Comparative Biochemistry and Physiology D-Genomics & Proteomics最新文献

{"title":"Effect of food enrichment based on diverse feeding regimes on the immunity of Nibea albiflora by biochemical and RNA-seq analysis of the spleen","authors":"Anle Xu ,&nbsp;Yuting Zheng ,&nbsp;Xiumei Zhang ,&nbsp;Dongdong Xu ,&nbsp;Jiaxing Wang ,&nbsp;Jipeng Sun","doi":"10.1016/j.cbd.2024.101363","DOIUrl":"10.1016/j.cbd.2024.101363","url":null,"abstract":"<div><div><em>Nibea albiflora</em> 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 <em>Exopalaemon carinicauda</em>); C: 90 % commercial diet+5 % ice-fresh <em>Exopalaemon carinicauda</em> + 5 % live <em>Perinereis nuntia</em>, 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 <em>BAX</em>, <em>ITPR3</em>, <em>NOS1</em>, <em>NLRP3</em> and down-regulating the gene <em>GOT1</em>. 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 <em>ADCY5</em>, <em>CACNA1C</em>, <em>SMAD4</em>, <em>NOS1</em> and <em>RXRB</em>. 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.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"53 ","pages":"Article 101363"},"PeriodicalIF":2.2,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142706265","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of temperature to the liver transcriptome in the hybrid puffer fish (Takifugu rubripes ♀ × Takifugu obscurus ♂)","authors":"Meiyuan Li ,&nbsp;Chenqi Wang ,&nbsp;Huiting Zhou ,&nbsp;Jinfeng Chen ,&nbsp;Liu Wang ,&nbsp;Yuyu Xiong ,&nbsp;Yushun Tian ,&nbsp;Hongwei Yan ,&nbsp;Xinyan Liang ,&nbsp;Qi Liu ,&nbsp;Xiuli Wang ,&nbsp;Yaohui Wang ,&nbsp;Chuang Fu","doi":"10.1016/j.cbd.2024.101360","DOIUrl":"10.1016/j.cbd.2024.101360","url":null,"abstract":"<div><div>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. <em>Takifugu rubripes</em> and <em>T. obscurus</em> are two important economic species in Asia. Here, to investigated the effect of temperature on the hybrid puffer larvae (<em>T. rubripes</em> ♀ × <em>T. obscurus</em> ♂), 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 (<em>P</em> &lt; 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.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"53 ","pages":"Article 101360"},"PeriodicalIF":2.2,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142723202","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Kidney transcriptome analysis reveals the molecular responses to salinity adaptation in largemouth bass (Micropterus salmoides)","authors":"Yichun Zhang ,&nbsp;Jinxin Zhang ,&nbsp;Yafang Tan ,&nbsp;Xinxin Wang ,&nbsp;Huapeng Chen ,&nbsp;Haoran Yu ,&nbsp;Feiyang Chen ,&nbsp;Xinling Yan ,&nbsp;Junlong Sun ,&nbsp;Jian Luo ,&nbsp;Feibiao Song","doi":"10.1016/j.cbd.2024.101362","DOIUrl":"10.1016/j.cbd.2024.101362","url":null,"abstract":"<div><div>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 <em>Micropterus salmoides</em>, a popular saline aquaculture species, remain poorly understood. We used RNA-seq to explore the differentially expressed genes (DEGs) in the kidney of <em>M. salmoides</em> 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 <em>M. salmoides</em> 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 <em>M. salmoides</em> to high salinity stress and provided valuable information for the future breeding of salinity-tolerant strains.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"53 ","pages":"Article 101362"},"PeriodicalIF":2.2,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142683887","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comprehensive analysis of hub mRNA, lncRNA and miRNA, and associated ceRNA networks implicated in cobia (Rachycentron canadum) scales under hypoosmotic adaption","authors":"Changgeng Yang ,&nbsp;Jingyi Gao ,&nbsp;Kailin Gong ,&nbsp;Qian Ma ,&nbsp;Gang Chen","doi":"10.1016/j.cbd.2024.101353","DOIUrl":"10.1016/j.cbd.2024.101353","url":null,"abstract":"<div><div>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 (<em>Rachycentron canadum</em>). 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.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"53 ","pages":"Article 101353"},"PeriodicalIF":2.2,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142706267","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Combined transcriptome and metabolome analysis reveals the mechanism of high nitrite tolerance in freshwater mussel Anodonta woodiana","authors":"Guochao Duan ,&nbsp;Xiubao Chen ,&nbsp;Yiran Hou ,&nbsp;Tao Jiang ,&nbsp;Hongbo Liu ,&nbsp;Jian Yang","doi":"10.1016/j.cbd.2024.101359","DOIUrl":"10.1016/j.cbd.2024.101359","url":null,"abstract":"<div><div>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 <em>Anodonta woodiana</em>. <em>A. woodiana</em> 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 LC₅₀). A combined transcriptome and metabolome analysis of the hemolymph (the most vital component of the bivalve immune system) was performed after exposing <em>A. woodiana</em> to 300 mg/L nitrite (approximately half the 96-h LC₅₀) for 96 h. The 96-h LC₅₀ of nitrite in <em>A. woodiana</em> 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 <em>A. woodiana</em> to nitrite and elucidate the molecular mechanisms underlying high nitrite tolerance in mussels.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"52 ","pages":"Article 101359"},"PeriodicalIF":2.2,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142640492","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Investigation of cold adaptation mechanisms by transcriptome analysis in the liver of yellowtail kingfish (Seriola aureovittata)","authors":"Xinyu Cao ,&nbsp;Xu Yang ,&nbsp;Shuhui Wang ,&nbsp;Minghong Gao ,&nbsp;Ruihu Zhao ,&nbsp;Zhen Yang ,&nbsp;Hongyu Peng ,&nbsp;Zhonglu Cai ,&nbsp;Chen Jiang","doi":"10.1016/j.cbd.2024.101358","DOIUrl":"10.1016/j.cbd.2024.101358","url":null,"abstract":"<div><div>Cold stress is an extreme environmental stressor that constrains the economic development of aquaculture. Yellowtail kingfish (<em>Seriola aureovittata</em>) 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.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"52 ","pages":"Article 101358"},"PeriodicalIF":2.2,"publicationDate":"2024-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142644278","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exosomes serve as a crucial mediator of epithelial–fibroblast communication during hair follicle morphogenesis in cashmere goats","authors":"Erhan Hai ,&nbsp;ChangShou Wang ,&nbsp;Zhihong Wu","doi":"10.1016/j.cbd.2024.101357","DOIUrl":"10.1016/j.cbd.2024.101357","url":null,"abstract":"<div><div>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.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"52 ","pages":"Article 101357"},"PeriodicalIF":2.2,"publicationDate":"2024-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142640493","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"FHL3 gene regulates bovine skeletal muscle cell growth through the PI3K/Akt/mTOR signaling pathway","authors":"Xiaonan Zhou,&nbsp;Yanling Ding,&nbsp;Chaoyun Yang,&nbsp;Chenglong Li,&nbsp;Zonghua Su,&nbsp;Junjie Xu,&nbsp;Chang Qu,&nbsp;Yuangang Shi,&nbsp;Xiaolong Kang","doi":"10.1016/j.cbd.2024.101356","DOIUrl":"10.1016/j.cbd.2024.101356","url":null,"abstract":"<div><div>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. <em>FHL3</em> 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 <em>FHL3</em> on BSMCs proliferation, differentiation, and muscle fiber types. The results revealed that the <em>FHL3</em> promoted BSMCs proliferation, inhibited differentiation, increased type II muscle fiber expression, and decreased type I muscle fiber expression. Meanwhile, the <em>FHL3</em> 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 <em>FHL3</em> 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 <em>FHL3</em> 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 <em>FHL3</em> in the development of BSMCs.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"52 ","pages":"Article 101356"},"PeriodicalIF":2.2,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142644271","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptome analysis reveals the immune response mechanism of golden cuttlefish (Sepia esculenta) larvae exposed to ink","authors":"Deyuan Chang ,&nbsp;Yancheng Zhao ,&nbsp;Ziwen Ren ,&nbsp;Xueyu Zhu ,&nbsp;Xiaokai Bao ,&nbsp;Yongjie Wang ,&nbsp;Weijun Wang ,&nbsp;Cuiju Cui ,&nbsp;Xiumei Liu ,&nbsp;Zan Li ,&nbsp;Yuan Shan ,&nbsp;Jianmin Yang","doi":"10.1016/j.cbd.2024.101355","DOIUrl":"10.1016/j.cbd.2024.101355","url":null,"abstract":"<div><div>The golden cuttlefish (<em>Sepia esculenta</em>), 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 <em>S. esculenta</em> are currently facing depletion due to the ongoing environmental degradation and overfishing. Secreted by the ink sac of the <em>S. esculenta</em>, 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 <em>S. esculenta</em> 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 <em>S. esculenta</em> 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 <em>S. esculenta</em> larvae. Through the enrichment analysis of genes and pathway functions, we understood the impact of ink exposure on the larvae of <em>S. esculenta</em> exhibit immune resistance, further improved our overall comprehension regarding the immune functionality exhibited by mollusks, and contributed to improving the survival rate of <em>S. esculenta</em> in factory farming.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"52 ","pages":"Article 101355"},"PeriodicalIF":2.2,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142633218","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Study of carbonate alkalinity-induced hepatic tissue damage in Hefang crucian carp (Carassius auratus) based on transcriptomic analysis","authors":"Xinyu Lei ,&nbsp;Xue Cao ,&nbsp;Faye Zhang ,&nbsp;Qifang Lai ,&nbsp;Pengcheng Gao ,&nbsp;Yue-hong Li","doi":"10.1016/j.cbd.2024.101351","DOIUrl":"10.1016/j.cbd.2024.101351","url":null,"abstract":"<div><div>This study investigated the effects of different sodium bicarbonate (NaHCO₃) 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 (<em>p</em> &lt; 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.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"52 ","pages":"Article 101351"},"PeriodicalIF":2.2,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142632897","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}