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

Molecular mechanisms of quercetin in regulating antioxidant defense and pyroptosis pathways in the redclaw crayfish (Cherax quadricarinatus) 槲皮素调控红爪小龙虾抗氧化防御和焦亡途径的分子机制

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-12-13 DOI: 10.1016/j.cbd.2025.101728

Zihan Zhou , Weiwei Lv , Qin Si , Bangyue Zhang , Aileen Tan Shau Hwai , Yi Juin Tay , Mingming Han , Zhengjun Zhan , Qichen Jiang

As a principal species in freshwater aquaculture, the redclaw crayfish (Cherax quadricarinatus) 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 C. quadricarinatus. 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.

作为淡水养殖的主要物种，红爪小龙虾（Cherax quadricarinatus）依赖于有效的免疫系统来减轻环境和病原体的挑战。槲皮素是一种普遍存在的植物源类黄酮，因其具有抗氧化、抗炎和免疫调节等多种生物活性而受到科学界的关注。本研究研究了槲皮素暴露对红腹金龟转录调控和抗氧化能力的影响。在28天的时间里，小龙虾受到5种槲皮素浓度（0、1.0、2.5、5.0和10.0 mg/L）的影响，并与未处理的对照进行结果评估。在5.0 mg/L浓度下，槲皮素暴露与NLRP3炎症小体通路关键转录物（NLRP3、GSDMD、Caspase-1）的显著下调相关，其影响在各浓度中表现得最为明显，表现为NLRP3、GSDMD、Caspase-1的下调。同时，转录变化与Nrf2信号轴的调节/激活一致，上调Nrf2、NQO1和Keap1的表达。这些转录变化表明槲皮素通过Nrf2-Keap1级联减轻焦亡并增强细胞抗氧化防御。相应地，肝胰腺SOD、CAT、GSH-Px活性显著升高，MDA水平显著降低，表明抗氧化能力增强，脂质过氧化作用减弱。该研究提供了有价值的毒理学见解，并阐明了槲皮素在淡水甲壳类动物中免疫调节和抗氧化作用的部分分子基础。

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引用次数: 0

Transcriptomic analysis of Cuvierian Organs regeneration in the sea cucumber Holothuria leucospilota 珠光海参居维尔器官再生的转录组学分析。

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-12-13 DOI: 10.1016/j.cbd.2025.101729

Xiaoli Zhang , Renhui Liu , Hua Ge , Ting Chen , Xinyue Ren , Caixia Long , Jiasheng Huang , Wenjie Pan , Haipeng Qin , Lihong Yuan , Aifen Yan

Sea cucumbers are renowned for their regenerative capabilities, making them ideal models for studying tissue and organ regeneration. Holothuria leucospilota 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 H. leucospilota 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.

海参以其再生能力而闻名，这使它们成为研究组织和器官再生的理想模型。白鳞海螺（Holothuria leucospilota）拥有一种独特的防御结构，即库维氏器官（Cuvierian organ， CO），它在受到威胁时射出，并在数周内再生。然而，CO再生的分子机制仍然知之甚少。在本研究中，我们采用机械刺激的方法诱导蓝叶青排CO，并在31天内观察其再生过程。组织学分析显示再生始于间皮形成，随后是结缔组织和上皮发育。转录组学分析鉴定了再生过程中许多差异表达的基因。细胞外基质（ECM）相关关键基因上调，基质蛋白酶基因下调。包括Wnt和Hippo在内的信号通路被抑制，而凋亡和细胞周期通路被激活。此外，一些结构外层蛋白表达改变。这些结果表明，ECM重组和细胞增殖和凋亡的协调调节是CO再生的核心。本研究为棘皮动物器官再生的分子机制提供了重要的见解，并为高等动物的再生研究提供了有价值的线索。

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引用次数: 0

Comparative transcriptome analysis provides novel insights into the evolution of enhanced cold tolerance in the northward invasion of the eel goby, Taenioides sp. 比较转录组分析为北侵鳗鱼虾虎鱼（Taenioides sp.）耐寒性增强的进化提供了新的见解。

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-12-11 DOI: 10.1016/j.cbd.2025.101709

Jing Liu, An Xu, Tianwei Liu, Kun Huang, Weihu Zhu, Jing Yu, Yijing Yang, Fenghui Li, Denghui Zhu, Li Gong, Liqin Liu, Zhenming Lü

Invasive species serve as an ideal model for investigating adaptation, since they are typically introduced to unfamiliar environments where adaptation is essential for survival. Taenioides 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 Taenioides 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., MYO18B) 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 Taenioides 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.

入侵物种是研究适应的理想模型，因为它们通常被引入不熟悉的环境，在那里适应是生存所必需的。Taenioides sp.是一种典型的入侵性虾虎鱼，最初栖息在中国东南部的热带和亚热带海岸，最近由于ESNT项目的实施而扩展到华北温带地区。然而，入侵种群在入侵期间如何适应中国北方气候的分子基础仍不清楚。本研究比较了长江口源种群和最北端入侵种群对冷胁迫的耐寒性和转录组学变化，以阐明这种气候适应的可能分子机制。我们的研究结果显示，与源种群相比，侵入性种群的耐寒性显著增强（CTmin: 7.11°C vs 10.66°C）。转录组分析发现56个差异表达基因（DEGs）在所有组织和群体中表达模式相似，表明它们在Taenioides sp.的冷响应中起核心作用。同时，多个DEGs表现出群体特异性表达谱，表明它们参与了不同的抗寒性。进一步的WGCNA分析显示，与肌肉结构和产热相关的冷反应中枢基因子集（例如MYO18B）在寒冷胁迫下的入侵种群中表现出不同的表达谱，突出了它们在增强耐寒性进化中的作用。本研究结果为水工程环境下带蚊北侵的热适应分子机制提供了新的见解，对预测其入侵潜力和制定有效控制策略具有重要意义。关于遗传和表观遗传力量如何驱动种群不同的基因表达调控，因此，不同的热适应将在未来进行进一步的分析。

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引用次数: 0

Epitranscriptomic variation in banded newts (Ommatotriton vittatus) across life stages and sexes in the semi-arid habitat in northern Israel 以色列北部半干旱地区带状蝾螈（Ommatotriton vittatus）跨生命阶段和性别的表转录组变异

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-12-09 DOI: 10.1016/j.cbd.2025.101727

Ari Meerson , Monika Almozlino , Gad Degani , Dani Bercovich

The banded newt, Ommatotriton vittatus, 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.

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 >30 differentially modified regions (DMRs, with a differential modification score > 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.

These findings provide the first evidence of m⁶A methylation patterns in O. vittatus and highlight their role in developmental transitions. The results advance understanding of transcriptomic–epitranscriptomic regulation in amphibian plasticity, and more generally, in vertebrate development.

带状蝾螈（Ommatotriton vittatus）在以色列被认为是濒危物种，以色列是其分布的南部边界，需要适应高度不稳定的栖息地。带状蝾螈有水栖和陆生两种形态，在其一生中经历了蜕变和各种表型变化。我们的团队之前已经报道了基于性别的广泛转录组重塑，特别是蝾螈的生命阶段。这些基因表达的戏剧性变化可能伴随着广泛的表转录组调控，这仍然知之甚少。在这项研究中，使用直接RNA测序来表征来自Nehalit种群的12只蝾螈的m6A RNA修饰。我们重点研究了127个转录本中有30个差异修饰区（DMRs，差异修饰评分为5）的基因，这些基因参与了结构、翻译和细胞外基质过程。其中，18个基因显示出不同生命阶段的甲基化模式聚类，尤其是角蛋白和翻译相关蛋白，提示m6A在结构重塑和发育转变中发挥调控作用。相比之下，大多数DMR基因与管家和压力反应功能有关，没有表现出生命阶段特异性聚类。与差异表达数据的交叉分析进一步表明，肌肉、免疫和结缔组织通路在转录和表转录组水平上共同调控。这些发现提供了m6A甲基化模式在O. vittatus中的第一个证据，并强调了它们在发育转变中的作用。这些结果促进了对两栖动物可塑性的转录组-表转录组调控的理解，更广泛地说，是对脊椎动物发育的理解。

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引用次数: 0

Profiling and functional validation of LPS-responsive miRNAs in the giant freshwater prawn, Macrobrachium rosenbergii 罗氏沼虾lps应答mirna的分析与功能验证

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-12-09 DOI: 10.1016/j.cbd.2025.101724

Tanapat Pangeson , Rattikon Thammason , Chalermporn Ongvarrasopone , Nalinnipa Wiengnak , Amnat Phetrungnapha

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 Macrobrachium rosenbergii 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 Rpn10, Rab11, Vps2, and ArfGAP3. 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 in vivo challenge experiment. In vivo overexpression of mro-miR-365-1-5p significantly increased mortality in prawns challenged with Vibrio harveyi, 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.

MicroRNAs （miRNAs）是甲壳类动物免疫应答的关键转录后调节因子，但其在模式识别受体激活过程中的作用仍知之甚少。在这项研究中，我们研究了罗氏沼虾（Macrobrachium rosenbergii）对脂多糖（LPS）的miRNA反应，脂多糖是一种保守的细菌病原体相关分子模式（PAMP）。高通量小RNA测序鉴定了LPS注射后肝胰腺中155个差异表达的mirna （dem）。途径富集分析显示，这些dem的靶基因与免疫途径显著相关，包括泛素-蛋白酶体途径（UPP）和内吞作用。网络分析表明，mir -365-1-5p是一个针对关键基因如Rpn10、Rab11、Vps2和ArfGAP3的中央调控因子。时间表达谱显示，LPS暴露后，mir -365-1-5p快速下调。通过双荧光素酶报告基因检测和体内激发实验验证了mir - mir -365-1-5p的调控作用。在体内，mir -365-1-5p的过表达显著增加了哈威弧菌攻击对虾的死亡率，表明免疫防御受损。这些发现为甲壳类动物lps反应性mirna的调节作用提供了新的见解，并表明特定mirna的调节可能对细菌感染期间有效的免疫激活至关重要。

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引用次数: 0

Physiological effects of long-term saline-alkaline stress on the gills of Acanthopagrus latus: A combined analysis of transcriptomics and metabolomics 长期盐碱胁迫对棘鱼鳃的生理影响：转录组学和代谢组学的联合分析。

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-12-08 DOI: 10.1016/j.cbd.2025.101701

Weiqing Huang , Fengfang Zhou , Zongqiang Lian , Zhideng Lin , Zipeng Zhang

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 Acanthopagrus latus 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.

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 p2ry12, LOC119021196, and LOC119027230 were linked to energy metabolism, while lyn, fynb, pik3r1, pik3cd, and akt1 were associated with apoptosis and immune regulation.

Overall, this study provides comprehensive molecular and physiological evidence of how A. latus 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.

盐碱胁迫对水产养殖鱼类构成了重大的环境挑战，但其适应盐碱胁迫的分子机制尚不清楚。在这项研究中，我们综合了转录组学、代谢组学、生理学和组织学分析来阐明棘鱼鳃在盐碱水（SAW）暴露下的适应机制。处理40天后，SAW引起了鳃结构的明显组织学改变，但对生长性能没有显著影响。生理分析显示，谷胱甘肽过氧化物酶（GSH-Px）、酸性磷酸酶（ACP）和碱性磷酸酶（ALP）活性无显著变化，丙二醛（MDA）水平升高，提示氧化应激和代谢紊乱。转录组学分析鉴定出2539个差异表达基因（DEGs），主要富集于免疫相关通路，如t细胞受体信号传导、Th17细胞分化和IL-17信号传导。代谢组学分析检测到892种差异表达代谢物（DEMs），主要参与能量代谢途径，包括花生四烯酸、α-亚麻酸和亚油酸代谢。综合多组学分析进一步揭示了血小板活化、磷脂酶D信号转导和谷胱甘肽代谢途径中显著的共富集。值得注意的是，29个DEGs和4个关键代谢物（ATP、前列腺素H₂、环AMP和ADP）在血小板活化途径中显著改变。其中，p2ry12、LOC119021196和LOC119027230等上调基因与能量代谢相关，lyn、fynb、pik3r1、pik3cd和akt1等上调基因与细胞凋亡和免疫调节相关。综上所述，本研究提供了水杨如何通过协调免疫调节和能量代谢来适应盐碱胁迫的分子和生理证据。这些发现增强了我们对鱼类适应机制的认识，为盐碱水资源在水产养殖中的可持续利用提供了理论支持。

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引用次数: 0

Multomics decipher the mechanisms of bisphenol S-induced oxidative stress and inflammation in Pseudobagrus ussuriensis 多组学揭示了双酚s诱导的乌苏里假袋氧化应激和炎症的机制

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-12-08 DOI: 10.1016/j.cbd.2025.101725

Lu Wang , Changchang Pu , Yimin Li , Jiaxiang Zhu , Mohammad Mehdi Ommati , Bingke Wang , Chunnuan Zhang

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 Pseudobagrus ussuriensis 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 (p < 0.05). 16S rRNA sequencing analysis demonstrated that 10 μg/L BPS exposure markedly altered gut microbial composition, with significant enrichment of Achromobacter and Acinetobacter. Liver transcriptome profiling identified substantial differential expression of immune-related genes (hmgb1, nfκb, and nfκbiα) in the 100 μg/L exposure group. Importantly, Pearson correlation analysis established a significant association between gut microbiota perturbation and hepatic immune-inflammatory responses (p < 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 P. ussuriensis, offering novel insights into the ecological risks of BPS contamination.

双酚S （BPS）是一种广泛存在的环境内分泌干扰化学物质，其生态毒理学效应引起了人们越来越多的关注。本研究以乌苏里假bagrus为模型水生物种，系统研究了BPS暴露的综合毒性。360尾鱼（平均初始体重：30.42±0.62 g）随机分为4组，分别暴露于0（对照）、1、10和100 μg/L BPS中14 d。组织病理学检查显示明显的组织损伤，包括鳃丝水肿、肠上皮脱屑和肝脏空泡化。氧化应激评估显示丙二醛（MDA）水平呈浓度依赖性升高（p < 0.05）。16S rRNA测序分析表明，10 μg/L BPS暴露显著改变了肠道微生物组成，无色杆菌和不动杆菌显著富集。肝脏转录组分析发现，在100 μg/L暴露组中，免疫相关基因（hmgb1、nfκb和nfκbiα）的表达存在显著差异。重要的是，Pearson相关分析建立了肠道菌群扰动与肝脏免疫炎症反应之间的显著关联（p < 0.05）。据我们所知，本研究首次证明了环境相关浓度（10 μg/L）的BPS可引起乌苏里江拟南鲷的显著生理损伤，为研究BPS污染的生态风险提供了新的视角。

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引用次数: 0

Knockout of zebrafish Clec3bb does cause vertebra density reduction 敲除斑马鱼的Clec3bb确实会导致椎骨密度降低

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-12-08 DOI: 10.1016/j.cbd.2025.101726

Feilong Shi , Xudong Wang , Yulong Chen , Zhengyu Xiao , Xuemei Xiong , Jianbo Wang , Zexia Gao , Chunhong Nie

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 clec3b 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 clec3b, namely clec3ba and clec3bb, whose functional divergence remains unclear. The amino acid sequence similarity between zebrafish clec3ba and clec3bb was 55.61 %. Tissue-specific expression analysis revealed distinct expression patterns of clec3ba and clec3bb across multiple tissues (brain, gonads, fin, skin, vertebra, eyes, ribs, muscle, kidney, liver, gills) and embryonic stages. Mutants of clec3ba and clec3bb were generated using CRISPR/Cas9 system. Micro-CT analysis revealed that vertebral bone density was significantly reduced in clec3bb⁻/⁻ mutants compared to wild type, whereas no significant change was observed in clec3ba⁻/⁻ mutants. Comparative transcriptome was used to analyze gene expression differences of vertebrae in clec3bb^+/+ and clec3bb⁻/⁻ zebrafish and identified 3316 differentially expressed genes were in vertebral tissues of clec3bb 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 (col1a1a, entpd5a, fgf23, bmp6, aspn, bglapl, tnmd, scxa, sp7, tnc) had a lower expression in vertebrae of clec3bb^−/− mutant. The above results highlight the critical role of clec3bb in zebrafish bone mineralization, providing insights into the functional specialization of clec3b paralogs and a theoretical basis for understanding skeletal development mechanisms in teleosts.

c型凝集素结构域家族3成员B （Clec3b）广泛参与多种生物过程，包括骨矿化、细胞增殖和疾病的发病机制。虽然在哺乳动物中已经很好地描述了cle3b与骨骼发育的关系，但它在鱼类骨骼发育中的作用仍不清楚。由于硬骨鱼基因组的重复，斑马鱼具有两个类似的clec3b基因，即clec3ba和clec3bb，其功能分化尚不清楚。斑马鱼clec3ba与clec3bb氨基酸序列相似性为55.61%。组织特异性表达分析显示，clec3ba和clec3bb在多个组织（脑、性腺、鳍、皮肤、脊椎、眼睛、肋骨、肌肉、肾脏、肝脏、鳃）和胚胎期的表达模式不同。利用CRISPR/Cas9系统生成了clec3ba和clec3bb突变体。Micro-CT分析显示，与野生型相比，clec3bb - / -突变体的椎体骨密度显著降低，而clec3ba - / -突变体的椎体骨密度没有明显变化。采用比较转录组分析clec3bb+/+和clec3bb−/−斑马鱼椎体基因表达差异，发现clec3bb突变体椎组织中存在3316个差异表达基因，主要富集于MAPK、TGF-β、钙和Wnt信号通路。RT-qPCR验证结果显示，10个骨骼相关基因（col1a1a、entpd5a、fgf23、bmp6、aspn、bglap、tnmd、scxa、sp7、tnc）在cle3bb−/−突变体的椎骨中表达量较低。上述结果突出了clec3bb在斑马鱼骨矿化中的关键作用，为了解clec3b类似物的功能专门化提供了见解，并为理解硬骨鱼骨骼发育机制提供了理论基础。

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引用次数: 0

Differential expression miRNAs in the gonad of sea cucumber Holothuria leucospilota 细鳞海参生殖腺mirna的差异表达

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-12-04 DOI: 10.1016/j.cbd.2025.101711

Jing Zhang , Xiao-qin Fu , Run-xin Lin , Yang Zhang , Pei-ming Zheng , Huo Li

MicroRNAs are defined as a class of short noncoding RNAs, which play important function in cell differentiation, developmental process and gender determination. The sea cucumber Holothuria leucospilota is a member of the Echinodermata, known for its excellent nutritional and economic value. Breeding efficiency of sea cucumbers is low due to the difficulty in distinguishing between male and female individuals. Discovering molecular markers that distinguish between genders will provide a robust strategy for elucidating the genetic mechanisms governing gender determination and differentiation. In this investigation, high-throughput sequencing was utilized to compare miRNA expression patterns in the gonadal tissues of male and female specimens of H. leucospilota. A total of 584 known miRNAs and 404 novel miRNAs were identified, of which 97 miRNAs were identified as significantly differentially expressed miRNAs (DEMs) between male and female sea cucumbers. These findings enabled the construction of a miRNA-mRNA regulatory network. Pathway analysis of target genes highlighted the potential roles of neuroactive ligand-receptor interactions, calcium signaling, Salmonella infection, endocytosis, and MAPK signaling in governing gender differentiation processes. The expression results of high-throughput sequencing were validated in sc-miR121, sc-miR41, sc-miR67, sc-miR90, sc-miR104 and sc-miR189 by quantitative real-time quantity polymerase chain reaction (RT-qPCR). In summary, our results will provide a foundation for future studies of miRNA regulation in gender differentiation of sea cucumber H. leucospilota.

MicroRNAs是一类短链非编码rna，在细胞分化、发育过程和性别决定中发挥重要作用。海参Holothuria leucospilota是棘皮科的一员，以其优良的营养和经济价值而闻名。由于雌雄个体难以区分，海参的繁殖效率较低。发现区分性别的分子标记将为阐明控制性别决定和分化的遗传机制提供强有力的策略。本研究利用高通量测序技术，比较了雄性和雌性标本的雄性和雌性标本性腺组织中miRNA的表达模式。共鉴定出584个已知mirna和404个新mirna，其中97个mirna在雄性和雌性海参之间被鉴定为显著差异表达mirna （dem）。这些发现使得构建miRNA-mRNA调控网络成为可能。靶基因的通路分析强调了神经活性配体-受体相互作用、钙信号、沙门氏菌感染、内吞作用和MAPK信号在调节性别分化过程中的潜在作用。采用实时定量聚合酶链反应（RT-qPCR）对高通量测序结果在sc-miR121、sc-miR41、sc-miR67、sc-miR90、sc-miR104和sc-miR189中的表达进行验证。综上所述，我们的研究结果将为进一步研究miRNA在海参性别分化中的调控作用提供基础。

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引用次数: 0

Astral-based DIA proteomics explored the cold response mechanism in the liver of juvenile greenfin horse-faced filefish (Thamnaconus septentrionalis) 基于星体的DIA蛋白质组学研究了绿鳍马面鱼幼鱼肝脏的冷反应机制。

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-12-04 DOI: 10.1016/j.cbd.2025.101710

Xuechun Zang , Yuxi Liu , Zijiao Wang , Yanqing Wu , Bo Qin , Shaowu Yin , Tao Wang

Thamnaconus septentrionalis, a high-value commercial fish, exhibits significant sensitivity to low temperatures. Understanding its cold response mechanism is vital for the aquaculture industry development. This study analyzed the hepatic response of T. septentrionalis to 24-h exposure at four temperature (10 °C, 15 °C, 20 °C, and 25 °C) using histology, biochemical parameters, and proteomics. Results showed that decreased temperature exacerbated hepatic damage, increased ROS accumulation, and induced oxidative stress. The cold-induced ROS accumulation was further validated by primary T. septentrionalis hepatocyte. Low-temperature groups (10 °C, 15 °C) exhibited elevated oxidative stress enzyme activities (SOD, CAT, GSH-Px), and the MDA level and decreased hepatic triglycerides compared to the control group (25 °C). Proteomic result revealed significant enrichment in energy metabolism pathways. It is hypothesized that cold stress tended to inhibited aerobic respiration and oxidative phosphorylation but enhanced fatty acid catabolism and potentially ketone body utilization as alternative fuels. The proteomic data also suggesting that liver also maintains cellular function by modulating lipid metabolism, activating autophagy, and suppressing apoptosis. This study reveals the physiological and proteomic response of T. septentrionalis to temperature variation, providing insights into its cold tolerance.

作为一种高价值的商品鱼，Thamnaconus septentrionalis对低温表现出显著的敏感性。了解其冷反应机制对水产养殖业的发展具有重要意义。本研究使用组织学、生化参数和蛋白质组学分析了在4种温度（10°C、15°C、20°C和25°C）下暴露24小时的七毛绦虫的肝脏反应。结果表明，温度降低会加重肝损伤，增加ROS积累，诱导氧化应激。低温诱导的ROS积累在原代七爪绦虫肝细胞中得到进一步验证。低温组（10°C, 15°C）与对照组（25°C）相比，氧化应激酶（SOD， CAT, GSH-Px）活性升高，MDA水平升高，肝脏甘油三酯降低。蛋白质组学结果显示能量代谢途径显著富集。假设冷应激倾向于抑制有氧呼吸和氧化磷酸化，但增强脂肪酸分解代谢和潜在的酮体利用作为替代燃料。蛋白质组学数据还表明肝脏还通过调节脂质代谢、激活自噬和抑制细胞凋亡来维持细胞功能。本研究揭示了七斑绦虫对温度变化的生理和蛋白质组反应，为其耐寒性提供了新的认识。

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引用次数: 0