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Yong-Xin Li

Publications and source records attributed to Yong-Xin Li.

13 recordsLinked to original sources
PubMed2026

Unlocking the unexplored AMPSphere in marine rare species.

BACKGROUND: Antimicrobial peptides (AMPs) have advantages over traditional antibiotics in fighting against drug-resistant bacterial infections. Natural microbial communities are considered as the priority targets for next-generation AMP bioprospecting initiatives. While progress has been made in characterizing AMPs from the dominant microbial taxa in natural ecosystems, current research largely overlooks the biosynthetic potential of rare species. Given their distinct evolutionary pressures, rare species likely produce AMPs with novel structures and unconventional mechanisms of action. RESULTS: In this study, enrichment cultivation of a marine biofilm was conducted in 138 carbon source- and oxygen level-based conditions, followed by metagenomic sequencing using both Illumina and Nanopore platforms. Analysis of 435 high-quality genomes derived from the metagenomes suggests that these bacterial strains are significantly underrepresented (<&#x2009;0.01%) in global marine biofilm communities. Through multi-model prediction, we identified 3,054,472 candidate AMPs from the genomes, including 1048 high-confidence ones, thereby significantly expanding the previously known AMPSphere. Furthermore, AMPs derived from the rare bacterial species exhibit unique sequence characteristics, structural diversity, remarkable stability under diverse pH conditions and pepsin exposure, and strong therapeutic potential in animal models, reflecting their specialized adaptive and defensive strategies developed within ecological systems. CONCLUSIONS: The features of the underexplored AMPs from low-abundance bacteria in marine biofilms provide valuable resources and theoretical foundations for the development of highly effective antimicrobial agents. Video Abstract.

Biofilms↗
PubMed2025

Systematically investigating and identifying bacteriocins in the human gut microbiome.

Human gut microbiota produces unmodified bacteriocins, natural antimicrobial peptides that protect against pathogens and regulate host physiology. However, current bioinformatic tools limit the comprehensive investigation of bacteriocins' biosynthesis, obstructing research into their biological functions. Here, we introduce IIBacFinder, a superior analysis pipeline for identifying unmodified class II bacteriocins. Through large-scale bioinformatic analysis and experimental validation, we demonstrate their widespread distribution across the bacterial kingdom, with most being habitat specific. Analyzing over 280,000 bacterial genomes, we reveal the diverse potential of human gut bacteria to produce these bacteriocins. Guided by meta-omics analysis, we synthesized 26 hypothetical bacteriocins from gut commensal species, with 16 showing antibacterial activities. Further ex vivo tests show minimal impact of narrow-spectrum bacteriocins on human fecal microbiota. Our study highlights the huge biosynthetic potential of unmodified bacteriocins in the human gut, paving the way for understanding their biological functions and health implications.

Humans↗
PubMed2025

Intratumoral fungus Neurospora crassa is associated with worsened prognosis in ovarian cancer via modulation of extracellular matrix.

Landmark studies on intratumoral fungi (ITF) have raised concerns due to irreproducible results and data-analysis errors. We aimed to determine whether ITF exist in ovarian cancer (OvCa) and, if so, whether they play a role in disease biology. Formalin-fixed, paraffin-embedded OvCa samples and multiple controls underwent operational decontamination, qPCR, internal transcribed spacer sequencing, and post-hoc data decontamination. We also leveraged updated fungal reads from The Cancer Genome Atlas generated by the TCMbio group, which addressed human-read contamination and artificial inflation, to validate findings and assess prognostic associations. A murine syngeneic model established using mouse ovarian cancer cell line (OVHM) with intratumoral Neurospora crassa injection was established. Transcriptomic and metabolomic analyses were performed to explore mechanisms. Tumor-containing blocks harbored significantly higher fungal loads than environmental controls but had loads comparable to paraffin controls. Applying a two-pass decontamination filter reduced raw sequence features from 9289 amplicon sequence variants (ASVs) to 659 ASVs. We focused on high-abundance features present in human tissues but absent from xenografts and paraffin controls and identified one candidate, N. crassa, associated with unfavorable prognosis in OvCa. Integrating human and murine data, we found Neurospora correlated with eosinophils, whereas N. crassa itself was not immune-related. Neurospora crassa promoted OvCa progression with downregulation of integrin-linked kinase and decreased extracellular matrix-receptor interaction. Most ITF signals are likely contaminants. We identified N. crassa as associated with unfavorable prognosis in OvCa, potentially via modulation of the extracellular matrix.

Neurospora crassa↗
PubMed2006

[Application of L-cysteine-capped nano-ZnS as a fluorescence probe to the determination of proteins in human serum].

Nanometer-sized L-cysteine-capped ZnS particles as a fluorescence probe were synthesized, and the effect of proteins on the fluorescence intensity has been investigated. With deltalambda = 190 nm, the maximum and constant synchronous fluorescence enhancement was produced at 268.0 nm and pH 5.12 in the presence of proteins. A highly sensitive synchronous fluorescence method for the rapid determination of proteins was developed. Under optimum conditions, the calibration curve was linear over the range 0.05-6.0 microg x mL(-1) for human serum albumin (HSA), and 0.05-8.0 microg x mL(-1) for gamma-globulin (gamma-G), respectively. The relative standard deviations of seven measurements were 1.90% for 1.0 microg x mL(-1) HSA, and 1.65% for 1.0 microg mL(-1) gamma-G.

Blood Proteins↗
PubMed2005

Comparisons between neural response imaging thresholds, electrically evoked auditory reflex thresholds and most comfortable loudness levels in CII bionic ear users with HiResolution sound processing strategies.

CONCLUSIONS: The data collected in this study indicated that first Neural Response Imaging (NRI) thresholds had a better correlation with HiResolution most comfortable loudness (M) levels than tNRI thresholds. Electrically evoked auditory reflex thresholds (EARTs) had a higher correlation with HiResolution M levels than tNRI thresholds and a lower correlation than first NRI thresholds. NRI is a very useful method for programming the cochlear implants of young children who cannot demonstrate a reliable judgment of loudness. OBJECTIVE: To investigate how HiResolution sound processing, designed to deliver high-rate stimuli, relates to EARTs and electrically evoked compound action potential measurements produced by low-rate stimuli. MATERIAL AND METHODS: Nine profoundly hearing-impaired children and adults aged 6-29 years participated in the study. NRI responses were elicited using pulse trains consisting of biphasic pulses at a pulse width per phase of 32 micros delivered at a frequency of 30 Hz using SoundWave programming software. Stimuli were delivered to the odd electrodes (1, 3, 5, 7, 9, 11, 13 and 15) along the array. tNRI (NRI threshold) and first NRI thresholds were recorded for each stimulating electrode. "Speech bursts" stimuli used in EARTs recording were delivered to four electrodes at a time and stapedial reflexes were recorded from the impedance bridge. The M levels used were those used by each patient in their everyday HiResolution programs. RESULTS: For 8 patients (53 stimulating electrodes) the correlation between tNRI threshold and M level was r=0.675 (p=0.000) and that between first NRI thresholds and M level was r=0.741 (p=0.000). On average the M-level value was 20 CU (Current Unit) lower than the first NRI threshold value and 12 CU higher than the tNRI threshold value. The M-level patterns across the electrode array overall were similar to the tNRI or first NRI threshold patterns. For 7 patients (112 stimulating electrodes) the correlation between EART and M levels was r=0.710 (p=0.000). On average the EART value was 14 CU higher than the M-level value.

Adolescent↗
PubMed2005

[Preparation and fluorescence study of anthracene, perylene and 1-aminoanthraquinone colloids].

Anthracene, perylene and 1-aminoanthraquinone colloids have been prepared by reprecipitation method. In comparison with the fluorescence emission spectra of colloids and molecules (in acetone solution), it was indicated that collids fluorescence spectra are red-shifted and easy emission. Base on the fluorescence emission and molecular structure theory, the authors conclude that these molecules overlap when they form particles. At the same time they are planar molecules. This results in the strong stacking electronic properties. So fluorescence excitation and emission become easy.

Acetone↗
PubMed2004

Fluorescence enhancement method for measuring anionic surfactants with a hydrophobic cyanine dye.

A novel fluorimetric method based on use of a hydrophobic cationic cyanine dye has been developed for determination of the anionic surfactant sodium dodecylbenzenesulfonate (DBS). The method is based on the enhancement effect of DBS on the fluorescence of the hydrophobic cyanine dye 2-[-4'-chloro-7'-(1"-ethyl-3",3"-dimethylindolin-2"-ylidene)-3',5'-(propane-1"',3"'-diyl)-1',3',5'-heptatrien-1'-yl]-1-ethyl-3,3-dimethyl-3 H-indolium iodide. Under the optimum conditions the extent of fluorescence enhancement is proportional to the concentration of DBS in the range 0.05-5.0 mg L(-1); the detection limit is 0.014 mg L(-1). The relative standard deviation for 0.35 mg L(-1) DBS was 1.1% (n=10). The proposed method, which avoided use of toxic solvents and tedious solvent-extraction, and was applied to the determination of DBS in natural water with recoveries between 99.9 and 107%. Preliminary research shows that the fluorescence enhancement is due to the formation of a dye aggregate facilitated by DBS.

Anions↗
PubMed2004

Cetyltrimethylammonium bromide sensitized resonance light-scattering of nucleic acid--Pyronine B and its analytical application.

This is the first report on the determination of nucleic acids with Pyronine B (PB) sensitized by cetyltrimethylammonium bromide (CTMAB) with resonance light-scattering (RLS) technique. Under the experimental conditions (1 x 10(-5) mol l(-1) PB, 1 x 10(-5) mol l(-1) CTMAB, pH 7.4, at room temperature, ionic strength 0.02 mol l(-1) NaCl), the interaction of PB with DNA sensitized by CTMAB results in enhanced RLS signals at 328 and 377 nm in the enhanced regions. It was found that the enhanced RLS intensity at 328 nm was proportional to the concentration of DNA in the suitable ranges. The linear range of this assay is 0.0-1.2 microg ml(-1) for calf thymus, 0.0-0.8 microg ml(-1) for fish sperm DNA (fsDNA), and 0.04-1.4 microg ml(-1) for yeast RNA, respectively. The detection limits (3 sigma) are 6.1 ng ml(-1) for calf thymus DNA (ctDNA), 11.2 ng ml(-1) for fish sperm DNA, and 8.6 ng ml(-1) for yeast RNA, respectively. Six synthetic samples were determined satisfactorily. This method is simple, rapid and the dye is inexpensive and stable.

Cetrimonium↗
PubMed2002

Tumor suppressor gene p16 and Rb expression in gastric cardia precancerous lesions from subjects at a high incidence area in northern China.

AIM: To further understand the molecular basis for gastric cardia carcinogenesis and to provide etiological clues. METHODS: Endoscopic mucosa biopsy and histopathological examinations were made on 37 subjects from a high incidence area for both esophageal and gastric cardia carcinomas in northern China. All the biopsy samples were fixed in 850 ml. (-1)L alcohol and embedded in paraffin. Each block contained one piece of tissue and was serially section at 5 microm. Immunohistochemistry (ABC) was carried out on these gastric cardia samples to determine the alterations of p16 and Rb. RESULTS: Based on the histopathlogical examination there were 11 cases of chronic superficial gastritis, 12 cases of chronic atrophic gastritis and 14 cases of dysplasia. The immunostaining demonstrated different levels of unclear immunostaining of p16 and Rb in normal gastric cardia tissue and the tissues with different severity of lesions. With the lesions progressing, the positive immunostaining rates for p16 protein had a decreasing tendency. In contrast, the positive immunostaining rate for Rb protein had an increasing tendency. There was a significant negative relationship between the two parameters. Changes of p16 was CSG 11(100%), CAG 7(58%), DYS 4(29%) and changes of Rb was CSG 2(18%), CAG 8(67%) and DYS 12(86%), (P<0.05). CONCLUSION: The alterations of p16 and Rb protein may play a role in the early stages of gastric cardia carcinogenesis.

China↗
PubMed2002

[Heparin-induced extacorporeal low-density lipoprotein-lipoprotein alpha-fibrinogen precipitation in 36 cases].

OBJECTIVE: To observe the efficacy of heparin-induced extracorporeal low-density lipoprotein-lipoprotein alpha- fibrinogen precipitation (HELP) in clearing blood lipids. METHODS: Thirty-six patients were subjected to extracorporeal plasma lipid separation procedures that utilized heparin to induce the formation of the complex consisted of heparin, low-density lipoprotein cholesterol (LDL-C), lipoprotein and fibrinogen which was precipitated and consequently separated from the plasma. Blood samples were obtained from the patients both before and after the procedures to assay serum total cholesterol (CH), triglyceride (TG), high-density lipoprotein cholesterol (HDL-C), LDL-C, apoliprotein A (ApoA) and apoliprotein B (ApoB). RESULT: Significant differences were observed between the pre- and postoperative levels of lipoprotein (P<0.001). CONCLUSION: Plasma lipoprotein can be partly cleared by way of HELP.

Adult↗
PubMed1998

Apoptosis and its relationship with cell proliferation, p53, Waf1p21, bcl-2 and c-myc in esophageal carcinogenesis studied with a high-risk population in northern China.

AIM:To determine the extent of apoptosis and its possible relationship with the changes of p53, Waflp21, bcl-2, and c-myc at different stages of esophageal carcinogenesis.METHODS:Two hundred and forty-one esophageal biopsy samples from symptom-free subjects and 38 surgically resected esophageal carcinoma tissues from a high-risk population for esophageal cancer in Henan, China were used in this study.Apoptotic cells and apoptotic bodies were identified by well-established morphological criteria. The extent of apoptosis and its possible relationship with the rate of cell proliferation (PCNA) and changes of p53, Waf1p21, bcl-2,and c-myc were analyzed in samples with esophageal precancerous and cancerous lesions.RESULTS:The apoptotic cells, identified morphologically, were located in the same proliferative compartment of hyperproliferative cell population in the esophageal epithelia as the cells immunostaining-positive for p53, bcl-2, c-myc and PCNA.The apoptotic indices (total number of apoptotic cells and apoptotic bodies per mm(2) of the tissue section) were low in the normal epithelia,and increased significantly as the lesions progressed from BCH to DYS and to SCC.The extent of apoptosis correlated well with the cell proliferation indices based on PCNA. The total number of positive cells for p53 stain was much higher than that of apoptotic cells. No difference in apoptotic indices was found between p53-positive and p53-negative samples. Waf1p21-positive cells resided in cell layers were higher in number than p53 and PCNA-positive cells. The number of immunostaining positive cells for Waflp21 increased slightly from normal to BCH,but decreased in DYS and SCC. Positive staining samples for bcl-2 and c-myc increased as the lesions progressed from BCH to DYS and to SCC. No apparent correlation between apoptosis and Waf1p21, bcl-2 or c-myc expression was observed.CONCLUSION:The extent of apoptosis was low in normal esophageal epithelium and increased as the lesions progressed. The apoptotic cells were located in the same hyperproliferative cell compartment as cells immunostaining-positive for p53, bcl-2,c-myc and PCNA,but no apparent correlation between apoptosis and these parameters was observed,possibly due to the complexities of molecular changes in esophageal carcinogenesis.

Journal Article↗
PubMed1998

Comparative studies on epithelial lesions at gastric cardia and pyloric antrum in subjects from a high incidence area for esophageal cancer in Henan, China.

AIM:To investigate the pathogenesis of gastric cardia and the distal part of stomach cancer and to further characterize the histopathogenesis model for gastric cardia cancer from the high-risk population for esophageal cancer.METHODS:Mass survey with endoscopic mucosa biopsy and histopathological examination were carried out on 226 subjects aged above 30 years. Three biopsies were collected one each from the middle part of the esophagus, the gastric cardia and the pyloric antrum. The biopsy tissue was fixed with 85% alcohol and paraffin-embedded.RESULTS:The incidence of intestinal metaplasia and dysplasia at gastric cardia epithelium was higher than that at the pyloric antrum from the subjects in the same area. And there were high incidences of both esophageal and gastric cardia cancer, but a low incidence of gastric cancer at the distal part of the stomach.CONCLUSION:There might be different etiology and pathogenesis of gastric cardia and pyloric cancer at the distal part of the stomach.

Journal Article↗