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.Antibiotic-Depleted Lung Microbiota Modulates Surfactant Proteins Expression and Reduces Experimental Silicosis.
Qiang ZHOU ; Mei Yu CHANG ; Ning LI ; Yi GUAN ; San Qiao YAO
Biomedical and Environmental Sciences 2025;38(4):469-483
OBJECTIVE:
Recent studies have overturned the traditional concept of the lung as a "sterile organ" revealing that pulmonary microbiota dysbiosis and abnormal surfactant proteins (SPs) expression are involved in the progression of silicosis. This study aimed to investigate the relationship between abnormal SPs expression and dysbiosis of lung microbiota in silica-induced lung fibrosis, providing insights into mechanisms of silicosis.
METHODS:
Lung pathology, SPs expression, and microbiota composition were evaluated in silica-exposed mice. A mouse model of antibiotic-induced microbiota depletion was established, and alveolar structure and SPs expression were assessed. The roles of the lung microbiota and SPs in silicosis progression were further evaluated in mice with antibiotic-induced microbiota depletion, both with and without silica exposure.
RESULTS:
Silica exposure induced lung inflammation and fibrosis, along with increased expression of SP-A expression. Antibiotics (Abx)-induced microbiota depletion elevated SP-A and SP-D expression. Furthermore, silica exposure altered lung microbiota composition, enriching potentially pathogenic taxa. However, antibiotic-induced microbiota depletion prior to silica exposure reduced silica-mediated lung fibrosis and inflammation.
CONCLUSION
Lung microbiota is associated with silica-induced lung injury. Overproduction of SP-A and SP-D, induced by Abx-induced microbiota depletion, may enhance the resistance of mouse lung tissue to silica-induced injury.
Animals
;
Silicosis/prevention & control*
;
Lung/metabolism*
;
Mice
;
Anti-Bacterial Agents/pharmacology*
;
Microbiota/drug effects*
;
Silicon Dioxide/toxicity*
;
Mice, Inbred C57BL
;
Male
;
Pulmonary Surfactant-Associated Proteins/genetics*
3.Hypertrophic Cardiomyopathy: Mechanisms of Pathogenicity.
Bao Xi WANG ; Yue Ting ZHOU ; Yi Pin ZHAO ; Yong CHENG ; Jun REN ; Guan Chang TAN ; Xiao Hu WANG
Biomedical and Environmental Sciences 2025;38(8):988-1000
Hypertrophic cardiomyopathy (HCM) is a major contributor to cardiovascular diseases (CVD), the leading cause of death globally. HCM can precipitate heart failure (HF) by causing the cardiac tissue to weaken and stretch, thereby impairing its pumping efficiency. Moreover, HCM increases the risk of atrial fibrillation, which in turn elevates the likelihood of thrombus formation and stroke. Given these significant clinical ramifications, research into the etiology and pathogenesis of HCM is intensifying at multiple levels. In this review, we discuss and synthesize the latest findings on HCM pathogenesis, drawing on key experimental studies conducted both in vitro and in vivo. We also offer our insights and perspectives on these mechanisms, while highlighting the limitations of current research. Advancing fundamental research in this area is essential for developing effective therapeutic interventions and enhancing the clinical management of HCM.
Cardiomyopathy, Hypertrophic/physiopathology*
;
Humans
;
Animals
4.Emerging role of Jumonji domain-containing protein D3 in inflammatory diseases
Li XIANG ; Chen RU-YI ; Shi JIN-JIN ; Li CHANG-YUN ; Liu YAN-JUN ; Gao CHANG ; Gao MING-RONG ; Zhang SHUN ; Lu JIAN-FEI ; Cao JIA-FENG ; Yang GUAN-JUN ; Chen JIONG
Journal of Pharmaceutical Analysis 2024;14(9):1282-1300
Jumonji domain-containing protein D3(JMJD3)is a 2-oxoglutarate-dependent dioxygenase that specif-ically removes transcriptional repression marks di-and tri-methylated groups from lysine 27 on histone 3(H3K27me2/3).The erasure of these marks leads to the activation of some associated genes,thereby influencing various biological processes,such as development,differentiation,and immune response.However,comprehensive descriptions regarding the relationship between JMJD3 and inflammation are lacking.Here,we provide a comprehensive overview of JMJD3,including its structure,functions,and involvement in inflammatory pathways.In addition,we summarize the evidence supporting JMJD3's role in several inflammatory diseases,as well as the potential therapeutic applications of JMJD3 inhibitors.Additionally,we also discuss the challenges and opportunities associated with investigating the functions of JMJD3 and developing targeted inhibitors and propose feasible solutions to provide valuable insights into the functional exploration and discovery of potential drugs targeting JMJD3 for inflammatory diseases.
5.Near-infrared targeted probe designed for intraoperative imaging of prostatic neurovascular bundles.
Zhan Yi ZHANG ; Fan ZHANG ; Ye YAN ; Cai Guang CAO ; Chang Jian LI ; Shao Hui DENG ; Yue Hao SUN ; Tian Liang HUANG ; Yun He GUAN ; Nan LI ; Min LU ; Zhen Hua HU ; Shu Dong ZHANG
Journal of Peking University(Health Sciences) 2023;55(5):843-850
OBJECTIVE:
To investigate the imaging effect of a near-infrared fluorescent targeted probe ICG-NP41 on the neurovascular bundles (NVB) around the prostate in rats.
METHODS:
A near-infrared fluorescent targeted probe ICG-NP41 was synthesized. An animal model for NVB imaging was established using Sprague-Dawley rats (250-400 g). Experiments were conducted using a custom-built near-infrared windowⅡ(NIR-Ⅱ) small animal in vivo imaging system, and images collected were processed using ImageJ and Origin. The fluorescence signal data were statistically analyzed using GraphPad Prism. The signal-to-background ratio (SBR) for NVB was quantitatively calculated to explore the effective dosage and imaging time points. Finally, paraffin pathology sections and HE staining were performed on the imaging structures.
RESULTS:
Except for rats in the control group (n=2), right-sided NVB of the rats injected with ICG-NP41 (n=2 per group) were all observed in NIR-Ⅱ fluorescence mode 2 h and 4 h after administration. At 2 h and 4 h, average SBR of cavernous nerve in 2 mg/kg group in fluorescence mode was 1.651±0.142 and 1.619±0.110, respectively, both higher than that in white light mode (1.111±0.036), with no significant difference (P>0.05); average SBR of 4 mg/kg group in fluorescence mode were 1.168±0.066 and 1.219±0.118, respectively, both higher than that in white light mode (1.081±0.040), with no significant difference (P>0.05). At 2 h and 4 h, the average SBR of 2 mg/kg and 4 mg/kg groups in fluorescence mode were higher than that of the control group (SBR=1), the average SBR of the 2 mg/kg group was higher than that of the 4 mg/kg group, and all the above with no significant difference (P>0.05). The average diameter of the nerve measured by full width at half maxima method was about (178±15) μm. HE staining of paraffin sections showed the right major pelvic ganglion.
CONCLUSION
The near-infrared fluorescent targeted probe ICG-NP41 can be used for real-time imaging of the NVB around the prostate in rats, providing a potential feasible solution for localizing NVB in real time during nerve-sparing radical prostatectomy.
Male
;
Rats
;
Animals
;
Prostate/diagnostic imaging*
;
Paraffin
;
Indocyanine Green
;
Rats, Sprague-Dawley
;
Fluorescent Dyes
7.Main chemical constituents in aerial parts of Glycyrrhiza uralensis by UPLC-Q-Exactive Orbitrap-MS.
Guan-Hua CHANG ; Ying-Yi BO ; Jie CUI ; Lu-Lu XU ; Zi-Han ZHAO ; Wen-Quan WANG ; Jun-Ling HOU
China Journal of Chinese Materia Medica 2021;46(6):1449-1459
Chemical constituents from aerial parts of Glycyrrhiza uralensis were analyzed and identified using ultra-high performance liquid chromatography coupled with hybrid quadrupole-orbitrap mass spectrometry(UPLC-Q-Exactive Orbitrap-MS). The chromatographic column of Waters Acquity UPLC BEH-C_(18)(2.1 mm×100 mm, 1.7 μm) was adopted, with acetonitrile-water(0.5% formic acid) as mobile phase at a flow rate of 0.2 mL·min~(-1). Data was collected in positive and negative modes of electrospray ionization(ESI). A total of 55 compounds, including 42 flavonoids, 9 stilbenes, 2 coumarins, 1 lignin and 1 phenolic acid, which were characterized in the aerial parts of G. uralensis based on accurate molecular mass information of molecular and product ions provided by UPLC-Q-Exactive Orbitrap-MS based on comparison with standard substances and references. It is an effective and accurate method to provide chemical information of constituents in aerial parts of G. uralensis, and can provide a reference for further study on pharmacodynamic material basis and resources development and utilization.
Chromatography, High Pressure Liquid
;
Drugs, Chinese Herbal
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Glycyrrhiza uralensis
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Mass Spectrometry
;
Plant Components, Aerial
8.Design and Feasibility Study of Tracheal Intubation Device Based on Magnetic Navigation Technology.
Rongfeng WANG ; Qianyun ZHANG ; Hongfan DING ; Haoyang ZHU ; Chang LIU ; Zheng GUAN ; Ge ZHAO ; Qiang WANG ; Yi LYU
Chinese Journal of Medical Instrumentation 2021;45(1):22-25
OBJECTIVE:
In the context of coronavirus disease 2019 (COVID-19) pandemic, the subject was designed to develop a new tracheal intubation device based on magnetic navigation technology to improve the success rate of tracheal intubation and reduce the risk of occupational exposure of medical staff.
METHODS:
The new tracheal intubation device was designed with the uniqueness of the magnetic field environment and magnetic steering of magnetic navigation technology. And preliminary magnetic navigation tracheal intubation experiments were performed on the tracheal intubation simulator.
RESULTS:
Magnetic navigation tracheal intubation can successfully implement tracheal intubation, and the time required is lower than that of traditional laryngoscopy.
CONCLUSIONS
The tracheal intubation based on magnetic navigation technology is feasible, with high efficiency and easy operation. That is expected to be widely used for tracheal intubation during treatment of patients outside the hospital in the future. At the same time, magnetic navigation endotracheal intubation technology will be the key technology for the development of endotracheal intubation robots.
COVID-19/therapy*
;
Equipment Design
;
Feasibility Studies
;
Humans
;
Intubation, Intratracheal
;
Magnetic Phenomena
;
SARS-CoV-2
;
Technology
9.Mis-estimation of coronary lesions and rectification by SYNTAX score feedback for coronary revascularization appropriateness.
Shen LIN ; Heng ZHANG ; Si-Peng CHEN ; Chen-Fei RAO ; Fan WU ; Fa-Jun ZHOU ; Yun WANG ; Hong-Bing YAN ; Ke-Fei DOU ; Yong-Jian WU ; Yi-Da TANG ; Li-Hua XIE ; Chang-Dong GUAN ; Bo XU ; Zhe ZHENG
Chinese Medical Journal 2020;133(11):1276-1284
BACKGROUND:
Imprecise interpretation of coronary angiograms was reported and resulted in inappropriate revascularization. Synergy Between Percutaneous Coronary Intervention with Taxus and Cardiac Surgery (SYNTAX) score is a comprehensive system to evaluate the complexity of the overall lesions. We hypothesized that a real-time SYNTAX score feedback from image analysts may rectify the mis-estimation and improve revascularization appropriateness in patients with stable coronary artery disease (CAD).
METHODS:
In this single-center, historical control study, patients with stable CAD with coronary lesion stenosis ≥50% were consecutively recruited. During the control period, SYNTAX scores were calculated by treating cardiologists. During the intervention period, SYNTAX scores were calculated by image analysts immediately after coronary angiography and were provided to cardiologists in real-time to aid decision-making. The primary outcome was revascularization deemed inappropriate by Chinese appropriate use criteria for coronary revascularization.
RESULTS:
A total of 3245 patients were enrolled and assigned to the control group (08/2016-03/2017, n = 1525) or the intervention group (03/2017-09/2017, n = 1720). For SYNTAX score tertiles, 17.9% patients were overestimated and 4.3% were underestimated by cardiologists in the control group. After adjustment, inappropriate revascularization significantly decreased in the intervention group compared with the control group (adjusted odds ratio [OR]: 0.83; 95% confidence interval [CI]: 0.73-0.95; P = 0.007). Both inappropriate percutaneous coronary intervention (adjusted OR: 0.82; 95% CI: 0.74-0.92; P < 0.001) and percutaneous coronary intervention utilization (adjusted OR: 0.88; 95% CI: 0.79-0.98; P = 0.016) decreased significantly in the intervention group. There was no significant difference in 1-year adverse cardiac events between the control group and the intervention group.
CONCLUSIONS:
Real-time SYNTAX score feedback significantly reduced inappropriate coronary revascularization in stable patients with CAD.
CLINICAL TRIAL REGISTRATION
Nos. NCT03068858 and NCT02880605; https://www.clinicaltrials.gov.
10.Visual analysis of coronavirus disease 2019 (COVID-19) studies based on bibliometrics.
Ying CHEN ; Yi-Bo GUO ; Ran GUO ; Xiu-Fen CHEN ; Guan-Hua CHANG ; Xin LI ; Li-Yu HAO ; Zhi-Rong SUN ; Zi-Long ZHANG
China Journal of Chinese Materia Medica 2020;45(10):2239-2248
To analyze the development of coronavirus disease 2019(COVID-19), this study systematically retrieved relevant Chinese and English literatures from both CNKI and Web of Science database platforms by bibliometric research method and CiteSpace 5.5.R2 software to obtain information and visualize relevant literatures. A total of 695 Chinese and 446 English literatures were included in this paper. Statistics showed that China had published most of the literatures and established close cooperation with the United States and the United Kingdom. Through the analysis, Tongji Medical College of Huazhong University of Science and Technology and its affiliated hospitals published the largest number of the publications. Moreover, the highly productive journals including Journal of Traditional Chinese Medicine and The Lancet covered eight major fields, such as medicine, medical virology, radiation medicine, infectious disease, and traditional Chinese medicine. Besides, a total of 35 special COVID-19 funds were recently established to subsidize these studies. The key words and themes analysis indicated that protein structure of COVID-19, receptor targets and mechanisms of action, integration of traditional Chinese and Western medicine, screening and development of antiviral drugs from traditional Chinese medicine and Western medicine, vaccine research as well as epidemiological characteristics and prediction are current study hotspots. This study provides a reference for researchers to rapidly master main study directions of COVID-19 and screen out relevant literatures.
Betacoronavirus
;
Bibliometrics
;
China
;
Coronavirus Infections
;
Humans
;
Pandemics
;
Pneumonia, Viral
;
United Kingdom
;
United States

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