1.Optimizing extraction of microbial DNA from urine: Advancing urinary microbiome research in bladder cancer
Chuang-Ming ZHENG ; Ho Won KANG ; Seongmin MOON ; Young Joon BYUN ; Won Tae KIM ; Yung Hyun CHOI ; Sung-Kwon MOON ; Xuan-Mei PIAO ; Seok Joong YUN
Investigative and Clinical Urology 2025;66(3):272-280
Purpose:
This study aimed to evaluate and optimize microbial DNA extraction methods from urine, a non-invasive sample source, to enhance DNA quality, purity, and reliability for urinary microbiome research and biomarker discovery in bladder cancer.
Materials and Methods:
A total of 302 individuals (258 with genitourinary cancers and 44 with benign urologic diseases) participated in this study. Urine samples were collected via sterile catheterization, resulting in 445 vials for microbial analysis. DNA extraction was performed using three protocols: the standard protocol (SP), water dilution protocol (WDP), and chelation-assisted protocol (CAP). DNA quality (concentration, purity, and contamination levels) was assessed using NanoDrop spectrophotometry.Microbial analysis was conducted on 138 samples (108 cancerous and 30 benign) using 16S rRNA sequencing. Prior to sequencing on the Illumina MiSeq platform, Victor 3 fluorometry was used for validation.
Results:
WDP outperformed other methods, achieving significantly higher 260/280 and 260/230 ratios, indicating superior DNA purity and reduced contamination, while maintaining reliable DNA yields. CAP was excluded due to poor performance across all metrics. Microbial abundance was significantly higher in WDP-extracted samples (p<0.0001), whereas SP demonstrated higher alpha diversity indices (p<0.01), likely due to improved detection of low-abundance taxa. Beta diversity analysis showed no significant compositional differences between SP and WDP (p=1.0), supporting the reliability of WDP for microbiome research.
Conclusions
WDP is a highly effective and reliable method for microbial DNA extraction from urine, ensuring high-quality and reproducible results. Future research should address sample variability and crystal precipitation to further refine microbiome-based diagnostics and therapeutics.
2.Molecular Mechanisms Underlying Sleep Deprivation-induced Acceleration of Alzheimer’s Disease Pathology
Si-Ru YAN ; Ming-Yang CAI ; Ya-Xuan SUN ; Qing HUO ; Xue-Ling DAI
Progress in Biochemistry and Biophysics 2025;52(10):2474-2485
Sleep deprivation (SD) has emerged as a significant modifiable risk factor for Alzheimer’s disease (AD), with mounting evidence demonstrating its multifaceted role in accelerating AD pathogenesis through diverse molecular, cellular, and systemic mechanisms. SD is refined within the broader spectrum of sleep-wake and circadian disruption, emphasizing that both acute total sleep loss and chronic sleep restriction destabilize the homeostatic and circadian processes governing glymphatic clearance of neurotoxic proteins. During normal sleep, concentrations of interstitial Aβ and tau fall as cerebrospinal fluid oscillations flush extracellular waste; SD abolishes this rhythm, causing overnight rises in soluble Aβ and tau species in rodent hippocampus and human CSF. Orexinergic neurons sustain arousal, and become hyperactive under SD, further delaying sleep onset and amplifying Aβ production. At the molecular level, SD disrupts Aβ homeostasis through multiple converging pathways, including enhanced production via beta-site APP cleaving enzyme 1 (BACE1) upregulation, coupled with impaired clearance mechanisms involving the glymphatic system dysfunction and reduced Aβ-degrading enzymes (neprilysin and insulin-degrading enzyme). Cellular and histological analyses revealed that these proteinopathies are significantly exacerbated by SD-induced neuroinflammatory cascades characterized by microglial overactivation, astrocyte reactivity, and sustained elevation of pro-inflammatory cytokines (IL-1β, TNF-α, IL-6) through NF‑κB signaling and NLRP3 inflammasome activation, creating a self-perpetuating cycle of neurotoxicity. The synaptic and neuronal consequences of chronic SD are particularly profound and potentially irreversible, featuring reduced expression of critical synaptic markers (PSD95, synaptophysin), impaired long-term potentiation (LTP), dendritic spine loss, and diminished neurotrophic support, especially brain-derived neurotrophic factor (BDNF) depletion, which collectively contribute to progressive cognitive decline and memory deficits. Mechanistic investigations identify three core pathways through which SD exerts its neurodegenerative effects: circadian rhythm disruption via BMAL1 suppression, orexin system hyperactivity leading to sustained wakefulness and metabolic stress, and oxidative stress accumulation through mitochondrial dysfunction and reactive oxygen species overproduction. The review critically evaluates promising therapeutic interventions including pharmacological approaches (melatonin, dual orexin receptor antagonists), metabolic strategies (ketogenic diets, and Mediterranean diets rich in omega-3 fatty acids), lifestyle modifications (targeted exercise regimens, cognitive behavioral therapy for insomnia), and emerging technologies (non-invasive photobiomodulation, transcranial magnetic stimulation). Current research limitations include insufficient understanding of dose-response relationships between SD duration/intensity and AD pathology progression, lack of long-term longitudinal clinical data in genetically vulnerable populations (particularly APOE ε4 carriers and those with familial AD mutations), the absence of standardized SD protocols across experimental models that accurately mimic human chronic sleep restriction patterns, and limited investigation of sex differences in SD-induced AD risk. The accumulated evidence underscores the importance of addressing sleep disturbances as part of multimodal AD prevention strategies and highlights the urgent need for clinical trials evaluating sleep-focused interventions in at-risk populations. The review proposes future directions focused on translating mechanistic insights into precision medicine approaches, emphasizing the need for biomarkers to identify SD-vulnerable individuals, chronotherapeutic strategies aligned with circadian biology, and multi-omics integration across sleep, proteostasis and immune profiles may delineate precision-medicine strategies for at-risk populations. By systematically examining these critical connections, this analysis positions sleep quality optimization as a viable strategy for AD prevention and early intervention while providing a comprehensive roadmap for future mechanistic and interventional research in this rapidly evolving field.
3.A Ten-Year Comparative Study on Ethical Cognition of Experimental Animals among Medical Students in a University
Xuan LEI ; Xiangyi MING ; Han YANG ; Zixu CHEN ; Dandan FENG ; Jing DENG ; Ziqiang LUO
Chinese Medical Ethics 2024;35(5):533-537
The study was carried out to understand the changes in the ethical cognition status of laboratory animals and the effectiveness of laboratory animal ethics education among medical students in Xiangya School of Medicine of Central South University (CSU), and provide new enlightenment for further strengthening the ethical education of laboratory animals. In the study, the same self-compiled questionnaire was used to investigate the ethical cognition of experimental animals among medical students in Xiangya School of Medicine of CSU in 2011 and 2021, and 359 and 363 questionnaires were collected respectively. Through comparative analysis of the questionnaire results before and after ten years, it was found that medical students’ animal experiment operation and attitudes towards laboratory animals, cognition of experimental animal ethics knowledge and their attitude to animal experiment ethics education were significantly improved. It showed that the state of experimental animal ethics cognition among medical students in Xiangya School of Medicine of CSU had improved significantly in recent 10 years, but the cognition of experimental animal ethics knowledge was higher than the actual behavior of caring for experimental animals, and there was the phenomenon of "separation of knowledge and action". The ethics education of experimental animals needs to pay more attention to the development of students’ behavior of caring for experimental animals.
4. Influence of quercetin on aging of bone marrow mesenchymal stem cells induced by microgravity
Yu-Tian YANG ; Ying-Ying XUAN ; Yu-Tian YANG ; Ying-Ying XUAN ; Yu-Hai GAO ; Long-Fei WANG ; Han-Qin TANG ; Zhi-Hui MA ; Liang LI ; Yi WU ; Ke-Ming CHEN ; Yu-Tian YANG ; Ying-Ying XUAN ; Yu-Hai GAO ; Long-Fei WANG ; Han-Qin TANG ; Zhi-Hui MA ; Liang LI ; Yi WU ; Ke-Ming CHEN
Chinese Pharmacological Bulletin 2024;40(1):38-45
Aim To investigate the effect of quercetin on the aging model of bone marrow mesenchymal stem cells established under microgravity. Methods Using 3D gyroscope, a aging model of bone marrow mesenchymal stem cells was constructed, and after receiving quercetin and microgravity treatment, the anti-aging effect of the quercetin was evaluated by detecting related proteins and oxidation indexes. Results Compared to the control group, the expressions of age-related proteins p21, pi6, p53 and RB in the microgravity group significantly increased, while the expressions of cyclin D1 and lamin B1 significantly decreased, with statistical significance (P<0.05). In the microgravity group, mitochondrial membrane potential significantly decreased (P<0.05), ROS accumulation significantly increased (P <0.05), SOD content significantly decreased and MDA content significantly increased (P<0.05). Compared to the microgravity group, the expressions of age-related proteins p21, pi6, p53 and RB in the quercetin group significantly decreased, while the expressions of cyclin D1 and lamin B1 significantly increased, with statistical significance (P<0.05). In the quercetin group, mitochondrial membrane potential significantly increased (P<0.05), ROS accumulation significantly decreased (P<0.05), SOD content significantly increased and MDA content significantly decreased (P<0.05). Conclusions Quercetin can resist oxidation, protect mitochondrial function and normal cell cycle, thus delaying the aging of bone marrow mesenchymal stem cells induced by microgravity.
5.Rapid Screening of 34 Emerging Contaminants in Surface Water by UHPLC-Q-TOF-MS
Chen-Shan LÜ ; Yi-Xuan CAO ; Xiao-Xi MU ; Hai-Yan CUI ; Tao WANG ; Zhi-Wen WEI ; Ke-Ming YUN ; Meng HU
Journal of Forensic Medicine 2024;40(1):30-36
Objective To establish a rapid screening method for 34 emerging contaminants in surface water by ultra-high performance liquid chromatography-quadrupole-time of flight mass spectrometry(UHPLC-Q-TOF-MS).Methods The pretreatment conditions of solid phase extraction(SPE)were op-timized by orthogonal experimental design and the surface water samples were concentrated and ex-tracted by Oasis? HLB and Oasis? MCX SPE columns in series.The extracts were separated by Kine-tex? EVO C18 column,with gradient elution of 0.1%formic acid aqueous solution and 0.1%formic acid methanol solution.Q-TOF-MS'fullscan'and'targeted MS/MS'modes were used to detect 34 emerging contaminants and to establish a database with 34 emerging contaminants precursor ion,prod-uct ion and retention times.Results The 34 emerging contaminants exhibited good linearity in the con-centration range respectively and the correlation coefficients(r)were higher than 0.97.The limit of de-tection was 0.2-10 ng/L and the recoveries were 81.2%-119.2%.The intra-day precision was 0.78%-18.70%.The method was applied to analyze multiple surface water samples and 6 emerging contaminants were detected,with a concentration range of 1.93-157.71 ng/L.Conclusion The method is simple and rapid for screening various emerging contaminants at the trace level in surface water.
6.Remote Virtual Companion via Tactile Codes and Voices for The People With Visual Impairment
Song GE ; Xuan-Tuo HUANG ; Yan-Ni LIN ; Yan-Cheng LI ; Wen-Tian DONG ; Wei-Min DANG ; Jing-Jing XU ; Ming YI ; Sheng-Yong XU
Progress in Biochemistry and Biophysics 2024;51(1):158-176
ObjectiveExisting artificial vision devices can be divided into two types: implanted devices and extracorporeal devices, both of which have some disadvantages. The former requires surgical implantation, which may lead to irreversible trauma, while the latter has some defects such as relatively simple instructions, limited application scenarios and relying too much on the judgment of artificial intelligence (AI) to provide enough security. Here we propose a system that has voice interaction and can convert surrounding environment information into tactile commands on head and neck. Compared with existing extracorporeal devices, our device can provide a larger capacity of information and has advantages such as lower cost, lower risk, suitable for a variety of life and work scenarios. MethodsWith the latest remote wireless communication and chip technologies, microelectronic devices, cameras and sensors worn by the user, as well as the huge database and computing power in the cloud, the backend staff can get a full insight into the scenario, environmental parameters and status of the user remotely (for example, across the city) in real time. In the meanwhile, by comparing the cloud database and in-memory database and with the help of AI-assisted recognition and manual analysis, they can quickly develop the most reasonable action plan and send instructions to the user. In addition, the backend staff can provide humanistic care and emotional sustenance through voice dialogs. ResultsThis study originally proposes the concept of “remote virtual companion” and demonstrates the related hardware and software as well as test results. The system can not only achieve basic guide functions, for example, helping a person with visual impairment to shop in supermarkets, find seats at cafes, walk on the streets, construct complex puzzles, and play cards, but also can meet the demand for fast-paced daily tasks such as cycling. ConclusionExperimental results show that this “remote virtual companion” is applicable for various scenarios and demands. It can help blind people with their travels, shopping and entertainment, or accompany the elderlies with their trips, wilderness explorations, and travels.
7.Development and Application of Detection Methods for Capture and Transcription Elongation Rate of Bacterial Nascent RNA
Yuan-Yuan LI ; Yu-Ting WANG ; Zi-Chun WU ; Hao-Xuan LI ; Ming-Yue FEI ; Dong-Chang SUN ; O. Claudio GUALERZI ; Attilio FABBRETTI ; Anna Maria GIULIODORI ; Hong-Xia MA ; Cheng-Guang HE
Progress in Biochemistry and Biophysics 2024;51(9):2249-2260
ObjectiveDetection and quantification of RNA synthesis in cells is a widely used technique for monitoring cell viability, health, and metabolic rate.After exposure to environmental stimuli, both the internal reference gene and target gene would be degraded. As a result, it is imperative to consider the accurate capture of nascent RNA and the detection of transcriptional levels of RNA following environmental stimulation. This study aims to create a Click Chemistry method that utilizes its property to capture nascent RNA from total RNA that was stimulated by the environment. MethodsThe new RNA was labeled with 5-ethyluridine (5-EU) instead of uracil, and the azido-biotin medium ligand was connected to the magnetic sphere using a combination of “Click Chemistry” and magnetic bead screening. Then the new RNA was captured and the transcription rate of 16S rRNA was detected by fluorescence molecular beacon (M.B.) and quantitative reverse transcription PCR (qRT-PCR). ResultsThe bacterial nascent RNA captured by “Click Chemistry” screening can be used as a reverse transcription template to form cDNA. Combined with the fluorescent molecular beacon M.B.1, the synthesis rate of rRNA at 37℃ is 1.2 times higher than that at 15℃. The 16S rRNA gene and cspI gene can be detected by fluorescent quantitative PCR,it was found that the measured relative gene expression changes were significantly enhanced at 25℃ and 16℃ when analyzed with nascent RNA rather than total RNA, enabling accurate detection of RNA transcription rates. ConclusionCompared to other article reported experimental methods that utilize screening magnetic columns, the technical scheme employed in this study is more suitable for bacteria, and the operation steps are simple and easy to implement, making it an effective RNA capture method for researchers.
8.Codonopsis polysaccharide protected LPS-induced acute lung injury by inhibiting MAPK/NF-κB signaling pathway in mice
Ling XIAO ; Chunlei GAO ; Wei GUO ; Ning WANG ; Xuan ZHANG ; Ming LIU
The Journal of Practical Medicine 2024;40(7):948-954
Objective To observe the protective effects of codonopsis pilosulae polysaccharide on lung tissues in mice with acute lung injury(ALI)induced by lipopolysaccharide(LPS)and its mechanism.Methods Fifty male Kunming mice were randomly divided into control group,model group,dexamethasone group,codonopsis polysaccharide high-dose group(300 mg/kg)and codonopsis polysaccharide low-dose group(150 mg/kg).The ALI model was established by intraperitoneal injection of LPS.All mice were given gavage administration according to the grouping except for the control group.0.3 s force expiratory volume(FEV 0.3)and force spirometry(FVC)and their ratios were measured using multiparametric lung function test system.The histopathology change of mouse lung was detected by hematoxylin-eosin(HE)staining,and the classification and count of inflammatory cells in alveolar lavage fluid(BALF)was detected by Richter-Giemsa staining.Levels of IL-1β,IL-6,MPO and TNF-α were measured by ELISA in BALF,and Western blot was used to detect the protein expression level of p-p38,p-IκB-α and p-p65.Results Compared with those in the control group,lung histopathological damage was more pronounced in the model mice,with significantly lower FEV 0.3,FVC,FEV0.3/FVC assay value,but signifi-cantly higher lung tissue wet mass/dry mass(W/D),neutrophils,lymphocytes,IL-1β,IL-6,MPO,TNF-α,p-p38 MAPK,p-IκB-α,and p-p65(P<0.05);while codonopsis pilosulae polysaccharide could significantly reverse these effects.Conclusion Codonopsis pilosulae polysaccharide plays a protective role against LPS-induced ALI via inhibiting MAPK/NF-κB pathway to reduce the pathological damage of lung tissue,and the level of inflammatory factors,thus to improve lung function in ALI model mice.
9.Tetrandrine ameliorates pulmonary fibrosis by inhibiting ROS-mediated fibroblast activation
Ye-chao YAN ; Chun-yi GUO ; Jia-ming ZHANG ; Yun-xuan LI ; Ke LI
Acta Pharmaceutica Sinica 2024;59(8):2216-2226
Pulmonary fibrosis is a chronic and progressive lung disease that poses a threat to human health. Current treatment options are limited, highlighting the urgent need for more effective therapeutic strategies. Tetrandrine (TET), a bis-benzylisoquinoline alkaloid extracted from
10.Decision-making experience of patients with abdominoplasty: a qualitative study
Hui WENG ; Chenzi XU ; Ming PANG ; Jinzhen REN ; Zhen WEI ; Handou LI ; Xuan HAO ; Zhirong LIU
Chinese Journal of Plastic Surgery 2024;40(11):1221-1227
Objective:To explore the decision-making experience of patients undergoing abdominoplasty in our country.Methods:A semi-structured interview was conducted with patients suffering from postpartum abdominal wall laxity who were treated at Union Hospital, Tongji Medical College, Huazhong University of Science and Technology from June to August 2023. The data were sort and analyzed using the Clolaizzi 7-step analysis method for thematic description.Results:A total of 15 patients, aged 29-53 years, were included in the study. 11 had a college education or higher, while 4 had less than a college education.Thirteen were married and two were divorced. According to the interview data, four themes were extracted: (1) negative perceptual experiences; (2) decision-making dilemmas; (3) peer support; (4) a physician-led decision-making model. According to the interview, the main decision-making dilemma faced by patients with postpartum abdominal wall laxity was lack of information and family support, and the support they get was mostly from information exchange among patients, and they had insufficient cognition of surgical knowledge, improvement degree and risk, and low participation in clinical decision making.Conclusion:Patients with postpartum abdominal wall laxity in China have an urgent psychological need for abdominoplasty, but there are many factors that have adverse effects on their decision-making experience.

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