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

{"title":"Identification of the mapk gene family in large yellow croaker (Larimichthys crocea): Involvement in immune response to Pseudomonas plecoglossicida infection and hypoxia exposure","authors":"Ziyu Wang ,&nbsp;Ping Han ,&nbsp;Yadong Xue ,&nbsp;Jianming Chen ,&nbsp;Xiumei Liu ,&nbsp;Xubo Wang","doi":"10.1016/j.cbd.2025.101732","DOIUrl":"10.1016/j.cbd.2025.101732","url":null,"abstract":"<div><div>Mitogen-activated protein kinases (MAPKs) are a family of evolutionarily conserved serine/threonine protein kinases that can be activated by diverse stimuli. They transmit signals from the cell membrane to the nucleus, regulating various biological processes such as apoptosis, hormone signaling, and immune responses. Members of the MAPK family have been extensively studied in multiple species and have been confirmed as a central hub for regulating antibacterial immunity and hypoxia adaptation in perciform fishes, such as Asian seabass and groupers. Given that the large yellow croaker, as an important mariculture species within this order, faces serious threats from <em>Pseudomonas plecoglossicida</em> infection and hypoxic stress, deciphering the functions of its MAPK family is of significant importance. To this end, this study identified 16 <em>mapk</em> genes in the large yellow croaker. Phylogenetic analysis revealed that these <em>mapk</em> genes were classified into three major subfamilies: ERK, JNK, and p38 MAPK. Comparative analyses of gene structures and conserved protein motifs demonstrated high conservation among MAPK family members. Meanwhile, RNA-seq data following bacterial and hypoxic stress revealed distinct expression patterns of <em>mapk</em> genes. <em>mapk7</em>, <em>mapk10</em>, and <em>mapk14a</em> exhibited significant differential expression in response to <em>P. plecoglossicida</em> challenge, and <em>mapk7</em>, <em>mapk8b</em>, and <em>mapk14a</em> were significantly induced under hypoxia stress, implying their potential involvement in stress adaptation. The protein-protein interaction (PPI) network analysis revealed that MAPK family members (including MAPK3, MAPK7, MAPK8b, MAPK12a, MAPK13, and MAPK14a) in <em>Larimichthys crocea</em> exhibit close interactions with key signaling proteins (such as MAP2K1, c-Fos, AP-1, and MAPKAPK2). These interactions suggested the potential formation of a complex signal transduction network involved in the immune stress response, collectively mediating the immune stress regulation in <em>Larimichthys crocea</em>. These findings enhanced the understanding of environmental adaptation mechanisms in large yellow croaker, and provided crucial candidate target genes and a theoretical basis for in-depth analysis of its molecular responses to pathogen infection and hypoxic stress.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101732"},"PeriodicalIF":2.2,"publicationDate":"2025-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145822310","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":"Serine proteases and serine protease inhibitors identified from the venom gland transcriptome of Rhitymna verruca","authors":"Zhi Li,&nbsp;Mengmeng Zhang,&nbsp;Wenhao Yin,&nbsp;Yulin Zheng,&nbsp;Heng Liu,&nbsp;Yu Zhao,&nbsp;Zizhong Yang","doi":"10.1016/j.cbd.2025.101719","DOIUrl":"10.1016/j.cbd.2025.101719","url":null,"abstract":"<div><div><em>Rhitymna verruca</em> is a large nocturnal wandering spider and an important natural predator of agricultural and forestry pests, with its venom playing a key role in prey capture. However, systematic studies on the composition of its venom remain scarce. In this study, we performed an integrated analysis of the venom gland and venom samples using high-throughput transcriptome sequencing combined with quantitative proteomics. The transcriptome yielded 43,244 representative unigene sequences, among which 102 toxin-like sequences were identified through functional annotation, encompassing 13 peptide toxin superfamilies and 7 protein toxin families. Proteomic analysis identified 35 venom components, including 14 peptide toxins and 21 functional proteins. The most abundantly expressed toxin families, Superfamily IX and VII, were highly expressed at both transcriptomic and proteomic levels, suggesting central roles in prey paralysis and neuroregulation. Most peptide toxins possessed ICK or Kunitz domains, indicating high structural stability and potential target specificity. In addition, the venom was rich in auxiliary components such as CAP protein superfamily, hyaluronidases, and metalloproteases, which may contribute to toxin synergy, diffusion, and tissue disruption. This study provides the first comprehensive characterization of the venom composition of <em>R. verruca</em>, offering fundamental insights into its functional mechanisms, evolutionary patterns, and potential applications in the development of novel bioactive agents.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101719"},"PeriodicalIF":2.2,"publicationDate":"2025-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145822342","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":"Molecular mechanisms of quercetin in regulating antioxidant defense and pyroptosis pathways in the redclaw crayfish (Cherax quadricarinatus)","authors":"Zihan Zhou ,&nbsp;Weiwei Lv ,&nbsp;Qin Si ,&nbsp;Bangyue Zhang ,&nbsp;Aileen Tan Shau Hwai ,&nbsp;Yi Juin Tay ,&nbsp;Mingming Han ,&nbsp;Zhengjun Zhan ,&nbsp;Qichen Jiang","doi":"10.1016/j.cbd.2025.101728","DOIUrl":"10.1016/j.cbd.2025.101728","url":null,"abstract":"<div><div>As a principal species in freshwater aquaculture, the redclaw crayfish (<em>Cherax quadricarinatus</em>) depends on a competent immune system to mitigate environmental and pathogenic challenges. Quercetin, a ubiquitous plant-derived flavonoid, has garnered scientific attention due to its pleiotropic bioactivities, including antioxidant, anti-inflammatory, and immunomodulatory properties. This study investigated the effects of waterborne quercetin exposure on transcriptional regulation and antioxidant capacity in <em>C. quadricarinatus</em>. Over a 28-day period, crayfish were subjected to five quercetin concentrations (0, 1.0, 2.5, 5.0, and 10.0 mg/L), with outcomes evaluated against an untreated control. At the concentration of 5.0 mg/L, which showed the most pronounced effects among the tested concentrations, quercetin exposure was associated with significant downregulation of key transcripts in the NLRP3 inflammasome pathway (NLRP3, GSDMD, Caspase-1), as evidenced by the downregulation of NLRP3, GSDMD, and Caspase-1. Simultaneously, the transcriptional changes were consistent with the modulation/activation of the Nrf2 signaling axis, upregulating the expression of Nrf2, NQO1, and Keap1. These transcriptional changes indicate that quercetin attenuates pyroptosis and augments cellular antioxidant defenses via the Nrf2-Keap1 cascade. Correspondingly, the hepatopancreas displayed markedly elevated activities of SOD, CAT, and GSH-Px, accompanied by a significant reduction in MDA levels, indicating enhanced antioxidative capacity and diminished lipid peroxidation. This study provides valuable toxicological insights and elucidates part of the molecular basis for quercetin's immunomodulatory and antioxidant roles in freshwater crustaceans.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101728"},"PeriodicalIF":2.2,"publicationDate":"2025-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145791248","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":"Transcriptomic analysis of Cuvierian Organs regeneration in the sea cucumber Holothuria leucospilota","authors":"Xiaoli Zhang ,&nbsp;Renhui Liu ,&nbsp;Hua Ge ,&nbsp;Ting Chen ,&nbsp;Xinyue Ren ,&nbsp;Caixia Long ,&nbsp;Jiasheng Huang ,&nbsp;Wenjie Pan ,&nbsp;Haipeng Qin ,&nbsp;Lihong Yuan ,&nbsp;Aifen Yan","doi":"10.1016/j.cbd.2025.101729","DOIUrl":"10.1016/j.cbd.2025.101729","url":null,"abstract":"<div><div>Sea cucumbers are renowned for their regenerative capabilities, making them ideal models for studying tissue and organ regeneration. <em>Holothuria leucospilota</em> possesses a unique defensive structure, the Cuvierian organ (CO), which is ejected upon threat and regenerates within weeks. However, the molecular mechanisms underlying CO regeneration remain poorly understood. In this study, we induced CO expulsion in <em>H. leucospilota</em> by mechanical stimulation and examined the regeneration process over 31 days. Histological analysis revealed that regeneration initiated with mesothelium formation, followed by connective tissue and epithelium development. Transcriptomic analysis identified numerous differentially expressed genes during regeneration. Key extracellular matrix (ECM)-related genes were upregulated, while matrix protease genes were downregulated. Signaling pathways including Wnt and Hippo were suppressed, whereas apoptosis and cell cycle pathways were activated. Additionally, several structural outer-layer proteins showed altered expression. These results indicate that ECM reorganization and coordinated regulation of cell proliferation and apoptosis are central to CO regeneration. This study provides important insights into the molecular mechanisms of organ regeneration in echinoderms and offers valuable clues for regenerative studies in higher animals.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101729"},"PeriodicalIF":2.2,"publicationDate":"2025-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145776674","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":"Comparative transcriptome analysis provides novel insights into the evolution of enhanced cold tolerance in the northward invasion of the eel goby, Taenioides sp.","authors":"Jing Liu,&nbsp;An Xu,&nbsp;Tianwei Liu,&nbsp;Kun Huang,&nbsp;Weihu Zhu,&nbsp;Jing Yu,&nbsp;Yijing Yang,&nbsp;Fenghui Li,&nbsp;Denghui Zhu,&nbsp;Li Gong,&nbsp;Liqin Liu,&nbsp;Zhenming Lü","doi":"10.1016/j.cbd.2025.101709","DOIUrl":"10.1016/j.cbd.2025.101709","url":null,"abstract":"<div><div>Invasive species serve as an ideal model for investigating adaptation, since they are typically introduced to unfamiliar environments where adaptation is essential for survival. <em>Taenioides</em> sp. is a typical invasive eel goby that originally inhabited the tropical and subtropical coasts of Southeast China but has recently expanded into the temperate regions of North China due to the implementation of ESNT Project. However, the molecular basis underlying how the invasive population adapted to the climate of northern China during the invasion remains largely unknown. Here, we compared the cold tolerance and transcriptomic changes to cold stress in source (Yangtze River estuary) and northernmost invasive (Zhaoyang Lake) populations to elucidate the possible molecular mechanisms underlying this climate adaptation. Our results revealed significantly enhanced cold tolerance in the invasive compared to the source population (CT_min: 7.11 °C vs 10.66 °C). Transcriptome analysis revealed 56 differentially expressed genes (DEGs) with similar expression patterns across all tissues and populations, suggesting their core roles in the cold response of <em>Taenioides</em> sp. Meanwhile, multiple DEGs exhibit population-specific expression profiles, indicating their involvement in divergent cold tolerance. Further WGCNA analyses revealed a subset of cold-response hub genes associated with muscle structure and thermogenesis (e.g., <em>MYO18B</em>) exhibiting a distinct expression profile in the invasive population under cold stress, highlighting their roles in the evolution of enhanced cold tolerance. Our findings provided novel insights into the molecular basis of thermal adaptation underpinning the northward invasion of <em>Taenioides</em> sp. in a hydraulic-project-facilitating context, thus had important implications for predicting their invasive potential and developing management strategies for their effective control. Further analyses regarding how genetic and epigenetic forces have driven population-distinct gene expression regulation and, hence, divergent thermal adaptation will be necessary in the future.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101709"},"PeriodicalIF":2.2,"publicationDate":"2025-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145791247","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":"Epitranscriptomic variation in banded newts (Ommatotriton vittatus) across life stages and sexes in the semi-arid habitat in northern Israel","authors":"Ari Meerson ,&nbsp;Monika Almozlino ,&nbsp;Gad Degani ,&nbsp;Dani Bercovich","doi":"10.1016/j.cbd.2025.101727","DOIUrl":"10.1016/j.cbd.2025.101727","url":null,"abstract":"<div><div>The banded newt, <em>Ommatotriton vittatus</em>, is considered endangered in Israel, which is the southern border of its distribution and requires adaptation to highly unstable habitats. Banded newts have both aquatic and terrestrial forms, going through metamorphosis and various phenotypic changes during their life. Our group has previously reported on the extensive transcriptomic remodeling based on sex and especially the life stage of the newt. These dramatic changes in gene expression are likely accompanied by extensive epitranscriptomic regulation, which remains poorly understood.</div><div>In this study, direct RNA sequencing was used to characterize m⁶A RNA modifications in 12 newts from the Nehalit population. We focused on 127 genes with &gt;30 differentially modified regions (DMRs, with a differential modification score &gt; 5) in their transcripts, involved in structural, translational, and extracellular matrix processes. Among them, 18 genes showed clustering of methylation patterns according to life stage, particularly keratins and translation-related proteins, suggesting that m⁶A plays a regulatory role in structural remodeling and developmental transitions. In contrast, the majority of DMR genes were associated with housekeeping and stress-response functions and did not show life-stage-specific clustering. Cross-analysis with differential expression data further indicated that muscle, immune, and connective tissue pathways are co-regulated at both the transcriptional and epitranscriptomic levels.</div><div>These findings provide the first evidence of m⁶A methylation patterns in <em>O. vittatus</em> and highlight their role in developmental transitions. The results advance understanding of transcriptomic–epitranscriptomic regulation in amphibian plasticity, and more generally, in vertebrate development.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101727"},"PeriodicalIF":2.2,"publicationDate":"2025-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145738491","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":"Profiling and functional validation of LPS-responsive miRNAs in the giant freshwater prawn, Macrobrachium rosenbergii","authors":"Tanapat Pangeson ,&nbsp;Rattikon Thammason ,&nbsp;Chalermporn Ongvarrasopone ,&nbsp;Nalinnipa Wiengnak ,&nbsp;Amnat Phetrungnapha","doi":"10.1016/j.cbd.2025.101724","DOIUrl":"10.1016/j.cbd.2025.101724","url":null,"abstract":"<div><div>MicroRNAs (miRNAs) are key post-transcriptional regulators involved in crustacean immune responses, yet their roles during pattern recognition receptor activation remain poorly understood. In this study, we investigated the miRNA response of <em>Macrobrachium rosenbergii</em> to lipopolysaccharide (LPS), a conserved bacterial pathogen-associated molecular pattern (PAMP). High-throughput small RNA sequencing identified 155 differentially expressed miRNAs (DEMs) in the hepatopancreas following LPS injection. Pathway enrichment analysis revealed that target genes of these DEMs were significantly associated with immune pathways, including the ubiquitin–proteasome pathway (UPP) and endocytosis. Network analysis highlighted mro-miR-365-1-5p as a central regulator targeting key genes such as <em>Rpn10, Rab11, Vps2,</em> and <em>ArfGAP3</em>. Temporal expression profiling revealed rapid downregulation of mro-miR-365-1-5p after LPS exposure. The regulatory role of mro-miR-365-1-5p was validated by dual-luciferase reporter assays and an <em>in vivo</em> challenge experiment. <em>In vivo</em> overexpression of mro-miR-365-1-5p significantly increased mortality in prawns challenged with <em>Vibrio harveyi</em>, indicating impaired immune defense. These findings provide novel insights into the regulatory roles of LPS-responsive miRNAs in crustaceans and suggest that modulation of specific miRNAs may be crucial for effective immune activation during bacterial infection.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101724"},"PeriodicalIF":2.2,"publicationDate":"2025-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145738578","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":"Physiological effects of long-term saline-alkaline stress on the gills of Acanthopagrus latus: A combined analysis of transcriptomics and metabolomics","authors":"Weiqing Huang ,&nbsp;Fengfang Zhou ,&nbsp;Zongqiang Lian ,&nbsp;Zhideng Lin ,&nbsp;Zipeng Zhang","doi":"10.1016/j.cbd.2025.101701","DOIUrl":"10.1016/j.cbd.2025.101701","url":null,"abstract":"<div><div>Saline-alkaline stress poses a significant environmental challenge to fish in aquaculture, yet the molecular mechanisms underlying adaptation remain poorly understood. In this study, we integrated transcriptomic, metabolomic, physiological, and histological analyses to elucidate the adaptive mechanisms of <em>Acanthopagrus latus</em> gills under saline-alkaline water (SAW) exposure. After 40 days of treatment, SAW caused evident histological alterations in gill structures but did not significantly affect growth performance. Physiological assays showed that glutathione peroxidase (GSH-Px), acid phosphatase (ACP) and alkaline phosphatase (ALP) activities showed no significant change, while malondialdehyde (MDA) levels increased, indicating oxidative stress and metabolic disturbance.</div><div>Transcriptomic analysis identified 2539 differentially expressed genes (DEGs), mainly enriched in immune-related pathways such as T-cell receptor signaling, Th17 cell differentiation, and IL-17 signaling. Metabolomic profiling detected 892 differentially expressed metabolites (DEMs), primarily involved in energy metabolism pathways, including arachidonic acid, α-linolenic acid, and linoleic acid metabolism. Integrated multi-omics analysis further revealed a significant co-enrichment in platelet activation, phospholipase D signaling, and glutathione metabolism pathways. Notably, 29 DEGs and 4 key metabolites (ATP, prostaglandin H₂, cyclic AMP, and ADP) were significantly altered in the platelet activation pathway. Among them, upregulated genes such as <em>p2ry12</em>, <em>LOC119021196</em>, and <em>LOC119027230</em> were linked to energy metabolism, while <em>lyn</em>, <em>fynb</em>, <em>pik3r1</em>, <em>pik3cd</em>, and <em>akt1</em> were associated with apoptosis and immune regulation.</div><div>Overall, this study provides comprehensive molecular and physiological evidence of how <em>A. latus</em> adapts to saline-alkaline stress through coordinated immune regulation and energy metabolism. These findings enhance our understanding of fish adaptive mechanisms and offer theoretical support for the sustainable utilization of saline-alkaline water resources in aquaculture.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101701"},"PeriodicalIF":2.2,"publicationDate":"2025-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145776697","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":"Multomics decipher the mechanisms of bisphenol S-induced oxidative stress and inflammation in Pseudobagrus ussuriensis","authors":"Lu Wang ,&nbsp;Changchang Pu ,&nbsp;Yimin Li ,&nbsp;Jiaxiang Zhu ,&nbsp;Mohammad Mehdi Ommati ,&nbsp;Bingke Wang ,&nbsp;Chunnuan Zhang","doi":"10.1016/j.cbd.2025.101725","DOIUrl":"10.1016/j.cbd.2025.101725","url":null,"abstract":"<div><div>Bisphenol S (BPS), a widespread environmental endocrine-disrupting chemical, has raised growing concerns regarding its ecotoxicological effects. In this study, we systematically investigated the integrated toxicity of BPS exposure using <em>Pseudobagrus ussuriensis</em> as a model aquatic species. Three hundred sixty fish (mean initial weight: 30.42 ± 0.62 g) were randomly allocated into four groups and exposed to 0 (control), 1, 10, or 100 μg/L BPS for 14 days. Histopathological examination revealed significant tissue damage, including gill filament edema, intestinal epithelial desquamation, and hepatic vacuolization. Oxidative stress assessment showed a concentration-dependent elevation in malondialdehyde (MDA) levels (<em>p</em> &lt; 0.05). 16S rRNA sequencing analysis demonstrated that 10 μg/L BPS exposure markedly altered gut microbial composition, with significant enrichment of <em>Achromobacter</em> and <em>Acinetobacter</em>. Liver transcriptome profiling identified substantial differential expression of immune-related genes (<em>hmgb1</em>, <em>nfκb</em>, and <em>nfκbiα</em>) in the 100 μg/L exposure group. Importantly, Pearson correlation analysis established a significant association between gut microbiota perturbation and hepatic immune-inflammatory responses (<em>p</em> &lt; 0.05). To our knowledge, this study provides the first evidence that environmentally relevant concentrations (10 μg/L) of BPS can induce significant physiological impairments in <em>P. ussuriensis</em>, offering novel insights into the ecological risks of BPS contamination.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101725"},"PeriodicalIF":2.2,"publicationDate":"2025-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145738493","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":"Knockout of zebrafish Clec3bb does cause vertebra density reduction","authors":"Feilong Shi ,&nbsp;Xudong Wang ,&nbsp;Yulong Chen ,&nbsp;Zhengyu Xiao ,&nbsp;Xuemei Xiong ,&nbsp;Jianbo Wang ,&nbsp;Zexia Gao ,&nbsp;Chunhong Nie","doi":"10.1016/j.cbd.2025.101726","DOIUrl":"10.1016/j.cbd.2025.101726","url":null,"abstract":"<div><div>C-type lectin domain family 3 member B (Clec3b) is widely involved in various biological processes, including bone mineralization, cell proliferation, and pathogenesis of diseases. While <em>clec3b</em> association with skeletal development has been well characterized in mammals, its role in fish skeletal development remains unclear. Due to genome duplication in teleosts, zebrafish possess two paralogous genes of <em>clec3b</em>, namely <em>clec3ba</em> and <em>clec3bb</em>, whose functional divergence remains unclear. The amino acid sequence similarity between zebrafish <em>clec3ba</em> and <em>clec3bb</em> was 55.61 %. Tissue-specific expression analysis revealed distinct expression patterns of <em>clec3ba</em> and <em>clec3bb</em> across multiple tissues (brain, gonads, fin, skin, vertebra, eyes, ribs, muscle, kidney, liver, gills) and embryonic stages. Mutants of <em>clec3ba</em> and <em>clec3bb</em> were generated using CRISPR/Cas9 system. Micro-CT analysis revealed that vertebral bone density was significantly reduced in <em>clec3bb</em>⁻/⁻ mutants compared to wild type, whereas no significant change was observed in <em>clec3ba</em>⁻/⁻ mutants. Comparative transcriptome was used to analyze gene expression differences of vertebrae in <em>clec3bb</em>^+/+ and <em>clec3bb</em>⁻/⁻ zebrafish and identified 3316 differentially expressed genes were in vertebral tissues of <em>clec3bb</em> mutants, which were mainly enriched in the MAPK, TGF-β, Calcium and Wnt signaling pathways. RT-qPCR validated results showed that 10 skeletal-related genes (<em>col1a1a</em>, <em>entpd5a</em>, <em>fgf23</em>, <em>bmp6</em>, <em>aspn</em>, <em>bglapl</em>, <em>tnmd</em>, <em>scxa</em>, <em>sp7</em>, <em>tnc</em>) had a lower expression in vertebrae of <em>clec3bb</em>^−/− mutant. The above results highlight the critical role of <em>clec3bb</em> in zebrafish bone mineralization, providing insights into the functional specialization of <em>clec3b</em> paralogs and a theoretical basis for understanding skeletal development mechanisms in teleosts.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101726"},"PeriodicalIF":2.2,"publicationDate":"2025-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145791276","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}