1.Risk factors for 90-day mortality in patients with acute-on-chronic liver failure and establishment of a predictive model
Jing SUN ; Tingji WANG ; Zhijiao DUAN ; Li ZHANG ; Yanmei LI
Journal of Clinical Hepatology 2026;42(1):151-159
ObjectiveTo investigate the independent predictive factors for 90-day mortality in patients with acute-on-chronic liver failure (ACLF), to establish a risk predictive model, and to assess its predictive efficacy in comparison with MELD, MELD-Na, MELD 3.0, and COSSH-ACLF Ⅱ. MethodsA retrospective analysis was performed for the clinical data of 394 patients with ACLF who were admitted to The Affiliated Hospital of Inner Mongolia Medical University and Hohhot Second Hospital from July 2018 to July 2024, and general information and laboratory markers on admission were collected from all patients. The independent-samples t test or the Mann-Whitney U test was used for comparison of quantitative data between two groups, and the chi-square test or the adjusted chi-square test was used for comparison of qualitative data between two groups. The LASSO regression analysis was used to identify related variables, and the multivariate logistic regression analysis was used to establish a predictive model and generate a nomogram. The receiver operating characteristic (ROC) curve, the area under the ROC curve (AUC), calibration curve, and clinical decision curve were used to assess the performance of the model. ResultsA total of 394 patients with ACLF were included in this study, with 136 patients in the training set, 58 in the internal validation set, and 200 in the external validation set. The cohort had a mean age of 52.9±11.7 years, among whom male patients accounted for 72.84% (287/394), the patients with HBV infection accounted for 22.33% (88/394), the patients with alcohol-related causes accounted for 45.94% (181/394), and the patients with other causes (including drug-induced and autoimmune diseases) accounted for 31.73% (125/394). The overall 90-day mortality rate was 27.41% (108/394). The multivariate logistic regression analysis showed that diabetes (odds ratio [OR]= 5.831, 95% confidence interval [CI]: 1.587 — 21.424, P=0.008), cystatin C (Cys-C) (OR=2.984, 95%CI: 1.501 — 5.933, P=0.002), and spontaneous peritonitis (SBP) (OR=5.692, 95%CI: 2.150 — 15.071, P<0.001) were independent risk factors, and a nomogram was generated based on these factors. This model had an AUC of 0.836 in the training set, 0.881 in the internal validation set, and 0.878 in the external validation set, showing a good discriminatory ability. The calibration curve showed a good degree of fitting, with a relatively high net clinical benefit. The subgroup analysis based on etiology showed that the model had an AUC of 0.850 in the patients with HBV infection, 0.858 in the patients with alcohol-induced ACLF, and 0.908 in the patients with other etiologies, indicating that the model had a good discriminatory ability across the populations with different etiologies. Compared with traditional scores, the model (AUC=0.836) had a significantly better predictive value than MELD (AUC=0.619, Z=3.197, P=0.001), MELD-Na (AUC=0.651, Z=2.998, P=0.003), MELD 3.0 (AUC=0.601, Z=3.682, P<0.001), and COSSH-ACLF Ⅱ (AUC=0.719, Z=2.396, P=0.017) alone. ConclusionDiabetes, SBP, and Cys-C are independent risk factors for 90-day mortality in patients with ACLF. Compared with MELD, MELD-Na, MELD 3.0, and COSSH-ACLF Ⅱ scores, this model has a higher predictive value for 90-day prognosis in patients with ACLF and is suitable for patients with ACLF caused by various etiologies.
2.Processing History and Modern Research of Bile-processed Coptidis Rhizoma: A Review
Zhaowei DONG ; Jing YANG ; Qinwan HUANG ; Jin WANG
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(2):269-278
Bile-processed Coptidis Rhizoma(B-pCR), first documented in Shengji Zonglu, is a unique processed products of Coptidis Rhizoma(CR) characterized by "mutual enhancement processing" and "enhancing the cold property of cold-natured herbs". Pig bile can enhance the bitter and cold properties of CR, yielding potent effects in purging excess fire from the liver and gallbladder. The processing increases the dissolution of alkaloids such as berberine, coptisine, and palmatine, while introducing bile acids from pig bile, including taurine-type and glycine-type cholic acids. This enhances its pharmacological effects, such as antipyretic activity, regulation of glucose and lipid metabolism disorders, and intestinal absorption. Traditional processing techniques and quality standards for B-pCR are outlined in the Shanghai Traditional Chinese Medicine(TCM) Decoction Pieces Processing Standard and the Gansu TCM Processing Standard. However, incomplete specifications for critical process parameters and quality criteria significantly impact its production and clinical application. A review of research over the past two decades on the processing history, process optimization, quality evaluation, material basis, and changes in pharmacological effects and properties of B-pCR reveals that the pretreatment method and dosage of pig bile, and processing temperature are key factors influencing its quality. Furthermore, current quality standards lack specific indicators. Additionally, the enhancement of the cold property and medicinal efficacy direction of B-pCR is not only associated with changes in alkaloid groups but also depend on the synergistic effects of bile acids. This review can provide insights for improving the quality evaluation system of B-pCR.
3.Herbal Textual Research on Inulae Flos in Famous Classical Formulas
Caixia LIU ; Yue HAN ; Yanzhu MA ; Lei GAO ; Sheng WANG ; Yan YANG ; Wenchuan LUO ; Ling JIN ; Jing SHAO ; Zhijia CUI ; Zhilai ZHAN
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(3):210-221
In this paper, by referring to ancient and modern literature, the textual research of Inulae Flos has been conducted to clarify the name, origin, production area, quality evaluation, harvesting, processing and others, so as to provide reference and basis for the development and utilization of famous classical formulas containing this herb. After textual research, it could be verified that the medicinal use of Inulae Flos was first recorded in Shennong Bencaojing of the Han dynasty. In successive dynasties, Xuanfuhua has been taken as the official name, and it also has other alternative names such as Jinfeicao, Daogeng and Jinqianhua. The period before the Song and Yuan dynasties, the main origin of Inulae Flos was the Asteraceae plant Inula japonica, and from the Ming and Qing dynasties to the present, I. japonica and I. britannica are the primary source. In addition to the dominant basal species, there are also regional species such as I. linariifolia, I. helianthus-aquatili, and I. hupehensis. The earliest recorded production areas in ancient times were Henan, Hubei and other places, and the literature records that it has been distributed throughout the country since modern times. The medicinal part is its flower, the harvesting and processing method recorded in the past dynasties is mainly harvested in the fifth and ninth lunar months, and dried in the sun, and the modern harvesting is mostly harvested in summer and autumn when the flowers bloom, in order to remove impurities, dry in the shade or dry in the sun. In addition, the roots, whole herbs and aerial parts are used as medicinal materials. In ancient times, there were no records about the quality of Inulae Flos, and in modern times, it is generally believed that the quality of complete flower structure, small receptacles, large blooms, yellow petals, long filaments, many fluffs, no fragments, and no branches is better. Ancient processing methods primarily involved cleaning, steaming, and sun-drying, supplemented by techniques such as boiling, roasting, burning, simmering, stir-frying, and honey-processing. Modern processing focuses mainly on cleaning the stems and leaves before use. Regarding the medicinal properties, ancient texts describe it as salty and sweet in taste, slightly warm in nature, and mildly toxic. Modern studies characterize it as bitter, pungent, and salty in taste, with a slightly warm nature. Its therapeutic effects remain consistent across eras, including descending Qi, resolving phlegm, promoting diuresis, and stopping vomiting. Based on the research results, it is recommended that when developing famous classical formulas containing Inulae Flos, either I. japonica or I. britannica should be used as the medicinal source. Processing methods should follow formula requirements, where no processing instructions are specified, the raw products may be used after cleaning.
4.Curcumin extraction and preparation and optimization of curcumin nanoparticles
Yuhang WANG ; Han ZHANG ; Chaojing ZHANG ; Xurong KOU ; Tongtong JING ; Rimei LIN ; Xinyu LIU ; Shilei LOU ; Hui YAN ; Cong SUN
Chinese Journal of Tissue Engineering Research 2026;30(2):362-374
BACKGROUND:Curcumin is the main active ingredient of turmeric and has significant medicinal value in anti-tumor,anti-inflammatory,antioxidant and other aspects.However,its poor water solubility,unstable chemical properties and easy decomposition lead to difficulty in extracting curcumin and low extraction yield.Therefore,it is particularly important to optimize the curcumin extraction method.OBJECTIVE:To enhance the extraction yield and utilization value of curcumin and optimize the curcumin extraction process and curcumin nanoparticle preparation process.METHODS:Curcumin was extracted from turmeric by ethanol extraction,ultrasonic extraction,ionic liquid extraction,enzyme extraction,and ionic liquid combined with ultrasonic assisted enzyme extraction.The curcumin extraction yield was detected by high performance liquid chromatography;the best extraction method was determined,and subsequent process optimization experiments were carried out.The curcumin extraction yield was the response value with the type of ionic liquid,reaction temperature,ultrasonic time,liquid-to-solid ratio,ionic liquid concentration,and enzyme-drug mass ratio as parameters.The optimal production process of ionic liquid combined with ultrasonic assisted enzyme extraction was determined by single factor combined response surface experiment.The optimal process for preparing curcumin nanoparticles by ionic crosslinking method was determined by single factor combined response surface experiment with acetic acid concentration,chitosan to sodium tripolyphosphate mass ratio,stirring rate,curcumin mass concentration,sodium tripolyphosphate mass concentration,and chitosan mass concentration as parameters,and drug encapsulation efficiency as response value.Curcumin nanoparticles were prepared under the optimal process,and the particle size,polydispersity index,Zata potential value,drug loading,stability,hemolysis rate,and antioxidant capacity in vivo and in vitro of the nanoparticles were detected.RESULTS AND CONCLUSION:(1)Among the five extraction methods,the curcumin yield of ionic liquid combined with ultrasound-assisted enzyme extraction was the highest,and this method was selected as the curcumin extraction method for subsequent experiments.The results of single factor combined response surface experiment showed that the optimal process for curcumin extraction was:ionic liquid selected 1-hexyl-3-methylimidazolium chloride,reaction temperature 55 ℃,liquid-to-solid ratio 40 mL/g,ultrasound time 57 minutes,ionic liquid concentration 57%,enzyme-drug mass ratio 3.5:10,and the obtained turmeric extraction yield was 3.10%.The optimal preparation process of curcumin nanoparticles was:glacial acetic acid concentration 0.5%,chitosan and sodium tripolyphosphate mass ratio 5.0:1,stirring speed 150 r/min,curcumin mass concentration 2.23 mg/mL,sodium tripolyphosphate mass concentration 1.45 mg/mL,chitosan mass concentration 3.63 mg/mL,and the obtained drug encapsulation efficiency was 90.61%.(2)The drug loading of curcumin nanoparticles was(14.49±0.23)%,the average particle size was(76.95±1.65)nm,the polydispersity coefficient was 0.15±0.02,and the Zata potential value was(32.37±1.46)mV.The curcumin nanoparticles had good stability and blood compatibility,did not induce hemolysis,and had stronger antioxidant capacity in vivo and in vitro than free curcumin.(3)The results show that the process optimization not only solves the problems of low extraction yield,poor solubility,and low bioavailability of curcumin,but also enhances its antioxidant activity in vivo and in vitro.
5.Constructing a rat animal model of pelvic organ prolapse:a comparison of three modeling methods
Jing YANG ; Houmei WANG ; Yi WANG ; Min SONG ; Jie REN ; Lujun DAI ; Ziwen XIAO
Chinese Journal of Tissue Engineering Research 2026;30(4):864-872
BACKGROUND:Currently,there are many modeling methods for pelvic organ prolapse animal models,and the commonly used methods are vaginal balloon dilatation,oophorectomy and the combination of the two.There is no study comparing the three modeling methods in detail.OBJECTIVE:To construct and validate a rat animal model of pelvic organ prolapse using three different methods and to identify the advantages and disadvantages of various models.METHODS:Seventy-two 8-week SPF-grade female Sprague-Dawley rats were selected and randomly divided into four groups,namely,vaginal balloon dilatation group,ovariectomy group,ovariectomy combined with vaginal balloon dilatation group(the combined group),and the sham-operated group(no ovariectomy and no vaginal dilatation).The vaginal wall tissues of rats were collected at 4,8 and 12 weeks after the operation for hematoxylin-eosin staining,Masson staining,EVG staining and immunohistochemical staining of α-smooth muscle actin,Vimentin and matrix metalloproteinase 9 detection,and the pelvic floor muscle tissues were taken at 4,8 and 12 weeks after the operation for hematoxylin-eosin staining,Masson staining and EVG staining.RESULTS AND CONCLUSION:(1)Hematoxylin-eosi staining showed that there was no significant difference in the decrease of vaginal epithelial layer thickness in the vaginal balloon dilatation group compared with the sham-operated group,(P>0.05),while the thickness of the vaginal epithelial layer was significantly reduced in the ovariectomy group and the ovariectomy combined with vaginal balloon dilation group(P<0.001),and the reduction was more significant in the ovariectomy combined with vaginal balloon dilation group,remained stable at 8 weeks after surgery and lasted until 12 weeks.(2)The changes in the content of collagen fibers and elastic fibers in the vaginal wall stained by Masson and EVG staining were the same as the changes in the thickness of the vaginal epithelial layer stained by hematoxylin-eosin,and there were no changes in collagen fibers and elastic fibers in the pelvic floor muscle tissues of the treatment groups.(3)At 4,8 and 12 weeks after treatment,there was no significant difference in the expression levels of α-smooth muscle actin,Vimentin and matrix metalloproteinase 9 in the vaginal wall tissue of the balloon dilation group compared with the control group(P>0.05),whereas the expression levels of α-smooth muscle actin and Vimentin were significantly decreased in the ovariectomy group and ovariectomy combined with vaginal balloon dilation group(P<0.01)and the expression of matrix metalloproteinase 9 showed a significant increase(P<0.01),with a more pronounced increase in the ovariectomy combined with vaginal balloon dilation group,and the increase reached a stable state at 8 weeks after surgery and could persist up to 12 weeks.To conclude,vaginal balloon dilatation could not maintain the degeneration of pelvic organ prolapse formed by the vaginal wall for a long period,and both ovariectomy and the combined method can be used.Ovariectomy combined with vaginal balloon dilatation can significantly accelerate and aggravate the formation of typical histological features of pelvic organ prolapse in vaginal wall tissues,effectively shorten the experimental period,and improve the efficiency.These effects reach a stable state at 8 weeks after surgery and can be sustained up to 12 weeks,which is practical and convenient for the study of pelvic organ prolapse animal models.
6.Assessing High-density Y-SNP Panels for Paternal Haplogroup Assignment in Forensic Practice
De-Qin ZHANG ; Chun-Nian WANG ; Lin-Lin LOU ; Meng NI ; Jing GAO ; Jiang HUANG ; Li JIANG
Progress in Biochemistry and Biophysics 2026;53(2):458-469
ObjectiveThe accuracy of Y-chromosome haplogroup assignment is crucial for tracing paternal lineage in male samples. With the advancement of high-throughput sequencing technologies, high-density Y-SNP genotyping from whole-genome or array-based data has become a standard method for determiningY-chromosome haplogroups. This study systematically evaluated the performance of 4 commonly used high-density SNP genotyping systems—namely, the Global Screening Array (GSA), Chinese Genotyping Array (CGA), Affymetrix array, and the 1240K capture panel—for haplogroup assignment. This work provides a reference for data comparison across different systems. MethodsWe extracted genotype data for the 4 Y-SNP panels from 30× whole-genome sequencing (WGS) data of 1 590 male samples from the 1000 Genomes Project. Additionally, GSA array genotype data from 384 relative pairs (spanning 1st- to 12th-degree relationships) from 109 Chinese Han families were collected. Haplogroup assignment was performed using Y-LineageTracker v1.3.0 software. We assessed the concordance and resolution of haplogroup assignments between the four Y-SNP panels and the WGS data. The consistency and resolution of haplogroup assignments were also evaluated for both the 1000 Genomes Project samples and the 109 family samples collected in this study. Furthermore, the impact of varying numbers of Y-SNPs on haplogroup assignment was examined. ResultsThe GSA and CGA panels demonstrated superior resolution and discrimination of haplogroup subclades compared with the other two panels. The haplogroup assignments from the GSA, CGA, and 1240K panels showed high concordance with WGS data, with consistency rates exceeding 88.70%, whereas the Affymetrix platform exhibited a significantly lower consistency rate of 61.89%. Specifically, the GSA and CGA panels consistently demonstrated superior performance compared with the other two panels in the assignment of haplogroups O-M175 and H-L901, achieving complete concordance (100%) for both haplogroups. In contrast, the Affymetrix panel erroneously assigned all individuals belonging to haplogroup O-M175 to haplogroup K2-M526. Furthermore, its accuracy for haplogroup H-L901 was exceedingly low, at merely 1.41%. This poor performance was characterized by the misassignment of 98.59% of H-L901 samples—specifically, 1.41% to J-M304 and a predominant 97.18% to F-M89. For haplogroup R-M207, all four panels exhibited uniformly high levels of consistency, with concordance values exceeding 94.00%. Notably, for haplogroup E-M96, the 1240K and Affymetrix panels outperformed the GSA and CGA panels in terms of concordance, representing the first instance in which these two panels surpassed the latter. Conversely, for haplogroups J-M304, Q-M242, and I-M170, all 4 panels showed relatively elevated misclassification rates, with the Affymetrix array demonstrating the poorest overall performance. None of the four panels showed any discordant haplogroup assignments among the familial relative pairs analyzed. A positive correlation was observed between the number of Y-SNPs (ranging from 1 000 to 10 000) and classification consistency; however, classification consistency plateaued when the number of Y-SNPs exceeded 10 000. Furthermore, a random sampling analysis conducted on the GSA and CGA panels demonstrated that the haplogroup misclassification rate exhibited negligible fluctuation across the Y-SNP range of 500 to 1 000. Conversely, a marked enhancement in classification consistency was observed as the number of markers increased from 1 000 to 5 000, ultimately reaching a plateau within the interval of 5 000 to 8 000 markers. ConclusionThese findings indicate that the GSA and CGA panels provide high resolution and concordance, delivering reliable Y-haplogroup assignment for forensic investigations.
7.Interaction Mechnisms Between Gut Microbiota and Ischemic Stroke——A Study Based on the “Microbiota-Gut-Brain Axis” Integrating 16S rRNA Sequencing with Fecal Microbiota Transplantation
Ting WANG ; Jing-Hao ZHANG ; Chao JIANG
Progress in Biochemistry and Biophysics 2026;53(2):470-484
ObjectiveThis Study was conducted to investigate the interaction mechemisms between gutmicrobiota dysregulation and ischemic stroke by establishing a rat model of ischemic stroke and employing fecal microbiota transplantation (FMT). MethodsA preliminary experiment was conducted to establish an antibiotic-induced pseudo-sterile (ABX) rat model through antibiotic treatment, and a cerebral ischemia model was prepared using the middle cerebral artery occlusion (MCAO) method. Fecal microbiota from stroke patients and healthy individuals were transplanted via FMT, followed by behavioral testing. 16S rRNA sequencing was used to analyze the microbial community, hematoxylin and eosin (HE) staining to observe histopathological status, transmission electron microscopy (TEM) to examine the tight junction structure of the small intestine, and enzyme-linked immunosorbent assay (ELISA) to detect levels of inflammatory factors and intestinal barrier-related markers. Results16S rRNA sequencing of fecal samples showed that compared with the normal control group and the metronidazole group, the abundance and diversity of fecal microorganisms in the quadruple antibiotic group were significantly reduced, indicating successful establishment of the ABX model. After transplanting fecal microbiota from stroke patients into ABX rats, significant changes in gut microbiota composition were observed. Behavioral tests revealed that the MCAO model group showed significant decreases in both horizontal movement and vertical exploration abilities. ELISA results indicated that IL-17 concentration in the ABX+mFMT (antibiotic-treated+model fecal microbiota transplantation) group was lower than in the ABX+cFMT (antibiotic-treated+control fecal microbiota transplantation) group, suggesting that IL-17 may serve as a key inflammatory indicator for evaluating the impact of stroke intervention on gut microbiota. Triphenyltetrazolium chloricle staining (TTC) staining suggested that gut microbiota intervention may increase the risk of stroke. HE staining showed that, except for the control group, all groups exhibited ischemic changes and inflammatory infiltration in brain tissues. TEM revealed that microvilli of small intestinal epithelial cells in the ABX+mFMT group were sparser than those in the ABX+cFMT group, indicating that microbial intervention affects intestinal barrier function. ConclusionThe ABX model established using broad-spectrum antibiotics showed no significant differences in physiological characteristics compared to normal rats, and the findings were consistent with those from germ-free rat models. Stroke prognosis appears to be influenced by intestinal dysbiosis, accompanied by significantly elevated levels of the pro-inflammatory cytokine IL-17, which may exacerbate neural injury via the gut-brain axis. Behavioral experiments indicated that transplantation of gut microbiota from stroke rats impaired cognitive function. Furthermore, IL-17 demonstrated sensitivity to alterations in the gut microbiota, suggesting its potential as a key therapeutic target for stroke intervention.
8.From Golgi Stress to Golgiphagy—a New Regulatory Model Involved in Glucose and Lipid Metabolism
Hai-Jun WEI ; He-Ming WANG ; Shu-Jing CHEN ; Shu-Zhi WANG ; Lin-Xi CHEN
Progress in Biochemistry and Biophysics 2026;53(2):275-292
The Golgi body, a core organelle in eukaryotic cells, plays a critical role in protein modification, sorting, vesicular transport, and serves as a key site for lipid synthesis and glycosylation. Glucose and lipid metabolism are central processes for cellular energy maintenance and biosynthesis, and are closely linked to Golgi function. Recent studies have revealed the extensive involvement of the Golgi body in regulating glucose and lipid metabolism, where maintaining its structural and functional homeostasis is crucial for normal physiological activity. Under various stress conditions such as acidosis, hypoxia, and nutrient deficiency, the Golgi body undergoes structural and functional disruption, leading to Golgi stress. This in turn activates specific signaling pathways, such as those mediated by the cAMP-responsive element binding protein 3 (CREB3) and proteoglycans, to alleviate Golgi stress and enhance Golgi function. Golgi stress contributes to glucose and lipid metabolic disorders by affecting the activity of insulin receptors, glucose transporters, and lipid metabolism-related enzymes. For example, Golgi stress triggers the cleavage and release of the active fragment of CREB3, which enters the nucleus and upregulates the transcription of ADP-ribosylation factor 4 (ARF4) and key gluconeogenic enzymes, including phosphoenolpyruvate carboxykinase (PEPCK) and glucose-6-phosphatase (G6Pase). ARF4 promotes vesicle retrograde transport between the Golgi and endoplasmic reticulum, maintains secretory capacity, and enhances hepatic glucose output. This pathway is particularly active under high-fat or lipotoxic stress, leading to fasting hyperglycemia. When damaged Golgi components accumulate beyond a tolerable threshold, the cell initiates an autophagic response, selectively encapsulating the damaged Golgi into autophagosomes, which then fuse with lysosomes to form autolysosomes, leading to Golgiphagy. This process results in the degradation and clearance of damaged Golgi, thereby regulating Golgi quantity, quality, and function. Golgiphagy also plays a significant role in regulating glucose and lipid metabolism. For instance, under high-glucose conditions, autophagic flux may be suppressed, impairing the timely clearance and renewal of damaged Golgi, compromising its normal function, and further exacerbating glucose metabolism disorders. Additionally, Golgiphagy may participate in lipid degradation and influence lipid synthesis and transport. Research indicates that Golgi stress and Golgiphagy play important roles in glucose and lipid metabolism-related diseases. For example, the leucine zipper protein (LZIP) under Golgi stress conditions can promote hepatic steatosis. In mouse primary cells and human tissues, LZIP induces the expression of apolipoprotein A-IV (APOA4), which increases peripheral free fatty acid uptake, resulting in lipid accumulation in the liver and contributing to the development of fatty liver disease. This review systematically outlines the structure and function of the Golgi apparatus, the molecular regulatory mechanisms of Golgi stress and Golgiphagy, and their synergistic roles. It further elaborates on how Golgi stress and Golgiphagy participate in the regulation of glucose and lipid metabolism, discusses their clinical significance in related diseases such as diabetes, fatty liver disease, and obesity, and highlights potential novel therapeutic strategies from the perspective of Golgi-targeted medicine
9.Assessing High-density Y-SNP Panels for Paternal Haplogroup Assignment in Forensic Practice
De-Qin ZHANG ; Chun-Nian WANG ; Lin-Lin LOU ; Meng NI ; Jing GAO ; Jiang HUANG ; Li JIANG
Progress in Biochemistry and Biophysics 2026;53(2):458-469
ObjectiveThe accuracy of Y-chromosome haplogroup assignment is crucial for tracing paternal lineage in male samples. With the advancement of high-throughput sequencing technologies, high-density Y-SNP genotyping from whole-genome or array-based data has become a standard method for determiningY-chromosome haplogroups. This study systematically evaluated the performance of 4 commonly used high-density SNP genotyping systems—namely, the Global Screening Array (GSA), Chinese Genotyping Array (CGA), Affymetrix array, and the 1240K capture panel—for haplogroup assignment. This work provides a reference for data comparison across different systems. MethodsWe extracted genotype data for the 4 Y-SNP panels from 30× whole-genome sequencing (WGS) data of 1 590 male samples from the 1000 Genomes Project. Additionally, GSA array genotype data from 384 relative pairs (spanning 1st- to 12th-degree relationships) from 109 Chinese Han families were collected. Haplogroup assignment was performed using Y-LineageTracker v1.3.0 software. We assessed the concordance and resolution of haplogroup assignments between the four Y-SNP panels and the WGS data. The consistency and resolution of haplogroup assignments were also evaluated for both the 1000 Genomes Project samples and the 109 family samples collected in this study. Furthermore, the impact of varying numbers of Y-SNPs on haplogroup assignment was examined. ResultsThe GSA and CGA panels demonstrated superior resolution and discrimination of haplogroup subclades compared with the other two panels. The haplogroup assignments from the GSA, CGA, and 1240K panels showed high concordance with WGS data, with consistency rates exceeding 88.70%, whereas the Affymetrix platform exhibited a significantly lower consistency rate of 61.89%. Specifically, the GSA and CGA panels consistently demonstrated superior performance compared with the other two panels in the assignment of haplogroups O-M175 and H-L901, achieving complete concordance (100%) for both haplogroups. In contrast, the Affymetrix panel erroneously assigned all individuals belonging to haplogroup O-M175 to haplogroup K2-M526. Furthermore, its accuracy for haplogroup H-L901 was exceedingly low, at merely 1.41%. This poor performance was characterized by the misassignment of 98.59% of H-L901 samples—specifically, 1.41% to J-M304 and a predominant 97.18% to F-M89. For haplogroup R-M207, all four panels exhibited uniformly high levels of consistency, with concordance values exceeding 94.00%. Notably, for haplogroup E-M96, the 1240K and Affymetrix panels outperformed the GSA and CGA panels in terms of concordance, representing the first instance in which these two panels surpassed the latter. Conversely, for haplogroups J-M304, Q-M242, and I-M170, all 4 panels showed relatively elevated misclassification rates, with the Affymetrix array demonstrating the poorest overall performance. None of the four panels showed any discordant haplogroup assignments among the familial relative pairs analyzed. A positive correlation was observed between the number of Y-SNPs (ranging from 1 000 to 10 000) and classification consistency; however, classification consistency plateaued when the number of Y-SNPs exceeded 10 000. Furthermore, a random sampling analysis conducted on the GSA and CGA panels demonstrated that the haplogroup misclassification rate exhibited negligible fluctuation across the Y-SNP range of 500 to 1 000. Conversely, a marked enhancement in classification consistency was observed as the number of markers increased from 1 000 to 5 000, ultimately reaching a plateau within the interval of 5 000 to 8 000 markers. ConclusionThese findings indicate that the GSA and CGA panels provide high resolution and concordance, delivering reliable Y-haplogroup assignment for forensic investigations.
10.Interaction Mechnisms Between Gut Microbiota and Ischemic Stroke——A Study Based on the “Microbiota-Gut-Brain Axis” Integrating 16S rRNA Sequencing with Fecal Microbiota Transplantation
Ting WANG ; Jing-Hao ZHANG ; Chao JIANG
Progress in Biochemistry and Biophysics 2026;53(2):470-484
ObjectiveThis Study was conducted to investigate the interaction mechemisms between gutmicrobiota dysregulation and ischemic stroke by establishing a rat model of ischemic stroke and employing fecal microbiota transplantation (FMT). MethodsA preliminary experiment was conducted to establish an antibiotic-induced pseudo-sterile (ABX) rat model through antibiotic treatment, and a cerebral ischemia model was prepared using the middle cerebral artery occlusion (MCAO) method. Fecal microbiota from stroke patients and healthy individuals were transplanted via FMT, followed by behavioral testing. 16S rRNA sequencing was used to analyze the microbial community, hematoxylin and eosin (HE) staining to observe histopathological status, transmission electron microscopy (TEM) to examine the tight junction structure of the small intestine, and enzyme-linked immunosorbent assay (ELISA) to detect levels of inflammatory factors and intestinal barrier-related markers. Results16S rRNA sequencing of fecal samples showed that compared with the normal control group and the metronidazole group, the abundance and diversity of fecal microorganisms in the quadruple antibiotic group were significantly reduced, indicating successful establishment of the ABX model. After transplanting fecal microbiota from stroke patients into ABX rats, significant changes in gut microbiota composition were observed. Behavioral tests revealed that the MCAO model group showed significant decreases in both horizontal movement and vertical exploration abilities. ELISA results indicated that IL-17 concentration in the ABX+mFMT (antibiotic-treated+model fecal microbiota transplantation) group was lower than in the ABX+cFMT (antibiotic-treated+control fecal microbiota transplantation) group, suggesting that IL-17 may serve as a key inflammatory indicator for evaluating the impact of stroke intervention on gut microbiota. Triphenyltetrazolium chloricle staining (TTC) staining suggested that gut microbiota intervention may increase the risk of stroke. HE staining showed that, except for the control group, all groups exhibited ischemic changes and inflammatory infiltration in brain tissues. TEM revealed that microvilli of small intestinal epithelial cells in the ABX+mFMT group were sparser than those in the ABX+cFMT group, indicating that microbial intervention affects intestinal barrier function. ConclusionThe ABX model established using broad-spectrum antibiotics showed no significant differences in physiological characteristics compared to normal rats, and the findings were consistent with those from germ-free rat models. Stroke prognosis appears to be influenced by intestinal dysbiosis, accompanied by significantly elevated levels of the pro-inflammatory cytokine IL-17, which may exacerbate neural injury via the gut-brain axis. Behavioral experiments indicated that transplantation of gut microbiota from stroke rats impaired cognitive function. Furthermore, IL-17 demonstrated sensitivity to alterations in the gut microbiota, suggesting its potential as a key therapeutic target for stroke intervention.

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