Comparative Biochemistry and Physiology D-Genomics & Proteomics最新文献_第9页

The sex-specific transcriptomic patterns in hypothalamic-pituitary-gonadal axis of Dabry's sturgeon (Acipenser dabryanus) 达布里鲟鱼下丘脑-垂体-性腺轴的性别特异性转录组模式。

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.2025.101687

Xuetao Shi , Yang Li , Hongtao Huang , Kan Xiao , Jing Yang

Dabry's sturgeon (Acipenser dabryanus) is one of the precious large fish species unique to the upper reaches of the Yangtze River in China. Investigating the molecular mechanisms that regulate the hypothalamic-pituitary-gonadal axis is crucial for the conservation of Dabry's sturgeon. In the present study, transcriptome sequencing and analysis were conducted on hypothalamus, pituitary, and gonad tissues of male and female Dabry's sturgeon. Raw sequence data were compiled and duplicate entries were eliminated, yielding 603,597 unigenes with an average length of 843 base pairs and an N50 value of 1056 bp. In the hypothalamus, the representative up-regulated pathways and genes include fatty acid biosynthesis (fasn, acsl) and fatty acid metabolism (acd), while down-regulated pathways and genes include neuroactive ligand-receptor interactions (lhcgr, npffr1, gabrd). In the pituitary, the representative up-regulated pathways and genes include neuroactive ligand-receptor interactions (drd2, trhr), while down-regulated pathways and genes are unsaturated fatty acid biosynthesis (elovl6). In the gonad, the representative up-regulated pathways and genes include unsaturated fatty acid biosynthesis (fads2), tryptophan metabolism (cyp1a1 and cyp1b1), while down-regulated pathways and genes are ovarian steroid production (fshr, igf1, and cyp11a). These representative pathways and genes play an important role in the gonadal development of Dabry's sturgeon. These potential determinants provide a glimpse into of the molecular mechanisms of hypothalamic-pituitary-gonadal axis regulation in Dabry's sturgeon.

Clinical trial number

All fish handling and experimental procedures in this study have been approved by the Chinese Sturgeon Research Institute of China Three Gorges Corporation, and the Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes (Chinese Sturgeon Research Institute of China Three Gorges Corporation).

大布里鲟（学名：Acipenser dabryanus）是中国长江上游特有的珍贵大型鱼类之一。研究下丘脑-垂体-性腺轴调控的分子机制对达布里鲟的保护至关重要。本研究对雌雄达布里鲟鱼的下丘脑、垂体和性腺组织进行了转录组测序和分析。对原始序列数据进行编译，剔除重复条目，得到603,597个单基因，平均长度为843个碱基对，N50值为1056 bp。在下丘脑中，代表性的上调途径和基因包括脂肪酸生物合成（fasn, acsl）和脂肪酸代谢（acd），下调途径和基因包括神经活性配体-受体相互作用（lhcgr, npffr1, gabrd）。在垂体中，代表性的上调途径和基因包括神经活性配体-受体相互作用（drd2, trhr），下调途径和基因为不饱和脂肪酸生物合成（elov16）。在性腺中，代表性的上调途径和基因包括不饱和脂肪酸生物合成（fads2）、色氨酸代谢（cyp1a1和cyp1b1），下调途径和基因为卵巢类固醇生成（fshr、igf1和cyp11a）。这些具有代表性的途径和基因在达布里鲟的性腺发育中起着重要的作用。这些潜在的决定因素提供了对达布里鲟鱼下丘脑-垂体-性腺轴调节的分子机制的一瞥。临床试验号：本研究中所有鱼类处理和实验程序均经中国三峡集团公司中华鲟研究所和三峡鱼类保护工程湖北省重点实验室（中国三峡集团公司中华鲟研究所）批准。

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引用次数: 0

Transcriptomic analysis reveals stage-specific cholesterol metabolism and steroidogenic in theca layer cells during follicular development in chickens 转录组学分析揭示了鸡卵泡发育过程中卵泡层细胞的阶段特异性胆固醇代谢和类固醇生成。

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-11-06 DOI: 10.1016/j.cbd.2025.101682

Yuechen Liao , Ashi Li , Yangqiwen Luo , Runbang Zhu , Cangning Zhang , Meng Ma , Yongfeng Li , Liumei Sun , Manman Shen , Liang Qu

Ovarian follicle development is a critical factor affecting laying performance in poultry. Follicles are mainly composed of the granulosa layer cells and theca layer cells (TLs). However, the regulatory role of TLs remains inadequately understood. This study explored the abundance of differentially expressed genes (DEGs) in chicken TLs across small yellow follicles (SYFT), the smallest hierarchical follicle (F6T), and the largest hierarchical follicle (F1T) through transcriptome analysis. Results revealed that the top abundance DEGs were linked to cholesterol metabolism (MSMO1, NPC1) and steroid hormone synthesis (STAR, CYP11A1, CYP19A1, POR, NR0B1). Notably, genes involved in steroid hormone synthesis (STAR, CYP11A1, and CYP19A1) were highly expressed at the F6T stage. Up-regulated DEGs in F6T were primarily enriched in metabolism pathways, including one carbon pool by folate and citrate cycle, which contribute to elevated cholesterol synthesis (MSMO1) at this stage. While cholesterol metabolism (NPC1, NR0B1, and POR) were prominent at the SYFT stage, where up-regulated DEGs were linked to cell differentiation such as Wnt and mTOR signaling pathways. Key genes including CYP19A1, CYP17A1, POR, NPC1, VLDLR, and NR0B1 were predominantly found in profiles 3 and 1, which represented significant trends identified through trend analysis. The main KEGG pathways included cell cycle, homologous recombination, metabolism and transport. This study highlights that TLs shift their transcriptional program from cholesterol transport in small yellow follicles to cholesterol synthesis and steroidogenesis in hierarchical follicles, revealing a key transcriptional program governing follicle development in chickens.

卵泡发育是影响家禽产蛋性能的关键因素。卵泡主要由颗粒层细胞和卵泡层细胞组成。然而，人们对TLs的调控作用仍然知之甚少。本研究通过转录组分析，探讨了鸡小黄卵泡（SYFT）、最小分层卵泡（F6T）和最大分层卵泡（F1T）的TLs中差异表达基因（DEGs）的丰度。结果显示，最高丰度的deg与胆固醇代谢（MSMO1, NPC1）和类固醇激素合成（STAR, CYP11A1, CYP19A1， POR, NR0B1）有关。值得注意的是，参与类固醇激素合成的基因（STAR、CYP11A1和CYP19A1）在F6T阶段高度表达。F6T中deg的上调主要富集在代谢途径中，包括叶酸和柠檬酸循环的碳库，这有助于提高该阶段的胆固醇合成（MSMO1）。而胆固醇代谢（NPC1， NR0B1和POR）在SYFT阶段表现突出，其中上调的deg与细胞分化（如Wnt和mTOR信号通路）有关。关键基因CYP19A1、CYP17A1、POR、NPC1、VLDLR和NR0B1主要出现在图谱3和1中，通过趋势分析发现了显著的趋势。KEGG的主要途径包括细胞周期、同源重组、代谢和转运。本研究强调，TLs将其转录程序从黄色小卵泡中的胆固醇转运转移到等级卵泡中的胆固醇合成和类固醇生成，揭示了控制鸡卵泡发育的关键转录程序。

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引用次数: 0

The metabolome of humpback whales (Megaptera novaeangliae) reveals clues as to their extreme fasting capabilities 座头鲸（Megaptera novaeangliae）的代谢组揭示了它们极端禁食能力的线索

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-11-03 DOI: 10.1016/j.cbd.2025.101670

Erika Oteri , Ido Bar , Steven D. Melvin , Eleanor Raffan , Susan Bengtson Nash

Southern Hemisphere humpback whales are capital breeders, relying on energy reserves accumulated through summer feeding in the Southern Ocean to fuel reproduction and migration. Understanding the fasting physiology of these populations, which lose up to 50 % of their post-summer feeding body mass during seasonal migration, is of great importance, particularly in the context of a rapidly changing Antarctic sea-ice ecosystem. Additionally, fluctuations in lipid reserves are known to mobilise lipophilic contaminants, potentially rendering seasonal fasting a time of elevated toxicological risk. This study analysed blubber biopsies from humpback whales migrating along the east coast of Australia. Biopsies were collected at two timepoints on the migration, corresponding to ∼3 and 6 months fasted, respectively. Nuclear Magnetic Resonance spectroscopy identified 32 polar metabolites in blubber, mainly involved in fatty acid and amino acid metabolism. Eleven of these metabolites showed significant differences between the two fasting stages, indicating changes in fatty acid oxidation, body condition, protein catabolism and glucose conservation. This is the first study to investigate the polar metabolomic alterations associated with migration in humpback whales, providing insights into biochemical pathways related to their fasting physiology. Metabolomic analysis holds the potential to identify metabolite patterns linked to nutritional and environmental stress, critical for ongoing biomonitoring of the Antarctic ecosystem.

南半球座头鲸是重要的繁殖者，依靠夏季在南大洋觅食积累的能量储备来繁殖和迁徙。了解这些种群的禁食生理是非常重要的，特别是在南极海冰生态系统迅速变化的背景下，这些种群在夏季后的摄食体重在季节性迁徙期间损失高达50%。此外，已知脂质储备的波动会调动亲脂污染物，可能使季节性禁食成为毒性风险升高的时间。这项研究分析了沿澳大利亚东海岸迁徙的座头鲸的鲸脂活检。在迁移的两个时间点采集活检，分别对应于禁食3个月和6个月。核磁共振波谱鉴定出鲸脂中32种极性代谢产物，主要参与脂肪酸和氨基酸代谢。其中11种代谢物在两个禁食阶段表现出显著差异，表明脂肪酸氧化、身体状况、蛋白质分解代谢和葡萄糖保存的变化。这是第一个研究与座头鲸迁移相关的极地代谢组学改变的研究，为其禁食生理学相关的生化途径提供了见解。代谢组学分析具有识别与营养和环境压力相关的代谢物模式的潜力，这对正在进行的南极生态系统生物监测至关重要。

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引用次数: 0

Transcriptomic analysis of the hepatopancreas response to low-pH stress in kuruma shrimp (Marsupenaeus japonicus) 日本袋虾肝胰腺对低ph胁迫响应的转录组学分析

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-11-01 DOI: 10.1016/j.cbd.2025.101667

Yongkang Hou , Caifeng Liang , Dekhkonova Dilorakhon Rasuljon Kizi , Jianyong Liu

Ocean acidification has emerged as a globally recognized environmental issue, posing a serious threat to marine ecosystems. To elucidate the adaptive mechanisms of Marsupenaeus japonicus under acidified conditions, both biochemical and transcriptomic analyses were performed following low-pH exposure. Biochemical assays revealed that low pH stress significantly SOD and CAT activities while markedly elevating MDA levels, indicating oxidative damage. T-AOC exhibited a transient rise followed by a sharp decline at later stages, suggesting initial activation and subsequent exhaustion of antioxidant defense. Transcriptomic profiling identified 2705 DEGs that were primarily enriched in pathways related to immune regulation, redox balance, apoptosis, and energy metabolism, including the lysosome, Toll-like receptor, and PPAR signaling pathways. Protein interaction analysis identified 9 hub genes, including NADH-GOGAT and MDHM, which may play key roles in antioxidant defense and metabolic regulation. The integration of enzyme activity and transcriptomic data indicates that acid stress initially induces oxidative imbalance, followed by compensatory activation of antioxidant and immune systems to restore cellular homeostasis. These findings provide comprehensive insights into the oxidative stress adaptation of M. japonicus and offer a genetic and physiological foundation for breeding acid-tolerant shrimp strains.

海洋酸化已成为全球公认的环境问题，对海洋生态系统构成严重威胁。为了阐明日本袋猴在酸化条件下的适应机制，在低ph条件下进行了生化和转录组学分析。生化分析显示，低pH胁迫显著提高SOD和CAT活性，同时显著升高MDA水平，提示氧化损伤。T-AOC表现出短暂的上升，随后在后期急剧下降，表明初始激活和随后的抗氧化防御耗尽。转录组学分析鉴定了2705个主要富集于免疫调节、氧化还原平衡、细胞凋亡和能量代谢相关通路的deg，包括溶酶体、toll样受体和PPAR信号通路。蛋白质互作分析鉴定出包括NADH-GOGAT和MDHM在内的9个枢纽基因，它们可能在抗氧化防御和代谢调节中发挥关键作用。酶活性和转录组学数据的整合表明，酸胁迫最初诱导氧化失衡，随后补偿性激活抗氧化和免疫系统以恢复细胞稳态。这些发现为日本对虾对氧化应激的适应提供了全面的认识，并为耐酸对虾品系的选育提供了遗传和生理基础。

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引用次数: 0

Identification and expression analysis of long noncoding RNAs in response to infection with VHSV in rainbow trout 虹鳟鱼VHSV感染应答长链非编码rna的鉴定与表达分析。

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-11-01 DOI: 10.1016/j.cbd.2025.101673

Mahmood Tavakoli-Alamouti , Ghodrat Rahimi-Mianji , Ardeshir Nejati-Javaremi , Ayoub Farhadi , Elham Younesi-Melerdi

Viral infections in the aquaculture industry present a significant challenge that requires further investigation. Emerging evidence suggests that long noncoding RNAs (lncRNAs) play a crucial role in regulating various biological processes, including immune responses. However, most studies have focused on model organisms, leaving a gap in knowledge about non-coding RNAs in response to viral hemorrhagic septicemia (VHS) in rainbow trout. In this study, we investigated the profile of non-coding RNAs (ncRNAs) and their targeting-related subjects in the spleen of rainbow trout challenged with the VHS virus. We explored their potential roles in immune defense responses through transcriptomic analysis of both virus-treated and control groups. Our analysis identified 4207 lncRNAs from 7753 transcripts, with many categorized as potentially novel isoforms (code = j) and intergenic lncRNAs (code = u). The expression analysis demonstrated the impact of viral infection on the expression levels of lncRNAs and their target genes. The results showed 182 lncRNAs and 1326 mRNAs with differential expression. We identified pairs of DElncRNA-DEmRNA interactions, such as “TP63-MSTRG.62, IL10-MSTRG.9783, IL10-MSTRG.9784, TK1-MSTRG.22826, and GLI1-MSTRG.17881” as cis interactions, while DOCK10-MSTRG.30015, MSTRG.36357-LOC101268921, and MSTRG.34190-ENPP2 exhibited trans interactions. Additionally, key signaling pathways, including the PPAR signaling pathway, Toll-like receptor signaling pathway, and p53 pathway, were revealed as critical responders to viral infection linked to lncRNAs. We also introduced quantitative trait loci (QTLs) associated with these lncRNAs, underscoring their potential regulatory roles in viral stress responses. Overall, our findings provide novel insights into the molecular mechanisms underlying viral infections and lncRNA-mediated host immune responses.

水产养殖业中的病毒感染是一项重大挑战，需要进一步调查。越来越多的证据表明，长链非编码rna （lncRNAs）在调节包括免疫应答在内的各种生物过程中起着至关重要的作用。然而，大多数研究都集中在模式生物上，对虹鳟鱼病毒性出血性败血症（VHS）的非编码rna反应的认识存在空白。在这项研究中，我们研究了VHS病毒攻击虹鳟鱼脾脏中的非编码rna （ncRNAs）及其靶向相关主体的谱图。我们通过对病毒处理组和对照组的转录组分析，探索了它们在免疫防御反应中的潜在作用。我们的分析从7753个转录本中鉴定出4207个lncrna，其中许多被归类为潜在的新亚型（代码= j）和基因间lncrna（代码= u）。表达分析证实了病毒感染对lncrna及其靶基因表达水平的影响。结果显示182个lncrna和1326个mrna存在差异表达。我们鉴定了DElncRNA-DEmRNA相互作用对，如“TP63-MSTRG”。62年,IL10-MSTRG。9783年,IL10-MSTRG。9784年,TK1-MSTRG。GLI1-MSTRG。作为cis相互作用，而DOCK10-MSTRG。30015、MSTRG.36357-LOC101268921和MSTRG.34190-ENPP2表现出反式相互作用。此外，关键的信号通路，包括PPAR信号通路、toll样受体信号通路和p53信号通路，被发现是与lncRNAs相关的病毒感染的关键应答者。我们还介绍了与这些lncrna相关的数量性状位点（qtl），强调了它们在病毒应激反应中的潜在调节作用。总的来说，我们的发现为病毒感染和lncrna介导的宿主免疫反应的分子机制提供了新的见解。

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引用次数: 0

Gut microbiota composition and antibiotic resistance ontology landscape in Micropterus salmoides: Insights from metagenomic and metabolomic analyses 沙尾小虾肠道菌群组成和抗生素耐药性本体景观：来自宏基因组学和代谢组学分析的见解。

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-10-31 DOI: 10.1016/j.cbd.2025.101666

Gang Zhou , Ying-Si Wang , Gui-Fang Zhang, Shu-Yao Zhang, Xia Wen, Zong-Bin Cui, Qing-Shan Shi, Xiao-Bao Xie

Micropterus salmoides, a pivotal aquaculture species in China, faces critical challenges including high disease susceptibility and insufficient characterization of gut microbiota-associated antibiotic resistance ontology (ARO). This study integrated metagenomic and metabolomic approaches to systematically characterize the compositional dynamics, diversity patterns, and spatiotemporal distribution of gut microbiota and AROs in M. salmoides across four developmental stages, while clarifying their interactions with metabolic pathways. Metagenomic profiling identified Proteobacteria, Firmicutes, and Fusobacteria as the dominant bacterial phyla, with Acinetobacter baumannii and Alcanivorax profundi exhibiting stage-specific abundance patterns. A total of 150 distinct ARO subtypes were identified, among which tetracycline- and glycopeptide-resistance genes (e.g., tetA and vanR) showing high abundance, with their resistance primarily mediated by efflux-driven mechanisms. Untargeted metabolomics uncovered 4459 metabolites, with robust correlations observed between core microbial genera (e.g., Flavobacterium and Herbaspirillum) and lipid/amino acid metabolic pathways. Co-occurrence network analysis further demonstrated significant interconnections between ARO subtypes and lineages of Proteobacteria/Firmicutes. Our multi-omics framework provides comprehensive insights into the gut microbiota-ARO-metabolism nexus in M. salmoides, thereby establishing a correlative framework for developing precision interventions to control the dissemination of antimicrobial resistance and improve disease management in sustainable aquaculture systems.

salmoides微翼鱼（Micropterus salmoides）是中国重要的水产养殖物种，面临着疾病易感性高、肠道菌群相关抗生素耐药性本体（ARO）表征不足等严峻挑战。本研究结合宏基因组学和代谢组学方法，系统表征了沙门沙门肠道微生物群和AROs在四个发育阶段的组成动态、多样性模式和时空分布，同时阐明了它们与代谢途径的相互作用。宏基因组分析鉴定出变形菌门、厚壁菌门和梭杆菌门是主要的细菌门，鲍曼不动杆菌和深铝菌门表现出特定阶段的丰度模式。共鉴定出150种不同的ARO亚型，其中四环素和糖肽耐药基因（如tetA和vanR）表现出高丰度，其耐药主要由外排驱动机制介导。非靶向代谢组学发现了4459种代谢物，在核心微生物属（如黄杆菌和Herbaspirillum）和脂质/氨基酸代谢途径之间观察到强大的相关性。共现网络分析进一步证明了ARO亚型与变形菌门/厚壁菌门谱系之间的显著相互联系。我们的多组学框架提供了salmoides肠道微生物- aro代谢关系的全面见解，从而为开发精确干预措施以控制抗菌素耐药性传播和改善可持续水产养殖系统中的疾病管理建立了相关框架。

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引用次数: 0

Hydrolyzed Debaryomyces hansenii yeasts as paraprobiotics in fish: Omics-based characterization of Atlantic salmon gut during a natural pathogen outbreak in seawater stage 水解的汉氏Debaryomyces hansenii酵母作为鱼类的副益生菌：大西洋鲑鱼肠道在海水阶段自然病原体爆发期间的组学特征。

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-10-30 DOI: 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.

饲料添加剂是在养殖条件下改善鱼类生产性能和健康（不影响生长）的一种替代方法。为了确定两种水解的汉氏德巴酵母（LAN4和LAN6）对大西洋鲑鱼（Salmo salar）幼鱼肠道的生理影响，在淡水和海水中分别添加0.1%的LAN4或LAN6，进行了7周和6周的体内实验。巧合的是，第5周在海水中报告了粘森氏菌（一种鱼类细菌病原体）的自然暴发。因此，目前的研究重点包括肠道蛋白质组和微生物群组成的疾病介导调节，分别通过宏蛋白质组学和16S rRNA测序进行估计。结果显示，共检测到52属的扩增子序列变异（asv） 1170个。此外，通过asv分析发现LAN4与对照组（Ctr）呈正相关。关于宏蛋白质组学数据和富集分析（使用KEGG或GO数据库），LAN4组显示出与48个功能术语相关的蛋白质丰度更高，如氨基酸生物合成和代谢、免疫稳态和细胞对氧化应激的反应。相反，LAN6中检测到的蛋白质与14个可能与炎症过程相关的术语（例如，铁下垂，花生四烯酸代谢和细胞投射组装的调节）有关。这些结果表明，汉氏酵母有潜力作为大西洋鲑鱼肠道蛋白质组和微生物群结构的副益生菌。因此，在生产周期中，汉氏菌是一种很有前途的水产养殖相关物种的饲料添加剂。

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引用次数: 0

Transcriptomic and physiological responses of rainbow trout (Oncorhynchus mykiss) gill tissues to hypoxic stress 虹鳟（Oncorhynchus mykiss）鳃组织对缺氧胁迫的转录组学和生理反应。

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-10-30 DOI: 10.1016/j.cbd.2025.101672

Ziyi Zhao, Mengqun Liu, Qiusheng Wang, Haishen Wen, Xin Qi

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.

低氧胁迫对水产养殖生产力构成重大挑战。虹鳟（Oncorhynchus mykiss）作为一种缺氧不耐受物种，其对长时间缺氧的分子和生理适应性有待进一步研究。在这项研究中，我们通过转录组学、组织病理学和生化分析的综合分析，研究了虹鳟鱼鳃细胞缺氧反应的时间动态。暴露于缺氧条件（3% O2） 0、24和48小时的原代鳃细胞表现出活性氧（ROS）水平的逐渐增加。通过RNA测序共鉴定出6744个差异表达基因（DEGs），其中糖酵解/糖异生和氨基酸生物合成途径在24和48 h均显著上调，表明代谢向厌氧能量产生和抗氧化防御转变。相反，类固醇生物合成在48 h时富集，可能支持膜修复和皮质醇介导的应激适应，而凋亡在24 h时从抑制转变为48 h时的激活，与不可逆的细胞损伤相关。加权基因共表达网络分析（Weighted Gene Co-expression Network Analysis， WGCNA）发现了与48小时缺氧最相关的模块，该模块也在这四条通路中富集。组织病理学和生理指标也证实了组织在缺氧胁迫下的时间依赖性变化。这些结果表明，在缺氧早期（24 h），虹鳟鱼的代谢适应，包括糖酵解/糖异生和氨基酸的生物合成，是优先的。然而，缺氧48小时后，诱导代谢适应向凋亡介导的细胞清除过渡，同时类固醇生物合成上调，以减轻持续的氧化损伤。

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引用次数: 0

Brain proteomics of rainbow trout at certain maturation stages: biological insights and fish by-products processing perspectives 虹鳟鱼在某些成熟阶段的脑蛋白质组学：生物学见解和鱼副产品加工的观点。

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-10-28 DOI: 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.

首次对虹鳟Oncorhynchus mykiss （Walbaum, 1792）在两个成熟阶段的脑蛋白质组学特征进行了描述和讨论。成熟和繁殖是鱼类生命周期的关键阶段，但这些阶段背后的生化和形态生理过程尚不清楚。鱼的大脑在成熟过程中发生的反应，调节生殖过程和伴随的代谢变化，是特别有趣的。是一种经济上重要的商业鲑科鱼类，是生物学研究的模式生物。我们分析了虹鳟鱼在性腺发育的不同阶段，包括II-III期（发育）和V期（产卵）的脑蛋白质组学。研究发现，脑蛋白质组在参与脂质代谢、免疫反应、应激反应、细胞结构和卵母细胞发育的蛋白质方面存在差异。这些发现为鱼类成熟过程中的复杂过程提供了有价值的见解，并有助于我们对生殖生物学的理解。展示了不同发育阶段大脑的生化差异，以及商业捕捞的副产品（在这种情况下是头部和大脑）可用于提取抗菌蛋白和肽的事实。

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引用次数: 0

Genome-wide identification and characterization of the HSP gene superfamily in the Ivory Shell (Babylonia areolata) 乳螺热休克蛋白基因超家族的全基因组鉴定与特征分析

IF 2.2 2区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Comparative Biochemistry and Physiology D-Genomics & Proteomics

Pub Date : 2025-10-27 DOI: 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.

热休克蛋白（HSPs）是一种高度保守的分子伴侣蛋白，在生物生长、发育和对环境胁迫的反应中起着重要作用。为了研究热休克蛋白在热胁迫下的功能，利用生物信息学方法在全基因组水平上鉴定了68个BaHsp基因。预测系统发育树、基因结构、染色体定位和蛋白质理化性质，并采用定量实时聚合酶链反应方法（qPCR）分析和表征热胁迫下不同组织中BaHsp基因的表达模式。结果显示，不同BaHsp基因的内含子数量和排列存在显著差异，内含子在26条染色体上分布不均匀。基因重复分析表明，在BaHsp20、BaHsp40和BaHsp90中存在串联重复事件，表明这些事件促进了BaHsp基因家族的扩展和功能多样化。RT-qPCR结果显示BaHsp基因有明显的组织特异性表达，总体表达水平在鳃组织中相对较高。热胁迫下，鳃组织中BaHsp基因的表达随温度升高而升高。时间表达分析进一步表明，大多数基因在热胁迫开始时迅速上调，随后逐渐下降，呈现出“先增加后减少”的动态模式。本研究为进一步研究乳霜小蠊热休克蛋白基因家族对热应激反应的分子机制提供了基础参考。

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引用次数: 0