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Structural Dynamics of Neutral Amino Acid Transporter SLC6A19 in Simple and Complex Lipid Bilayers 中性氨基酸转运体SLC6A19在简单和复杂脂质双分子层中的结构动力学。
IF 3 3区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-01-03 DOI: 10.1002/jcb.30693
Budheswar Dehury, Sarbani Mishra, Sunita Panda, Mahender Kumar Singh, Nischal L. Simha, Sanghamitra Pati

B0AT1 (SLC6A19) is a major sodium-coupled neutral amino acid transporter that relies on angiotensin converting enzyme 2 (ACE2) or collectrin for membrane trafficking. Despite its significant role in disorders associated with amino acid metabolism, there is a deficit of comprehensive structure-function understanding of B0AT1 in lipid environment. Herein, we have employed molecular dynamics (MD) simulations to explore the architectural characteristics of B0AT1 in two distinct environments: a simplified POPC bilayer and a complex lipid system replicating the native membrane composition. Notably, our B0AT1 analysis in terms of structural stability and regions of maximum flexibility shows consistency in both the systems with enhanced structural features in the case of complex lipid system. Our findings suggest that diacylglycerol phospholipids significantly alter the pore radius, hydrophobic index, and surface charge distribution of B0AT1, thereby affecting the flexibility of transmembrane helices TM7, TM12, and loop connecting TM7-TM8, crucial for ACE2-B0AT1 interaction. Pro41, Ser190, Arg214, Arg240, Ser413, Pro414, Cys463, and Val582 are among the most prominent lipid binding residues that might influence B0AT1 functionality. We also perceive notable lipid mediated deviation in the degree of tilt and loss of helicity in TM1 and TM6 which might affect the substrate binding sites S1 and S2 in B0AT1. Considerably, destabilization in the structure of B0AT1 in lipid environment was evident upon mutation in TM domain, associated with Hartnup disorder through various structure-based protein stability tools. Our two-tiered approach allowed us to validate the use of POPC as a baseline for initial analyses of SLC transporters. Altogether, our all-atoms MD study provides a platform for future investigations into the structure-function mechanism of B0AT1 in realistic lipid mimetic bilayers and offers a framework for developing new therapeutic agents targeting this transporter.

B0AT1(SLC6A19)是一种主要的钠偶联中性氨基酸转运体,其膜转运依赖于血管紧张素转换酶 2(ACE2)或收集蛋白。尽管 B0AT1 在与氨基酸代谢相关的疾病中发挥着重要作用,但人们对其在脂质环境中的结构-功能还缺乏全面的了解。在此,我们采用分子动力学(MD)模拟来探索 B0AT1 在两种不同环境中的结构特征:简化的 POPC 双层和复制原生膜组成的复杂脂质系统。值得注意的是,我们从结构稳定性和最大灵活性区域方面对 B0AT1 进行的分析表明,这两种体系具有一致性,而在复杂脂质体系中,结构特征得到了增强。我们的研究结果表明,二酰甘油磷脂显著改变了 B0AT1 的孔半径、疏水指数和表面电荷分布,从而影响了跨膜螺旋 TM7、TM12 和连接 TM7-TM8 的环的灵活性,而这对 ACE2 与 B0AT1 的相互作用至关重要。Pro41、Ser190、Arg214、Arg240、Ser413、Pro414、Cys463 和 Val582 是可能影响 B0AT1 功能的最显著的脂质结合残基。我们还发现,在脂质介导下,TM1 和 TM6 的倾斜度和螺旋度的损失发生了明显的偏差,这可能会影响 B0AT1 中的底物结合位点 S1 和 S2。通过各种基于结构的蛋白质稳定性工具,我们发现当 TM 结构域发生突变时,B0AT1 在脂质环境中的结构稳定性明显下降,这与哈特努普紊乱有关。我们的双层方法使我们验证了使用 POPC 作为 SLC 转运体初步分析的基线。总之,我们的全原子 MD 研究为今后研究 B0AT1 在仿脂双分子层中的结构-功能机制提供了一个平台,并为开发针对这种转运体的新治疗药物提供了一个框架。
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引用次数: 0
Supervillin-Mediated ZO-1 Downregulation Facilitates Migration of Cisplatin-Resistant HCT116 Colorectal Cancer Cells 超级绒毛蛋白介导的ZO-1下调促进顺铂耐药HCT116结直肠癌细胞的迁移
IF 3 3区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-01-02 DOI: 10.1002/jcb.30699
Yali Hong, Xu Li, Rongchen Mao, Feier Zhou, Shengnan Li, Chao Zhu, Lai Jin

Supervillin (SVIL), the biggest member of the villin/gelsolin superfamily, has recently been reported to promote the metastasis of hepatocellular carcinoma by stimulating epithelial-mesenchymal transition (EMT). However, little is known about the roles of SVIL in the migration of colorectal cancer cells. Here, we investigated the effects of SVIL on the migration of cisplatin-resistant colorectal cancer cells. The model of cisplatin-resistant HCT116 cells (HCT116/DDP) was established. Migration was assessed after SVIL knockdown. Tumor metastasis was assessed using a mouse model with tail vein injection of colorectal cancer cells. The results showed that the expression of SVIL was upregulated in HCT116/DDP cells compared to that in their parental cells. Also, the HCT116/DDP cells showed increased cell migration and lung metastasis. Furthermore, we revealed that the expression of SVIL was associated with the migration of HCT116/DDP cells. Reduced SVIL expression inhibited migration and lung metastasis in HCT116/DDP cells. Further work showed that SVIL knockdown blocked cell migration by targeting zona occludens-1 (ZO-1) mediated tight-junction remodeling. The expression of ZO-1, but not occludin and cludin5, was downregulated after SVIL knockdown. Immunofluorescence indicated that the linear ZO-1 was interrupted while the SVIL knockdown reversed the interruption. This study displayed the relationship between SVIL and ZO-1 in cisplatin-resistant colon cancer cells, providing a new insight into the mechanism of colorectal cancer migration.

超级绒毛蛋白(Supervillin, SVIL)是绒毛蛋白/凝胶蛋白超家族中最大的成员,最近被报道通过刺激上皮-间质转化(EMT)促进肝细胞癌的转移。然而,对SVIL在结直肠癌细胞迁移中的作用知之甚少。在这里,我们研究了SVIL对顺铂耐药结直肠癌细胞迁移的影响。建立顺铂耐药HCT116细胞(HCT116/DDP)模型。SVIL敲除后评估迁移。采用小鼠尾静脉注射结直肠癌细胞模型评估肿瘤转移。结果表明,与亲本细胞相比,HCT116/DDP细胞中SVIL的表达上调。HCT116/DDP细胞的细胞迁移和肺转移增加。此外,我们发现SVIL的表达与HCT116/DDP细胞的迁移有关。降低SVIL表达可抑制HCT116/DDP细胞的迁移和肺转移。进一步的研究表明,SVIL敲低通过靶向ZO-1介导的紧密连接重塑来阻断细胞迁移。SVIL敲除后ZO-1表达下调,occludin和cludin5表达下调。免疫荧光显示线性ZO-1被中断,而SVIL敲除逆转了这种中断。本研究揭示了SVIL与ZO-1在顺铂耐药结肠癌细胞中的关系,为结直肠癌迁移机制提供了新的认识。
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引用次数: 0
Pleiotropic Function of Cellular Prion Protein: Encompassing Endoplasmic-Reticulum Stress, Cell Proliferation in Vascular Smooth Muscle Cells 细胞朊蛋白的多功能性:包括内质网应激、血管平滑肌细胞的细胞增殖。
IF 3 3区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2025-01-02 DOI: 10.1002/jcb.30692
Rumela Bose, Madhubanti Ghosh, Rupasri Ain

Cellular prion protein (PRNP) has been implicated in various physiological processes in different cell types, for decades. Little has been known how PRNP functions in multiple, yet related processes within a particular system. In our current study, with the aid of high-throughput RNA-sequencing technique, we have presented an overall transcriptome profile of rat vascular smooth muscle cells (VSMCs) with Prnp knockdown. Fifty-one genes were found to be differentially regulated, of which, genes involved in cell proliferation and endoplasmic reticulum (ER) stress pathway, show significant upregulation. That PRNP negatively regulates VSMC proliferation, has been demonstrated using immunoblot assays, BrdU incorporation assay and Ki-67 immunofluorescence staining. As revealed from our RNA-Seq data, ATF4, a downstream effector of the PERK arm of ER stress pathway is upregulated upon RNA interference of Prnp in VSMCs. As a result, the expression of the functional phosphorylated isoform of translation initiation factor eIF2α (p-eIF2α) is elevated. Additionally, we also showed that downregulation of Prnp leads to excess intracellular ROS accumulation, subsequently leading to splicing of Xbp1 mRNA and triggering unfolded protein response (UPR) within the cell. Therefore, our findings highlight that PRNP directly or indirectly modulates an array of biological processes and plays a pivotal role in preserving the equilibrium between excess proliferation and optimal endoplasmic reticulum function, in VSMCs.

几十年来,细胞朊病毒蛋白(PRNP)参与了不同细胞类型的各种生理过程。很少有人知道PRNP如何在一个特定系统内的多个相关过程中起作用。在我们目前的研究中,借助高通量rna测序技术,我们展示了Prnp敲低的大鼠血管平滑肌细胞(VSMCs)的整体转录组图谱。51个基因被差异调控,其中涉及细胞增殖和内质网(ER)应激通路的基因显著上调。免疫印迹实验、BrdU掺入实验和Ki-67免疫荧光染色证实了PRNP对VSMC增殖的负调控作用。我们的RNA- seq数据显示,在VSMCs中,内质网应激途径PERK臂的下游效应物ATF4在Prnp的RNA干扰下上调。结果,翻译起始因子eIF2α (p-eIF2α)功能性磷酸化异构体的表达升高。此外,我们还发现下调Prnp会导致细胞内ROS积累过多,随后导致Xbp1 mRNA剪接并触发细胞内未折叠蛋白反应(UPR)。因此,我们的研究结果强调,PRNP直接或间接地调节了一系列生物过程,并在vsmc中保持过度增殖和最佳内质网功能之间的平衡中发挥关键作用。
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引用次数: 0
RETRACTION: Effect of Oridonin on Experimental Animal Model of Bronchopulmonary Dysplasia 撤回:冬凌草苷对支气管肺发育不良动物模型的影响。
IF 3 3区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-12-30 DOI: 10.1002/jcb.30696

RETRACTION: S. Zhang, J. Wang, Z. Xin, C. Sun, Z. Ju, X. Xue, W. Jiang, Q. Xin, J. Wang, Z. Zhang, and Y. Luan, “Effect of Oridonin on Experimental Animal Model of Bronchopulmonary Dysplasia,” Journal of Cellular Biochemistry 125, no. 9 (2024): e30632, https://doi.org/10.1002/jcb.30632.

The above article, published online on 16 July 2024 in Wiley Online Library (wileyonlinelibrary.com), has been retracted by agreement between the journal Editor-in-Chief, Christian Behl; and Wiley Periodicals LLC. Following publication, it has come to the attention of the journal that the article was accepted solely on the basis of compromised peer review processes. Furthermore, multiple conclusions are not sufficiently supported by the data. Accordingly, the article is retracted as the editors consider its conclusions to be invalid.

引用本文:张淑娟,王军,辛志强,孙超,鞠志强,薛旭,姜文,辛琪,王军,张志强,栾毅,“冬凌草苷对支气管肺发育不良动物模型的影响”,《细胞生物化学》,第125期。9 (2024): e30632, https://doi.org/10.1002/jcb.30632。上述文章于2024年7月16日在Wiley在线图书馆(wileyonlinelibrary.com)上发表,经该杂志主编Christian Behl;和Wiley期刊有限责任公司。在发表之后,该杂志注意到,这篇文章完全是基于折衷的同行评议过程而被接受的。此外,多重结论没有得到充分的数据支持。因此,这篇文章被撤回,因为编辑认为其结论无效。
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引用次数: 0
MicroRNAs as Biomarker in Rheumatoid Arthritis: Pathogenesis to Clinical Relevance MicroRNAs作为类风湿性关节炎的生物标志物:发病机制和临床相关性。
IF 3 3区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-12-22 DOI: 10.1002/jcb.30690
Tooba Qamar, Md. Samsuddin Ansari,  Masihuddin, Sayali Mukherjee

MicroRNAs (miRNAs) have emerged as intricate players in rheumatoid arthritis (RA), holding promise as discerning biomarkers for diagnostic and prognostic purposes. The lack of sensitivity and specificity in current diagnostic techniques, such as rheumatoid factor (RF) and anti-citrullinated protein antibodies (ACPA), causes diagnosis delays in RA. The miR-146a and miR-155 act in inflammatory cascades and reduce joint deterioration, and miR-223 is paradoxical, acting differently in different illness scenarios. The microenvironment of RA is shaped by the complex modulation of gene expression and cytokine dynamics by miR-126 and miR-24. miRNAs serve as a promising candidate for precision medicine in the management of RA. There are obstacles encountered in validation, delivery optimization, and off-target effect mitigation before miRNA-based biomarkers may be applied in clinical settings. Machine learning (ML) and artificial intelligence (AI) have been used to integrate miRNA expression patterns with clinical data to greatly advance the treatment of RA. Because of the disease's inherent complexity and variability, these state-of-the-art models provide accurate predictions regarding the onset, development, and response to treatment of RA. By using clinical information and miRNA expression data, ML algorithms are revolutionizing the treatment of RA by predicting the onset and course of the disease with remarkably high accuracy. The development of therapeutic modalities and miRNA profiling has great potential to transform the diagnosis, prognosis, and treatment of RA, providing fresh hope for better patient outcomes.

MicroRNAs (miRNAs)在类风湿关节炎(RA)中扮演着复杂的角色,有望成为诊断和预后目的的鉴别生物标志物。目前的诊断技术缺乏敏感性和特异性,如类风湿因子(RF)和抗瓜氨酸化蛋白抗体(ACPA),导致RA的诊断延迟。miR-146a和miR-155在炎症级联反应中起作用并减少关节恶化,而miR-223则是矛盾的,在不同的疾病情况下起不同的作用。RA的微环境是由miR-126和miR-24对基因表达和细胞因子动力学的复杂调节形成的。mirna是精准医学治疗类风湿性关节炎的一个有希望的候选药物。在基于mirna的生物标志物应用于临床环境之前,在验证、递送优化和脱靶效应缓解方面遇到了障碍。机器学习(ML)和人工智能(AI)已被用于将miRNA表达模式与临床数据相结合,以极大地推进RA的治疗。由于这种疾病固有的复杂性和可变性,这些最先进的模型提供了关于RA的发病、发展和治疗反应的准确预测。通过使用临床信息和miRNA表达数据,ML算法以非常高的准确性预测RA的发病和病程,从而彻底改变了RA的治疗。治疗方式和miRNA分析的发展有很大的潜力来改变RA的诊断、预后和治疗,为更好的患者预后提供了新的希望。
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引用次数: 0
In Silico and In Vitro Verification of the Effects of Chemotherapeutic Doxorubicin and 5-Fluorouracil in Combination With Curcumin and Vitamin C on MCF-7 Cells 多柔比星、5-氟尿嘧啶联合姜黄素和维生素C化疗对MCF-7细胞影响的实验和体外验证
IF 3 3区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-12-18 DOI: 10.1002/jcb.30688
Aslı Akyüz, Duygu YAŞAR Şirin

Breast cancer ranks among the most prevalent cancers. Enhancing the effectiveness of chemotherapy and patient survival is the objective of many studies. In the literature, no study has investigated the combined effect of vitamin c and curcumin with chemotherapy drugs on cell viability in the MCF-7 cell line, nor the mechanism of inflammation induced by cancer drugs, both in vitro and in silico. Thus, the purpose of this study was to assess the synergistic effect of curcumin and vitamin c in combination with the chemotherapy drugs 5-fluorouracil and doxorubicin. The cytokine hub genes of the Toll-like receptor pathway for the administered drugs were identified using the Cytoscape program, and docking studies were conducted via the Cb Dock2 website. In silico analyses indicated that doxorubicin and curcumin displayed comparable characteristics, achieving the highest interaction scores (-10) with marker proteins, whereas 5-fluorouracil and vitamin c showed lower interaction scores. Cell viability was evaluated through MTT analysis and AO/PI staining, while the expression of inflammation-related markers IL-6, IL-10, and TNF-α proteins determined using the ELISA method. After 24 h, the cell viability of the chemotherapeutic drugs administered in combination with curcumin decreased by up to 28%. Subsequently, applications at 48 and 72 h were performed. These results indicate that the effect of curcumin on cell viability is significant when combined with chemotherapy drugs. In the ELISA test, a 52% expression of IL-6 was noted in MCF-7 cells treated with curcumin, whereas the IL-6 level decreased to 15% in the other experimental groups. An increase was observed in the TNF-α expression with 5-fluorouracil and doxorubicin compared to the control, while a notable decrease was recorded in the applications with vitamin c and curcumin (p < 0.05). This study demonstrates that vitamin c and curcumin exhibit a synergistic effect with chemotherapeutic agents in the inflammatory system.

乳腺癌是最常见的癌症之一。提高化疗的有效性和患者的生存是许多研究的目标。在文献中,目前还没有研究维生素c和姜黄素联合化疗药物对MCF-7细胞系细胞活力的影响,也没有研究癌症药物诱导炎症的机制,无论是体外还是体内。因此,本研究的目的是评估姜黄素和维生素c与化疗药物5-氟尿嘧啶和阿霉素联合使用的协同作用。使用Cytoscape程序鉴定给药药物toll样受体途径的细胞因子中心基因,并通过Cb Dock2网站进行对接研究。计算机分析表明,阿霉素和姜黄素表现出类似的特征,与标记蛋白的相互作用得分最高(-10),而5-氟尿嘧啶和维生素c的相互作用得分较低。通过MTT分析和AO/PI染色评估细胞活力,ELISA法检测炎症相关标志物IL-6、IL-10和TNF-α蛋白的表达。24小时后,化疗药物与姜黄素联合施用的细胞活力下降了28%。随后,在48和72小时进行应用。这些结果表明,姜黄素与化疗药物联合使用对细胞活力的影响是显著的。在ELISA测试中,姜黄素处理的MCF-7细胞中IL-6的表达量为52%,而在其他实验组中IL-6的表达量降至15%。与对照组相比,5-氟尿嘧啶和阿霉素组的TNF-α表达增加,而维生素c和姜黄素组的TNF-α表达明显减少(p
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引用次数: 0
FKBP51, a multitasker in protein function, pathway activity, and physiology FKBP51,蛋白质功能、通路活动和生理学中的多面手。
IF 3 3区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-12-16 DOI: 10.1002/jcb.30448
Mario D. Galigniana, Theo Rein
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引用次数: 0
Lactate-Dependent HIF1A Transcriptional Activation Exacerbates Severe Acute Pancreatitis Through the ACSL4/LPCAT3/ALOX15 Pathway Induced Ferroptosis 乳酸依赖性HIF1A转录激活通过ACSL4/LPCAT3/ALOX15途径诱导铁下垂加重严重急性胰腺炎
IF 3 3区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-12-16 DOI: 10.1002/jcb.30687
Tingyuan Zhang, Xiaopei Huang, Shengnan Feng, Huanzhang Shao

Acute pancreatitis (AP) is a common emergency in the digestive system, and in severe cases, it can progress to severe acute pancreatitis (SAP), with a mortality rate of up to 30%, representing a dire situation. SAP in mice was induced by l-arginine (l-Arg). HE, IHC, WB and ELISA were used to study the role and regulation of HIF1A in SAP. At the same time, QPCR, WB, CHIP-QPCR and luciferase report were used to explore the specific mechanism of HIF1A regulation of SAP in vitro. The research results indicate that following SAP induction, the pancreatic tissue of mice exhibited significant glycolytic abnormalities, accompanied by a marked upregulation of HIF1A expression. This led to apparent damage in the pancreatic tissue, lungs, and kidneys. However, in sh-HIF1A mice, the degree of these injuries was significantly alleviated, along with a reduction in the production of inflammatory factors, oxidative products, and lipid peroxidation markers. This suggests that HIF1A plays a crucial role in the inflammatory and oxidative stress processes during SAP. Further exploration revealed that the absence or overexpression of HIF1A affects SAP by inducing ferroptosis through the ACSL4/LPCAT3/ALOX15 pathway. Notably, the elevated lactate level resulting from glycolytic abnormalities further enhances the histone lactylation in the HIF1A promoter region, thereby aggravating the expression of HIF1A. Lactate-dependent HIF1A transcriptional activation exacerbates severe acute pancreatitis through the ACSL4/LPCAT3/ALOX15 pathway induced ferroptosis.

急性胰腺炎(AP)是一种常见的消化系统急症,严重者可发展为严重急性胰腺炎(SAP),死亡率高达30%,是一种可怕的情况。l-精氨酸(l-Arg)诱导小鼠SAP。采用HE、IHC、WB和ELISA等方法研究HIF1A在SAP中的作用和调控,同时采用QPCR、WB、CHIP-QPCR和荧光素酶报告等方法探讨HIF1A在体外调控SAP的具体机制。研究结果表明,在SAP诱导后,小鼠胰腺组织出现明显的糖酵解异常,并伴有HIF1A表达明显上调。这导致胰腺组织、肺和肾脏明显受损。然而,在sh-HIF1A小鼠中,这些损伤的程度显著减轻,炎症因子、氧化产物和脂质过氧化标志物的产生也减少。这表明HIF1A在SAP的炎症和氧化应激过程中起着至关重要的作用。进一步的研究发现,HIF1A的缺失或过表达通过ACSL4/LPCAT3/ALOX15途径诱导铁凋亡,从而影响SAP。值得注意的是,糖酵解异常引起的乳酸水平升高进一步增强了HIF1A启动子区域的组蛋白乳酸化,从而加重了HIF1A的表达。乳酸依赖性HIF1A转录激活通过ACSL4/LPCAT3/ALOX15途径诱导铁下垂加重严重急性胰腺炎。
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引用次数: 0
Cover Image, Volume 125, Number 12, December 2024 封面图片,第125卷,第12期,2024年12月
IF 3 3区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-12-16 DOI: 10.1002/jcb.30697

Front Cover: This special issue features articles by experts in the field highlighting various molecular and physiological aspects of the versatile multitasker protein FKBP51. Created in BioRender”

封面:这期特刊刊登了该领域专家的文章,重点介绍了多功能多任务蛋白FKBP51的各种分子和生理方面。在BioRender中创建”
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引用次数: 0
Cover Image, Volume 125, Number 12, December 2024 封面图片,第125卷,第12期,2024年12月
IF 3 3区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-12-16 DOI: 10.1002/jcb.30698

Inside Front Cover: A full-length structural model of the Large T protein of Merkel Cell Polyomavirus reveals a predominance of intrinsic disorder.

封面内页:梅克尔细胞多瘤病毒大 T 蛋白的全长结构模型揭示了主要的内在紊乱。
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引用次数: 0
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Journal of cellular biochemistry
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