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学者姓名：刘若愚
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Abstract ：
Pseudomonas plecoglossicida is a pathogen bacterium responsible for visceral white spot disease (VWND) in Large Yellow Croakers (Larimichthys crocea), causing significant economic losses in commercial fish farms. The prolinealanine-alanine-arginine repeats protein (PAAR) is a core component of the spike structure in the type VI secretion system (T6SS), which injects toxic effectors into host and contributes to bacterial virulence. However, the role of the PAAR gene in P. plecoglossicida and its impact on bacterial infection and host immune responses remain unexplored. In this study, PAAR-1 was identified for the first time in P. plecoglossicida as an effector gene within the T6SS-1 gene cluster, which is regulated and secreted by T6SS-1. The P. plecoglossicida mutant strain (z.PAAR-1) and its complementary strain (C-z.PAAR-1) were constructed for subsequent investigation. Compared to the wild-type strain, z.PAAR-1 exhibited reduced biofilm formation, adhesion, total antioxidant capacity, and secretion of T6SS core protein Hcp-1. In vitro, z.PAAR-1 showed decreased survival rates in Large Yellow Croaker macrophage cell line (LYC-FM) due to impaired oxidative stress tolerance. In vivo, infection with z.PAAR-1 led to a significant reduction in mortality, bacterial colonization, and the formation of spleen nodules in Large Yellow Croakers. Comparative transcriptome analysis revealed that PAAR-1 predominantly influences the host Toll-like receptor (TLR) signaling pathway and apoptosis by upregulating the expression of plasma membrane-associated TLRs, including TLR1, TLR2, and TLR5, while downregulating the expression of endosomal TLRs like TLR3, TLR7, TLR8, and TLR9, along with its downstream molecules such as MyD88 and TRAF3. Additionally, knockout PAAR1 downregulates apoptosis-related genes including AP-1, NF-kappa B, FAS-L TNF alpha, Caspase8, and FAS-L. Real-time quantitative polymerase chain reaction (RT-qPCR) further confirmed these findings. Furthermore, the proportion of apoptotic cells was significantly lower in the z.PAAR-1 infected LYC-PKM cells. These results indicate that PAAR-1 is involved in regulating TLR signaling pathway and apoptosis in Large Yellow Croaker. This study provides the first identification of the core T6SS-1 gene PAAR-1 in P. plecoglossicida, offering valuable insights into its pathogenic mechanisms and presenting a potential target for attenuated vaccine development.
Keyword ：
Immune response Immune response Large yellow croaker Large yellow croaker PAAR-1 PAAR-1 Pathogenicity Pathogenicity Pseudomonas plecoglossicida Pseudomonas plecoglossicida
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| GB/T 7714 | Zhang, Baoyu , Li, Youshen , Li, Jianxin et al. Identification and characterization of the PAAR-1 gene in Pseudomonas plecoglossicida: Insights into bacterial phenotypes and host immune responses in Large Yellow Croaker (Larimichthys crocea) [J]. | AQUACULTURE , 2026 , 610 . |
| MLA | Zhang, Baoyu et al. "Identification and characterization of the PAAR-1 gene in Pseudomonas plecoglossicida: Insights into bacterial phenotypes and host immune responses in Large Yellow Croaker (Larimichthys crocea)" . | AQUACULTURE 610 (2026) . |
| APA | Zhang, Baoyu , Li, Youshen , Li, Jianxin , Zhai, Yu , Meng, Ziyu , Huang, Xiyue et al. Identification and characterization of the PAAR-1 gene in Pseudomonas plecoglossicida: Insights into bacterial phenotypes and host immune responses in Large Yellow Croaker (Larimichthys crocea) . | AQUACULTURE , 2026 , 610 . |
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Antifreeze proteins (AFPs) are crucial for enhancing an organism's ability to adapt to low temperatures, with broad applications in medicine, frozen food storage and processing, aquaculture, and agriculture. The accurate identification of AFPs is a prerequisite for their utilization, but the high structural and sequence heterogeneity among different AFPs has made their identification a challenging task. To improve AFP prediction performance and enable classification of different AFP types, we propose a novel deep learning-based prediction model, BERT-DomainAFP. Firstly, we integrated existing AFP data using a novel annotation strategy to establish the AntiFreezeDomains dataset. This dataset was then used to train the pre-trained ProteinBERT model, resulting in the development of the BERT-DomainAFP model for AFP prediction. Secondly, for handling of the unbalanced datasets, our BERT-DomainAFP model innovates employing oversampling and undersampling techniques. This ensures the model can fully learn the features of various data types during training and maintain high predictive ability even on more unbalanced datasets. Most importantly, Structural domain annotations are used as training labels, which enables the model to not only accurate predict the presence of AFPs (with an accuracy 98.48%, the highest among existing models), but also classify different types of AFPs based on their unique structural domain features. In summary, our proposed BERT-DomainAFP model not only outperforms existing models in AFP recognition but also supports the classification of different AFP types, offering a promising recognition and classification tool for advancing AFP research and related applications. © 2024, The Authors. All rights reserved.
Keyword ：
Food storage Food storage Prediction models Prediction models
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| GB/T 7714 | Chen, Shengzhen , Zheng, Ping , Zheng, Lele et al. BERT-DomainAFP: Antifreeze Protein Recognition and Classification Model Based on BERT and Structural Domain Annotation [J]. | SSRN , 2025 . |
| MLA | Chen, Shengzhen et al. "BERT-DomainAFP: Antifreeze Protein Recognition and Classification Model Based on BERT and Structural Domain Annotation" . | SSRN (2025) . |
| APA | Chen, Shengzhen , Zheng, Ping , Zheng, Lele , Yao, Qinglong , Meng, Ziyu , Lin, Longshan et al. BERT-DomainAFP: Antifreeze Protein Recognition and Classification Model Based on BERT and Structural Domain Annotation . | SSRN , 2025 . |
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Clinacanthus nutans is a valuable traditional medicinal plant that contains enriched active compounds such as triterpenoids and flavonoids. Understanding the accuulation process of these secondary metabolites in C. nutans requires exploring gene expression regulation under abiotic stresses and hormonal stimuli. qRT-PCR is a powerful method for gene expression analysis, with the selection of suitable reference genes being paramount. However, reports on stably expressed reference genes in C. nutans and even across the entire family Acanthaceae are limited. In this study, we evaluated the expression stability of 12 candidate reference genes (CnUBQ, CnRPL, CnRPS, CnPTB1, CnTIP41, CnACT, CnUBC, CnGAPDH, Cn18S, CnCYP, CnEF1 alpha, and CnTUB) in C. nutans across different tissues and under abiotic stresses and MeJA treatment using three programs (geNorm, NormFinder, and BestKeeper). The integrated ranking results indicated that CnUBC, CnRPL, and CnCYP were the most stably expressed genes across different tissues. Under abiotic stress conditions, CnUBC, CnRPL, and CnEF1 alpha were the most stable, while under MeJA treatment, CnRPL, CnEF1 alpha, and CnGAPDH exhibited the highest stability. Additionally, CnRPL, CnUBC, and CnEF1 alpha were the most stable reference genes across all tested samples, whereas CnGAPDH was the least stable. CnRPL, consistently ranking among the top three most stable genes, may therefore serve as an ideal reference gene for qRT-PCR analysis in C. nutans. To further validate the selected reference genes, we assessed the expression of two key biosynthetic genes, CnPAL and CnHMGR. The results confirmed that using the most stable reference genes yielded expression patterns consistent with biological expectations, while using unstable reference genes led to significant deviations. These findings offer valuable insights for accurately quantifying target genes via qRT-PCR in C. nutans, facilitating investigations into the mechanisms underlying active compound accumulation.
Keyword ：
Clinacanthus nutans Clinacanthus nutans molecular biology techniques molecular biology techniques plant stress response plant stress response quantitative real-time PCR quantitative real-time PCR reference genes reference genes
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| GB/T 7714 | An, Chang , Lu, Lin , Yao, Yixin et al. Selection and Validation of Reference Genes in Clinacanthus nutans Under Abiotic Stresses, MeJA Treatment, and in Different Tissues [J]. | INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES , 2025 , 26 (6) . |
| MLA | An, Chang et al. "Selection and Validation of Reference Genes in Clinacanthus nutans Under Abiotic Stresses, MeJA Treatment, and in Different Tissues" . | INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 26 . 6 (2025) . |
| APA | An, Chang , Lu, Lin , Yao, Yixin , Liu, Ruoyu , Cheng, Yan , Lin, Yanxiang et al. Selection and Validation of Reference Genes in Clinacanthus nutans Under Abiotic Stresses, MeJA Treatment, and in Different Tissues . | INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES , 2025 , 26 (6) . |
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C-type lectins (CTLs), a vital group of soluble pattern recognition receptors (PRRs), are essential to the shrimp's innate immune system. However, little is known about the CTLs composed of a C-type lectin domain (CTLD) and another domain. In this study, a novel C-type lectin containing a leucine-rich repeat (LRR) domain, designated LRRCTL, was identified in Penaeus vannamei and found to exhibit immune regulatory functions. First, LRRCTL expression was highest in the hepatopancreas. The mRNA expression levels of LRRCTL showed a significant upregulation under the different stimuli, including Vibrio parahaemolyticus, Staphylococcus aureus, Aspergillus niger, Lipopolysaccharide (LPS). Second, knockdown of the expression of LRRCTL increased the bacterial load of V. parahaemolyticus, whereas injection of rLRRCTL or r triangle LRR-LRRCTL recombinant proteins enhanced the survival rate of V. parahaemolyticus-infected shrimp. Additionally, the knockdown of LRRCTL expression reduced the mRNA level of multiple immune-related genes, encompassing both immune signaling components and antimicrobial peptide genes, suggesting an important role in immune regulation. Our findings reveal that LRRCTL is essential for regulating humoral immune responses, particularly antimicrobial peptide production, against V. parahaemolyticus infection. The findings provide a theoretical foundation for further investigation into the functional mechanisms of composite CTLs in shrimp innate immunity and potential molecular targets for developing strategies to prevent and control shrimp diseases.
Keyword ：
Immune regulatory Immune regulatory LRRCTL LRRCTL Penaeus vannamei Penaeus vannamei Vibrio parahaemolyticus Vibrio parahaemolyticus
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| GB/T 7714 | Weng, Kejia , Liu, Ruoyu , Xiong, Chengqi et al. A novel LRR domain-containing C-type lectin gene with immune regulatory functions protects Penaeus vannamei against Vibrio parahaemolyticus infection [J]. | FISH & SHELLFISH IMMUNOLOGY , 2025 , 165 . |
| MLA | Weng, Kejia et al. "A novel LRR domain-containing C-type lectin gene with immune regulatory functions protects Penaeus vannamei against Vibrio parahaemolyticus infection" . | FISH & SHELLFISH IMMUNOLOGY 165 (2025) . |
| APA | Weng, Kejia , Liu, Ruoyu , Xiong, Chengqi , Shi, Yuxin , Chen, Wenqian , Wang, Chuanqi et al. A novel LRR domain-containing C-type lectin gene with immune regulatory functions protects Penaeus vannamei against Vibrio parahaemolyticus infection . | FISH & SHELLFISH IMMUNOLOGY , 2025 , 165 . |
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BackgroundPineapple (Ananas comosus L.), an economically significant tropical fruit crop, is highly susceptible to low-temperature during cultivation. The abscisic acid (ABA) and stress-inducible HVA22 gene family is known to play important roles in growth regulation and abiotic stress response, but its functions in pineapple remain unclear.ResultsWe identified 11 HVA22 genes (AcHVA22A - AcHVA22K) in the pineapple genome and grouped them into four phylogenetic clades. Expression analysis showed that most AcHVA22 genes displayed tissue- or developmental stage-specific expression patterns, suggesting their diverse functions in pineapple growth and development. Subcellular localization analyses revealed diverse localizations of AcHVA22 proteins, including plasma membrane, cytoplasm, and nucleus. And regulatory predictions indicated control by multiple cis-elements, transcription factors, and miRNAs, which may contribute to their functional diversification. Most AcHVA22 genes responded consistently to ABA, GA, and drought treatments, but their responses to high and low-temperatures varied. Notably, AcHVA22C/D/E/G/I/K were up-regulated under both short- and long-term cold treatments in two different pineapple varieties, highlighting their potential key roles in cold stress tolerance.ConclusionsThis study provided the first genome-wide characterization of the HVA22 gene family in pineapple. The identification of candidate genes involved in cold stress response offers new insights into HVA22 functions in tropical fruits and provides valuable resources for improving cold resistance in pineapple breeding.
Keyword ：
Cold response Cold response Expression profiling Expression profiling HVA22 genes HVA22 genes Pineapple Pineapple Tissue-specific Tissue-specific
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| GB/T 7714 | Hou, Zhimin , Cai, Xinkai , Wu, Jiahao et al. Identification and characterization of HVA22 genes in pineapple (Ananas comosus L.) revealed their potential roles in development regulation and cold stress response [J]. | BMC PLANT BIOLOGY , 2025 , 25 (1) . |
| MLA | Hou, Zhimin et al. "Identification and characterization of HVA22 genes in pineapple (Ananas comosus L.) revealed their potential roles in development regulation and cold stress response" . | BMC PLANT BIOLOGY 25 . 1 (2025) . |
| APA | Hou, Zhimin , Cai, Xinkai , Wu, Jiahao , Lu, Lin , Liu, Chaojia , Zhang, Yangmei et al. Identification and characterization of HVA22 genes in pineapple (Ananas comosus L.) revealed their potential roles in development regulation and cold stress response . | BMC PLANT BIOLOGY , 2025 , 25 (1) . |
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Understanding the metabolic characteristics of pineapple varieties is crucial for market expansion and diversity. This study performed comparative metabolomic analysis on the "Comte de Paris" (BL) and three Taiwan-introduced varieties: "Tainong No. 11" (XS), "Tainong No. 23" (MG), and "Tainong No. 13" (DM). A total of 551 metabolites were identified across the four varieties, with 231 metabolites exhibiting no significant differences between all varieties. This included major sugars such as sucrose, glucose, and fructose, as well as key acids like citric, malic, and quinic acids, indicating that the in-season maturing fruits of different pineapple varieties can all achieve good sugar-acid accumulation under suitable conditions. The differentially accumulated metabolites (DAMs) that were identified among the four varieties all primarily belonged to several major subclasses, including phenolic acids, flavonoids, amino acids and derivatives, and alkaloids, but the preferentially accumulated metabolites in each variety varied greatly. Specifically, branched-chain amino acids (L-leucine, L-isoleucine, and L-valine) and many DAMs in the flavonoid, phenolic acid, lignan, and coumarin categories were most abundant in MG, which might contribute to its distinct and enriched flavor and nutritional value. XS, meanwhile, exhibited a notable accumulation of aromatic amino acids (L-phenylalanine, L-tryptophan), various phenolic acids, and many lignans and coumarins, which may be related to its unique flavor profile. In DM, the dominant accumulation of jasmonic acid might contribute to its greater adaptability to low temperatures during autumn and winter, allowing off-season fruits to maintain good quality. The main cultivar BL exhibited the highest accumulation of L-ascorbic acid and many relatively abundant flavonoids, making it a good choice for antioxidant benefits. These findings offer valuable insights for promoting different varieties and advancing metabolome-based pineapple improvement programs.
Keyword ：
comparative analysis comparative analysis fruit quality fruit quality metabolome metabolome pineapple pineapple
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| GB/T 7714 | Zheng, Ping , Wu, Jiahao , Li, Denglin et al. Comparative Metabolomics Analysis of Four Pineapple (Ananas comosus L. Merr) Varieties with Different Fruit Quality [J]. | PLANTS-BASEL , 2025 , 14 (15) . |
| MLA | Zheng, Ping et al. "Comparative Metabolomics Analysis of Four Pineapple (Ananas comosus L. Merr) Varieties with Different Fruit Quality" . | PLANTS-BASEL 14 . 15 (2025) . |
| APA | Zheng, Ping , Wu, Jiahao , Li, Denglin , Xie, Shiyu , Cai, Xinkai , Xiao, Qiang et al. Comparative Metabolomics Analysis of Four Pineapple (Ananas comosus L. Merr) Varieties with Different Fruit Quality . | PLANTS-BASEL , 2025 , 14 (15) . |
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Anisarchus medius (Reinhardt, 1837) is a widely distributed Arctic fish, serving as an indicator of climate change impacts on coastal Arctic ecosystems. This study presents a chromosome-level genome assembly for A. medius using PacBio sequencing and Hi-C technology. The PacBio assembly totaled 739.07 Mb across 697 contigs, with a Contig N50 of 10.004 Mb. Hi-C mapping yielded 23 chromosomes, with a successful mapping rate of 90.53% and a Scaffold N50 of 30.20 Mb. Genome BUSCO integrity was 97.05%. Repetitive sequences accounted for 240.83 Mb (32.58%) of the genome. Non-coding RNA annotations included 4,928 rRNAs, 9,663 tRNAs, 347 snRNAs, and 21 snoRNAs. A total of 30,345 protein-coding genes were identified, encoding 46,603 proteins, with a BUSCO completeness of 94.98%. Molecular pathway related to the endocrine system, carbohydrate metabolism, folding, sorting, and degradation, signal transduction, and transport and catabolism contribute to A. medius adaptation to extreme Arctic environments. This high-quality genome provides valuable genetic resources for understanding Arctic adaptations and supporting polar ecological conservation and management.
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| GB/T 7714 | Liu, Ruoyu , Meng, Ziyu , Mu, Yinan et al. Chromosome-level reference genome and annotation of the Arctic fish Anisarchus medius [J]. | SCIENTIFIC DATA , 2025 , 12 (1) . |
| MLA | Liu, Ruoyu et al. "Chromosome-level reference genome and annotation of the Arctic fish Anisarchus medius" . | SCIENTIFIC DATA 12 . 1 (2025) . |
| APA | Liu, Ruoyu , Meng, Ziyu , Mu, Yinan , Zhang, Ran , Ma, Hanhui , Hu, Jingjing et al. Chromosome-level reference genome and annotation of the Arctic fish Anisarchus medius . | SCIENTIFIC DATA , 2025 , 12 (1) . |
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本发明公开一种基于迁移学习的抗冻蛋白分型预测方法，属于生物信息技术领域。本发明方法包括：收集已经过结构域注释的抗冻蛋白和非抗冻蛋白序列作为正负数据集；采取过采样和欠采样方法进行数据平衡；选择ProteinBert模型对抗冻蛋白序列数据集进行训练，使抗冻蛋白序列与结构域标签之间形成对应关系，以构建BERT‑DomainAFP模型；将待鉴定蛋白序列数据输入BERT‑DomainAFP模型中进行预测，得到对应的结构域预测值；设定目标数据标签，若BERT‑DomainAFP模型输出的结构域预测值与目标数据标签相同，则判定待鉴定的蛋白序列中存在抗冻蛋白序列结构域。本发明的模型特征提取能力强，能够自动从蛋白质序列中提取出复杂的特征信息，对抗冻蛋白预测的准确率高、特异性好、灵敏度高、预测精度高。
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| GB/T 7714 | 刘若愚 , 陈盛圳 , 陈新华 et al. 一种基于迁移学习的抗冻蛋白分型预测方法 : CN202410678242.X[P]. | 2024-05-29 . |
| MLA | 刘若愚 et al. "一种基于迁移学习的抗冻蛋白分型预测方法" : CN202410678242.X. | 2024-05-29 . |
| APA | 刘若愚 , 陈盛圳 , 陈新华 , 郑平 , 孟子钰 . 一种基于迁移学习的抗冻蛋白分型预测方法 : CN202410678242.X. | 2024-05-29 . |
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Background Glehnia littoralis F. Schmidt ex Miq., an endangered plant species with significant medicinal, edible, and ecological value, is now a central concern for conservation and sustainable utilization. Investigating the physiological and ecological mechanisms leading to its endangerment and elucidating its genetic background constitutes the foundation for conducting in-depth research on G. littoralis. Results Our observations have revealed a significant degree of floral sterility in wild populations of G. littoralis. The inflorescences of G. littoralis are classified into three types: completely fertile, completely sterile, and partially fertile compound umbels. Moreover, the flowers of G. littoralis can be categorized into fertile and sterile types. Sterile flowers exhibited abnormalities in the stigma, ovary, and ovules. This study is the first to discover that the presence or absence of a giant cell at the funiculus during the initiation of ovule primordium determines whether the flower can develop normally, providing cytological evidence for female sterility in G. littoralis. Conversely, both fertile and sterile flowers produced normally developed pollen. Field observations have suggested that robust plants bear more fertile umbels, while weaker ones have fewer or even no fertile umbels, indicating a close relationship between flower fertility and plant nutritional status. Our model correctly predicted that the eastern coastal regions of China, as well as prospective areas in Neimenggu and Sichuan, are suitable environments for its cultivation. Additionally, Using flow cytometry and genome survey, we estimated the genome size of G. littoralis to be 3.06 Gb and the heterozygosity to be 4.58%. Conclusion The observations and findings presented in this study were expected to provide valuable insights for further conserving its genetic resources and sustainable utilization of G. littoralis.
Keyword ：
Flower development Flower development Genomic background Genomic background Glehnia littoralis Glehnia littoralis Suitable growth area Suitable growth area
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| GB/T 7714 | An, Chang , Ye, Kangzhuo , Jiang, Runfa et al. Cytological analysis of flower development, insights into suitable growth area and genomic background: implications for Glehnia littoralis conservation and sustainable utilization [J]. | BMC PLANT BIOLOGY , 2024 , 24 (1) . |
| MLA | An, Chang et al. "Cytological analysis of flower development, insights into suitable growth area and genomic background: implications for Glehnia littoralis conservation and sustainable utilization" . | BMC PLANT BIOLOGY 24 . 1 (2024) . |
| APA | An, Chang , Ye, Kangzhuo , Jiang, Runfa , Chen, Jiayi , Yao, Yixin , Lu, Lin et al. Cytological analysis of flower development, insights into suitable growth area and genomic background: implications for Glehnia littoralis conservation and sustainable utilization . | BMC PLANT BIOLOGY , 2024 , 24 (1) . |
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Passion fruit, an economically valuable fruit crop, is highly vulnerable to adverse climate conditions. The HVA22 genes, recognized as abscisic acid (ABA) and stress-inducible, play vital roles in stress response and growth regulation in diverse eukaryotic organisms. Here, six HVA22 genes were firstly identified in passion fruit genome and all predicted to be localized within the endoplasmic reticulum. Phylogenetic analyses showed that all PeHVA22s were divided into four subgroups. The gene structural features of PeHVA22 genes clustered in the same subgroup were relatively conserved, while the gene structure characteristics of PeHVA22s from different subgroups varied significantly. PeHVA22A and PeHVA22C closely clustered with barley HVA22 in Group II, were also induced by ABA and drought stress treatment, suggesting conserved roles similar to barley HVA22. Meanwhile, most PeHVA22s exhibited induced expression post-drought treatment but were suppressed under salt, low and high-temperature conditions, indicating a unique role in drought response. Additionally, PeHVA22s displayed tissue-specific expression patterns across diverse tissues, except for PeHVA22B which maybe a pseudogene. Notably, PeHVA22C, PeHVA22E, and PeHVA22F predominantly expressed in fruit, indicating their involvement in fruit development. Almost all PeHVA22s showed variable expression at different developmental stages of stamens or ovules, implying their roles in passion fruit's sexual reproduction. The intricate roles of PeHVA22s may result from diverse regulatory factors including transcription factors and CREs related to plant growth and development, hormone and stress responsiveness. These observations highlighted that PeHVA22s might play conserved roles in ABA response and drought stress tolerance, and also be participated in the regulation of passion fruit growth and floral development.
Keyword ：
expression analysis expression analysis floral development floral development HVA22 genes HVA22 genes passion fruit passion fruit phytohormone and stress response phytohormone and stress response
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| GB/T 7714 | Hou, Zhimin , Liang, Jianxiang , Cai, Xinkai et al. PeHVA22 gene family in passion fruit (Passiflora edulis): initial characterization and expression profiling diversity [J]. | FRONTIERS IN PLANT SCIENCE , 2024 , 14 . |
| MLA | Hou, Zhimin et al. "PeHVA22 gene family in passion fruit (Passiflora edulis): initial characterization and expression profiling diversity" . | FRONTIERS IN PLANT SCIENCE 14 (2024) . |
| APA | Hou, Zhimin , Liang, Jianxiang , Cai, Xinkai , Lin, Jingting , Wang, Xiaomei , Liu, Ruoyu et al. PeHVA22 gene family in passion fruit (Passiflora edulis): initial characterization and expression profiling diversity . | FRONTIERS IN PLANT SCIENCE , 2024 , 14 . |
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