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| 1 | A complete sequence and comparative analysis of a SARS-associated virus(Isolate BJ01)显示文摘The genome sequence of the Severe Acute Respiratory Syndrome (SARS)-associated virus provides essential information for the identification of pathogen(s), exploration of etiology and evolution, interpretation of transmission and pathogenesis, development of diagnostics, prevention by future vaccination, and treatment by developing new drugs. We report the complete genome sequence and comparative analysis of an isolate (BJ01) of the coronavirus that has been recognized as a pathogen for SARS. The genome is 29725 nt in size and has 11 ORFs (Open Reading Frames). It is composed of a stable region encoding an RNA-dependent RNA polymerase (composed of 2 ORFs) and a variable region representing 4 CDSs (coding sequences) for viral structural genes (the S, E, M, N proteins) and 5 PUPs (putative uncharacterized proteins). Its gene order is identical to that of other known coronaviruses. The sequence alignment with all known RNA viruses places this virus as a member in the family of Coronaviridae. Thirty putative substitutions have been identified by comparative analysis of the 5 SARS- associated virus genome sequences in GenBank. Fifteen of them lead to possible amino acid changes (non-synonymous mutations) in the proteins. Three amino acid changes, with predicted alteration of physical and chemical features, have been detected in the S protein that is postulated to beinvolved in the immunoreactions between the virus and its host. Two amino acid changes have been detected in the Mprotein, which could be related to viral envelope formation. Phylogenetic analysis suggests the possibility of non-human origin of the SARS-associated viruses but provides noevidence that they are man-made. Further efforts should focus on identifying the etiology of the SARS-associated virus and ruling out conclusively the existence of otherpossible SARS-related pathogen(s). | QIN E'de ZHU Qingyu YU Man FAN Baochang CHANG Guohui SI Bingyin YANG Bao PENG Wenming JIANG Tao LIU Bohua DENG Yongqiang LIU Hong ZHANG Yu WANG Cui LI Yuquan GAN Yonghua LI Xiaoyu L Fushuang TAN Gang CAO Wuchun, YANG Ruifu Institute of Microbiology and Epidemiology, Chinese Academy of Military Medical Sciences, Beijing 100071, China WANG Jian, LI Wei, XU Zuyuan, LI Yan, WU Qingfa, LIN Wei, CHEN Weijun, TANG Lin, DENG Yajun, HAN Yujun, LI Changfeng, LEI Meng, LI Guoqing, LI Wenjie, L Hong, SHI Jianping, TONG Zongzhong, ZHANG Feng, LI Songgang, LIU Bin, LIU Siqi, DONG Wei, WANG Jun, Gane K-S Wong, YU Jun & YANG Huanming* Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300 National Center for Genome Information, Beijing 101300, China | 2003 | Chinese Science Bulletin2003，48，10： | 121 |
| 2 | An Ebola virus-encoded microRNA-like fragment serves as a biomarker for early diagnosis of Ebola virus disease显示文摘 | Zeliang Chen Hongwei Liang Xi Chen Yuehua Ke Zhen Zhou Mingjuan Yang Ke Zen Ruifu Yang Chao Liu Chen-Yu Zhang | 2016 | Cell Research2016，26，3： | 7 |
| 3 | Formation and regulation of Yersinia biofilms显示文摘Flea-borne transmission is a recent evolutionary adaptation that distinguishes the deadly Yersinia pestis from its progenitor Y.pseudotuberculosis,a mild pathogen transmitted via the food-borne route.Y.pestis synthesizes biofilms in the flea gut,which is important for fleaborne transmission.Yersinia biofilms are bacterial colonies surrounded by extracellular matrix primarily containing a homopolymer of N-acetyl-D-glucosamine that are synthesized by a set of specific enzymes.Yersinia biofilm production is tightly regulated at both transcriptional and post-transcriptional levels.All the known structural genes responsible for biofilm production are harbored in both Y.pseudotuberculosis and Y.pestis,but Y.pestis has evolved changes in the regulation of biofilm development,thereby acquiring efficient arthropod-borne transmission. | Dongsheng Zhou Ruifu Yang | 2011 | Protein & Cell2011，2，3： | 6 |
| 4 | Shiga toxin-producing Escherichia coli O104:H4: An emerging 0important pathogen in food safety显示文摘In 2011, Shiga toxin-producing Escherichia coli O104 : H4 resulted in a large outbreak of bloody diarrhea and hemolytic uremic syndrome (HUS) in Germany and 15 other countries in Europe and North America. This event raised a serious public health crisis and caused more than two billion US dollars in economic losses. In this review, we describe the classification of E. coli, the Germany outbreak, and the characteristics and epidemical source-tracing of the causative agent. We also discuss the genomics analysis of the outbreak organism and propose an open-source genomics analysis as a new strategy in combating the emerging infectious diseases. | CUI YuJun LI DongFang YANG RuiFu | 2013 | Chinese Science Bulletin2013，58，14： | 5 |
| 5 | IL-17A-dependent gut microbiota is essential for regulating diet-induced disorders in mice显示文摘The gut microbiota plays a key role in obesity and related metabolic disorders, and multiple factors including diet, host genotype, and age regulate it. Many studies have examined the contribution of extrinsic factors to the regulation of the gut microbiota, but the importance of the host genetic constitution cannot be ignored. Interleukin 17A(IL-17A), a pro-inflammatory cytokine, is important in the defense against infection and diseases. Here, we investigated the association among IL-17, a high-fat diet(HFD), and the gut microbiota. Mice deficient in IL-17A were resistant to diet-induced obesity and related diseases. Compared with the Ⅱ-17^(-/-)mice, wild-type(WT) mice challenged with HFD showed obvious weight fluctuations, such as those seen in type 2 diabetes, and hematological changes similar to those associated with metabolic syndrome. However, housing WT mice and Ⅱ-17a^(-/-)mice together significantly alleviated these symptoms in the WT mice. A metagenomic analysis of the mouse feces indicated that the microbial community compositions of these two groups differed before HFD feeding. The HFD mediated shifts in the gut microbial compositions, which were associated with the mouse phenotypes.We also identified potentially beneficial and harmful species present during this period, and drew networks of the most abundant species. A functional analysis indicated pathway changes in the WT and Ⅱ-17a^(-/-)mice when fed the HFD. Collectively, these data underscore the importance of the host factor IL-17 A in shaping and regulating the gut microbiota, which conversely, influences the host health. | Yujing Bi Chunxiao Li Lin Liu Jiyuan Zhou Zhengchao Li Huimin Deng Chunyan Wu Yanping Han Yajun Song Yafang Tan Xiaoyi Wang Zongmin Du Yujun Cui Yanfeng Yan Fachao Zhi Guangwei Liu Nan Qin Heping Zhang Ruifu Yang | 2017 | Science Bulletin2017，62，15： | 5 |
| 6 | Alterations in gut microbiota and metabolites associated with altitude-induced cardiac hypertrophy in rats during hypobaric hypoxia challenge显示文摘The gut microbiota is involved in host responses to high altitude.However,the dynamics of intestinal microecology and their association with altitude-related illness are poorly understood.Here,we used a rat model of hypobaric hypoxia challenge to mimic plateau exposure and monitored the gut microbiome,short-chain fatty acids(SCFAs),and bile acids(BAs)over 28 d.We identified weight loss,polycythemia,and pathological cardiac hypertrophy in hypoxic rats,accompanied by a large compositional shift in the gut microbiota,which is mainly driven by the bacterial families of Prevotellaceae,Porphyromonadaceae,and Streptococcaceae.The aberrant gut microbiota was characterized by increased abundance of the Parabacteroides,Alistipes,and Lactococcus genera and a larger Bacteroides to Prevotella ratio.Trans-omics analyses showed that the gut microbiome was significantly correlated with the metabolic abnormalities of SCFAs and BAs in feces,suggesting an interaction network remodeling of the microbiome-metabolome after the hypobaric hypoxia challenge.Interestingly,the transplantation of fecal microbiota significantly increased the diversity of the gut microbiota,partially inhibited the increased abundance of the Bacteroides and Alistipes genera,restored the decrease of plasma propionate,and moderately ameliorated cardiac hypertrophy in hypoxic rats.Our results provide an insight into the longitudinal changes in intestinal microecology during the hypobaric hypoxia challenge.Abnormalities in the gut microbiota and microbial metabolites contribute to the development of high-altitude heart disease in rats. | Zhiyuan Pan Yichen Hu Zongyu Huang Ni Han Yan Li Xiaomei Zhuang Jiye Yin Hui Peng Quansheng Gao Wenpeng Zhang Yong Huang Yujun Cui Yujing Bi Zhenjiang Zech Xu Ruifu Yang | 2022 | Science China(Life Sciences)2022，65，10： | 5 |
| 7 | Transcriptomic Response to Yersinia pestis:RIG-I Like Receptor Signaling Response Is Detrimental to the Host against Plague显示文摘Bacterial pathogens have evolved various mechanisms to modulate host immune responses for successful infection.In this study,RNAsequencing technology was used to analyze the responses of human monocytes THP1 to Yersinia pestis infection.Over 6000 genes were differentially expressed over the 12 h infection.Kinetic responses of pathogen recognition receptor signaling pathways,apoptosis,antigen processing,and presentation pathway and coagulation system were analyzed in detail.Among them,RIG-I-like receptor(RLR) signaling pathway,which was established for antiviral defense,was significantly affected.Mice lacking MAVS,the adaptor of the RLR signahng pathway,were less sensitive to infection and exhibited lower IFN-P production,higher Thl-type cytokines IFN-y and IL-12 production,and lower Th2-type cytokines EL-4 and IL-13 production in the serum compared with wild-type mice.Moreover,infection of pathogenic bacteria other than Y.pestis also altered the expression of the RLR pathway,suggesting that the response of RLR pathway to bacterial infection is a universal mechanism. | Zongmin Du Huiying Yang Yafang Tan Guang Tian Qingwen Zhang Yujun Cui Yanfeng Yan Xiaohong Wu Zuyun Chen Shiyang Cao Yujing Bi Yanping Han Xiaoyi Wang Yajun Song Ruifu Yan | 2014 | Journal of Genetics and Genomics2014，41，7： | 2 |
| 8 | Transcriptional regulation of the waaAE-coaD operon by PhoP and RcsAB in Yersinia pestis biovar Microtus显示文摘亲爱的编辑, | Lei Liu Nan Fang Yicheng Sun Huiying Yang Yiquan Zhang Yanping Han Dongsheng Zhou Ruifu Yang | 2014 | Protein & Cell2014，5，12： | 2 |
| 9 | Pandora of Ebola virus: are we ready?显示文摘在 2014 年 3 月 23 日,畿尼的健康的部通知了在东南的 forested 区域的 Ebola 病毒疾病(EVD ) 的很快传播的爆发,并且 4 ? 天以后,疾病被证实被传给 Conakry,畿尼的首都。疾病很快也传播了到利比里亚,尼日利亚和塞拉利昂。2014 年 7 月 27 日,累积数字证实(909 ) ,可能(276 ) 并且在上述四个国家的嫌疑犯(138 ) EVD 盒子到达了 1,323,包括 729 死亡(与 55.1 的死亡率 ?%)(http://www.who.int/csr/don/2014_07_31_ebola/en/) 。这是 EVD 的最大的爆发直到现在并且第一次疾病在韦斯特检测了非洲。 | Ruifu Yang | 2014 | Chinese Science Bulletin2014，59，32： | 1 |
| 10 | Distinctness of spore and vegetative cellular fatty acid profiles of some aerobic endospore-forming bacilli显示文摘 | SONG Yajun YANG Ruifu GUO Zhaobiao | 2000 | J Microbiol Methods2000，39，3： | 1 |
| 11 | Detection of Francisella tularensis by the polymerase chain reaction 显示文摘 | Zhai Junhui Yang Ruifu Lu Jianchun | 1996 | J Med Microbiol1996，45，： | 1 |
| 12 | Seven facts and five initiatives for gut microbiome research显示文摘The gut microbiome has attracted increasing attention over the past 15 years.Along with the fast-growing body of research literature and media reports,the public's opinions on the gut microbiome have begun to appear polarized.Some believe that the gut microbiome is at the core of human health and is related to every single disease.To the opposite,some people question the scientific basis of gut microbiome studies and criticize that many of them are farfetched;there is even a joke spreading in the biomedical research field—'keeping gut microbiome in mind,no mechanism is hard to find'. | Danyi Li Chunhui Gao Faming Zhang Ruifu Yang Canhui Lan Yonghui Ma Jun Wang | 2020 | Protein & Cell2020，11，6： | 1 |
| 13 | Enhanced root colonization and biocontrol activity of Bacillus amyloliquefaciens SQR9 by abrB gene disruption显示文摘 | Jun Weng Yang Wang Juan Li Qirong Shen Ruifu Zhang | 2013 | Applied Microbiology and Biotechnology2013，，19： | 1 |
| 14 | Mobile laboratory in Sierra Leone during outbreak of Ebola: practices and implications显示文摘Dear Editors,Ebola virus disease(EVD)is an acute,serious and fatal illness caused by the Ebola virus.EVD was first identified in 1976 during two simultaneous outbreaks,one in Nzara,Sudan,and the other in Yambuku,Democratic Republic of Congo[1].The latter o ccurred in a village near the Ebola River,from which the disease takes its name.Since | CHEN ZeLiang CHANG GuoHui ZHANG WenYi CHEN Yong WANG XueSong YANG RuiFu LIU Chao | 2015 | Science China(Life Sciences)2015，58，9： | 1 |
| 15 | Y ersinia protein kinase A phosphorylates vasodilator‐stimulated phosphoprotein to modify the host cytoskeleton显示文摘 | Yuehua Ke Yafang Tan Na Wei Fen Yang Huiying Yang Shiyang Cao Xiaohui Wang Jian Wang Yanping Han Yujing Bi Yujun Cui Yanfeng Yan Yajun Song Xiaoming Yang Zongmin Du Ruifu Yang | 2015 | Cell Microbiol2015，，： | 1 |
| 16 | The supernatant of Bacillus pumilus SQR‐N43 has antifungal activity towards Rhizoctonia solani显示文摘 | Xinqi Huang Xiaoyu Yong Ruifu Zhang Qirong Shen Xingming Yang | 2013 | Basic Microbiol2013，，8： | 1 |
| 17 | Development of an up-converting phosphor technology-based 10-channel lateral flow assay for profiling antibodies against Yersinia pestis显示文摘 | Wenyan Hong Lihua Huang Haoran Wang Jianfeng Qu Zhaobiao Guo Chengke Xie Ziwen Zhu Youbao Zhang Zongmin Du Yanfeng Yan Yan Zheng Huijie Huang Ruifu Yang Lei Zhou | 2010 | Journal of Microbiological Methods2010，，2： | 1 |
| 18 | Genetic and Functional Differences of Escherichia coli Strains from Colorectal Cancer Mucosal Tissues显示文摘Colorectal cancer(CRC)is the third leading cancer globally.Metagenomics has been widely used to analyze the association between the gut microbiota and CRC based on bacterial genus-or species-level comparisons,providing evidence of dysbiosis in CRC development.However,this kind of analysis is unable to provide strain-level information for understanding the individual role of a species in CRC.Here,we used culturomics to isolate CRC mucosal samples and selected 158 Escherichia coli strains to reveal their differences in both genomics and functions by means of phylogenetic analysis and inflammatory induction based on cell and animal experiments.Through genomic comparison,these strains were divided into five phylogroups.The representative strains of each phylogroup significantly induced different levels of cytokine secretion by human leukemic monocyte(THP-1 cell)-based Transwell and animal experiments.Further bioinformatic analysis revealed different profiles of single-nucleotide polymorphisms,genes,and metabolic pathways in the different phylogroups,which can improve the current understanding of the phenotypic differences between these strains.The strain differences revealed in both genomics and functions indicate that the microbiota’s function at the strain level should be investigated in order to understand the interacting mechanisms between hosts and gut bacteria. | Yuxiao Chang Xiang Li Lei Ding Chao Yang Zhiyuan Pan Ni Han Yujun Cui Fachao Zhi Ruifu Yang Hong Gao Yujing Bi | 2022 | Engineering2022，，9： | 0 |
| 19 | Single-cell transcriptomics of immune cells in lymph nodes reveals their composition and alterations in functional dynamics during the early stages of bubonic plague显示文摘Bubonic plague caused by Yersinia pestis is highly infectious and often fatal.Characterization of the host immune response and its subsequent suppression by Y.pestis is critical to understanding the pathogenesis of Y.pestis.Here,we utilized single-cell RNA sequencing to systematically profile the transcriptomes of immune cells in draining lymph nodes(d LNs)during the early stage of Y.pestis infection.Dendritic cells responded to Y.pestis within 2 h post-infection(hpi),followed by the activation of macrophages/monocytes(Mφs/Mons)and recruitment of polymorphonuclear neutrophils(PMNs)to d LNs at 24 hpi.Analysis of cell-to-cell communication suggests that PMNs may be recruited to lymph nodes following the secretion of CCL9 by Mφs/Mons stimulated through CCR1-CCL9 interaction.Significant functional suppression of all the three innate immune cell types occurred during the early stage of infection.In summary,we present a dynamic immune landscape,at single-cell resolution,of murine d LNs involved in the response to Y.pestis infection,which may facilitate the understanding of the plague pathogenesis of during the early stage of infection. | Yifan Zhao Tong Wang Ziyang Liu Yuehua Ke Ruoyan Li Hongyan Chen Yang You Gengshan Wu Shiyang Cao Zongmin Du Fan Bai Ruifu Yang | 2023 | Science China(Life Sciences)2023，66，1： | 0 |
| 20 | 高产酒精肺炎克雷伯菌引起的非酒精性脂肪肝病显示文摘文章简介非酒精性脂肪肝(NAFLD)具有进展为肝硬化和肝细胞癌的风险,其潜在病因多种多样,目前认为NAFLD与肠道微生物群的变化有关,然而,它们之间的因果关系尚不清楚。研究团队发现肠道菌群中高产酒精的肺炎克雷伯菌(HiAlc Kpn)可能是NAFLD的一个病因。在NAFLD患者人群中,高达60%的患者肠道菌群中含有HiAlc Kpn。 | 袁静 Chen Chen Jinghua Cui Jing Lu Chao Yan Xiao Wei Xiangna Zhao NanNan Li Shaoli Li Guanhua Xue Weiwei Cheng Boxing Li Huan Li Weishi Lin Changyu Tian Jiangtao Zhao Juqiang Han Daizhi An Qiong Zhang Hong Wei Minghua Zheng Xuejun Ma Wei Li Xiao Chen Zheng Zhang Hui Zeng Sun Ying JianXin Wu Ruifu Yang 刘翟 | 2020 | 科学新闻2020，，2： | 0 |
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