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.The Mechanism of Blue Light in Inactivating Microorganisms and Its Applications in The Food and Medical Fields
Ruo-Hong BI ; Rong-Qian WU ; Yi LÜ ; Xiao-Fei LIU
Progress in Biochemistry and Biophysics 2025;52(5):1219-1228
Blue light inactivation technology, particularly at the 405 nm wavelength, has demonstrated distinct and multifaceted mechanisms of action against both Gram-positive and Gram-negative bacteria, offering a promising alternative to conventional antibiotic therapies. For Gram-positive pathogens such as Bacillus cereus, Listeria monocytogenes, and methicillin-resistant Staphylococcus aureus (MRSA), the bactericidal effects are primarily mediated by endogenous porphyrins (e.g., protoporphyrin III, coproporphyrin III, and uroporphyrin III), which exhibit strong absorption peaks between 400-430 nm. Upon irradiation, these porphyrins are photoexcited to generate cytotoxic reactive oxygen species (ROS), including singlet oxygen, hydroxyl radicals, and superoxide anions, which collectively induce oxidative damage to cellular components. Early studies by Endarko et al. revealed that (405±5) nm blue light at 185 J/cm² effectively inactivated L. monocytogenes without exogenous photosensitizers, supporting the hypothesis of intrinsic photosensitizer involvement. Subsequent work by Masson-Meyers et al. demonstrated that 405 nm light at 121 J/cm² suppressed MRSA growth by activating endogenous porphyrins, leading to ROS accumulation. Kim et al. further elucidated that ROS generated under 405 nm irradiation directly interact with unsaturated fatty acids in bacterial membranes, initiating lipid peroxidation. This process disrupts membrane fluidity, compromises structural integrity, and impairs membrane-bound proteins, ultimately causing cell death. In contrast, Gram-negative bacteria such as Salmonella, Escherichia coli, Helicobacter pylori, Pseudomonas aeruginosa, and Acinetobacter baumannii exhibit more complex inactivation pathways. While endogenous porphyrins remain central to ROS generation, studies reveal additional photodynamic contributors, including flavins (e.g., riboflavin) and bacterial pigments. For instance, H. pylori naturally accumulates protoporphyrin and coproporphyrin mixtures, enabling efficient 405 nm light-mediated inactivation without antibiotic resistance concerns. Kim et al. demonstrated that 405 nm light at 288 J/cm² inactivates Salmonella by inducing genomic DNA oxidation (e.g., 8-hydroxy-deoxyguanosine formation) and disrupting membrane functions, particularly efflux pumps and glucose uptake systems. Huang et al. highlighted the enhanced efficacy of pulsed 405 nm light over continuous irradiation for E. coli, attributing this to increased membrane damage and optimized ROS generation through frequency-dependent photodynamic effects. Environmental factors such as temperature, pH, and osmotic stress further modulate susceptibility, sublethal stress conditions (e.g., high salinity or acidic environments) weaken bacterial membranes, rendering cells more vulnerable to subsequent ROS-mediated damage. The 405 nm blue light inactivates drug-resistant Pseudomonas aeruginosa through endogenous porphyrins, pyocyanin, and pyoverdine, with the inactivation efficacy influenced by bacterial growth phase and culture medium composition. Intriguingly, repeated 405 nm exposure (20 cycles) failed to induce resistance in A. baumannii, with transient tolerance linked to transient overexpression of antioxidant enzymes (e.g., superoxide dismutase) or stress-response genes (e.g., oxyR). For Gram-positive bacteria, porphyrin abundance dictates sensitivity, whereas in Gram-negative species, membrane architecture and accessory pigments modulate outcomes. Critically, ROS-mediated damage is nonspecific, targeting DNA, proteins, and lipids simultaneously, thereby minimizing resistance evolution. The 405 nm blue light technology, as a non-chemical sterilization method, shows promise in medical and food industries. It enhances infection control through photodynamic therapy and disinfection, synergizing with red light for anti-inflammatory treatments (e.g., acne). In food processing, it effectively inactivates pathogens (e.g., E. coli, S. aureus) without altering food quality. Despite efficacy against multidrug-resistant A. baumannii, challenges include device standardization, limited penetration in complex materials, and optimization of photosensitizers/light parameters. Interdisciplinary research is needed to address these limitations and scale applications in healthcare, food safety, and environmental decontamination.
3.A comparative study of four combined methods for planning access to the anterior acetabular column for nail place-ment
Li-Yang YI ; Bi-Wen LI ; Peng TANG ; Hu TANG ; Wen-Fu TAN
China Journal of Orthopaedics and Traumatology 2024;37(8):801-807
Objective To investigate global optimisation of anterior acetabular column pinning channels can be achieved based on large density point cloud data.Methods Data were collected on the CT scans of the normal pelvis in 40 adults from January 2022 to January 2023,including 22 males and 18 females,aged 20 to 54 years old.Medical imaging data from three of the samples were selected for experimental study.In planning access for anterior acetabular column pinning,to address the is-sue of whether the current CAD planning methods were advanced or not,four combinations of the same point cloud acquisition channels,different directional line creation software,and the same 3D design and virtual experiment software were proposed:Mimics+Imageware+UG,Mimics+3DReshaper+UG,Mimics+ZEISS Quality Suite+UG and Mimics+Design X+UG,and direc-tional lines created based on the centroid point set and solid point cloud of the secondary pruning model,respectively,and it applied to the planning of the left anterior column pinning channel of the three acetabular samples.The maximum internally connected cylinder without acetabular socket and pubic bone penetration was used as a safe passage for nailing of the anterior acetabular column to evaluate the advancement of each method.Results The fitting effect of the directional line was better than that of the unnoised solid point cloud when the central point set with obvious relevant features was selected as the sample points;and the combination of Mimics+Imageware+UG and Mimics+3DReshaper+UG could efficiently and stably obtain the desirable planning results when planning with the central point set,respectively,in the three acetabular samples 1,2,3.The maximum internal joint circle diameters obtained in samples 1,2,and 3 were 10.35 mm,9.62 mm,and 9.24 mm;and when the directional lines were based on the solid point cloud the combined methods of Mimics+ZEISS Quality Suite+UG and Mimics+Design X+UG were not applicable;whereas the Mimics+3 DReshaper+UG the solid point cloud denoising planning method could stably obtain the maximum value of the safe channel for nail placement,and the maximum internal joint circle diameters obtained in acetabular samples 1,2,and 3 are 10.66 mm,10.96 mm,and 9.48 mm,respectively.Conclusion It is recommend-ed that the nail placement channel planners use robust Mimics+Imageware+UG or Mimics+3DReshaper+UG centre point set planning method,and if there is enough time,it is recommended to use the solid point cloud denoising planning method of Mimics+3DReshaper+UG in order to obtain the maximum value of safe channels for nail placement.
4.Predictive values of PNI,LMR and MELD for early lung infection after liver transplantation
Kai YANG ; Dingcong HOU ; Shaoxian DUAN ; Yi BI ; Yan XIE ; Li ZHANG ; Wentao JIANG
Tianjin Medical Journal 2024;52(10):1041-1045
Objective To explore risk factors of early lung infection after liver transplantation and to construct a prediction model of early lung infection after liver transplantation.Methods The clinical data of 269 patients who underwent orthotopic liver transplantation for the first time were retrospectively analyzed.Patients were divided into the infected group(n=97)and the non-infected group(n=172)according to whether pulmonary infection occurred within 30 days after operation.The preoperative general data,preoperative laboratory examination results,intraoperative and postoperative data of the patients were collected.Multivariate Logistic regression analysis were used to screen risk factors of pulmonary infection.Based on the results of multivariate analysis,the prediction model was constructed and the prediction efficiency of the model was evaluated.Results Univariate and multivariate Logistic regression analysis showed that preoperative PNI≤41.70(OR=1.972,95%CI:1.047-3.714,P=0.036),LMR≤1.52(OR=2.020,95%CI:1.102-3.705,P=0.023),MELD score>10.72(OR=1.985,95%CI:1.103-3.573,P=0.022),operative time>448.00 min(OR=2.676,95%CI:1.515-4.727,P=0.001)and intensive care unit(ICU)hospitalization time>4.0 days(OR=2.623,95%CI:1.335-5.154,P=0.005)were independent risk factors for early pulmonary infection after liver transplantation.The ROC area under the curve(AUC)of the prediction model based on the results of multivariate Logistic regression analysis was 0.768,the sensitivity was 80.41%and the specificity was 60.47%.Conclusion The prediction model based on PNI,LMR,MELD score,operation time and ICU hospitalization time can effectively predict the occurrence of early pulmonary infection after liver transplantation.
5.mfat-1 gene therapy prevents and ameliorates multiple sclerosis in mice
Min-Yi TANG ; Xin-Yun BI ; Shuai WANG ; Chao-Feng XING ; Xiao-Li WU ; Zi-Jian ZHAO ; Fang-Hong LI
Chinese Pharmacological Bulletin 2024;40(10):1930-1936
Aim To investigate the preventive and therapeutic effects of the mfat-1 gene therapy on exper-imental autoimmune encephalomyelitis in mice.Meth-ods mfat-1 gene therapy was used to render the host endogenous capability of producing ω-3 PUFAs,con-comitantly reduce the levels of ω-6 PUFAs,and change the proportion of ω-3/ω-6 PUFAs.Then,the levels of PUFAs in blood were analyzed by gas chromatography.The neurological deficits in mice were evaluated by neurological dysfunction score.HE staining and LFB staining of mouse spinal cord slices were used to ob-serve central nervous system inflammation infiltration and demyelinating lesions.Flow cytometry microsphere microarray technology was used to detect the content of cytokines in serum.Results The mfat-1 gene therapy could significantly raise the proportion of ω-3/ω-6 PU-FAs(P<0.05),markedly delay the incubation period and peak period and reduce neurological dysfunction scores(P<0.05),and improve inflammation and de-myelination of spinal cords(P<0.05).It could also greatly increase the levels of IL-2,IFN-γ,IL-4 and IL-17 in serum(P<0.05).Conclusion The pro-portion of ω-3/ω-6 PUFAs in blood circulation en-hanced by mfat-1 gene therapy can effectively prevent and treat experimental autoimmune encephalomyelitis in mice.
6.The protective effect of licorice on cisplatin-induced liver injury in rats based on untargeted metabolomics study
Ting-Mei YIN ; Bi-Qian YANG ; Guang-Miao GAO ; Xiao-Yan FU ; Xiao-Long LIAN ; Ling-Ling YANG ; Jie LI ; Yi DENG
Chinese Pharmacological Bulletin 2024;40(12):2246-2255
Aim To study the mechanism of action of licorice in alleviating cisplatin liver injury.Methods Forty-eight SD rats were randomly divided into a blank group,a model group,a positive control group and lico-rice administration groups(450,900 and 1 800 mg·kg-1).After 5 days of prophylactic administration,8 mg·kg-1 of cisplatin was injected intraperitoneally in-to the model,positive control,and licorice administra-tion groups to establish an acute liver injury model.LC-MS/MS untargeted metabolomics was used to ana-lyze the differential metabolites and metabolic pathways of licorice to alleviate cisplatin acute liver injury.Re-sults PLS-DA score plots showed significant separa-tion of metabolomics samples.The analysis yielded 119 differential metabolites associated with cisplatin liver injury,of which 31 differential metabolites were signifi-cantly regressed after licorice intervention and were mainly involved in D-arginine and D-ornithine metabo-lism;parathyroid hormone synthesis,secretion,and ac-tion;tyrosine metabolism;biosynthesis of phenylala-nine,tyrosine,and tryptophan;β-alanine metabolism;and amino acid and nucleotide sugar metabolism.Con-clusions Metabolomics analysis indicates that licorice can alter the metabolic profile of cisplatin-induced he-patic injury rats,and its mechanism of action may be related to its improvement of the levels of differential metabolites and its involvement in the regulation of a-mino acid metabolism and other related pathways.
7.Clinical comprehensive evaluation of finerenone in the treatment of diabetic nephropathy
Yahong BI ; Ying ZHENG ; Fengyong JIN ; Jianxun FENG ; Yi FANG ; Junqin SHENG
Chinese Journal of Pharmacoepidemiology 2024;33(5):561-571
Objective To investigate the clinical comprehensive value of finerenone in the treatment of diabetic nephropathy(DN),and to provide evidence-based medicine evidence for clinical drug decision.Methods PubMed,Web of Science,Embase,Cochrane Library,WanFang Data,CNKI and health technology assessment(HTA)official website were systematically searched to collect the systematic review/Meta-analysis and pharmacoeconomic evaluation on finerenone in treatment of DN from the inception to November 31,2023.The method of rapid HTA was used to evaluate the effectiveness,safety and economic evaluation.The innovation,suitability and accessibility of finerenone were analyzed by relevant data from drug instructions,professional websites such as the National Medical Products Administration(NMPA)and Center for Drug Evaluation,NMPA.Results In terms of effectiveness,finerenone significantly reduced the risk of the renal composite events and composite cardiovascular outcomes in DN compared with placebo and traditional mineralocorticoid receptor antagonist(MRA).In terms of safety,the incidence of adverse reactions and acute kidney injury of finerenone was similar to that of placebo and traditional MRA,but the incidence of hyperkalemia was higher than that of placebo.In terms of economy,two foreign HTA reports showed that finerenone was more economical than standard treatment.In terms of innovation,finerenone was the world's first approved non-steroidal,selective MRA innovative drug for the treatment of type 2 DN,making its efficacy and adverse reactions more advantageous.In terms of suitability,finerenone should only be taken once a day,which had good suitability in pharmaceutical properties and clinical use.In terms of accessibility,the domestic price of finerenone was lower than the international price,and it was included in the medical insurance,and the market coverage was high,it had a good affordability and availability.Conclusion Finerenone has good effectiveness and safety in the treatment of DN,but attention should be paid to the risk of hyperkalemia,and its economy requires further economic research in China.As the world's first approved non-steroidal,selective MRA innovative drug,finerenone has better innovation,suitability and accessibility.
8.Chemical constituents from the leaves of Citrus reticulata and their anti-inflammatory activities
Fa-Ke YANG ; Xing YANG ; Zhi-Bi ZHANG ; Rui YIN ; Hong-Chuan ZHANG ; Xu-Li DENG ; Wei-Mao DONG ; Yi-Mou WANG ; Hong-Ping HE ; Fa-Wu DONG
Chinese Traditional Patent Medicine 2024;46(9):2972-2979
AIM To study the chemical constituents from the leaves of Citrus reticulata Blanco and their anti-inflammatory activities.METHODS The 85%ethanol extract from the leaves of C.reticulata was isolated and purified by silica gel,D101 macroporous resin,MCI,ODS and Sephadex LH-20,then the structures of obtained compounds were identified by physicochemical properties and spectral data.The Griess method was used to determine their inhibitory activities on lipopolysaccharide-induced NO production in macrophages RAW 264.7 cells.The mice foot swelling inflammation model induced by carrageenan was established,and the levels of IL-1β,TNF-α were detected.RESULTS Twelve compounds were isolated and identified as nobiletin(1),tangeretin(2),5-demethylinoblitin(3),5,4'-dihydroxy-6,7,8,3'-tetramethoxy flavone(4),5-hydroxy-7,8,3',4'-trimethoxyflavanone(5),3,5,6,7,8,3',4'-heptamethoxyflavanone(6),hesperetin(7),5-hydroxy-6,7,3',4'-tetramethoxyphenone(8),β-balsam alcohol(9),stigmaster-5-en-3β-alcohol(10),p-hydroxybenzaldehyde(11),vanillin(12).Compounds 1,4,6,7,10 and 12 had strong inhibitory activites on NO release in LPS-induced RAW 264.7 cells,and the IC50 values were(25.21±2.10),(37.77±0.50),(38.19±1.58),(21.89±1.73),(43.81±1.18),(47.98±2.55),(41.23±1.11),(43.80±1.43)μmol/mL,respectively.Compounds 2-3 reduced IL-1β and TNF-α levels(P<0.05,P<0.01).CONCLUSION Compounds 6-7,9 are isolated from this plant for the first time.Compounds 1-4,8 exhibit strong in vitro anti-inflammatory activities,and compounds 2-3 exhibit significant in vivo anti-inflammatory activities.
9.Immune checkpoint inhibitor related tuberculosis:a case report and literature analysis
Wen-Ting JIN ; Jia-Yi NI ; Bi-Jie HU ; Jue PAN
Fudan University Journal of Medical Sciences 2024;51(2):272-276
With the increasing application of immune checkpoint inhibitors(ICI)in anti-tumor therapy,ICI related infections are often neglected.Mycobacterium tuberculosis(MTB)is also a common pathogen.We reported a case of ICI related pulmonary tuberculosis from Zhongshan Hospital,Fudan University.Meanwhile,18 cases of ICI related tuberculosis infection were collected through literature search,and the characteristics of ICI related tuberculosis were analyzed to improve the understanding in clinic practice.All the cases were confirmed TB including 15 cases of pulmonary tuberculosis(1 case with complication of intestinal tuberculosis)and 4 cases of extra-pulmonary tuberculosis(1 case of disseminated tuberculosis,bone tuberculosis,tuberculous pericarditis and tuberculous pleurisy,respectively).The chest CT characteristics of pulmonary tuberculosis mainly included centrilobular nodules,ground glass nodules,empty lesions,patchy shadows,consolidation and large infiltration.Eighteen cases started anti-tuberculosis treatment,while 4 cases continued ICI treatment.Three cases suspended ICI(2 cases had remission after reuse)and 11 cases stopped ICI,and 1 case was not mentioned.ICI related tuberculosis may be a direct complication of tumor immunotherapy.It is necessary to screen tuberculosis infection and exclude active tuberculosis before immunotherapy.If there are suspected symptoms such as fever,cough and sputum during ICI treatment,active tuberculosis should be taken into account.
10.Molecular biological mechanism of acquired heterotopic ossification
Yang XIONG ; Shibo ZHOU ; Xing YU ; Lianyong BI ; Jizhou YANG ; Fengxian WANG ; Yi QU ; Yongdong YANG ; Dingyan ZHAO ; He ZHAO ; Ziye QIU ; Guozheng JIANG
Chinese Journal of Tissue Engineering Research 2024;28(30):4881-4888
BACKGROUND:Heterotopic ossification is a dynamic growth process.Diverse heterotopic ossification subtypes have diverse etiologies or induction factors,but they exhibit a similar clinical process in the intermediate and later phases of the disease.Acquired heterotopic ossification produced by trauma and other circumstances has a high incidence. OBJECTIVE:To summarize the molecular biological mechanisms linked to the occurrence and progression of acquired heterotopic ossification in recent years. METHODS:The keywords"molecular biology,heterotopic ossification,mechanisms"were searched in CNKI,Wanfang,PubMed,Embase,Web of Science,and Google Scholar databases for articles published from January 2016 to August 2022.Supplementary searches were conducted based on the obtained articles.After the collected literature was screened,131 articles were finally included and summarized. RESULTS AND CONCLUSION:(1)The occurrence and development of acquired heterotopic ossification is a dynamic process with certain concealment,making diagnosis and treatment of the disease difficult.(2)By reviewing relevant literature,it was found that acquired heterotopic ossification involves signaling pathways such as bone morphogenetic protein,transforming growth factor-β,Hedgehog,Wnt,and mTOR,as well as core factors such as Runx-2,vascular endothelial growth factor,hypoxia-inducing factor,fibroblast growth factor,and Sox9.The core mechanism may be the interaction between different signaling pathways,affecting the body's osteoblast precursor cells,osteoblast microenvironment,and related cytokines,thereby affecting the body's bone metabolism and leading to the occurrence of acquired heterotopic ossification.(3)In the future,it is possible to take the heterotopic ossification-related single-cell osteogenic homeostasis as the research direction,take the osteoblast precursor cells-osteogenic microenvironment-signaling pathways and cytokines as the research elements,explore the characteristics of each element under different temporal and spatial conditions,compare the similarities and differences of the osteogenic homeostasis of different types and individuals,observe the regulatory mechanism of the molecular signaling network of heterotopic ossification from a holistic perspective.It is beneficial to the exploration of new methods for the future clinical prevention and treatment of heterotopic ossification.(4)Meanwhile,the treatment methods represented by traditional Chinese medicine and targeted therapy have become research hotspots in recent years.How to link traditional Chinese medicine with the osteogenic homeostasis in the body and combine it with targeted therapy is also one of the future research directions.(5)At present,the research on acquired heterotopic ossification is still limited to basic experimental research and the clinical prevention and treatment methods still have defects such as uncertain efficacy and obvious side effects.The safety and effectiveness of relevant targeted prevention and treatment drugs in clinical application still need to be verified.Future research should focus on clinical prevention and treatment based on basic experimental research combined with the mechanism of occurrence and development.

Result Analysis
Print
Save
E-mail