1.Geographical Inference Study of Dust Samples From Four Cities in China Based on ITS2 Sequencing
Wen-Jun ZHANG ; Yao-Sen FENG ; Jia-Jin PENG ; Kai FENG ; Ye DENG ; Ke-Lai KANG ; Le WANG
Progress in Biochemistry and Biophysics 2025;52(4):970-981
ObjectiveIn the realm of forensic science, dust is a valuable type of trace evidence with immense potential for intricate investigations. With the development of DNA sequencing technologies, there is a heightened interest among researchers in unraveling the complex tapestry of microbial communities found within dust samples. Furthermore, striking disparities in the microbial community composition have been noted among dust samples from diverse geographical regions, heralding new possibilities for geographical inference based on microbial DNA analysis. The pivotal role of microbial community data from dust in geographical inference is significant, underscoring its critical importance within the field of forensic science. This study aims to delve deeply into the nuances of fungal community composition across the urban landscapes of Beijing, Fuzhou, Kunming, and Urumqi in China. It evaluates the accuracy of biogeographic inference facilitated by the internal transcribed spacer 2 (ITS2) fungal sequencing while concurrently laying a robust foundation for the operational integration of environmental DNA into geographical inference mechanisms. MethodsITS2 region of the fungal genomes was amplified using universal primers known as 5.8S-Fun/ITS4-Fun, and the resulting DNA fragments were sequenced on the Illumina MiSeq FGx platform. Non-metric multidimensional scaling analysis (NMDS) was employed to visually represent the differences between samples, while analysis of similarities (ANOSIM) and permutational multivariate analysis of variance (PERMANOVA) were utilized to statistically evaluate the dissimilarities in community composition across samples. Furthermore, using Linear Discriminant Analysis Effect Size (LEfSe) analysis to identify and filter out species that exhibit significant differences between various cities. In addition, we leveraged SourceTracker to predict the geographic origins of the dust samples. ResultsAmong the four cities of Beijing, Fuzhou, Kunming and Urumqi, Beijing has the highest species richness. The results of species annotation showed that there were significant differences in the species composition and relative abundance of fungal communities in the four cities. NMDS analysis revealed distinct clustering patterns of samples based on their biogeographic origins in multidimensional space. Samples from the same city exhibited clear clustering, while samples from different cities showed separation along the first axis. The results from ANOSIM and PERMANOVA confirmed the significant differences in fungal community composition between the four cities, with the most pronounced distinctions observed between Fuzhou and Urumqi. Notably, the biogeographic origins of all known dust samples were successfully predicted. ConclusionSignificant differences are observed in the fungal species composition and relative abundance among the cities of Beijing, Fuzhou, Kunming, and Urumqi. Employing fungal ITS2 sequencing on dust samples from these urban areas enables accurate inference of biogeographical locations. The high feasibility of utilizing fungal community data in dust for biogeographical inferences holds particular promise in the field of forensic science.
2.Value of third lumbar skeletal muscle mass index in predicting the prognosis of patients with acute-on-chronic liver failure
Yewen HAN ; Jing LI ; Ninghui ZHAO ; Jia YAO ; Juan WANG
Journal of Clinical Hepatology 2025;41(4):698-702
ObjectiveTo investigate the value of third lumbar skeletal muscle mass index (L3-SMI) in predicting the long-term prognosis of patients with acute-on-chronic liver failure (ACLF), and to provide a useful tool for prognostic scoring of ACLF patients. MethodsA retrospective analysis was performed for the data of 126 patients who underwent abdominal computed tomography (CT) scanning and were diagnosed with ACLF in Shanxi Bethune Hospital from December 2017 to December 2021, including clinical indicators, biochemical parameters, and model for end-stage liver disease (MELD) score, and L3-SMI was calculated. The independent-samples t test was used for comparison of normally distributed continuous data between groups, and the Mann-Whitney U test was used for comparison of non-normally distributed continuous data between groups; the chi-square test was used for comparison of categorical data between groups. The receiver operating characteristic (ROC) curve was used to assess the diagnostic value of L3-SMI and other variables (MELD score and Child-Pugh score), and the DeLong test was used for comparison of the area under the ROC curve (AUC). ResultsAmong the 126 patients enrolled, 44 (35%) died within 2 years and 82 (65%) survived. Compared with the survival group, the death group had significantly higher age, incidence rate of ascites, international normalized ratio, MELD score, and Child-Pugh score (all P<0.05) and a significantly lower value of L3-SMI [38.40 (35.95 — 46.29) cm²/m² vs 44.19 (40.20 — 48.58) cm²/m², Z=-2.855, P=0.004]. L3-SMI had an AUC of 0.720 in predicting 2-year mortality in ACLF patients, with a sensitivity of 63.6% and a specificity of 80.5%, and a combination of L3-SMI, MELD score, and Child-Pugh score had a significantly better AUC than a combination of MELD score and Child-Pugh score in predicting 2-year mortality (0.809 vs 0.757, Z=2.015, P<0.05). ConclusionL3-SMI has a high predictive value for the prognosis of ACLF patients, and the combination of L3-SMI、MELD score and Child-Pugh score has a higher predictive value for ACLF patients, and the inclusion of L3-SMI or sarcopenia in the conventional prognostic scores of ACLF patients may increase the ability to predict disease progression.
3.Application of middle hepatic vein splitting and reconstruction technique in split liver transplantation from low-age donor livers
Hui TANG ; Binsheng FU ; Qing YANG ; Jia YAO ; Kaining ZENG ; Xiao FENG ; Shuhong YI ; Yang YANG
Organ Transplantation 2025;16(3):453-459
Objective To explore the feasibility and clinical experience of the middle hepatic vein splitting-reconstruction technique in split liver transplantation from low-age donor livers. Methods A retrospective analysis was conducted on the cases of two low-age donor livers that underwent middle hepatic vein splitting-reconstruction, which were transplanted into four child recipients at the Liver Transplantation Center of the Third Affiliated Hospital of Sun Yat-sen University from January 2017 to July 2023. The surgical and postoperative conditions were summarized and analyzed. Results Donor 1 was a 6-year-old and 4-month-old girl with a body weight of 21 kg, and the obtained donor liver weighed 496 g. After splitting, the left and right liver weights were 201 g and 280 g, and transplanted into a 9-month-old boy weighing 6.5 kg and a 9-month-old boy weighing 7.5 kg, respectively. The graft to recipient weight ratio (GRWR) was 3.09% and 3.73%, respectively. Donor 2 was a 5-year-old and 8-month-old boy with a body weight of 19 kg, and the donor liver weighed 673 g. After splitting, the left and right liver weights were 230 g and 400 g, and transplanted into a 13-month-old girl weighing 9.5 kg and a 15-month-old boy weighing 12 kg. The GRWR was 2.42% and 3.33%, respectively. Both donor livers were split ex vivo, with the middle hepatic vein being completely split in the middle and reconstructed using allogeneic iliac vein and iliac artery vascular patches. According to GRWR, none of the 4 transplant livers were reduced in volume. Among the 4 recipients, one died due to postoperative portal vein thrombosis and non-function of the transplant liver, while the other three cases recovered smoothly without early or late complications. Regular follow-up was conducted until July 31, 2023, and liver function recovered well. Conclusions Under the premise of detailed assessment of the donor liver and meticulous intraoperative operation, as well as matching with suitable child recipients, low-age donor livers may be selected for splitting. The complete splitting and reconstruction of the middle hepatic vein in the middle may effectively ensure the adequate venous return of the left and right liver and provide sufficient functional liver volume.
4.Preliminary exploration of differentiating and treating multiple system atrophy from the perspective of the eight extraordinary meridians
Di ZHAO ; Zhigang CHEN ; Nannan LI ; Lu CHEN ; Yao WANG ; Jing XUE ; Xinning ZHANG ; Chengru JIA ; Xuan XU ; Kaige ZHANG
Journal of Beijing University of Traditional Chinese Medicine 2025;48(3):392-397
Multiple system atrophy (MSA) is a rare neurodegenerative disease with complex clinical manifestations, presenting substantial challenges in clinical diagnosis and treatment. Its symptoms and the eight extraordinary meridians are potentially correlated; therefore, this article explores the association between MSA symptom clusters and the eight extraordinary meridians based on their circulation and physiological functions, as well as their treatment strategies. The progression from deficiency to damage in the eight extraordinary meridians aligns with the core pathogenesis of MSA, which is characterized by "the continuous accumulation of impacts from the vital qi deficiency leading to eventual damage". Liver and kidney deficiency and the emptiness of the eight extraordinary meridians are required for the onset of MSA; the stagnation of qi deficiency and the gradual damage to the eight extraordinary meridians are the key stages in the prolonged progression of MSA. The disease often begins with the involvement of the yin and yang qiao mai, governor vessel, thoroughfare vessel, and conception vessel before progressing to multiple meridian involvements, ultimately affecting all eight extraordinary meridians simultaneously. The treatment approach emphasizes that "the direct method may be used for joining battle, but indirect method will be needed in order to secure victory" and focuses on "eliminate pathogenic factors and reinforce healthy qi". Distinguishing the extraordinary meridians and focusing on the primary symptoms are pivotal to improving efficacy. Clinical treatment is aimed at the target, and tailored treatment based on careful clinical observation ensures precision in targeting the disease using the eight extraordinary meridians as the framework and core symptoms as the specific focus. Additionally, combining acupuncture, daoyin therapy, and other method may help prolong survival. This article classifies clinical manifestations based on the theory of the eight extraordinary meridians and explores treatment.
5.Research on BP Neural Network Method for Identifying Cell Suspension Concentration Based on GHz Electrochemical Impedance Spectroscopy
An ZHANG ; A-Long TAO ; Qi-Hang RAN ; Xia-Yi LIU ; Zhi-Long WANG ; Bo SUN ; Jia-Feng YAO ; Tong ZHAO
Progress in Biochemistry and Biophysics 2025;52(5):1302-1312
ObjectiveThe rapid advancement of bioanalytical technologies has heightened the demand for high-throughput, label-free, and real-time cellular analysis. Electrochemical impedance spectroscopy (EIS) operating in the GHz frequency range (GHz-EIS) has emerged as a promising tool for characterizing cell suspensions due to its ability to rapidly and non-invasively capture the dielectric properties of cells and their microenvironment. Although GHz-EIS enables rapid and label-free detection of cell suspensions, significant challenges remain in interpreting GHz impedance data for complex samples, limiting the broader application of this technique in cellular research. To address these challenges, this study presents a novel method that integrates GHz-EIS with deep learning algorithms, aiming to improve the precision of cell suspension concentration identification and quantification. This method provides a more efficient and accurate solution for the analysis of GHz impedance data. MethodsThe proposed method comprises two key components: dielectric property dataset construction and backpropagation (BP) neural network modeling. Yeast cell suspensions at varying concentrations were prepared and separately introduced into a coaxial sensor for impedance measurement. The dielectric properties of these suspensions were extracted using a GHz-EIS dielectric property extraction method applied to the measured impedance data. A dielectric properties dataset incorporating concentration labels was subsequently established and divided into training and testing subsets. A BP neural network model employing specific activation functions (ReLU and Leaky ReLU) was then designed. The model was trained and tested using the constructed dataset, and optimal model parameters were obtained through this process. This BP neural network enables automated extraction and analytical processing of dielectric properties, facilitating precise recognition of cell suspension concentrations through data-driven training. ResultsThrough comparative analysis with conventional centrifugal methods, the recognized concentration values of cell suspensions showed high consistency, with relative errors consistently below 5%. Notably, high-concentration samples exhibited even smaller deviations, further validating the precision and reliability of the proposed methodology. To benchmark the recognition performance against different algorithms, two typical approaches—support vector machines (SVM) and K-nearest neighbor (KNN)—were selected for comparison. The proposed method demonstrated superior performance in quantifying cell concentrations. Specifically, the BP neural network achieved a mean absolute percentage error (MAPE) of 2.06% and an R² value of 0.997 across the entire concentration range, demonstrating both high predictive accuracy and excellent model fit. ConclusionThis study demonstrates that the proposed method enables accurate and rapid determination of unknown sample concentrations. By combining GHz-EIS with BP neural network algorithms, efficient identification of cell concentrations is achieved, laying the foundation for the development of a convenient online cell analysis platform and showing significant application prospects. Compared to typical recognition approaches, the proposed method exhibits superior capabilities in recognizing cell suspension concentrations. Furthermore, this methodology not only accelerates research in cell biology and precision medicine but also paves the way for future EIS biosensors capable of intelligent, adaptive analysis in dynamic biological research.
6.Application of Ferroptosis Regulation in Chronic Atrophic Gastritis Based on Spleen Deficiency and Turbid Toxin
Yuxi GUO ; Xuemei JIA ; Jie WANG ; Yanru CAI ; Pengli DU ; Yao DU ; Diangui LI ; Qian YANG
Chinese Journal of Experimental Traditional Medical Formulae 2025;31(13):279-285
Chronic atrophic gastritis (CAG), a common digestive system disease, has an unclear pathogenesis. Currently, it is mostly believed to be related to Helicobacter pylori (Hp) infection, immune factors, dietary factors, bile reflux, long-term use of antibiotics and anti-inflammatory drugs, and other factors. Ferroptosis is a regulated cell death mechanism that is iron-dependent and characterized by disruption of iron metabolism and accumulation of lipid peroxides. More and more studies have found that ferroptosis is closely related to the onset of CAG. Professor LI Diangui, a master of traditional Chinese medicine, first proposed the turbid toxin theory, which holds that spleen deficiency and turbid toxin is the main pathogenic mechanism of CAG. Abnormal iron metabolism regulation is a prerequisite for the accumulation of turbid toxin in CAG, and ferroptosis is in accordance with the pathogenic mechanism (spleen deficiency and turbid toxin) of CAG. This article explores the pathological mechanism of spleen deficiency and turbid toxin in CAG from the perspectives of iron metabolism, oxidative stress, and lipid peroxidation, providing theoretical support of traditional Chinese medicine for the modern research on CAG. It enriches the modern scientific connotation of the turbid toxicity theory and provides new ideas and breakthrough points for the clinical treatment of CAG.
7.Application of Ferroptosis Regulation in Chronic Atrophic Gastritis Based on Spleen Deficiency and Turbid Toxin
Yuxi GUO ; Xuemei JIA ; Jie WANG ; Yanru CAI ; Pengli DU ; Yao DU ; Diangui LI ; Qian YANG
Chinese Journal of Experimental Traditional Medical Formulae 2025;31(13):279-285
Chronic atrophic gastritis (CAG), a common digestive system disease, has an unclear pathogenesis. Currently, it is mostly believed to be related to Helicobacter pylori (Hp) infection, immune factors, dietary factors, bile reflux, long-term use of antibiotics and anti-inflammatory drugs, and other factors. Ferroptosis is a regulated cell death mechanism that is iron-dependent and characterized by disruption of iron metabolism and accumulation of lipid peroxides. More and more studies have found that ferroptosis is closely related to the onset of CAG. Professor LI Diangui, a master of traditional Chinese medicine, first proposed the turbid toxin theory, which holds that spleen deficiency and turbid toxin is the main pathogenic mechanism of CAG. Abnormal iron metabolism regulation is a prerequisite for the accumulation of turbid toxin in CAG, and ferroptosis is in accordance with the pathogenic mechanism (spleen deficiency and turbid toxin) of CAG. This article explores the pathological mechanism of spleen deficiency and turbid toxin in CAG from the perspectives of iron metabolism, oxidative stress, and lipid peroxidation, providing theoretical support of traditional Chinese medicine for the modern research on CAG. It enriches the modern scientific connotation of the turbid toxicity theory and provides new ideas and breakthrough points for the clinical treatment of CAG.
8.Daurisoline Inhibits Progression of Triple-Negative Breast Cancer by Regulating the γγ-Secretase/Notch Axis
Xiangyi ZHAN ; Xiaoyong CHEN ; Mei FENG ; Kuo YAO ; Kefan YANG ; Hui JIA
Biomolecules & Therapeutics 2025;33(2):331-343
Triple-negative breast cancer (TNBC) is a subtype of breast cancer that is challenging to treat and lacks targeted therapeutic drugs in the clinic. Natural active ingredients provide promising opportunities for discovering and developing targeted therapies for TNBC. This study investigated the effects of daurisoline on TNBC and elucidated its potential mechanisms. Using network pharmacology, a correlation was identified between daurisoline, derived from Menispermum dauricum, and breast cancer, particularly involving the Notch signaling pathway. The effects of daurisoline on the proliferation, migration, and apoptosis of MDA-MB-231 and MDA-MB-468 cells were evaluated in vitro. Additionally, the impact of daurisoline on the growth of MDA-MB-231 xenograft tumors in nude mice was assessed through in vivo experiments. Expression levels of Notch signaling pathway-related proteins, including Notch-1, NICD, PSEN-1, Bax, and Bcl-2, were examined using molecular docking and Western blotting to explore the underlying mechanisms of daurisoline’s anti-breast cancer effects. It was revealed that daurisoline could effectively inhibit the proliferation and migration of MDA-MB-231 and MDA-MB-468 cells and promote apoptosis. Furthermore, it significantly reduced the growth of subcutaneous tumors in nude mice. Notably, daurisoline could reduce the hydrolytic activity of γ-secretase by binding to the catalytic core PSEN-1, thereby inhibiting activation of the γ-secretase/Notch axis and contributing to its anti-TNBC effects.This study supported the development of naturally targeted drugs for TNBC and provided insights into the research on dibenzylisoquinoline alkaloids, such as daurisoline.
9.Daurisoline Inhibits Progression of Triple-Negative Breast Cancer by Regulating the γγ-Secretase/Notch Axis
Xiangyi ZHAN ; Xiaoyong CHEN ; Mei FENG ; Kuo YAO ; Kefan YANG ; Hui JIA
Biomolecules & Therapeutics 2025;33(2):331-343
Triple-negative breast cancer (TNBC) is a subtype of breast cancer that is challenging to treat and lacks targeted therapeutic drugs in the clinic. Natural active ingredients provide promising opportunities for discovering and developing targeted therapies for TNBC. This study investigated the effects of daurisoline on TNBC and elucidated its potential mechanisms. Using network pharmacology, a correlation was identified between daurisoline, derived from Menispermum dauricum, and breast cancer, particularly involving the Notch signaling pathway. The effects of daurisoline on the proliferation, migration, and apoptosis of MDA-MB-231 and MDA-MB-468 cells were evaluated in vitro. Additionally, the impact of daurisoline on the growth of MDA-MB-231 xenograft tumors in nude mice was assessed through in vivo experiments. Expression levels of Notch signaling pathway-related proteins, including Notch-1, NICD, PSEN-1, Bax, and Bcl-2, were examined using molecular docking and Western blotting to explore the underlying mechanisms of daurisoline’s anti-breast cancer effects. It was revealed that daurisoline could effectively inhibit the proliferation and migration of MDA-MB-231 and MDA-MB-468 cells and promote apoptosis. Furthermore, it significantly reduced the growth of subcutaneous tumors in nude mice. Notably, daurisoline could reduce the hydrolytic activity of γ-secretase by binding to the catalytic core PSEN-1, thereby inhibiting activation of the γ-secretase/Notch axis and contributing to its anti-TNBC effects.This study supported the development of naturally targeted drugs for TNBC and provided insights into the research on dibenzylisoquinoline alkaloids, such as daurisoline.
10.Treatment of Hyperuricemia and Gouty Arthritis by Buyang Huanwu Tongfeng Decoction via Inhibition of PPAR-γ/NF-κB/AGEs/RAGE Pathway Based on Network Pharmacology
Yue CAO ; Wanmei YAO ; Tao YANG ; Man YANG ; Ruimin JIA ; Rongrong LU ; Xue FENG ; Biwang LIU
Chinese Journal of Experimental Traditional Medical Formulae 2025;31(1):182-192
ObjectiveThis paper aims to investigate the potential molecular biological mechanism of Buyang Huanwu Tongfeng decoction in treating hyperuricemia and gouty arthritis by network pharmacology and molecular docking technology and preliminarily verify the mechanism through animal experiments. MethodsThe active ingredients and targets in the Buyang Huanwu Tongfeng decoction were obtained by the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) and ETCM databases. The DisGeNET and GeneCards databases were utilized to acquire disease targets associated with hyperuricemia and gouty arthritis. These disease targets were then intersected with drug targets to identify key targets. The R language ClusterProfiler package and Python were employed for conducting gene ontology(GO) enrichment analysis and Kyoto encyclopedia of genes and genomes(KEGG) enrichment analysis. The regulatory network diagram of the drug-key target-function-pathway was visualized using Cytoscape 3.9.1 software, and the protein-protein interaction (PPI) network for key targets was depicted. Finally, the hub gene was determined through topological analysis. Auto Dock, PyMOL, and other software were used for molecular docking to explore the possible therapeutic mechanism of Buyang Huanwu Tongfeng decoction for hyperuricemia and gouty arthritis. In animal experiments, a composite rat model of hyperuricemia induced by intraperitoneal injection of oteracil potassium combined with gouty arthritis induced by the modified Coderre method was established. Through hematoxylin-eosin(HE) staining, uric acid test, enzyme linked immunosorbent assay(ELISA), Western blot, and real-time polymerase chain reaction(Real-time PCR), the molecular mechanism and key targets of Buyang Huanwu Tongfeng decoction for treating hyperuricemia and gouty arthritis were observed. ResultsAfter screening and removing duplicate values, 76 active ingredients and 15 key targets were finally obtained. GO enrichment analysis yielded that the treatment of hyperuricemia and gouty arthritis with Buyang Huanwu Tongfeng decoction was significantly associated with acute inflammatory response, astrocyte activation, regulation of interleukin (IL)-8 production, nuclear receptor activity, and binding of growth factor receptor. KEGG pathway enrichment analysis obtained that the key target genes were significantly associated with the IL-17 signaling pathway, advanced glycosylation end/receptor of advanced glycation endproducts(AGE/RAGE) signaling pathway, anti-inflammatory, and other pathways. PPI network indicated that albumin(ALB), peroxisome proliferator-activated receptor-γ (PPAR-γ), IL-6, IL-1β, and C-reactive protein(CRP) were the key protein targets. The molecular docking results showed that ALB had the strongest binding force with beta-carotene (β-carotene). Biochemical results showed that blood uric acid decreased in the Buyang Huanwu Tongfeng decoction groups. HE staining results showed that the low-dose (7.76 g·kg-1·d-1), medium-dose (15.53 g·kg-1·d-1), and high-dose (31.05 g·kg-1·d-1) groups of Buyang Huanwu Tongfeng decoction had different degrees of remission, and the remission of the high-dose group was the most obvious. Fibroblastic tissue hyperplasia in synovial joints accompanied with inflammatory cell infiltration, as well as inflammatory cell infiltration in renal tissue of the high-dose group was significantly reduced, followed by the medium-dose and low-dose groups, and the expression of ALB, PPAR-γ, IL-6, IL-1β, and CRP was down-regulated to different degrees. ConclusionBy regulating the targets such as ALB, PPAR-γ, IL-6, IL-1β, and CRP, inhibiting the PPAR-γ/nuclear transcription factor (NF)-κB pathway, and reducing AGEs/RAGE-mediated inflammation, Buyang Huanwu Tongfeng decoction exerts anti-inflammatory and analgesic effects and activates blood circulation and diuresis in the treatment of hyperuricemia and gouty arthritis.


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