1.Structural and Spatial Analysis of The Recognition Relationship Between Influenza A Virus Neuraminidase Antigenic Epitopes and Antibodies
Zheng ZHU ; Zheng-Shan CHEN ; Guan-Ying ZHANG ; Ting FANG ; Pu FAN ; Lei BI ; Yue CUI ; Ze-Ya LI ; Chun-Yi SU ; Xiang-Yang CHI ; Chang-Ming YU
Progress in Biochemistry and Biophysics 2025;52(4):957-969
ObjectiveThis study leverages structural data from antigen-antibody complexes of the influenza A virus neuraminidase (NA) protein to investigate the spatial recognition relationship between the antigenic epitopes and antibody paratopes. MethodsStructural data on NA protein antigen-antibody complexes were comprehensively collected from the SAbDab database, and processed to obtain the amino acid sequences and spatial distribution information on antigenic epitopes and corresponding antibody paratopes. Statistical analysis was conducted on the antibody sequences, frequency of use of genes, amino acid preferences, and the lengths of complementarity determining regions (CDR). Epitope hotspots for antibody binding were analyzed, and the spatial structural similarity of antibody paratopes was calculated and subjected to clustering, which allowed for a comprehensively exploration of the spatial recognition relationship between antigenic epitopes and antibodies. The specificity of antibodies targeting different antigenic epitope clusters was further validated through bio-layer interferometry (BLI) experiments. ResultsThe collected data revealed that the antigen-antibody complex structure data of influenza A virus NA protein in SAbDab database were mainly from H3N2, H7N9 and H1N1 subtypes. The hotspot regions of antigen epitopes were primarily located around the catalytic active site. The antibodies used for structural analysis were primarily derived from human and murine sources. Among murine antibodies, the most frequently used V-J gene combination was IGHV1-12*01/IGHJ2*01, while for human antibodies, the most common combination was IGHV1-69*01/IGHJ6*01. There were significant differences in the lengths and usage preferences of heavy chain CDR amino acids between antibodies that bind within the catalytic active site and those that bind to regions outside the catalytic active site. The results revealed that structurally similar antibodies could recognize the same epitopes, indicating a specific spatial recognition between antibody and antigen epitopes. Structural overlap in the binding regions was observed for antibodies with similar paratope structures, and the competitive binding of these antibodies to the epitope was confirmed through BLI experiments. ConclusionThe antigen epitopes of NA protein mainly ditributed around the catalytic active site and its surrounding loops. Spatial complementarity and electrostatic interactions play crucial roles in the recognition and binding of antibodies to antigenic epitopes in the catalytic region. There existed a spatial recognition relationship between antigens and antibodies that was independent of the uniqueness of antibody sequences, which means that antibodies with different sequences could potentially form similar local spatial structures and recognize the same epitopes.
2.Terms Related to The Study of Biomacromolecular Condensates
Ke RUAN ; Xiao-Feng FANG ; Dan LI ; Pi-Long LI ; Yi LIN ; Zheng WANG ; Yun-Yu SHI ; Ming-Jie ZHANG ; Hong ZHANG ; Cong LIU
Progress in Biochemistry and Biophysics 2025;52(4):1027-1035
Biomolecular condensates are formed through phase separation of biomacromolecules such as proteins and RNAs. These condensates exhibit liquid-like properties that can futher transition into more stable material states. They form complex internal structures via multivalent weak interactions, enabling precise spatiotemporal regulations. However, the use of inconsistent and non-standardized terminology has become increasingly problematic, hindering academic exchange and the dissemination of scientific knowledge. Therefore, it is necessary to discuss the terminology related to biomolecular condensates in order to clarify concepts, promote interdisciplinary cooperation, enhance research efficiency, and support the healthy development of this field.
3.DIA Proteomics Reveals Mechanism of Acanthopanacis Senticosi Radix et Rhizoma seu Caulis Extract in Treating α-Syn Transgenic Parkinson's Disease in Mice
Qi ZHENG ; Yi LU ; Donghua YU ; Liangyou ZHAO ; Chunsheng LIN ; Fang LU ; Shumin LIU
Chinese Journal of Experimental Traditional Medical Formulae 2025;31(8):40-50
ObjectiveTo investigate the mechanism of Acanthopanacis Senticosi Radix et Rhizoma seu Caulis extract (ASH) in treating Parkinson's disease (PD) in mice by Data-Independent Acquisition (DIA) proteomics. MethodsThe α-Synuclein (α-Syn) transgenic PD mice were selected as suitable models for PD, and they were randomly assigned into PD, ASH (61.25 mg·kg-1), and Madopar (97.5 mg·kg-1) groups. Male C57BL/6 mice of the same age were selected as the control group, with eight mice in each group. Mice were administrated with corresponding drugs by gavage once a day for 20 days. The pole climbing time and the number of autonomic activities were recorded to evaluate the exercise ability of mice. Hematoxylin-eosin staining was employed to observe neuronal changes in the substantia nigra of PD mice. Immunohistochemistry (IHC) was employed to measure the tyrosine hydroxylase (TH) activity in the substantia nigra and assess the areal density of α-Syn in the striatum. DIA proteomics was used to compare protein expression in the substantia nigra between groups. IHC was utilized to validate key differentially expressed proteins, including Lactotransferrin, Notch2, Ndrg2, and TMEM 166. The cell counting kit-8 (CCK-8) method was used to investigate the effect of ASH on the viability of PD cells with overexpression of α-Syn. Real-time fluorescence quantitative polymerase chain reaction (Real-time PCR) and Western blot were employed to determine the protein and mRNA levels of Lactotransferrin, Notch2, Ndrg2, and TMEM 166 in PD cells. ResultsCompared with the control group, the model group showed prolonged pole climbing time, diminished coordination ability, reduced autonomic activities (P<0.01), and reduced swelling neurons. Compared with the model group, ASH and Madopar reduced the climbing time, increased autonomic activities (P<0.01), and ameliorated neuronal damage. Compared with the control group, the model group showed a decrease in TH activity in the substantia nigra and an increase in α-Syn accumulation in the striatum (P<0.01). Compared with the model group, the ASH group showed an increase in TH activity and a reduction in α-Syn accumulation (P<0.05). DIA proteomics revealed a total of 464 differentially expressed proteins in the model group compared with the control group, with 323 proteins being up-regulated and 141 down-regulated. A total of 262 differentially expressed proteins were screened in the ASH group compared with the model group, including 85 proteins being up-regulated and 177 down-regulated. Kyoto encylopedia of genes and genomes (KEGG) pathway analysis indicated that ASH primarily regulated the Notch signaling pathway. The model group showed up-regulation in protein levels of Notch2, Ndrg2, and TMEM 166 and down-regulation in the protein level of Lactotransferrin compared with the control group (P<0.01). Compared with the model group, ASH down-regulated the protein levels of Notch2, Ndrg2, and TMEM 166 (P<0.05) while up-regulating the protein level of Lactotransferrin (P<0.01). The IHC results corroborated the proteomics findings. The cell experiment results showed that compared with the control group, the modeling up-regulated the mRNA and protein levels of Notch2, Ndrg2, and TMEM 166 (P<0.01), while down-regulating the mRNA and protein levels of Lactotransferrin (P<0.01). Compared with the model group, ASH reduced the mRNA and protein levels of Notch2, Ndrg2, and TMEM 166 (P<0.01), while increasing the mRNA and protein levels of Lactotransferrin (P<0.05, P<0.01). ConclusionASH may Synergistically inhibit the Notch signaling pathway and mitigate neuronal damage by down-regulating the expression of Notch2 and Ndrg2. Additionally, by up-regulating the expression of Lactotransferrin and down-regulating the expression of TMEM166, ASH can address brain iron accumulation, intervene in ferroptosis, inhibit mitophagy, and mitigate reactive oxygen species damage, thereby protecting nerve cells and contributing to the treatment of PD.
4.Status Analysis of Acupoint Selection and Stimulation Parameters Application for Acupuncture Treatment of Functional Dyspepsia
Siyi ZHENG ; Han ZHANG ; Yang YU ; Chuanlong ZHOU ; Yan SHI ; Xiaohu YIN ; Shouhai HONG ; Na NIE ; Jianqiao FANG ; Yi LIANG
Journal of Traditional Chinese Medicine 2025;66(12):1293-1299
Based on commonly used acupoints in the clinical acupuncture treatment of functional dyspepsia (FD), this study systematically analyzes the therapeutic differences and synergistic effects between local and distal point selection. It also examines the suitability of primary acupoint selection for different FD subtypes, postprandial distress syndrome (PDS) and epigastric pain syndrome (EPS). The findings suggest that a combination of local and distal acupoints may be more appropriate as primary points for PDS, whereas local acupoints alone may be more suitable for EPS. Additionally, the study explores the impact of various factors, such as stimulation techniques, needling order, intensity or stimulation parameters, and depth, on the efficacy of acupuncture. It concludes that the intrinsic properties of acupoints are the primary determinants of therapeutic direction. Other factors mainly influence the magnitude rather than the direction of the effect. Future research may further investigate how different acupoint combinations, local versus distal, affect the treatment outcomes of FD subtypes, providing new insights for clinical acupuncture prescriptions.
5.Association of parent-child connectedness and peers romantic behaviors with romantic relationships of secondary vocational school students
XU Simin, ZUO Xiayun, FANG Yuhang, YU Chunyan, LIAN Qiguo, LOU Chaohua, ZHENG Yujia, TU Xiaowen
Chinese Journal of School Health 2025;46(10):1422-1426
Objective:
To explore the association between parent-child connectedness and romantic relationships of secondary vocational school students and the moderating effect of peers romantic behavior, providing scientific basis for family and school health education.
Methods:
From March to April 2021,2 426 students from six secondary vocational and technical schools in Shanghai and Shaanxi Province were selected to conduct the survey by combining convenience sampling and cluster sampling.Electronic questionnaires were used to collect data on students family characteristics,oneself and peer romantic behaviors, and parent-child bonding. The t-test was employed for inter group comparisons, and binary Logistic regression analysis was conducted to examine the relationship between parent-child bonding levels, peer romantic behavior, and the romantic behavior of secondary vocational students.
Results:
The mother-child connection (2.63±0.77) was higher than that of father-child connection (2.48±0.78), with statistically significant difference ( t =6.83, P <0.01). Multivariable Logistic regression showed that overall father-child connectedness was negatively associated with students romantic relationships( OR =0.86,95% CI =0.76-0.97, P =0.02)and was only associated to girls romantic relationships when stratified by gender( OR =0.79,95% CI =0.66-0.93, P =0.01). Peers romantic relationships were positively associated with students romantic relationships ( OR =3.19-5.12, all P <0.01), and there was a moderating effect of the association between maternal connectedness and boys romantic relationships ( OR =1.67, 95% CI =1.05-2.66, P =0.03). Among boys without romantic peers, mother-child connectedness was negatively associated with their romantic relationships ( OR = 0.60 , 95% CI =0.36-0.99, P <0.05). In the total sample of Shanghai and girls of Shaanxi, father-child connectedness was negatively correlated with the romantic relationships of secondary vocational school students ( OR =0.84,0.65,95% CI =0.71-1.00,0.50-0.85,both P <0.05). Peer romantic relationships exhibited a negative moderating effect on the influence of mother-child connectedness on the romantic relationships of males in Shanghai ( OR =1.91, 95% CI =1.03-3.57, P <0.05).
Conclusions
The father-daughter connectedness is negatively correlated with girls romantic behavior, and peer romantic behavior weakens the correlation between mother-child connectedness and boys romantic behavior. Efforts should be made to enhance the parent-child connectedness of secondary vocational students and their ability to cope with peer influence, providing proper guidance for adolescents heterosexual interactions.
6.An advanced machine learning method for simultaneous breast cancer risk prediction and risk ranking in Chinese population: A prospective cohort and modeling study
Liyuan LIU ; Yong HE ; Chunyu KAO ; Yeye FAN ; Fu YANG ; Fei WANG ; Lixiang YU ; Fei ZHOU ; Yujuan XIANG ; Shuya HUANG ; Chao ZHENG ; Han CAI ; Heling BAO ; Liwen FANG ; Linhong WANG ; Zengjing CHEN ; Zhigang YU
Chinese Medical Journal 2024;137(17):2084-2091
Background::Breast cancer (BC) risk-stratification tools for Asian women that are highly accurate and can provide improved interpretation ability are lacking. We aimed to develop risk-stratification models to predict long- and short-term BC risk among Chinese women and to simultaneously rank potential non-experimental risk factors.Methods::The Breast Cancer Cohort Study in Chinese Women, a large ongoing prospective dynamic cohort study, includes 122,058 women aged 25-70 years old from the eastern part of China. We developed multiple machine-learning risk prediction models using parametric models (penalized logistic regression, bootstrap, and ensemble learning), which were the short-term ensemble penalized logistic regression (EPLR) risk prediction model and the ensemble penalized long-term (EPLT) risk prediction model to estimate BC risk. The models were assessed based on calibration and discrimination, and following this assessment, they were externally validated in new study participants from 2017 to 2020.Results::The AUC values of the short-term EPLR risk prediction model were 0.800 for the internal validation and 0.751 for the external validation set. For the long-term EPLT risk prediction model, the area under the receiver operating characteristic curve was 0.692 and 0.760 in internal and external validations, respectively. The net reclassification improvement index of the EPLT relative to the Gail and the Han Chinese Breast Cancer Prediction Model (HCBCP) models for external validation was 0.193 and 0.233, respectively, indicating that the EPLT model has higher classification accuracy.Conclusions::We developed the EPLR and EPLT models to screen populations with a high risk of developing BC. These can serve as useful tools to aid in risk-stratified screening and BC prevention.
7.Effect of salidroside on ischemic brain injury in rats
Qing-Qing WU ; Hui-Lin WU ; Bin-Bin ZHOU ; Zheng-Shuang YU ; Ze-Lin YANG ; Wen-Fang LAI ; Gui-Zhu HONG
Chinese Pharmacological Bulletin 2024;40(5):873-880
Aim To study the permeability of salidro-side(Sal)to the blood brain barrier(BBB)by high-performance liquid chromatography electrospray ioniza-tion tandem mass spectrometry(UPLC-ESI-MS-MS),and to explore the target and mechanism of Sal in the treatment of ischemic stroke(IS)by network pharma-cology,molecular docking technique and animal exper-iment.Methods UPLC-ESI-MS/MS was used to study the BBB penetration of Sal.Multiple databases were used to predict the target of Sal and the disease target of IS,GO and KEGG enrichment analysis were performed and verified by molecular docking technique and animal experiments.Results After Sal adminis-tration to normal rats and MCAO rats,Sal prototype and the metabolite tyrosol were detected in plasma and brain tissue of rats.A total of 191 targets were identi-fied by network pharmacology,the enrichment analysis of GO mainly involved in the biological processes of proteolysis and positive regulation of cell migration,and the analysis of KEGG pathway suggested that PI3K-Akt,MAPK,FOXO and other signaling path-ways played a key role in the treatment of IS by Sal The results of molecular docking showed that Sal had good binding ability with the core target of docking,and the results of animal experiments showed that Sal could significantly improve the neurologic impairment of MCAO rats,the number of Nissl-positive cells in is-chemic side significantly increased,and the expression of VEGF,EGFR and IGF1 increased,while the ex-pression of IL-6 and MMP9 was inhibited.Conclu-sions Sal is able to penetrate the BBB and enter the central nervous system for its pharmacological effects.Network pharmacology predicts the core targets of Sal in the treatment of IS,including VEGFA,EGFR,IL-6,MMP9,IGF1,CASP3,ALB,SRC.The effects of Sal on some core targets can be verified by animal ex-periments,to provide a reference for further study of the mechanism of Sal in the treatment of IS.
8.Effect of recombinant glycoprotein hormone beta5/alpha2 on promoting lipolysis via regulation of cAMP/PKA/CREB pathway in 3T3-L1 adipocytes and its mechanism
Ai-Jun QIAN ; Geng-Miao XIAO ; Zhuang LI ; Xue TIAN ; Xiao-Hong LIU ; Yu-Ping SONG ; Zheng-Gang ZHAO ; Zi-Jian ZHAO ; Fang-Hong LI
Chinese Pharmacological Bulletin 2024;40(7):1272-1278
Aim To investigate the effect of recombi-nant glycoprotein hormone β5/α2(rCGH)on lipolysis in 3T3-L1 adipocytes,and explore the underlying mechanism.Methods 3T3-L1 preadipocytes were cultured and induced to differentiate into mature adipo-cytes,then treated with different concentrations of rCGH for 24 h in vitro.Cell viability of 3T3-L1 adipo-cytes was evaluated by CCK-8 assay,the levels of in-tracellular triglyceride(TG)and glycerol in the culture supernatant were measured by enzymatic method,and the changes of lipid droplets were observed by oil red O staining.The expression levels of HSL and ATGL lipo-lytic proteins in adipocytes were detected by Western blot.To carry out the intervention experiment with dif-ferent concentrations of rCGH with or without the PKA inhibitor,H89,on the mature 3T3-L1 adipocytes,the cultured cells were divided into the control group,H89 pre treatment group,1 μmol·L-1 rCGH group,and(1 μmol·L-1 rCGH+H89)combined intervention group.The contents of intracellular TG and free glycer-ol were measured by enzymatic method,and the ex-pression of CREB and lipolysis-related proteins was de-tected using Western blot.Results Different concen-trations of rCGH(0.25,0.5,1,and 2 μmol·L-1)had no significant effect on the cell viability of adipo-cytes(P>0.05).Compared with the control group,the treatment with rCGH significantly decreased the size of lipid droplets and intracellular TG content,while significantly elevated glycerol concentration in cell supernatant.rCGH treatment also stimulated the protein expression of p-HSL,ATGL,and p-PKA.In addition,the addition of a PKA inhibitor,H89,atten-uated the effects of rCGH on free glycerol level,intra-cellular TG content,and the expression of p-HSL,p-PLIN1,and p-CREB.Conclusions rCGH enhances the lipolysis of 3T3-L1 adipocytes by up-regulating the activities of HSL,ATGL and PKA,promoting glycerol release,inhibiting TG synthesis and lipid accumula-tion,and its mechanism of action is related to the acti-vation of cAMP/PKA/CREB signaling pathway.
9.Development of nanographene oxide as clinical drug carrier in cancer therapy
Chun-Lian ZHONG ; Chang-Jian FANG ; Gui-Yu ZHOU ; Hui-Ling ZHU ; Tang ZHENG ; Wan-Jing ZHUANG ; Jian LIU ; Yu-Sheng LU
Chinese Pharmacological Bulletin 2024;40(8):1413-1418
Immunotherapy is an important breakthrough in canc-er treatment.Unfortunately,low drug concentration in tumor sites almost ineffectively initiates immune responses and thereby severely limits immune therapy applications in clinics.Nanoma-terials are well-recognized drug delivery system in cancer thera-py.Nanographene oxide(NGO)have shown immense perti-nence for anti-cancer drug delivery owing to their ultra-high sur-face area,chemical stability,good biocompatibility and excel-lent photosensitivity.In addition,functionalized modifications on the surface of NGO increase tumor targeting and minimize cy-totoxicity.This study focuses on reviewing the literature and up-dates on NGO in drug delivery and discussing the possibilities and challenges of NGO in cancer synergetic therapy.
10.Effect of salidroside combined with rosavin on ischemic brain injury in rats
Wen-Fang LAI ; Yu-Ting JIANG ; Hui-Ling WU ; Qing-Qing WU ; Jing-Quan CHEN ; Xue-Rui ZHENG ; Gui-Zhu HONG
Chinese Pharmacological Bulletin 2024;40(12):2303-2311
Aim To study the effect of salidroside combined with rosavin on ischemic stroke in rats.Methods The model of MCAO was established by u-sing thread-embolic method.The rats were divided into the sham group,MCAO group,salidroside combined with rosavin group,positive control group,and the drug was given continuously for seven days.The infarct volume was measured by MRI and neurological deficit score was evaluated by Zea-Longa.The levels of Ne-uN,BDNF,TGF-β1,p-Smad were observed by West-ern blot and immunofluorescence staining.The expres-sions of IL-1β,TNF-α and IL-6 were performed by RT-qPCR/ELISA.The primary cortical neurons were isolated,OGD/R inducted,divided into the normal group,OGD/R group,salidroside combined with rosa-vin group,and TGF-β1 inhibitor+salidroside com-bined with rosavin group,the drug was given for 24 hours,and the expressions of NeuN,BDNF,IL-1β,TNF-α and IL-6 were measured.Results Salidroside combined with rosavin could decrease the infarct vol-ume,improve the neurological function,promote the levels of Neun,BDNF,TGF-β1,p-Smad,and inhibit the expressions of IL-1β,TNF-α and IL-6.Salidroside combined with rosavin could promote NeuN,BDNF,inhibit IL-1β,TNF-α,IL-6 in primary nerve cells in-duced by OGD/R,and these effects were blocked by TGF-β1 inhibitor.Conclusions Salidroside combined with rosavin has neuroprotective effects on MCAO rats,and primary neurons are induced by OGD/R,and these effects are closely related to the TGF-β pathway.


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