Biomedical subjects

Yi Xie

Publications and source records attributed to Yi Xie.

At least 19 recordsLinked to original sources

PubMed2026

Lineage structure and penicillin-binding protein variability in clinical Streptococcus pneumoniae isolates from Southwest China exhibiting reduced susceptibility to penicillin.

BACKGROUND: Reduced susceptibility to penicillin in Streptococcus pneumoniae is mediated primarily by alterations in penicillin-binding proteins (PBPs) and often coexists with multidrug resistance within successful lineages. The region-specific genomic characterization of clinically relevant pneumococci with reduced penicillin susceptibility in Southwest China remains limited. METHODS: We performed whole-genome sequencing of 204 clinical S. pneumoniae isolates collected from five institutions in Southwest China (2018-2022) that met our operational screening definition of reduced susceptibility to penicillin (PEN MIC ≥0.12 μg/mL). Molecular serotypes, MLST types, and Global Pneumococcal Sequence Clusters (GPSCs) were assigned; virulence and antimicrobial resistance determinants were profiled; and a core genome phylogeny was reconstructed with international contextualization through the use of PubMLST genomes meeting the same MIC criterion. Amino acid variability in PBP1a/PBP2b/PBP2x was quantified using TIGR4 numbering, and highly variable noncatalytic residues located within 15 Å of catalytic motifs were prioritized via structure-guided screening. RESULTS: The isolates showed a high burden of resistance to non-β-lactam antibiotics (erythromycin, 98.5%; tetracycline, 82.8%; trimethoprim-sulfamethoxazole, 64.7%), while fluoroquinolone susceptibility was largely preserved (≥97%), and vancomycin/linezolid resistance was not detected. Twenty-seven serotypes were identified, among which 19F (23.5%) and 19A (14.2%) were dominant, and the estimated PCV13 coverage was 69.6%. GPSC1 was the dominant lineage (36.8%), and the lineage composition among our isolates differed markedly from those in the PubMLST-USA and PubMLST-Thailand subsets. Virulence and resistance gene carriage differed markedly between GPSC1 and non-GPSC1 isolates, with enrichment of pilus operons, mef(A)/msr(D), and folA/folP in GPSC1. PBP variations were clustered in transpeptidase domains and motif-adjacent regions while essential catalytic residues were conserved; with the structure-guided filter, 12, 11, and 11 motif-proximal noncatalytic candidate sites were prioritized in PBP1a, PBP2b, and PBP2x, respectively. CONCLUSION: Clinical S. pneumoniae isolates with reduced penicillin susceptibility collected in Southwest China demonstrated resistance and accessory gene profiles that were strongly structured by a GPSC-defined lineage background. Our site-resolved, structure-guided PBP analysis provides a regional PBP variability landscape and a compact set of recurrent motif-proximal candidate substitutions to support surveillance and downstream functional validation.

Streptococcus pneumoniae↗

PubMed2026

STK11 Mutations and Deletions Define an Aggressive Molecular Subgroup of Cervical Adenocarcinoma.

Cervical adenocarcinoma accounts for 15%-20% of cervical cancers and is associated with poorer survival and reduced response to screening and immunotherapy compared with squamous cell carcinoma (SCC). The genomic drivers underlying this molecular subgroup remain incompletely characterized. Whole-exome sequencing was performed on 302 invasive cervical cancers from Guatemala and Venezuela. Structural variation analysis was conducted using SNP-array and whole-genome sequencing data. Findings were replicated in more than 4600 additional cervical cancer samples from TCGA, AACR Project GENIE, MSKCC, and Caris datasets. TP53 mutations were more frequent in adenocarcinoma than SCC, particularly in HPV-negative tumors. STK11 alterations, including mutations and focal deletions, were significantly enriched in HPV-positive adenocarcinomas compared with SCC and affected 23% of adenocarcinomas overall. Whole-genome analyses identified recurrent focal deletions, inversions, chromosomal rearrangements, and breakage-fusion-bridge events involving chromosome 19p and STK11 that were not detected by exome sequencing alone. STK11 alterations were associated with younger age at diagnosis, poorer overall survival, and inferior outcomes following immune checkpoint inhibitor (ICI) therapy. STK11 alterations significantly co-occurred with YAP1 amplification but were largely mutually exclusive with PIK3CA mutation. Cervical adenocarcinomas also demonstrated significantly lower CD274 (PD-L1) expression than SCC. STK11 alterations define a distinct molecular subgroup of cervical adenocarcinoma characterized by structural disruption of chromosome 19p, younger age at onset, and poorer clinical outcomes. These findings have implications for molecular classification and future targeted therapeutic approaches in cervical cancer.

Humans↗

PubMed2007

Identification of genes differentially regulated by transcription factor, AP-2delta.

In an effort to better understand the transcriptional program regulated by transcription factor, AP-2delta, we used cDNA microarray to evaluate the relative expression of human genes in AD293 cells by exogenous expression of AP-2delta. Microarray showed 29 genes that were up-regulated and 39 genes with a down-regulated expression pattern. Among the identified genes were those encoding transcription factors, signal transduction molecules, kinases, as well as genes regulating cell growth, differentiation, and cell adhesion, a set of genes suggested to be regulated by AP-2. The results of microarray was validated for some regulated genes by real-time PCR analysis. These observations shed novel insight into the mechanism of AP-2delta action and provide a range of target genes for further investigation.

Binding Sites↗

PubMed2006

A novel and simple biomolecules immobilization method: electro-deposition ZrO2 doped with HRP for fabrication of hydrogen peroxide biosensor.

For the first time, a very novel and simple immobilization method for fabrication of hydrogen peroxide biosensor was reported in this paper. The biocompatible composite HRP-ZrO(2) thin films were synthesized on gold electrode surface based on electro-deposition zirconia doped with horseradish peroxidase (HRP) by cyclic voltammetry scanning in KCl solution containing ZrO(2) and HRP. The fabricated process of biosensor was characterized by electrochemical impedance spectroscopy (EIS) and the surface topography of the prepared films was imaged by atomic force microscope (AFM). The HRP in HRP-ZrO(2) thin films kept its bioactivity and exhibited excellent electrocatalytical response to the reduction of H(2)O(2). Experimental conditions influencing the biosensor performance such as pH, potential were optimized. The resulting biosensor (HRP-ZrO(2)/Au electrode) showed a linear response to H(2)O(2) over a concentration range from 0.02 to 9.45mM with a detection limit of 2muM based on a signal-to-noise ratio of 3 under optimized conditions. The apparent Michaelis-Menten constant (K(M)(app)) was evaluated to be 8.01mM, which indicated the HRP in HRP-ZrO(2) thin films kept its native bioactivity and had high affinity for H(2)O(2). Moreover, the proposed biosensor showed high sensitivity, good reproducibility and long-term stability. What is more, this immobilization methodology widened biosensor application in biomolecules immobilization and could further develop for other protein and biomolecules immobilization.

Biocompatible Materials↗

PubMed2006

Cloning and characterization of a gene encoding the human putative ubiquitin conjugating enzyme E2Z (UBE2Z).

Ubiquitination, the covalent attachment of the protein ubiquitin (Ub) to other cellular proteins, has been implicated in a number of important physiological processes. ubiquitin conjugating enzyme (E2) plays an important role in the ubiquitin system. Here we report the research about a human putative ubiquitin conjugating enzyme gene, UBE2Z. The length of UBE2Z cDNA is 3054 base pairs and contains an open reading frame encoding 246 amino acids. The UBE2Z gene was mapped to human chromosome 17q21.32 and consisted of 6 exons. RT-PCR showed that UBE2Z was widely expressed in human tissues, especially high in placenta, pancreas, spleen and testis. The UBE2Z-GFP fusion protein was located in both nucleus and cytoplasm of AD293 cells.

Amino Acid Sequence↗

PubMed2006

Different roles of MTHFR C677T and A1298C polymorphisms in colorectal adenoma and colorectal cancer: a meta-analysis.

Association studies on the MTHFR polymorphisms (C677T and A1298C) in colorectal cancer (CRC) and colorectal adenoma have shown conflicting results. We performed a meta-analysis to better assess the purported associations. Overall, the 677T allele (10,131 patients and 15,362 controls) showed a small but significant protective effect against CRC compared to the 677C allele [P=0.0003, odds ratio (OR)=0.93; 95% confidence interval (CI) 0.89-0.98, P=0.22 (for heterogeneity)] for a worldwide population. Meta-analyses of other genetic contrasts suggested that the 677T allele is more likely to affect CRC in a recessive genetic model worldwide (P<0.0001, OR=0.86; 95% CI 0.76-0.96, P=0.06) and in Asians (P=0.0005, OR=0.75; 95% CI 0.64-0.88, P=0.71). Similarly, we found a significantly decreased risk of CRC for 1298C polymorphism (4,764 CRC patients and 6,592 controls) for a recessive genetic model worldwide (P=0.005, OR=0.81; 95% CI 0.70-0.94, P=0.40) and in Caucasians (P=0.04, OR=0.75 95% CI 0.57-0.99, P=0.35). No evidence of association of C677T (4,616 patients and 6,338 controls) and A1298C (1,272 patients and 1,684 controls) with colorectal adenoma were found. The evidence accumulated suggests that MTHFR may represent a low-penetrance susceptible gene for CRC, and that the two polymorphisms might protect against colorectal adenoma developing into cancer. A larger single study is required to further evaluate gene-gene and gene-environment interactions for MTHFR polymorphisms and the cancer risk in a specific population.

Adenoma↗

PubMed2006

In2O3 hollow microspheres: synthesis from designed In(OH)3 precursors and applications in gas sensors and photocatalysis.

In this work, well-shaped In(OH)3 hollow microspheres have been successfully prepared via a novel surfactant-free vesicle-template-interface route in the "formamide-resorcinol-water" system, in which spontaneous vesicles were formed under hydrothermal conditions and NH3 from the hydrolysis of formamide acted as the OH- provider. Morphological and structural characterizations indicate that the shells of as-prepared In(OH)3 hollow microspheres were constructed by numerous nanocubes about 80 nm in size. As desired, In2O3 hollow microspheres were obtained from annealing the designed In(OH)3 precursors, and the as-obtained In2O3 hollow microspheres performed well as a gas-sensing material in response to both ethanol and formaldehyde gases and as a photocatalyst for photocatalytic degradation of rhodamine B. The facile preparation method and the improved properties derived from special microstructures are significant in the synthesis and future applications of functional nanomaterials.

Journal Article↗

PubMed2006

Necklace-like hollow carbon nanospheres from the pentagon-including reactants: synthesis and electrochemical properties.

Necklace-like hollow carbon nanospheres (CNSs) have been successfully synthesized from the pentagon-including reactants, which provide an auxiliary example for the theoretical prediction that necklace-like hollow CNSs are assumed to be composed of the regular occurrence of nonhexagonal rings at the atomic level. Benefits of the as-obtained hollow CNSs also arise from the high Brunauer-Emmett-Teller value of 594.32 m(2)/g and a narrow pore distribution at 5 nm. The electrochemical hydrogen storage experiments for the as-obtained necklace-like hollow CNSs exhibit a capacity of 242 mAh/g at the current density of 200 mA/g, corresponding to a hydrogen storage of 0.89 wt %, which is higher than the previously reported electrochemical capacities for the multiwalled carbon nanotubes (MWCNTs). Furthermore, the as-obtained necklace-like hollow CNSs show a lithium capacity advantage compared with the carbon solid particles for application in lithium batteries. These results indicate that the necklace-like hollow CNSs provide a new candidate for the application in hydrogen storage and lithium batteries.

Journal Article↗

PubMed2006

Stromal cell-derived factor-1/CXCR4 signaling modifies the capillary-like organization of human embryonic stem cell-derived endothelium in vitro.

The molecular mechanisms that regulate human blood vessel formation during early development are largely unknown. Here we used human ESCs (hESCs) as an in vitro model to explore early human vasculogenesis. We demonstrated that stromal cell-derived factor-1 (SDF-1) and CXCR4 were expressed concurrently with hESC-derived embryonic endothelial differentiation. Human ESC-derived embryonic endothelial cells underwent dose-dependent chemotaxis to SDF-1, which enhanced vascular network formation in Matrigel. Blocking of CXCR4 signaling abolished capillary-like structures induced by SDF-1. Inhibition of the SDF-1/CXCR4 signaling pathway by AMD3100, a CXCR4 antagonist, disrupted the endothelial sprouting outgrowth from human embryoid bodies, suggesting that the SDF-1/CXCR4 axis plays a critical role in regulating initial vessel formation, and may function as a morphogen during human embryonic vascular development.

Animals↗

PubMed2006

MoS2 hierarchical hollow cubic cages assembled by bilayers: one-step synthesis and their electrochemical hydrogen storage properties.

Micrometer scaled MoS2 hierarchical hollow cubic cages assembled by bilayers can be synthesized via a one-step self-assembly coupled with intermediate crystal templating process without any surfactant, in which the intermediate K2NaMoO3F3 crystal formed in-situ and then served as the self-sacrificed template based on the Kirkendall Effect; The MoS2 hierarchical hollow cubic cages were employed for electrochemical hydrogen storage with a high capacity of 375 mAh g(-1) due to the more active edges exposing on the upright-standing nanoplates.

Disulfides↗

PubMed2006

Synthesis of hematite (alpha-Fe2O3) nanorods: diameter-size and shape effects on their applications in magnetism, lithium ion battery, and gas sensors.

We demonstrated in this paper the shape-controlled synthesis of hematite (alpha-Fe(2)O(3)) nanostructures with a gradient in the diameters (from less than 20 nm to larger than 300 nm) and surface areas (from 5.9 to 52.3 m(2)/g) through an improved synthetic strategy by adopting a high concentration of inorganic salts and high temperature in the synthesis systems to influence the final products of hematite nanostructures. The benefits of the present work also stem from the first report on the <20-nm-diameter and porous hematite nanorods, as well as a new facile strategy to the less-than-20-nm nanorods, because the less-than-20-nm diameter size meets the vital size domain for magnetization properties in hematite. Note that the porous and nonporous hematite one-dimensional nanostructures with diameter gradients give us the first opportunity to investigate the Morin temperature evolution of nanorod diameter and porosity. Evidently, the magnetic properties for nanorods exhibit differences compared with those for the spherical particle counterparts. Hematite nanorods are strongly dependent on their diameter size and porosity, where the magnetization is not sensitive to the size evolution from submicron particles to the 60-90 nm nanorods, while the magnetic properties change significantly in the case of <20 nm. In other words, for the magnetic properties of nanorods, in a comparable size range, the porous existence could also influence the magnetic behavior. Moreover, applications in formaldehyde (HCHO) gas sensors and lithium batteries for the hematite nanostructures with the diameter/surface area gradient reveal that the performance of electrochemical and gas-sensor properties strongly depends on the diameter size and Brunauer-Emmett-Teller (BET) surface areas, which is consistent with the crystalline point of view. Thus, this work not only provides the first example of the fabrication of hematite nanostructure sensors for detecting HCHO gas, but also reveals that the surface area or diameter size of hematite nanorods can also influence the lithium intercalation performances. These results give us a guideline for the study of the size-dependent properties for functional materials as well as further applications for magnetic materials, lithium-ion batteries, and gas sensors.

Journal Article↗

PubMed2006

Dual specificity phosphotase 18, interacting with SAPK, dephosphorylates SAPK and inhibits SAPK/JNK signal pathway in vivo.

The SAPK/JNKs play important roles in numerous cellular processes, and for this reason they have become putative drug targets. Most dual-specificity protein phosphatases (DSPs) play important roles in the regulation of mitogenic signal transduction and cell cycle control in response to extracellular stimuli. Dual-specificity phosphatase 18 (DUSP18), a newly recognized SAPK/JNK phosphatase, is widely expressed. This expression is modulated in response to extracellular stimuli. By phosphorylation assay, pull down and coimmunoprecipitation experiments, it is shown here that DUSP18 interacts with SAPK/JNK and dephosphorylates it both in vitro and in vivo. DUSP18 does not dephosphorylate p38 or p44ERK1. Furthermore, DUSP18 inhibits SAPK/JNK pathway in vivo. Based on these findings, DUSP18 appears to serve an important role by regulation of SAPK/JNK pathway.

Blotting, Western↗

PubMed2006

Pyrrolidine dithiocarbamate inhibits interleukin-6 signaling through impaired STAT3 activation and association with transcriptional coactivators in hepatocytes.

Interleukin (IL)-6 is a proinflammatory cytokine that has been implicated in the expression of acute phase plasma proteins and hepatic insulin resistance through activation of the JAK/STAT3 pathway. Although previous studies have demonstrated that pyrrolidine dithiocarbamate (PDTC) exerts protection against inflammatory responses, its role in the regulation of IL-6 receptor signaling remains unclear. Here we show that treatment of cultured HepG2 hepatoma cells with PDTC inhibits IL-6-stimulated tyrosine phosphorylation and subsequent nuclear translocation of STAT3 in a dose- and time-dependent fashion. No inhibition of JAK-1 activity was observed. To provide insight into PDTC signaling, we constructed a conditionally active STAT3 by fusing it with the ligand binding domain of the estrogen receptor (STAT3-ER). In the presence of 4-hydroxytamoxifen STAT3-ER was translocated in the nucleus of HepG2 cells in a phosphorylation-independent manner, and treatment with PDTC mitigated the response. Although STAT3 coprecipitated with heat-shock protein 90 (Hsp90) in control cells, coprecipitation of the two proteins was greatly reduced after PDTC treatment or after exposure to geldanamycin, an Hsp90 inhibitor. As a result there was a decrease in IL-6-induced association of STAT3 with the transcriptional coactivators FOXO1a and C/EBPbeta together with significant reduction in the expression of SOCS-3 protein and that of two major acute phase plasma proteins. Importantly, treatment of HepG2 cells and a primary culture of rat hepatocytes with PDTC restored insulin responsiveness that was abrogated by IL-6. These studies are consistent with the ability of PDTC to down-regulate IL-6-induced STAT3 activation by altering the stability of STAT3-Hsp90 complex.

Active Transport, Cell Nucleus↗

PubMed2006

A novel full-length gene of human ribosomal protein L14.22 related to human glioma.

BACKGROUND: This study was undertaken to obtain differentially expressed genes related to human glioma by cDNA microarray and the characterization of a novel full-length gene. METHODS: Total RNA was extracted form human glioma and normal brain tissue, and mRNA was used as a probe. The results of hybridization procedure were scanned with the computer system. The gene named 507E08 cone was subsequently analyzed by northern blot, bioinformatic approach, and protein expression. RESULTS: Fifteen differentially expressed genes were obtained from human glioma by hybridization and scanning for four times. Northern blot analysis confirmed that the 507E08 clone was low expressed in human brain tissue and over expressed in human glioma tissues. The analysis of BLASTn and BLASTx showed that the 507E08 clone was a novel full-length gene, which codes 203 amino acid of protein and is called human ribosomal protein 14.22 gene. The nucleotide sequence had been submitted to the GenBank with the accession number of AF329277. After expression in E. coli., protein yielded a major band of apparent molecular mass 22 kDa on an SDS-PAGE gel. CONCLUSIONS: cDNA microarray technology can be successfully used to identify differentially expressed genes. The novel full-length gene of human ribosomal protein 13.22 may be correlated with the development of human glioma.

Amino Acid Sequence↗

PubMed2006

Breast cancer metastasis suppressor 1 (BRMS1) is stabilized by the Hsp90 chaperone.

Breast cancer metastasis suppressor 1 (BRMS1) is a member of the mSin3-HDAC transcription co-repressor complex. However, the proteins associated with BRMS1 have not been fully identified. Yeast two-hybrid screen, immuno-affinity chromatography, and co-immunoprecipitation experiments were performed to identify BRMS1 interacting proteins (BIPs). In addition to known core mSin3 transcriptional complex components RBBP1 and mSDS3, BRMS1 interacted with other proteins including three chaperones: DNAJB6 (MRJ), Hsp90, and Hsp70. Hsp90 is a known target of HDAC6 and reversible acetylation is one of the mechanisms that is implicated in regulation of Hsp90 chaperone complex activity. BRMS1 interacted with class II HDACs, HDAC 4, 5, and 6. We further found that BRMS1 is stabilized by Hsp90, and its turnover is proteasome dependent. The stability of BRMS1 protein may be important in maintaining the functional role of BRMS1 in metastasis suppression.

Animals↗

PubMed2006

Facile synthesis and catalytic property of porous tin dioxide nanostructures.

Porous tin dioxide (SnO(2)) nanostructures consisting of nanoplates are prepared through thermal decomposition of the mixed solution composed of dibutyltin dilaurate and acetic acid. The aggregations of the nanoplates give rise to large macropores with the size of about 100-300 nm. These nanoplates have a wormhole-like porous structure with the size of about 4 nm and possess high surface area. X-ray powder diffraction, transmission electron microscopy, scanning electron microscopy, infrared spectroscopy, and nitrogen sorption have been employed to characterize the obtained porous structures. It is found that the obtained nanostructures exhibit excellent catalytic activity toward methanol decomposition. Such porous structures with high surface area have promising industrial applications as catalysts.

Journal Article↗

PubMed2006

Low-temperature synthesis of alpha-MnO2 hollow urchins and their application in rechargeable Li+ batteries.

Novel alpha-MnO2 hollow urchins were synthesized on a large scale by a facile and efficient low-temperature (60 degrees C) mild reduction route, without templates or surfactants in the system. The formation mechanism for the hollow urchins was proved to be the Ostwald ripening process by tracking the crystallization and morphology of the product at different reaction stages. The as-prepared hollow-urchin sample has a high Brunauer-Emmett-Teller surface area of 132 m(2)/g and a mesoporous structure, which were expected to help improve the electrochemical property in Li+ batteries. When the alpha-MnO2 hollow urchins were used as the cathode material in Li batteries, they performed better than the other alpha-MnO2 samples (solid urchins and dispersed nanorods), indicating that the electrochemical performance of the electrode material is sensitive to its morphology. This synthetic procedure is straightforward and inexpensive and thus facilitates mass production of alpha-MnO2 hollow urchins.

Cold Temperature↗

PubMed2006

Application of HLA-DRB1 genotyping by oligonucleotide micro-array technology in forensic medicine.

UNLABELLED: The human leukocyte antigen (HLA) system is known to be the most complex polymorphic system in the human genome. Among all of the HLA loci, HLA-DRB1 has the second largest number of alleles. The purpose of this study is to develop an oligonucleotide micro-array based HLA-DRB1 typing system for use in forensic identification, anthropology, tissue transplantation, and other genetic research fields. The system was developed by analyzing the HLA-DRB1 (DRB1) genotypes in 1198 unrelated healthy Chinese Han individuals originating from various parts of China and residing in Shanghai, China. METHOD: Polymerase chain reaction (PCR) coupled with the oligonucleotide micro-array technology was used to detect and type HLA-DRB1 alleles of the sample individuals. The reliability, sensitivity, consistency and specificity were evaluated for use in forensic identification. Furthermore, a meta-analysis was carried out by comparing the allele frequencies of the HLA-DRB1 locus with those of other Chinese Han groups, Chinese minorities and other ethnic populations. RESULTS: All the DNA samples yielded a 273 bp amplification product, with no other amplification products in this length range. The minimum quantity of DNA detected by this method is 15 ng in a PCR reaction system of 25 microl. The population studied appeared to be not in Hardy-Weinberg equilibrium. Observed heterozygosity (Ho), expected heterozygosity (He), expected probability of exclusion (PE), polymorphic information content (PIC), and discrimination power (DP) of the HLA-DRB1 locus from the Shanghai Han ethnic group were evaluated to be 0.8022, 0.8870, 0.7741, 0.8771, 0.9750, respectively. A total of 25 HLA-DRB1 alleles were identified. HLA-DRB1*09XX, *04XX, *12XX and *15XX were the most frequent DRB1 alleles, which were observed in 58.76% of the sample. One hundred and sixteen genotypes were found. The five most frequent genotypes were: *04XX/*04XX (0.0626), *09XX/*09XX (0.0593), *04XX/*09XX (0.0551), *09XX/*15XX (0.0384) and *08XX/*12XX (0.0351). The meta-analysis showed that there were uniquely distributed features of DRB1 alleles among various ethnic populations and among the studied population groups from various regions with the same ethnic origin. CONCLUSIONS: An HLA-DRB1 genotyping system has been developed and established based on the oligonucleotide micro-array technology. The HLA-DRB1 typing of the Han population in Shanghai has revealed a relatively high heterogeneity. Information obtained in this study will be useful for medical and forensic applications as well as in anthropology research. Large-scale micro-array detection is highly accurate and reliable for DNA-based HLA-DRB1 genotyping. These results suggest that HLA-DRB1 DNA polymorphisms and the database of the Shanghai Han group have useful applications in processing forensic casework (as personal identification, paternity test), tracing population migration and genetic diagnosis.

Animals↗