1.Effects of Modified Buyang Huanwu Tang on Mice with Cerebral Ischemia-reperfusion Injury by Regulating PINK1/Parkin Signaling Pathway-mediated Mitochondrial Autophagy
Li GUO ; Hengwen CHEN ; Cun ZHAN ; Zhenzhen YING ; Zuomin WU ; Shaoju JIN ; Shangmei CAO ; Shengming HUANG ; Jin WANG ; Xiaotao YU
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(11):34-43
ObjectiveTo investigate the effects of modified Buyang Huanwu Tang on cerebral ischemia-reperfusion injury (CI/RI) in mice via the PTEN-induced putative kinase 1/E3 ubiquitin ligase (PINK1/Parkin) signaling pathway-mediated mitophagy, and to explore the underlying mechanism by which modified Buyang Huanwu Tang improves CI/RI. MethodsSeventy-two male C57BL/6J mice were randomly divided into six groups (n = 12 per group): Sham-operated group, middle cerebral artery occlusion/reperfusion (MCAO/R) model group, low-, medium-, and high-dose modified Buyang Huanwu Tang groups (8.84, 17.68, 35.36 g·kg-1·d-1), and an aspirin group (13.00 mg·kg-1·d-1). Neurological deficit scores were assessed using the Zea-Longa method. Cerebral infarct volume ratio was measured by 2,3,5-triphenyltetrazolium chloride (TTC) staining. Histopathological changes and neuronal injury in brain tissues were observed using hematoxylin-eosin (HE) staining and Nissl staining. Apoptosis was detected by terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling (TUNEL) assay. Mitochondrial ultrastructure in brain tissue was observed by transmission electron microscopy (TEM). Serum levels of superoxide dismutase (SOD) and malondialdehyde (MDA) were determined by enzyme-linked immunosorbent assay (ELISA). The mRNA and protein expression levels of PINK1, Parkin, microtubule-associated protein 1 light chain 3B (LC3B, LC3Ⅱ/Ⅰ), and p62 in brain tissues were detected by real-time quantitative reverse transcription PCR (Real-time PCR) and Western blot, respectively. ResultsCompared with the sham-operated group, the MCAO/R model group showed significantly increased neurological deficit scores and cerebral infarct volume ratios (P<0.01). Severe cortical injury on the infarct side was observed, characterized by decreased neuronal density, cytoplasmic vacuolation, nuclear pyknosis, a marked reduction in Nissl bodies, dissolution of Nissl bodies in the cytoplasm of some pyramidal neurons, and blurred cellular boundaries. The number of TUNEL-positive cells increased significantly (P<0.01). Mitochondria exhibited cristae membrane rupture and matrix vacuolation, with rupture of the outer mitochondrial membrane and formation of autophagosomes, the number of which increased significantly. Serum SOD activity decreased significantly (P<0.01), while MDA content increased significantly (P<0.01). In infarcted brain tissues of model mice, the relative mRNA expression and protein levels of PINK1, Parkin and LC3B were significantly increased (P<0.05, P<0.01), whereas p62 mRNA and protein expression were significantly decreased (P<0.05, P<0.01), showing statistical significance. Compared with the model group, all treatment groups showed significantly decreased neurological deficit scores and cerebral infarct volume ratios (P<0.01). Neuronal density increased significantly, cytoplasmic vacuolation was alleviated, nuclear morphology tended to be more regular and clearer, Nissl body density increased significantly with reduced dissolution and improved contour clarity. The mitochondrial cristae structure was partially restored, with some mitochondria showing autophagosome encapsulation, and the degree of mitochondrial damage was alleviated. Serum SOD activity increased significantly (P<0.01), while MDA content decreased significantly. The mRNA and protein expression levels of PINK1, Parkin, and LC3Ⅱ/Ⅰ were significantly increased (P<0.05, P<0.01), while p62 mRNA and protein expression in the low- and medium-dose modified Buyang Huanwu Tang groups were significantly decreased (P<0.05, P<0.01), showing statistical significance. ConclusionModified Buyang Huanwu Tang can upregulate the protein expression levels of PINK1, Parkin, and LC3Ⅱ/Ⅰ and downregulate p62 protein expression, suggesting that it may improve CI/RI by regulating the expression of proteins related to the PINK1/Parkin signaling pathway. Regulation of the mitophagy pathway may be one of the mechanisms by which modified Buyang Huanwu Tang alleviates CI/RI in mice.
2.Epidemic trends and prevention and control effectiveness of notifiable infectious diseases in Yichang City based on interrupted time series
Qian WU ; Hao ZHANG ; Zhongcheng YANG ; Ling ZHOU ; Yi LIANG ; Yajun CAO
Journal of Public Health and Preventive Medicine 2026;37(1):88-92
Objective To analyze the epidemiological characteristics of statutory infectious diseases in Yichang City from 2015 to 2023 and evaluate the effectiveness of non-pharmaceutical interventions (NPIs) in infectious disease prevention and control, and to provide a basis for formulating prevention and control strategies. Methods Descriptive epidemiological methods were used to analyze annual incidence rates. SARIMA and SARIMA intervention models were constructed to predict the incidence rates of infectious diseases. Interrupted time series analysis (ITS) was applied to assess the control effectiveness. Results The average annual incidence rate from 2015 to 2023 was 787.47/100 000, with the top five diseases being influenza, hand-foot-and-mouth disease, hepatitis B, tuberculosis, and diarrheal diseases. The average incidence rate from 2015 to 2019 (654.31/100 000) was significantly higher than that from 2020 to 2022 (489.01/100 000) (χ2= 3 499.6, P < 0.05). The total incidence rate in 2023 (2 396.51/100 000) was significantly higher than the average annual incidence rates from 2015-2019 (χ2= 108 186.1, P < 0.05) and 2020-2022 (χ2= 112 869.4, P < 0.05). SARIMA model results indicated that the actual incidence rate from 2020 to 2022 decreased by 73.49% compared to the predicted rate without intervention, with the highest decline observed in respiratory infectious diseases (79.57%). The SARIMA-intervention model showed a 55.48% relative decrease in the total incidence rate for 2023, with the largest reduction in respiratory infectious diseases (63.28%) and a slight increase in intestinal infectious diseases (5.48%). Conclusion NPIs effectively reduce the incidence of statutory infectious diseases in the short term, especially for acute respiratory and intestinal infectious diseases. However, long-term effectiveness faces challenges, necessitating the development of differentiated prevention and control strategies.
3.Association of outdoor activity time and sleep duration with screening myopia in primary school students
LIU Xiaoling, LI Tingting, CAO Caiyun, YANG Feng, TAO Shuman, WU Xiaoyan, XU Shaojun, TAO Fangbiao
Chinese Journal of School Health 2026;47(2):279-282
Objective:
To explore the association of outdoor activity time and sleep duration with screening myopia in primary school students, so as to provide strategies for myopia prevention.
Methods:
Through a convenience sampling method, a survey was conducted among 4 248 primary school students aged 7-13 years from three primary schools in Xihu District, Nanchang City, Jiangxi Province from May to July, 2023. The average daily outdoor activity time and sleep duration on both weekdays and weekends were investigated in primary school students by using a self designed questionnaire. Uncorrected visual acuity tests and non cycloplegic autorefraction were measured by professional optometrists. Inter group comparisons were conducted using the Chi square test. Logistic regression model was used to analyze the association of outdoor activity time and sleep duration with screening myopia.
Results:
The detection rate of screening myopia in primary school students was 33.6%, with the rate in boys (32.0%) lower than that in girls (35.3%), and the difference was statistically significant ( χ 2=5.11, P =0.02). The analysis results of Logistic regression showed that after adjusting for factors such as gender, grade and parental education level, both average daily outdoor activity time <2 h on both weekdays and weekends ( OR =1.27, 95% CI =1.11-1.46) and sleep duration <10 h ( OR =1.17, 95% CI =1.01- 1.35 ), as well as their combined effect ( OR =1.57, 95% CI =1.25-1.98), were associated with an increased risk of screening myopia in primary school students(all P <0.05). Subgroup analysis results indicated that compared to boys ( OR =1.46, 95% CI = 1.07 -1.99), girls( OR =1.73, 95% CI =1.22-2.44) with insufficient outdoor activity time and sleep duration had a higher risk of screening myopia(both P <0.05).
Conclusions
There is a negative correlation of outdoor activity time and sleep duration with screening myopia in primary school students. Outdoor activity time and extending sleep duration should be increased to reduce the risk of myopia in primary school students.
4.Study on the mechanism of Juanxiao decoction in improving bronchial asthma
Bangqing CAO ; Qiangqiang YU ; Meinian LIU ; Zhixi WU ; Lizhen ZENG ; Mengyao TONG ; Yunhua DENG ; Hanrong XUE
China Pharmacy 2026;37(2):155-160
OBJECTIVE To investigate the potential mechanism by which Juanxiao decoction improves bronchial asthma (hereinafter referred to as “asthma”) based on the nucleotide-binding domain leucine-rich repeat and pyrin domain-containing receptor 3 (NLRP3) inflammasome signaling pathway. METHODS Female SD rats were randomly assigned to normal group, model group and Juanxiao decoction low-, medium- and high-dose groups (0.36, 0.72 and 1.44 g/kg, calculated based on crude drug weight), as well as positive control group (Dexamethasone acetate tablets, 0.2 mg/kg), with 10 rats in each group. Except for the normal group, asthma models were established in the remaining groups via intraperitoneal injection of ovalbumin combined with aluminum hydroxide, followed by nebulized inhalation of ovalbumin. On day 14 of the experiment, rats in each group received intragastric administration of the corresponding solution or normal saline, once a day, for 7 consecutive days. Following the final administration, the following parameters were measured in each group: lung function indexes (forced vital capacity, forced expiratory volume in 0.3 second, peak expiratory flow), serum levels of inflammatory markers (interleukin-1β, interleukin- 18), and the percentages of inflammatory cells (lymphocytes, eosinophils, neutrophils) in bronchoalveolar lavage fluid. Histopathological changes in lung tissue were observed, and the protein and mRNA expressions of nuclear factor-kappa B (NF- κB), NLRP3 and caspase-1 in lung tissue were detected. RESULTS Compared with the normal group, pathological changes such as alveolar wall thickening and inflammatory cell infiltration were observed in rats in the model group. All pulmonary function indicators were significantly reduced in rats in the model group and the administration groups. The levels of inflammatory markers, the percentages of inflammatory cells, and the protein and mRNA expressions of NF-κB, NLRP3 and caspase-1 were significantly elevated or up-regulated (P<0.05). Compared with the model group, pathological changes in rats in each dosage group of Juanxiao decoction were significantly alleviated, and all quantitative indicators showed dose-dependent improvements (P<0.05). CONCLUSIONS Juanxiao decoction can reduce airway inflammatory responses in asthmatic rats, alleviate lung function impairment, and improve pathological changes such as inflammatory cell infiltration. Those effects may be related to the inhibition of the NLRP3 inflammasome signaling pathway.
5.Association between snack consumption and depressive symptoms among first year junior high school students with different left behind experiences in Yunnan Province
LIU Na, WU Huijuan, WANG Liangui, LUO Chengyong, CAO Yanrong, FU Yun, ZHANG Tai,〖JZ〗 KONG Jing, HU Mengdie, XIONG Yuan, XU Honglü ;
Chinese Journal of School Health 2026;47(1):18-22
Objective:
To explore the relationship between snack consumption and depressive symptoms in first year junior high school students with different left behind experiences in Yunnan Province, so as to provide a basis for improving depressive symptoms among first year junior high school students with different left behind experiences.
Methods:
From October to December 2022,a cluster random sampling method was used to select 8 500 first year junior high school students from 11 ethnic minority areas (Fugong County, Longling County, Longyang District, Luchun County, Mojiang County, Nanjian County, Qiaojia County, Shuangjiang County, Tengchong City, Yuanmou County, Zhenyuan County) in Yunnan Province for a questionnaire survey. The Chinese version of Depression Anxiety Stress Scale-21 was applied to assess depressive symptoms in first year junior high school students, and snack consumption was collected by employing food frequency questionnaire. The generalized linear model was used to analyze the association between first year junior high school students snack consumption and depressive symptoms, and the analysis was stratified according to left behind experience.
Results:
The detection rates of depressive symptoms among firstyear junior high school students with and without left behind experience were 36.25% and 26.91%, respectively. After controlling for confounding variables, the generalized linear model analysis showed that sweet snacks ( β=0.16, 95%CI =0.07-0.25), fast food ( β=0.14, 95%CI =0.04-0.23) and carbonated drinks ( β=0.09, 95%CI =0.01-0.17) of first year junior high school students with left behind experience (all P <0.05). Compared with those without such behavior, the risk of depressive symptoms was higher in consumption of fast food ( β=0.13, 95%CI =0.07-0.18) and carbonated drinks ( β=0.10, 95%CI =0.06-0.15)among first year junior high school students without left behind experience (both P <0.05).
Conclusion
Snack consumption among first year junior high school students in Yunnan may increase the risk of developing depressive symptoms, while first year junior high school students with left behind experience may have a greater risk of developing depressive symptoms.
6.Multi-dimensional Holographic Characterization of Zhejiang Characteristic Atractylodis Macrocephalae Rhizoma with Nine-time Repeating Steaming and Processing
Xin WU ; Cuiwei CHEN ; Qiao YU ; Chao FENG ; Hongyan ZHANG ; Yan CHEN ; Caihua SUN ; Gang CAO
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(6):197-205
ObjectiveHistorically documented Zhejiang Atractylodis Macrocephalae Rhizoma(Baizhu) possesses premium characteristics such as phoenix-like head and crane-like neck, pronounced sweetness, and fragrant aroma. However, its current market circulation is low, and the processed products with Zhejiang-style characteristics are at the risk of being lost. This study aims to preserve the ancient Zhejiang-style processing techniques and evaluate them using modern scientific methods. MethodsMultidimensional intelligent sensory evaluation was used to digitally characterize the "quality-structure" of the external appearance of nine-steamed and nine-processed Baizhu medicinal materials(intermediate processed products) and the "odor-taste" of the internal quality of its decoction pieces(slices), and the appearance parameters were digitally characterized by colorimeter, texture analyzer, electronic nose and electronic tongue, the chemical composition was analyzed via ultra-performance liquid chromatography-quadrupole-time-of-flight mass spectrometry(UPLC-Q-TOF-MS/MS). Then, cluster analysis on the differences in odor between the medicinal materials(intermediate processed products) and decoction pieces(slices) of nine-steamed and nine-processed Baizhu was conducted, as well as the differences in taste between water-soluble and alcohol-soluble extracts of the decoction pieces(slices), and the correlation analysis of chroma value-alcohol-soluble extract content-component response value. ResultsThe nine-steamed and nine-processed Baizhu had a dark brown to black epidermis, a brownish-yellow to brownish-gray cross-section, a slightly tough texture, a faint odor, and a slightly sweet, bitter and pungent taste. Texture analyzer measurements revealed minimal adhesion and maximum recovery in the middle section of the characteristic processed Baizhu, consistent with the processing endpoint of thorough steaming and cooking. The head section showed the highest internal hardness, elasticity and chewiness, indicating a denser texture in this area. The electronic nose sensor could clearly distinguish the difference between the medicinal materials and its decoction pieces, with a more significant clustering effect at 60 ℃ for 30 minutes compared to ambient temperature headspace for 2 hours, highlighting the significant impact of the baking degree before slicing on the quality. The electronic tongue taste signal map clearly distinguished the differences between water-soluble and alcohol-soluble extracts of nine-steamed and nine-processed Baizhu decoction pieces, and the addition of auxiliary materials during processing could enhance its alcohol-soluble extract content. A total of 82 chemical components were identified in the characteristic processed Baizhu. After processing, the contents of 58 components increased, while 24 components decreased. Correlation analysis revealed significant negative correlations(P<0.01) between ethanol-soluble extract content and colorimetric values of brightness(L*), yellow-bule value(b*), and total color difference(E*ab). E*ab showed marked negative correlations(P<0.05) with the response values of isochlorogenic acid A and C. ConclusionThis study establishes a modern intelligent sensory evaluation model for multidimensional holographic characterization of nine-steamed and nine-processed Baizhu, clarifying the correlation between increased isochlorogenic acid content and the visual color appearance after different steaming cycles, as well as its intrinsic alcohol-soluble extracts. This provides a reference for quality evaluation and processing standards of the Zhejiang-style characteristic processed products.
7.Kinesiophobia in relation to illness perception and cardiac discomfort among convalescent AMI patients
Ying WU ; Xinting CAO ; Wenjing GAO ; Qian MA
Journal of Public Health and Preventive Medicine 2026;37(3):104-107
Objective To explore the correlation between kinesiophobia and disease uncertainty, personal mastery, cardiac discomfort symptoms in patients with acute myocardial infarction (AMI) during recovery period. Methods A total of 320 patients with AMI admitted to the hospital were enrolled between January 2020 and January 2024. According to the results of Tampa Scale for Kinesiophobia Heart (TSK-H), they were divided into AMI kinesiophobia group (n=166) and simple AMI group (n=154). The disease uncertainty was evaluated by Mishel Uncertainty in Illness Scale for Adults (MUIS-A), personal mastery was evaluated by Personal Mastery Scale (PMS), and cardiac discomfort symptoms were evaluated by cardiac discomfort symptom scale. The correlation between kinesiophobia and disease uncertainty, personal mastery, cardiac discomfort symptoms in AMI patients was analyzed by Pearson correlation analysis. Results The scores of MUIS-A and cardiac discomfort symptoms in AMI kinesiophobia group were higher than those in simple AMI group (P<0.05), and PMS scores were lower than those in simple AMI group (P<0.05). The score of kinesiophobia was significantly positively correlated with scores of disease uncertainty and cardiac discomfort symptoms (r=0.628, 0.689, P<0.05), while significantly negatively correlated with the score of personal mastery (r=-0.526, P<0.05). Conclusion Kinesiophobia is related to disease uncertainty, personal mastery and cardiac discomfort symptoms in AMI patients during recovery period. Clinical medical staffs should focus on patients with the above characteristics. The targeted intervention measures can improve kinesiophobia and promote recovery of patients.
8.A Computational Perspective on Differences Between MHC-I and MHC-II in TCR-pMHC Structure Prediction Resources: Review and Benchmarking
Xiao-Qin WU ; Da-Wei LIU ; Bin-Yu LI ; Yang LIU ; Yang CAO ; Wen-Tao DAI
Progress in Biochemistry and Biophysics 2026;53(5):1376-1399
The initiation of adaptive immune responses relies on the precise recognition and interpretation of antigenic information. In this process, the specific binding of T cell receptors (TCRs) to peptide-major histocompatibility complex (pMHC) molecules represents one of the key molecular events in the initiation of adaptive immune responses. Accordingly, the structural features of TCR-pMHC complexes provide a fundamental basis for dissecting antigen recognition mechanisms and support rational vaccine design, therapeutic target discovery in TCR-based immunotherapy, and TCR identification and optimization. However, experimental determination of TCR-pMHC structures remains costly, time-consuming, and limited in coverage, making computational approaches essential for rapidly obtaining reliable structural information. Computational methods for predicting the structures of TCR-pMHC complexes have advanced rapidly in recent years, driven by progress in deep learning-based modeling frameworks and the increasing availability of structural and sequence resources. Despite these developments, most existing tools do not adequately distinguish the key structural and biophysical differences between MHC class I (MHC-I) and MHC class II (MHC-II) complexes during model construction. As a consequence, their predictive performance differs substantially between class I and class II complexes. In general, structural predictions for class I complexes outperform those for class II complexes. This discrepancy may be related to several fundamental differences between the two systems, including the architecture of the peptide-binding groove, the distribution of peptide lengths, and the properties of peptide flanking residues (PFRs). Compared with MHC-I molecules, MHC-II molecules usually bind longer antigenic peptides, which typically range from 13 to 25 amino acids in length. PFRs at both termini of these peptides participate in regulating the overall conformation of TCR-pMHC class II complexes and exert a pronounced effect on the geometric and physicochemical characteristics of the TCR-pMHC binding interface. Furthermore, within the TCR recognition interface, the complementarity-determining regions (CDRs) consist of segments that differ markedly in conformational behavior. They commonly include regions that are relatively rigid and structurally stable, together with highly flexible segments exhibiting substantial conformational plasticity. These rigidity-flexibility features constitute an essential structural basis enabling TCRs to recognize diverse peptide-MHC ligands and to accommodate conformational heterogeneity at the interface. However, many current modeling tools, in an effort to enforce global conformational stability or reduce structural noise, tend to over-constrain intrinsically flexible regions. Such oversimplification may lead to inappropriate rigidification of flexible CDR loops, resulting in local structural distortions, compromised interface geometry, or even complete modeling failure for specific complexes. Against this background, the review approaches the field from the perspective of computational differences between MHC-I and MHC-II complexes. We first systematically organize and summarize available resources related to TCRs and pMHCs, including structural datasets, sequence databases, prediction tools, and benchmarking studies. We then focus on five representative tools capable of predicting both class I and class II complexes—AlphaFold2, AlphaFold3, TCRmodel2, tFold-TCR, and TCR-pHLA_ModellerS. After excluding structures present in the training sets of these tools, we constructed a benchmark dataset comprising 25 class I and 10 class II TCR-pMHC complexes in the bound state and conducted a systematic evaluation using this dataset. We first employ widely used general evaluation metrics, including All-Atom Root Mean Square Deviation (All-Atom RMSD), Backbone RMSD, Template Modeling score (TM-score), and DockQ, to assess the global conformational accuracy and interface modeling quality of class I and class II complexes. For class II complexes, we propose for the first time a peptide flanking residue deviation index, including the PFRs-Deviation Index (PFRs-DI), N-PFR-Deviation Index (N-PFR-DI), and C-PFR-Deviation Index (C-PFR-DI), to quantitatively characterize conformational deviations in PFRs. In addition, we propose the CDR conformational consistency index (CCC) designed to qualitatively evaluate the ability of prediction tools to capture TCR CDR conformational flexibility. These metrics collectively assess a tool’s ability to model both overall conformation and critical functional regions, thereby addressing the limitations of existing evaluation criteria that overemphasize global structure while inadequately capturing modeling quality in key functional areas. This establishes a unified analytical framework for MHC-I and MHC-II complexes to guide data resource selection, modeling strategy formulation, and evaluation system development. The framework further advances computational modeling and provides crucial support for multi-scale analysis of TCR-pMHC recognition mechanisms and their biological functions.
9.A Computational Perspective on Differences Between MHC-I and MHC-II in TCR-pMHC Structure Prediction Resources: Review and Benchmarking
Xiao-Qin WU ; Da-Wei LIU ; Bin-Yu LI ; Yang LIU ; Yang CAO ; Wen-Tao DAI
Progress in Biochemistry and Biophysics 2026;53(5):1376-1399
The initiation of adaptive immune responses relies on the precise recognition and interpretation of antigenic information. In this process, the specific binding of T cell receptors (TCRs) to peptide-major histocompatibility complex (pMHC) molecules represents one of the key molecular events in the initiation of adaptive immune responses. Accordingly, the structural features of TCR-pMHC complexes provide a fundamental basis for dissecting antigen recognition mechanisms and support rational vaccine design, therapeutic target discovery in TCR-based immunotherapy, and TCR identification and optimization. However, experimental determination of TCR-pMHC structures remains costly, time-consuming, and limited in coverage, making computational approaches essential for rapidly obtaining reliable structural information. Computational methods for predicting the structures of TCR-pMHC complexes have advanced rapidly in recent years, driven by progress in deep learning-based modeling frameworks and the increasing availability of structural and sequence resources. Despite these developments, most existing tools do not adequately distinguish the key structural and biophysical differences between MHC class I (MHC-I) and MHC class II (MHC-II) complexes during model construction. As a consequence, their predictive performance differs substantially between class I and class II complexes. In general, structural predictions for class I complexes outperform those for class II complexes. This discrepancy may be related to several fundamental differences between the two systems, including the architecture of the peptide-binding groove, the distribution of peptide lengths, and the properties of peptide flanking residues (PFRs). Compared with MHC-I molecules, MHC-II molecules usually bind longer antigenic peptides, which typically range from 13 to 25 amino acids in length. PFRs at both termini of these peptides participate in regulating the overall conformation of TCR-pMHC class II complexes and exert a pronounced effect on the geometric and physicochemical characteristics of the TCR-pMHC binding interface. Furthermore, within the TCR recognition interface, the complementarity-determining regions (CDRs) consist of segments that differ markedly in conformational behavior. They commonly include regions that are relatively rigid and structurally stable, together with highly flexible segments exhibiting substantial conformational plasticity. These rigidity-flexibility features constitute an essential structural basis enabling TCRs to recognize diverse peptide-MHC ligands and to accommodate conformational heterogeneity at the interface. However, many current modeling tools, in an effort to enforce global conformational stability or reduce structural noise, tend to over-constrain intrinsically flexible regions. Such oversimplification may lead to inappropriate rigidification of flexible CDR loops, resulting in local structural distortions, compromised interface geometry, or even complete modeling failure for specific complexes. Against this background, the review approaches the field from the perspective of computational differences between MHC-I and MHC-II complexes. We first systematically organize and summarize available resources related to TCRs and pMHCs, including structural datasets, sequence databases, prediction tools, and benchmarking studies. We then focus on five representative tools capable of predicting both class I and class II complexes—AlphaFold2, AlphaFold3, TCRmodel2, tFold-TCR, and TCR-pHLA_ModellerS. After excluding structures present in the training sets of these tools, we constructed a benchmark dataset comprising 25 class I and 10 class II TCR-pMHC complexes in the bound state and conducted a systematic evaluation using this dataset. We first employ widely used general evaluation metrics, including All-Atom Root Mean Square Deviation (All-Atom RMSD), Backbone RMSD, Template Modeling score (TM-score), and DockQ, to assess the global conformational accuracy and interface modeling quality of class I and class II complexes. For class II complexes, we propose for the first time a peptide flanking residue deviation index, including the PFRs-Deviation Index (PFRs-DI), N-PFR-Deviation Index (N-PFR-DI), and C-PFR-Deviation Index (C-PFR-DI), to quantitatively characterize conformational deviations in PFRs. In addition, we propose the CDR conformational consistency index (CCC) designed to qualitatively evaluate the ability of prediction tools to capture TCR CDR conformational flexibility. These metrics collectively assess a tool’s ability to model both overall conformation and critical functional regions, thereby addressing the limitations of existing evaluation criteria that overemphasize global structure while inadequately capturing modeling quality in key functional areas. This establishes a unified analytical framework for MHC-I and MHC-II complexes to guide data resource selection, modeling strategy formulation, and evaluation system development. The framework further advances computational modeling and provides crucial support for multi-scale analysis of TCR-pMHC recognition mechanisms and their biological functions.
10.Shaoyaotang Regulates miRNA-155-mediated SOCS1/JAK1/STAT1 Signaling Pathway to Affect Macrophage Polarization
Qi CHENG ; Bo ZOU ; Youwei XIAO ; Yiqian YU ; Ruoru HUANG ; Yan GONG ; Jiachun XIONG ; Jun XIONG ; Dichang LAI ; Dongsheng WU ; Hui CAO
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(13):43-52
ObjectiveTo investigate the mechanism by which Shaoyaotang regulates the miRNA-155-mediated suppressor of cytokine signaling 1 (SOCS1)/Janus kinase 1 (JAK1)/signal transducer and activator of transcription 1 (STAT1) signaling pathway and thereby affects macrophage polarization. MethodsThe cell-counting kit-8 (CCK-8) assay was used to detect the effect of drug-containing serum of Shaoyaotang at different concentrations on the viability of RAW 264.7 cells. A cell model of inflammation was established by stimulating RAW264.7 cells with lipopolysaccharide (LPS) at a concentration of 10 mg·L-1 The modeled cells were assigned by the random number table method into seven groups: LPS-induced M1 polarization (model), M1+miRNA-155 mimics, M1+miRNA-155 inhibitor, M1+Shaoyaotang-containing serum, M1+miRNA-155 mimics+Shaoyaotang-containing serum, M1+miRNA-155 inhibitor+Shaoyaotang-containing serum, and M1+blank serum. Enzyme-linked immunosorbent assay was employed to measure the levels of inflammatory factors [tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6), and interleukin-1β (IL-1β)]. Immunofluorescence assay was used to detect the expression of macrophage polarization markers [inducible nitric oxide synthase (iNOS) and macrophage mannose receptor 1 (CD206)]. Real-time PCR was employed to measure the expression of miRNA-155 in cells. Western blot was performed to determine the protein levels of SOCS1, STAT1, and JAK1. ResultsCompared with the LPS-induced M1 polarization (model) group, the M1+miRNA-155 mimics group showed up-regulated expression of miRNA-155, JAK1, STAT1, TNF-α, IL-6, IL-1β, and iNOS (P<0.05) and down-regulated expression of CD206 (P<0.05). In both the M1+miRNA-155 inhibitor group and the M1+Shaoyaotang-containing serum group, the expression levels of miRNA-155, JAK1, STAT1, TNF-α, IL-6, IL-1β, and iNOS were down-regulated (P<0.05), while those of SOCS1 and CD206 were up-regulated (P<0.05). Compared with the M1+miRNA-155 mimics group, the M1+miRNA-155 mimics+Shaoyaotang-containing serum group showed down-regulated expression of miRNA-155, JAK1, STAT1, TNF-α, IL-6, IL-1β, and iNOS (P<0.05) and up-regulated expression of SOCS1 and CD206 (P<0.05). Compared with the M1+miRNA-155 inhibitor group, the M1+miRNA-155 inhibitor+Shaoyaotang-containing serum group showed down-regulated expression of miRNA-155, JAK1, STAT1, TNF-α, IL-6, IL-1β, and iNOS (P<0.05) and up-regulated expression of SOCS1 and CD206 (P<0.05). ConclusionShaoyaotang regulates macrophage polarization by modulating miRNA-155 expression and interfering with the SOCS1/JAK1/STAT1 signaling pathway. The findings provide new experimental evidence for the treatment of ulcerative colitis with Shaoyaotang.


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