakened. The findings of this study highlight the ecological risks associated with unique biological responses in plants co-exposed to Cd and PAHs in polluted soils.

Effect of Biosilicate® Addition on Physical-Mechanical and Biological Properties of Dental Glass Ionomer Cements

This study investigated the influence of incorporating Biosilicate^® on the physico-mechanical and biological properties of glass ionomer cement (GIC). This bioactive glass ceramic (23.75% Na₂O, 23.75% CaO, 48.5% SiO₂, and 4% P₂O₅) was incorporated by weight (5%, 10%, or 15%) into commercially available GICs (Maxxion R and Fuji IX GP). Surface characterization was made by SEM (n = 3), EDS (n = 3), and FTIR (n = 1). The setting and working (S/W time) times (n = 3) and compressive strength (CS) were analyzed (n = 10) according to ISO 9917-1:2007. The ion release (n = 6) was determined and quantified by ICP OES and by UV-Vis for Ca, Na, Al, Si, P, and F. To verify cell cytotoxicity, stem cells from the apical papilla (SCAP) were exposed to eluates (n = 3, at a ratio of 1.8 cm²/mL) and analyzed 24 h post-exposure. Antimicrobial activity against Streptococcus mutans (ATCC 25175, NCTC 10449) was analyzed by direct contact for 2 h (n = 5). The data were submitted for normality and lognormality testing. One-way ANOVA and Tukey's test were applied for the working and setting time, compressive strength, and ion release data. Data from cytotoxicity and antimicrobial activity were submitted for Kruskal-Wallis' testing and Dunn's post hoc test (α = 0.05). Among all experimental groups, only those with 5% (wt) of Biosilicate^® showed better surface quality. Only M5% showed a comparable W/S time to the original material (p = 0.7254 and p = 0.5912). CS was maintained for all Maxxion R groups (p > 0.0001) and declined for Fuji IX experimental groups (p < 0.0001). The Na, Si, P, and F ions released were significantly increased for all Maxxion R and Fuji IX groups (p < 0.0001). Cytotoxicity was increased only for Maxxion R with 5% and 10% of Biosilicate^®. A higher inhibition of S. mutans growth was observed for Maxxion R with 5% of Biosilicate^® (less than 100 CFU/mL), followed by Maxxion R with 10% of Biosilicate^® (p = 0.0053) and Maxxion R without the glass ceramic (p = 0.0093). Maxxion R and Fuji IX presented different behaviors regarding Biosilicate^® incorporation. The impacts on physico-mechanical and biological properties were different depending on the GIC, but therapeutic ion release was increased for both materials.

Single and combined genotoxicity of metals and fluoroquinolones to zebrafish embryos at environmentally relevant concentrations

Fluoroquinolones (FQs) are known to have genotoxicity to aquatic organisms. However, their genotoxicity mechanisms, individually and in combination with heavy metals, are poorly understood. Here, we investigated the single and joint genotoxicity of FQs, ciprofloxacin (CIP) and enrofloxacin (ENR), and metals (Cd and Cu) at environmentally relevant concentrations (0.2 µM) to zebrafish embryos. We found that FQs or/and metals induced genotoxicity (i.e., DNA damage and cell apoptosis) to zebrafish embryos. Compared with their single exposure, the combined exposure of FQs and metals elicited less ROS overproduction but higher genotoxicity, suggesting other toxicity mechanisms may also act in addition to oxidation stress. The upregulation of nucleic acid metabolites and the dysregulation of proteins confirmed the occurrence of DNA damage and apoptosis, and further revealed the inhibition of DNA repair by Cd and binding of DNA or DNA topoisomerase by FQs. This study deepens the knowledge on the responses of zebrafish embryos to exposure of multiple pollutants, and highlights the genotoxicity of FQs and heavy metals to aquatic organisms.

Geosmin disrupts energy metabolism and locomotor behavior of zebrafish in early life stages

Geosmin has been commonly detected both in various aquatic environments and biota, but its exact toxicological mechanisms to organisms need further experimentation. In the present study, zebrafish embryos were exposed to geosmin at nominal concentrations of 50, 500 and 5000 ng/L for 120 h post-fertilization (hpf), followed by locomotor activity and biochemical parameter examination, and multi-omics investigation of the transcriptome and metabolome. The results showed that geosmin exposure significantly reduced the mitochondrial electron transport chain (ETC) complexes I-V, ATP content and mitochondrial respiration and suppressed the locomotor behavior of zebrafish larvae. Transcriptomics analysis revealed that the transcripts of genes involved in oxidative phosphorylation, glycolysis, and lipid metabolism were significantly affected, indicating that geosmin disrupts energy metabolism. Furthermore, metabolomics results showed that 3 classes of lipids, namely glycerophospholipids (GPs), sphingolipids (SLs) and fatty acyls (FAs) were significantly decreased after geosmin exposure. This study provides novel insight into the underlying mechanisms of geosmin-induced energy metabolism and highlights the need for concern about geosmin exposure.

Metabolomics analysis reveals the response mechanism to carbonate alkalinity toxicity in the gills of Eriocheir sinensis

Aquatic water with carbonate alkalinity presents a survival challenge to aquatic animals. As an economically important crab, large quantities of Eriocheir sinensis are cultured in carbonate-type saline-alkali ponds, while the toxic effect on E. sinensis from carbonate alkalinity is still unclear. In this study, untargeted liquid chromatography-mass spectrometry metabolomics was performed to investigate the metabolic change caused by culture alkalinity, and confirmed distinct physiological response under gradient alkalinities. There were 39 differential metabolites obtained in the low-alkalinity group (4.35 mmol/L) versus control group, and "arachidonic acid metabolism" was enriched as a core response pathway. 93 differential metabolites were identified in the high-alkalinity group (17.43 mmol/L) versus control group, and a complex response net was manifested through integrated analysis, building by "steroid hormone biosynthesis", "phenylalanine, tyrosine and tryptophan biosynthesis", "phosphonate and phosphinate metabolism", "phenylalanine metabolism", "mineral absorption", "purine metabolism" and "carbon metabolism". This indicated the mobilization of energy reserves and the suppression of protein and amino acid catabolism were manifested in E. sinensis gills to defense high alkalinity stress. In addition, the persistently regulation of key metabolites under various alkalinity, including diuretic compound "spironolactone" and the antiphlogistic compound "LXB₄", suggested anti-inflammatory action and excretion regulation were initiated to defend the stress.

What happens to Hoplias malabaricus fed on live prey (Astyanax altiparanae) previously exposed to copper? A multiple biomarker approach

Copper waterborne toxicity is well understood in aquatic organisms. However, the dietary copper effects are much less known, especially in tropical fish. The toxicity of copper via the trophic route could be influenced by the composition of the food, and diets naturally impregnated with copper seem to have greater toxicity at lower concentrations than artificially impregnated ones. Thus, our objective was to investigate the effects of copper on juveniles of the Neotropical fish Hoplias malabaricus fed on live prey (Astyanax altiparanae) previously exposed to the metal (20 µg L ^- 1) for 96 h. The prey fish were given to H. malabaricus every 96 h, totaling 10 doses at the end of the experiment. Thus, after 40 days fish were killed and tissues were sampled. Blood showed to be the only tissue in which copper accumulated. Anemia was found and there was damage to the DNA of erythrocytes. Furthermore, ionic imbalances were observed in plasma. There was an increase in the concentration of Na⁺ and Cl^- and a decrease in Ca²⁺, which were associated with increased copper uptake in the gastrointestinal tract of fish fed on copper exposed prey. All the antioxidant enzymes evaluated in the gills showed decreased activity compared to the control group. Copper seems to have interfered in the energy metabolism of H. malabaricus, since a lower condition factor and feed conversion efficiency rate were observed in fish fed with copper diet. The present study confirms the trophic route as an important copper toxicity pathway for H. malabaricus and reinforces the idea that metal toxicity can be increased when it is naturally impregnated in the prey tissues, even if the prey has been exposed to the metal only for a short period of time.

Effects of Copper Exposure on Oxidative Stress, Apoptosis, Endoplasmic Reticulum Stress, Autophagy and Immune Response in Different Tissues of Chinese Mitten Crab (Eriocheir sinensis)

High concentrations of copper (Cu²⁺) pose a great threat to aquatic animals. However, the mechanisms underlying the response of crustaceans to Cu²⁺ exposure have not been well studied. Therefore, we investigated the alterations of physiological and molecular parameters in Chinese mitten crab (Eriocheir sinensis) after Cu²⁺ exposure. The crabs were exposed to 0 (control), 0.04, 0.18, and 0.70 mg/L of Cu²⁺ for 5 days, and the hemolymph, hepatopancreas, gills, and muscle were sampled. The results showed that Cu²⁺ exposure decreased the antioxidative capacity and promoted lipid peroxidation in different tissues. Apoptosis was induced by Cu²⁺ exposure, and this activation was associated with the mitochondrial and ERK pathways in the hepatopancreas. ER stress-related genes were upregulated in the hepatopancreas but downregulated in the gills at higher doses of Cu²⁺. Autophagy was considerably influenced by Cu²⁺ exposure, as evidenced by the upregulation of autophagy-related genes in the hepatopancreas and gills. Cu²⁺ exposure also caused an immune response in different tissues, especially the hepatopancreas, where the TLR2-MyD88-NF-κB pathway was initiated to mediate the inflammatory response. Overall, our results suggest that Cu²⁺ exposure induces oxidative stress, ER stress, apoptosis, autophagy, and immune response in E. sinensis, and the toxicity may be implicated following the activation of the ERK, AMPK, and TLR2-MyD88-NF-κB pathways.

Effects of short-term exposure to the heavy metal, nickel chloride (Nicl2) on gill histology and osmoregulation components of the gray mullet, Mugil cephalus

The gray mullet, Mugil cephalus is an inshore and bottom-feeding fish species of Oman sea. Therefore, the gray mullet may be more exposed to heavy metal contamination, as the toxic impacts of heavy metals mullet has been reported in various studies. This study was conducted to evaluate the toxic effects of the heavy metal, nickel (as NiCl₂) on osmoregulation of the gray mullet by measuring blood biochemicals, hormones, minerals and gill histology. Fish (10 fish/tank) were experimentally exposed to NiCl₂ at three environmentally relevant concentrations of 5, 10 and 15 μg/l for 96 h. Then, fish were challenged with seawater (35 mg/l) for a period of 120 min. The samples (blood and gill tissue) were collected After 96 exposure to NiCl2 and during salinity challenge (30, 60 and 120 min post challenge). The plasma levels of cortisol and glucose significantly increased in NiCl_2-exposed fish. In addition, cortisol increased in all experimental groups 30 min after salinity challenge and then returned gradually to the same levels as the control at 120 min post salinity challenge (PSC). The triiodothyronine (T3) and thyroxine (T4) levels significantly decreased in response to 10 and 15 μg/l NiCl₂. In all groups, the thyroid hormones significantly elevated at 30 min PSC. After 30 min PSC, T3 levels in all NiCl_2-exposed fish and T4 in the treatment, 10 μg/l NiCl₂ remained unchanged throughout the salinity challenge. In the treatment, 5 μg/l NiCl₂, T4 levels were recovered at 120 min PSC and reached the same levels as the control. Exposure of fish to high concentrations of NiCl₂ and salinity stress increased the lactate levels. However, lactate levels in 5 and 10 μg/l NiCl₂ groups were recovered at 120 min PSC and reached the same levels as the control. Furthermore, plasma protein increased in response to 10 and 15 μg/l NiCl₂. At 30 PSC, the protein levels decreased in control and 5 μg/l NiCl₂ group, while it remained unchanged in fish exposed to 10 and 15 μg/l NiCl₂ throughout the salinity challenge. Exposure of fish to NiCl₂ disrupted the electrolyte (Na⁺, Cl^-) balance both before and after salinity challenge, which may be due to gill lesions induced by the heavy metal and following alternations in gill permeability. However, fish in 5 μg/l NiCl₂ re-established the ionic balance in the blood at the end of salinity challenge period. The malondialdehyde (MDA) levels significantly increased in response to 10 and 15 μg/l NiCl₂. The MDA levels returned to the same levels as the control group at 120 min PSC. The results of the present study showed that nickel-induced toxicity (especially at high concentrations) can reduce the osmoregulation capabilities of mullet. However, fish are able to recover from the toxic effects over time, if contamination be eliminated.

Metal Accumulation and Ion Regulation in the Fish Hyphessobrycon luetkenii Living in a Site Chronically Contaminated by Copper: Insights from Translocation Experiments

Fish living in the João Dias creek (southern Brazil) have to deal with trace-metal contamination in the long-term basis, as this aquatic environment has been historically impacted by copper mining activities. In order to survive in this harsh environment, the local biota had to develop adaptations related to pollution tolerance. The aim of this study was to test if biochemical mechanisms related to osmoregulation were among these adaptations, using translocation experiments. Water ionic and trace-metal compositions were measured in a nonmetal impacted site (NMIS) and in a metal impacted site (MIS) of this creek. Also, whole-body metal accumulation, ion concentration and branchial enzyme activity (Na,K-ATPase and carbonic anhydrase) were evaluated in Hyphessobrycon luetkenii. In both NMIS and MIS, fish were collected and immediately stored, kept caged or translocated from sites. The result shows that waterborne Cu was 3.4-fold higher at the MIS. Accordingly, animals that had contact with this site showed elevated whole-body Cu levels. Moreover, both translocated groups showed elevated Na,K-ATPase activity. Additionally, fish translocated from the NMIS to the MIS showed lower carbonic anhydrase activity. These findings indicate that H. luetkenii chronically or acutely exposed to naturally elevated waterborne Cu showed a rapid Cu bioaccumulation but was unable to readily excrete it. Moreover, classic Cu osmoregulatory toxicity related to Na,K-ATPase inhibition was not observed. Conversely, impacts in ammonia excretion related to carbonic anhydrase inhibition may have occurred.

Study on toxicity effects of environmental pollutants based on metabolomics: A review

In the past few decades, the toxic effects of environmental pollutants on non-target organisms have received more and more attention. As a new omics technology, metabolomics can clarify the metabolic homeostasis of the organism at the overall level by studying the changes in the relative contents of endogenous metabolites in the organism. Recently, a large number of studies have used metabolomics technology to study the toxic effects of environmental pollutants on organisms. In this review, we reviewed the analysis processes and data processes of metabolomics and its application in the study of the toxic effects of environmental pollutants including heavy metals, pesticides, polychlorinated biphenyls, polycyclic aromatic hydrocarbons, polybrominated diphenyl ethers and microplastics. In addition, we emphasized that the combination of metabolomics and other omics technologies will help to explore the toxic mechanism of environmental pollutants and provide new research ideas for the toxicological evaluation of environmental pollutants.

Immune defense, detoxification, and metabolic changes in juvenile Eriocheir sinensis exposed to acute ammonia

Ammonia-N accumulation in the rice-crab co-culture system may have negative effects on the health of juvenile Eriocheir sinensis. In this study, physiological, transcriptomic, and metabolomic analyses were performed to explore the toxic responses in the hepatopancreas of juvenile E. sinensis exposed to 0, 0.75, and 2.99 mmol/L total ammonia-N for 24 h. We observed that the content of most amino acids and glycogen was significantly decreased after ammonia exposure. Acid phosphatase and alkaline phosphatase activities showed marginally increased trends after low ammonia exposure. Transcriptomic analysis indicated that immune defense, detoxification, and metabolic pathways were altered. Metabolomic analysis revealed that ammonia exposure affected energy metabolism and nucleotide metabolism. The combination of transcriptomic and metabolomic analyses revealed that the tricarboxylic acid cycle and amino acid consumption were enhanced for additional energy supply to cope with ammonia stress. Ammonia stress activated the immune defense system in juvenile E. sinensis. Moreover, the upregulation of detoxification genes and the acceleration of glycogen degradation for glucose supply are important adaptive mechanisms in response to high ammonia stress. Notably, ammonia stress may affect the nervous system of juvenile E. sinensis. Thus, our data provide a better understanding of the defensive mechanisms of E. sinensis against ammonia toxicity.

An NMR-based metabolomics study on sea anemones Exaiptasia diaphana (Rapp, 1829) with atrazine exposure

Sea anemones have been recommended as critical bioindicators for marine environmental stressors; however, the understanding of the biological effects in response to sublethal pollutant exposure is still limited. In this study, NMR-based metabolomics was performed to investigate the effects of atrazine on Exaiptasia diaphana with concentrations ranging from 3 to 90 ppb. As a result, the metabolic profiling of E. diaphana was significantly affected after 70 ppb treatment while a partial perturbation was observed as early as 3 ppb treatment. Glutamate was significantly changed at low atrazine concentrations with increased upregulation in concentrated atrazine experiments which is a potential biomarker for E. diaphana exposed to atrazine stressors. The TCA intermediates succinate and malate as well as the TCA cycle-related metabolites such as alanine, glycine, and taurine downregulated after atrazine treatment which also indicated the lower energy supply of E. diaphana. In summary, our study demonstrated that significant metabolic level perturbation could be detected at low atrazine concentrations before a physical change could be observed, and glutamate or the nitrogen metabolism may be the initial target for sea anemones by atrazine. The study may provide pioneering results for using E. diaphana to predict the impacts of exposure to atrazine toxin in marine systems.

Exposure to pollutants present in Iguaçu River Southern Brazil affect the health of Oreochromis niloticus (Linnaeus, 1758): Assessment histological, genotoxic and biochemical

Urban sewage is a source of major contamination in aquatic systems and contributes to environmental and human health disturbances. This study investigates the effects of sewage-polluted waters from Iguaçu River on the health of juvenile Oreochromis niloticus. Two hundred four specimens were exposed to riverine water in four groups: no diluted, 25 and 50 % diluted water and a control group without tested water for 72 days. Biological samples were obtained for histopathological, neurotoxicity, antioxidant defenses, genotoxicity, metallothionines expression and polycyclic aromatic hydrocarbons (PAHs) metabolites. The results showed histopathological alterations in liver and gills, genotoxic alteration in erythrocytes, reduction of acetylcholinesterase activity in brain and muscle, activation of antioxidant defenses in the liver, recruitment of metals by metallothionein and the detection of PAHs metabolites in bile. These results demonstrate that juveniles of O. niloticus are susceptible to Iguaçu River exposure water and they can be used as indicator of water quality.

Integrated metabolome and transcriptome analyses revealing the effects of thermal stress on lipid metabolism in juvenile turbot Scophthalmus maximus

To gain insights into the influence of heat stress on lipid metabolism in juvenile turbot (Scophthalmus maximus), we analyzed the correlations between data obtained by transcriptome sequencing and metabolome sequencing of the kidney under different high temperature stimuli (20 °C, 25 °C and 28 °C) and control conditions (14 °C). We identified the differentially expressed genes and metabolites, which were found to be enriched in seven pathways (steroid hormone biosynthesis, primary bile acid biosynthesis, glycerophospholipid metabolism, linoleic acid metabolism, sphingolipid metabolism, glycerolipid metabolism and biosynthesis of unsaturated fatty acids) associated with lipid metabolism, according to KEGG pathway analysis. After correlation analysis of these differentially expressed genes, the most representative genes (lpcat2, Etnk1, TAZ, SCP2, ch25hl and gpd1l) and metabolites (citicoline, UPD-6-sulfoquinovose, dihydroxyacetone, taurine and o-phosphocholine) were selected according to their correlation coefficients. These genes and metabolites were found to be the key points to regulate lipid deposition and maintain lipid homeostasis through varying degrees of up-regulation or down-regulation under heat stress, so as to relieve the disorder of lipid metabolism caused by heat stress, which is of great significance for breeding new heat-resistant varieties of turbot and provides a reliable theoretical basis for optimizing actual production. These results provide new clues for understanding the roles of lipid metabolism in fish under heat stress.

Metabolite profiling, histological and oxidative stress responses in the grey mullet, Mugil cephalus exposed to the environmentally relevant concentrations of the heavy metal, Pb (NO3)2

In this study, a metabolomics approach was applied to investigate the metabolic responses of grey mullet, Mugil cephalus to toxicity induced by heavy metal, Pb (NO3)₂. In addition, the study was followed by assessing the peroxidation index and histology of liver as supplementary data. Pb (NO3)₂ exposure affected the plasma metabolome, especially four group metabolites including amino acids, methylated metabolites, energetic metabolites and citric acid intermediates. Pb (NO3)₂ in medium and high concentrations (15 and 25 μg/l) increased the levels of plasma amino acids compared to control (P < 0.01). In contrast, Pb (NO3)₂ decreased the plasma levels of methylated metabolites (P < 0.01). The ketogenic metabolites and glycerol levels significantly elevated in fish exposed to 25 μg/l Pb (NO3)₂ (P < 0.01). The plasma glucose levels increased in treatment, 5 μg/l Pb (NO3)₂ and after a decline in treatment 15 μg/l Pb (NO3)₂ elevated again in treatment 25 μg/l Pb (NO3)₂ (P < 0.01).The plasma levels of lactate significantly increased in fish exposed to 5 and 15 μg/l Pb (NO3)₂ and then declined to initial levels in treatment, 25 μg/l Pb (NO3)₂ (P < 0.01). The plasma levels of TCA cycle intermediates significantly elevated in treatments 15 and 25 μg/l Pb (NO3)₂ (P < 0.01). As a biomarker of oxidative stress, the plasma levels of malondialdehyde (MDA) showed significant increases in Pb (NO3)₂ exposed fish (P < 0.01). During exposure period, wide ranges of liver tissue damages were also observed in Pb (NO3)₂ exposed fish. In conclusion, exposure to Pb (NO3)₂ affected the metabolome content of blood in grey mullet, mainly through inducing the biochemical pathways related to the metabolism of the amino acids, energetic metabolites and methylated metabolites. Our results may help to understand the effects of heavy metals on fish hematology from a molecular point of view.

Zn Induces Lipophagy via the Deacetylation of Beclin1 and Alleviates Cu-Induced Lipotoxicity at Their Environmentally Relevant Concentrations

In this study, the mechanisms of environmentally relevant doses of Cu and Zn mixtures influencing lipid deposition and metabolism were investigated in freshwater teleost yellow catfish Pelteobagrus fulvidraco (2 months old, 4.95 (t0.01 g, mean ± SEM). Our study indicated that waterborne Cu exposure increased lipid content, while Zn activated lipophagic flux and alleviated Cu-induced lipid accumulation. Yellow catfish hepatocytes treated with Zn or Zn + Cu activated autophagy-specific lipophagy, decreased lipid storage, and increased nonesterified fatty acid (NEFA) release, suggesting a causal relationship between lipophagy and lipid droplet (LD) breakdown under Zn and Zn + Cu conditions. Our further investigation found that Beclin1 deacetylation by sirtuin 1 (SIRT1) was required for Zn- and Zn + Cu-induced lipophagy and lipolysis, and lysine residues 427 and 434 were key sites for Beclin1 deacetylation. Taken together, these findings show that the Zn-induced deacetylation of Beclin1 promotes lipophagy as an important pathway to alleviate Cu-induced lipid accumulation in fish, which reveals a previously unidentified mechanism for understanding the antagonistic effects of Cu and Zn on metabolism at their environmentally relevant concentrations. Our results highlight the importance of combined exposure when the biological effects of heavy metals are evaluated during environmental risk assessments.

Approaches to Integrating Metabolomics and Multi-Omics Data: A Primer

Metabolomics deals with multiple and complex chemical reactions within living organisms and how these are influenced by external or internal perturbations. It lies at the heart of omics profiling technologies not only as the underlying biochemical layer that reflects information expressed by the genome, the transcriptome and the proteome, but also as the closest layer to the phenome. The combination of metabolomics data with the information available from genomics, transcriptomics, and proteomics offers unprecedented possibilities to enhance current understanding of biological functions, elucidate their underlying mechanisms and uncover hidden associations between omics variables. As a result, a vast array of computational tools have been developed to assist with integrative analysis of metabolomics data with different omics. Here, we review and propose five criteria-hypothesis, data types, strategies, study design and study focus- to classify statistical multi-omics data integration approaches into state-of-the-art classes under which all existing statistical methods fall. The purpose of this review is to look at various aspects that lead the choice of the statistical integrative analysis pipeline in terms of the different classes. We will draw particular attention to metabolomics and genomics data to assist those new to this field in the choice of the integrative analysis pipeline.

Integrative analyses of transcriptomics and metabolomics in Raphidocelis subcapitata treated with clarithromycin

As a macrolide antibiotic, clarithromycin (CLA) has a high detection rate in surface water and sewage treatment plant effluents worldwide, posing a considerably high ecological risk to aquatic ecosystem. However, algal transcriptome and metabolome in response to CLA remains largely unknown. In this study, a model alga Raphidocelis subcapitata (R. subcapitata), was exposed to CLA at the concentrations of 0, 3, 10, and 15 μg L^-1. Transcriptomic analysis was performed for all the treatment groups, whereas metabolomics was merely applied to 0, 3, and 10 μg L^-1 groups because of the limited amount of algal biomass. After 7 d cultivation, the growth of R. subcapitata was significantly hindered at the concentrations above 10 μg L^-1. A total of 115, 1833, 2911 genes were differentially expressed in 3, 10, and 15 μg L^-1 groups, respectively; meanwhile, 134 and 84 differentially accumulated metabolites (DAMs) were found in the 3 and 10 μg L^-1 groups. Specifically, expression levels of DEGs and DAMs related to xenobiotic metabolism, electron transport and energy synthesis were dysregulated, leading to the produced reactive oxygen species (ROS). To confront the CLA-induced injury, the biosynthesis of unsaturated fatty acids and carotenoids of R. subcapitata in 3 μg L^-1 were up-regulated; although the photosynthesis was up-regulated in both 10 μg L^-1 and 15 μg L^-1 groups, the energy synthesis and the ability to resist ROS in these two groups were down-regulated. Overall, this study shed light on the mechanism underlying the inhibitory effects of macrolide antibiotics in algae.

Dietary uptake and effects of copper in Sticklebacks at environmentally relevant exposures utilizing stable isotope-labeled 65CuCl2 and 65CuO NPs

Copper oxide nanoparticles (CuO NPs) accumulating in sediment can be taken up by invertebrates that serve as prey for fish. Thus, it is likely that the latter are exposed to CuO NPs via the gut. However, to this day it is unknown if CuO NPs can be taken up via the gastrointestinal tract and if and in which tissues/organs they accumulate. To address this knowledge gap, we synthesized CuO NPs enriched in the stable isotope ⁶⁵Cu and incorporated them at low concentration (5 μg ⁶⁵Cu g^-1 ww food) into a practical diet prepared from worm homogenate, which was then fed to Three-spined Stickleback (Gasterosteus aculeatus) for 16 days. For comparison, fish were exposed to a diet spiked with a ⁶⁵CuCl₂ solution. Background Cu and newly taken up ⁶⁵Cu in fish tissues/organs including gill, stomach, intestine, liver, spleen, gonad and carcass and feces were quantified by ICP-MS. In addition, expression levels of genes encoding for proteins related to Cu uptake, detoxification and toxicity (ctr-1, gcl, gr, gpx, sod-1, cat, mta and zo-1) were measured in selected tissues using RT-qPCR. The obtained results showed that feces of fish fed ⁶⁵CuO NP-spiked diet contained important amounts of ⁶⁵Cu. Furthermore, there was no significant accumulation of ⁶⁵Cu in any of the analyzed internal organs, though ⁶⁵Cu levels were slightly elevated in liver. No significant modulation in gene expression was measured in fish exposed to ⁶⁵CuO NP-spiked diet, except for metallothionein, which was significantly upregulated in intestinal tissue compared to control fish. Altogether, our results suggests that dietary absorption efficiency of CuO NPs, their uptake across the gastrointestinal barrier into the organism, and effects on Cu-related genes is limited at low, environmentally relevant exposure doses (0.2 μg ⁶⁵Cu ^-1 fish ww day^-1).

Integrated analysis of transcriptomic and metabolomic data to evaluate responses to hypersalinity stress in the gill of the razor clam (Sinonovacula constricta)

Salinity is an important ecological factor that affects physiological metabolism, survival, and distribution of marine organisms. Despite changes in the osmolarity and composition of the cytosol during salinity shifts, marine mollusks are able to maintain their metabolic function. The razor clam (Sinonovacula constricta) survives the wide range of salinity in the intertidal zone via changes in behavior and physiology. To explore the stress responses and mechanisms of salinity tolerance in razor clams, we collected transcriptomic and metabolomic data from a control group (salinity 20‰, S20) and a salinity-stress group (salinity 35‰, S35). The transcriptome data showed that genes related to the immune system, cytoskeleton remodeling, and signal transduction pathways dominated in the S35 group to counteract hypersalinity stress in the gill. The metabolomic analysis showed that 142 metabolites were significantly different between the S35 and S20 groups and that amino acid and carbohydrate metabolism were affected by hypersalinity stress. Levels of amino acids and energy substances, such as l-proline, isoleucine, and fructose, were higher in the gill of the S35 group. The combination of transcriptomic and metabolomic data indicated that metabolism of amino acids, carbohydrates, and lipids was enhanced in the gill during adaptation to high salinity. These results clarified the complex physiological processes involved in the response to hyperosmotic stress and maintenance of metabolism in the gill of razor clams. These findings provide a reference for further study of the biological responses of euryhaline shellfish to hyperosmotic stress and a molecular basis for the search for populations with high salinity tolerance.

Effect of short-chain chlorinated paraffins on metabolic profiling of male SD rats

The toxic effect of high-dose of short-chain chlorinated paraffins (SCCPs) has been extensively studied, however the possible health risks induced by SCCPs at low-dose remain largely unknown. In this study, a comprehensive toxicology analysis of SCCPs was conducted with the exposure levels from the environmental dose to the Lowest Observed Adverse Effect Level (LOAEL) of 100 mg/kg/day. General toxicology analysis revealed inconspicuous toxicity of the environmental dose of SCCPs, high dose SCCP exposure inhibited the growth rate and increased the liver weight of rat. Metabolomics analysis indicated that SCCP-induced toxicity was triggered at environmentally relevant doses. First, inhibition of energy metabolism was observed with the decrease in blood glucose and the dysfunction of TCA cycle, which may have contributed to lower body weight gain in rats exposed to a high dose of SCCPs. Second, the increase of free fatty acids indicated the acceleration of lipid metabolism to compensate for the energy deficiency caused by hypoglycemia. Lipid oxidative metabolism inevitably leads to oxidative stress and stimulates the up-regulation of antioxidant metabolites such as GSH and GSSH. The up-regulation of polyunsaturated fatty acids (PUFAs) and phospholipids composed of arachidonic acid indicates the occurrence of inflammation. Dysfunction of lipid metabolism can be an indicator of SCCP-induced liver injury.

Waterborne copper exposure up-regulated lipid deposition through the methylation of GRP78 and PGC1α of grass carp Ctenopharyngodon idella

Early molecular events after the exposure of heavy metals, such as aberrant DNA methylation, suggest that DNA methylation was important in regulating physiological processes for animals and accordingly could be used as environmental biomarkers. In the present study, we found that copper (Cu) exposure increased lipid content and induced the DNA hypermethylation at the whole genome level. Especially, Cu induced hypermethylation of glucose-regulated protein 78 (grp78) and peroxisome proliferator-activated receptor gamma coactivator-1α (pgc1α). CCAAT/enhancer binding protein α (C/EBPα) could bind to the methylated sequence of grp78, whereas C/EBPβ could not bind to the methylated sequence of grp78. These synergistically influenced grp78 expression and increased lipogenesis. In contrast, DNA methylation of PGC1α blocked the specific protein 1 (SP1) binding and interfered mitochondrial function. Moreover, Cu increased reactive oxygen species (ROS) production, activated endoplasmic reticulum (ER) stress and damaged mitochondrial function, and accordingly increased lipid deposition. Notably, we found a new toxicological mechanism for Cu-induced lipid deposition at DNA methylation level. The measurement of DNA methylation facilitated the use of these epigenetic biomarkers for the evaluation of environmental risk.

Integrated proteomics, metabolomics and physiological analyses for dissecting the toxic effects of halosulfuron-methyl on soybean seedlings (Glycine max merr.)

Halosulfuron methyl (HSM) is a herbicide widely used to control sedge and broad-leaved weeds during crop production, but its environmental residue may damage non-target crops. Here, proteomics and metabolomics methods were used to explore the phytotoxicity mechanisms of HSM against soybean (Glycine max Merr.). Soybean seedlings were exposed to 0.01, 0.05 and 0.5 mg/L HSM for 8 d. The HSM applications significantly reduced chlorophyll and carotenoid contents in HSM-treated seedlings. Additionally, chlorophyll a fluorescence was seriously affected. The glutathione, hydrogen peroxide and malondialdehyde contents, as well as antioxidant enzyme activities, significantly increased in seedlings exposed to HSM. Furthermore, five enzymes involved in the tricarboxylic acid (TCA) cycle, α-ketoglutarate dehydrogenase, isocitrate dehydrogenase, aconitase, malic dehydrogenase and succinate dehydrogenase, were inhibited to varying degrees in HSM-treated seedlings compared with controls. Proteomics results showed multiple differentially abundant proteins involved in chlorophyll synthesis, photosystem processes and chloroplast ATP synthetase were down-regulated. Metabolomics analyses revealed that metabolites involved in the TCA cycle decreased significantly. Moreover, metabolites and proteins related to reactive oxygen species detoxification accumulated. In conclusion, the phytotoxicity mechanisms of HSM against soybean mainly act by damaging the photosynthetic machinery, inhibiting chlorophyll synthesis, interrupting the TCA cycle and causing oxidative stress. These results provide new insights into the toxicity mechanisms of sulfonylurea herbicides against non-target crops.

Cross-Taxa Distinctions in Mechanisms of Developmental Effects for Aquatic Species Exposed to Trifluralin

Standard ecological risk assessment practices often rely on larval and juvenile fish toxicity data as representative of the amphibian aquatic phase. Empirical evidence suggests that endpoints measured in fish early life stage tests are often sufficient to protect larval amphibians. However, the process of amphibian metamorphosis relies on endocrine cues that affect development and morphological restructuring and are not represented by these test endpoints. The present study compares developmental endpoints for zebrafish (Danio rerio) and the African clawed frog (Xenopus laevis), 2 standard test species, exposed to the herbicide trifluralin throughout the larval period. Danio rerio were more sensitive and demonstrated a reduction in growth measurements with increasing trifluralin exposure. Size of X. laevis at metamorphosis was not correlated with exposure concentration; however, time to metamorphosis was delayed relative to trifluralin concentration. Gene expression patterns indicate discrepancies in response by D. rerio and X. laevis, and dose-dependent metabolic activity suggests that trifluralin exposure perturbed biological pathways differently within the 2 species. Although many metabolites were correlated with exposure concentration in D. rerio, nontargeted hepatic metabolomics identified a subset of metabolites that exhibited a nonmonotonic response to trifluralin exposure in X. laevis. Linking taxonomic distinctions in cellular-level response with ecologically relevant endpoints will refine assumptions used in interspecies extrapolation of standard test effects and improve assessment of sublethal impacts on amphibian populations. Environ Toxicol Chem 2020;39:1797-1812. Published 2020. This article is a US government work and is in the public domain in the USA.

Sublethal exposure to copper supresses the ability to acclimate to hypoxia in a model fish species

Hypoxia is one of the major threats to biodiversity in aquatic systems. The association of hypoxia with nutrient-rich effluent input into aquatic systems results in scenarios where hypoxic waters could be contaminated with a wide range of chemicals, including metals. Despite this, little is known about the ability of fish to respond to hypoxia when exposures occur in the presence of environmental toxicants. We address this knowledge gap by investigating the effects of exposures to different levels of oxygen in the presence or absence of copper using the three-spined sticklebacks (Gasterosteus aculeatus) model. Fish were exposed to different air saturations (AS; 100%, 75% and 50%) in combination with copper (20 μg/L) over a 4 day period. The critical oxygen level (P_crit), an indicator of acute hypoxia tolerance, was 54.64 ± 2.51% AS under control conditions, and 36.21 ± 2.14% when fish were chronically exposed to hypoxia (50% AS) for 4 days, revealing the ability of fish to acclimate to low oxygen conditions. Importantly, the additional exposure to copper (20 μg/L) prevented this improvement in P_crit, impairing hypoxia acclimation. In addition, an increase in ventilation rate was observed for combined copper and hypoxia exposure, compared to the single stressors or the controls. Interestingly, in the groups exposed to copper, a large increase in variation in the measured P_crit was observed between individuals, both under normoxic and hypoxic conditions. This variation, if observed in wild populations, may lead to selection for a tolerant phenotype and alterations in the gene pool of the populations, with consequences for their sustainability. Our findings provide strong evidence that copper reduces the capacity of fish to respond to hypoxia by preventing acclimation and will inform predictions of the consequences of global increases of hypoxia in water systems affected by other pollutants worldwide.

Dysregulated Choline, Methionine, and Aromatic Amino Acid Metabolism in Patients with Wilson Disease: Exploratory Metabolomic Profiling and Implications for Hepatic and Neurologic Phenotypes

Wilson disease (WD) is a genetic copper overload condition characterized by hepatic and neuropsychiatric symptoms with a not well-understood pathogenesis. Dysregulated methionine cycle is reported in animal models of WD, though not verified in humans. Choline is essential for lipid and methionine metabolism. Defects in neurotransmitters as acetylcholine, and biogenic amines are reported in WD; however, less is known about their circulating precursors. We aimed to study choline, methionine, aromatic amino acids, and phospholipids in serum of WD subjects. Hydrophilic interaction chromatography-quadrupole time-of-flight mass spectrometry was employed to profile serum of WD subjects categorized as hepatic, neurologic, and pre-clinical. Hepatic transcript levels of genes related to choline and methionine metabolism were verified in the Jackson Laboratory toxic milk mouse model of WD (tx-j). Compared to healthy subjects, choline, methionine, ornithine, proline, phenylalanine, tyrosine, and histidine were significantly elevated in WD, with marked alterations in phosphatidylcholines and reductions in sphingosine-1-phosphate, sphingomyelins, and acylcarnitines. In tx-j mice, choline, methionine, and phosphatidylcholine were similarly dysregulated. Elevated choline is a hallmark dysregulation in WD interconnected with alterations in methionine and phospholipid metabolism, which are relevant to hepatic steatosis. The elevated phenylalanine, tyrosine, and histidine carry implications for neurologic manifestations and are worth further investigation.

Responses in the crucian carp (Carassius auratus) exposed to environmentally relevant concentration of 17α-Ethinylestradiol based on metabolomics

17α-ethynylestradiol (EE2), a ubiquitous synthetic endocrine disrupting chemical, was the principal component of contraceptive drugs and one of common hormone medications. The detrimental impact of EE2 on the reproduction of organisms was widely recognized. However, the underlying mechanisms of physiological and metabolome effects of EE2 on freshwater fish are still unclear. This study investigated the toxic effects and related mechanisms of EE2 on freshwater fish crucian carp (Carassius auratus) based on metabolomics. Crucian carp were exposed to EE2 at environmentally relevant concentration for 9 days, 18 days, and 27 days, and the biological responses were explored through analysis of the physiological endpoints, steroid hormones, and metabolome. The physiological endpoints of crucian carp had no distinct change after EE2 exposure. However, metabolomics analysis probed significant deviation based on chemometrics, indicating that the metabolomics approach was more sensitive to the effects of EE2 at environmentally relevant concentration to freshwater fish than the traditional endpoints. The alterations of 24 metabolites in gonad and 16 metabolites in kidney were induced by treatment with EE2, respectively, which suggesting the perturbations in amino acid metabolism, lipid metabolism, energy metabolism, and oxidative stress. Moreover, EE2 exposure could induce the disruption of lipid metabolism and then broke the homeostasis of endogenous steroid hormones. Metabolomics provided a new strategy for the studies on contaminant exposure at a low dose in the short term and gave important information for the toxicology and mechanism of EE2.

Genotoxic Response and Mortality in 3 Marine Copepods Exposed to Waterborne Copper

Copper (Cu) is an essential trace metal, but may also be toxic to aquatic organisms. Although many studies have investigated the cytotoxicity of Cu, little is known about the in vivo genotoxic potential of Cu in marine invertebrates. We investigated the genotoxicity of Cu in 2 pelagic calanoid copepods, Acartia tonsa and Temora longicornis, and the intertidal harpacticoid copepod Tigriopus brevicornis by exposing them for 6 and 72 h to waterborne Cu (0, 6, and 60 µg Cu/L). A subsequent 24-h period in filtered seawater was used to investigate delayed effects or recovery. Genotoxicity was evaluated as DNA strand breaks in individual copepods using the comet assay. Copper did not increase DNA strand breaks in any of the species at any concentration or time point. The treatment did, however, cause 100% mortality in A. tonsa following exposure to 60 µg Cu/L. Acartia tonsa and T. longicornis were more susceptible to Cu-induced mortality than the benthic harpacticoid T. brevicornis, which appeared to be unaffected by the treatments. The results show major differences in Cu susceptibility among the 3 copepods and also that acute toxicity of Cu to A. tonsa is not directly associated with genotoxicity. We also show that the comet assay can be used to quantify genotoxicity in individual copepods. Environ Toxicol Chem 2019;38:2224-2232. © 2019 SETAC.

Combined effects of polystyrene microplastics and natural organic matter on the accumulation and toxicity of copper in zebrafish

As emerging contaminants, microplastics (MPs) are predicted to act as vectors for other contaminants and their combined effects are largely unknown. In this study, the combined effects of MPs and natural organic matter (NOM) on the accumulation and toxicity of copper (Cu) in zebrafish (Danio rerio) were investigated. As a result, small-size MPs could absorb more Cu than large-size MPs. The presence of NOM promoted Cu adsorption on MPs in the pH range of 6-8. Our results demonstrate that the combination of MPs and NOM increased Cu accumulation in the livers and guts in a size-depended manner. Correspondingly, the results of biochemical test showed that MPs and NOM could aggravate Cu-toxicity in the livers and guts, which is manifested in the increased levels of malonaldehyde (MDA) and metallothionein (MT) and decreased levels of superoxide dismutase (SOD). Furthermore, the results of transcriptomic analysis suggested that such aggravation of toxicity was mainly attributed to the inhibition of Cu-ion transport and the enhanced oxidative stress. Since the co-existence of MPs and NOM in the environment is inevitable, their enhancement effects on the bioaccumulation and toxicity of other pollutants such as heavy metals deserve more attention.

Metabolomic analysis reveals the mechanism of aluminum cytotoxicity in HT-29 cells

BACKGROUND

Aluminum (Al) is toxic to animals and humans. The most common sources of human exposure to Al are food and beverages. The intestinal epithelium is the first barrier against Al-induced toxicity. In this study, HT-29, a human colon cancer cell line, was selected as an in vitro model to evaluate the Al-induced alteration in metabolomic profiles and explore the possible mechanisms of Al toxicity.

METHODS

MTT assay was performed to determine the half-maximal inhibitory concentration of Al ions. Liquid chromatography-mass spectrometry (LC-MS) was used for metabolomic analysis, and its results were further confirmed using quantitative reverse transcription polymerase chain reaction (RT-qPCR) of nine selected genes.

RESULTS

Al inhibited the growth of the HT-29 cells, and its half-maximal dose for the inhibition of cell proliferation was found to be four mM. This dose was selected for further metabolomic analysis, which revealed that 81 metabolites, such glutathione (GSH), phosphatidylcholines, phosphatidylethanolamines, and creatine, and 17 metabolic pathways, such as the tricarboxylic acid cycle, pyruvate metabolism, and GSH metabolism, were significantly altered after Al exposure. The RT-qPCR results further confirmed these findings.

CONCLUSION

The metabolomics and RT-qPCR results indicate that the mechanisms of Al-induced cytotoxicity in HT-29 cells include cellular apoptosis, oxidative stress, and alteration of lipid, energy, and amino acid metabolism.

Integrated application of multi-omics provides insights into cold stress responses in pufferfish Takifugu fasciatus

BACKGROUND

T. fasciatus (Takifugu fasciatus) faces the same problem as most warm water fish: the water temperature falls far below the optimal growth temperature in winter, causing a massive death of T. fasciatus and large economic losses. Understanding of the cold-tolerance mechanisms of this species is still limited. Integrated application of multi-omics research can provide a wealth of information to help us improve our understanding of low-temperature tolerance in fish.

RESULTS

To gain a comprehensive and unbiased molecular understanding of cold-tolerance in T. fasciatus, we characterized mRNA-seq and metabolomics of T. fasciatus livers using Illumina HiSeq 2500 and UHPLC-Q-TOF MS. We identified 2544 up-regulated and 2622 down-regulated genes in the liver of T. fasciatus. A total of 40 differential metabolites were identified, including 9 down-regulated and 31 up-regulated metabolites. In combination with previous studies on proteomics, we have established an mRNA-protein-metabolite interaction network. There are 17 DEMs (differentially-expressed metabolites) and 14 DEGs-DEPs (differentially co-expressed genes and proteins) in the interaction network that are mainly involved in fatty acids metabolism, membrane transport, signal transduction, and DNA damage and defense. We then validated a number of genes in the interaction network by qRT-PCR. Additionally, a number of SNPs (single nucleotide polymorphisms) were revealed through the transcriptome data. These results provide key information for further understanding of the molecular mechanisms of T. fasciatus under cold stress.

CONCLUSION

The data generated by integrated application of multi-omics can facilitate our understanding of the molecular mechanisms of fish response to low temperature stress. We have not only identified potential genes and SNPs involved in cold tolerance, but also show that some nutrient metabolites may be added to the diet to help the overwintering of T. fasciatus.

Sub-lethal effects of waterborne copper in early developmental stages of rainbow trout (Oncorhynchus mykiss)

The aim of this work was to study the impact of copper during a sub-chronic exposure to environmental concentrations in the early life stages of rainbow trout (Oncorhynchus mykiss). Eyed-stage embryos of rainbow trout, at 265 °D, were exposed in semi-static conditions to sub-lethal concentrations of CuSO₄ up to the larval stage (528 °D) under laboratory-controlled conditions. During 3 weeks, they were exposed to the environmentally-realistic concentration of 2 µg/L Cu and to a 10-fold higher concentration, 20 µg/L Cu. Several biological (survival, hatching success, malformation, growth) and behavioral (swimming activity) and molecular endpoints (genotoxicity and gene transcription) were studied. Exposure to 20 µg/L Cu had an inhibitory effect on hatching and increased half-hatched embryos (25%). At the end of the exposure, no significant differences were observed in growth of the larvae exposed to the highest Cu concentration. However, larvae exposed to 2 µg/L Cu exhibited increased growth in comparison with non-exposed larvae. The percentage of malformed larvae was significantly higher for both copper conditions, with skeletal malformations being the most observed. Expression of several genes was evaluated in whole larvae using quantitative real-time PCR. Genes involved in detoxification (gst, mt1 and mt2) and in cell cycle arrest (p53) were significantly repressed in both copper conditions when compared to control. In addition, potential genotoxic effects on larvae were investigated by the comet assay on blood cells, but this test did not demonstrate any significant DNA damage on larvae exposed to copper. This study confirms the adverse effects of copper on early life stages of rainbow trout even at the lowest environmentally relevant tested concentration.

Proteomic and metabolomic responses in hepatopancreas of whiteleg shrimp Litopenaeus vannamei infected by microsporidian Enterocytozoon hepatopenaei

Enterocytozoon hepatopenaei (EHP) causes hepatopancreatic microsporidiosis (HPM) in shrimp. HPM is not normally associated with shrimp mortality, but is associated with significant growth retardation. In this study, the responses induced by EHP were investigated in hepatopancreas of shrimp Litopenaeus vannamei using proteomics and metabolomics. Among differential proteins identified, several (e.g., peritrophin-44-like protein, alpha2 macroglobulin isoform 2, prophenoloxidase-activating enzymes, ferritin, Rab11A and cathepsin C) were related to pathogen infection and host immunity. Other proteomic biomarkers (i.e., farnesoic acid o-methyltransferase, juvenile hormone esterase-like carboxylesterase 1 and ecdysteroid-regulated protein) resulted in a growth hormone disorder that prevented the shrimp from molting. Both proteomic KEGG pathway (e.g., "Glycolysis/gluconeogenesis" and "Glyoxylate and dicarboxylate metabolism") and metabolomic KEGG pathway (e.g., "Galactose metabolism" and "Biosynthesis of unsaturated fatty acids") data indicated that energy metabolism pathway was down-regulated in the hepatopancreas when infected by EHP. More importantly, the changes of hormone regulation and energy metabolism could provide much-needed insight into the underlying mechanisms of stunted growth in shrimp after EHP infection. Altogether, this study demonstrated that proteomics and metabolomics could provide an insightful view into the effects of microsporidial infection in the shrimp L. vannamei.

Whole-transcriptome response to wastewater treatment plant and stormwater effluents in the Asian clam, Corbicula fluminea

The increase in human population and urbanization are resulting in an increase in the volume of wastewater and urban runoff effluents entering natural ecosystems. These effluents may contain multiple pollutants to which the biological response of aquatic organisms is still poorly understood mainly due to mixture toxicity and interactions with other environmental factors. In this context, RNA sequencing was used to assess the impact of a chronic exposure to wastewater treatment plant and stormwater effluents at the whole-transcriptome level and evaluate the potential physiological outcomes in the Asian clam Corbicula fluminea. We de-novo assembled a transcriptome from C. fluminea digestive gland and identified a set of 3,181 transcripts with altered abundance in response to water quality. The largest differences in transcriptomic profiles were observed between C. fluminea from the reference site and those exposed to wastewater treatment plant effluents. On both anthropogenically impacted sites, most differentially expressed transcripts were involved in signaling pathways in relation to energy metabolism such as mTOR and FoxO, suggesting an energy/nutrient deficit and hypoxic conditions. These conditions were likely responsible for damages to proteins and transcripts in response to wastewater treatment effluents whereas exposure to urban runoff might result in immune and endocrine disruptions. In absence of comprehensive chemical characterization, the RNAseq approach could provide information regarding the mode of action of pollutants and then be useful for the identification of which parameters must be studied at higher integration level in order to diagnose sites where the presence of complex and variable mixtures of chemicals is suspected.

Integrated metabolomic and transcriptomic analysis of brain energy metabolism in the male Oriental river prawn (Macrobrachium nipponense) in response to hypoxia and reoxygenation

Hypoxia is as an endocrine disruptor, and, in crustaceans, the energy metabolic consequences of hypoxia in the brain tissue are still poorly understood. We combined gas chromatography-mass spectrometry (GC-MS)-based metabolomic analysis and high-throughput RNA sequencing to evaluate the metabolic effects and subjacent regulatory pathways in the brain tissue of the male Oriental river prawn (Macrobrachium nipponense) in response to hypoxia and reoxygenation. We recorded LC₅₀ and heartbeats per minute of male M. nipponense juveniles. Hypoxia resulted in the generation of reactive oxygen species in the brain cells and alterations in gene expression and metabolite concentrations in the prawn brain tissue in a time-dependent manner. The transcriptomic analyses revealed specific changes in the expression of genes associated with metabolism pathways, which was consistent with the changes in energy metabolism indicated by the GC-MS metabolomic analysis. Quantitative real-time polymerase chain reaction and western blot confirmed the transcriptional induction of these genes because of hypoxia. The lactate levels increased significantly during hypoxia and decreased to normal after reoxygenation; this is consistent with a shift towards anaerobic metabolism, which may cause metabolic abnormalities in the brain tissue of M. nipponense. Overall, these results are consistent with metabolic disruption in the brain of M. nipponense exposed to hypoxia and will help in understanding how crustacean brain tissue adapts and responds to hypoxia and reoxygenation.

Waterborne exposure of adult zebrafish to silver nanoparticles and to ionic silver results in differential silver accumulation and effects at cellular and molecular levels

Effects of silver nanoparticles (Ag NPs) on freshwater species have been reported in several studies, but there is not information on the potential long-term consequences of a previous exposure. In this work, we investigated the long-term effects of maltose-coated Ag NPs (20 nm) and of ionic silver (10 μg/L) after 21 days of exposure and at 6 months post-exposure (mpe) in adult zebrafish. Exposure resulted in significant silver accumulation in the whole body of fish exposed to ionic silver, but not in those exposed to Ag NPs. However, autometallography revealed metal accumulation in the liver and intestine of fish treated with the two silver forms and especially in the intestine of fish exposed to Ag NPs. X-ray microanalysis showed the presence of silver in gills, liver and intestine and of Ag NPs in gill and liver cells. Inflammation and hyperplasia were evident in the gills after both treatments and these histopathological conditions remained at 6 mpe. According to the hepatic transcriptome analysis, at 3 days ionic silver regulated a larger number of transcripts (410) than Ag NPs (129), while at 21 days Ag NPs provoked a stronger effect (799 vs 165 regulated sequences). Gene ontology terms such as "metabolic processes" and "response to stimulus" appeared enriched after all treatments, while "immune system" or "reproductive processes" were specifically enriched after the exposure to Ag NPs. This suggests that the toxicity of Ag NPs may not be solely related to the release of Ag ions, but also to the NP form. No evident effects were found on protein oxidation or on hepatocyte lysosomal membrane stability during exposure, but effects recorded on liver lysosomes and persistent damage on gill tissue at 6 mpe could indicate potential for long-term effects in exposed fish.

Assessing the impact of wastewater treatment plant effluent on downstream drinking water-source quality using a zebrafish (Danio Rerio) liver cell-based metabolomics approach

Cell-based metabolomics was used in a proof-of-concept fashion to investigate the biological effects of contaminants as they traveled from a wastewater treatment plant (WWTP) discharge to a drinking water treatment plant (DWTP) intake in a surface-water usage cycle. Zebrafish liver (ZFL) cells were exposed to water samples collected along a surface-water flowpath, where a WWTP was located ∼14.5 km upstream of a DWTP. The sampling sites included: 1) upstream of the WWTP, 2) the WWTP effluent discharging point, 3) a proximal location downstream of the WWTP outfall, 4) a distal location downstream of the WWTP outfall, 5) the drinking water intake, and 6) the treated drinking water collected prior to discharge to the distribution system. After a 48-h laboratory exposure, the hydrophilic and lipophilic metabolites in ZFL cell extracts were analyzed by proton nuclear magnetic resonance (¹H NMR) spectroscopy and gas chromatography-mass spectrometry (GC-MS), respectively. Multivariate statistical analysis revealed distinct changes in metabolite profiles in response to WWTP effluent exposure. These effects on the hydrophilic metabolome gradually diminished downstream of the WWTP, becoming non-significant at the drinking water intake (comparable to upstream of the WWTP, p = 0.98). However, effects on the lipophilic metabolome increased significantly as the river flowed from the distal location downstream of the WWTP to the drinking water intake (p < 0.001), suggesting a source of bioactive compounds in this watershed other than the WWTP. ZFL cells exposed to treated drinking water did not exhibit significant changes in either the hydrophilic (p = 0.15) or lipophilic metabolome (p = 0.83) compared to the upstream site, suggesting that constituents in the WWTP effluent were efficiently removed by the drinking water treatment process. Impacts on ZFL cells from the WWTP effluent included disrupted energy metabolism, a global decrease in amino acids, and altered lipid metabolism pathways. Overall, this study demonstrated the utility of cell-based metabolomics as an effective tool for assessing the biological effects of complex pollutant mixtures, particularly when used as a complement to conventional chemical monitoring.

Comparative Metabolic Response between Cucumber ( Cucumis sativus) and Corn ( Zea mays) to a Cu(OH)2 Nanopesticide

Due to their unique properties, copper-based nanopesticides are emerging in the market. Thus, understanding their effect on crop plants is very important. Metabolomics can capture a snapshot of cellular metabolic responses to a stressor. We selected maize and cucumber as model plants for exposure to different doses of Cu(OH)₂ nanopesticide. GC-TOF-MS-based metabolomics was employed to determine the metabolic responses of these two species. Results revealed significant differences in metabolite profile changes between maize and cucumber. Furthermore, the Cu(OH)₂ nanopesticide induced metabolic reprogramming in both species, but in different manners. In maize, several intermediate metabolites of the glycolysis pathway and tricarboxylic acid cycle (TCA) were up-regulated, indicating the energy metabolism was activated. In addition, the levels of aromatic compounds (4-hydroxycinnamic acid and 1,2,4-benzenetriol) and their precursors (phenylalanine, tyrosine) were enhanced, indicating the activation of shikimate-phenylpropanoid biosynthesis in maize leaves, which is an antioxidant defense-related pathway. In cucumber, arginine and proline metabolic pathways were the most significantly altered pathway. Both species exhibited altered levels of fatty acids and polysaccharides, suggesting the cell membrane and cell wall composition may change in response to Cu(OH)₂ nanopesticide. Thus, metabolomics helps to deeply understand the differential response of these plants to the same nanopesticide stressor.

Expression of genes related to metal metabolism in the freshwater fish Hyphessobrycon luetkenii living in a historically contaminated area associated with copper mining

Copper (Cu) mining in Minas do Camaquã-Brazil, released significant amounts of metals into the João Dias creek, where Hyphessobrycon luetkenii inhabit. Because the involvement of Cu in biological processes its concentration and availability is regulated by molecules as the metal regulatory transcription factor (MTF-1), metallothionein (MT) and transporters (ATP7A and CTR1). These genes were whole sequenced and their expression (GE) evaluated in gills, liver and intestine. Were collected fish in non-contaminated and contaminated (Cu 3.4-fold higher) sites of the creek (CC and PP) and respectively translocated (CP and PC) for 96 h. The GE of the non-translocated groups evidenced that MT, MTF-1 and CTR1 have organ specific differences between both communities. Additionally the translocation allowed to identify organ specific changes associated with the activation/inactivation of protective mechanisms. These findings indicate that MTF-1, MT and CTR-1 GE play an important role in the tolerance of H. luetkenii to Cu contamination.

Chloride-accelerated Cu-Fenton chemistry for biofilm removal

Biofilms present challenges to numerous industries. Herein, a simple approach was developed based on chloride-accelerated Fenton chemistry, where copper oxide nanoparticles facilitate efficient generation of reactive chlorine species for biofilm removal.

Omics in Zebrafish Teratogenesis

The genome revolution represents a complete change on our view of biological systems. The quantitative determination of changes in all major molecular components of the living cells, the "omics" approach, opened whole new fields for all health sciences. Genomics, transcriptomics, proteomics, metabolomics, and others, together with appropriate prediction and modeling tools, will mark the future of developmental toxicity assessment both for wildlife and humans. This is especially true for disciplines, like teratology, which rely on studies in model organisms, as studies at lower levels of organization are difficult to implement. Rodents and frogs have been the favorite models for studying human reproductive and developmental disorders for decades. Recently, the study of the development of zebrafish embryos (ZE) is becoming a major alternative tool to adult animal testing. ZE intrinsic characteristics makes this model a unique system to analyze in vivo developmental alterations that only can be studied applying in toto approaches. Moreover, under actual legislations, ZE is considered as a replacement model (and therefore, excluded from animal welfare regulations) during the first 5 days after fertilization. Here we review the most important components of the zebrafish toolbox available for analyzing early stages of embryotoxic events that could eventually lead to teratogenesis.

Cellular and molecular responses of adult zebrafish after exposure to CuO nanoparticles or ionic copper

Due to their antimicrobial, electrical and magnetic properties, copper nanoparticles (NPs) are suitable for a vast array of applications. Copper can be toxic to biota, making it necessary to assess the potential hazard of copper nanomaterials. Zebrafish (Danio rerio) were exposed to 10 µg Cu/L of CuO NPs of ≈100 nm (CuO-poly) or ionic copper to compare the effects provoked after 3 and 21 days of exposure and at 6 months post-exposure (mpe). At 21 days, significant copper accumulation was only detected in fish exposed to ionic copper. Exposure to both copper forms caused histopathological alterations that could reduce gill functionality, more markedly in the case of ionic copper. Nevertheless, at 6 mpe higher prevalences of gill lesions were detected in fish previously exposed to CuO-poly NPs. No relevant histological alterations were detected in liver, but the lysosomal membrane stability test showed significantly impaired general health status after exposure to both metal forms that lasted up to 6 mpe. 69 transcripts appeared regulated after 3 days of exposure to CuO-poly NPs, suggesting that NPs could produce oxidative stress and reduce metabolism and transport processes. Thirty transcripts were regulated after 21 days of exposure to ionic copper, indicating possible DNA damage. Genes of the circadian clock were identified as the key genes involved in time-dependent differences between the two copper forms. In conclusion, each copper form showed a distinct pattern of liver transcriptome regulation, but both caused gill histopathological alterations and long lasting impaired health status in adult zebrafish.

Metabolomics and transcriptomics reveal the toxicity of difenoconazole to the early life stages of zebrafish (Danio rerio)

Difenoconazole is widely used to inhibit the growth of fungi, but its residue in the water environment may threaten ecosystem and human health. Here, ¹H nuclear magnetic resonance (NMR) and LC-MS/MS based metabolomics and transcriptomics approaches were used to assess the response of zebrafish to difenoconazole exposure. Early life stages of zebrafish were exposed to difenoconazole at environmentally relevant concentrations for 168h. Their comparison with the control group suggested an adverse development and disturbance of steroid hormones and VTG. KEGG pathway analysis identified five biological processes on the basis of differentially expressed genes (DEGs), as well as altered metabolites and amino acids in zebrafish following difenoconazole exposure. These affected processes included energy metabolism, amino acids metabolism, lipid metabolism, nucleotide metabolism, and an immune-related pathway. Collectively, these results bring us closer to an incremental understanding of the toxic effects of difenoconazole on zebrafish in its early development, and lend support to the continued use of the early life stages of zebrafish as a classical model to evaluate underlying environmental risks of xenobiotics in aquatic organisms.

Subacute oral toxicity assessment of benalaxyl in mice based on metabolomics methods

In this study, the metabolic responses of mice after 30 days of exposure to benalaxyl were assessed using NMR-based untargeted metabolomics and LC-MS-based targeted profiling of 20 amino acids. Urinary ¹H NMR analyses revealed alterations in energy metabolism, lipid metabolism, vitamin B metabolism, the urea cycle and amino acid metabolism, and targeted analyses indicated that the serum levels of asparagine, histidine, lysine and aspartic acid were significantly altered. Additionally, significant oxidative stress was observed in the liver and kidney, although no apparent histopathological injury was observed. The tissue distribution indicated a significant stereoselectivity in the brain, where (-)-R-benalaxyl was enriched. These data provide a comprehensive picture of the subacute toxic effects of benalaxyl in mice. The results of this study suggested that, for a toxicity evaluation, metabolomics analysis is much more sensitive than traditional toxicological methods. The results also highlight the combined use of untargeted and targeted metabolomics approaches in evaluating the health risks of xenobiotics.