Pub Date : 2025-10-30DOI: 10.1016/j.cbd.2025.101671
Byron Morales-Lange , Sérgio D.C. Rocha , Arturo Vera-Ponce de León , Matthias Hötzinger , Liv Torunn Mydland , Brankica Djordjevic , Phillip B. Pope , Margareth Øverland
Feed additives are an alternative to improve fish performance and health (without compromising growth) during farming conditions. To determine the physiological effects of two hydrolyzed Debaryomyces hansenii yeasts (LAN4 and LAN6 from Lallemand SAS) on the gut of post-smolts Atlantic salmon (Salmo salar), an in vivo experiment was conducted (7 weeks in freshwater and 6 weeks in seawater) using 0.1 % LAN4 or LAN6 in diets for vaccinated fish. Coincidentally, a natural outbreak of Moritella viscosa (a bacterial fish pathogen) was reported at week 5 in seawater. Thus, the current study focus incorporated the disease-inflicted modulation of intestinal proteome and microbiota composition, which was estimated through metaproteomics and 16S rRNA sequencing, respectively. Results showed a detection of 1170 amplicon sequence variants (ASVs) belonging to 52 genera (modulated among dietary groups). Moreover, a positive correlation between LAN4 and control group (Ctr) was detected based on ASVs analysis. Regarding metaproteomics data and enrichment analysis (using KEGG or GO databases), LAN4 group showed a higher abundance of proteins linked to 48 functional terms such as amino acid biosynthesis and metabolism, immune homeostasis and cellular response to oxidative stress. On contrary, the proteins detected in LAN6 were linked with 14 terms (e.g., ferroptosis, arachidonic acid metabolism and regulation of cell projection assembly) that can be related to the inflammatory process. These results suggest the potential of D. hansenii yeasts as a paraprobiotics for the intestinal proteome and microbiota structure of Atlantic salmon. Therefore, D. hansenii is a promising feed additive for aquaculture-related species during the production cycle.
{"title":"Hydrolyzed Debaryomyces hansenii yeasts as paraprobiotics in fish: Omics-based characterization of Atlantic salmon gut during a natural pathogen outbreak in seawater stage","authors":"Byron Morales-Lange , Sérgio D.C. Rocha , Arturo Vera-Ponce de León , Matthias Hötzinger , Liv Torunn Mydland , Brankica Djordjevic , Phillip B. Pope , Margareth Øverland","doi":"10.1016/j.cbd.2025.101671","DOIUrl":"10.1016/j.cbd.2025.101671","url":null,"abstract":"<div><div>Feed additives are an alternative to improve fish performance and health (without compromising growth) during farming conditions. To determine the physiological effects of two hydrolyzed <em>Debaryomyces hansenii</em> yeasts (LAN4 and LAN6 from Lallemand SAS) on the gut of post-smolts Atlantic salmon (<em>Salmo salar</em>), an <em>in vivo</em> experiment was conducted (7 weeks in freshwater and 6 weeks in seawater) using 0.1 % LAN4 or LAN6 in diets for vaccinated fish. Coincidentally, a natural outbreak of <em>Moritella viscosa</em> (a bacterial fish pathogen) was reported at week 5 in seawater. Thus, the current study focus incorporated the disease-inflicted modulation of intestinal proteome and microbiota composition, which was estimated through metaproteomics and 16S rRNA sequencing, respectively. Results showed a detection of 1170 amplicon sequence variants (ASVs) belonging to 52 genera (modulated among dietary groups). Moreover, a positive correlation between LAN4 and control group (Ctr) was detected based on ASVs analysis. Regarding metaproteomics data and enrichment analysis (using KEGG or GO databases), LAN4 group showed a higher abundance of proteins linked to 48 functional terms such as amino acid biosynthesis and metabolism, immune homeostasis and cellular response to oxidative stress. On contrary, the proteins detected in LAN6 were linked with 14 terms (e.g., ferroptosis, arachidonic acid metabolism and regulation of cell projection assembly) that can be related to the inflammatory process. These results suggest the potential of <em>D. hansenii</em> yeasts as a paraprobiotics for the intestinal proteome and microbiota structure of Atlantic salmon. Therefore, <em>D. hansenii</em> is a promising feed additive for aquaculture-related species during the production cycle.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"57 ","pages":"Article 101671"},"PeriodicalIF":2.2,"publicationDate":"2025-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145460906","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}
Hypoxic stress poses a significant challenge to aquaculture productivity. As a hypoxia-intolerant species, rainbow trout (Oncorhynchus mykiss) requires further investigation regarding their molecular and physiological adaptations to prolonged hypoxia. In this study, we investigated the temporal dynamics of the hypoxic response in rainbow trout gill cells through an integrated analysis of transcriptomics, histopathology, and biochemical analysis. Primary gill cells exposed to hypoxic conditions (3 % O2) for 0, 24, and 48 h exhibited a progressive increase in reactive oxygen species (ROS) levels. A total of 6744 differentially expressed genes (DEGs) were identified through RNA sequencing, with the Glycolysis/Gluconeogenesis and Biosynthesis of amino acids pathways significantly upregulated at both 24 and 48 h, indicating a metabolic shift toward anaerobic energy production and antioxidant defense. In contrast, steroid biosynthesis was enriched at 48 h, potentially supporting membrane repair and cortisol-mediated stress adaptation, whereas apoptosis transitioned from inhibition at 24 h to activation at 48 h, correlating with irreversible cellular damage. Weighted Gene Co-expression Network Analysis (WGCNA) identified the module most associated with 48-h hypoxia, which was also enriched in these four pathways. Histopathological and physiological indicators also proved time-dependent changes in tissues upon hypoxic stress. These findings indicated that during early hypoxia (24 h), metabolic adaptation, including Glycolysis/Gluconeogenesis and Biosynthesis of amino acids, was prioritized in rainbow trout. However, after 48 h of hypoxia, a transition from metabolic adaptation to apoptosis-mediated cell clearance was induced, accompanied by the upregulation of steroid biosynthesis to mitigate sustained oxidative damage.
{"title":"Transcriptomic and physiological responses of rainbow trout (Oncorhynchus mykiss) gill tissues to hypoxic stress","authors":"Ziyi Zhao, Mengqun Liu, Qiusheng Wang, Haishen Wen, Xin Qi","doi":"10.1016/j.cbd.2025.101672","DOIUrl":"10.1016/j.cbd.2025.101672","url":null,"abstract":"<div><div>Hypoxic stress poses a significant challenge to aquaculture productivity. As a hypoxia-intolerant species, rainbow trout (<em>Oncorhynchus mykiss</em>) requires further investigation regarding their molecular and physiological adaptations to prolonged hypoxia. In this study, we investigated the temporal dynamics of the hypoxic response in rainbow trout gill cells through an integrated analysis of transcriptomics, histopathology, and biochemical analysis. Primary gill cells exposed to hypoxic conditions (3 % O<sub>2</sub>) for 0, 24, and 48 h exhibited a progressive increase in reactive oxygen species (ROS) levels. A total of 6744 differentially expressed genes (DEGs) were identified through RNA sequencing, with the Glycolysis/Gluconeogenesis and Biosynthesis of amino acids pathways significantly upregulated at both 24 and 48 h, indicating a metabolic shift toward anaerobic energy production and antioxidant defense. In contrast, steroid biosynthesis was enriched at 48 h, potentially supporting membrane repair and cortisol-mediated stress adaptation, whereas apoptosis transitioned from inhibition at 24 h to activation at 48 h, correlating with irreversible cellular damage. Weighted Gene Co-expression Network Analysis (WGCNA) identified the module most associated with 48-h hypoxia, which was also enriched in these four pathways. Histopathological and physiological indicators also proved time-dependent changes in tissues upon hypoxic stress. These findings indicated that during early hypoxia (24 h), metabolic adaptation, including Glycolysis/Gluconeogenesis and Biosynthesis of amino acids, was prioritized in rainbow trout. However, after 48 h of hypoxia, a transition from metabolic adaptation to apoptosis-mediated cell clearance was induced, accompanied by the upregulation of steroid biosynthesis to mitigate sustained oxidative damage.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"57 ","pages":"Article 101672"},"PeriodicalIF":2.2,"publicationDate":"2025-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145446733","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 : 2025-10-28DOI: 10.1016/j.cbd.2025.101669
A.A. Tsekova, A.E. Kuritsyn, S.A. Murzina
For the first time, the brain proteomic profiles of rainbow trout Oncorhynchus mykiss (Walbaum, 1792) at two maturation stages were described and discussed. Maturation and reproduction are critical stages in the fish life cycle, but the biochemical and morphophysiological processes underlying these stages are not well understood. The reactions that occur in the fish brain during maturation, regulating the reproductive process and accompanying metabolic changes, are of particular interest. O. mykiss is an economically significant commercial species of salmonid fish that is a model organism for biological research. We analyzed the brain proteomes of rainbow trout at different stages of gonadal development, including stages II–III (developing) and stage V (spawning). It was revealed that the brain proteomes differed in terms of proteins involved in lipid metabolism, immune responses, stress response, cell structure, and oocyte development. These findings provide valuable insights into the complex processes that occur during fish maturation and can contribute to our understanding of reproductive biology. The biochemical differences in the brain at different stages of development are shown, as well as the fact that the by-products of commercial fishing, in this case, heads and brains, can be used to extract antimicrobial proteins and peptides.
{"title":"Brain proteomics of rainbow trout at certain maturation stages: biological insights and fish by-products processing perspectives","authors":"A.A. Tsekova, A.E. Kuritsyn, S.A. Murzina","doi":"10.1016/j.cbd.2025.101669","DOIUrl":"10.1016/j.cbd.2025.101669","url":null,"abstract":"<div><div>For the first time, the brain proteomic profiles of rainbow trout <em>Oncorhynchus mykiss</em> (Walbaum, 1792) at two maturation stages were described and discussed. Maturation and reproduction are critical stages in the fish life cycle, but the biochemical and morphophysiological processes underlying these stages are not well understood. The reactions that occur in the fish brain during maturation, regulating the reproductive process and accompanying metabolic changes, are of particular interest. <em>O. mykiss</em> is an economically significant commercial species of salmonid fish that is a model organism for biological research. We analyzed the brain proteomes of rainbow trout at different stages of gonadal development, including stages II–III (developing) and stage V (spawning). It was revealed that the brain proteomes differed in terms of proteins involved in lipid metabolism, immune responses, stress response, cell structure, and oocyte development. These findings provide valuable insights into the complex processes that occur during fish maturation and can contribute to our understanding of reproductive biology. The biochemical differences in the brain at different stages of development are shown, as well as the fact that the by-products of commercial fishing, in this case, heads and brains, can be used to extract antimicrobial proteins and peptides.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"57 ","pages":"Article 101669"},"PeriodicalIF":2.2,"publicationDate":"2025-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145454227","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 : 2025-10-27DOI: 10.1016/j.cbd.2025.101668
Deng Fu , Yingyin Wu , Xin Hong , Yanyun Zhu , Querui Luo , Guanyi Li , Kun Tian , Xing Zheng , Chunsheng Liu , Shifeng Wang , Aiming Wang , Zhifeng Gu , Feng Yu
Heat shock proteins (HSPs) are highly conserved molecular chaperones that play essential roles in biological growth, development, and responses to environmental stress. To investigate the functions of HSPs in Babylonia areolata (BaHsps) under heat stress, a total of 68 BaHsp genes were identified at the genome-wide level using bioinformatics approaches. The phylogenetic tree, gene structure, chromosome location and protein physicochemical properties were predicted, and the expression patterns of BaHsp genes in different tissues under heat stress were analyzed and characterized by Quantitative Real-time polymerase chain reaction method (qPCR). The results revealed significant variation in the number and arrangement of introns among different BaHsp genes, with introns unevenly distributed across 26 chromosomes. Gene duplication analysis indicated tandem duplication events in the BaHsp20, BaHsp40 and BaHsp90, suggesting that these events contributed to the expansion and functional diversification of the BaHsp gene families. RT-qPCR results demonstrated clear tissue-specific expression of BaHsp genes, with overall expression levels being relatively high in gill tissue. Under heat stress, expression of BaHsp genes in gill tissue increased with rising temperatures. Temporal expression analysis further showed that most genes were rapidly upregulated at the onset of heat stress, followed by a gradual decline, exhibiting a dynamic pattern of “increase-then-decrease”. This study provides a fundamental reference for further investigations into the molecular mechanisms of HSP gene family response to heat stress in B. areolata.
{"title":"Genome-wide identification and characterization of the HSP gene superfamily in the Ivory Shell (Babylonia areolata)","authors":"Deng Fu , Yingyin Wu , Xin Hong , Yanyun Zhu , Querui Luo , Guanyi Li , Kun Tian , Xing Zheng , Chunsheng Liu , Shifeng Wang , Aiming Wang , Zhifeng Gu , Feng Yu","doi":"10.1016/j.cbd.2025.101668","DOIUrl":"10.1016/j.cbd.2025.101668","url":null,"abstract":"<div><div>Heat shock proteins (HSPs) are highly conserved molecular chaperones that play essential roles in biological growth, development, and responses to environmental stress. To investigate the functions of HSPs in <em>Babylonia areolata</em> (BaHsps) under heat stress, a total of 68 BaHsp genes were identified at the genome-wide level using bioinformatics approaches. The phylogenetic tree, gene structure, chromosome location and protein physicochemical properties were predicted, and the expression patterns of BaHsp genes in different tissues under heat stress were analyzed and characterized by Quantitative Real-time polymerase chain reaction method (qPCR). The results revealed significant variation in the number and arrangement of introns among different BaHsp genes, with introns unevenly distributed across 26 chromosomes. Gene duplication analysis indicated tandem duplication events in the <em>BaHsp20</em>, <em>BaHsp40</em> and <em>BaHsp90</em>, suggesting that these events contributed to the expansion and functional diversification of the BaHsp gene families. RT-qPCR results demonstrated clear tissue-specific expression of BaHsp genes, with overall expression levels being relatively high in gill tissue. Under heat stress, expression of BaHsp genes in gill tissue increased with rising temperatures. Temporal expression analysis further showed that most genes were rapidly upregulated at the onset of heat stress, followed by a gradual decline, exhibiting a dynamic pattern of “increase-then-decrease”. This study provides a fundamental reference for further investigations into the molecular mechanisms of HSP gene family response to heat stress in <em>B. areolata.</em></div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"57 ","pages":"Article 101668"},"PeriodicalIF":2.2,"publicationDate":"2025-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145425806","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 : 2025-10-24DOI: 10.1016/j.cbd.2025.101664
Jianghao Chang , Rong Huang , Wei Peng , Yibing Yue , Huawei Su , Yang He , Weiru Song , Chuzhao Lei , Rende Song , Jun Zhang , Yongzhen Huang
This study investigated genomic structural variations and their association with muscle development in Qinghai-Tibetan Plateau yaks to elucidate their genetic diversity and adaptive mechanisms. Whole-genome resequencing was performed on 145 Qinghai-Tibetan Plateau yaks, supplemented with sequence data from 12 wild yaks obtained from the National Center for Biotechnology Information (NCBI) database. Analyses characterized runs of homozygosity (ROH), copy number variations (CNV), and structural variations (SV). A genome-wide copy number variation map for Qinghai Plateau yaks was constructed. Qinghai-Tibetan Plateau yaks exhibited numerous ROHs (totaling 61,074 segments, covering 19,947.56 Mb), showing relatively high levels of genomic homozygosity compared to wild yaks (3255 segments, 1056.66 total length), and 1175 CNV regions and 59,694 SVs, primarily located in non-coding regions, were identified. Publicly available transcriptome data were integrated to identify candidate genes related to muscle development, followed by statistical validation of key candidates. Integrating genomic and transcriptomic data revealed 84 overlapping genes potentially involved in muscle development. Subsequent bioinformatic prioritization identified PTPN6, ATP2A1, LCP1, GNA15, ALOX5AP, FLT3, SLC34A3, and BCL11A as high-priority candidate genes potentially influencing this trait. These findings demonstrate that genomic variations significantly impact muscle development in Qinghai-Tibetan Plateau yaks, providing a valuable molecular basis for future yak breeding programs and adaptation research.
{"title":"Genomic runs of homozygosity and structural variation reveal muscle development-related genes in Qinghai-Tibetan Plateau yaks","authors":"Jianghao Chang , Rong Huang , Wei Peng , Yibing Yue , Huawei Su , Yang He , Weiru Song , Chuzhao Lei , Rende Song , Jun Zhang , Yongzhen Huang","doi":"10.1016/j.cbd.2025.101664","DOIUrl":"10.1016/j.cbd.2025.101664","url":null,"abstract":"<div><div>This study investigated genomic structural variations and their association with muscle development in Qinghai-Tibetan Plateau yaks to elucidate their genetic diversity and adaptive mechanisms. Whole-genome resequencing was performed on 145 Qinghai-Tibetan Plateau yaks, supplemented with sequence data from 12 wild yaks obtained from the National Center for Biotechnology Information (NCBI) database. Analyses characterized runs of homozygosity (ROH), copy number variations (CNV), and structural variations (SV). A genome-wide copy number variation map for Qinghai Plateau yaks was constructed. Qinghai-Tibetan Plateau yaks exhibited numerous ROHs (totaling 61,074 segments, covering 19,947.56 Mb), showing relatively high levels of genomic homozygosity compared to wild yaks (3255 segments, 1056.66 total length), and 1175 CNV regions and 59,694 SVs, primarily located in non-coding regions, were identified. Publicly available transcriptome data were integrated to identify candidate genes related to muscle development, followed by statistical validation of key candidates. Integrating genomic and transcriptomic data revealed 84 overlapping genes potentially involved in muscle development. Subsequent bioinformatic prioritization identified PTPN6, ATP2A1, LCP1, GNA15, ALOX5AP, FLT3, SLC34A3, and BCL11A as high-priority candidate genes potentially influencing this trait. These findings demonstrate that genomic variations significantly impact muscle development in Qinghai-Tibetan Plateau yaks, providing a valuable molecular basis for future yak breeding programs and adaptation research.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"57 ","pages":"Article 101664"},"PeriodicalIF":2.2,"publicationDate":"2025-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145411055","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 : 2025-10-24DOI: 10.1016/j.cbd.2025.101663
Jing Yu , Hongfang Wang , Zhenguo Liu , Baohua Xu
20-hydroxyecdysone (20E) plays a crucial role in insect metamorphosis and has been reported to be involved in fat body lipolysis during pupation in many insects, although this has not been reported in honeybees. Here, we investigated how 20E regulates lipid metabolism during pupation in Apis mellifera. We found that 20E promotes fat body lipolysis by inducing autophagy. 20E treatment reduced fat body triglyceride (TG) content, upregulated lipase-1 and adipokinetic hormone receptor (akhr) expression, and promoted fat body lipolysis. Our lipidomic results showed that honeybee larvae treated with 20E showed significant changes in their TG and phosphatidylcholine (PC) fatty acid levels. In conclusion, we conclude that 20E promotes pupal development by coordinating autophagy and lipid mobilization. This work reveals a novel regulatory mechanism of insect metamorphosis in honeybees and expands our understanding of steroid hormone action in holometabolous insects.
{"title":"20-Hydroxyecdysone promotes fat body lipolysis through autophagy during pupation in Apis mellifera","authors":"Jing Yu , Hongfang Wang , Zhenguo Liu , Baohua Xu","doi":"10.1016/j.cbd.2025.101663","DOIUrl":"10.1016/j.cbd.2025.101663","url":null,"abstract":"<div><div>20-hydroxyecdysone (20E) plays a crucial role in insect metamorphosis and has been reported to be involved in fat body lipolysis during pupation in many insects, although this has not been reported in honeybees. Here, we investigated how 20E regulates lipid metabolism during pupation in <em>Apis mellifera</em>. We found that 20E promotes fat body lipolysis by inducing autophagy. 20E treatment reduced fat body triglyceride (TG) content, upregulated <em>lipase-1</em> and <em>adipokinetic hormone receptor</em> (<em>akhr</em>) expression, and promoted fat body lipolysis. Our lipidomic results showed that honeybee larvae treated with 20E showed significant changes in their TG and phosphatidylcholine (PC) fatty acid levels. In conclusion, we conclude that 20E promotes pupal development by coordinating autophagy and lipid mobilization. This work reveals a novel regulatory mechanism of insect metamorphosis in honeybees and expands our understanding of steroid hormone action in holometabolous insects.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"57 ","pages":"Article 101663"},"PeriodicalIF":2.2,"publicationDate":"2025-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145454293","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 : 2025-10-23DOI: 10.1016/j.cbd.2025.101665
Xiaolan Huang , Jingjing Gu , Zhen Huang , Xuebo Cui , Daowen Qiu , Zan Li , Yanwei Feng , Xiaohui Xu , Jianmin Yang
Amphioctopus fangsiao is a commercially valuable cephalopod species prized for its distinctive flavor and nutritional profile. However, its large-scale aquaculture is hampered by significant challenges, particularly outbreaks of infectious diseases. Viral pathogens, which can be co-transmitted among marine species, pose a severe threat to sustainable population development. To elucidate the antiviral defense mechanisms in A. fangsiao, we conducted transcriptomic profiling of hepatopancreatic tissue following stimulation with polyinosinic-polycytidylic acid (Poly(I:C)), a well-established viral mimic known to activate innate immune pathways. Comparative transcriptomic profiling of the hepatopancreas—a key immune organ—at 6 h and 24 h post-stimulation identified 1406 and 904 differentially expressed genes (DEGs), respectively. Functional enrichment analysis revealed that these DEGs were significantly involved in critical immune-related pathways, including apoptosis, ECM-receptor interaction, and the MAPK and Hippo signaling pathways. Furthermore, by integrating protein-protein interaction (PPI) network analysis with KEGG pathway data, we identified 18 hub genes—such as TNFSF10, JUN, EGFR, and CTSB—that were potential key regulators of the antiviral response. The expression patterns of the aforementioned hub genes were successfully validated by means of quantitative reverse transcription polymerase chain reaction (qRT-PCR). This study comprehensively revealed the transcriptome characteristics of antiviral immune response of A. fangsiao for the first time. Our findings not only advance the understanding of innate immunity in cephalopods but also offer valuable genetic resources and potential molecular targets for developing strategies against viral diseases in octopus aquaculture.
{"title":"Transcriptome analysis and exploration of immune key genes of hepatopancreas after Poly(I:C) stimulation in Amphioctopus fangsiao","authors":"Xiaolan Huang , Jingjing Gu , Zhen Huang , Xuebo Cui , Daowen Qiu , Zan Li , Yanwei Feng , Xiaohui Xu , Jianmin Yang","doi":"10.1016/j.cbd.2025.101665","DOIUrl":"10.1016/j.cbd.2025.101665","url":null,"abstract":"<div><div><em>Amphioctopus fangsiao</em> is a commercially valuable cephalopod species prized for its distinctive flavor and nutritional profile. However, its large-scale aquaculture is hampered by significant challenges, particularly outbreaks of infectious diseases. Viral pathogens, which can be co-transmitted among marine species, pose a severe threat to sustainable population development. To elucidate the antiviral defense mechanisms in <em>A</em>. <em>fangsiao</em>, we conducted transcriptomic profiling of hepatopancreatic tissue following stimulation with polyinosinic-polycytidylic acid (Poly(I:C)), a well-established viral mimic known to activate innate immune pathways. Comparative transcriptomic profiling of the hepatopancreas—a key immune organ—at 6 h and 24 h post-stimulation identified 1406 and 904 differentially expressed genes (DEGs), respectively. Functional enrichment analysis revealed that these DEGs were significantly involved in critical immune-related pathways, including apoptosis, ECM-receptor interaction, and the MAPK and Hippo signaling pathways. Furthermore, by integrating protein-protein interaction (PPI) network analysis with KEGG pathway data, we identified 18 hub genes—such as <em>TNFSF10, JUN, EGFR</em>, and <em>CTSB</em>—that were potential key regulators of the antiviral response. The expression patterns of the aforementioned hub genes were successfully validated by means of quantitative reverse transcription polymerase chain reaction (qRT-PCR). This study comprehensively revealed the transcriptome characteristics of antiviral immune response of <em>A. fangsiao</em> for the first time. Our findings not only advance the understanding of innate immunity in cephalopods but also offer valuable genetic resources and potential molecular targets for developing strategies against viral diseases in octopus aquaculture.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"57 ","pages":"Article 101665"},"PeriodicalIF":2.2,"publicationDate":"2025-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145411095","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}
Decapoda crabs inhabit diverse environments, which are mainly aquatic, while some intertidal crabs are semi-terrestrial. However, current research on the molecular basis of terrestrial adaptation in crabs remains insufficiently characterized. Orisarma neglectum (Sesarmidae), which inhabits low-salinity semi-terrestrial environments such as the Yangtze River Estuary and its surrounding wetland areas, is an ideal model for studying terrestrial adaptation mechanisms. Thus, the transcriptomic and histological methods were used to explore the terrestrial adaptation mechanism of O. neglectum in this study. Three experimental groups (aquatic, semi-terrestrial, terrestrial) under controlled habitat simulations were set up. Histological analyses revealed marked branchial lamellar hypertrophy with concomitant cytoplasmic exudation in terrestrial-acclimated O. neglectum compared to aquatic/semi-terrestrial groups under xeric conditions. Furthermore, the transcriptomics results of gills revealed that the desiccation stress imposed on O. neglectum mainly manifests in energy metabolism, RNA synthesis and Ribosome pathways, and immune-related genes. The results of histology and transcriptomics suggested that gills were more sensitive to habitat changes than hepatopancreas. Given all this, a completely terrestrial habitat may be detrimental to the survival of O. neglectum, and intertidal crabs cannot live completely without water. Investigating the adaptive mechanisms of O. neglectum to diverse habitats through histology and transcriptomics can provide critical insights into understanding the terrestrial adaptation of semi-terrestrial crab species, and references for solving the problems of oxygen supply and air exposure during crab breeding and transportation.
{"title":"Analysis of the histology and transcriptomics of Orisarma neglectum provides new insights into the terrestrial adaptation mechanisms of intertidal crabs","authors":"Zhengfei Wang , Zhilin Guo , Chenchen Shen , Lijie Cui , Jing Zhu , Sijia Hao , Yayun Guan , Yanhan Peng","doi":"10.1016/j.cbd.2025.101658","DOIUrl":"10.1016/j.cbd.2025.101658","url":null,"abstract":"<div><div>Decapoda crabs inhabit diverse environments, which are mainly aquatic, while some intertidal crabs are semi-terrestrial. However, current research on the molecular basis of terrestrial adaptation in crabs remains insufficiently characterized. <em>Orisarma neglectum</em> (Sesarmidae), which inhabits low-salinity semi-terrestrial environments such as the Yangtze River Estuary and its surrounding wetland areas, is an ideal model for studying terrestrial adaptation mechanisms. Thus, the transcriptomic and histological methods were used to explore the terrestrial adaptation mechanism of <em>O. neglectum</em> in this study. Three experimental groups (aquatic, semi-terrestrial, terrestrial) under controlled habitat simulations were set up. Histological analyses revealed marked branchial lamellar hypertrophy with concomitant cytoplasmic exudation in terrestrial-acclimated <em>O. neglectum</em> compared to aquatic/semi-terrestrial groups under xeric conditions. Furthermore, the transcriptomics results of gills revealed that the desiccation stress imposed on <em>O. neglectum</em> mainly manifests in energy metabolism, RNA synthesis and Ribosome pathways, and immune-related genes. The results of histology and transcriptomics suggested that gills were more sensitive to habitat changes than hepatopancreas. Given all this, a completely terrestrial habitat may be detrimental to the survival of <em>O. neglectum</em>, and intertidal crabs cannot live completely without water. Investigating the adaptive mechanisms of <em>O. neglectum</em> to diverse habitats through histology and transcriptomics can provide critical insights into understanding the terrestrial adaptation of semi-terrestrial crab species, and references for solving the problems of oxygen supply and air exposure during crab breeding and transportation.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"57 ","pages":"Article 101658"},"PeriodicalIF":2.2,"publicationDate":"2025-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145369817","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 : 2025-10-22DOI: 10.1016/j.cbd.2025.101660
Suhan Peng , Jie Lai , Shengyue Lin , Sixun Li , Binhua Deng , Weijian Chen , Weibin Li , Chong Han , Qiang Li
The demand for synthetic progesterone has surged due to its widespread use in contraceptives and veterinary drugs. However, these compounds are not fully removed by wastewater treatment plants, leading to their release into aquatic environments and potential disruption of fish reproduction and development. Etonogestrel (ETO), a third-generation synthetic progestogen, is widely used in oral contraceptives. In this study, adult female mosquitofish were exposed to ETO at measured concentrations of 0 ng/L, 3.88 ng/L, 39.5 ng/L, and 385.18 ng/L for 36 days. Morphology, ovarian histology, and transcriptomic analyses were conducted to assess the effects of ETO. Results showed that ETO exposure reduced the body weight-to-total length ratio and promoted gonopodia and skeletal modifications. Particularly notable was the finding of decreased ovarian weight and the induction of testicular structures in the 385.18 ng/L ETO group, indicating a significant masculinization effect. Transcriptomic analysis revealed that genes related to sexual differentiation (cyp17a1, hsd17b3 and sox9), which were enriched in the GnRH signaling pathway and steroid hormone biosynthesis, may drive masculinization by promoting androgen production and inhibiting estrogen synthesis. Additionally, ETO may promote morphological masculinization by altering lipid metabolism patterns. These findings indicate that ETO could induce masculinization and negatively impact reproductive health in mosquitofish, an effect potentially exacerbated by changes in lipid metabolism.
{"title":"Induction of masculinization in mosquitofish (Gambusia affinis) by the synthetic progestin etonogestrel exposure: Insights from morphology, ovarian histology, and transcriptomic analyses","authors":"Suhan Peng , Jie Lai , Shengyue Lin , Sixun Li , Binhua Deng , Weijian Chen , Weibin Li , Chong Han , Qiang Li","doi":"10.1016/j.cbd.2025.101660","DOIUrl":"10.1016/j.cbd.2025.101660","url":null,"abstract":"<div><div>The demand for synthetic progesterone has surged due to its widespread use in contraceptives and veterinary drugs. However, these compounds are not fully removed by wastewater treatment plants, leading to their release into aquatic environments and potential disruption of fish reproduction and development. Etonogestrel (ETO), a third-generation synthetic progestogen, is widely used in oral contraceptives. In this study, adult female mosquitofish were exposed to ETO at measured concentrations of 0 ng/L, 3.88 ng/L, 39.5 ng/L, and 385.18 ng/L for 36 days. Morphology, ovarian histology, and transcriptomic analyses were conducted to assess the effects of ETO. Results showed that ETO exposure reduced the body weight-to-total length ratio and promoted gonopodia and skeletal modifications. Particularly notable was the finding of decreased ovarian weight and the induction of testicular structures in the 385.18 ng/L ETO group, indicating a significant masculinization effect. Transcriptomic analysis revealed that genes related to sexual differentiation (<em>cyp17a1</em>, <em>hsd17b3</em> and <em>sox9</em>), which were enriched in the GnRH signaling pathway and steroid hormone biosynthesis, may drive masculinization by promoting androgen production and inhibiting estrogen synthesis. Additionally, ETO may promote morphological masculinization by altering lipid metabolism patterns. These findings indicate that ETO could induce masculinization and negatively impact reproductive health in mosquitofish, an effect potentially exacerbated by changes in lipid metabolism.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"57 ","pages":"Article 101660"},"PeriodicalIF":2.2,"publicationDate":"2025-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145402882","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 : 2025-10-21DOI: 10.1016/j.cbd.2025.101661
Minghui Ye , Dayan Zhou , Lingwei Kong , Yulei Zhang , Chuanhao Pan , Cailin Huang , Guangli Li , Huapu Chen , Changxu Tian
Thermal stress poses a significant challenge to fish physiology and aquaculture sustainability, necessitating an in-depth understanding of molecular responses to temperature fluctuations. This study characterizes the Hsp40 gene family in Hong Kong catfish (Clarias fuscus), a species known for its thermal resilience, to elucidate their roles in proteostasis and immune modulation. A total of 55 Hsp40 genes were identified and categorized into three subfamilies: DnaJa (n = 6), DnaJb (n = 16), and DnaJc (n = 33). These genes exhibit conserved J-domains and diverse motifs, indicating adaptations to aquatic stressors. Phylogenetic analysis reveals that the Hsp40 gene family in C. fuscus exhibits the closest evolutionary relationship to Ictalurus punctatus, followed by Danio rerio, with distinct clustering patterns across the subtypes. Collinearity and synteny analyses indicated substantial genomic conservation of Hsp40 genes between C. fuscus, I. punctatus, and D. rerio, with evidence of gene duplication and homologous relationships. The subcellular localization of Hsp40 proteins was observed in the cytoplasm, endoplasmic reticulum, mitochondria, nucleus, and extracellular regions, supporting their roles in chaperone activity and immune response regulation. Protein interaction networks identified two major clusters: one associated with protein folding and another with Hsp90-dependent immune signaling. Molecular docking confirmed stable interactions between Hsp40 and Hsp70, aiding in the mitigation of thermal-induced protein misfolding. Transcriptomic analysis under thermal stress showed significant differential expression of 30 Hsp40 genes, with dnajb11 and dnajc5.1 notably differentially expressed in the liver, gills, and kidneys. Under normal-temperature conditions, 10, 6, and 12 genes were differentially expressed in the liver, gills, and kidneys, respectively. High-temperature acclimation significantly increased the number of differentially expressed genes in the kidneys (20 genes), indicating enhanced thermal tolerance. These genes bolster immunity by stabilizing proteins and modulating inflammatory pathways. These findings suggest that key Hsp40s, such as dnajb11 and dnajc5.1, serve as biomarkers for selective breeding and support the development of strategies like immunomodulatory feed additives to enhance thermal resilience in C. fuscus aquaculture.
{"title":"Genome-wide characterization of the Hsp40 gene family in Clarias fuscus reveals their roles in thermal stress adaptation and immune modulation","authors":"Minghui Ye , Dayan Zhou , Lingwei Kong , Yulei Zhang , Chuanhao Pan , Cailin Huang , Guangli Li , Huapu Chen , Changxu Tian","doi":"10.1016/j.cbd.2025.101661","DOIUrl":"10.1016/j.cbd.2025.101661","url":null,"abstract":"<div><div>Thermal stress poses a significant challenge to fish physiology and aquaculture sustainability, necessitating an in-depth understanding of molecular responses to temperature fluctuations. This study characterizes the Hsp40 gene family in Hong Kong catfish (<em>Clarias fuscus</em>), a species known for its thermal resilience, to elucidate their roles in proteostasis and immune modulation. A total of 55 <em>Hsp40</em> genes were identified and categorized into three subfamilies: DnaJa (<em>n</em> = 6), DnaJb (<em>n</em> = 16), and DnaJc (<em>n</em> = 33). These genes exhibit conserved J-domains and diverse motifs, indicating adaptations to aquatic stressors. Phylogenetic analysis reveals that the Hsp40 gene family in <em>C. fuscus</em> exhibits the closest evolutionary relationship to <em>Ictalurus punctatus</em>, followed by <em>Danio rerio</em>, with distinct clustering patterns across the subtypes. Collinearity and synteny analyses indicated substantial genomic conservation of <em>Hsp40</em> genes between <em>C. fuscus</em>, <em>I. punctatus</em>, and <em>D. rerio,</em> with evidence of gene duplication and homologous relationships. The subcellular localization of Hsp40 proteins was observed in the cytoplasm, endoplasmic reticulum, mitochondria, nucleus, and extracellular regions, supporting their roles in chaperone activity and immune response regulation. Protein interaction networks identified two major clusters: one associated with protein folding and another with Hsp90-dependent immune signaling. Molecular docking confirmed stable interactions between Hsp40 and Hsp70, aiding in the mitigation of thermal-induced protein misfolding. Transcriptomic analysis under thermal stress showed significant differential expression of 30 <em>Hsp40</em> genes, with <em>dnajb11</em> and <em>dnajc5.1</em> notably differentially expressed in the liver, gills, and kidneys. Under normal-temperature conditions, 10, 6, and 12 genes were differentially expressed in the liver, gills, and kidneys, respectively. High-temperature acclimation significantly increased the number of differentially expressed genes in the kidneys (20 genes), indicating enhanced thermal tolerance. These genes bolster immunity by stabilizing proteins and modulating inflammatory pathways. These findings suggest that key Hsp40s, such as <em>dnajb11</em> and <em>dnajc5.1</em>, serve as biomarkers for selective breeding and support the development of strategies like immunomodulatory feed additives to enhance thermal resilience in <em>C. fuscus</em> aquaculture.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"57 ","pages":"Article 101661"},"PeriodicalIF":2.2,"publicationDate":"2025-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145369759","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