Discovery of novel glycoside hydrolases from C-glycoside-degrading bacteria using sequence similarity network analysis

Wei Bin,Wang Ya-Kun,Yu Jin-Biao,Wang Si-Jia,Yu Yan-Lei,Xu Xue-Wei,Wang Hong 한국미생물학회 2021 The journal of microbiology Vol.59 No.10

C-Glycosides are an important type of natural product with significant bioactivities, and the C-glycosidic bonds of C-glycosides can be cleaved by several intestinal bacteria, as exemplified by the human faeces-derived puerarin-degrading bacterium Dorea strain PUE. However, glycoside hydrolases in these bacteria, which may be involved in the C-glycosidic bond cleavage of C-glycosides, remain largely unknown. In this study, the genomes of the closest phylogenetic neighbours of five puerarin-degrading intestinal bacteria (including Dorea strain PUE) were retrieved, and the protein-coding genes in the genomes were subjected to sequence similarity network (SSN) analysis. Only four clusters of genes were annotated as glycoside hydrolases and observed in the genome of D. longicatena DSM 13814T (the closest phylogenetic neighbour of Dorea strain PUE); therefore, genes from D. longicatena DSM 13814T belonging to these clusters were selected to overexpress recombinant proteins (CG1, CG2, CG3, and CG4) in Escherichia coli BL21(DE3). In vitro assays indicated that CG4 efficiently cleaved the O-glycosidic bond of daidzin and showed moderate β-D-glucosidase and β-D-xylosidase activity. CG2 showed weak activity in hydrolyzing daidzin and pNP- β-D-fucopyranoside, while CG3 was identified as a highly selective and efficient α-glycosidase. Interestingly, CG3 and CG4 could be selectively inhibited by daidzein, explaining their different performance in kinetic studies. Molecular docking studies predicted the molecular determinants of CG2, CG3, and CG4 in substrate selectivity and inhibition propensity. The present study identified three novel and distinctive glycoside hydrolases, highlighting the potential of SSN in the discovery of novel enzymes from genomic data.

Characteristic and pathogenicity of Autographa californica nucleopolyhedrovirus single ORF-turncated mutants

Xue Ying Tao,Jong Yul Roh,Jae Young Choi,Yong Wang,Qin Liu,Jong Bin Park,Soo Dong Woo,Byung Rae Jin,Yeon Ho Je 한국응용곤충학회 2010 한국응용곤충학회 학술대회논문집 Vol.2010 No.10

Autographa californica nucleopolyhedrovirus (AcMNPV) has a large doublestrand DNA genome of approximately 134 kbp and harbors 156 open reading frames (ORFs). To elucidate DNA replication cascade of AcMNPV, we developed a novel baculovirus genome that can be maintained in Escherichia coli as a plasmid and can infect susceptible lepidopteran insect cells. This genome, named bAc-MK, contains a mini-F replicon and a kanamycin resistance marker. Using a convenient Tn7 transposon-based system, pPCS-S, 55 single ORF-truncated mutants were generated by random insertion into bAc-MK genome. These single ORF-truncated mutants were independently transfected into Sf9 cells, 16 of them were found affecting viral replication since they defected in producing polyhedra. Furthermore, to verify the pathogenicity of the single ORF-truncated mutants, the remaining 39 mutants were subjected to bioassay to Spodoptera exigua 3rd instar larvae. Among them, ac9-, ac49-, ac103- and ac105-knockout mutants showed higher mortality compared to that of bAc-MK. These results suggested that these ORFs could be related to pathogenicity of AcMNPV.

Experimental and Numerical Study on the Stability Capacity of Q690 High-strength Circular Steel Tubes Under Axial Compression

Wang Hui,Guo Yonghua,Bai Yongtao,Zhang Bin,Sun Qing,Xue Jianyang 한국강구조학회 2017 International Journal of Steel Structures Vol.17 No.3

This paper presents experimental investigation on the local and overall buckling capacity of Q690 high-strength circular steel tubes under axial compression. Coupon tests are undertaken to obtain the Young’s modulus, Poisson’s ratio, tensile yield stress and ultimate tensile strength of Q690 steel material. Forty-two specimens under axial compression are tested to evaluate the buckling behavior and the failure mode. Test results indicate that most of the existing design standards are conservative for the design of Q690 steel tubes. The distribution model of residual stress is measured by cutting ring method. Then, a finite element model based on modified column deflection curve method (CDC) is built to assess the effects of initial imperfection and residual stress on the stability capacity of the steel tubes. Finally, design methods and recommendations are provided for estimating the stability capacity of high-strength circular steel tubes.

The Clustering Coefficient of Multiple Parallel Airlines AANET

Xue Liu,Xiaoping Zeng,Zhiming Wang,Bin Zhu,Li Chen 보안공학연구지원센터 2016 International Journal of Future Generation Communi Vol.9 No.7

Biotransformation of natural polyacetylene in red ginseng by Chaetomium globosum

Wang, Bang-Yan,Yang, Xue-Qiong,Hu, Ming,Shi, Li-Jiao,Yin, Hai-Yue,Wu, Ya-Mei,Yang, Ya-Bin,Zhou, Hao,Ding, Zhong-Tao The Korean Society of Ginseng 2020 Journal of Ginseng Research Vol.44 No.6

Background: Fermentation has been shown to improve the biological properties of plants and herbs. Specifically, fermentation causes decomposition and/or biotransformation of active metabolites into high-value products. Polyacetylenes are a class of polyketides with a pleiotropic profile of bioactivity. Methods: Column chromatography was used to isolate compounds, and extensive NMR experiments were used to determine their structures. The transformation of polyacetylene in red ginseng (RG) and the production of cazaldehyde B induced by the extract of RG were identified by TLC and HPLC analyses. Results: A new metabolite was isolated from RG fermented by Chaetomium globosum, and this new metabolite can be obtained by the biotransformation of polyacetylene in RG. Panaxytriol was found to exhibit the highest antifungal activity against C. globosum compared with other major ingredients in RG. The fungus C. globosum cultured in RG extract can metabolize panaxytriol to Metabolite A to survive, with no antifungal activity against itself. Metabolites A and B showed obvious inhibition against NO production, with ratios of 42.75 ± 1.60 and 63.95 ± 1.45% at 50 µM, respectively. A higher inhibitory rate on NO production was observed for Metabolite B than for a positive drug. Conclusion: Metabolite A is a rare example of natural polyacetylene biotransformation by microbial fermentation. This biotransformation only occurred in fermented RG. The extract of RG also stimulated the production of a new natural product, cazaldehyde B, from C. globosum. The lactone in Metabolite A can decrease the cytotoxicity, which was deemed to be the intrinsic activity of polyacetylene in ginseng.

Functional Characterization of Autographa californica Multiple Nucleopolyhedrovirus ORF43 and Phenotypic Changes of ORF43-Knockout Mutant

Xue Ying Tao,최재영,Yong Wang,노종열,이주현,Qin Liu,Jong Bin Park,김재수,김우진,제연호 한국미생물학회 2013 The journal of microbiology Vol.51 No.4

ORF43 (ac43) of Autographa californica multiple nucleopolyhedrovirus (AcMNPV) is a highly conserved baculovirus gene of unknown function. To investigate the role of ac43 in the baculovirus lifecycle, we constructed an ac43-deleted mutant AcMNPV, Ac43KO. After transfection into Spodoptera frugiperda cells, Ac43KO produced polyhedra much larger in size than those of wild-type AcMNPV. Interestingly, some of the nucleocapsids were singly enveloped in the polyhedrin matrix while the nucleocapsids of AcMNPV are known to be multiply enveloped. Furthermore, Ac43KO led to a defect in the transcription and expression of polyhedrin, which resulted in reduced occlusion body production. However,Ac43KO did not affect production of budded virus as there was no remarkable difference in budded virus titer. These results suggest that ac43 plays an important role in the expression of polyhedrin, the morphogenesis of occlusion body,and the assembly of virions occluded in occlusion bodies.

A Novel Method to Predict Connectivity Probability of a Plane in Multi-Airline AANET

Xue Liu,Xiaoping Zeng,Zhiming Wang,Ya Wen,Bin Zhu 보안공학연구지원센터 2016 International Journal of Future Generation Communi Vol.9 No.6

A novel method is introduced for approximate calculation of the probability that a plane can connect to a base station in an aeronautical ad hoc networks (AANET) where planes move along multiple specified airlines. Since the communication coverage of a plane can covers segments of airlines, for each of these segments, there is a probability that the communication of the plane (FCOM) can extend to it, from which FCOM can extend again to others segments of airlines until it reaches a base station. As multiple airlines are in AANET, there are plenty of extension paths for FCOM to reach a base station and each path has an existing probability, which is used to calculate the probability that the plane can connects to a base station. Thus, our method is in fact some kind of probabilistic diffusion, which works out the probability that the communication of a plane can diffuse to a base station. We choose the flight routes above the North Pacific Ocean and also generate some random scenarios in simulations to show the correctness and universality of our work. In the conclusion, several future works of AANET based on our method are introduced.

Integrin-linked Kinase Functions as a Tumor Promoter in Bladder Transitional Cell Carcinoma

Wang, De-Lin,Lan, Jian-Hua,Chen, Liang,Huang, Biao,Li, Zeng,Zhao, Xiu-Min,Ma, Qiang,Sheng, Xia,Li, Wen-Bin,Tang, Wei-Xue Asian Pacific Journal of Cancer Prevention 2012 Asian Pacific journal of cancer prevention Vol.13 No.6

The aim of this study was to elucidate the role of the integrin-linked kinase (ILK) gene in development of human bladder transitional cell carcinoma (BTCC). Expression of ILK protein and ILK mRNA in 56 cases of human BTCC tissue and in 30 cases of adjacent normal bladder tissue was detected by immunohistochemistry S-P and reverse transcription polymerase chain reaction (RT-PCR), respectively. Four specific miRNA RNAi vectors targeting human ILK were synthesized and transfected into BIU-87 cells by liposome to obtain stable expression cell strains. The influence of ILK on proliferation of BTCC was detected by MTT, FCM on athymic mouse tumorigenesis. The positive rate of ILK protein in BTCC tissue (53.6%) was much higher than adjacent normal bladder tissue (10.0%) (p<0.05). Similarly, expression of ILK mRNA in BTCC tissue ($0.540{\pm}0.083$) was significantly higher than in adjacent normal bladder tissue ($0.492{\pm}0.070$) (p<0.05). MTT showed that the proliferation ability of miRNA-ILK transfected group was clearly decreased (p<0.05), the cell cycle being arrested in G0/G1-S, an tumorigenesis in vivo was also significantly reduced (p<0.05). ILK gene transcription and protein expression may be involved in the development of BTCC, so that ILK might be the new marker for early diagnosis and the new target for gene treatment.

The Impact of Carrier Transport Confinement on the Energy Transfer Between InGaN/GaN Quantum‐Well Nanorods and Colloidal Nanocrystals

Jiang, Bin,Zhang, Chunfeng,Wang, Xiaoyong,Park, Min Joo,Kwak, Joon Seop,Xu, Jian,Zhang, Huichao,Zhang, Jiayu,Xue, Fei,Xiao, Min WILEY‐VCH Verlag 2012 Advanced Functional Materials Vol.22 No.15

<P><B>Abstract</B></P><P>The energy transfer (ET) between InGaN/GaN multiple‐quantum‐well (MQW) nanorods (NRs) and semiconductor nanocrystals (NCs) for efficient color conversion is studied. An exceptional contribution of carrier transport confinement to the ET mechanisms is observed in the proximal side‐wall coupling system, which consists of InGaN/GaN NRs and CdSe NCs. Under relatively low or high excitation, the ET rate shows different carrier‐density dependence, resulting from different electron‐hole configurations, i.e., bound excitons and free carriers. In the localized exciton regime, the ET rate decreases when increasing temperature from 20 K to 200 K. However, in the free‐carrier regime, the ET rate varies insignificantly in the same temperature range. The temperature dependence in this NR‐NC coupling system is different from that in the previously studied planar MQW‐NC coupling system. It is suggested that the carrier transport confinement in NRs is a major factor for these divergences. The highly efficient ET with efficiency up to 80% shows a promising potential of using such NR‐NC coupled structures for ET‐pumped, NC‐based, light‐emitting devices.</P>

Circulating Lymphocytes as Predictors of Sensitivity to Preoperative Chemoradiotherapy in Rectal Cancer Cases

Dou, Xue,Wang, Ren-Ben,Yan, Hong-Jiang,Jiang, Shu-Mei,Meng, Xiang-Jiao,Zhu, Kun-Li,Xu, Xiao-Qing,Mu, Dian-Bin Asian Pacific Journal of Cancer Prevention 2013 Asian Pacific journal of cancer prevention Vol.14 No.6

Objective: The objective of this study was to identify clinical predictive factors for tumor response after neoadjuvant chemoradiotherapy (nCRT) in locally advanced rectal cancer (LARC). Methods: All factors were evaluated in 88 patients with LARC treated with nCRT. After a long period of 4-8 weeks of chemoradiotherapy, 3 patients achieved clinical complete response (cCR) and thus aggressive surgery was avoided, and the remaining 85 patients underwent a curative-intent operation. The response to nCRT was evaluated by tumor regression grade (TRG) system. Results: There were 32 patients (36.4%) with good tumor regression (TRG 3-4) and 56 (63.6%) with poor tumor regression (TRG 0-2). Lymphocyte counts and ratios were higher in good response cases (P=0.01, 0.03, respectively) while neutrophil ratios and N/L ratios were higher in poor response cases (P=0.04, 0.02, respectively). High lymphocyte ratios before nCRT and good tumor regression (TRG3-4) were significantly associated with improved 5-year disease-free survival (P<0.05). Pretreatment nodal status was also significantly associated with 5-year disease-free survival and 5-year overall survival (P<0.05). Multivariate analysis confirmed that the pretreatment lymphocyte ratio and lymph nodal status were independent prognostic factors. Conclusion: Our study suggested that LARC patients with high lymphocyte ratios before nCRT would have good tumor response and high 5-year DFS and OS.