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.Review of chemical constituents, pharmacological effects, and quality control status of Eucommiae Cortex and prediction of its Q-markers.
Meng-Fan PENG ; Bao-Song LIU ; Pei-Pei YAN ; Cai-Xia LI ; Xiao-Fang ZHANG ; Yi ZHENG ; Ya-Gang SONG ; Tong LIU ; Lei YANG ; Ming-San MIAO
China Journal of Chinese Materia Medica 2025;50(4):946-958
Eucommiae Cortex, the dried bark of Eucommia ulmoides( Eucommiaceae), has both medicinal and edible values.Modern research has shown that Eucommiae Cortex contains various components such as flavonoids, lignans, iridoids, phenolic acids,terpenoids, and steroids, which have anti-osteoporosis, antioxidant, anti-inflammatory, blood glucose-lowering, and gastrointestinal tract-protecting effects. Eucommiae Cortex has applications in multiple fields such as healthcare, industry, and animal husbandry,demonstrating broad development prospects. This article reviews the chemical constituents, pharmacological effects, and quality control status of Eucommiae Cortex. Furthermore, according to the concept of quality marker(Q-marker), this article predicts the Q-markers of Eucommiae Cortex from traditional medicinal properties, traditional medicinal effects, new medicinal effects, measurability of chemical components, compatibility, harvesting periods, and geographical origins. The components such as pinoresinol diglucoside,chlorogenic acid, caffeic acid, quercetin, baicalein, baicalin, olivil, coniferyl ferulate, and kaempferol can be used as Q-markers for Eucommiae Cortex, which provide reference for establishing a systematic quality control system for Eucommiae Cortex.
Eucommiaceae/chemistry*
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Drugs, Chinese Herbal/pharmacology*
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Quality Control
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Humans
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Animals
4.Quality evaluation of Hibisci Mutabilis Folium based on fingerprint and quantitative analysis of multi-components by single-marker method.
Ming CHEN ; Zhen-Hai YUAN ; Xuan TANG ; Dong WANG ; Zhi-Yong ZHENG ; Jing FENG ; Dai-Zhou ZHANG ; Fang WANG
China Journal of Chinese Materia Medica 2025;50(16):4619-4629
To improve the quality evaluation system of Hibisci Mutabilis Folium, this study established high performance liquid chromatography(HPLC) fingerprints of Hibisci Mutabilis Folium and evaluated the quality differences of medicinal materials from different places of production by chemometrics. Furthermore, a content measurement method of differential components was established based on quantitative analysis of multi-components by single-marker(QAMS). The fingerprints of 17 batches of Hibisci Mutabilis Folium from different places of production were constructed, with a total of 19 common peaks marked and seven components confirmed. The similarity between the sample fingerprints and the reference fingerprints ranged from 0.890 to 0.974. By utilizing principal component analysis(PCA), hierarchical cluster analysis(HCA), and orthogonal partial least squares-discriminant analysis(OPLS-DA), the chemical patterns of fingerprints were identified. Five components that could be used to evaluate the quality differences of Hibisci Mutabilis Folium were screened, namely peak 6(quercetin 3-O-β-robinobioside), peak 7(rutin), peak 9(kaempferol-3-O-β-robinobioside), peak 10(kaempferol-3-O-rutinoside), and peak 14(tiliroside). The relative correction factors of isoquercitrin, kaempferol-3-O-β-robinobioside, kaempferol-3-O-rutinoside, kaempferol-3-O-β-D-glucoside, and tiliroside were measured with rutin as the internal reference. The QAMS method was established for the content measurement of six flavonoids, and the results showed there was no significant difference compared to the results obtained by an external standard method. In summary, the HPLC fingerprints and QAMS method established in the study, demonstrating stability and accuracy, can provide a reference for the overall quality evaluation of Hibisci Mutabilis Folium.
Chromatography, High Pressure Liquid/methods*
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Drugs, Chinese Herbal/chemistry*
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Quality Control
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Principal Component Analysis
5.Expert consensus on prognostic evaluation of cochlear implantation in hereditary hearing loss.
Xinyu SHI ; Xianbao CAO ; Renjie CHAI ; Suijun CHEN ; Juan FENG ; Ningyu FENG ; Xia GAO ; Lulu GUO ; Yuhe LIU ; Ling LU ; Lingyun MEI ; Xiaoyun QIAN ; Dongdong REN ; Haibo SHI ; Duoduo TAO ; Qin WANG ; Zhaoyan WANG ; Shuo WANG ; Wei WANG ; Ming XIA ; Hao XIONG ; Baicheng XU ; Kai XU ; Lei XU ; Hua YANG ; Jun YANG ; Pingli YANG ; Wei YUAN ; Dingjun ZHA ; Chunming ZHANG ; Hongzheng ZHANG ; Juan ZHANG ; Tianhong ZHANG ; Wenqi ZUO ; Wenyan LI ; Yongyi YUAN ; Jie ZHANG ; Yu ZHAO ; Fang ZHENG ; Yu SUN
Journal of Clinical Otorhinolaryngology Head and Neck Surgery 2025;39(9):798-808
Hearing loss is the most prevalent disabling disease. Cochlear implantation(CI) serves as the primary intervention for severe to profound hearing loss. This consensus systematically explores the value of genetic diagnosis in the pre-operative assessment and efficacy prognosis for CI. Drawing upon domestic and international research and clinical experience, it proposes an evidence-based medicine three-tiered prognostic classification system(Favorable, Marginal, Poor). The consensus focuses on common hereditary non-syndromic hearing loss(such as that caused by mutations in genes like GJB2, SLC26A4, OTOF, LOXHD1) and syndromic hereditary hearing loss(such as Jervell & Lange-Nielsen syndrome and Waardenburg syndrome), which are closely associated with congenital hearing loss, analyzing the impact of their pathological mechanisms on CI outcomes. The consensus provides recommendations based on multiple round of expert discussion and voting. It emphasizes that genetic diagnosis can optimize patient selection, predict prognosis, guide post-operative rehabilitation, offer stratified management strategies for patients with different genotypes, and advance the application of precision medicine in the field of CI.
Humans
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Cochlear Implantation
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Prognosis
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Hearing Loss/surgery*
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Consensus
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Connexin 26
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Mutation
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Sulfate Transporters
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Connexins/genetics*
6.A computational medicine framework integrating multi-omics, systems biology, and artificial neural networks for Alzheimer's disease therapeutic discovery.
Yisheng YANG ; Yizhu DIAO ; Lulu JIANG ; Fanlu LI ; Liye CHEN ; Ming NI ; Zheng WANG ; Hai FANG
Acta Pharmaceutica Sinica B 2025;15(9):4411-4426
The translation of genetic findings from genome-wide association studies into actionable therapeutics persists as a critical challenge in Alzheimer's disease (AD) research. Here, we present PI4AD, a computational medicine framework that integrates multi-omics data, systems biology, and artificial neural networks for therapeutic discovery. This framework leverages multi-omic and network evidence to deliver three core functionalities: clinical target prioritisation; self-organising prioritisation map construction, distinguishing AD-specific targets from those linked to neuropsychiatric disorders; and pathway crosstalk-informed therapeutic discovery. PI4AD successfully recovers clinically validated targets like APP and ESR1, confirming its prioritisation efficacy. Its artificial neural network component identifies disease-specific molecular signatures, while pathway crosstalk analysis reveals critical nodal genes (e.g., HRAS and MAPK1), drug repurposing candidates, and clinically relevant network modules. By validating targets, elucidating disease-specific therapeutic potentials, and exploring crosstalk mechanisms, PI4AD bridges genetic insights with pathway-level biology, establishing a systems genetics foundation for rational therapeutic development. Importantly, its emphasis on Ras-centred pathways-implicated in synaptic dysfunction and neuroinflammation-provides a strategy to disrupt AD progression, complementing conventional amyloid/tau-focused paradigms, with the future potential to redefine treatment strategies in conjunction with mRNA therapeutics and thereby advance translational medicine in neurodegeneration.
7.Research Progress of Using Canine Olfactory Search for Human Remains
Wei FANG ; Ji-Long ZHENG ; Yi-Ming FU ; Yi LIU
Journal of Forensic Medicine 2024;40(3):269-275
In the process of murder investigation,it is of great significance to find the discarded and buried human remains accurately.The main methods of searching for human remains include human vi-sual search,aerial detection,geophysical technology,remote imaging technology and canine olfactory search technique.Canine olfactory search for human remains is a recognized time-effective and non-invasive search method,making dogs the most valuable search tool in forensic investigation.By sys-tematically reviewing and summarizing relevant literature,and based on the theory of volatile organic compound produced by the decomposition of human remains,this paper explores the basic principle of the canine olfactory search technique for human remains.This paper also reviews the application of training canine search technique for human remains in forensic investigation by using human blood,tissue,cadaver putrefying fluid and odor substitutes as sniffing sources.The application prospect of canine olfactory search for human remains was prospected from the perspectives of detection of vola-tile organic compound during cadaver decay,development of odor substitutes and adsorption devices,and technology tactics used in canine training and use,to provide references for the relevant research of canine olfactory search for human remains in China.
8.Pregnancy and the disease recurrence of patients previously treated for differentiated thyroid cancer: A systematic review and meta analysis
Rui SHAN ; Xin LI ; Ming TAO ; Wucai XIAO ; Jing CHEN ; Fang MEI ; Shibing SONG ; Bangkai SUN ; Chunhui YUAN ; Zheng LIU
Chinese Medical Journal 2024;137(5):547-555
Background::Differentiated thyroid cancer (DTC) is commonly diagnosed in women of child-bearing age, but whether pregnancy influences the prognosis of DTC remains controversial. This study aimed to summarize existing evidence regarding the association of pregnancy with recurrence risk in patients previously treated for DTC.Methods::We searched PubMed, Embase, Web of Science, Cochrane, and Scopus based on the prespecified protocol registered at PROSPERO (CRD42022367896). After study selection, two researchers independently extracted data from the included studies. For quantitative data synthesis, we used random-effects meta-analysis models to pool the proportion of recurrence (for pregnant women only) and odds ratio (OR; comparing the risk of recurrence between the pregnancy group and the nonpregnancy group), respectively. Then we conducted subgroup analyses to explore whether risk of recurrence differed by response to therapy status or duration of follow-up time. We also assessed quality of the included studies.Results::A total of ten studies were included. The sample size ranged from 8 to 235, with participants’ age at pregnancy or delivery ranging from 28 to 35 years. The follow-up time varied from 0.1 to 36.0 years. The pooled proportion of recurrence in all pregnant patients was 0.13 (95% confidence intervals [CI]: 0.06-0.25; I2: 0.58). Among six included studies reporting response to therapy status before pregnancy, we observed a trend for increasingly higher risk of recurrence from excellent, indeterminate, and biochemically incomplete to structurally incomplete response to therapy ( Ptrend <0.05). The pooled risk of recurrence in the pregnancy group showed no evidence of a significant difference from that in the nonpregnancy group (OR: 0.75; 95% CI: 0.45-1.23; I2: 0). The difference in follow-up time (below/above five years) was not associated with either the proportion of recurrence in all pregnant patients ( P >0.05) or the OR of recurrence in studies with a comparison group ( P >0.05). Two included studies that focused on patients with distant metastasis also did not show a significant difference in disease recurrence between pregnancy and nonpregnancy groups (OR: 0.51 [95% CI: 0.14-1.87; I2: 59%]). Conclusion::In general, pregnancy appears to have a minimal association with the disease recurrence of DTC with initial treatment. Clinicians should pay more attention to progression of DTC among pregnant women with biochemical and/or structural persistence.Registration::PROSPERO, https://www.crd.york.ac.uk/PROSPERO/; No. CRD42022367896.
9.Antimicrobial resistance of Escherichia spp.:surveillance report from Hunan Province Antimicrobial Resistance Surveillance System,2012-2021
Fang-Wei LONG ; Li-Hua CHEN ; Chen-Chao FU ; Chen LI ; Yan-Ming LI ; Xing-Wang NING ; Jun LIU ; Guo-Min SHI ; Jing-Min WU ; Hong-Xia YUAN ; Ming ZHENG ; An-Hua WU ; Xun HUANG ; Huai-De YANG ; Nan REN
Chinese Journal of Infection Control 2024;23(8):975-983
Objective To understand the antimicrobial resistance of Escherichia spp.from member units of Hu-nan Province Antimicrobial Resistance Surveillance System from 2012 to 2021.Methods According to the technical scheme of China Antimicrobial Resistance Surveillance System(CARSS),data about Escherichia spp.and the anti-microbial susceptibility testing results reported from member units of Hunan Province Antimicrobial Resistance Sur-veillance System were analyzed by WHONET 5.6 software.Results From 2012 to 2021,a total of 476 351 clini-cally isolated Escherichia spp.were collected,475 520 of which were Escherichia coli,accounting for 99.8%;92.6%were isolated from inpatients;39.3%were isolated from urine specimens.Over the past 10 years,the proportion of Escherichia spp.in total detected pathogens remained relatively stable,ranging 20%-23%,the lowest rate was 18.7%in 2012,and the highest rate was 22.9%in 2015.In the past 10 years,the resistance rates of Escherichia spp.to ampicillin,ceftriaxone,cefotaxime and ampicillin/sulbactam were>80%,>47%,>45%,and>39%,respectively;resistance rates to piperacillin/tazobactam,cefoperazone/sulbactam,and nitrofurantoin were all<8%,to tigecycline,amikacin,imipenem,and meropenem(except in 2012)were all<5%.Resistance of Escherichia spp.to 22 commonly clinically used antimicrobial agents fluctuated,but overall trend decreased year by year.The resistance rates of Escherichia spp.from patients in the intensive care unit(ICU),non-ICU patients,outpatients,and emergency patients to 22 clinically commonly used antimicrobial agents were compared among different depart-ments,and the differences were statistically significant(all P<0.05).The resistance rates of Escherichia spp.iso-lated from ICU and non-ICU patients were compared,and except for tigecycline,the resistance rates to the other 21 antimicrobial agents were statistically different(all P<0.05).The resistance rates of Escherichia spp.isolated from patients to commonly clinically used antimicrobial agents were statistically different among patients of different age groups(all P<0.05).Conclusion Escherichia spp.isolated from patients in different years,departments,specimens,and ages have different resistance to commonly used antimicrobial agents.It is necessary to continue to strengthen the surveillance on bacterial resistance,so as to guide the rational choice of antimicrobial agents.
10.Clinical effect of personalized pars plana vitrectomy for proliferative diabetic retinopathy
Xinbao ZHENG ; Jiayu CHEN ; Jiahong WEI ; Jing XIA ; Aiping YANG ; Chunfeng CHEN ; Ming-Fang LI ; Cheng FENG ; Yongwang ZHAO ; Jingfa ZHANG
Recent Advances in Ophthalmology 2024;44(6):449-453
Objective To explore the clinical effect of personalized pars plana vitrectomy(PPV)for proliferative di-abetic retinopathy(PDR).Methods In this retrospective case study,76 patients(86 eyes)diagnosed with PDR and re-ceiving PPV in the Department of Ophthalmology of Songjiang Hospital affiliated to Shanghai Jiao Tong University School of Medicine,from October 2019 to November 2022,were divided into the observation group(40 patients,46 eyes)and the control group(36 patients,40 eyes).Patients in the obseration group were treated with personalized PPV,while patients in the control group were treated with conventional PPV,After treatment,all patients were followed up for 12 months.The operation time,intraoperative use of heavy water and silicone oil,incidence of iatrogenic retinal tears and heavy water resi-dues,proportion of scleral buckling,preoperative and postoperative best corrected visual acuity(BCVA)and intraocular pressure(IOP),retinal reattachment rate at 12 months after surgery,and the incidence of post-vitrectomy vitreous hemor-rhage(PVH),diabetic macular edema(DME)and neovascular glaucoma(NVG)were compared between the two groups.Results The operation time of patients in the observation group was shorter than that in the control group(P<0.05).Intraoperative use of heavy water and silicone oil in the observation group was lower than that in the control group(both P<0.05).The incidence of iatrogenic retinal tears and heavy water residues and the proportion of scleral buckling showed no statistically significant difference between the two groups(all P>0.05).There was no statistically significant difference between the two groups in BCVA preoperatively,3,6 and 12 months postoperatively(all P>0.05).BCVA in the observa-tion group was better than that in the control group at 1 day,1 week and 1 month after surgery(all P<0.05).Compared with the preoperative value,BCVA increased in the observation group at 1 day,1 week,1 month,3 months,6 months,and 12 months after surgery(all P<0.05);in the control group,BCVA increased slightly at 1 day and 1 week(both P>0.05)and then increased significantly at 1 month,3 months,6 months,and 12 months after surgery(all P<0.05).The two groups showed no statistically significant difference in IOP at 1 day,1 week,1 month,3 months,6 months,and 12 months postoperatively(all P>0.05).There was no statistically significant difference in the retinal reattachment rate and the inci-dence of complications such as PVH,DME,and NVG between the two groups at 12 months postoperatively(all P>0.05).Conclusion Personalized PPV can shorten the operation time,reduce the intraoperative use of heavy water and silicone oil,enhance the efficiency of the operation,and rapidly improve the visual acuity of PDR patients.

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