Transcriptome analysis reveals the importance of exogenous nutrition in regulating antioxidant defenses during the mouth-opening stage in oviparous fish

Induction of oxidative stress and cardiac developmental toxicity in zebrafish embryos by arsenate at environmentally relevant concentrations

The contamination of water by arsenic (As) has emerged as a significant environmental concern due to its well-documented toxicity. Environmentally relevant concentrations of As have been reported to pose a considerable threat to fish. However, previous studies mainly focused on the impacts of As at environmentally relevant concentrations on adult fish, and limited information is available regarding its impacts on fish at early life stage. In this study, zebrafish embryos were employed to evaluate the environmental risks following exposure to different concentrations (0, 25, 50, 75 and 150 μg/L) of pentavalent arsenate (AsV) for 120 hours post fertilization. Our findings indicated that concentrations ≤ 150 μg/L AsV did not exert significant effects on survival or aberration; however, it conspicuously inhibited heart rate of zebrafish larvae. Furthermore, exposure to AsV significantly disrupted mRNA transcription of genes associated with cardiac development, and elongated the distance between the sinus venosus and bulbus arteriosus at 75 μg/L and 150 μg/L treatments. Additionally, AsV exposure enhanced superoxide dismutase (SOD) activity at 50, 75 and 150 μg/L treatments, and increased mRNA transcriptional levels of Cu/ZnSOD and MnSOD at 75 and 150 μg/L treatments. Concurrently, AsV suppressed metallothionein1 (MT1) and MT2 mRNA transcriptions while elevating heat shock protein70 mRNA transcription levels in zebrafish larvae resulting in elevated malondialdehyde (MDA) levels. These findings provide novel insights into the toxic effects exerted by low concentrations of AsV on fish at early life stage, thereby contributing to an exploration into the environmental risks associated with environmentally relevant concentrations.

Liver Transcriptome Analysis Reveals Energy Regulation and Functional Impairment of Onychostoma sima During Starvation

Releasing juvenile fish into resource-depleted waters is regarded as an effective way to restore fishery resources. However, during this stage, released fish are most vulnerable to long-term food deprivation due to environmental changes and low adaptability. Therefore, research regarding the energy regulation of fish under starvation stress is crucial to the optimization of release strategies. In this study, we performed a transcriptome analysis of the liver of Onychostoma sima subjected to starvation for 14 days. The results showed that, under long-term starvation, the liver regulated glucose homeostasis by activating the gluconeogenesis pathway. Meanwhile, the fatty acid metabolism pathway was activated to supply acetyl-coA to the TCA cycle, thus increasing mitochondrial ATP production and maintaining the balance of energy metabolism. Nevertheless, the activation of energy metabolism could not completely compensate for the role of exogenous nutrients, as evidenced by the downregulation of many genes involved in antioxidant defenses (e.g., cat, gpx3, mgst1, and mgst2) and immune response (e.g., c3, cd22, trnfrsf14, and a2ml). In summary, our data reveal the effects of long-term starvation on the energy metabolism and defensive regulation of starved juvenile fish, and these findings will provide important reference for the optimization of artificial release.

Delayed First Feeding Chronically Impairs Larval Fish Growth Performance, Hepatic Lipid Metabolism, and Visceral Lipid Deposition at the Mouth-Opening Stage

During the mouth-opening stage, fish larvae are susceptible to delayed first feeding (DFF). In this study, we explored the effects of DFF for two days on later growth and energy metabolism in larval fish. Results showed that DFF chronically impaired larval growth performance, thereby reducing the efficiency of feed utilization by larvae. In DFF larvae, the mRNA levels of growth inhibitors (i.e., igfbp1a and igfbp1b) were significantly upregulated and consistently maintained at high expression levels, which may be an important attribution of larval growth retardation. Concomitantly, DFF retarded the growth of adipose tissue and reduced lipid deposition in larval viscera, suggesting lipid metabolism is disordered in DFF larvae and generates inefficient lipid reserves. In the liver, we observed that DFF resulted in a significant accumulation of neutral lipids, and this phenotype did not disappear rapidly after DFF larvae received exogenous nutrition. As to the transcript analyses, we found that the expression of genes related to hepatic lipid synthesis (e.g., srebf1, srebf2, dgat1a, dgat1b, fasn, and scdb) in DFF larvae was consistently upregulated, while the expression of genes involved in lipid transport (e.g., apoa2, apoa4b.1, and apoa4b.3) was downregulated. Therefore, it appears that the inefficient lipid reserves in DFF larvae are associated with their hepatic lipid transport dysfunction. Taken together, our findings contribute to understanding the impairments to fish larvae caused by delayed first feeding during the mouth-opening stage and to aiding larval management in the aquaculture industry.

An Integrated Bioinformatics Approach to Identify Network-Derived Hub Genes in Starving Zebrafish

The present study was aimed at identifying causative hub genes within modules formed by co-expression and protein-protein interaction (PPI) networks, followed by Bayesian network (BN) construction in the liver transcriptome of starved zebrafish. To this end, the GSE11107 and GSE112272 datasets from the GEO databases were downloaded and meta-analyzed using the MetaDE package, an add-on R package. Differentially expressed genes (DEGs) were identified based upon expression intensity N(µ = 0.2, σ² = 0.4). Reconstruction of BNs was performed by the bnlearn R package on genes within modules using STRINGdb and CEMiTool. ndufs5 (shared among PPI, BN and COEX), rps26, rpl10, sdhc (shared between PPI and BN), ndufa6, ndufa10, ndufb8 (shared between PPI and COEX), skp1, atp5h, ndufb10, rpl5b, zgc:193613, zgc:123327, zgc:123178, wu:fc58f10, zgc:111986, wu:fc37b12, taldo1, wu:fb62f08, zgc:64133 and acp5a (shared between COEX and BN) were identified as causative hub genes affecting gene expression in the liver of starving zebrafish. Future work will shed light on using integrative analyses of miRNA and DNA microarrays simultaneously, and performing in silico and experimental validation of these hub-causative (CST) genes affecting starvation in zebrafish.

Transcriptome analysis reveals the early resistance of zebrafish larvae to oxidative stress

Oxidative stress is one of most common environmental stresses encountered by fish, especially during their fragile larval stage. More and more studies are aimed at understanding the antioxidant defense mechanism of fish larvae. Herein we characterized the early resistance of zebrafish larvae to oxidative stress and investigated the underlying transcriptional regulations using RNA-seq. We found that pre-exposure of zebrafish larvae to 2 mM H₂O₂ for 1 or 3 h significantly improved their survival under higher doses of H₂O₂ (3 mM), suggesting the antioxidant defenses of zebrafish larvae were rapidly built under pre-exposure of H₂O₂. Comparative transcriptome analysis showed that 310 (185 up and 125 down) and 512 (331 up and 181 down) differentially expressed genes were generated after 1 and 3 h of pre-exposure, respectively. KEGG enrichment analysis revealed that protein processing in endoplasmic reticulum is a highly enriched pathway; multiple genes (e.g., hsp70.1, hsp70.2, and hsp90aa1.2) encoding heat shock proteins in this pathway were sharply upregulated presumably to correct protein misfolding and maintaining the cellular normal functions during oxidative stress. More importantly, the Keap1/Nrf2 system-mediated detoxification enzyme system was significantly activated, which regulates the upregulation of target genes (e.g., gstp1, gsr, and prdx1) to scavenger reactive oxygen species, thereby defending against apoptosis. In addition, the MAPK, as a transmitter of stress signals, was activated, which may play an important role in activating antioxidant system in the early stages of oxidative stress. Altogether, these findings demonstrate that zebrafish larvae rapidly establish resistance to oxidative stress, and this involves changes in protein processing, stress signal transmission, and the activation of detoxification pathways.