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| 1 | Efficient and Specific Modifications of the Drosophila Genome by Means of an Easy TALEN Strategy显示文摘技术开发总是是在生物医学的研究驾驶突破的力量之一。自从托马斯·摩根的时间起,一步一步地, Drosophilists 为操作并且机能上地把开发了强大的基因工具为改进这些技术并且开发新技术的果蝇染色体,而是房间仍然大,今天特别作为生物学家开始系统地学习不同模型有机体的功能的 genomics ,包括人,以一种高产量的方式。这里,我们报导,第一次在果蝇,为借助于改进抄写在很高的效率修改果蝇染色体的一个快速、容易、高度特定的方法像使活跃之物的受动器核酸酶(TALEN ) 策略。我们利用了最近发达的单位集会策略装配设计修改黄基因的二特定的 TALEN (在性染色体上) 并且新奇正染色体的基因。TALEN 的 mRNAs 随后被注入果蝇胚胎。从 31.2% 注射 F0 肥沃的苍蝇,我们检测了包含黄基因的可继承的修正。从到可继承的修正的察觉的特定的 TALEN 的建设的全部过程能在一个月以内被完成。在果蝇的这个调停 TALEN 的染色体修正方法的潜在的应用程序被讨论。 | Jiyong Liu Changqing Li Zhongsheng Yu Peng Huang Honggang Wu Chuanxian Wei Nannan Zhu Yan Shen Yixu Chen Bo Zhang Wu-Min Deng Renjie Jiao | 2012 | Journal of Genetics and Genomics2012，39，5： | 43 |
| 2 | Identification of an epitope of SARS-coronavirus nucleocapsid protein显示文摘The nucleocapsid (N) protein of severe acute respiratory syndrome-coronavirus (SARS-CoV) is a majorvirion structural protein. In this study, two epitopes (N1 and N2) of the N protein of SARS-CoV werepredicted by bioinformatics analysis. After immunization with two peptides, the peptides-specific antibodieswere isolated from the immunized rabbits. The further experiments demonstrated that N1 peptide-inducedpolyclonal antibodies had a high affinity to bind to E. coli expressed N protein of SARS-CoV. Furthermore, itwas confirmed that N1 peptide-specific IgG antibodies were detectable in the sera of severe acute respiratorysyndrome (SARS) patients. The results indicated that an epitope of the N protein has been identified andN protein specific Abs were produced by peptide immunization, which will be useful for the study of SARS-CoV. | YINGLIN XuSHEN RUIFuYANG YIXUELI YONGYONGJI YouYuHE MuDESHI WEILU TIELIUSHI BINGSUN JINWANG HONGXIAWANG HUALIANGJIANG JIANHUASHEN YOUHUAXIE YUANWANG GANGPEI BBIFENSHEN JIARUIWU | 2003 | Cell Research2003，13，3： | 22 |
| 3 | Bow-tie topological features of metabolic networks and the functional significance显示文摘Exploring the structural topology of genome-based large-scale metabolic network is essential for in- vestigating possible relations between structure and functionality.Visualization would be helpful for obtaining immediate information about structural organization.In this work,metabolic networks of 75 organisms were investigated from a topological point of view.A spread bow-tie model was proposed to give a clear visualization of the bow-tie structure for metabolic networks.The revealed topological pattern helps to design more efficient algorithm specifically for metabolic networks.This coarse- grained graph also visualizes the vulnerable connections in the network,and thus could have important implication for disease studies and drug target identifications.In addition,analysis on the reciprocal links and main cores in the GSC part of bow-tie also reveals that the bow-tie structure of metabolic networks has its own intrinsic and significant features which are significantly different from those of random networks. | ZHAO Jing TAO Lin YU Hong LUO JianHua CAO ZhiWei LI YiXue | 2007 | Chinese Science Bulletin2007，52，8： | 19 |
| 4 | Comparative profiling of genes and miRNAs expressed in the newborn, young adult, and aged human epididymides显示文摘在通过老化从出生后的开发在 epididymis 调整基因表示理解 transcriptional 因素和 miRNAs 的角色,在新生儿,年轻成年人,和年老的人表示的基因和 miRNAs 的系统的介绍 epididymides 被 cDNA 数组和 miRNA 数组分析分别地执行。新生的人的 epididymis 表示了 fewest mRNAs 但是 miRNAs 的最大的数字而成年、年老的 epididymides 表示了大多数 mRNAs 但是 fewest miRNAs,在 mRNAs 和 miRNA 之间的否定关联在老化期间。由综合分析,一套 miRNA 目标基于 miRNA 和 cDNA 数组被预言。在新生的 epididymis, 127 miRNAs 只或优先地被表示,但是仅仅 3 和 2 miRNAs 分别地在成年、年老的 epididymides 显示出一个充实年龄的表示模式。这研究在 epididymis 在基因表示的复杂规定上为进一步的研究象新卓见和基础一样提供一个基本数据库。 | Jinsong Zhang Qiang Liu Wei Zhang Jianyuan Li Zheng Li Zhongyi Tang Yixue Li Chunsheng Han Susan H. Hall Yonglian Zhang | 2010 | Acta Biochimica et Biophysica Sinica2010，42，2： | 15 |
| 5 | Microvessel changes in the gerbil hippocampus after cerebral ischemia and reperfusion by Buyang Huanwu decoction pretreatment显示文摘Buyang Huanwu decoction(BYHWD) is a classic recipe for the prevention and treatment of ischemic cerebrovascular disease.Gerbils were pretreated with BYHWD,and then subjected to cerebral ischemia and reperfusion.Microvascular changes were determined with laser Doppler monitoring,tannic acid-ferric chloride mordant,and electron microscopy.Results showed that BYHWD pretreatment could enhance the function of hippocampal microvessels,prevent injury,and increase microvasular density and microvasular area density.Thus,these results suggest that BYHWD pretreatment could prevent microvascular occlusion,enhance the capacity of microvascular reperfusion,increase cerebral blood flow,and inhibit neuronal damage,and may be an effective therapy against brain ischemic injury. | Xiaoguang Wu Yixue Li Haixia Liu Yuhua Yin Shumin Zhao Yuanyuan Guo | 2011 | Neural Regeneration Research2011，6，9： | 11 |
| 6 | Effect of updating training on fluid intelligence in children显示文摘Recent studies have indicated that working memory (WM) training can improve fluid intelligence.However,these earlier studies confused the impact of WM storage and central executive function on the effects of training.The current study used the running memory task to train the updating ability of 9-11 year-old children using a double-blind controlled design.The results revealed that children's fluid intelligence was significantly improved by memory-updating training.Overall,our findings suggest that the increase in fluid intelligence achieved with WM training is related to improving central executive function. | ZHAO Xin WANG YiXue LIU DanWei2 ZHOU RenLai1 | 2011 | Chinese Science Bulletin2011，56，21： | 11 |
| 7 | Suppression dampens unpleasant emotion faster than reappraisal:Neural dynamics in a Chinese sample显示文摘The timing dynamics of regulating negative emotion with expressive suppression and cognitive reappraisal were investigated in a Chinese sample. Event-Related Potentials were recorded while subjects were required to view, suppress emotion expression to, or reappraise emotional pictures. The results showed a similar reduction in self-reported negative emotion during both strategies. Additionally, expressive suppression elicited larger amplitudes than reappraisal in central-frontal P3 component(340–480 ms). More importantly, the Late Positive Potential(LPP) amplitudes were decreased in each 200 ms of the 800–1600 ms time intervals during suppression vs. viewing conditions. In contrast, LPP amplitudes were similar for reappraisal and viewing conditions in all the time windows, except for the decreased amplitudes during reappraisal in the 1400–1600 ms. The LPP(but not P3) amplitudes were positively related to negative mood ratings, whereas the amplitudes of P3, rather than LPP, predict self-reported expressive suppression. These results suggest that expressive suppression decreases emotion responding more rapidly than reappraisal, at the cost of greater cognitive resource involvements in Chinese individuals. | YUAN JiaJin LONG QuanShan DING NanXiang LOU YiXue LIU YingYing YANG JieMin | 2015 | Science China(Life Sciences)2015，58，5： | 11 |
| 8 | Comparative proteogenomic analysis of the Leptospira interrogans virulence-attenuated strain IPAV against the pathogenic strain 56601显示文摘稀释毒力的螺旋体 interrogans serovar Lai 紧张 IPAV 被延长实验室经过从在中国孤立的高度剧毒的祖先的紧张导出。我们学习了 IPAV 的基因变化对病原的 L 经由比较分析使它变为无毒害。interrogans serovar Lai 紧张 56601。IPAV 紧张的完全的染色体顺序决心、使用与作比较,然后修正并且重新注解紧张 56601 的染色体顺序。除了他们的高度类似的 genomic,结构和基因顺序, 33 插入的一个总数, 53 删除和 301 个单个核苷酸的变化(SNV ) 在整个直接影响 101 基因的 IPAV 的染色体被检测,在他们的 5 ′ 的任何一个;在上游的区域或在他们的编码区域以内。在他们之中, 44 功能的基因的多数涉及信号 transduction,压力反应, transmembrane 运输和氮新陈代谢。基于量的液体,层析(LC )-MS/MS 数据揭示了的比较 proteomic 分析在 orthologs 的 1 627 选择的对之中,在 IPAV 的 174 基因拉紧,这是 upregulated,与主要在精力的班上的丰富生产和类脂化合物新陈代谢。相反,在紧张 56601 的 228 基因是 upregulated,与在蛋白质翻译和 DNA 复制 / 修理的范畴充实的多数。 genomic 和 proteomic 途径的联合在批评基因说明了那改变的表情或变化,例如编码 Ser/Thr kinase ,碳饥饿蛋白质 CstA ,夫酸安合成酶,GTP有约束力的蛋白质 BipA , ribonucleotide-diphosphate reductase 和磷酸盐 transporter 的那些,并且在脂蛋白或外部膜蛋白质的翻译侧面的改变是可能的在紧张 IPAV 说明毒力变细。 | Yi Zhong Xiao Chang Xing-Jun Cao Yan Zhang Huajun Zheng Yongzhang Zhu Chengsong Cai Zelin Cui Yunyi Zhang Yuan-Yuan Li Xiu-Gao Jiang Guo-Ping Zhao Shengyue Wang Yixue Li Rong Zeng Xuan Li Xiao-Kui Guo | 2011 | Cell Research2011，21，8： | 10 |
| 9 | Complex networks theory for analyzing metabolic networks显示文摘One of the main tasks of post-genomic informatics is to systematically investigate all mole- cules and their interactions within a living cell so as to understand how these molecules and the interactions between them relate to the function of the organism, while networks are appropriate abstract description of all kinds of interactions. In the past few years, great achievement has been made in developing theory of complex networks for revealing the organizing prin- ciples that govern the formation and evolution of various complex biological, technological and social networks. This paper reviews the accomplishments in constructing genome-based metabolic networks and describes how the theory of complex networks is applied to analyze metabolic networks. | ZHAO Jing YU Hong LUO Jianhua CAO Z. W. LI Yixue | 2006 | Chinese Science Bulletin2006，51，13： | 10 |
| 10 | Processing and Microstructural Evolution of Superalloy Inconel 718 during Hot Tube Extrusion显示文摘The processing parameters of tube extrusion for superalloy Inconel 718 (IN 718), such as slug temperature, tools temperature, choice of lubricant, extrusion ratio and extrusion speed, were determined by experiment in this paper. An appropriate temperature range recommended for the slug is 1080~1120℃, and the temperature range recommended for the tools is 350~500℃. The microstructural evolution of superalloy IN 718 during tube extrusion was analyzed.With the increase of the deformation the cross crystal grains were slightly refined. While the vertical crystal grain is elongated evidently and the tensile strength increased along the axial rake. Glass lubricants have to be spread on the slug surface after being heated to 150~200℃, vegetable oil or animal oil can be used as the lubricant on the surface of the tools to reduce the extrusion force remarkably. | ShihongZHANG ZhongtangWANG BingQIAO YiXU TingfengXU | 2005 | Journal of Materials Science & Technology2005，21，2： | 8 |
| 11 | FluxExplorer: A general platform for modeling and analyses of metabolic net-works based on stoichiometry显示文摘Stoichiometry-based analyses of meta- bolic networks have aroused significant interest of systems biology researchers in recent years. It is necessary to develop a more convenient modeling platform on which users can reconstruct their network models using completely graphical operations, and explore them with powerful analyzing modules to get a better understanding of the properties of metabolic systems. Herein, an in silico platform, FluxExplorer, for metabolic modeling and analyses based on stoichiometry has been developed as a publicly available tool for systems biology research. This platform integrates various analytic approaches, in- cluding flux balance analysis, minimization of meta- bolic adjustment, extreme pathways analysis, shadow prices analysis, and singular value decom- position, providing a thorough characterization of the metabolic system. Using a graphic modeling process, metabolic networks can be reconstructed and modi- fied intuitively and conveniently. The inconsistencies of a model with respect to the FBA principles can be proved automatically. In addition, this platform sup- ports systems biology markup language (SBML). FluxExplorer has been applied to rebuild a metabolic network in mammalian mitochondria, producing meaningful results. Generally, it is a powerful and very convenient tool for metabolic network modeling and analysis. | LUO Ruoyu LIAO Sha ZENG Shaoqun LI Yixue LUO Qingming | 2006 | Chinese Science Bulletin2006，51，6： | 6 |
| 12 | Highly efficient base editing in human tripronuclear zygotes显示文摘 | Changyang Zhou Meiling Zhang Yu Wei Yidi Sun Yun Sun Hong Pan Ning Yao Wanxia Zhong Yixue Li Weiping Li3 Hui Yang Zi-jiang Chen | 2017 | Protein & Cell2017，8，10： | 6 |
| 13 | Antigenic and immunogenic changes due to mutation of sgene of HBV显示文摘AIM: To investigate the change of immunological characteristics of HBsAg caused by the mutation at codon 145 of HBsAg using DNA-based immunization.METHODS: Plasmids expressing mutant and wild type envelope antigens were transfected into human hepatocellular carcinoma cells via electrotransformation. The antigenicity of HBsAg was studied with EIA and immunocytochemical staining. Then plasmids were used to immunize 5 C57BL/6 mice. Sera of mice were detected for anti-HBs and anti-preS2with ELISA. RESULTS: The mutant HBsAg could be detected by native antibody in EIA and immunocytochemical study. But the A(450nm) value of the mutant HBsAg in the supernatant was apparently lower than that of the wild-type. Both mutant and native HBsAg expression plasmid could stimulate a strong humoral immune response to HBsAg and preS2 antigen in mice. Protective antibodies against HBsAg elicited by the native HBsAg occurred earlier than that elicited by the mutant HBsAg about one to two weeks. The occurrence of protective antibodies against preS2 antigen was one to two weeks earlier than that of anti-HBs.CONCLUSION: The amino acid substitution causes changes of the antigenicity and immunogenicity of HBsAg, but mutant HBsAg can still induce a protective humoral immune responsein mice. | Jun-HuiGe Hui-MinLiu JingSun Le-ZhiZhang ]inHe Yu-LiLi HongLiu YiXu Hong-YuYu Yi-PingHu | 2004 | World Journal of Gastroenterology2004，10，21： | 6 |
| 14 | Adsorption of Basic Dyes Using Walnut Shell-based Biochar Produced by Hydrothermal Carbonization显示文摘 | KANG Chunli ZHU Ling WANG Yixue WANG Yuhan XIAO Kunkun TIAN Tao | 2018 | Chemical Research in Chinese Universities2018，34，4： | 5 |
| 15 | A Brief Review of Computational Gene Prediction Methods显示文摘With the development of genome sequencing for many organisms, more and more raw sequences need to be annotated. Gene prediction by computational methods for finding the location of protein coding regions is one of the essential issues in bioinformatics. Two classes of methods are generally adopted: similarity based searches and ab initio prediction. Here, we review the development of gene prediction methods, summarize the measures for evaluating predictor quality, highlight open problems in this area, and discuss future research directions. | ZhuoWang YazhuChen YixueLi | 2004 | Genomics, Proteomics & Bioinformatics2004，2，4： | 5 |
| 16 | Drosophila RecQ5 is required for efficient SSA repair and suppression of LOH in vivo显示文摘RecQ5 in mammalian cells has been suggested to suppress inappropriate homologous recombination.However,the specific pathway(s)in which it is involved and the underlining mechanism(s)remain poorly understood.We took advantage of genetic tools in Drosophila to investigate how Drosophila RecQ5(dRecQ5)functions in vivo in homologous recombination-mediated double strand break(DSB)repair.We generated null alleles of dRecQ5 using the targeted recombination technique.The mutant animals are homozygous viable,but with growth retardation during development.The mutants are sensitive to both exogenous DSB-inducing treatment,such as gamma-irradiation,and endogenously induced double strand breaks(DSBs)by I-Sce I endonuclease.In the absence of dRecQ5,single strand annealing(SSA)-mediated DSB repair is compromised with compensatory increases in either inter-homologous gene conversion,or non-homologous end joining(NHEJ)when inter-chromosomal homologous sequence is unavailable.Loss of function of dRecQ5 also leads to genome instability in loss of heterozygosity(LOH)assays.Together,our data demonstrate that dRecQ5 functions in SSA-mediated DSB repair to achieve its full efficiency and in suppression of LOH in Drosophila. | Yixu Chen Wen Dui Zhongsheng Yu Changqing Li Jun Ma Renjie Jiao | 2010 | Protein & Cell2010，1，5： | 5 |
| 17 | Effects of electroacupuncture on astrocytes in the marginal zone of focal cerebral ischemia in rats显示文摘BACKGROUND:Astrocytes react sensitively to cerebral ischemia,causing reactive proliferation and activation,which may contribute to their effect in protecting or injuring neuronal regeneration. Whether acupuncture,as a treatment for cerebral ischemia,regulates the activated state of astrocytes has become a focus of recent investigations. OBJECTIVE:To observe the effects of electroacupuncture(EA) on ultrastructure changes and reactive proliferation of astrocytes in the marginal zone of focal cerebral ischemia in rats. DESIGN,TIME AND SETTING:Randomized,controlled animal study.This study was performed at the Experimental Animal Center of Guangzhou University of Traditional Chinese Medicine between December 2007 and July 2008. MATERIALS:A total of 90 male Wistar rats were randomly divided into sham operated,model and EA groups.Each group was subdivided into 1 hour,1,3,7,and 21 days post-cerebral ischemia groups,with six animals for each time point.Rabbit anti-rat glial fibrillary acidic protein (GFAP) and goat anti-rabbit IgG/tetramethylrhodamine isothiocyanate were provided by Beijing Biosynthesis Biotechnology.The G-6805 electric acupuncture apparatus was provided by Shanghai Huayi. METHODS:Heat-coagulation-induced occlusion of the middle cerebral artery was performed to establish a model of focal cerebral ischemia,in the model and EA groups.Middle cerebral arteries were exposed without occlusion in sham operated group.EA was applied immediately after surgery in the EA group,4/20 Hz,2.0-3.0 V,1-3 mA,to Baihui(GV 20) and Dazhui(GV 14),for 30 minutes.The treatment was performed once a day.The sham operated and model groups did not receive acupuncture. MAIN OUTCOME MEASURES:In the marginal zone of focal cerebral ischemia in rats at different time points after intervention,the ultrastructure changes of astrocytes were observed by using transmission electronic microscopy.GFAP expression in astrocytes was also measured by laser confocal scanning microscopy. RESULTS:Cell swelling and rapid proliferation of astrocytes were observed following cerebral ischemia.In comparison to the model group,the degree of swelling of astrocytes was significantly decreased in the EA group.Compared with the sham operated group at hour 1 post-surgery,there was no significant difference in the expression of average fluorescence intensity of GFAP between the EA and model groups(P>0.05),while the expression of GFAP in both the EA and model groups increased significantly at days 1,3,7 and 21 post-surgery(P<0.01).The expression of GFAP in EA group was also significantly lower than in the model group(P<0.01,P<0.05). CONCLUSION:Ultrastructural changes and reactive proliferation of astrocytes appear in the marginal zone of focal cerebral ischemia in rats.EA can relieve the degree of swelling of astrocytes and inhibit GFAP overexpression by activated astrocytes.These effects may be related to its ability to regulate the activated state of astrocytes. | Yan Luo Nenggui Xu Wei Yi Yong Zi Yixu Du | 2009 | Neural Regeneration Research2009，4，4： | 4 |
| 18 | Determination of Feature Line Equation for Self-adapting Incremental Press Bending显示文摘The basic idea and method about determination of the feature line equations and how to apply them to the numerical control of the press bending of panel skins were introduced. Research indicates that it is feasible to realize the self adapting incremental press bending by adopting the feature line equation. The feature line equation, which is based on the database of the status of practical processes, can be adjusted in time, and the forming precision can be improved.It is important to correctly select and reasonably predict the feature line equations to enhance the accuracy of the incremental press bending based on the feature line database and algorithm. The determination of the feature line equation settles necessary data foundation for further research on the database of self-adapting incremental press bending, and it supplies a new clue for the development of self-adapting incremental press bending. | JinsongLIU ShihongZHANG YuansongZENG ZhiqiangLI WeiWU ZhongtangWANG YiXU LimeiREN | 2004 | Journal of Materials Science & Technology2004，20，6： | 4 |
| 19 | Prediction and systematic study of protein-protein interaction networks of Leptospira interrogans显示文摘Leptospira interrogans serovar Lai is a pathogenic bacterium that causes a spirochetal zoonosis in humans and some animals. With its complete genome sequence available, it is possible to analyze protein-protein interactions from a whole- genome standpoint. Here we combine four recently developed computational approaches (gene fusion method, gene neighbor method, phylogenetic profiles method, and operon method) to predict protein-pro- tein interaction networks of Leptospira interrogans strain Lai. Through comprehensive analysis on in- teractions among proteins of motility and chemotaxis system, signal transduction, lipopolysaccaride bio- synthesis and a series of proteins related to adhesion and invasion, we provided information for further studying on its pathogenic mechanism. In addition, we also assigned 203 previously uncharacterized proteins with possible functions based on the known functions of its interacting partners. This work is helpful for further investigating L. interrogans strain Lai. | SUN Jingchun XU Jinlin CAO Jianping LIU Qi GUO Xiaokui SHI Tieliu LI Yixue | 2006 | Chinese Science Bulletin2006，51，11： | 3 |
| 20 | Big Biological Data:Challenges and Opportunities显示文摘In‘‘Omics’’era of the life sciences,data is presented in many forms,which represent the information at various levels of bio logical systems,including data about genome,transcriptome epigenome,proteome,metabolome,molecular imaging,molec ular pathways,different population of people and clinical/med ical records.The biological data is big,and its scale has already been well beyond petabyte(PB)even exabyte(EB). | Yixue Li Luonan Chen | 2014 | Genomics, Proteomics & Bioinformatics2014，12，5： | 3 |
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