Genomics最新文献

英文中文

Molecular insights into temperature-driven color variation in Stropharia rugosoannulata mushrooms.

IF 3.4 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genomics

Pub Date : 2025-03-28 DOI: 10.1016/j.ygeno.2025.111044

Meng Shen, Guoying Lv, Ruisen Wang, Mengyu Wang, Ye Yuan, Xinhua Quan, Xiangtan Yao

Stropharia rugosoannulata is a widely distributed edible mushroom rich in nutrients and bioactive compounds with various pharmacological properties. This study explores the mechanism involved in color variation in S. rugosoannulata mushroom cap under different temperature conditions. Transcriptome analysis revealed the role of cytochrome P450 (CYP) gene family members and the flavonoid biosynthesis pathway in color development. The study found that under low-temperature conditions, the expression of key genes in the flavonoid synthesis pathway was upregulated in red varieties, potentially leading to an accumulation of flavonoids and a change in color. Color changes in yellow varieties were related to genes in the terpenoid synthesis pathway. Gene Set Enrichment Analysis (GSEA) highlighted the role of zeaxanthin epoxidase genes in carotenoid synthesis, affecting color formation and possessing photoprotective and antioxidant functions. Additionally, Weighted correlation network analysis, also known as weighted gene co-expression network analysis (WGCNA) analysis revealed the role of C2H2-type transcription factors in color regulation, which may directly or indirectly regulate the genes responsible for pigment synthesis, influencing mushroom color. These factors may directly or indirectly regulate the genes responsible for pigment synthesis, influencing the mushroom color. This research offers insights into the molecular mechanisms underlying color variation in S. rugosoannulata and establishes a foundation for developing varieties in different colors, which could enhance their market appeal and application value in the food industry.

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引用次数: 0

Resveratrol-stimulated macrophage exosomes delivering lncRNA Snhg6 inhibit liver fibrosis by modulating the NF-κB pathway

IF 3.4 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genomics

Pub Date : 2025-03-25 DOI: 10.1016/j.ygeno.2025.111043

Taicheng Zhang , Jie Jing , Yaodan Liang , Jianming Luo, Dongyu Cheng, Shanyu Qin, Haixing Jiang

Objective

To investigate the role of lncRNA Snhg6 in liver fibrosis, delivered by resveratrol-stimulated macrophage exosomes.

Methods

Resveratrol-stimulated and unstimulated exosomes were generated from RAW 264.7 cells, confirmed by electron microscopy, nanoparticle analysis, and Western blotting. JS1 cells were used as an HSC model, activated with TGF-β1 and treated with exosomes. Exosome uptake was observed via confocal microscopy, and acta2 expression was measured with immunofluorescence. RNA sequencing and RT-qPCR were used to analyze exosomal lncRNA profiles. KEGG GSEA enrichment was conducted on differentially expressed genes, and nf-κb expression was detected in HSCs using WB. Serum from liver fibrosis patients was analyzed for SNHG6 levels.

Results

Resveratrol-stimulated exosomes inhibited TGF-β1-induced HSC activation, with 132 differentially expressed lncRNAs, including upregulated Snhg6. NF-κB signaling was downregulated. Silencing Snhg6 weakened this inhibitory effect.

Conclusion

Resveratrol-stimulated macrophage exosomes may inhibit liver fibrosis by delivering lncRNA Snhg6, which suppresses the NF-κB pathway.

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引用次数: 0

The noncausal association between a loss-of-function CLCN2 variant and childhood absence epilepsy

IF 3.4 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genomics

Pub Date : 2025-03-25 DOI: 10.1016/j.ygeno.2025.111042

Wei Li , Zhijie Wang , Zishan Xu , Xiaoli Zhang , Renjun Gu , Guoyang He

Childhood absence epilepsy (CAE) is a subtype of idiopathic (genetic) generalized epilepsies (IGEs). In this study, four heterozygous variants in CLCN2 were found in 10 CAE patients using whole exome sequencing (WES). We used genetics, bioinformatics, molecular biology, and electrophysiology to study the four variants. Bioinformatics analysis showed that the four variants were probably damaging, and the c.1141C > G (p.Pro381Ala) and c.1885C > T (p.Arg629Cys) variants affected the tertiary structure of the ClC-2 chloride channel. Functional studies showed that the c.1141C > G (p.Pro381Ala) variant significantly reduced the expression of CLCN2 in the plasma membrane, and affected the Cl⁻ currents of ClC-2 chloride channel, indicating that the c.1141C > G (p.Pro381Ala) variant was a loss-of-function mutation. Furthermore, the minor allele frequency (MAF) of the variant was higher than the incidence of CAE. Therefore, we postulated that the c.1141C > G (p.Pro381Ala) variant was noncausal association with CAE. This study was valuable for further exploring the pathogenic variants of CAE.

儿童失神性癫痫（CAE）是特发性（遗传性）全身性癫痫（IGEs）的一种亚型。本研究利用全外显子组测序（WES）在10名CAE患者中发现了CLCN2的四个杂合变异。我们利用遗传学、生物信息学、分子生物学和电生理学对这四个变异进行了研究。生物信息学分析表明，这四个变异体可能具有损伤性，其中c.1141C >G（p.Pro381Ala）和c.1885C >T（p.Arg629Cys）变异体影响了ClC-2氯离子通道的三级结构。功能研究表明，c.1141C > G (p.Pro381Ala)变异显著降低了CLCN2在质膜中的表达，并影响了ClC-2氯离子通道的Cl-电流，表明c.1141C > G (p.Pro381Ala)变异是一个功能缺失突变。此外，该变异的小等位基因频率（MAF）高于 CAE 的发病率。因此，我们推测c.1141C > G (p.Pro381Ala)变异与CAE无因果关系。这项研究对进一步探索CAE的致病变异具有重要价值。

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引用次数: 0

Identification of potential modulators of intrauterine adhesion pathogenesis with RNA sequencing, histology and in vitro assays

IF 3.4 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genomics

Pub Date : 2025-03-25 DOI: 10.1016/j.ygeno.2025.111038

Bao Liu , Mingqian Chen , Yugang Chi , Li-Na Hu

Intrauterine adhesion (IUA), also referred to as intrauterine stenosis or synechiae, is a prevalent gynecological issue, which is characterized by the fusion of the walls of the intrauterine canal. However, the molecular changes during its pathogenesis are still unclear. In the present work, tissue samples from patients with IUA and normal endometrial tissues from healthy subjects were collected, and then RNA sequencing and bioinformatics analyses were performed to screen the differentially expressed genes (DEGs). Subsequently, immunohistochemistry was used for detecting the protein expression level of the representative genes including XDH, VNN1, CD36, and after transfection, enzyme-linked immunosorbent assay and Western blotting were used to evaluate their functions in regulating inflammatory response and the expression level of matrix metalloproteinases. It was revealed that multiple genes were dysregulated in the pathological tissues of patients with IUA, and these DEGs were associated with multiple biological processes and signal pathways including Hedgehog pathway. DEGs including XDH, VNN1, CD36 were also highly expressed in IUA tissues at protein level, and their expression levels correlated with the expression levels of inflammation mediators NLRP3 and STING. XHD, VNN1 and CD36 also promoted the expression and secretion of TNF-α, IL-1β and IL-6 in ishikawa cells, and up-regulated the expression level of MMP-2 and MMP-9. Collectively, our data suggested that Hedgehog signaling is a potential crucial pathway in IUA pathogenesis, and some DEGs contribute to endometrial fibrosis by regulating inflammatory response and matrix remodeling.

{"title":"Identification of potential modulators of intrauterine adhesion pathogenesis with RNA sequencing, histology and in vitro assays","authors":"Bao Liu , Mingqian Chen , Yugang Chi , Li-Na Hu","doi":"10.1016/j.ygeno.2025.111038","DOIUrl":"10.1016/j.ygeno.2025.111038","url":null,"abstract":"<div><div>Intrauterine adhesion (IUA), also referred to as intrauterine stenosis or synechiae, is a prevalent gynecological issue, which is characterized by the fusion of the walls of the intrauterine canal. However, the molecular changes during its pathogenesis are still unclear. In the present work, tissue samples from patients with IUA and normal endometrial tissues from healthy subjects were collected, and then RNA sequencing and bioinformatics analyses were performed to screen the differentially expressed genes (DEGs). Subsequently, immunohistochemistry was used for detecting the protein expression level of the representative genes including XDH, VNN1, CD36, and after transfection, enzyme-linked immunosorbent assay and Western blotting were used to evaluate their functions in regulating inflammatory response and the expression level of matrix metalloproteinases. It was revealed that multiple genes were dysregulated in the pathological tissues of patients with IUA, and these DEGs were associated with multiple biological processes and signal pathways including Hedgehog pathway. DEGs including XDH, VNN1, CD36 were also highly expressed in IUA tissues at protein level, and their expression levels correlated with the expression levels of inflammation mediators NLRP3 and STING. XHD, VNN1 and CD36 also promoted the expression and secretion of TNF-α, IL-1β and IL-6 in ishikawa cells, and up-regulated the expression level of MMP-2 and MMP-9. Collectively, our data suggested that Hedgehog signaling is a potential crucial pathway in IUA pathogenesis, and some DEGs contribute to endometrial fibrosis by regulating inflammatory response and matrix remodeling.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 3","pages":"Article 111038"},"PeriodicalIF":3.4,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729512","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Exome analyses unravel the genetic architecture of Mendelian dominant nonsyndromic orofacial clefts

IF 3.4 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genomics

Pub Date : 2025-03-25 DOI: 10.1016/j.ygeno.2025.111039

Yining Zuo , Ji-Wei Chang , Nian-Nian Zhong, Zhuo Huang, Haitang Yue, Haiyan Cao, Zhaoyi Wu, Miao He, Zhuan Bian

Nonsyndromic orofacial clefts (NSOFC) represents a prevalent congenital anomalies, the etiology of which likely involves a complex interplay between genetic and environmental factors. To elucidate potential pathogenic variants, exome sequencing (ES) was conducted on 123 Chinese pedigrees demonstrating Mendelian dominant inheritance of NSOFC, including 251 patients and 130 unaffected relatives. This was followed by a standardized process of variant screening and filtering to identify novel variants within established candidate genes associated with clefting phenotypes. The study unveiled rare pathogenic variants in recognized genes with clefting across 101 pedigrees. These genes are implicated in essential biological processes such as primary ciliary function, bone formation and development, cell adhesion, and transcription regulation. Notably, the investigation into random X chromosome inactivation assay posited FLNA and GPC3 as factors contributing to NSOFC's incomplete dominance. Moreover, in vitro functional experiments targeting variants in two ciliary genes, TBC1D32 and SCLT1, elucidated their roles in NSOFC pathogenesis.

非综合征性口唇裂（NSOFC）是一种常见的先天性畸形，其病因可能涉及遗传和环境因素之间复杂的相互作用。为了阐明潜在的致病变异，我们对 123 个显示 NSOFC 孟德尔显性遗传的中国血统进行了外显子组测序（ES），其中包括 253 名患者和 130 名未受影响的亲属。随后进行了标准化的变异筛选和过滤过程，以确定与裂隙表型相关的已确定候选基因中的新变异。研究揭示了 101 个血统中与裂隙有关的公认基因中的罕见致病变异。这些基因与重要的生物过程有关，如原发性睫状肌功能、骨骼形成和发育、细胞粘附和转录调控。值得注意的是，对随机 X 染色体失活试验的调查认为，FLNA 和 GPC3 是导致 NSOFC 不完全显性的因素。此外，针对 TBC1D32 和 SCLT1 这两个睫状体基因变异的体外功能实验阐明了它们在 NSOFC 发病机制中的作用。

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引用次数: 0

Maternal genetic architecture of Guizhou's Hmong-Mien populations via whole mitogenome

IF 3.4 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genomics

Pub Date : 2025-03-24 DOI: 10.1016/j.ygeno.2025.111041

Li Chen , Yuhang Feng , Shuaiji Pan , Lin Wang , Hongling Zhang , Xiaoye Jin , Qiyan Wang , Yubo Liu , Meiqing Yang , Xiaolan Huang , Shunyi Tian , Changyun Gu , Jiang Huang , Zheng Ren

The Hmong-Mien (HM) language family, majorly distributed across southern China and Southeast Asia, has remained underexplored in population genetics, particularly concerning whole mitogenome studies. In this study, we sequenced the whole mitogenomes of 261 individuals from Guizhou Hmong-Mien-speaking populations (HM-G), comprising Miao, Yao, and She individuals. The haplogroup distribution was dominated by southern East Asian haplogroups (B, M7, and F). The neutrality test revealed significantly negative values, and mismatch distribution analyses showed a pronounced unimodal distribution, indicating high genetic diversity and recent population expansion in populations. For a comprehensive understanding of the matrilineal genetic background of the HM-speaking population, we merged whole mitogenome data from 83 populations worldwide. Our findings showed that the HM-G exhibited relatively close genetic distances to HM- and Tai-Kadai-speaking populations from East and Southeast Asia. These results provide crucial insights into the genetic structure and evolutionary history of HM-G.

{"title":"Maternal genetic architecture of Guizhou's Hmong-Mien populations via whole mitogenome","authors":"Li Chen , Yuhang Feng , Shuaiji Pan , Lin Wang , Hongling Zhang , Xiaoye Jin , Qiyan Wang , Yubo Liu , Meiqing Yang , Xiaolan Huang , Shunyi Tian , Changyun Gu , Jiang Huang , Zheng Ren","doi":"10.1016/j.ygeno.2025.111041","DOIUrl":"10.1016/j.ygeno.2025.111041","url":null,"abstract":"<div><div>The Hmong-Mien (HM) language family, majorly distributed across southern China and Southeast Asia, has remained underexplored in population genetics, particularly concerning whole mitogenome studies. In this study, we sequenced the whole mitogenomes of 261 individuals from Guizhou Hmong-Mien-speaking populations (HM-G), comprising Miao, Yao, and She individuals. The haplogroup distribution was dominated by southern East Asian haplogroups (B, M7, and F). The neutrality test revealed significantly negative values, and mismatch distribution analyses showed a pronounced unimodal distribution, indicating high genetic diversity and recent population expansion in populations. For a comprehensive understanding of the matrilineal genetic background of the HM-speaking population, we merged whole mitogenome data from 83 populations worldwide. Our findings showed that the HM-G exhibited relatively close genetic distances to HM- and Tai-Kadai-speaking populations from East and Southeast Asia. These results provide crucial insights into the genetic structure and evolutionary history of HM-G.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 3","pages":"Article 111041"},"PeriodicalIF":3.4,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143724424","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Heterogeneity of fibroblasts from different anatomical sites in healthy human knee ligaments revealed by single-cell RNA sequencing

IF 3.4 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genomics

Pub Date : 2025-03-24 DOI: 10.1016/j.ygeno.2025.111040

Haibo Zhao , Yizhi Yao , Fan Jiang , Xuesai Zhu , Tengbo Yu , Xiao Xiao

Knee ligaments are important structures that determine the locomotor function of the knee. In this paper, we identified and analyzed the cell types and compositions of ligaments from different parts of the healthy knee joint. By single-cell sequencing of approximately 106,077 extracted cells, we established a comprehensive cellular profile of ligaments in other parts of the knee joints of 15 healthy subjects and explored the more critical heterogeneity of fibroblasts. Three subpopulations of fibroblasts that may be associated with knee ligament anatomy were identified and their differentiation relationships were revealed, and the FTH1/FTL_SCARA5 signaling pathway that may be associated with knee ligament anatomical function was identified. This ligament atlas provides a molecular cytological basis for studying the physiological functions and properties of knee ligaments as well as the relationship between ligament structure and function at different sites. It offers certain clues for future studies of rated knee ligament diseases.

膝关节韧带是决定膝关节运动功能的重要结构。在本文中，我们鉴定并分析了健康膝关节不同部位韧带的细胞类型和组成。通过对提取的约 106,077 个细胞进行单细胞测序，我们建立了 15 名健康受试者膝关节其他部位韧带的全面细胞概况，并探索了成纤维细胞更为关键的异质性。我们确定了可能与膝关节韧带解剖有关的三个成纤维细胞亚群，并揭示了它们的分化关系，还确定了可能与膝关节韧带解剖功能有关的 FTH1/FTL_SCARA5 信号通路。该韧带图谱为研究膝关节韧带的生理功能和特性以及不同部位韧带结构和功能之间的关系提供了分子细胞学基础。它为今后研究额定膝关节韧带疾病提供了一定的线索。

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引用次数: 0

Feadm5C: Enhancing prediction of RNA 5-Methylcytosine modification sites with physicochemical molecular graph features

IF 3.4 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genomics

Pub Date : 2025-03-22 DOI: 10.1016/j.ygeno.2025.111037

Dongdong Jiang , Chunyan Ao , Yan Li , Liang Yu

One common post-transcriptional modification that is essential to biological activities is RNA 5-methylcytosine (m5C). A large amount of RNA data containing m5C modification sites has been gathered as a result of the rapid development of high-throughput sequencing technology. While there are a lot of machine learning based techniques available for identifying m5C alteration sites, these models' accuracy still has to be raised. This study proposed a novel method, Feadm5C, which predicts m5C based on fusing molecular graph features and sequencing information together. 10-fold cross-validation was used to assess the model's predictive performance. In addition, we used t-SNE visualization to assess the model's stability and effectiveness. While keeping feature encoding and model structure straightforward, the approach suggested in this work outperforms the most recent approaches in use. The dataset and code of the model can be downloaded from GitHub (https://github.com/LiangYu-Xidian/Feadm5C).

引用次数: 0

Insights for variant clinical interpretation based on a benchmark of 65 variant effect predictors

IF 3.4 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genomics

Pub Date : 2025-03-22 DOI: 10.1016/j.ygeno.2025.111036

Ragousandirane Radjasandirane, Julien Diharce, Jean-Christophe Gelly , Alexandre G. de Brevern

Single amino acid substitutions in protein sequences are generally harmless, but a certain number of these changes can lead to disease. Accurately predicting the effect of genetic variants is crucial for clinicians as it accelerates the diagnosis of patients with missense variants associated with health problems. Many computational tools have been developed to predict the pathogenicity of genetic variants with various approaches. Analysing the performance of these different computational tools is crucial to provide guidance to both future users and especially clinicians. In this study, a large-scale investigation of 65 tools was conducted. Variants from both clinical and functional contexts were used, incorporating data from the ClinVar database and bibliographic sources. The analysis showed that AlphaMissense often performed very well and was in fact one of the best options among the existing tools. In addition, as expected, meta-predictors perform well on average. Tools using evolutionary information showed the best performance for functional variants. These results also highlighted some heterogeneity in the difficulty of predicting some specific variants while others are always well categorized. Strikingly, the majority of variants from the ClinVar database appear to be easy to predict, while variants from other sources of data are more challenging. This raises questions about the use of ClinVar and the dataset used to validate tools accuracy. In addition, these results show that this variant predictability can be divided into three distinct classes: easy, moderate and hard to predict. We analyzed the parameters leading to these differences and showed that the classes are related to structural and functional information.

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引用次数: 0

Transcriptome analysis reveals that the injection of mesenchymal stem cells remodels extracellular matrix and complement components of the brain through PI3K/AKT/FOXO1 signaling pathway in a neuroinflammation mouse model

IF 3.4 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genomics

Pub Date : 2025-03-21 DOI: 10.1016/j.ygeno.2025.111033

Zhihao Xu , Keqin Liu , Guoqing Zhang , Fen Yang , Ya'’nan He , Wenbin Nan , Yonghai Li , Juntang Lin

Neurological disorders are often accompanied by neuroinflammatory responses. Our previous research indicated that mesenchymal stem cells (MSCs) suppressed neuroinflammation in the brain. The mechanism of action remains not fully understood. In this study, we analyzed the impact of injected MSCs on the transcriptome in the brains of neuroinflammatory mouse model (NIM) with bioinformatical methods and conducted experimental validation with qPCR and Western blot. The results showed that the expression of extracellular matrix components changed, and the complement cascade was activated in the NIM brains. Injection of MSCs reversed the expression of ECM components and inhibited complement activation. MSCs may promote the improvement of neuronal synaptic function and alter the infiltration of immune cells into the brain. MSCs regulated the PI3K/AKT/Foxo1 signaling pathway. These findings will be very helpful for the development of MSCs-based therapy and the treatment of neuroinflammation-related diseases.

{"title":"Transcriptome analysis reveals that the injection of mesenchymal stem cells remodels extracellular matrix and complement components of the brain through PI3K/AKT/FOXO1 signaling pathway in a neuroinflammation mouse model","authors":"Zhihao Xu , Keqin Liu , Guoqing Zhang , Fen Yang , Ya'’nan He , Wenbin Nan , Yonghai Li , Juntang Lin","doi":"10.1016/j.ygeno.2025.111033","DOIUrl":"10.1016/j.ygeno.2025.111033","url":null,"abstract":"<div><div>Neurological disorders are often accompanied by neuroinflammatory responses. Our previous research indicated that mesenchymal stem cells (MSCs) suppressed neuroinflammation in the brain. The mechanism of action remains not fully understood. In this study, we analyzed the impact of injected MSCs on the transcriptome in the brains of neuroinflammatory mouse model (NIM) with bioinformatical methods and conducted experimental validation with qPCR and Western blot. The results showed that the expression of extracellular matrix components changed, and the complement cascade was activated in the NIM brains. Injection of MSCs reversed the expression of ECM components and inhibited complement activation. MSCs may promote the improvement of neuronal synaptic function and alter the infiltration of immune cells into the brain. MSCs regulated the PI3K/AKT/Foxo1 signaling pathway. These findings will be very helpful for the development of MSCs-based therapy and the treatment of neuroinflammation-related diseases.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 3","pages":"Article 111033"},"PeriodicalIF":3.4,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143686522","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

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