The formation of dermal condensates (DCs) through fibroblasts is a pivotal event in hair follicle morphogenesis in cashmere goats, a process that intricately involves epithelial-fibroblast communication. Exosomes (Exos), as essential mediators of intercellular communication, have garnered increasing attention in recent years, yet their precise role in hair follicle morphogenesis remains largely unknown. In this study, we focused on isolating and identifying epithelial cell-derived exosomes (Epi-Exos) from Inner Mongolian cashmere goats. Our experiments demonstrated that Epi-Exos could efficiently enter fibroblasts within 12 h of co-culture. Both direct co-culture of epithelial cells with fibroblasts and co-culture with Epi-Exos alone revealed that Epi-Exos promoted fibroblast migration while inhibiting their proliferation, changes that mirror the cellular biological characteristics observed during DC formation. Furthermore, recognizing the abundance of miRNAs carried by Exos, we conducted small RNA sequencing (small RNA-seq) on Epi-Exos. This analysis identified a panel of 54 highly expressed miRNAs within the Epi-Exos, 34 of which were also found to be abundant in fetal skin tissues of Inner Mongolian cashmere goats. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that these miRNAs were significantly enriched in cellular processes and signaling pathways related to hair follicle morphogenesis. Notably, our findings offer new perspectives on the role of miRNAs in Epi-Exos regulating DC formation and hair follicle morphogenesis in cashmere goats, with significant implications for understanding hair follicle development mechanisms and potential clinical or production benefits, including improved cashmere quality and yield through targeted exosome-mediated signaling manipulation.

Nitrite contamination and stress on aquatic organisms are increasingly emphasized in freshwater ecosystems. Freshwater bivalves exhibit high tolerance to nitrite; however, the underlying mechanism is unknown. Accordingly, this study investigated the tolerance mechanism of the globally occurring freshwater bivalve Anodonta woodiana. A. woodiana were exposed to nominal concentrations of 0, 250, 500, 1000, 2000, and 4000 mg/L nitrite for 96 h to calculate the 96-h median lethal concentration (96-h LC). A combined transcriptome and metabolome analysis of the hemolymph (the most vital component of the bivalve immune system) was performed after exposing A. woodiana to 300 mg/L nitrite (approximately half the 96-h LC) for 96 h. The 96-h LC of nitrite in A. woodiana was 618.7 mg/L. Transcriptome analysis identified 5600 differentially expressed genes (DEGs) primarily related to ribosomes, lysosomes, DNA replication, and nucleotide excision repair. Metabolome analysis identified 216 differentially expressed metabolites (DEMs) primarily involved in biosynthesis of amino acids, 2-oxocarboxylic acid metabolism, protein digestion and absorption, aminoacyl-tRNA biosynthesis, nucleotide metabolism, ABC transporters, and valine, leucine and isoleucine degradation. Combined transcriptome and metabolome analysis revealed that DEGs and DEMs were primarily associated with nucleotide (purine and pyrimidine) and amino acid metabolism (including aminoacyl-tRNA biosynthesis, cysteine and methionine metabolism, arginine and proline metabolism, and valine, leucine and isoleucine degradation) as well as the immune system (necroptosis and glutathione metabolism). This study is the first to describe the high tolerance of A. woodiana to nitrite and elucidate the molecular mechanisms underlying high nitrite tolerance in mussels.

Cold stress is an extreme environmental stressor that constrains the economic development of aquaculture. Yellowtail kingfish (Seriola aureovittata) is a commercially important fish species, but its molecular mechanisms in response to cold stress remain unknown. In this study, we investigated the transcriptional response of yellowtail kingfish liver to cold stress (10 °C) using RNA-sequencing analysis. We obtained 83.21 Gb of clean data from fish in the control group (0 h) and at 6, 12, and 24 h post-stimulation. A total of 2900 differentially expressed genes were identified from the comparison of the bioinformatic data from cold-stressed and control groups. Enrichment analysis suggested that protein processing, energy and lipid metabolism, signal transduction, and stress-induced cell cycle changes were highly involved during cold adaptation. Transport and utilization of fatty acids and cell cycle arrest were enhanced, whereas the rate of glycogen metabolism and protein biosynthesis were inhibited to maintain energy balance and normal fluidity of the cell membrane, thereby enhancing the tolerance of yellowtail kingfish to cold stress. Our study uncovered molecular pathways and key regulatory genes that are crucial for cold adaptation in yellowtail kingfish. These results provide new insights that could inform selective breeding programs aimed at enhancing cold resistance in aquaculture.

Sturgeon aquaculture has grown in recent years, driven by increasing global demand for its highly valued products. Russian sturgeon (Acipenser gueldenstaedtii), recognised as one of the most valuable species for caviar production, is farmed in several warm-temperate regions. However, the substantial temperature increase due to global warming represents a challenge for developing sturgeon aquaculture. Previously we demonstrated that Russian sturgeon under chronic heat stress (CHS) exhibited a liver metabolic reprogramming to meet energy demands, weakening their innate defences and leading to increased mortality and economic losses. Here, we used RNA-seq technology to analyse regulated genes in the spleen of Russian sturgeons exposed to CHS and challenged with Aeromonas hydrophila. The assembly gave 253,415 unigenes, with 13.7 % having at least one reliable functional annotation. We found that CHS caused mild splenitis and upregulated genes related to protein folding, heat shock response, apoptosis and autophagy while downregulated genes associated with the cell cycle. The cell cycle arrest was maintained upon A. hydrophila challenge in heat-stressed fish, potentially inducing cell senescence. Surprisingly, immunoglobulin heavy and light chains were upregulated in the spleen of stressed sturgeons but not in those maintained at tolerable temperatures; however, no changes in IgM serum levels were observed in any condition. Our findings indicate that long-term exposure to non-tolerable temperatures induced a heat shock response and activated apoptosis and autophagy processes in the spleen. These mechanisms may enable the control of tissue damage and facilitate the recycling of cell components in a condition where the nutrient supply by the liver might be insufficient. Stressed sturgeons challenged with A. hydrophila maintain these mechanisms, which could culminate in cellular senescence.

Recently, against the background of increasing land salinization and global warming, many studies have examined the mechanisms of freshwater fish adaptation to elevated salinity. However, the mechanisms underlying salinity tolerance in the kidney of Micropterus salmoides, a popular saline aquaculture species, remain poorly understood. We used RNA-seq to explore the differentially expressed genes (DEGs) in the kidney of M. salmoides at 0 ‰, 5 ‰, and 10 ‰ salinity for 24 d and 48 d. These DEGs mainly affected metabolism-related pathways, such as secondary metabolite biosynthesis, arachidonic acid metabolism, etc., and immunity-related pathways, such as IL-17 signaling and ECM-receptor interaction. Trend analysis on days 24 and 48 showed that, as salinity increased, the up-regulated genes were notably enriched in the cytochrome P450 xenobiotic metabolic pathway, and down-regulated genes substantially linked to cell cycle, phagosome, etc. More importantly, we identified a total of 22 genes enriched in the cytochrome P450 xenobiotic metabolic pathway, including seven UDP-glucuronosyltransferase genes (UGTs) and five glutathione S-transferase genes (GSTs). We speculated that M. salmoides kidneys removed toxic substances produced due to salinity stress and mitigated oxidative damage by up-regulating UGTs and GSTs, hence maintaining normal physiological function. In addition, genes such as Cystatin A1, significantly up-regulated with increasing salinity stress and duration, favoured the recovery of kidney injury. This research delved into the molecular processes involved in the adaptability of M. salmoides to high salinity stress and provided valuable information for the future breeding of salinity-tolerant strains.

The greater amberjack (Seriola dumerili) is a valuable marine fish with significant breeding potential, but does not exhibit clear sexual dimorphism in morphology. Sex research and the development of sex identification technology are important for breeding purposes. Through genome-wide association analysis (GWAS), we identified one significant sex-related SNP and 18 candidate sex-related SNPs, then obtained one significant sex-related gene (hsd17β1) and 20 candidate sex-related genes (hmbox1, ahcyl1, pdzd2, etc.). Key sex-biased genes (sox2, dmrt2, hsd17β3, rnf145, foxo3, etc.) were identified in mature gonads by transcriptome analysis. These genes are important in greater amberjack sex determination and gonad development. In addition, we developed classical PCR and kompetitive allele-specific PCR (KASP) primers to identify the sex of greater amberjack, with an accuracy of 94.87 % and 100 %, respectively. The sex-specific markers can effectively determine the gender of greater amberjack and evaluate the sex ratio and reproductive potential of the breeding population.

Herbicides pose a threat to various non-target organisms, including fish. A widely used herbicide, glyphosate, and its main breakdown product, aminomethylphosphonic acid (AMPA), are quite ubiquitous in freshwater systems. The aim of this work was to analyze changes in the relative abundance of hepatic proteins participating in the biotransformation and response to chemical stress in adult zebrafish Danio rerio exposed to environmentally relevant concentrations of glyphosate (100 μg/L), AMPA (100 μg/L), and their mixture (50 μg/L + 50 μg/L) for two weeks. Proteomic analysis showed that the tested concentrations caused dysregulation of various biotransformation proteins, the most upregulated of which in all treatment groups was the Phase I enzyme cyp27a7. While glyphosate had a more pronounced impact on the biotransformation pathways, AMPA showed stronger interference with redox homeostasis. When acting together, the parent compound and its metabolite were more potent to disturb fish metabolic processes, including nucleotide metabolism and proteasome pathway, and to downregulate proteins known for their roles in protection from oxidative modifications of cellular constituents and disruption of redox signaling.

This study investigated the effects of different sodium bicarbonate (NaHCO) concentrations (0 g/L, 1 g/L, and 3 g/L) on Hefang crucian carp (12.0 ± 1.1 g) over a 96-hour period. The experiment is divided into three groups, each with three replicates, and each replicate contains 30 fish. We employed a comprehensive approach integrating histology, physiological and biochemical assays, transcriptomics, as well as artificial intelligence (AI)-assisted analysis. This multifaceted method allowed us to examine changes in gill and liver morphology, osmoregulation, antioxidant capacity, immune response, and physiological metabolism. Results showed that gill and liver tissue damage increased with rising water alkalinity. Serum sodium (Na), potassium (K), blood ammonia, and gill Na/K-ATPase (NKA) levels increased significantly (p < 0.05). Hepatic antioxidant enzymes initially increased, then decreased with prolonged stress. Serum and liver immunoenzyme indices were higher in bicarbonate-treated groups compared to controls. Carbonate treatment altered lipid and glucose metabolism in both serum and liver. Transcriptome analysis, enhanced by large language models (LLMs), revealed differentially expressed genes (DEGs) significantly associated with ion binding, transport, apoptosis, and metabolism. In conclusion, excessive carbonate intake in fish alters serum physiological functions and affects hepatic metabolic functions. Crucian carp primarily regulate hepatic antioxidant systems, utilize carbohydrate breakdown for energy requirements, and employ lipids in osmoregulation. This study provides insights into fish adaptation to saline-alkaline environments and offers support for the development of aquaculture in saline-alkaline waters.

The infraclass Pteriomorphia within the phylum Mollusca, class Bivalvia, encompasses a diverse group of bivalve mollusks characterized by their unique morphological and ecological traits. However, the molecular data of Pteriomorphia remains limited, constraining classification and phylogenetic analysis within the infraclass Pteriomorphia. In this study, we sequenced the mitogenomes of 15 pteriomorphians using high-throughput sequencing technology and conducted comparative genomic analysis with 58 sequences available on GenBank. The newly sequenced mitogenomes all exhibited a circular double-stranded structure, ranging in size from 12,844 to 28,105 bp. Mitogenome features, including nucleotide composition, codon usage, and amino acid content, exhibited significant deviations. The mitochondrial gene orders (MGOs) in pteriomorphians also exhibited significant diversity, with 44 distinct patterns identified (excluding the tRNA gene). The gene rearrangement analysis inferred that the ancestral MGO evolution pathway supported the hypothesis that the common ancestor MGO of Mytilida is the closest to that of the entire infraclass Pteriomorphia. The reconstructed phylogeny also indicated the order Mytilida as the basal group of Pteriomorphia. Furthermore, the analysis revealed that Ostreida and Pectinida were sister taxa, while Ostreoidea and the Pinnoidea were sister taxa within Ostreida. Gene rearrangement analysis further suggested that the MGOs of Arcida and Pectinida likely evolved from the ancestral MGO of Ostreida. Our study provided new insights into the phylogenetic relationships and evolution of gene rearrangements within the subclass Pteriomorphia.

Salinity plays a vital role in fish aquaculture, profoundly influencing the growth and development of fish. Scales, as the protective outer layer of fish, function as a critical defense against external factors. In this study, we employed transcriptome sequencing to analyze the ceRNA expression profiles to reveal the effect of salinity acclimation on transcriptional expression changes in the scales of cobia (Rachycentron canadum). The results revealed that after being exposed to a salinity level of 15 ‰ for just one day (1D), a total of 407 mRNAs/genes were significantly regulated; 66 miRNAs were respectively significantly regulated; and 109 target genes of the differentially expressed miRNAs were significantly regulated; a total of 185 differently expressed lncRNAs and 292 differently expressed target genes (DetGenes) of differently expressed lncRNAs were also identified. After 7 days (7D), a total of 2195 mRNAs/genes were found to be significantly regulated and 82 miRNAs were significantly regulated; among the target genes of the differentially expressed miRNAs, 245 were regulated. Moreover, 438 differently expressed lncRNAs and 681 DetGenes of these lncRNAs were identified. Subsequent analysis through GO, KEGG pathway, in 1D vs. CG (control group), DeGenes, which first respond to changes in salinity, are mainly involved in negative regulation of macrophage differentiation, negative regulation of granulocyte differentiation and negative regulation of phagocytosis, and are mainly related to biological processes related to the immune function of fish. After a 7-day process, DeGenes were enriched in the collagen fibril organization, regulation of nodal signaling pathway and cell recognition biology processes. These biological processes are not only related to the immune function of fish, but more importantly, to the physiological structure of fish. By analyzing the co down-regulated miRNAs of 1D vs. CG, as well as 7D vs. CG, the functions of these miRNAs are mainly related to bone differentiation and development. In addition，ceRNA network uncovered that the effect of salinity is temporal. The first competing lncRNAs mainly regulated genes related to physiological processes and biological development, while target genes related to immunity and body defense were less competitive. On the contrary, after a period of salinity treatment, the types of competing lncRNAs involved changed.

The Largemouth bass (Micropterus salmoides; LMB) is a freshwater fish that plays a significant role in aquaculture, and its cultural base is expanding into inland saline water areas. To study the effect of short-term salt exposure on LMB, fish with an average body weight of 11.69 (±1.82) g were cultured for 14 days at three different salt concentrations (0 ‰, 6 ‰, and 12 ‰). After 14 days, the second gill arch was collected for tissue sectioning and transcriptome sequencing, while serum samples were collected to analyze serum components. The results showed that the mortality rate in the 0 ‰ and 6 ‰ groups was 0 %, whereas the mortality rate in the 12 ‰ group was 62 %. In the gill tissue sections, no apparent damage was observed in the 0 ‰ and 6 ‰ groups. However, in the 12 ‰ group, the secondary lamellae became shorter, thicker, and exhibited a disordered arrangement. The serum component test results showed that osmolality and K significantly increased in the 12 ‰ group, while Na, K, and Cl concentrations showed slight increases, but the differences were not significant. Comparative transcriptome analysis revealed that, along the salinity gradient, gene expression exhibited five profiles. Genes related to ion transport and immunity were highly expressed in the 6 ‰ and 12 ‰ groups, while genes associated with biosynthesis and ATP production showed decreased expression levels as salinity increased. Notably, seven solute carrier genes, two Na/K-ATPase genes, and two insulin-like growth factor genes were significantly highly expressed in the 12 ‰ salinity group, playing important roles in the transmembrane transport of ions. Based on the results, the LMB can acclimatize to a salt concentration of at least 6 ‰. However, exposure to 12 ‰ salinity can lead to a series of adverse effects, including organ damage, reduced energy metabolism efficiency, and disruption of ion homeostasis.

Water temperature exerts a crucial impact on the growth and development of fish. Hybrids may integrate the superior traits of their parents, thereby leading to higher economic benefits. Takifugu rubripes and T. obscurus are two important economic species in Asia. Here, to investigated the effect of temperature on the hybrid puffer larvae (T. rubripes ♀ × T. obscurus ♂), the larvae (0.79 ± 0.02 cm in body length) were treated to three temperatures: 15 °C (T15), 20 °C (T20), and 25 °C (T25) for 45 days. At the end of the study, the body length and weight were measured, the survival rate was calculated, and liver transcriptome analysis was performed on liver tissues. The hybrid puffer larvae in the T25 group showed a significant increase in average body length and body weight compared to the T15 and T20 groups (P < 0.05). 1292, 329, and 1927 differentially expressed genes (DEGs) were identified in T15 vs. T20, T20 vs. T25, and T15 vs. T25 groups, respectively. KEGG enrichment analyses showed that DEGs were primarily involved in the citrate cycle (TCA cycle), PPAR signaling, glycine, serine and threonine metabolism, and protein digestion and absorption pathways. These results indicated that temperature affects metabolism, signal transduction and protein digestion and absorption in hybrid puffer fish. In addition, twelve DEGs were randomly selected for RNA-seq validation, and the transcriptome results were consistent with the qPCR validation results, illustrating the accuracy of transcriptome sequencing. These findings deepen our understanding of the complex molecular mechanism of the response of hybrid puffer fish to temperature changes and contribute to the development of hybrid puffer fish breeding.

Sperm storage in females is widespread among vertebrates and insects, and the expression of proteins in the female reproductive tract is influenced by the presence of sperm, allowing for adaptation to this phenomenon. Through histological observation, we confirmed that sperm were stored in the isthmic fossa outside the oocyte during the post-mating (POM) stage, and closer to the epithelial cells during the pre-fertilization (PRF) stage. In addition, we observed asynchronous ovarian development in black rockfish, where oocytes at various stages could be identified during the PRF phase. This study investigated the ovarian protein expression changes in black rockfish (Sebastes schlegelii) during key reproductive stages: pre-mating (PRM), POM, unmated control (POM-CT), and PRF. A total of 5012 proteins were identified, with notable fluctuations in protein expression observed at the PRF stage. Specifically, 140 proteins were upregulated and 615 downregulated when compared to the PRM stage, while 101 proteins were upregulated and 531 downregulated in comparison to the POM stage. The functional enrichment analysis of differentially expressed proteins (DEPs) revealed distinct pathways: POM vs. PRM showed involvement in vesicle sorting and hormone signaling; PRF vs. POM indicated pathways related to chromatin remodeling and gene expression regulation; and POM vs. POM-CT highlighted pathways associated with immune response. These findings suggested that these signaling pathways may play a crucial role in oocyte development and sperm storage. The majority of DEPs were localized in the nucleus, with key interactions involving proteins such as GSK3B and MED1. These findings enhance our understanding of the molecular mechanisms underlying oocyte maturation and sperm storage, providing insights relevant to reproductive biology and aquaculture practices.

The golden cuttlefish (Sepia esculenta), a significant cephalopod in the Yellow and Bohai Seas of China, is highly esteemed for its exceptional medicinal and commercial value. The natural resources of the S. esculenta are currently facing depletion due to the ongoing environmental degradation and overfishing. Secreted by the ink sac of the S. esculenta, the ink contains a diverse array of nutrients and active ingredients, which can exert a substantial impact on biological immune cells' proliferation and differentiation, the occurrence of inflammation, autophagy, along with other processes pertaining to immune response, and thus affects their survival. In the actual production, the high-density artificial cultivation and transportation process of S. esculenta often leads to large-scale inkjet phenomenon, posing a significant threat to the survival of this species. The present study employed RNA-seq as the basis to investigate the mechanisms of immune response in S. esculenta larvae when exposed to ink. Conduct functional enrichment analysis (GO and KEGG) as well as protein-protein interaction (PPI) network analysis for the 1951 differentially expressed genes (DEGs). In addition, this study is the pioneering attempt to employ a combined analysis of KEGG and PPI network construction and further reveal a set of 20 key genes associated with immunity, which have higher numbers of PPI or KEGG pathway participation. It is evident that the ink exposure has an impact on the inflammatory response, immune cell propagation and specialization, transmission of signals in the immune system, and autophagy in S. esculenta larvae. Through the enrichment analysis of genes and pathway functions, we understood the impact of ink exposure on the larvae of S. esculenta exhibit immune resistance, further improved our overall comprehension regarding the immune functionality exhibited by mollusks, and contributed to improving the survival rate of S. esculenta in factory farming.

Nibea albiflora is an economically valuable aquaculture species but suffers from various diseases caused by bacteria and parasites. It is necessary to investigate some novel methods to improve the immunity. In this study, three feeding regimes (A: commercial diet; B: 90 % commercial diet+10 % ice-fresh Exopalaemon carinicauda); C: 90 % commercial diet+5 % ice-fresh Exopalaemon carinicauda + 5 % live Perinereis nuntia, named Control group, Group 1 and Group 2 with similar nutrient and energy content were designed to construct the food enrichment model to investigate their effects on the immunity of this species. The study was focused on spleen tissue where biochemical and RNA-seq analysis were performed to reach our goals. The results showed that fish fed the enriched food showed higher immunity than the Control group fish. Food enrichment feeding also could enhance fish adaptive capacity which contributes to enhancing immunity. Compared to the Control group, the diet B feeding enhanced the fish immunity and adaptive capacity by up-regulating important genes like BAX, ITPR3, NOS1, NLRP3 and down-regulating the gene GOT1. Similarly for the diet C feeding, it improved not only fish immunity but also the neurotransmission activity associated with a good physiological condition by up regulating the genes ADCY5, CACNA1C, SMAD4, NOS1 and RXRB. The diet C feeding was the best in improving fish immunity. Above all, our study revealed the positive effects of such a food enrichment model on the fish and provided evidences and data which support the application of the feeding strategies in the healthy culturing of the fish.

Hippotiscus dorsalis (Hemiptera: Pentatomidae) is a common pest that feeds on the stems of Moso bamboo. Therefore, investigating the molecular processes related to its fundamental physiology is important. In this study, transcriptome sequencing was employed to compare gene expression in different tissues of male and female adults. A total of 36,238 annotated unigenes were identified through the NR database and compared with those of other known species. Among these, Halyomorpha halys and Nezara viridula showed the highest homology with H. dorsalis, with a total similarity exceeding 86 %. The top significant differentially expressed genes were mainly associated with protein digestion, carbohydrates metabolism, as well as reproduce regulation between sexes. The Gene Ontology enrichment analysis across three different segments of each sex revealed some terms associated with detoxification such like IMP biosynthetic process and acetyl-CoA metabolic process. Additionally, Kyoto Encyclopedia of Genes and Genomes enrichment analysis highlighted significant pathways related to glucose metabolism and pancreatic secretion. Further investigation of these DEGs, particularly in the calcium signaling pathway and glycan biosynthesis and metabolism, is essential for understanding sugar metabolism and transport in phytophagous insects.

Beef quality is a critical factor in evaluating the effectiveness of beef cattle production. Fiber types play key roles in determining muscle growth and meat quality characteristics. FHL3 is de novo expressed in skeletal muscle and is responsible for MyHC isoform expression in C2C12 cells. Nevertheless, the precise function of this factor in regulating the proliferation, differentiation, and fiber type of bovine skeletal muscle cells (BSMCs) have yet to be identified. This study aimed to investigate the impact of the FHL3 on BSMCs proliferation, differentiation, and muscle fiber types. The results revealed that the FHL3 promoted BSMCs proliferation, inhibited differentiation, increased type II muscle fiber expression, and decreased type I muscle fiber expression. Meanwhile, the FHL3 promoted the expression and phosphorylation levels of PI3K, Akt, and mTOR in the PI3K/Akt/mTOR signaling pathway, and inhibited the expression and phosphorylation levels of PI3K, Akt, and mTOR after treatment with the pathway inhibitor LY294002, furthermore, it promoted differentiation and inhibited proliferation of BSMCs, while promoting the expression of type II muscle fibers and inhibiting the expression of type I muscle fibers. The results suggest that the FHL3 has an effect on promoting the proliferation and inhibiting the differentiation of BSMCs through the PI3K/Akt/mTOR signaling pathway, but the effect of the FHL3 on myofiber type conversion is not regulated by this pathway. The objective of this study is to enhance our understanding of the molecular function of FHL3 in the development of BSMCs.

Studies showed that toxicants that adhered to the surface of nano-microplastics (NPs) have toxicological effects. Juvenile tilapia were divided into four groups namely the control group (A), 100 ng·L sulfamethoxazole (SMZ) group (B), 75 nm NPs group (C) and SMZ + 75 nm NPs group (D), and were exposed to an acute test for 2, 4 and 8 days. The hepatic histopathological changes, enzymatic activities, transcriptomics and proteomics analysis have been performed. The results showed that; the enzymatic activities of anti-oxidative enzymes (ROS, SOD, EROD), energy (ATP), lipid metabolism (TC, TG, FAS, LPL, ACC), pro-inflammatory factors (TNFα, IL-1β) and apoptosis (Caspase 3) have decreased significantly at 8 d. Hepatic histopathological results revealed the narrowed hepatic sinuses, displaced nucleus, and vacuoles under SMZ exposure. Transcriptome results demonstrated that endocytosis, MAPK signaling pathway, apoptosis, lysosome and herpes simplex infection were enriched in group C at 8 d. apaf1, casp3a, nfkbiaa (apoptosis, except for 8 d) were significantly increased, il1b and tgfb3, fgfr2 showed significant increase and decrease in group C/D. ctsd and ctsk associated with apoptosis have been especially significantly increased at 8 d, while MAPK signaling pathway, gadd45ga, gadd45gb/gadd45gg have been significantly decreased and increased, as well as map3k3/map3k2 significantly decreased at 8 d. Apoptosis and MAPK signaling pathway were affected and the synergistic effect was verified in tilapia liver following NPs and SMZ acute co-exposure.

This project focused on evaluating the effects of maternal dietary choline intake on global DNA methylation profiles and related transcriptional changes in rainbow trout offspring. Three experimental diets were formulated to test different levels of choline intake: (a) 2065 ppm choline (Low Choline, 0 % supplementation), (b) 5657 ppm choline (Medium Choline, 0.6 % supplementation), and (c) 9248 ppm choline (High Choline, 1.2 % choline supplementation). Six rainbow trout families were fed experimental diets beginning 18 months post-hatch until spawning; their offspring were fed a commercial diet. Reduced representation bisulfite sequencing (RRBS) was utilized to measure genome-wide methylation in offspring immediately after hatching. When comparing to the Medium Choline offspring, differential DNA methylation occurred more in the Low Choline offspring than High Choline, especially in genic features like promoters. The differentially methylated CpGs (q ≤ 0.01) were identified evenly between CpG islands and shores in the genome, mostly found in the introns of genes. Genes such as fabp2 and leap2B associated with protein binding, fatty acid binding, DNA binding, and response to bacteria were differentially methylated and detected as differentially regulated genes by previous RNA-seq analysis. Although these findings indicate that levels of dietary choline available in broodstock diets alter offspring DNA methylation;, most differentially expressed genes were not associated with differential DNA methylation, suggesting additional mechanisms playing a role in regulating gene expression in response to maternal choline intake.

This study investigated the genetic response of tilapia (Oreochromis mossambicus) brain cells to hypertonic stress, focusing on miRNAs regulation. Three hundred and thirty-one known miRNAs and 163 novel miRNAs which responded to hypertonic stress were identified by high-throughput sequencing in tilapia brain cells. Differential expression analysis revealed that 16 miRNAs were significantly upregulated, while 11 miRNAs were significantly downregulated. These differentially expressed miRNAs are closely related to metabolism, immune response, and neural regulation. The target genes of these miRNAs are implicated in neurotrophic and synaptic signaling pathways, potentially affecting metabolic and apoptotic processes. GO and KEGG enrichment analyses provided insights into the biological processes and pathways affected by hypertonic stress. Furthermore, correlation analysis between mRNA and miRNA highlighted miRNA-mRNA interactions related to cell cycle and apoptosis regulation. These results indicated significant changes of miRNA expression under hypertonic stress and their crucial role in osmotic pressure regulation. This study offers a basis for further exploration of miRNA functions and molecular mechanisms in tilapia, potentially informing practices for aquaculture in challenging environments such as saline-alkaline waters.

Induction of spawning in catfish is well demonstrated in females while stimulation of spermiation in males seems difficult. This has led to least understanding of gene profile changes during testicular maturation. Expression of the factors after hormonal induction that control reproductive processes has become an intense research area in fish endocrinology. In view of this, de novo assemblies of testicular transcriptomes of the Asian catfish, Clarias batrachus and the African catfish, C. gariepinus, were performed to identify genes/factors involved in testicular maturation. For testicular induction, human chorionic gonadotropin (hCG) was administered in vivo to both the catfish species during active phase of reproduction. 1,68,071 and 1,26,232 assembled transcripts were obtained from C. batrachus and C. gariepinus testicular transcriptomes and were annotated using different databases. Further, in silico analysis suggested the presence of several transcripts that were involved in steroidogenesis and male reproduction. Comparison of transcriptomes of both species revealed the presence of certain unique genes related to reproduction differentially. Expression profiles after hCG induction in testis showed higher expression of certain steroidogenesis related genes such as star, cyp11b1, cyp17a and cyp21a in both the species. Further, expression levels of crucial factors related to testis, such as dmrt1/2/3, were also found to be significantly higher after gonadotropin induction. However, amh, tgfα and dmrt4/5 expression levels were significantly low. Factors related to male reproduction i.e., tekt1, tekt2, sox9, spag1, spata2 and spata7 were found to be differentially upregulated in hCG treated testicular tissues of both the species. Histology analysis indicated that the gonadotropin induction either short or long term is a better strategy to highlight expression profile changes during testicular maturation in teleost.