Comparative Biochemistry and Physiology D-Genomics & Proteomics最新文献_第8页

Key lncRNA-mRNA networks regulated by Polyascus sp. infection: A comparative transcriptomic analysis of the eyestalk in the Eriocheir sinensis 中华绒螯蟹眼柄的转录组学比较分析：多曲霉感染调控的关键lncRNA-mRNA网络

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-11-22 DOI: 10.1016/j.cbd.2025.101693

Jing Xie , Congping Ying , Zhen Tang , Yanping Yang , Kai Liu

The Chinese mitten crab (Eriocheir sinensis) is a crustacean widely distributed in coastal and estuarine waters across China. Due to its high nutritional value, it has become a significant commercial aquaculture species in China, generating substantial economic value. Polyascus sp., which is called crab slave, can parasitize on crabs, altering the host's morphological appearance and disrupting its endocrine regulation, thereby inhibiting growth and development. To further elucidate the molecular mechanisms underlying the host crab's response to crab slave parasitism and to elucidate the role of lncRNAs in this process, we performed comparative transcriptome sequencing analysis on the eyestalk tissues of parasitized and non-parasitized crabs. This study identified 2746 novel lncRNAs, including 735 differentially expressed lncRNAs in the male comparison groups and 394 differentially expressed lncRNAs in the female comparison groups. Concurrently, GSEA analysis of target mRNAs for differentially expressed lncRNAs revealed that Polyascus sp. parasitism influences lncRNA regulation of GO:0042302 (structural components of the cuticle), GO:0006040 (amino acid metabolism processes), and GO:0006030 (chitin metabolic process) were enriched in the male comparison (T1 vs. CK1), while GO:0044282 (small molecule catabolic process) and GO:0016627 (oxidoreductase activity, acting on the CH-CH group of donors), etc., were enriched in the female comparison (T2 vs. CK2). Furthermore, a molecular regulatory network of key lncRNA-mRNA interactions was constructed based on transcriptomic profiles. These findings provide new insights into lncRNA-mediated physiological regulation in crustaceans and highlight the pivotal role of lncRNAs in modulating expression patterns.

中华绒螯蟹（Eriocheir sinensis）是一种广泛分布于中国沿海和河口水域的甲壳类动物。由于其高营养价值，已成为中国重要的商业养殖品种，产生了可观的经济价值。Polyascus sp.被称为蟹奴，它可以寄生在螃蟹身上，改变寄主的形态外观，扰乱寄主的内分泌调节，从而抑制其生长发育。为了进一步阐明寄主蟹对从寄生反应的分子机制以及lncrna在这一过程中的作用，我们对被寄生和未被寄生的寄主蟹眼柄组织进行了转录组测序比较分析。本研究鉴定出2746个新的lncrna，其中男性对照组差异表达的lncrna为735个，女性对照组差异表达的lncrna为394个。同时，对lncRNAs差异表达的靶mrna进行GSEA分析发现，雄性对照（T1 vs CK1）中，Polyascus寄生影响GO:0042302（表皮结构成分）、GO:0006040（氨基酸代谢过程）和GO:0006030（几丁质代谢过程）的lncRNA调控富集，而GO:0044282（小分子分解代谢过程）和GO:0016627（氧化还原酶活性，作用于CH-CH供体组）等lncRNA调控富集。在女性对照中（T2 vs. CK2）表达丰富。此外，基于转录组谱构建了lncRNA-mRNA关键相互作用的分子调控网络。这些发现为研究lncrna介导的甲壳类动物生理调控提供了新的见解，并突出了lncrna在调节表达模式中的关键作用。

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引用次数: 0

Harnessing genomics for identifying disease-resistant eels: Advances, applications, and sustainable aquaculture 利用基因组学鉴定抗病鳗鱼：进展、应用和可持续水产养殖

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-11-19 DOI: 10.1016/j.cbd.2025.101695

Mingmei Liu , Keyu Zhou , Zhuoling Liu , Sen Wei , Laia Ribas , Quanquan Cao

Globally, eel aquaculture holds significant economic and ecological importance, but it faces severe challenges from various diseases that hinder its sustainable development. This review aims to systematically explore how genomics can be utilized to enhance the disease resistance of eels, thereby promoting sustainable aquaculture practices. To achieve this goal, we first review the current status of eel aquaculture and the main disease threats, and then focus on the application of genomic technologies in understanding eel disease resistance. We elaborate on the progress in genome sequencing of multiple eel species, which provides a fundamental resource for identifying disease-resistant traits. We discuss the role of functional genomics tools such as CRISPR-Cas9 in accelerating the screening of favorable disease-resistant traits. We also detail how immune system genomics (e.g., genes like Tollip, interferon, and MHC), genome-wide association studies, and the interaction between epigenetics and the environment contribute to the identification of disease-resistant traits. In addition, this review analyzes the applications of marker-assisted selection and genomic selection in eel breeding programs, as well as biotechnological intervention methods such as gene editing, probiotics, and vaccine development as novel strategies to improve disease resistance. Finally, we present future prospects for eel disease-resistant breeding efforts.

在全球范围内，鳗鱼养殖具有重要的经济和生态意义，但它面临着各种疾病的严峻挑战，阻碍了其可持续发展。本文旨在系统地探讨如何利用基因组学来增强鳗鱼的抗病能力，从而促进可持续的水产养殖实践。为了实现这一目标，我们首先回顾了鳗鱼养殖的现状和主要的疾病威胁，然后重点介绍了基因组技术在了解鳗鱼抗病方面的应用。本文阐述了多种鳗鲡基因组测序的研究进展，为鉴定其抗病性状提供了基础资源。我们讨论了功能基因组学工具如CRISPR-Cas9在加速筛选有利的抗病性状中的作用。我们还详细介绍了免疫系统基因组学（例如，Tollip、干扰素和MHC等基因）、全基因组关联研究以及表观遗传学和环境之间的相互作用如何有助于鉴定抗病性状。此外，本文还分析了标记辅助选择和基因组选择在鳗鱼育种计划中的应用，以及基因编辑、益生菌和疫苗开发等生物技术干预方法作为提高抗病性的新策略。最后，对今后鳗鱼抗病育种工作进行了展望。

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引用次数: 0

Integrated miRNA and mRNA analysis in gills of Amur ide (Leuciscus waleckii) reveals novel insights into the molecular regulatory mechanism of alkaline acclimation 对阿穆尔鱼鳃miRNA和mRNA的综合分析揭示了碱驯化分子调控机制的新见解

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-11-19 DOI: 10.1016/j.cbd.2025.101688

Haochen Yang , Chenghao Li , Jing Huang , Haotong Jia , Yu Du , Yumei Chang

Leuciscus waleckii, a cyprinid fish of significant commercial value, exhibits remarkable adaptability to a range of environmental conditions, including extreme alkaline and saline environments. This adaptability positions it an important model for investigating the mechanisms underlying saline-alkali adaptation and osmoregulation. In light of the global challenge of land salinization and the increasing trend of aquaculture in saline-alkali environments, understanding the adaptation mechanisms of fish species such as L. waleckii is crucial for the success of aquaculture in these areas. In this study, gill tissue samples were collected from fish at 1, 5, and 10 days during alkali stress (AW1, AW5, AW10) and after transfer to freshwater (FW1, FW5, FW10), with AW10 serving as the control group. RNA sequencing identified a total of 444 and 856 differentially expressed genes (DEGs) during the stress and recovery phases, respectively. KEGG enrichment analysis highlighted key pathways: alkali stress activated ECM-receptor interaction, focal adhesion, and steroid hormone biosynthesis, while recovery involved cytokine-cytokine receptor interaction and Toll-like/FoxO signaling. Small RNA sequencing, combined with differential expression analysis, identified links between miRNAs and primary bile acid biosynthesis as well as immune regulation. Integrated miRNA-mRNA network analysis implicated specific genes and miRNAs in regulating ECM integrity, steroid metabolism, and immune response. These results demonstrate that L. waleckii employs ECM remodeling, steroid hormone dynamics, and miRNA-mediated immune modulation to survive extreme alkalinity, providing valuable insights for breeding saline-alkali tolerant aquaculture species. These findings not only enhance our understanding of the adaptive physiology of fish but also provide insights into strategies for improving stress resistance in commercially valuable species, thereby enhancing aquaculture productivity in saline-alkali ecosystems.

waleckii Leuciscus waleckii是一种具有重要商业价值的鲤科鱼类，对一系列环境条件表现出卓越的适应性，包括极端碱性和盐水环境。这种适应性使其成为研究盐碱适应和渗透调节机制的重要模型。鉴于全球土地盐碱化的挑战和盐碱环境下水产养殖的增加趋势，了解waleckii等鱼类的适应机制对于这些地区水产养殖的成功至关重要。本研究分别在碱胁迫（AW1、AW5、AW10）和转入淡水（FW1、FW5、FW10）后的第1、5、10天采集鱼鳃组织样本，以AW10为对照组。RNA测序在胁迫和恢复阶段分别鉴定出444和856个差异表达基因（deg）。KEGG富集分析强调了关键途径：碱胁迫激活ecm受体相互作用、局灶黏附和类固醇激素生物合成，而恢复涉及细胞因子-细胞因子受体相互作用和toll样/FoxO信号传导。小RNA测序结合差异表达分析，确定了mirna与初级胆汁酸生物合成以及免疫调节之间的联系。综合miRNA-mRNA网络分析表明，特定基因和mirna参与调节ECM完整性、类固醇代谢和免疫反应。这些结果表明，waleckii通过ECM重塑、类固醇激素动力学和mirna介导的免疫调节来适应极端碱性，为培育耐盐碱水产养殖品种提供了有价值的见解。这些发现不仅增强了我们对鱼类适应性生理的理解，而且为提高商业价值物种的抗逆性策略提供了见解，从而提高了盐碱生态系统的水产养殖生产力。

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引用次数: 0

Mechanism study of selenium nanoparticles alleviating heat stress in rainbow trout hepatocytes by regulating lncRNA expression 纳米硒通过调控lncRNA表达缓解虹鳟鱼肝细胞热应激的机制研究

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-11-17 DOI: 10.1016/j.cbd.2025.101691

Jun Sun , Zhe Liu

This study investigated the role of selenium nanoparticles (SeNPs) in modulating long non-coding RNA (lncRNA) expression and their regulatory networks in rainbow trout hepatocytes under heat stress using transcriptomic and bioinformatic approaches. Exposure to 5 μg/mL SeNPs alleviated heat stress-induced damage, with trans-target prediction identifying 1360 differentially expressed lncRNAs (DElncRNAs) and 4355 differentially expressed mRNAs (DEmRNAs). A competing endogenous RNA (ceRNA) network was constructed based on DElncRNAs, DEmiRNAs, and DEmRNAs with Pearson correlation coefficients >0.99 and P < 0.05, ultimately comprising 37 DElncRNAs, 18 DEmiRNAs, and 14 DEmRNAs. Functional enrichment analysis revealed that target genes of DElncRNAs were significantly enriched in biological processes related to stimulus response, immune regulation, and antioxidant activity. KEGG pathway analysis indicated that these genes are primarily involved in endoplasmic reticulum signaling, potentially activating downstream MAPK, IL-17, B-cell receptor, and TNF signaling pathways. These regulatory mechanisms may enhance thermal tolerance in rainbow trout hepatocytes by suppressing apoptosis and promoting cell proliferation. Our findings highlight the critical role of SeNP-mediated lncRNA regulatory networks in mitigating heat stress, providing novel insights into the molecular basis of stress resilience in fish.

本研究利用转录组学和生物信息学方法研究了硒纳米颗粒（SeNPs）在热应激条件下虹鳟鱼肝细胞中调节长链非编码RNA （lncRNA）表达及其调控网络的作用。暴露于5 μg/mL SeNPs可减轻热应激诱导的损伤，通过跨靶预测鉴定出1360个差异表达lncRNAs （DElncRNAs）和4355个差异表达mrna （DEmRNAs）。基于DElncRNAs、DEmiRNAs和demmrnas构建了一个竞争性内源RNA （ceRNA）网络，Pearson相关系数>；0.99和P <； 0.05，最终包括37个DElncRNAs、18个DEmiRNAs和14个demmrnas。功能富集分析显示，DElncRNAs靶基因在刺激反应、免疫调节和抗氧化活性相关的生物过程中显著富集。KEGG通路分析表明，这些基因主要参与内质网信号通路，可能激活下游的MAPK、IL-17、b细胞受体和TNF信号通路。这些调节机制可能通过抑制细胞凋亡和促进细胞增殖来增强虹鳟肝细胞的热耐受性。我们的研究结果强调了senp介导的lncRNA调节网络在减轻热应激中的关键作用，为鱼类应激恢复的分子基础提供了新的见解。

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引用次数: 0

Acute injury of liver in hybrid groupers (Epinephelus lanceolatus ♂ × Epinephelus fuscoguttatus ♀) under high-dose Edwardsiella ictaluri infection 高剂量爱德华氏菌感染杂交石斑鱼（斑点石斑鱼♂×褐斑石斑鱼♀）肝脏的急性损伤。

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-11-17 DOI: 10.1016/j.cbd.2025.101692

Xiaomin Zheng , Zhuojin He , Lixin Ma, Linjie Zheng, Li Lin, Fei Shi

Edwardsiella ictaluri is a major fish pathogen that poses a serious threat to hybrid grouper in intensive aquaculture. This study evaluated the impact of E. ictaluri on liver health by analyzing histopathological changes, enzyme activity, and gene expression in infected hybrid grouper. Compared with the control group, infected fish exhibited markedly increased cytoplasmic vacuolation, inflammatory cell infiltration, nuclear pyknosis, and hepatocyte apoptosis. Moreover, biochemical assays revealed significantly elevated activities of glutamate oxaloacetate transaminase (GOT), glutamate pyruvate transaminase (GPT), and catalase (CAT). Transcriptomic analysis showed altered expression of genes associated with steroid hormone biosynthesis, PPAR signaling pathway, and protein digestion and absorption. Quantitative real-time polymerase chain reaction (qRT-PCR) further demonstrated increased mRNA expression of Nuclear Factor Kappa-B p65 (NF-κB p65), Toll-like Receptor 3 (TLR-3), Occludin (OCLD), Zonula Occludens-3 (ZO-3), and Fas cell surface death receptor (Fas). Redundancy analysis (RDA) revealed correlations of differentially expressed genes (DEGs) with cytoplasmic vacuolation and enzyme activities. Collectively, these findings reveal that E. ictaluri infection profoundly impairs liver health in hybrid grouper by disrupting hepatic structure, altering enzyme activity, and dysregulating pathways associated with immunity and metabolism.

Edwardsiella ictaluri是集约化养殖中对杂交石斑鱼造成严重威胁的主要鱼类病原体。本研究通过分析受感染杂交石斑鱼的组织病理学变化、酶活性和基因表达，评估了伊氏石斑鱼对肝脏健康的影响。与对照组相比，感染鱼表现出明显增加的细胞质空泡化、炎症细胞浸润、核固缩和肝细胞凋亡。此外，生化分析显示谷氨酸草酰乙酸转氨酶（GOT）、谷氨酸丙酮酸转氨酶（GPT）和过氧化氢酶（CAT）活性显著升高。转录组学分析显示，与类固醇激素生物合成、PPAR信号通路和蛋白质消化吸收相关的基因表达发生了改变。定量实时聚合酶链反应（qRT-PCR）进一步证实核因子κ b p65 （NF-κB p65）、toll样受体3 （TLR-3）、Occludin （OCLD）、Zonula occluden -3 （ZO-3）和Fas细胞表面死亡受体（Fas） mRNA表达增加。冗余分析（RDA）揭示了差异表达基因（DEGs）与细胞质空泡形成和酶活性的相关性。综上所述，这些发现表明，伊克塔乌里杆菌感染通过破坏肝脏结构、改变酶活性和失调与免疫和代谢相关的途径，严重损害杂交石斑鱼的肝脏健康。

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引用次数: 0

Genome-wide identification, characterization, molecular evolution and expression profiling analysis of COMMD gene family in black rockfish (Sebastes schlegelii) 黑岩鱼comd基因家族的全基因组鉴定、表征、分子进化及表达谱分析

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-11-15 DOI: 10.1016/j.cbd.2025.101694

Xuechen Li , Zhentao Chen , Jingrun Pu, Xuangang Wang, Ze Tao, Zhixiang Duan, Gan Yu, Ping Han, Fan Zhang, Haiyang Yu

The Copper Metabolism gene MURR1 Domain (COMMD) gene family is recognized as a highly conserved gene family in diverse species and involved in various important biological processes, including copper metabolism, NF-κB signaling and membrane transport. However, current research regarding the systematic identification of the COMMD gene family in teleosts and its role in the innate immunity of Sebastes schlegelii (S. schlegelii) remains limited. In this study, we identified and annotated 9 COMMD genes in S. schlegelii. Through phylogenetic analysis, analysis of gene structure, motif compositions, and molecular evolutionary patterns of the COMMD gene family, we found that COMMD gene maintains a highly conserved state in evolutionary process, and bears similar importance in metabolism of different species. Moreover, we analyzed the expression patterns of COMMD genes in macrophage and immune-relevant tissues of healthy S. schlegelii and those infected with Acinetobacter johnsonii by using qRT-PCR. The results revealed distinct tissue-specific expression profiles for COMMD genes, and their expression was significantly altered after A. johnsonii infection. We confirmed that SsCOMMD1 could up-regulate the activity of NF-κB pathway. This study elaborates COMMD genes of S. schlegelii, providing a valuable reference for future research on understanding of the functions of COMMD gene family in the innate immune response of teleosts.

铜代谢基因MURR1结构域（COMMD）基因家族是广泛存在于多种物种中的高度保守的基因家族，参与铜代谢、NF-κB信号传导、膜转运等多种重要的生物过程。然而，目前关于硬骨鱼COMMD基因家族的系统鉴定及其在schlegelii （S. schlegelii）先天免疫中的作用的研究仍然有限。在这项研究中，我们鉴定并注释了9个schlegeli的COMMD基因。通过系统发育分析，分析COMMD基因家族的基因结构、基序组成和分子进化模式，我们发现COMMD基因在进化过程中保持高度保守状态，在不同物种的代谢中具有相似的重要性。此外，我们还利用qRT-PCR分析了健康schlegeli链球菌和感染johnsoni不动杆菌的巨噬细胞和免疫相关组织中COMMD基因的表达模式。结果显示，comd基因具有明显的组织特异性表达谱，且其表达在约翰氏单胞杆菌感染后显著改变。我们证实SsCOMMD1可以上调NF-κB通路的活性。本研究详细阐述了schlegelii的COMMD基因，为进一步研究COMMD基因家族在硬骨鱼先天免疫应答中的功能提供了有价值的参考。

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引用次数: 0

Quercetin enhances antioxidant defense and modulates immune homeostasis in mandarin fish (Siniperca chuatsi): Insights from biochemical and transcriptomic analyses 槲皮素增强鳜鱼的抗氧化防御和调节免疫稳态：来自生化和转录组学分析的见解。

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-11-13 DOI: 10.1016/j.cbd.2025.101690

Zihan Zhou , Qichen Jiang , Mingming Han , Chenxi Zhu , Tian Zhu , Yi Juin Tay , Guoxing Liu

Revealing the molecular basis of stress resistance in aquaculture species is the key to achieving sustainable breeding strategies. Based on the two-species complementation strategy, this study systematically evaluated the cross-species protection of natural flavonoid quercetin in mandarin fish (Siniperca chuatsi) and zebrafish (Danio rerio). In this study, the effects of quercetin on the transcription and antioxidant capacity of S. chuatsi gene and the antioxidant capacity of D. rerio were tested. S. chuatsi and D. rerio were immersed in four concentrations (0, 1, 2.5, 5.0 mg/L) of quercetin for 28 days. At 2.5 mg/L, quercetin boosted antioxidant defenses by elevating SOD activity and lowering lipid peroxidation, while modulating immune homeostasis in a dose-dependent manner. Although the two fish species showed a consistent trend in oxidative stress indicators, there were significant species differences in their immune responses. Transcriptome results revealed that S. chuatsi activated key functional modules such as cell structure remodeling, transmembrane transport and protein folding under quercetin intervention, and was enriched in signal transduction, nutrient absorption and fat metabolism pathways, forming a multi-level and synergistically regulated stress defense network. The results show that quercetin can mediate a set of evolutionarily conserved systemic protection mechanisms and has the potential to be used as a functional molecule for aquaculture stress resistance breeding.

揭示水产养殖物种抗逆性的分子基础是实现可持续养殖策略的关键。基于两种互补策略，系统评价了天然类黄酮槲皮素对鳜鱼和斑马鱼的跨种保护作用。本研究考察了槲皮素对荸荠基因转录和抗氧化能力的影响，以及对金黄色葡萄球菌抗氧化能力的影响。槲皮素浓度分别为0、1、2.5、5.0 mg/L的槲皮素溶液中，对翘丝桃和黑绒桃进行浸泡28 d。在2.5 mg/L时，槲皮素通过提高SOD活性和降低脂质过氧化来增强抗氧化防御，同时以剂量依赖的方式调节免疫稳态。虽然两种鱼类在氧化应激指标上表现出一致的趋势，但在免疫反应上却存在显著的物种差异。转录组研究结果显示，槲皮素干预下，翘子激活了细胞结构重塑、跨膜转运和蛋白质折叠等关键功能模块，并在信号转导、营养吸收和脂肪代谢途径中富集，形成了一个多层次、协同调节的应激防御网络。结果表明，槲皮素可介导一套进化保守的系统保护机制，具有作为水产养殖抗逆性育种功能分子的潜力。

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引用次数: 0

The effects of interfering with gs and gls genes on intestinal genes expression and metabolic pathways in Trachinotus blochii 干扰gs和gls基因对布氏沙眼虫肠道基因表达和代谢途径的影响。

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-11-13 DOI: 10.1016/j.cbd.2025.101689

Changlin Chen, Lei Wang, Chaoyue Deng, Wenyan Lin, Huapeng Chen, Xinxin Wang, Haoran Yu, Junlong Sun, Jian Luo, Feibiao Song

Previous research has demonstrated that the addition of exogenous glutamine in feed can enhance the growth and development of Trachinotus blochii. Nonetheless, there is limited knowledge about the specific regulatory pathways and essential regulatory genes implicated in glutamine's influence on the growth and development of T. blochii. This research utilized RNA interference technology to achieve sustained suppression of the gs and gls genes in live T. blochii. After 52 days of interference, we analyzed the growth and development of T. blochii, intestinal morphology, digestive and antioxidant enzyme activity, and intestinal transcriptome. The development of T. blochii was markedly inhibited by interference, with the intestinal diameter, villus length, width, and muscle layer in the interference group being greatly reduced compared to the control group. Measurements of intestinal enzyme activity showed a significant decrease in LPS content in T. blochii following interference, and antioxidant-related enzyme activities (T-AOC and GSH) were lowered, and MDA content was significantly raised. Transcriptome analysis indicated that following the knockdown of the gs and gls genes, there was a significant enrichment of growth-related serine metabolism pathways and lipid metabolism pathways, as well as immune inflammation-related pathways, including the complement and coagulation cascade and PPAR signaling pathway. Co-expression mRNA network analysis revealed a significant enrichment of genes associated with purine de novo synthesis and the coenzyme Q oxidoreductase family. In summary, knockdown of the gs and gls genes diminishes amino acid metabolism and fat utilization in the intestines of T. blochii, thus impacting intestinal structure and hindering growth. These findings offer significant insights for the control of intestinal health and agricultural practices of T. blochii.

已有研究表明，在饲料中添加外源谷氨酰胺可促进布氏沙眼虫的生长发育。然而，关于谷氨酰胺对blochi生长发育影响的具体调控途径和必要调控基因的知识有限。本研究利用RNA干扰技术实现了活体blochi中gs和gls基因的持续抑制。经过52 d的干扰，我们分析了blochi的生长发育、肠道形态、消化酶和抗氧化酶活性以及肠道转录组。干扰显著抑制blochi的发育，干扰组肠道直径、绒毛长度、宽度、肌肉层数均较对照组显著减小。肠道酶活性测定结果显示，干扰后斑衣多糖含量显著降低，抗氧化相关酶活性（T-AOC和GSH）显著降低，MDA含量显著升高。转录组分析显示，gs和gls基因敲低后，生长相关的丝氨酸代谢途径和脂质代谢途径以及免疫炎症相关的途径，包括补体和凝血级联以及PPAR信号通路显著富集。共表达mRNA网络分析显示，与嘌呤从头合成和辅酶Q氧化还原酶家族相关的基因显著富集。综上所述，gs和gls基因的敲低减少了blochi肠内氨基酸代谢和脂肪利用，从而影响肠道结构，阻碍生长。这些发现为控制肠道健康和农业实践提供了重要的见解。

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引用次数: 0

Integrative analysis of FOX genes in fish: Evolution, structure, and functional roles in environmental stress tolerance and growth regulation in Mugil cephalus 鱼类FOX基因的综合分析：Mugil cephalus在环境胁迫耐受和生长调节中的进化、结构和功能作用。

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-11-08 DOI: 10.1016/j.cbd.2025.101685

Urwah Ishaque , Saima Naz , Jhan Zeb , Ahmad Manan Mustafa Chatha , Ghazi Alatawi , Saba Iqbal , Bushra Irfan

The forkhead box (FOX) gene family encodes transcription factors that control growth, development, stress response, and metabolism across vertebrates. While FOX genes have been widely explored in a few model fish species, their roles in Mugil cephalus, a commercially and ecologically important euryhaline species, are still not well described. Current study, explored the first ever genomic and structural analysis of FOX genes in M. cephalus. In this study, 42 FOX genes were identified in the genome of M. cephalus and the presence of conserved forkhead domains was confirmed. The study showed that there are significant differences in the physicochemical traits of studied proteins and the phylogenetic analysis grouped these proteins into 18 clades. Duplication history pointed toward a number of genome-wide duplication events, with all of them shaped mainly by purifying selection. The synteny analysis suggested that chromosomal arrangements were mostly conserved with humans, indicating a deep evolutionary link. The organization of Motif and domains pointed toward functional diversification, while structure modeling (2D and 3D) revealed noticeable variation in folding patterns of amino acids. Moreover, mutation predictions reported various destabilizing substitutions that could weaken the stability of proteins. In conclusion, this study gives the first integrated overview of FOX genes in M. cephalus, opening new perspectives on their evolution and possible functions in vertebrate species. Experimental studies are aimed in future to confirm the role of FOX genes for improved aquaculture practices, stress tolerance, and bio-conservation of M. cephalus.

叉头盒（FOX）基因家族编码控制脊椎动物生长、发育、应激反应和代谢的转录因子。虽然FOX基因已经在一些模式鱼类中得到了广泛的探索，但它们在Mugil cephalus（一种具有商业和生态重要性的广盐物种）中的作用仍然没有得到很好的描述。本研究首次探索了头头棘球蚴FOX基因的基因组和结构分析。在本研究中，在头头猪基因组中鉴定出42个FOX基因，并证实了保守叉头结构域的存在。研究表明，所研究的蛋白质在理化性状上存在显著差异，系统发育分析将这些蛋白质归为18支。复制历史指出了许多全基因组复制事件，所有这些事件都主要是由纯化选择形成的。合成分析表明，染色体排列大多与人类保守，表明一个深刻的进化联系。Motif和结构域的组织指向功能多样化，而结构建模（2D和3D）揭示了氨基酸折叠模式的显著变化。此外，突变预测报告了各种不稳定的取代，这些取代可能削弱蛋白质的稳定性。综上所述，本研究首次对头头螺杆菌FOX基因进行了全面的综述，为其在脊椎动物物种中的进化及其可能的功能开辟了新的视角。未来的实验研究旨在证实FOX基因在改善头头m.s cephalus的养殖方式、抗逆性和生物保护方面的作用。

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引用次数: 0

Transcriptome analysis reveals intestinal gene expression and metabolic pathways in yaks 转录组分析揭示了牦牛肠道基因表达和代谢途径。

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-11-08 DOI: 10.1016/j.cbd.2025.101686

Xiaofeng Luo , Junru Pan , Haiyan Li , Wenrui Ye , Shehr Bano Mustafa , Siraj Ahmed , Khuram Shahzad , Yonggang Sun , Wangsheng Zhao

The yak, a ruminant species native to high-altitude plateaus, serves as a vulnerable model for studying adaptation to extreme environments. Exposed to hypoxia, low temperatures, and strong ultraviolet radiation, yaks have evolved unique physiological mechanisms to thrive under such conditions. Among its organs, the intestine is a crucial metabolic organ and plays a key role in environmental adaptation. Therefore, this study systematically compared the transcriptional regulatory mechanisms of the small and large intestine between yaks and cattle, thereby revealing the metabolic mechanisms underlying the high-altitude adaptation of yaks. The results showed that the expression of several key metabolic genes, including IDO1, KYNU (tryptophan metabolism), ACSL1 (lipid metabolism), and ABCG2 (vitamin transport), was significantly upregulated in the yak small intestine. This indicates that the yak small intestine has stronger physiological potential in nutrient metabolism and barrier function. In the large intestine, the expression of key genes in pathways such as lipid metabolism (PLA2), detoxification (UGT), cAMP signaling (ADCY, CREB3L), and bile secretion (ABCC) was significantly upregulated, indicating that the yak possesses unique physiological advantages in energy regulation and maintaining intestinal homeostasis. This study systematically elucidates the metabolic mechanisms of the yak intestine under the extreme conditions of the plateau, providing a basis for in-depth analysis of ruminant intestinal function and molecular breeding.

牦牛是一种原产于高海拔高原的反刍动物，是研究极端环境适应性的脆弱模型。在缺氧、低温和强紫外线辐射的环境下，牦牛进化出了独特的生理机制，在这样的条件下茁壮成长。在其器官中，肠道是一个重要的代谢器官，在环境适应中起着关键作用。因此，本研究系统比较了牦牛和牛小肠和大肠的转录调控机制，揭示了牦牛高原适应的代谢机制。结果表明，牦牛小肠中IDO1、KYNU（色氨酸代谢）、ACSL1（脂质代谢）和ABCG2（维生素运输）等关键代谢基因的表达显著上调。说明牦牛小肠在营养物质代谢和屏障功能方面具有较强的生理潜力。在大肠中，脂质代谢（PLA2）、解毒（UGT）、cAMP信号通路（ADCY、CREB3L）和胆汁分泌（ABCC）等关键基因的表达显著上调，表明牦牛在能量调节和维持肠道稳态方面具有独特的生理优势。本研究系统阐明了高原极端条件下牦牛肠道代谢机制，为深入分析反刍动物肠道功能及分子育种提供依据。

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引用次数: 0