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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 | A draft sequence of the rice (Oryza sativa ssp. indica) genome显示文摘The sequence of the rice genome holds fundamental information for its biology, including physiology, genetics, development, and evolution, as well as information on many beneficial phenotypes of economic significance. Using a 'whole genome shotgun' approach, we have pro-duced a draft rice genome sequence of Oryza sativa ssp. in-dica, the major crop rice subspecies in China and many other regions of Asia. The draft genome sequence is constructed from over 4.3 million successful sequencing traces with an accumulative total length of 2214.9 Mb. The initial assembly of the non-redundant sequences reached 409.76 Mb in length, based on 3.30 million successful sequencing traces with a total length of 1797.4 Mb from an indica variant cultivar 93-11, giving an estimated coverage of 95.29% of the rice genome with an average base accuracy of higher than 99%. The coverage of the draft sequence, the randomness of the sequence distribution, and the consistency of BIG-ASSEM-BLER, a custom-designed software package | YU Jun, HU Songnian, WANG Jun,LI Songgang WONG Ka-Shu Gane, LIU Bin,DENG Yajun, DAI Li, ZHOU Yan,ZHANG Xiuqing, CAO Mengliang, LIU Jing,SUN Jiandong , TANG Jiabin, CHEN Yanjiong,HUANG Xiaobing, LIN Wei, YE Chen, TONG Wei,CONG Lijuan, GENG Jianing, HAN Yujun, LI Lin,LI Wei, HU Guangqiang, HUANG Xiangang,LI Wenjie, LI Jian, LIU Zhanwei, LI Long,LIU Jianping, Ql Qiuhui, LIU Jinsong, LI Li,WANG Xuegang, LU Hong, WU Tingling,ZHU Miao, Nl Peixiang, HAN Hua, DONG Wei,REN Xiaoyu, FENG Xiaoli, GUI Peng,LI Xianran, WANG Hao, XU Xin, ZHAI Wenxue,XU Zhao, ZHANG Jinsong, HE Sijie,ZHANG Jianguo, XU Jichen, ZHANG Kunlin,ZHENG Xianwu, DONG Jianhai, ZENG Wanyong,TAO Lin, CHEN Xuewei, HE Jun, LIU Daofeng,TIAN Wei, TIAN Chaoguang, XIA Hongai,LI Gang, GAO Hui, LI Ping, CHEN Wei ,WANG Xudong, ZHANG Yong, HU Jianfei,WANG Jing, LIU Song, YANG Jian,ZHANG Guangyu, XIONG Yuqing, LI Zhijie,MAO Long, ZHOU Chengshu, ZHU Zhen,CHEN Runsheng, HAO Bailin,ZHENG Weimou, CHEN Shouyi, QUO Wei,LI Guojie, LIU Siqi, HUANG Guyang,TAO Ming, WANG Jian, ZHU Lihuang,YUAN Longping& YANG HuanmingBeijing Genomics Institute/Center of Genomics & Bioinformatics, Chinese Academy of Sciences, Beijing 101300, China Hangzhou Genomics Institute/Institute of Bioinformatics of Zhejiang University/Key Laboratory of Bioinformatics of Zhejiang Province, Hangzhou 310007, China Institute of Genetics, Chinese Academy of Sciences, Beijing 100101, China National Hybrid Rice R & D Center, Changsha 410125, China Laboratory of Bioinformatics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China College of Life Sciences, Peking University, Beijing 100871, China Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 1Q0080, China Digital China Ltd., Beijing 100080, China Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100080, China Medical College, Xi’an Jiaotong University, Xi’an 710061, ChinaThese authors contributed equally to this work.Corresponding author.Corresponden | 2001 | Chinese Science Bulletin2001，46，23： | 6 |
| 3 | Toward High Per- formance Graphene Fibers显示文摘 | Chen Li He Yuling Chai Songgang | 2013 | Nanoscale2013，5，： | 1 |
| 4 | mda-7/IL-24 induces apoptosis in human GBC-SD gallbladder carcinomacells via mitochondrial apoptotic pathway显示文摘 | Jianguang Jia Songgang Li Wei Gong Jing Ding Cuifu Fang Zhiwei Quan | 2011 | Oncology Reports2011，，1： | 1 |
| 5 | A role for p21‐activated kinase 7 in the development of gastric cancer显示文摘 | Jun Gu Keqiang Li Maolan Li Xiangsong Wu Lin Zhang Qichen Ding Wenguang Wu Jiahua Yang Jiasheng Mu Hao Wen Qian Ding Jianhua Lu Yuan Hao Lei Chen Wenjie Zhang Songgang Li Yingbin Liu | 2012 | FEBS J2012，，1： | 1 |
| 6 | Differences in Carbon Nutrition between On-season and Off-season Longan during the Flowering Process显示文摘Flower-bud differentiation is the most critical stage of fruit yield formation,as well as a complicated carbon transfer process. To understand the changes of carbon during the flower bud differentiation process of longan,it is very important to adopt suitable planting measures and control flowering time. This study focused on the changes of sugar and starch content of on-season and off-season longan during the flowering process. The results showed that the accumulation and transformation of carbon differed between on-season and off-season longan during flower-bud differentiation process; to be specific,sugar and starch content in tissues differentiated from apical buds of on-season longan were reduced at the late flower-bud physiological differentiation stage except in leaf buds; on the contrary,sugar and starch content in off-season longan increased at the late flower-bud physiological differentiation stage: specifically,total sugar content increased from15. 43(- 7 d) to 31. 38 mg /g( 7 d); starch content increased from 5. 42 to 8. 31 mg /g during this time,which may be relevant to the external environment or tree original metabolism damaged by potassium chlorate. | Ziqin YANG Xingxing CHEN Jiwang HONG Lei ZHANG Jianbin LUO Songgang LI | 2014 | Agricultural Biotechnology2014，3，2： | 1 |
| 7 | A role for p21‐activated kinase 7 in the development of gastric cancer显示文摘 | Jun Gu Keqiang Li Maolan Li Xiangsong Wu Lin Zhang Qichen Ding Wenguang Wu Jiahua Yang Jiasheng Mu Hao Wen Qian Ding Jianhua Lu Yuan Hao Lei Chen Wenjie Zhang Songgang Li Yingbin Liu | 2012 | FEBS J2012，，1： | 1 |
| 8 | A role for p21‐activated kinase 7 in the development of gastric cancer显示文摘 | Jun Gu Keqiang Li Maolan Li Xiangsong Wu Lin Zhang Qichen Ding Wenguang Wu Jiahua Yang Jiasheng Mu Hao Wen Qian Ding Jianhua Lu Yuan Hao Lei Chen Wenjie Zhang Songgang Li Yingbin Liu | 2012 | FEBS J2012，，1： | 1 |
| 9 | Effects of Matrine on Proliferation and Apoptosis in Gallbladder Carcinoma Cells (GBC‐SD)显示文摘 | Zhiping Zhang Xuefeng Wang Wenguang Wu Jianwei Wang Yong Wang Xiangsong Wu Xiaozhou Fei Songgang Li Jie Zhang Ping Dong Jun Gu Yingbin Liu | 2011 | Phytother Res2011，，6： | 1 |
| 10 | Wogonin, an active ingredient of Chinese herb medicine Scutellaria baicalensis , inhibits the mobility and invasion of human gallbladder carcinoma GBC-SD cells by inducing the expression of maspin显示文摘 | Ping Dong Yong Zhang Jun Gu Wenguang Wu Maolan Li Jiahua Yang Lin Zhang Jianhua Lu Jiasheng Mu Lei Chen Songgang Li Jianwei Wang Yingbin Liu | 2011 | Journal of Ethnopharmacology2011，，3： | 1 |
| 11 | Reactive oxygen species-mediated endoplasmic reticulum stress and mitochondrial dysfunction contribute to cirsimaritin-induced apoptosis in human gallbladder carcinoma GBC-SD cells显示文摘 | Zhiwei Quan Jun Gu Ping Dong Jianhua Lu Xiangsong Wu Wenguang Wu Xiaozhou Fei Songgang Li Yong Wang Jianwei Wang Yingbin Liu | 2010 | Cancer Letters2010，，2： | 1 |
| 12 | Analysis of Carbon Content in Off-season Flowering and Non-flowering Longan Trees显示文摘After flower induction,some longan trees can successfully blossom and bear fruit,while others with similar tree body status can only sprout leaf buds.In order to investigate the main reason for these differences,in this study,off-season flowering and non-flowering longan trees were used as experimental materials to analyze the changes of carbon content in mature leaves,tender leaves,mature shoots,tender shoots and terminal buds of longan trees after flower induction by potassium chlorate. The result showed that carbon content played an important role in flowering process. Off-season longan trees with carbon content in mature leaves reached 50. 93 mg /g could successfully blossom,but those with carbon content in mature leaves lower than 37. 40 mg /g were usually difficult to blossom. In addition,the maturity of tender leaves posed great influence on flowering. Specifically,tender leaves with a higher maturity contained higher carbon content and could easily blossom,which could be used as a new indicator to evaluate flower induction in off-season longan trees. | Ziqin YANG Xingxing CHEN Lei ZHANG Jiwang HONG Songgang LI | 2014 | Agricultural Biotechnology2014，3，4： | 1 |
| 13 | Evolutionary Transients in the Rice Transcriptome显示文摘In the canonical version of evolution by gene duplication, one copy is kept unaltered while the other is free to evolve. This process of evolutionary experimentation can persist for millions of years. Since it is so short lived in comparison to the lifetime of the core genes that make up the majority of most genomes, a substantial fraction of the genome and the transcriptome may-in principle-be attributable to what we will refer to as 'evolutionary transients', referring here to both the process and the genes that have gone or are undergoing this process. Using the rice gene set as a test case, we argue that this phenomenon goes a long way towards explaining why there are so many more rice genes than Arabidopsis genes, and why most excess rice genes show low similarity to eudicots. | Jun Wang Jianguo Zhang Ruiqiang Li Hongkun Zheng Jun Li Yong Zhang Heng Li Peixiang Ni Songgang Li Shengting Li Jingqiang Wang Dongyuan Liu Jason McDermott Ram Samudrala Siqi Liu Jian Wang Huanming Yang Jun Yu Gane Ka-Shu Wong | 2010 | Genomics, Proteomics & Bioinformatics2010，8，4： | 0 |
| 14 | Effects of Boron on Spore Germination and Integrity of Colletotrictum gloeosporioides( Penz) Saec显示文摘Litchi anthracnose caused by Colletotrictum gloeosporioides( Penz) Saec. is an extremely destructive and widely distributed disease,which results in poor market value. Borate,an essential plant micronutrient that helps plant growth and has been used extensively in industry and agriculture as a safe method for control of fungi,was effective in the form of potassium tetraborate for control of C. gloeosporioides( Penz). In this study,boron strongly inhibited spore germination,germ tube elongation,and mycelial spread of C. gloeosporioides( Penz) in the culture medium. Application of boron at 1% caused the appearance of abnormal spores( disrupted) in some cases. On the basis of propidium iodide fluorescent staining,the loss of membrane integrity in C. gloeosporioides( Penz) was observed after boron treatment. Furthermore,Boron led to the leakage of cellular constituents( soluble proteins and carbohydrates) from hyphae of C. gloeosporioides( Penz). These data suggest that the mechanisms may be directly related with the disruption effect of boron on cell membrane of the fungal pathogen,resulting in the breakdown of cell membrane structure and loss of cytoplasmic materials from the hyphae. | Ying LU Yixian XIE Lei ZHANG Songgang LI | 2014 | Agricultural Biotechnology2014，3，6： | 0 |
| 15 | Positive correlation between recombination rate and nucleotide diversity is shown under domestication selection in the chicken genome显示文摘Positive correlation between recombination rate and nucleotide diversity has been observed in a wide variety of eukaryotes on megabase scale. On the basis of genome-wide chicken genetic variation map generated by comparing three domestic breeds with wild ancestor and the positions of markers on the genetic linkage map, we found that SNPs rates were similar for all chromosomes while the recombina-tion rates increased in micro chromosomes. In other words no correlation exists in chromosome size. Nevertheless, when we scanned the genome by calculating the values of each characteristic within non-overlapping windows, instead of single value for each chromosomes, the nucleotide diversity was found to be significantly correlated with the recombination rate (r=0.27, P<0.0005). Furthermore, the significant association not only existed between these two features, but also existed between all 6 pairwise combinations of nucleotide diversity, recombination rate, GC content and average gene length. This co-variation is very meaningful for the studies of sequence evolution. | FANG Lin YE Jia LI Ning ZHANG Yong LI SongGang GANE Ka-Shu WONG WANG Jun | 2008 | Chinese Science Bulletin2008，53，5： | 0 |
| 16 | Probable lumbar acute noncompressive nucleus pulposus extrusion: a case report of acute pain caused by a hydrated nucleus pulposus and review of the literature显示文摘Acute noncompressive nucleus pulposus(NP)extrusion has been widely described in veterinary medicine,especially in dogs and cats;however,caseshave rarely been reported in humans.We report a rare case of acute pain caused by a hydrated NP.Magnetic resonance imaging revealed an obvious hyperintense signal on T2-weighted images at the L5/S1 segments,while computed tomography imaging and radiography revealed amildly herniated discat the L4/5 level and slightlumbar spondylo listhesis at the L5/S1 segments.The operation was performed to confirm the presence of ared and swollen nerve root on the right side of the hydrated L5/S1 segment.The patient’s severe pain disappeared,and full recovery was achieved months after surgery.Thus,our case demonstrated a probable lumbar acute noncompressive NP extrusion in humans and reported associated symptoms and imaging characteristics.In such circumstances,surgical management is indicated and may be associated with a good outcome. | Changjun Chen Xianlei Gao Hao Li Xin Pan Songgang Wang | 2022 | Emergency and Critical Care Medicine2022，2，2： | 0 |
| 17 | Effects of H_2O_2 and NO on Flower Development and AP1 Gene Expression of Off-season Longan显示文摘[Objective] T his study aimed to investigate the effects of H_2O_2 and NO on flower development and AP1 gene expression of off-season longan. [Method] N ine-year-old off-season Chuliang longan was sprayed with enhancers and blockers of H_2O_2 and NO to analyze dynamic changes of flower development and AP1 expression. [Result] T he expression level of AP1 gene in off-season longan was improved during flower development. SNP and MV treatments up-regulated the expression level of AP1 gene in leaves and terminal buds to varying degrees during lateral primordium formation. Especially,SNP treatment exhibited the most remarkable effect. DMTU treatment significantly inhibited the expression of AP1 gene in leaves and terminal buds during lateral primordium formation. L-NNA treatment slightly inhibited the expression of AP1 gene in leaves and exerted no significant effect on expression of AP1 gene in terminal buds. [Conclusion]It can be speculated that the enhancement of NO and H_2O_2 signals is conducive to flower development of off-season longan,while blocking H_2O_2 signals may inhibit flower development of off-season longan. | Songgang LI Xinjun ZHANG Lei ZHANG Jiwang HONG Yeyuan CHEN | 2016 | Agricultural Biotechnology2016，5，4： | 0 |
| 18 | Applications of the double-barreled data in whole-genome shotgun sequence assembly and analysis显示文摘Double-barreled (DB) data have been widely used for the assembly of large ge- nomes. Based on the experience of building the whole-genome working draft of Oryza sativa L. ssp. Indica, we present here the prevailing and improved uses of DB data in the assembly pro- cedure and report on novel applications during the following data-mining processes such as ac- quiring precise insert fragment information of each clone across the genome, and a new kind of low-cost whole-genome microarray. With the increasing number of organisms being sequenced, we believe that DB data will play an important role both in other assembly procedures and in future genomic studies. | HAN Yujun 1,2 , NI Peixiang 2 , Lü Hong 2 , YE Jia 3 , HU Jianfei 1 , CHEN Chen 2 , HUANG Xiangang 2 , CONG Lijuan 2 , LI Guangyuan 2 , WANG Jing 1 , GU Xiaocheng 1 , YU Jun 2 & LI Songgang 1,2 1. College of Life Sciences, Peking University, Beijing 100871, China 2. Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China 3. James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310012, China | 2005 | Science China(Life Sciences)2005，48，3： | 0 |
| 19 | Indicator Analysis of Off-season Longan Flower Reversal显示文摘[Objectives] This study was conducted to analyze the internal causes of flower reversal in Longan( Dimocarpus longan Lour.) trees. [Methods]With flowering trees and flower reversal trees as experimental materials,the variations in sugar and starch in mature leaves,tender leaves,mature branches,twigs and terminal buds after flower forcing were analyzed. [Results]During flowering process,sugar content showed the greatest difference between flowering and flower reversal trees,and the difference was the greatest in mature leaves. Trees with mature leaves having a sugar content above 44. 71 mg/g were found to be more prone to flowering,while those with leaf sugar content lower than 27. 80 mg/g were susceptible to flower reversal. In addition,longan trees with a higher sugar content in tender leaves were not prone to flower reversal. [Conclusions] In future,whether off-season flower forcing can be performed on longan trees could be judged through the detection of tree leaves,which is of great significance to prevention of flower reversal in off-season longan production. | Ziqin YANG Lei ZHANG Jiwang HONG Songgang LI | 2018 | Agricultural Biotechnology2018，7，5： | 0 |
| 20 | Magnetically tunable zero-index metamaterials显示文摘Zero-index metamaterials(ZIMs)feature a uniform electromagnetic mode over a large area in arbitrary shapes,enabling many applications including high-transmission supercouplers with arbitrary shapes,directionindependent phase matching for nonlinear optics,and collective emission of many quantum emitters.However,most ZIMs reported to date are passive;active ZIMs that allow for dynamic modulation of their electromagnetic properties have rarely been reported.Here,we design and fabricate a magnetically tunable ZIM consisting of yttrium iron garnet(YIG)pillars sandwiched between two copper clad laminates in the microwave regime.By harnessing the Cotton–Mouton effect of YIG,the metamaterial was successfully toggled between gapless and bandgap states,leading to a“phase transition”between a zero-index phase and a single negative phase of the metamaterial.Using an S-shaped ZIM supercoupler,we experimentally demonstrated a tunable supercoupling state with a low intrinsic loss of 0.95 d B and a high extinction ratio of up to 30.63 d B at 9 GHz.We have also engineered a transition between the supercoupling state and the topological one-way transmission state at10.6 GHz.Our work enables dynamic modulation of the electromagnetic characteristics of ZIMs,enabling various applications in tunable linear,nonlinear,quantum,and nonreciprocal electromagnetic devices. | YUCONG YANG YUEYANG LIU JUN QIN SONGGANG CAI JIEJUN SU PEIHENG ZHOU LONGJIANG DENG YANG LI LEI BI | 2023 | Photonics Research2023，11，10： | 0 |
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