1.DIA Proteomics Reveals Mechanism of Acanthopanacis Senticosi Radix et Rhizoma seu Caulis Extract in Treating α-Syn Transgenic Parkinson's Disease in Mice
Qi ZHENG ; Yi LU ; Donghua YU ; Liangyou ZHAO ; Chunsheng LIN ; Fang LU ; Shumin LIU
Chinese Journal of Experimental Traditional Medical Formulae 2025;31(8):40-50
ObjectiveTo investigate the mechanism of Acanthopanacis Senticosi Radix et Rhizoma seu Caulis extract (ASH) in treating Parkinson's disease (PD) in mice by Data-Independent Acquisition (DIA) proteomics. MethodsThe α-Synuclein (α-Syn) transgenic PD mice were selected as suitable models for PD, and they were randomly assigned into PD, ASH (61.25 mg·kg-1), and Madopar (97.5 mg·kg-1) groups. Male C57BL/6 mice of the same age were selected as the control group, with eight mice in each group. Mice were administrated with corresponding drugs by gavage once a day for 20 days. The pole climbing time and the number of autonomic activities were recorded to evaluate the exercise ability of mice. Hematoxylin-eosin staining was employed to observe neuronal changes in the substantia nigra of PD mice. Immunohistochemistry (IHC) was employed to measure the tyrosine hydroxylase (TH) activity in the substantia nigra and assess the areal density of α-Syn in the striatum. DIA proteomics was used to compare protein expression in the substantia nigra between groups. IHC was utilized to validate key differentially expressed proteins, including Lactotransferrin, Notch2, Ndrg2, and TMEM 166. The cell counting kit-8 (CCK-8) method was used to investigate the effect of ASH on the viability of PD cells with overexpression of α-Syn. Real-time fluorescence quantitative polymerase chain reaction (Real-time PCR) and Western blot were employed to determine the protein and mRNA levels of Lactotransferrin, Notch2, Ndrg2, and TMEM 166 in PD cells. ResultsCompared with the control group, the model group showed prolonged pole climbing time, diminished coordination ability, reduced autonomic activities (P<0.01), and reduced swelling neurons. Compared with the model group, ASH and Madopar reduced the climbing time, increased autonomic activities (P<0.01), and ameliorated neuronal damage. Compared with the control group, the model group showed a decrease in TH activity in the substantia nigra and an increase in α-Syn accumulation in the striatum (P<0.01). Compared with the model group, the ASH group showed an increase in TH activity and a reduction in α-Syn accumulation (P<0.05). DIA proteomics revealed a total of 464 differentially expressed proteins in the model group compared with the control group, with 323 proteins being up-regulated and 141 down-regulated. A total of 262 differentially expressed proteins were screened in the ASH group compared with the model group, including 85 proteins being up-regulated and 177 down-regulated. Kyoto encylopedia of genes and genomes (KEGG) pathway analysis indicated that ASH primarily regulated the Notch signaling pathway. The model group showed up-regulation in protein levels of Notch2, Ndrg2, and TMEM 166 and down-regulation in the protein level of Lactotransferrin compared with the control group (P<0.01). Compared with the model group, ASH down-regulated the protein levels of Notch2, Ndrg2, and TMEM 166 (P<0.05) while up-regulating the protein level of Lactotransferrin (P<0.01). The IHC results corroborated the proteomics findings. The cell experiment results showed that compared with the control group, the modeling up-regulated the mRNA and protein levels of Notch2, Ndrg2, and TMEM 166 (P<0.01), while down-regulating the mRNA and protein levels of Lactotransferrin (P<0.01). Compared with the model group, ASH reduced the mRNA and protein levels of Notch2, Ndrg2, and TMEM 166 (P<0.01), while increasing the mRNA and protein levels of Lactotransferrin (P<0.05, P<0.01). ConclusionASH may Synergistically inhibit the Notch signaling pathway and mitigate neuronal damage by down-regulating the expression of Notch2 and Ndrg2. Additionally, by up-regulating the expression of Lactotransferrin and down-regulating the expression of TMEM166, ASH can address brain iron accumulation, intervene in ferroptosis, inhibit mitophagy, and mitigate reactive oxygen species damage, thereby protecting nerve cells and contributing to the treatment of PD.
2.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.
3.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.
4.Status Analysis of Acupoint Selection and Stimulation Parameters Application for Acupuncture Treatment of Functional Dyspepsia
Siyi ZHENG ; Han ZHANG ; Yang YU ; Chuanlong ZHOU ; Yan SHI ; Xiaohu YIN ; Shouhai HONG ; Na NIE ; Jianqiao FANG ; Yi LIANG
Journal of Traditional Chinese Medicine 2025;66(12):1293-1299
Based on commonly used acupoints in the clinical acupuncture treatment of functional dyspepsia (FD), this study systematically analyzes the therapeutic differences and synergistic effects between local and distal point selection. It also examines the suitability of primary acupoint selection for different FD subtypes, postprandial distress syndrome (PDS) and epigastric pain syndrome (EPS). The findings suggest that a combination of local and distal acupoints may be more appropriate as primary points for PDS, whereas local acupoints alone may be more suitable for EPS. Additionally, the study explores the impact of various factors, such as stimulation techniques, needling order, intensity or stimulation parameters, and depth, on the efficacy of acupuncture. It concludes that the intrinsic properties of acupoints are the primary determinants of therapeutic direction. Other factors mainly influence the magnitude rather than the direction of the effect. Future research may further investigate how different acupoint combinations, local versus distal, affect the treatment outcomes of FD subtypes, providing new insights for clinical acupuncture prescriptions.
5.Hypoxia Exercise Mediates The miR-27/PPARγ Pathway to Improve Lipid Metabolism in Obese Rats at Target Genes and Protein Levels
Wei KONG ; Jie SHAO ; Teng ZHAI ; Qian CHENG ; Fang-Zheng HAN ; Yi QU ; Lei ZHU
Progress in Biochemistry and Biophysics 2025;52(6):1386-1400
ObjectiveTo explore the sequential effects of hypoxic exercising on miR-27/PPARγ and lipid metabolism target gene and protein expression levels in the obesity rats’ liver. Methods13-week-old male diet-induced obesity rats were randomly divided into three groups (n=10): normal oxygen concentration quiet group (N), hypoxia quiet group (H), hypoxic exercise group (HE). Exercise training on the horizontal animal treadmill for 1 h/d, 5 d/week for a total of 4 week, and the intensity of horizontal treadmill training was 20 m/min (hypoxic concentration was 13.6%). Comparison of the weights of perirenal fat and epididymal fat in rats across different groups and calculation of Lee’s index based on body weight and body length of rats in each group were done. And the serum concentrations of total cholesterol (TC), triglyceride (TG), low density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C) levels were detected. RT-PCR and Western Blot were used to detect the levels of miR-27, PPARγ, CYP7A1 and CD36. ResultsHypoxic exercise decreased the expression levels of miR-27 in the obese rats’ liver, however, the expression level of PPARγ was gradually increased. The expression levels of miR-27 in HE group were significantly lower than N group (P<0.05). The expression levels of PPARγ mRNA in N group were significantly lower than H group (P<0.05), especially lower than HE group (P<0.01). The protein expression of PPARγ protein in N group was significantly lower than that other groups (P<0.01). The expression of lipid metabolism-related genes and proteins increased in the obese rats’ liver. The expression of CYP7A1 mRNA in N group was significantly lower than H group (P<0.05), especially lower than HE group (P<0.01). The expression of CYP7A1 protein in the obese rats’ liver in N group was extremely lower than H group and HE group (P<0.01). The protein expression of CD36 in N group was significantly lower than that in HE group (P<0.05). Hypoxia exercise improved the related physiological and biochemical indexes of lipid metabolism disorder. The perirenal fat weight of obese rats in HE group was extremely lower than N group and H group (P<0.01), and the perirenal fat weight in N group was significantly higher than H group (P<0.05). The epididymal fat weight in N group was significantly higher than H group (P<0.05), and extremely higher than HE group (P<0.01). The Lee’s index in HE group was extremely lower than N group and H group (P<0.01). The serum concentration of TC in obese rats in HE group was extremely lower than N group and H group (P<0.01). The serum concentration of TG in HE group was extremely lower than N group and H group (P<0.01). The serum concentration of LDL-C in N group was extremely higher than HE group (P<0.01). The serum concentration of HDL-C in N group was extremely lower than H group (P<0.01). ConclusionHypoxia and hypoxia exercise may negatively regulate the levels of PPARγ by inhibiting miR-27 in the obese rats’ liver, thereby affecting the expression of downstream target genes CYP7A1 and CD36, and promoting cholesterol, fatty acid oxidation and HDL-C transport in the liver, and ultimately the lipid levels in obese rats were improved. The effect of hypoxia exercise on improving blood lipid is better than simple hypoxia intervention.
6.Experts consensus on standard items of the cohort construction and quality control of temporomandibular joint diseases (2024)
Min HU ; Chi YANG ; Huawei LIU ; Haixia LU ; Chen YAO ; Qiufei XIE ; Yongjin CHEN ; Kaiyuan FU ; Bing FANG ; Songsong ZHU ; Qing ZHOU ; Zhiye CHEN ; Yaomin ZHU ; Qingbin ZHANG ; Ying YAN ; Xing LONG ; Zhiyong LI ; Yehua GAN ; Shibin YU ; Yuxing BAI ; Yi ZHANG ; Yanyi WANG ; Jie LEI ; Yong CHENG ; Changkui LIU ; Ye CAO ; Dongmei HE ; Ning WEN ; Shanyong ZHANG ; Minjie CHEN ; Guoliang JIAO ; Xinhua LIU ; Hua JIANG ; Yang HE ; Pei SHEN ; Haitao HUANG ; Yongfeng LI ; Jisi ZHENG ; Jing GUO ; Lisheng ZHAO ; Laiqing XU
Chinese Journal of Stomatology 2024;59(10):977-987
Temporomandibular joint (TMJ) diseases are common clinical conditions. The number of patients with TMJ diseases is large, and the etiology, epidemiology, disease spectrum, and treatment of the disease remain controversial and unknown. To understand and master the current situation of the occurrence, development and prevention of TMJ diseases, as well as to identify the patterns in etiology, incidence, drug sensitivity, and prognosis is crucial for alleviating patients′suffering.This will facilitate in-depth medical research, effective disease prevention measures, and the formulation of corresponding health policies. Cohort construction and research has an irreplaceable role in precise disease prevention and significant improvement in diagnosis and treatment levels. Large-scale cohort studies are needed to explore the relationship between potential risk factors and outcomes of TMJ diseases, and to observe disease prognoses through long-term follw-ups. The consensus aims to establish a standard conceptual frame work for a cohort study on patients with TMJ disease while providing ideas for cohort data standards to this condition. TMJ disease cohort data consists of both common data standards applicable to all specific disease cohorts as well as disease-specific data standards. Common data were available for each specific disease cohort. By integrating different cohort research resources, standard problems or study variables can be unified. Long-term follow-up can be performed using consistent definitions and criteria across different projects for better core data collection. It is hoped that this consensus will be facilitate the development cohort studies of TMJ diseases.
7.Model summary and application analysis of surface sensitization point detection
Wei PAN ; Linan LIN ; Xiaoshuai YU ; Xiaoying WANG ; Qiongying SHEN ; Siyi ZHENG ; Na NIE ; Yi LIANG ; Jianqiao FANG
Journal of Beijing University of Traditional Chinese Medicine 2024;47(11):1623-1628
The acupoint sensitization theory,a breakthrough in acupuncture and moxibustion over the past two decades,has greatly enhanced the understanding of meridians and acupoints while increasing the effectiveness of clinical diagnosis and treatment in acupuncture and moxibustion practices.The number of studies on surface sensitization site detection for different diseases is increasing.However,systematic sorting and a summary of the detection mode of surface sensitization points are lacking.Therefore,this study categorizes the method of surface sensitization point detection into two modes:pan-scanning and focused scanning.The classification is based on the characteristics of the openness of the research purpose,the precision of the target range,and the degree of variation during detection.The two modes have considerable differences in the exploration efficiency and the presentation of result.The pan-scanning mode can be further subdivided into holistic and localized pan-scanning modes,whereas the focused-scanning mode can be subdivided into fixed-and variable-focused scanning modes.This study analyzes the application scenarios,characteristics,advantages,and limitations of each detection mode and presents opinions on mode selection,mode innovation,and future development directions.This study aims to provide valuable insights and guidance for the follow-up research on surface sensitization site detection of various diseases.
8.Application progress of radiolabeling strategies in human mass balance studies
Yi-fei HE ; Yuan-dong ZHENG ; Da-fang ZHONG ; Xing-xing DIAO
Acta Pharmaceutica Sinica 2024;59(9):2470-2483
Human mass balance study is a pivotal research in the field of clinical pharmacology, aiming at elucidating the metabolic and excretion pathways of drugs in humans. Currently, human mass balance studies predominantly employ radiolabeling techniques. Recently, both the U.S. Food and Drug Administration (FDA) and the Center for Drug Evaluation (CDE) of the China National Medical Products Administration (NMPA) issued related research drafts and guidelines to encourage and guide the pharmaceutical industry to conduct research in compliance with established standards. The selection of radiolabeling sites is crucial for obtaining critical information on drug metabolism. However,
9.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.
10.Quantitative diagnosis of annular pancreas in neonates with saline-contrast ultrasound
Boyang YANG ; Qian FANG ; Yi ZHENG ; Hongying WANG
The Journal of Practical Medicine 2024;40(18):2618-2622
Objective To investigate the clinical utility of ultrasound parameters in diagnosing neonatal annular pancreas.Methods A total of 56 neonates with descending duodenal obstruction underwent saline-contrast ultrasound examination.Ultrasonic parameters,including dilated duodenum diameter(DDD),dilated duodenum thickness(DDT),and stenosis duodenum diameter(SDD),were measured.The cases were categorized into three groups:annular pancreas(group A,n=28),descending duodenal atresia(group B,n=3),and descending duodenal septum(group C,n=25).One-way ANOVA was employed to compare statistical differences among the three ultrasonic parameters across the groups,followed by LSD-t test for pairwise comparisons between two groups showing significant differences.Receiver operating characteristics analysis was conducted to calculate the area under the curve and determine the cut-off value if there were statistically significant differences observed.Results In group A,group B,group C,the diameters of DDD were measured as(23.2±2.4)mm,(25±1.0)mm,(19.4±2.6)mm,respectively.When comparing these three groups,there was a statistically significant difference between group A or group B and group C in terms of DDD diameter measurements(t=5.7,P<0.05;t=3.793,P<0.05).However,no statistically significant difference was observed between group A and group B for DDD diameter measurements(t=1.232,P>0.05).The corresponding values for DDT were measured as(3.0±0.6)mm,(3.2±0.4)mm,and(2.4±0.3)mm,respectively.When comparing these three groups,the results showed a statistically significant differ-ence between either Group A or Group B compared to Group C in terms of DDT measurement(t=4.695,P<0.05;t=2.778,P<0.05).However,no statistically significant difference was found between Group A and Group B regard-ing the measurement of DDT(t=0.666,P>0.05).The SDD measurements in the three groups were(1.9±0.3)mm,(3.6±0.8)mm,(5.5±0.7)mm,respectively.Statistical analysis using LSD-t test revealed significant differences between the three groups(t=5.521,P<0.05;t=6.142,P<0.05;t=25.828,P<0.05).The sensitivity,specificity,positive predictive value,and negative predictive value for detecting annular pancreas at a cutoff of 2.3 mm were determined to be 96.4%,100%,100%,and 96.6%,respectively,with an area under the receiver operating charac-teristic curve of 0.999.Conclusion SDD could be employed for the diagnosis of neonatal annular pancreas.

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