Starvation stress affects the maternal development and larval fitness in zebrafish (Danio rerio)

Early stress exposure on zebrafish development: effects on survival, malformations and molecular alterations

The effects of stress during early vertebrate development can be especially harmful. Avoiding stressors in fish larvae is essential to ensure the health of adult fish and their reproductive performance and overall production. We examined the consequences of direct exposure to successive acute stressors during early development, including their effects on miR-29a and its targets, survival, hatching and malformation rates, larval behaviour and cartilage and eye development. Our aim was to shed light on the pleiotropic effects of early-induced stress in this vertebrate model species. Our results showed that direct exposure to successive acute stressors during early development significantly upregulated miR-29a and downregulated essential collagen transcripts col2a1a, col6a2 and col11a1a, decreased survival and increased malformation rates (swim bladder, otoliths, cardiac oedema and ocular malformations), promoting higher rates of immobility in larvae. Our results revealed that stress in early stages can induce different eye tissular architecture and cranioencephalic cartilage development alterations. Our research contributes to the understanding of the impact of stressful conditions during the early stages of zebrafish development, serving as a valuable model for vertebrate research. This holds paramount significance in the fields of developmental biology and aquaculture and also highlights miR-29a as a potential molecular marker for assessing novel larval rearing programmes in teleost species.

Combined Pituitary Hormone Deficiency in lhx4-Knockout Zebrafish

LIM homeobox 4 (LHX4) is a transcription factor crucial for anterior pituitary (AP) development. Patients with LHX4 mutation suffer from combined pituitary hormone deficiency (CPHD), short statures, reproductive and metabolic disorders and lethality in some cases. Lhx4-knockout (KO) mice fail to develop a normal AP and die shortly after birth. Here, we characterize a zebrafish lhx4-KO model to further investigate the importance of LHX4 in pituitary gland development and regulation. At the embryonic and larval stages, these fish express lower levels of tshb mRNA compared with their wildtype siblings. In adult lhx4-KO fish, the expressions of pituitary hormone-encoding transcripts, including growth hormone (gh), thyroid stimulating hormone (tshb), proopiomelanocortin (pomca) and follicle stimulating hormone (fshb), are reduced, the pomca promoter-driven expression in corticotrophs is dampened and luteinizing hormone (lhb)-producing gonadotrophs are severely depleted. In contrast to Lhx4-KO mice, Lhx4-deficient fish survive to adulthood, but with a reduced body size. Importantly, lhx4-KO males reach sexual maturity and are reproductively competent, whereas the females remain infertile with undeveloped ovaries. These phenotypes, which are reminiscent of those observed in CPHD patients, along with the advantages of the zebrafish for developmental genetics research, make this lhx4-KO fish an ideal vertebrate model to study the outcomes of LHX4 mutation.

Oxidative damage to mitochondrial DNA in maternal zebrafish (Danio rerio) exposed to dibutyl phthalate at environmentally relevant level

Dibutyl phthalate (DBP) is a widely-used plasticizer that is dispersed in various environments, causing significant pollution and health risks. The toxic mechanism of DBP has been discussed in recent years, while the susceptibility of mitochondrial DNA (mtDNA) to DBP exposure and the resulting damage remain unclear. In this study, maternal zebrafish were exposed to environmentally relevant concentration of DBP for 0, 2, 4, and 6 weeks. Results showed that DBP exposure impaired health status, leading to the reduced body length and weight, condition factor, hepatosomatic index, and gonadosomatic index. Furthermore, DBP exposure induced oxidative stress and ATP deficiency in the gill and liver in a time-dependent manner. The oxidized mtDNA (ox-mtDNA) levels in the D-loop and ND1 regions were assessed in different tissues, showing distinct response patterns. The high energy-consuming tissues such as heart, brain, gill, and liver exhibited elevated susceptibility to mitochondrial damage, with a rapid increase in ox-mtDNA levels in the short term. Conversely, in muscle, ovary, eggs, and offspring, ox-mtDNA gradually accumulated over the exposure period. Notably, the ox-mtDNA levels in the D-loop region of blood showed a prompt response to DBP exposure, making it convenient for evaluation. Additionally, decreased hatching rates, increased mortality, lipoperoxidation, and depressed swimming performance were observed in offspring following maternal DBP exposure, suggesting the inherited impairments of maternal mtDNA. These findings highlight the potential for ox-mtDNA to serve as a convenient biomarker for environmental contamination, aiding in ecological risk assessment and forewarning systems in aquatic environment.

Starvation-induced changes in the proteome and transcriptome of the salivary glands of leech (Hirudo nipponia)

Hirudo nipponia is an important medicinal animal in China. Its salivary gland secretions contain a variety of protein bioactive substances. Investigations of its salivary glands are of great significance in the study of the medicinal value and mechanism of leech secretions. Illumina RNA-Seq technology was used to perform transcriptome sequencing of salivary gland tissue of H. nipponia under starvation (D30) and fed (D0) states. A total of 2,650 differentially expressed genes (DEGs) were screened. Using the label-free protein quantification technique and bioinformatics analysis, the expression of differentially expressed proteins (DEPs) in the salivary gland tissue of H. nipponia was compared. A total of 2,021 proteins were identified, among which 181 proteins were differentially expressed between the starvation and fed states, with 72 significantly upregulated and 109 significantly downregulated. The salivary glands of H. nipponia synthesized protein-based active substances after 30 days of starvation and adapted to the starvation environment by weakening respiratory activity and reducing metabolic activity to reduce energy expenditure. Energy was produced by glycolysis and the tricarboxylic acid cycle for the synthesis of substances such as antibiotics. This study combined transcriptome and proteome sequencing data to provide a data reference for an in-depth study of the regulatory mechanism of salivary gland secretions of H. nipponia under starvation stress by analyzing DEGs and DEPs.

A short-term of starvation improved the antioxidant activity and quality of African catfish (Clarias gariepinus)

Clarias gariepinus is an important freshwater fish with high economic value and breeding potential in China. It is a fast-growing and adaptable catfish, but the main problems facing the current market are its low price and poor taste, although starvation is a good solution to these problems. In this study, the effects of starvation on the physiology, biochemistry, and muscle quality of C. gariepinus were investigated. The results showed that compared with the control group, the weight gain rate and specific growth rate of the starvation group were significantly different. Body weight, visceral weight, condition factor, viscerosomatic index, hepatosomatic index, and viscera fat index all decreased, while visceral weight and hepatosomatic index decreased significantly after starvation for 30 days. The hardness and crude protein of muscle increased significantly and crude lipid decreased significantly. Taste-enhancing amino acids increased slightly, and fatty acids increased significantly. Compared with the control group, starvation led to changes in antioxidant defense parameters. The level of malondialdehyde (MDA) in liver increased significantly; the activities of superoxide dismutase (SOD) increased in serum after 30 days; the activities of glutathione peroxidase (GSH-Px) increased considerably in the serum and liver after 15 days; the activities of alanine aminotransferase (ALT) increased considerably in the serum and liver after 30 days. The in-depth study of changes in physiological, biochemical, and nutritional components of fish under starvation is helpful to understand the ecological strategy of fish to adapt to starvation and of great guiding significance for fishery resource management and aquaculture production.

The physiological response of oriental river prawn Macrobrachium nipponense to starvation-induced stress

Environmental stresses play critical roles in the physiology of crustaceans. Food deprivation is an important environmental factor and a regular occurrence in both natural aquatic habitats and artificial ponds. However, the underlying physiological response mechanisms to starvation-caused stress in crustaceans are yet to be established. In the present study, the hepatopancreas tissue of Macrobrachium nipponense was transcriptome analyzed and examined for starvation effects on oxidative stress, DNA damage, autophagy, and apoptosis across four fasting stages (0 (control group), 7, 14, and 21 days). These results indicated that a ROS-mediated regulatory mechanism is critical to the entire fasting process. At the initial stage of starvation (fasting 0 d ~ 7 d), ROS concentration increased gradually, activating antioxidant enzymes to protect the cellular machinery from the detrimental effects of oxidative stress triggered by starvation-induced stress. ROS content production (hydrogen peroxide and superoxide anion) then rose continuously with prolonged starvation (fasting 7 d ~ 14 d), reaching peak levels and resulting in autophagy in hepatopancreas cells. During the final stages of starvation (fasting 14 d ~ 21 d), excessive ROS induced DNA damage and cell apoptosis. Furthermore, autophagolysosomes and apoptosis body were further identified with transmission electron microscopy. These findings lay a foundation for further scrutiny of the molecular mechanisms combating starvation-generated stress in M. nipponense and provide fishermen with the theoretical guidance for adopting fasting strategies in M. nipponense aquaculture.

Mitochondrial DNA Stress-Mediated Health Risk to Dibutyl Phthalate Contamination on Zebrafish (Danio rerio) at Early Life Stage

Plastics contaminations are found globally and fit the exposure profile of the planetary boundary threat. The plasticizer of dibutyl phthalate (DBP) leaching has occurred and poses a great threat to human health and the ecosystem for decades, and its toxic mechanism needs further comprehensive elucidation. In this study, environmentally relevant levels of DBP were used for exposure, and the developmental process, oxidative stress, mitochondrial ultrastructure and function, mitochondrial DNA (mtDNA) instability and release, and mtDNA-cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) signaling pathway with inflammatory responses were measured in zebrafish at early life stage. Results showed that DBP exposure caused developmental impairments of heart rate, hatching rate, body length, and mortality in zebrafish embryo. Additionally, the elevated oxidative stress damaged mitochondrial ultrastructure and function and induced oxidative damage to the mtDNA with mutations and instability of replication, transcription, and DNA methylation. The stressed mtDNA leaked into the cytosol and activated the cGAS-STING signaling pathway and inflammation, which were ameliorated by co-treatment with DBP and mitochondrial reactive oxygen species (ROS) scavenger, inhibitors of cGAS or STING. Furthermore, the larval results suggest that DBP-induced mitochondrial toxicity of energy disorder and inflammation were involved in the developmental defects of impaired swimming capability. These results enhance the interpretation of mtDNA stress-mediated health risk to environmental contaminants and contribute to the scrutiny of mitochondrial toxicants.

Characterization of three lamp genes from largemouth bass (Micropterus salmoides): molecular cloning, expression patterns, and their transcriptional levels in response to fast and refeeding strategy

Lysosomes-associated membrane proteins (LAMPs), a family of glycosylated proteins and major constituents of the lysosomal membranes, play a dominant role in various cellular processes, including phagocytosis, autophagy and immunity in mammals. However, their roles in aquatic species remain poorly known. In the present study, three lamp genes were cloned and characterized from Micropterus salmoides. Subsequently, their transcriptional levels in response to different nutritional status were investigated. The full-length coding sequences of lamp1, lamp2 and lamp3 were 1251bp, 1224bp and 771bp, encoding 416, 407 and 256 amino acids, respectively. Multiple sequence alignment showed that LAMP1-3 were highly conserved among the different fish species, respectively. 3-D structure prediction, genomic survey, and phylogenetic analysis were further confirmed that these genes are widely existed in vertebrates. The mRNA expression of the three genes was ubiquitously expressed in all selected tissues, including liver, brain, gill, heart, muscle, spleen, kidney, stomach, adipose and intestine, lamp1 shows highly transcript levels in brain and muscle, lamp2 displays highly expression level in heart, muscle and spleen, but lamp3 shows highly transcript level in spleen, liver and kidney. To analyze the function of the three genes under starvation stress in largemouth bass, three experimental treatment groups (fasted group and refeeding group, control group) were established in the current study. The results indicated that the expression of lamp1 was significant induced after starvation, and then returned to normal levels after refeeding in the liver. The expression of lamp2 and lamp3 exhibited the same trend in the liver. In addition, in the spleen and the kidney, the transcript level of lamp1 and lamp2 was remarkably increased in the fasted treatment group and slightly decreased in the refed treatment group, respectively. Collectively, our findings suggest that three lamp genes may have differential function in the immune and energetic organism in largemouth bass, which is helpful in understanding roles of lamps in aquatic species.

Paternal starvation affects metabolic gene expression during zebrafish offspring development and lifelong fitness

Dietary restriction in the form of fasting is a putative key to a healthier and longer life, but these benefits may come at a trade-off with reproductive fitness and may affect the following generation(s). The potential inter- and transgenerational effects of long-term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split-egg clutch design to explore the male-specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected, we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 h post-fertilisation in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra-embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism-associated genes. These similarities suggest a physiologically relevant, directed and potentially adaptive response transmitted by the father, independently from the offspring's nutritional state, which was defined by the mother.

Whole-Genome Methylation Sequencing of Large Yellow Croaker (Larimichthys crocea) Liver Under Hypoxia and Acidification Stress

Large yellow croaker (Larimichthys crocea) is an important aquaculture species in China. This study analysed whole-genome methylation differences in liver tissues of young fish under different hypoxic and acidification conditions. Differentially methylated regions (DMRs) and differentially methylated genes (DMGs) were identified. Gene ontology (GO) and Kyoto encyclopaedia of genes and genomes (KEGG) enrichment analyses of DMGs were conducted to explore the mechanism of coping with hypoxic acidification. The main methylation type was CG, accounting for > 70% of total methylation, significantly higher than CHG and CHH methylation types. GO enrichment analysis of DMGs revealed strong enrichment of nervous system development, cell periphery, plasma membrane, cell junction organisation, cell junction, signalling receptor activity, molecular sensor activity, cell-linked tissue junction organisation, cell-cell adhesion and nervous system development. KEGG enrichment analysis of DMR-related genes identified cell adhesion molecules, cortisol synthesis and secretion and aldosterone synthesis and secretion as the three key pathways regulating the physiological responses to hypoxia and acidification. Long-term hypoxic and acidification stress affected the immune system, nervous system and stress responses of large yellow croaker. Whole-genome sequencing analysis of exposed tissues was used to investigate changes that occur in L. crocea in response to hypoxic and acidic conditions at the DNA methylation level. The findings contribute to our comprehensive understanding of functional methylation in large yellow croaker and will support future research on the response mechanisms of this species under different environmental pressures.

Insight into the health risk implicated in mitochondrial toxicity of dibutyl phthalate exposure on zebrafish (Danio rerio) cells

Dibutyl phthalate (DBP) is commonly applied plasticizer in plastic products such as face masks, easily leaches or migrates into environment and its widespread contamination posed profound health risks. Further concerns rise regarding to the toxicity of DBP at subcellular level, while little is known about the ranging effects on mitochondrial susceptibility. Present study investigated the mitochondrial impairments with implicated cell death upon DBP exposure on zebrafish cells. Elevated mitochondrial oxidative stress reduced its membrane potential and count, enhanced fragmentation, and impaired ultrastructure that showed smaller size and cristae rupture. Afterwards, the critical function of ATP synthesis was damaged and the stabilized binding capacity between DBP with mitochondrial respiratory complexes was simulated by the molecular docking. And the top pathways enrichment of mitochondrion and metabolism by transcriptome analyses verified the mitochondrial dysfunction that indicated the human diseases risks. The mitochondrial DNA (mtDNA) replication and transcription with DNA methylation modifications were also disrupted, reflecting the genotoxicity on mtDNA. Moreover, the activated autophagy and apoptosis underlying mitochondrial susceptibility integrated into cellular homeostasis changes. These findings provide the first systemic evidence broadening and illustrating the mitochondrial toxicity of DBP exposure on zebrafish model that raise concern on phthalates contamination and ecotoxicological evaluation.

Starvation-induced changes in sex ratio involve alterations in sex-related gene expression and methylation in Pacific oyster Crassostrea gigas

Aquatic animals are subject to varying degrees of starvation stress in their natural habitats due to food limitations. Consequently, starvation is a crucial environmental factor for sex determination in many species; however, limited research has been conducted on the effects of starvation on sex determination in shellfish. Here, four full sibling families of Pacific oysters were established and subjected to starvation stress. The results demonstrated that starvation caused the sex ratio (female to male) to change from 1:0.78 to 1:1.44 and resulted in a delay in gonadal development. Further studies revealed that the expression levels of DNA methylation-related genes Dnmt1 (DNA methyltransferase 1), Dnmt3a/b (DNA methyltransferase 3a/b) and Tet3 (tet methylcytosine dioxygenase 3) decreased under starvation stress. Conversely, the upregulation of Dmrt1 (doublesex and mab-3 related transcription factor 1), a gene typically associated with males, in females suggests that the increased proportion of males may be linked to starvation-induced high expression of this particular gene. In addition, the gene Dgkd (diacylglycerol kinase delta), which is involved in the regulation of second messenger protein kinase C, was differentially methylated between males and females, with the methylation level of this gene gradually increasing with male development, while the methylation level of this gene decreased under starvation stress. Correlation analysis of Dgkd methylation levels with expression levels showed a negative correlation between DNA methylation and gene expression. Finally dual fluorescence reporter experiments confirmed that DNA methylation suppressed Dgkd expression in vitro. In summary, the results suggest that starvation may regulate Dgkd gene expression through DNA methylation and thus affect Dmrt1 expression, thereby causing sex reversal in the Pacific oyster. The outcomes resolved how environmental factors are involved in sex reversal from an epigenetic perspective and provided a theoretical basis for sex control breeding in the Pacific oyster.

Field-realistic dose of cefotaxime enhances potential mobility of β-lactam resistance genes in the gut microbiota of zebrafish (Danio rerio)

With large amounts of cephalosporin end up in natural ecosystems, water has been acknowledged as the large reservoir of β-lactam resistance over the past decades. However, there is still insufficient knowledge available on the function of the living organisms to the transmission of antibiotic resistance. For this reason, in this study, using adult zebrafish (Danio rerio) as animal model, exposing them to environmentally relevant dose of cefotaxime for 150 days, we asked whether cefotaxime contamination accelerated β-lactam resistance in gut microbiota as well as its potential transmission. Results showed that some of β-lactam resistance genes (βRGs) were intrinsic embedded in intestinal microbiome of zebrafish even without antibiotic stressor. Across cefotaxime treatment, the abundance of most βRGs in fish gut microbiome decreased apparently in the short term firstly, and then increased with the prolonged exposure, forming distinctly divergent βRG profiles with antibiotic-untreated zebrafish. Meanwhile, with the rising concentration of cefotaxime, the range of βRGs' host-taxa expanded and the co-occurrence relationships of mobile genetics elements (MGEs) with βRGs intensified, indicating the enhancement of βRGs' mobility in gut microbiome when the fish suffered from cefotaxime contamination. Furthermore, the path of partial least squares path modeling (PLS-PM) gave an integral assessment on the specific causality of cefotaxime treatment to βRG profiles, showing that cefotaxime-mediated βRGs variation was most ascribed to the alteration of MGEs under cefotaxime stress, followed by bacterial community, functioning both direct influence as βRG-hosts and indirect effects via affecting MGEs. Finally, pathogenic bacteria Aeromonas was identified as the critical host for multiple βRGs in fish guts, and its β-lactam resistance increased over the duration time of cefotaxime exposure, suggesting the potential spreading risks for the antibiotic-resistant pathogens from environmental ecosystems to clinic. Overall, our finding emphasized cefotaxime contamination in aquatic surroundings could enhance the β-lactam resistance and its transmission mobility in fish bodies.

Previous stress causes a contrasting response to cadmium toxicity in the aquatic snail Potamopyrgus antipodarum: lethal and behavioral endpoints

In aquatic ecosystems, animals are often exposed to a combination of stressors, including both natural and anthropogenic factors. Combined stressors may have additive or interactive effects on animals, either magnifying or reducing the effects caused by each stressor alone. Therefore, standardized bioassays can lead to overestimations or underestimations of the risk of toxicants if natural stressors are not bear in mind. The inclusion of natural stress in laboratory bioassays may help to extrapolate the laboratory results to ecosystems. This study assesses the effects of successive exposure to two sources of stress (high water conductivity and cadmium toxicity) on the behavior and survival of the aquatic snail Potamopyrgus antipodarum (Tateidae, Mollusca). I conducted a bioassay consisting on exposure to high conductivity (5000 mg NaCl/L, 7 days), followed by exposure to cadmium (0.03, 0.125, and 0.25 mg Cd/L for 7 days) and by a post-exposure period (7 days). Mortality, inactivity, and the time to start activity of active animals were monitored in each animal. In general, cadmium lethality was higher in animals previously undergoing high conductivity than in non-stressed ones. Previously stressed animals showed longer time to start activity, with a noticeable effect at the two highest cadmium concentrations. Animals submitted to the two highest cadmium concentration both, stressed and non-stressed, showed a moderate recovery during the post-exposure period. It is concluded that previous stress caused a worsening of the cadmium toxicity on the aquatic snail Potamopyrgus antipodarum, which is especially noticeable for mortality. However, there was no interactive effect between cadmium and conductivity on snail activity, which may be indicative of recovery after cadmium exposure regardless the previous stress suffered by the snails.

Transcriptome and DNA Methylation Responses in the Liver of Yellowfin Seabream Under Starvation Stress

Fish suffer from starvation due to environmental risks such as extreme weather in the wild and due to insufficient feedings in farms. Nutrient problems from short-term or long-term starvation conditions can result in stress-related health problems for fish. Yellowfin seabream (Acanthopagrus latus) is an important marine economic fish in China. Understanding the molecular responses to starvation stress is vital for propagation and culturing yellowfin seabream. In this study, the transcriptome and genome-wide DNA methylation levels in the livers of yellowfin seabream under 14-days starvation stress were analyzed. One hundred sixty differentially expressed genes (DEGs) by RNA-Seq analysis and 737 differentially methylated-related genes by whole genome bisulfite sequencing analysis were identified. GO and KEGG pathway enrichment analysis found that energy metabolism-related pathways such as glucose metabolism and lipid metabolism were in response to starvation. Using bisulfite sequencing PCR, we confirmed the presence of CpG methylation differences within the regulatory region of a DEG ppargc1a in response to 14-days starvation stress. This study revealed the molecular responses of livers in response to starvation stress at the transcriptomic and whole genome DNA methylation levels in yellowfin seabream.

Post-exposure Period as a key Factor to Assess Cadmium Toxicity: Lethal vs. Behavioral Responses

The exposure of animals to pollution in ecosystems is not always chronic. Toxicants can remain in aquatic ecosystems for a short-term. To improve the extrapolation of laboratory results to natural scenarios the inclusion of post-exposure periods is a relevant issue. The present study focuses on the assessment of cadmium toxicity on survival and behavior of the aquatic snail Potamopyrgus antipodarum (Tateidae, Mollusca) during exposure and post-exposure. Animals were exposed for 48 h to cadmium (0.05, 0.14, 0.44 and 1.34 mg Cd/L) and 168 h of post-exposure. During the post-exposure period an increase in mortality in all concentrations was observed. The effects observed during the post-exposure period on the LC50 and EC50 were significant. During the post-exposure, behavior showed a clear recovery in surviving animals exposed to 0.44 mg Cd/L. Animals exposed to 0.05 mg Cd/L did not show differences with control. Therefore, mortality after exposure should be included in the ecotoxicological bioassays for a more realistic estimation of the cadmium effects. To assess the degree of animal recovery after cadmium exposure, behaviour has been shown as an adequate parameter.

Partial immune responses in Sichuan bream (Sinibrama taeniatus) after starvation

Background

Food deprivation is a severe stress across multiple fields and it might be a challenge to immune system.

Methods

In the present study, adult male Sinibrama taeniatus were deprived of feed for 7 to 28 days. We explored the effects of starvation on immunity in S. taeniatus through hematological analysis, antioxidant capacity analysis, detection of the content or activity of immune factors in plasma, and transcriptomic analysis.

Results

The results indicated that biometric indexes significantly decreased in the fish after starvation, the proportion of thrombocyte, neutrophil and monocyte increased and, conversely, the proportion of lymphocyte decreased. The antioxidant indexes (SOD and CAT) and innate immune parameters (LZM, C3) were upregulated in fish suffering from a short period of starvation, while adaptive immune parameter (IgM) conversely declined. The transcriptome analysis revealed the changes of various metabolic regulatory pathways involved in fatty acids and amino acids, as well as the immune responses and antioxidant capacity.

Conclusions

Taken together, this research in the present study suggested an induced innate immunity while a partly suppressed adaptive immunity under a short period starvation.

DNA methylation of pck1 might contribute to the programming effects of early high-carbohydrate diets feeding to the glucose metabolism across two generations in zebrafish (Danio rerio)

The purpose of this study is to assess the effects of early high-carbohydrate stimulus on glucose metabolism in zebrafish (Danio rerio) over two generations and explore the mechanisms that explain those nutritional programming effects via epigenetic modifications. The larvae were delivered a high-carbohydrate diet (53.66%) that was used as an early nutritional stimulus from the first feeding to the end of the yolk sac (FF) and 5 days after yolk-sac exhaustion (YE). The larvae (F0) and their offspring (F1) were then both fed the control diet (22.69%) until adulthood (15 weeks), and they were challenged with a high-carbohydrate diet (35.36%) at the 16th week. The results indicated that early stimulus immediately raised the mRNA levels of genes involved in glycolysis and gluconeogenesis. At the end of F0 challenge, both treatment groups decreased the plasma glucose levels, increased the expression levels of glucokinase (gck), and inhibited the mRNA during gluconeogenesis. When challenged in F1, the glucose levels were lower in FF (F1), and the mRNA levels of phosphoenolpyruvate carboxykinase 1 (pck1) were decreased in FF (F1) and YE (F1). Besides, in both experimental groups (F0 and F1), the CpG island of pck1 maintained lower levels of hypermethylated expression from F0 adult, 24 h post-fertilization embryo, to F1 adult. In conclusion, these results indicated that an early high-carbohydrate stimulus could significantly reprogram glucose metabolism in adult zebrafish, that those modifications could be partially transmitted to the next generation, and that the DNA methylation of pck1 might work as a stable epigenetic marker to contribute to those processes.

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.

Mitochondrial changes in fish cells in vitro in response to serum deprivation

Mitochondria are critical to cellular activity that implicated in expansive networks to maintain organismal homeostasis under external stimuli of nutrient variability, a common and severe stress to fish performance during the intensive culture conditions. In the present study, zebrafish embryonic fibroblast cells were used to investigate the fish mitochondrial changes upon serum deprivation. Results showed that mitochondrial content and membrane potential were significantly reduced with increased intracellular ROS level in the serum deprivation treated fish cells. And the impaired mitochondria were characterized by rough and fracted outer membrane, and more fused mitochondria were frequently observed with the upregulated mRNA expressions of mitochondrial fusion genes (mfn1b, mfn2, and opa1). Besides, the mitochondrial DNA (mtDNA) copy numbers of mtatp6, mtcox1, mtcytb, mtnd4, and mtnd6 were overall showing the highly significant reduction, together with the mRNA expressions of these genes significantly increased, exhibiting the compensatory effects in mitochondria. Furthermore, the methyl-cytosine of whole mtDNA was compared and the methyl-reads numbers were distinctly increased in the treatment group, reflecting the instability of fish mtDNA with mitochondrial dysfunction under nutrient fluctuations. Collectively, current findings could facilitate the integrated research between fish mitochondrial response and external variables that indicates the potentially profound and durative deficits in fish health during the aquaculture processes.

Environmentally relevant concentrations of benzophenones triggered DNA damage and apoptosis in male Chinese rare minnows (Gobiocypris rarus)

Benzophenone-type ultraviolet (UV) filters (BPs) are commonly used as sunscreen agents, fragrance enhancers and plastic additives, and are great threats to aquatic organisms due to their high detected concentrations in the aquatic environment. However, few studies on their toxicity and mechanism in fish have been clearly reported. In this study, Chinese rare minnows (Gobiocypris rarus) were exposed to benzophenone (BP), 2,4-dihydroxybenzophenone (BP-1), and 5-benzoyl-4-hydroxy-2-methoxybenzenesulfonic acid (BP-4) at 5, 50, 500 µg/L for 28 d to assess their toxicity. Transcriptomics screening showed that cell cycle, DNA replication and repair were significantly altered pathways (p < 0.05). The altered transcripts were similar to those identified by RNA-seq. DNA damage and 8-OHdG levels were significantly increased at 50 and 500 μg/L groups (p < 0.05). The DNA methylcytosine level was not significantly changed exposure to BP, BP-1 and BP-4. TUNEL assays indicated that hepatic apoptosis was significantly improved at 500 μg/L BP and BP-4 and 50 and 500 μg/L BP-1 (p < 0.05), with the significantly increasing the activity of caspase-3, -8 and -9 (p < 0.05). Molecular docking analysis revealed that BP, BP-1 and BP-4 could bind differently to caspase-3 through different binding interactions. Therefore, BP-1 induced more serious oxidative DNA damage and apoptosis by activating caspase-3 than BP and BP-4, which will provide theoretical basis and data support for ecological evaluation of aquatic organisms induced by BPs.

Genomic selection signatures in farmed Colossoma macropomum from tropical and subtropical regions in South America

Tambaqui or cachama (Colossoma macropomum) is one of the most important neotropical freshwater fish used for aquaculture in South America, and its production is concentrated at low latitudes (close to the Equator, 0°), where the water temperature is warm. Therefore, understanding how selection shapes genetic variations and structure in farmed populations is of paramount importance in evolutionary biology. High‐throughput sequencing to generate genome‐wide data for fish species allows for elucidating the genomic basis of adaptation to local or farmed conditions and uncovering genes that control the phenotypes of interest. The present study aimed to detect genomic selection signatures and analyze the genetic variability in farmed populations of tambaqui in South America using single‐nucleotide polymorphism (SNP) markers obtained with double‐digest restriction site‐associated DNA sequencing. Initially, 199 samples of tambaqui farmed populations from different locations (located in Brazil, Colombia, and Peru), a wild population (Amazon River, Brazil), and the base population of a breeding program (Aquaculture Center, CAUNESP, Jaboticabal, SP, Brazil) were genotyped. Observed and expected heterozygosity was 0.231–0.350 and 0.288–0.360, respectively. Significant genetic differentiation was observed using global FST analyses of SNP loci (FST = 0.064, p < 0.050). Farmed populations from Colombia and Peru that differentiated from the Brazilian populations formed distinct groups. Several regions, particularly those harboring the genes of significance to aquaculture, were identified to be under positive selection, suggesting local adaptation to stress under different farming conditions and management practices. Studies aimed at improving the knowledge of genomics of tambaqui farmed populations are essential for aquaculture to gain deeper insights into the evolutionary history of these fish and provide resources for the establishment of breeding programs.

The Effects of Early Life Stress on the Brain and Behaviour: Insights From Zebrafish Models

The early life period represents a window of increased vulnerability to stress, during which exposure can lead to long-lasting effects on brain structure and function. This stress-induced developmental programming may contribute to the behavioural changes observed in mental illness. In recent decades, rodent studies have significantly advanced our understanding of how early life stress (ELS) affects brain development and behaviour. These studies reveal that ELS has long-term consequences on the brain such as impairment of adult hippocampal neurogenesis, altering learning and memory. Despite such advances, several key questions remain inadequately answered, including a comprehensive overview of brain regions and molecular pathways that are altered by ELS and how ELS-induced molecular changes ultimately lead to behavioural changes in adulthood. The zebrafish represents a novel ELS model, with the potential to contribute to answering some of these questions. The zebrafish offers some important advantages such as the ability to non-invasively modulate stress hormone levels in a whole animal and to visualise whole brain activity in freely behaving animals. This review discusses the current status of the zebrafish ELS field and its potential as a new ELS model.

Exposure to artificial light at night (ALAN) alters RNA:DNA ratios in a sandy beach coleopteran insect

Coastal habitats worldwide, including sandy beaches, are becoming increasingly exposed to Artificial Light at Night (ALAN). Despite the spread of this global stressor, research assessing ALAN potential impacts remain scarce, particularly at the molecular level. This study addressed this gap by assessing the influence of ALAN on the physiological condition of the sandy beach insect Phalerisida maculata Kulzer (Coleoptera, Tenebrionidae). RNA:DNA ratios were used here as a proxy of the insect's nutritional condition in laboratory trials that lasted 20 d. Insects were exposed to two representative ALAN conditions (either 60 or 120 lx) and compared with those maintained in a natural daylight/night cycle (0 lx at nigth; control). After the trial, organisms from each treatment were frozen in liquid nitrogen and standard protocols were followed to estimate RNA, DNA and RNA:DNA ratios. Estimates of RNA:DNA ratios from insects maintained in control conditions were significantly higher (P < 0.05) than those from insects exposed to ALAN. The reduced nutritional condition of insects exposed to light pollution is explained by the lower in situ biosynthetic capacity in these organisms resulting from a reduction in their feeding. ALAN likely altered P. maculata normal locomotor activity, which takes place primarily at night, forcing the insects to remain buried in the sand for extended periods of time. As ALAN continues to spread along coastlines worldwide, there is a likelihood of growing impacts on these and other species living on sandy beaches and other coastal habitats.

Stress responses of testicular development, inflammatory and apoptotic activities in male zebrafish (Danio rerio) under starvation

Food deprivation is a severe stress across multiple fields and challenged to organismal development and immune system. Here, adult male zebrafish were used to investigate the starvation stress on organismal development, spermatogenesis, testicular inflammation and apoptosis. Results showed that the biological indexes, blood parameters, and RNA/DNA ratio in testis dramatically decreased after 1-3 weeks of starvation. The testicular architecture was impaired and the spermatogenesis was retarded with increased proportions of spermatogonia and spermatocytes, and decreased proportion of spermatozoa in the starved fish. The mRNA expressions of amh and sycp3 were downregulated, the retinoic acid content increased at later stage of starvation through the transcriptional regulation of aldh1a2 and cyp26a1. Besides, the immune response was elevated with upregulated mRNA and protein expressions of TNF-α, IL-6, and IL-1β, which indicated the inflammation of opportunistic risk in testis. The apoptotic activity was stimulated, accompanied by differentially upregulated expressions of baxa, casp9, casp3, casp2, and decreased ratio of Bcl-2/Bax in the attenuate testis. Taken together, our findings revealed that the stress responses of testicular development, inflammatory and apoptotic activities in male zebrafish under starvation and pointed out the susceptibility of fish gonad to food fluctuation.

Rearing environment affects the genetic architecture and plasticity of DNA methylation in Chinook salmon

Genetic architecture and phenotypic plasticity are important considerations when studying trait variation within and among populations. Since environmental change can induce shifts in the genetic architecture and plasticity of traits, it is important to consider both genetic and environmental sources of phenotypic variation. While there is overwhelming evidence for environmental effects on phenotype, the underlying mechanisms are less clear. Variation in DNA methylation is a potential mechanism mediating environmental effects on phenotype due to its sensitivity to environmental stimuli, transgenerational inheritance, and influences on transcription. To characterize the effect of environment on methylation, we created two 6 × 6 (North Carolina II) Chinook salmon breeding crosses and reared the offspring in two environments: uniform hatchery tanks and seminatural stream channels. We sampled the fish twice during development, at the alevin (larval) and fry (juvenile) stages. We measured DNA methylation at 13 genes using a PCR-based bisulfite sequencing protocol. The genetic architecture of DNA methylation differed between rearing environments, with greater additive and nonadditive genetic variance in hatchery fish and greater maternal effects in seminatural channel fish, though gene-specific variation was evident. We observed plasticity in methylation across all assayed genes, as well as gene-specific effects at two genes in alevin and six genes in fry, indicating developmental stage-specific effects of rearing environment on methylation. Characterizing genetic and environmental influences on methylation is critical for future studies on DNA methylation as a potential mechanism for acclimation and adaptation.

DNA Methylation Profiles Suggest Intergenerational Transfer of Maternal Effects

The view of maternal effects (nongenetic maternal environmental influence on offspring phenotype) has changed from one of distracting complications in evolutionary genetics to an important evolutionary mechanism for improving offspring fitness. Recent studies have shown that maternal effects act as an adaptive mechanism to prepare offspring for stressful environments. Although research into the magnitude of maternal effects is abundant, the molecular mechanisms of maternal influences on offspring phenotypic variation are not fully understood. Despite recent work identifying DNA methylation as a potential mechanism of nongenetic inheritance, currently proposed links between DNA methylation and parental effects are indirect and primarily involve genomic imprinting. We combined a factorial breeding design and gene-targeted sequencing methods to assess inheritance of methylation during early life stages at 14 genes involved in growth, development, metabolism, stress response, and immune function of Chinook salmon (Oncorhynchus tshawytscha). We found little evidence for additive or nonadditive genetic effects acting on methylation levels during early development; however, we detected significant maternal effects. Consistent with conventional maternal effect data, maternal effects on methylation declined through development and were replaced with nonadditive effects when offspring began exogenous feeding. We mapped methylation at individual CpG sites across the selected candidate genes to test for variation in site-specific methylation profiles and found significant maternal effects at selected CpG sites that also declined with development stage. While intergenerational inheritance of methylated DNA is controversial, we show that CpG-specific methylation may function as an underlying molecular mechanism for maternal effects, with important implications for offspring fitness.

Genomic responses of DNA methylation and transcript profiles in zebrafish cells upon nutrient deprivation stress

Environmental stress such as nutrient deprivation across multiple fields in nature causes physiological and biochemical changes in organism. Understanding the potential epigenetic modulations to phenotypic variation upon nutrient deprivation stress is crucial for environmental assessments. Here, the methyl-cytosine at single-base resolution was mapped across the whole genome and the methylation patterns and methylation levels coordinated with transcript analysis were systemically elaborated in zebrafish embryonic fibroblast cells under serum starvation stress. The down-regulated genes mainly annotated to the pathways of DNA replication and cell cycle that were consistent with cell physiological changes. Vast differentially methylated regions were identified in genomic chromosome and showed enrichment in the intron and intergenic regions. In an integrated transcriptome and DNA methylation analyses, 135 negatively correlated genes were determined, wherein the hub genes of gins2, cdca5, fbxo5, slc29a2, suv39h1b, and zgc:174160 were predominant responsive to the nutrient condition changes. Besides, nutrient recovery and DNA methyltransferases inhibitor supplements partly rescued cell proliferation with decrease of DNA methylation and reactivation of several depressed genes, implying the possible intrinsic relationships among cell physiological state, mRNA expression, and DNA methylation. Collectively, current study proved the broad role of DNA methylation in governing cellular responses to nutrient deprivation and revealed the epigenetic risk of starvation stress in zebrafish.

Discrepant dose responses of bisphenol A on oxidative stress and DNA methylation in grass carp ovary cells

Bisphenol A (BPA), is a common contaminant in diverse environmental compartments and its endocrine disruptive effect on living organisms has been widely reported. Further works are still required to facilitate the research on cytotoxicity and genotoxicity. In the present study, grass carp ovary (GCO) cells were used to investigate cellular oxidative stress and genomic DNA methylation under BPA exposure. Results showed that BPA exposure for 48 h arrested cell proliferation and viability. The oxidative stress was distinctly enhanced with increased reactive oxygen species (ROS), malondialdehyde level, and oxidation of reduced glutathione (GSH) in 30 μM BPA group. Furthermore, the global 5-methylcytosine (5 mC) level was elevated and showed inverted U-shaped responses to the BPA doses. Besides, one-carbon metabolism and de novo GSH synthesis were disrupted at 30 μM BPA. Current data suggested that low dose of BPA exposure could exhibit hormesis in recycling circular biosynthesis of GSH and scavenging ROS to create a relatively reductive intracellular environment, and up-regulate transcripts of methyltransferases that increased the 5 mC level in GCO cells. While high dose of BPA distinctly induced oxidative stress, elevated de novo GSH synthesis, and then attenuated transmethylation activity and decreased 5 mC level. Current study highlighted the discrepant dose responses of BPA in fish ovary cells that facilitated the understanding of pleiotropic consequences in organisms.

The cellular responses of autophagy, apoptosis, and 5-methylcytosine level in zebrafish cells upon nutrient deprivation stress

Here we reported the stress responses of nutrient deprivation and extended observation of autophagy, apoptosis, and DNA methylation in zebrafish embryonic fibroblast (ZF4) cells. Our results showed that serum deprivation resulted in the changes of cell shape and adherent ability, the suppressed cell growth and viability, and the inhibited proliferation and cell cycle. Besides, the appearance of lysosome and autophagosome/autolysosome with significantly increased expression of mRNAs (ulk1a, becn1, atg12, sqstm1, maplc3, and lamp1) and proteins (Atg12, Becn1, Sqstm1, and Lamp1) indicate the autophagic activity was boosted at initial stage but relatively weakened at 48 h of serum starvation. When autophagy no longer mitigate for the stress, cell apoptosis detected by the mRNA expression of caspases, Bcl-2/Bax expression, and Annexin V/PI was gradually enhanced to execute the death plan upon prolonged starvation process. Furthermore, the methyl group metabolism was increased in accordance with autophagic activity and was suppressed by enhanced apoptotic activity. These data suggested that the recycle activity induced by autophagy could compensate the substrates and reactions of DNA transmethylation, which obviously increased 5-methylcytosine (5 mC) level in ZF4 cells. In summary, our results discovered the cellular responses under prolonged serum starvation stress and elaborated the switch from autophagy to apoptosis and corresponding correlation with 5 mC level changes in teleost fish in vitro.