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- 저자 : Xiaobo Xing (검색결과 6 건)
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Comparative genomic and functional analysis of Akkermansia muciniphila and closely related species
Juyuan Xing,Xiaobo Li,Yingjiao Sun,Juanjuan Zhao,Shaohua Miao,Qin Xiong,Yonggang Zhang,Guishan Zhang 한국유전학회 2019 Genes & Genomics Vol.41 No.11
Background Akkermansia muciniphila is an important bacterium that resides on the mucus layer of the intestinal tract. Akkermansia muciniphila has a high abundance in human feces and plays an important role in human health. Objective In this article, 23 whole genome sequences of the Akkermansia genus were comparatively studied. Methods Phylogenetic trees were constructed with three methods: All amino acid sequences of each strain were used to construct the first phylogenetic tree using the web server of Composition Vector Tree Version 3. The matrix of Genome-to- Genome Distances which were obtained from GGDC 2.0 was used to construct the second phylogenetic tree using FastME. The concatenated single-copy core gene-based phylogenetic tree was generated through MEGA. The single-copy genes were obtained using OrthoMCL. Population structure was assessed by STRU CTU RE 2.3.4 using the SNPs in core genes. PROKKA and Roary were used to do pan-genome analyses. The biosynthetic gene clusters were predicted using antiSMASH 4.0. IalandViewer 4 was used to detect the genomic islands. Results The results of comparative genomic analysis revealed that: (1) The 23 Akkermansia strains formed 4 clades in phylogenetic trees. The A. muciniphila strains isolated from different geographic regions and ecological niches, formed a closely related clade. (2) The 23 Akkermansia strains were divided into 4 species based on digital DNA-DNA hybridization (dDDH) values. (3) Pan-genome of A. muciniphila is in an open state and increases with addition of new sequenced genomes. (4) SNPs were not evenly distributed throughout the A. muciniphila genomes. The genes in regions with high SNP density are related to metabolism and cell wall/membrane envelope biogenesis. (5) The thermostable outer-membrane protein, Amuc_1100, was conserved in the Akkermansia genus, except for Akkermansia glycaniphila PytT. Conclusion Overall, applying comparative genomic and pan-genomic analyses, we classified and illuminated the phylogenetic relationship of the 23 Akkermansia strains. Insights of the evolutionary, population structure, gene clusters and genome islands of Akkermansia provided more information about the possible physiological and probiotic mechanisms of the Akkermansia strains, and gave some instructions for the in-depth researches about the use of Akkermansia as a gut probiotic in the future.
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Zongbao Li,Xia Wang,Xiaobo Xing,Ying Wang 한국물리학회 2017 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.70 No.3
Using density functional theory, we calculated the geometries, band structures and densities of states of W-doped, N-doped, and W/N-codoped anatase TiO2 (001) and (101) surfaces, as well as while the formation energies, based on the overall reaction energy diagram. The calculated results reveal that, on the two surfaces, the absorption of W atoms are more stable than that of N atoms while a larger energy barrier blocks the transfer of W atoms from the surfaces to the body. For TiO2(001), the W-doping and the N/W-codoping lead to a visible lattice distortion while the recombination of photo-generated electron-holes pairs is reduced. A comprehensive analysis of the electronic structures show that the band-gap narrows and a new W-N bond appears, which obviously enhance the photocatalytic activity.
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Meng Yue Wang,Sun Xing Qin,Fen He,Xiaobo Li 대한약학회 2011 Archives of Pharmacal Research Vol.34 No.6
A novel protein with antitumor activity, Hailongin, was purified from the aqueous extract of the whole body of Trachyrhamphus serratus, which is commonly used in traditional Chinese medicine, by bioassay-guided fractionation. Hailongin exhibited strong inhibition of proliferation of the tested human cell lines, such as A549, HeLa, LoVo and CCRF-CEM. The IC_50 values of Hailongin ranged from 5.4 to 25.7 μg/mL. An in vivo study showed that the growth of implanted S-180 solid tumors in mice was significantly inhibited by Hailongin treatment, while the immunological function of the tumor-bearing mice was enhanced. The molecular weight and the isoelectric point of Hailongin were 57.074 kDa (by MALDI-TOF-MS) and 6.2 (by isoelectric focusing-polyacrylamide gel electrophoresis), respectively. Seventeen amino acids were identified in Hailongin. The acidic amino acids accounted for the majority of Hailongin’s amino acid composition. The N-terminal amino acid sequence of Hailongin was determined to be IVPYSHNAGNKGLTQMR and showed no significant homology with known proteins.
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Xia Wang,Zongbao Li,Lichao Jia,Xiaobo Xing 한국물리학회 2018 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.72 No.10
A simple strategy to greatly increase the photocatalytic ability of nanocrystalline anatase has been put forward to fabricate efficient TiO2-based photocatalysts under visible irradiation. By surface modification with V ion, samples with different ratios were synthesized by using an incipient wetness impregnation method. The as-prepared specimens were characterized using X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), and UV-vis diffuse reflectance spectroscopy. The photocatalytic activities were evaluated by using methylene blue degradations. Meanwhile, the optimized loading structure and electronic structures were calculated by using the density function theory (DFT). This work should provide a practical route to reasonably design and synthesize high-performance TiO2-based nanostructured photocatalysts.
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Jianhui Zhang,Jun Ge,Juyin Li,Jianqiang Li,Yong Zhang,Yinghui Shi,Jiaojiao Sun,Qiongjin Wang,Xiaobo Zhang,Xing-xu Zhao 대한수의학회 2023 Journal of Veterinary Science Vol.24 No.1
Background: Inactivated vaccines are limited in preventing foot-and-mouth disease (FMD) due to safety problems. Recombinant virus-like particles (VLPs) are an excellent candidate for a novel vaccine for preventing FMD, given that VLPs have similar immunogenicity as natural viruses and are replication- and infection-incompetent. Objectives: The 3C protease and P1 polyprotein of type O FMD virus (FDMV) was expressed in yeast Hansenula polymorpha to generate self-resembling VLPs, and the potential of recombinant VLPs as an FMD vaccine was evaluated. Methods: BALB/c mice were immunized with recombinant purified VLPs using CpG oligodeoxynucleotide and aluminum hydroxide gel as an adjuvant. Cytokines and lymphocytes from serum and spleen were analyzed by enzyme-linked immunosorbent assay, enzyme-linked immunospot assay, and flow cytometry. Results: The VLPs of FMD were purified successfully from yeast protein with a diameter of approximately 25 nm. The immunization of mice showed that animals produced high levels of FMDV antibodies and a higher level of antibodies for a longer time. In addition, higher levels of interferon-γ and CD4+ T cells were observed in mice immunized with VLPs. Conclusions: The expression of VLPs of FMD in H. polymorpha provides a novel strategy for the generation of the FMDV vaccine.
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