Pub Date : 2024-12-09DOI: 10.1016/j.cbd.2024.101397
Xinhai Zhu , Qi Dong , Xiaoyu Cai , Jia Yin , Yan Liu , Xiaojian Gao , Qun Jiang , Guoxing Liu , Xiaojun Zhang
Aeromonas salmonicida belongs to the Aeromonas family, which could widely infect economic fish, causing diseases and huge economic losses. Recently, A. salmonicida was also detected in diseased Odontobutis potamophila. Transcriptomic model of A. salmonicida-infected O. potamophila was analyzed to reveal immune response. A total of 113,282 unigenes were obtained and annotated in six databases. After 12 h of infection with A. salmonicides, a total of 614 differentially expressed genes (DEGs) (355 up-regulated genes and 259 down-regulated genes) were identified in the head kidney tissues. Following 24 h of infection, a total of 1689 DEGs were detected in the head kidney tissues, including 313 up-regulated genes and 1376 down-regulated genes. GO and KEGG pathway analyses were conducted to provide functional insights and a clearer understanding of the signal transduction pathways associated with the DEGs. Further analysis of the complement and coagulation cascades pathway and PPAR signaling pathway exhibited that the expression of immune genes was widely activated at the beginning of A. salmonicides infection. Additionally, six DEGs were randomly selected and validated using quantitative real-time PCR, showing expression patterns consistent with the high-throughput sequencing data. These results offer important insights that enhance the understanding of immune response in O. potamophila against A. salmonicida infection.
{"title":"The immune defense response and immune-related genes expression in Odontobutis potamophila infected by Aeromonas salmonicida","authors":"Xinhai Zhu , Qi Dong , Xiaoyu Cai , Jia Yin , Yan Liu , Xiaojian Gao , Qun Jiang , Guoxing Liu , Xiaojun Zhang","doi":"10.1016/j.cbd.2024.101397","DOIUrl":"10.1016/j.cbd.2024.101397","url":null,"abstract":"<div><div><em>Aeromonas salmonicida</em> belongs to the <em>Aeromonas</em> family, which could widely infect economic fish, causing diseases and huge economic losses. Recently, <em>A. salmonicida</em> was also detected in diseased <em>Odontobutis potamophila</em>. Transcriptomic model of <em>A. salmonicida</em>-infected <em>O. potamophila</em> was analyzed to reveal immune response. A total of 113,282 unigenes were obtained and annotated in six databases. After 12 h of infection with <em>A. salmonicides</em>, a total of 614 differentially expressed genes (DEGs) (355 up-regulated genes and 259 down-regulated genes) were identified in the head kidney tissues. Following 24 h of infection, a total of 1689 DEGs were detected in the head kidney tissues, including 313 up-regulated genes and 1376 down-regulated genes. GO and KEGG pathway analyses were conducted to provide functional insights and a clearer understanding of the signal transduction pathways associated with the DEGs. Further analysis of the complement and coagulation cascades pathway and PPAR signaling pathway exhibited that the expression of immune genes was widely activated at the beginning of <em>A. salmonicides</em> infection. Additionally, six DEGs were randomly selected and validated using quantitative real-time PCR, showing expression patterns consistent with the high-throughput sequencing data. These results offer important insights that enhance the understanding of immune response in <em>O. potamophila</em> against <em>A. salmonicida</em> infection.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101397"},"PeriodicalIF":2.2,"publicationDate":"2024-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142820271","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}
Pub Date : 2024-12-07DOI: 10.1016/j.cbd.2024.101379
Chunhua Zhou , Xinyang Lian , Rongrong Wang , Xiaoping Wu , Feng Lin , Shan Ouyang , Shaoqing Jian , Qi Hua
Opsariichthys bidens is a unique economically important freshwater fish in China. Male O. bidens grow faster than females, and male fish have attractive blue-green stripes on the body surface during the breeding period. The breeding of all-male stocks can significantly improve the efficiency of breeding. To accelerate the breeding of all-male stocks, additional studies of the mechanism regulating sex differentiation and gonad development are needed. In this study, transcriptome sequencing of the ovaries and testes of O. bidens was performed using Illumina high-throughput sequencing. The results revealed a total of 21,703 differentially expressed genes, including 8645 up-regulated genes and 5880 down-regulated genes expressed in the ovary compared with the testis. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses revealed multiple differentially expressed genes involved in sex differentiation and gonad development. Eight differentially expressed genes (zp3, cyp19a, hsd17b1, msh4, dmrt1, rspo2, kif23, and gdf9) that play a key role in sex differentiation and gonadal development were selected for RT-qPCR validation. The expression levels of selected genes in the testes and ovaries were significantly different (P < 0.05). zp3, cyp19a, hsd17b1, and gdf9 were female-biased genes, and msh4, dmrt1, rspo2, and kif23 were male-biased genes. zp3, cyp19a, hsd17b, and msh4 were only slightly expressed in the kidney and liver, and dmrt1, rspo2, kif23, and gdf9 were all expressed in gill, kidney, and liver tissue. None of the genes were expressed in the heart or muscle. In this study, differentially expressed genes related to the sex determination and differentiation of O. bidens were identified. Overall, our findings provide important data for future studies of the molecular mechanisms of sex differentiation and gonad development of O. bidens and will aid the breeding of all-male species.
{"title":"Gonadal transcriptome analysis of Opsariichthys bidens reveals sex-associated genes","authors":"Chunhua Zhou , Xinyang Lian , Rongrong Wang , Xiaoping Wu , Feng Lin , Shan Ouyang , Shaoqing Jian , Qi Hua","doi":"10.1016/j.cbd.2024.101379","DOIUrl":"10.1016/j.cbd.2024.101379","url":null,"abstract":"<div><div><em>Opsariichthys bidens</em> is a unique economically important freshwater fish in China. Male <em>O. bidens</em> grow faster than females, and male fish have attractive blue-green stripes on the body surface during the breeding period. The breeding of all-male stocks can significantly improve the efficiency of breeding. To accelerate the breeding of all-male stocks, additional studies of the mechanism regulating sex differentiation and gonad development are needed. In this study, transcriptome sequencing of the ovaries and testes of <em>O. bidens</em> was performed using Illumina high-throughput sequencing. The results revealed a total of 21,703 differentially expressed genes, including 8645 up-regulated genes and 5880 down-regulated genes expressed in the ovary compared with the testis. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses revealed multiple differentially expressed genes involved in sex differentiation and gonad development. Eight differentially expressed genes (<em>zp3</em>, <em>cyp19a</em>, <em>hsd17b1</em>, <em>msh4</em>, <em>dmrt1</em>, <em>rspo2</em>, <em>kif23</em>, and <em>gdf9</em>) that play a key role in sex differentiation and gonadal development were selected for RT-qPCR validation. The expression levels of selected genes in the testes and ovaries were significantly different (<em>P</em> < 0.05). <em>zp3</em>, <em>cyp19a</em>, <em>hsd17b1</em>, and <em>gdf9</em> were female-biased genes, and <em>msh4</em>, <em>dmrt1</em>, <em>rspo2</em>, and <em>kif23</em> were male-biased genes. <em>zp3</em>, <em>cyp19a</em>, <em>hsd17b</em>, and <em>msh4</em> were only slightly expressed in the kidney and liver, and <em>dmrt1</em>, <em>rspo2</em>, <em>kif23</em>, and <em>gdf9</em> were all expressed in gill, kidney, and liver tissue. None of the genes were expressed in the heart or muscle. In this study, differentially expressed genes related to the sex determination and differentiation of <em>O. bidens</em> were identified. Overall, our findings provide important data for future studies of the molecular mechanisms of sex differentiation and gonad development of <em>O. bidens</em> and will aid the breeding of all-male species.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101379"},"PeriodicalIF":2.2,"publicationDate":"2024-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142820261","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}
Pub Date : 2024-12-05DOI: 10.1016/j.cbd.2024.101392
Xiumei Liu , Weijun Wang , Haitao Zhao , Yongjie Wang , Liming Jiang , Enshuo Zhang , Yanwei Feng , Xumin Wang , Jiangyong Qu , Jianmin Yang , Zan Li
As an important member of global aquaculture, oysters (Crassostrea gigas) have significant economic value. With the development of commercial aquaculture, the frequent occurrence of diseases caused by Vibrio alginolyticus has become a hindrance to high-density aquaculture. Gill tissue, as an important component of immune system of the oysters, plays the key point in the face of invasion by foreign substances. Compared to the diploid oyster, the triploid oyster presents a higher growth rate and lower growth investment, making it a more ideal model for studying oyster immune defense. In this study, triploid oysters were as the research subject, and gill tissues attacked by V. alginolyticus were sequenced. By analyzing samples from different time points, 1746 DEGs were obtained. The KEGG and GO functional enrichment analysis showed that gill tissues mainly participate in immune function through the PIK3-Akt signaling pathway and the MAPK signaling pathway. The protein interaction network revealed three genes (CASP8, CASP9 and PIK3CA) that play core roles in immune defense by analyzing the interaction relationship between genes. Finally, qRT-PCR verified the expression of key genes. This study provides a more effective scientific basis for disease prevention and control of oysters and other bivalve shellfish, and helps to promote the sustainable development of aquaculture.
{"title":"Transcriptome profiling of triploid Crassostrea gigas gills indicates the host immune mechanism against bacterial infection","authors":"Xiumei Liu , Weijun Wang , Haitao Zhao , Yongjie Wang , Liming Jiang , Enshuo Zhang , Yanwei Feng , Xumin Wang , Jiangyong Qu , Jianmin Yang , Zan Li","doi":"10.1016/j.cbd.2024.101392","DOIUrl":"10.1016/j.cbd.2024.101392","url":null,"abstract":"<div><div>As an important member of global aquaculture, oysters (<em>Crassostrea gigas</em>) have significant economic value. With the development of commercial aquaculture, the frequent occurrence of diseases caused by <em>Vibrio alginolyticus</em> has become a hindrance to high-density aquaculture. Gill tissue, as an important component of immune system of the oysters, plays the key point in the face of invasion by foreign substances. Compared to the diploid oyster, the triploid oyster presents a higher growth rate and lower growth investment, making it a more ideal model for studying oyster immune defense. In this study, triploid oysters were as the research subject, and gill tissues attacked by <em>V. alginolyticus</em> were sequenced. By analyzing samples from different time points, 1746 DEGs were obtained. The KEGG and GO functional enrichment analysis showed that gill tissues mainly participate in immune function through the PIK3-Akt signaling pathway and the MAPK signaling pathway. The protein interaction network revealed three genes (CASP8, CASP9 and PIK3CA) that play core roles in immune defense by analyzing the interaction relationship between genes. Finally, qRT-PCR verified the expression of key genes. This study provides a more effective scientific basis for disease prevention and control of oysters and other bivalve shellfish, and helps to promote the sustainable development of aquaculture.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101392"},"PeriodicalIF":2.2,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142796673","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}
Pub Date : 2024-11-28DOI: 10.1016/j.cbd.2024.101370
Yao Zheng , Jiajia Li , Jiancao Gao , Wei Jin , Jiawen Hu , Yi Sun , Haojun Zhu , Gangchun Xu
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−1 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.
{"title":"Apoptosis, MAPK signaling pathway affected in tilapia liver following nano-microplastics and sulfamethoxazole acute co-exposure","authors":"Yao Zheng , Jiajia Li , Jiancao Gao , Wei Jin , Jiawen Hu , Yi Sun , Haojun Zhu , Gangchun Xu","doi":"10.1016/j.cbd.2024.101370","DOIUrl":"10.1016/j.cbd.2024.101370","url":null,"abstract":"<div><div>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<sup>−1</sup> 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. <em>apaf1</em>, <em>casp3a</em>, <em>nfkbiaa</em> (apoptosis, except for 8 d) were significantly increased, <em>il1b</em> and <em>tgfb3</em>, <em>fgfr2</em> showed significant increase and decrease in group C/D. <em>ctsd</em> and <em>ctsk</em> associated with apoptosis have been especially significantly increased at 8 d, while MAPK signaling pathway, <em>gadd45ga</em>, <em>gadd45gb/gadd45gg</em> have been significantly decreased and increased, as well as <em>map3k3</em>/<em>map3k2</em> 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.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"53 ","pages":"Article 101370"},"PeriodicalIF":2.2,"publicationDate":"2024-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142744347","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}
Pub Date : 2024-11-28DOI: 10.1016/j.cbd.2024.101371
Huiting Zhou , Jia Wang , Mingtao Hu , Xufang Shen , Rui Gao , Hongwei Yan , Qi Liu , Ying Liu , Yushun Tian , Heng Wang , Xiuli Wang , Shaodong Qu , Chuang Fu
Water temperature plays a vital role in shaping the physical conditions crucial for the growth, development and reproduction of fish species. Since limited comprehensive multi-omics analyses exploring the molecular mechanisms of temperature influences on the early life stages of fish. Here, the effects of temperature variations on the growth of Takifugu rubripes, a commercial teleost farmed in Asia were investigated. Nineteen-days-old fugu larvae were subjected to different temperature (15 °C-T15, 20 °C-T20, 25 °C-T25) for 30 days. Liver tissues were harvested at the end of the study for transcriptomic and metabolomic assessments. The T. rubripes larvae in the T15 group showed a significant decrease in total length and body weight compared to the T20 and T25 groups (p < 0.05). 1344, 416, and 2080 differentially expressed genes (DEGs) were identified in T15-vs-T20, T20-vs-T25, and T15-vs-T25 comparisons, respectively. Those DEGs were mainly enriched in metabolic, protein digestion and absorption, steroid biosynthesis, and glycerophospholipid metabolism pathways. 15 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. 340, 238, and 330 significantly different metabolites (SDMs) were identified in positive modes when comparing in T15-vs-T20, T20-vs-T25, and T15-vs-T25, respectively. Additionally, 145, 137, and 159 SDMs were identified in negative modes within the three comparisons. Those SDMs enriched in biosynthesis of secondary metabolites, glycerophospholipid metabolism, linoleic acid metabolism, and metabolic pathways. The integration of transcriptomic and metabolomic analyses indicated that DEGs and SDMs mainly enriched in metabolic pathways. These discoveries provide valuable insights into the effects of temperature on fish larvae in aquaculture, laying a foundation for future breeding approaches aimed at improving the growth of T. rubripes.
{"title":"Physiological responses to different temperature in the liver of Takifugu rubripes larvae revealed by integrated transcriptomic and metabolomic analyses","authors":"Huiting Zhou , Jia Wang , Mingtao Hu , Xufang Shen , Rui Gao , Hongwei Yan , Qi Liu , Ying Liu , Yushun Tian , Heng Wang , Xiuli Wang , Shaodong Qu , Chuang Fu","doi":"10.1016/j.cbd.2024.101371","DOIUrl":"10.1016/j.cbd.2024.101371","url":null,"abstract":"<div><div>Water temperature plays a vital role in shaping the physical conditions crucial for the growth, development and reproduction of fish species. Since limited comprehensive multi-omics analyses exploring the molecular mechanisms of temperature influences on the early life stages of fish. Here, the effects of temperature variations on the growth of <em>Takifugu rubripes</em>, a commercial teleost farmed in Asia were investigated. Nineteen-days-old fugu larvae were subjected to different temperature (15 °C-T15, 20 °C-T20, 25 °C-T25) for 30 days. Liver tissues were harvested at the end of the study for transcriptomic and metabolomic assessments. The <em>T. rubripes</em> larvae in the T15 group showed a significant decrease in total length and body weight compared to the T20 and T25 groups (<em>p</em> < 0.05). 1344, 416, and 2080 differentially expressed genes (DEGs) were identified in T15-vs-T20, T20-vs-T25, and T15-vs-T25 comparisons, respectively. Those DEGs were mainly enriched in metabolic, protein digestion and absorption, steroid biosynthesis, and glycerophospholipid metabolism pathways. 15 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. 340, 238, and 330 significantly different metabolites (SDMs) were identified in positive modes when comparing in T15-vs-T20, T20-vs-T25, and T15-vs-T25, respectively. Additionally, 145, 137, and 159 SDMs were identified in negative modes within the three comparisons. Those SDMs enriched in biosynthesis of secondary metabolites, glycerophospholipid metabolism, linoleic acid metabolism, and metabolic pathways. The integration of transcriptomic and metabolomic analyses indicated that DEGs and SDMs mainly enriched in metabolic pathways. These discoveries provide valuable insights into the effects of temperature on fish larvae in aquaculture, laying a foundation for future breeding approaches aimed at improving the growth of <em>T. rubripes</em>.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101371"},"PeriodicalIF":2.2,"publicationDate":"2024-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142792988","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}
Pub Date : 2024-11-28DOI: 10.1016/j.cbd.2024.101369
Mingming Han , Xiaohua Zhu , Daming Li , Qin Si , Tian Zhu , Zihan Zhou , Guoxing Liu , Di Ren , Qichen Jiang , Shengkai Tang
This study investigated the effects of short-term exposure to flavonoids, specifically quercetin and taxifolin, on the transcriptomic responses of Chinese sucker (Myxocyprinus asiaticus) to validate their influence on gene expression related to immunity, antioxidant activity, and metabolism. Using transcriptomic data, we also analyzed their influence on relevant immune genes and examined the Chinese suckers' resistance to A. hydrophila. Oxidative stress, immune defense, and glucose metabolism of Chinese suckers were tested to assess potential enhancements. Significant alterations were observed in multiple immune-related Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in the liver of Chinese suckers, notably the complement and coagulation cascades, degradation of aromatic compounds, and xenobiotic metabolism by cytochrome P450. The key immune markers such as UGT, MPO, C3, and C4 were highlighted in these pathways, underlining their importance in fish immunity. Additionally, oxidative stress related KEGG pathways were notably influenced after exposure to quercetin and taxifolin, displaying markers such as CYP3A, superoxide dismutase, GST, malondialdehyde, and catalase. Quercetin particularly affected the enzymatic activity of glucose oxidase, hexokinase, phosphofructokinase, and ATPase, which are enzymes related to stress responses in fish. Antimicrobial tests revealed that both flavonoids enhanced Chinese suckers' defense against A. hydrophila by bolstering oxidative stress resistance and immunity. These results provided valuable insights for using flavonoids to enhance fish immunity.
{"title":"Quercetin and taxifolin enhance immunity in Chinese sucker (Myxocyprinus asiaticus) and increase its resistance to Aeromonas hydrophila","authors":"Mingming Han , Xiaohua Zhu , Daming Li , Qin Si , Tian Zhu , Zihan Zhou , Guoxing Liu , Di Ren , Qichen Jiang , Shengkai Tang","doi":"10.1016/j.cbd.2024.101369","DOIUrl":"10.1016/j.cbd.2024.101369","url":null,"abstract":"<div><div>This study investigated the effects of short-term exposure to flavonoids, specifically quercetin and taxifolin, on the transcriptomic responses of Chinese sucker (<em>Myxocyprinus asiaticus</em>) to validate their influence on gene expression related to immunity, antioxidant activity, and metabolism. Using transcriptomic data, we also analyzed their influence on relevant immune genes and examined the Chinese suckers' resistance to <em>A. hydrophila</em>. Oxidative stress, immune defense, and glucose metabolism of Chinese suckers were tested to assess potential enhancements. Significant alterations were observed in multiple immune-related Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in the liver of Chinese suckers, notably the complement and coagulation cascades, degradation of aromatic compounds, and xenobiotic metabolism by cytochrome P450. The key immune markers such as <em>UGT</em>, <em>MPO</em>, <em>C3</em>, and <em>C4</em> were highlighted in these pathways, underlining their importance in fish immunity. Additionally, oxidative stress related KEGG pathways were notably influenced after exposure to quercetin and taxifolin, displaying markers such as CYP3A, superoxide dismutase, GST, malondialdehyde, and catalase. Quercetin particularly affected the enzymatic activity of glucose oxidase, hexokinase, phosphofructokinase, and ATPase, which are enzymes related to stress responses in fish. Antimicrobial tests revealed that both flavonoids enhanced Chinese suckers' defense against <em>A. hydrophila</em> by bolstering oxidative stress resistance and immunity. These results provided valuable insights for using flavonoids to enhance fish immunity.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101369"},"PeriodicalIF":2.2,"publicationDate":"2024-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142792992","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}
Pub Date : 2024-11-26DOI: 10.1016/j.cbd.2024.101367
Weidong Ding, Liping Cao, Zheming Cao, Xuwen Bing
The oxygen content in the fish ponds is facing greater challenges than before in the aquaculture of mandarin fish (Siniperca chuatsi) due to the change of climate and eutrophication. Until now, little is known about the molecular mechanisms underlying the harmful effects of hypoxia on this species. In this work, we built transcriptomes for the mandarin fish that were exposed to decreased oxygen concentration at two times points (24 h and 96 h). The respiratory metabolism activities of pyruvate kinase (PK), hexokinase (HK), lactate dehydrogenase (LDH), succinate dehydrogenase (SDH) and malate dehydrogenase (MDH) had different significantly changes during hypoxic treatment. Histological observation of the gill and brain also revealed some damages by hypoxia. A total of 196,355 transcripts were involved in the Gene Ontology analysis, and the numbers of differentially expressed genes (DEGs) in the brain and the gill between the control and experiment groups are 141 and 552 respectively involved in the different hypoxic stress time. The DEGs were then analyzed using KEGG enrichment analysis. The results showed significant differences in the expression of some genes involved in ribosome pathways,biosynthesis of amino acids, hippo signaling pathway, and pentose phosphate pathway,glycolysis/gluconeogenesis pathway and the TCA cycle. The huge number of transcriptome sequences collected in this study has enhanced the mandarin fish gene resources, and the identified DEGs and related pathway analysis give essential information for understanding biological responses to hypoxia.
{"title":"Gill and brain transcriptomic analysis of mandarin fish(Siniperca chuatsi)reveals hypoxia-induced mitochondrial dysfunction and modulation of metabolism","authors":"Weidong Ding, Liping Cao, Zheming Cao, Xuwen Bing","doi":"10.1016/j.cbd.2024.101367","DOIUrl":"10.1016/j.cbd.2024.101367","url":null,"abstract":"<div><div>The oxygen content in the fish ponds is facing greater challenges than before in the aquaculture of mandarin fish (<em>Siniperca chuatsi</em>) due to the change of climate and eutrophication. Until now, little is known about the molecular mechanisms underlying the harmful effects of hypoxia on this species. In this work, we built transcriptomes for the mandarin fish that were exposed to decreased oxygen concentration at two times points (24 h and 96 h). The respiratory metabolism activities of pyruvate kinase (PK), hexokinase (HK), lactate dehydrogenase (LDH), succinate dehydrogenase (SDH) and malate dehydrogenase (MDH) had different significantly changes during hypoxic treatment. Histological observation of the gill and brain also revealed some damages by hypoxia. A total of 196,355 transcripts were involved in the Gene Ontology analysis, and the numbers of differentially expressed genes (DEGs) in the brain and the gill between the control and experiment groups are 141 and 552 respectively involved in the different hypoxic stress time. The DEGs were then analyzed using KEGG enrichment analysis. The results showed significant differences in the expression of some genes involved in ribosome pathways,biosynthesis of amino acids, hippo signaling pathway, and pentose phosphate pathway,glycolysis/gluconeogenesis pathway and the TCA cycle. The huge number of transcriptome sequences collected in this study has enhanced the mandarin fish gene resources, and the identified DEGs and related pathway analysis give essential information for understanding biological responses to hypoxia.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"53 ","pages":"Article 101367"},"PeriodicalIF":2.2,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142775674","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}
Pub Date : 2024-11-25DOI: 10.1016/j.cbd.2024.101368
Ying Chen, Wajid Ali, Yu Men, Kai Yan, Zibin Li, Wenxiu Cai, Yan He, Jie Qi
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.
{"title":"Molecular insights into oocyte development and sperm storage in black rockfish (Sebastes schlegelii): Proteomic changes across reproductive stages","authors":"Ying Chen, Wajid Ali, Yu Men, Kai Yan, Zibin Li, Wenxiu Cai, Yan He, Jie Qi","doi":"10.1016/j.cbd.2024.101368","DOIUrl":"10.1016/j.cbd.2024.101368","url":null,"abstract":"<div><div>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 (<em>Sebastes schlegelii</em>) 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.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"53 ","pages":"Article 101368"},"PeriodicalIF":2.2,"publicationDate":"2024-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142744346","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}
Pub Date : 2024-11-23DOI: 10.1016/j.cbd.2024.101364
Duo Li , Leilei Zeng , Weiwei Zhang , Qinghua Wang , Jinhui Wu , Chunhua Zhu , Zining Meng
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.
{"title":"Multi-omics study of sex in greater amberjack (Seriola dumerili): Identifying related genes, analyzing sex-biased expression, and developing sex-specific markers","authors":"Duo Li , Leilei Zeng , Weiwei Zhang , Qinghua Wang , Jinhui Wu , Chunhua Zhu , Zining Meng","doi":"10.1016/j.cbd.2024.101364","DOIUrl":"10.1016/j.cbd.2024.101364","url":null,"abstract":"<div><div>The greater amberjack (<em>Seriola dumerili</em>) 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 (<em>hsd17β1</em>) and 20 candidate sex-related genes (<em>hmbox1</em>, <em>ahcyl1</em>, <em>pdzd2</em>, etc.). Key sex-biased genes (<em>sox2</em>, <em>dmrt2</em>, <em>hsd17β3</em>, <em>rnf145</em>, <em>foxo3</em>, 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.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"53 ","pages":"Article 101364"},"PeriodicalIF":2.2,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142723092","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}
Pub Date : 2024-11-22DOI: 10.1016/j.cbd.2024.101366
Alexey A. Morozov, Victoria V. Yurchenko
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.
{"title":"Effects of environmentally relevant concentrations of glyphosate and aminomethylphosphonic acid on biotransformation and stress response proteins in the liver of zebrafish (Danio rerio)","authors":"Alexey A. Morozov, Victoria V. Yurchenko","doi":"10.1016/j.cbd.2024.101366","DOIUrl":"10.1016/j.cbd.2024.101366","url":null,"abstract":"<div><div>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 <em>Danio rerio</em> 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.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"53 ","pages":"Article 101366"},"PeriodicalIF":2.2,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142706266","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}
扫码关注我们
求助内容：
应助结果提醒方式：
京公网安备 11010802042870号