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| 1 | A structural view of the antibiotic degradation enzyme NDM-1 from a superbug显示文摘Gram-negative Enterobacteriaceae with resistance to carbapenem conferred by New Delhi metallo-β-lactamase 1(NDM-1)are a type of newly discovered antibioticresistant bacteria.The rapid pandemic spread of NDM-1 bacteria worldwide(spreading to India,Pakistan,Europe,America,and Chinese Taiwan)in less than 2 months characterizes these microbes as a potentially major global health problem.The drug resistance of NDM-1 bacteria is largely due to plasmids containing the blaNDM-1 gene shuttling through bacterial populations.The NDM-1 enzyme encoded by the blaNDM-1 gene hydrolyzes β-lactam antibiotics,allowing the bacteria to escape the action of antibiotics.Although the biological functions and structural features of NDM-1 have been proposed according to results from functional and structural investigation of its homologues,the precise molecular characteristics and mechanism of action of NDM-1 have not been clarified.Here,we report the threedimensional structure of NDM-1 with two catalytic zinc ions in its active site.Biological and mass spectroscopy results revealed that D-captopril can effectively inhibit the enzymatic activity of NDM-1 by binding to its active site with high binding affinity.The unique features concerning the primary sequence and structural conformation of the active site distinguish NDM-1 from other reported metallo-β-lactamases(MBLs)and implicate its role in wide spectrum drug resistance.We also discuss the molecular mechanism of NDM-1 action and its essential role in the pandemic of drug-resistant NDM-1 bacteria.Our results will provide helpful information for future drug discovery targeting drug resistance caused by NDM-1 and related metallo-β-lactamases. | Yu Guo Jing Wang Guojun Niu Wenqing Shui Yuna Sun Honggang Zhou Yaozhou Zhang Cheng Yang Zhiyong Lou Zihe Rao | 2011 | Protein & Cell2011，2，5： | 16 |
| 2 | Accurate authentication of Dendrobium officinale and its closely related species by comparative analysis of complete plastomes显示文摘Owing to its great medicinal and ornamental values, Dendrobium officinale is frequently adulterated with other Dendrobium species on the market. Unfortunately, the utilization of the common DNA markers ITS,ITS2, and mat Ktrbc L is unable to distinguish D. officinale from 5 closely related species of it(D. tosaense, D.shixingense, D. flexicaule, D. scoriarum and D. aduncum). Here, we compared 63 Dendrobium plastomes comprising 40 newly sequenced plastomes of the 6 species and 23 previously published plastomes. The plastomes of D. officinale and its closely related species were shown to have conserved genome structure and gene content. Comparative analyses revealed that small single copy region contained higher variation than large single copy and inverted repeat regions, which was mainly attributed to the loss/retention of ndh genes.Furthermore, the intraspecific sequence variability among different Dendrobium species was shown to be diversified, which necessitates a cautious evaluation of genetic markers specific for different Dendrobium species.By evaluating the maximum likelihood trees inferred from different datasets, we found that the complete plastome sequence dataset had the highest discriminatory power for D. officinale and its closely related species,indicating that complete plastome sequences can be used to accurately authenticate Dendrobium species.& 2018 Chinese Pharmaceutical Association and Institute of Materia Medica, Chinese Academy of Medical Sciences. Production and hosting by Elsevier B.V. This is an open access article under the CC BY-NC-ND license(http://creativecommons.org/licenses/by-nc-nd/4.0/). | Shuying Zhu Zhitao Niu Qingyun Xue Hui Wang Xuezhu Xie Xiaoyu Ding | 2018 | Acta Pharmaceutica Sinica B2018，8，6： | 14 |
| 3 | Plastome-wide comparison reveals new SNV resources for the authentication of Dendrobium huoshanense and its corresponding medicinal slice(Huoshan Fengdou)显示文摘Dendrobium species and their corresponding medicinal slices have been extensively used as traditional Chinese medicine(TCM) in many Asian countries. However, it is extremely difficult to identify Dendrobium species based on their morphological and chemical features. In this study, the plastomes of D. huoshanense were used as a model system to investigate the hypothesis that plastomic mutational hotspot regions could provide a useful single nucleotide variants(SNVs) resource for authentication studies. We surveyed the plastomes of 17 Dendrobium species, including the newly sequenced plastome of D. huoshanense. A total of 19 SNVs that could be used for the authentication of D. huoshanense were detected. On the basis of this comprehensive comparison, we identified the four most informative hotspot regions in the Dendrobium plastome that encompass ccsA to ndhF, matK to 3′trnG, rpoB to psbD, and trnT to rbcL. Furthermore, to established a simple and accurate method for the authentication of D. huoshanense and its medicinal slices, a total of 127 samples from 20 Dendrobium species including their corresponding medicinal slices(Fengdous) were used in this study. Our results suggest that D. huoshanense and its medicinal slices can be rapidly and unequivocally identified using this method that combines real-time PCR with the amplification refractory mutation system(ARMS). | Zhitao Niu Jiajia Pan Qingyun Xue Shuying Zhu Wei Liu Xiaoyu Ding | 2018 | Acta Pharmaceutica Sinica B2018，8，3： | 6 |
| 4 | The role of MAPK and FAS death receptor pathways in testicular germ cell apoptosis induced by lead显示文摘现在的学习的目的是调查在阴囊的细菌房间的导致铅的 apoptosis 涉及 MAPK 的信号小径和船边交货的死亡信号受体小径的基因表示。首先,房间生存能力被 MTT 试金决定。第二,使用单个房间胶化电气泳动测试(彗星试金) 和染色技术, apoptotic 率和阴囊的细菌房间的房间 apoptosis 本地化的 TUNEL 在分别地与 0.15% , 0.3% ,和 0.6% 铅一起对待的老鼠被测量。第三, K 地岬, c-fos,船边交货,和活跃 caspase-3 蛋白质的 immunolocalization 被 immunohistochemistry 决定。最后,在 K 地岬, c-fos,船边交货,和活跃 caspase-3 的翻译层次的变化被西方的污点分析进一步检测。我们的结果证明铅能显著地以一种剂量依赖者方式导致阴囊的细菌房间 apoptosis (P < 0.01 ) 。机制是仔细与在 apoptotic 细菌房间的 K 地岬, c-fos,船边交货,和活跃 caspase-3 的增加的表情有关。在结论, K-ras/c-fos 和 Fas/caspase-3 死亡发信号受体小径在老鼠涉及阴囊的细菌房间的导致铅的 apoptosis。 | Shuying Dong Duoping Liang Na An Li Jia Yujuan Shan Chao Chen Kuo Sun Fei Niu Huiyan Li Songbin Fu | 2009 | Acta Biochimica et Biophysica Sinica2009，41，9： | 4 |
| 5 | Circular BANP knockdown inhibits the malignant progression of residual hepatocellular carcinoma after insufficient radiofrequency ablation显示文摘Background:Circular RNAs(circRNAs)are endogenous non-coding RNAs,some of which have pathological roles.The current study aimed to explore the role of circRNA BTG3-associated nuclear protein(circ-BANP)binding with let-7f-5p and its regulation of the toll-like receptor 4(TLR4)/signal transducer and activator of transcription 3(STAT3)signaling pathway in residual hepatocellular carcinoma(HCC)after insufficient radiofrequency ablation(RFA).Methods:Circ-BANP,let-7f-5p,and TLR4 expressions in HCC samples were assessed using reverse transcription-quantitative polymerase chain reaction(RT-qPCR)and Western blotting.Bioinformatics prediction,RNA pull-down assay,and dual luciferase reporter gene assay were used to analyze the relationships among circ-BANP,let-7f-5p,and TLR4.Huh7 cells were used to generate an in vitro model of residual HCC,defined as Huh7-H cells,which were transfected with either a plasmid or the sequence of circ-BANP,let-7f-5p,or TLR4.Expression of circ-BANP,let-7f-5p,and TLR4 mRNA was determined by RT-qPCR.TLR4,STAT3,p-STAT3,vascular endothelial growth factor A,vascular endothelial growth factor receptor-2,and epithelialmesenchymal transformation(EMT)-related factors proteins were determined by Western blotting.Cell proliferation was determined by cell counting kit-8 and 5-Ethynyl-2’-deoxyuridine(EdU)assay and cell migration and invasion by Transwell assay.Animal studies were performed by inducing xenograft tumors in nude mice.Results:Circ-BANP and TLR4 mRNAs were upregulated in HCC tissues(the fold change for circ-BANP was 1.958 and that for TLR4 was 1.736 relative to para-tumors)and expression further increased following insufficient RFA(fold change for circBANP was 2.407 and that of TLR4 was 2.224 relative to para-tumors).Expression of let-7f-5p showed an opposite tendency(fold change for let-7f-5p in HCC tissues was 0.491 and that in tumors after insufficient RFA was 0.300 relative to paratumors).Competitive binding of circ-BANP to let-7f-5p was demonstrated and TLR4 was identified as a target of let-7f-5p(P<0.01).Knockdown of circ-BANP or elevation of let-7f-5p expression inhibited the TLR4/STAT3 signaling pathway,proliferation,invasion,migration,angiogenesis,and EMT in Huh7 and Huh7-H cells(P<0.01).The effects induced by circBANP knockdown were reversed by let-7f-5p inhibition.Overexpression of TLR4 reversed the impact of let-7f-5p upregulation on the cells(P<0.01).Silencing of circ-BANP inhibited the in vivo growth of residual HCC cells after insufficient RFA(P<0.01).Conclusions:Knockdown of circ-BANP upregulated let-7f-5p to inhibit proliferation,migration,and EMT formation in residual HCC remaining after insufficient RFA.Effects occur via regulation of the TLR4/STAT3 signaling pathway. | Guoming Li Jian Kong Shuying Dong Haigang Niu Shilun Wu Wenbing Sun | 2022 | Chinese Medical Journal2022，，13： | 2 |
| 6 | Effect of ginseng polysaccharide on the urinary excretion of type 2 diabetic rats studied by liquid chromatography–mass spectrometry显示文摘 | Jun Niu Zifeng Pi Hao Yue Yang Wang Qing Yu Shuying Liu | 2012 | Journal of Chromatography B2012，，： | 1 |
| 7 | Improving Data Utility Through Game Theory in Personalized Differential Privacy显示文摘Due to dramatically increasing information published in social networks,privacy issues have given rise to public concerns.Although the presence of differential privacy provides privacy protection with theoretical foundations,the trade-off between privacy and data utility still demands further improvement.However,most existing studies do not consider the quantitative impact of the adversary when measuring data utility.In this paper,we firstly propose a personalized differential privacy method based on social distance.Then,we analyze the maximum data utility when users and adversaries are blind to the strategy sets of each other.We formalize all the payoff functions in the differential privacy sense,which is followed by the establishment of a static Bayesian game.The trade-off is calculated by deriving the Bayesian Nash equilibrium with a modified reinforcement learning algorithm.The proposed method achieves fast convergence by reducing the cardinality from n to 2.In addition,the in-place trade-off can maximize the user's data utility if the action sets of the user and the adversary are public while the strategy sets are unrevealed.Our extensive experiments on the real-world dataset prove the proposed model is effective and feasible. | Lei Cui Youyang Qu Mohammad Reza Nosouhi Shui Yu Jian-Wei Niu Gang Xie | 2019 | Journal of Computer Science & Technology2019，34，2： | 0 |
| 8 | Integration of rhythmic metabolome and transcriptome provides insights into the transmission of rhythmic fluctuations and temporal diversity of metabolism in rice显示文摘Various aspects of the organisms adapt to cyclically changing environmental conditions via transcriptional regulation.However,the role of rhythmicity in altering the global aspects of metabolism is poorly characterized.Here,we subjected four rice(Oryza sativa)varieties to a range of metabolic profiles and RNA-seq to investigate the temporal relationships of rhythm between transcription and metabolism.More than 40%of the rhythmic genes and a quarter of metabolites conservatively oscillated across four rice accessions.Compared with the metabolome,the transcriptome was more strongly regulated by rhythm;however,the rhythm of metabolites had an obvious opposite trend between day and night.Through association analysis,the time delay of rhythmic transmission from the transcript to the metabolite level was~4 h under long-day conditions,although the transmission was nearly synchronous for carbohydrate and nucleotide metabolism.The rhythmic accumulation of metabolites maintained highly coordinated temporal relationships in the metabolic network,whereas the correlation of some rhythmic metabolites,such as branched-chain amino acids(BCAAs),was significantly different intervariety.We further demonstrated that the cumulative diversity of BCAAs was due to the differential expression of branched-chain aminotransferase 2 at dawn.Our research reveals the flexible pattern of rice metabolic rhythm existing with conservation and diversity. | Junjie Zhou Chengyuan Liu Qiyu Chen Ling Liu Shuying Niu Ridong Chen Kang Li Yangyang Sun Yuheng Shi Chenkun Yang Shuangqian Shen Yufei Li Junwei Xing Honglun Yuan Xianqing Liu Chuanying Fang Alisdair R.Fernie Jie Luo | 2022 | Science China(Life Sciences)2022，65，9： | 0 |
| 9 | Quality of Life in Terms of Mental Stress and Physical Activities among Community Elder Residents in Shenzhen in the Post-COVID-19 Period显示文摘Coronavirus disease 2019(COVID-19)is a deadly infectious disease that has caused a total of 318 million cases and 5.5 million deaths as of January 14,2022[1].A series of preventive measures such as border restrictions,quarantine and isolation,and social distancing were implemented by the government,which resulted in a substantial disruption of daily life,reduced physical activity(PA). | ZHANG Xiao Ying DENG Shu LU Sen ZHANG Xu Chang NIU Tian Shui LYU Zhong Wei YANG Jian She | 2022 | Biomedical and Environmental Sciences2022，35，12： | 0 |
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