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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 | Characterizations and identification of the candidate gene of rice thermo-sensitive genic male sterile gene tms5 by mapping显示文摘Previous study indicated that the thermo-sensitive genic malesterile(TGMS) gene in rice was regulated by temperature.TGMS rice plays an important role in hybrid rice production,because the application of the TGMS system in two-line breeding is laborsaving,timesaving,simple,inexpensive,efficient,and eliminating the limitations of the cytoplasmic male sterility(CMS) system.'AnnongS' is the first discovered and deeply studied TGMS rice lines in China.'AnnongS-1' and 'Y58S',two derivatives of TGMS line AnnongS,were both controlled by a single recessive gene named tms5,which was genetically mapped on chromosome 2.In this study,three populations('AnnongS-1' × 'Nanjing11','Y58S' × 'Q611',and 'Y58S' × 'Guanghui122') were developed and used for the molecular fine mapping of the tms5 gene.By analyzing recombination events in the sterile individuals using a total of 125 probes covering the tms5 region,the tms5 gene was physically mapped to a 19-kb DNA fragment between two markers 4039-1 and 4039-2,which were located on the BAC clone AP004039.After the construction of the physical map between two markers 4039-1 and 4039-2,a member(ONAC023) of the NAC(NAM-ATAF-CUC-related) gene family was identified as the candidate gene of the tms5 gene. | YANG Qing-kai1,LIANG Chun-yang1,LI Jun1,JIN De-min1,AHUANG Wen2,DENG Qi-yun2,WANG Bin1(1.The State Key Laboratory of Plant Genomics,Institute of Genetics and Developmental Biology,Chinese Academy of Sciences,Beijing,100101 2. Hunan Hybrid Rice Research Center,Changsha 410125) | 2007 | 湖南农业大学学报(自然科学版)2007，33，S1： | 34 |
| 3 | Identification and mapping of quantitative trait loci controlling cold-tolerance of Chinese common wild rice (O. rufipogon Griff.) at booting to flowering stages显示文摘An advanced backcross population of rice was used to identify the quantitative trait locus (QTL) controlling the cold-tolerance at booting to flowering stages. The recipient, Guichao 2 (GC2), was a commercial Indica rice; the donor Dongxiang common wild rice, was an accession of common wild rice (DXCWR, Oryza rufipogon Griff.). Three QTLs for cold-tolerance were detected on chromosomes 1, 6 and 11. Two of them coming from DXCWR could enhance the cold-tolerance of the backcross progenies. Moreover, one sterility QTL that could reduce the seed set rate of the backcross progenies by 78% was mapped on chromosome 5. | LIU Fengxia, SUN Chuanqing, TAN Lubin, FU Yongcai, LI Dejun & WANG Xiangkun Department of Plant Genetics and Breeding, China Agricultural University, National Key Laboratory of Agrobiology, Key Laboratory of Crop Genetic Improvement and Genome of the Ministry of Agriculture, Beijing 100094, China | 2003 | Chinese Science Bulletin2003，48，19： | 29 |
| 4 | Next-generation sequencing technology:A technology review and future perspective显示文摘As one of the most powerful tools in biomedical research,DNA sequencing not only has been improving its productivity at an exponential growth rate but has also been evolving into a new layout of technological territories toward engineering and physical disciplines over the past three decades.In this technical review,we look into technical characteristics of the next-generation sequencers and provide insights into their future development and applications.We envisage that some of the emerging platforms are capable of supporting the USD1000 genome and USD100 genome goals if given a few years for technical maturation.We also suggest that scientists from China should play an active role in this campaign that will have a profound impact on both scientific research and societal healthcare systems. | ZHOU XiaoGuang1,REN LuFeng1,LI YunTao2,ZHANG Meng1,YU YuDe2 & YU Jun1 1 Key Laboratory of Genome Sciences and Information,Beijing Institute of Genomics,Chinese Academy of Sciences,Beijing 100029,China 2 Institute of Semiconductors,Chinese Academy of Sciences,Beijing 100083,China | 2010 | Science China(Life Sciences)2010，53，1： | 27 |
| 5 | Identification of quantitative trait loci associated with salt tolerance at seedling stage from Oryza rufipogon显示文摘土壤咸度是影响工厂生长和庄稼生产的主要不能生活的压力之一。在现在的学习,在米饭幼苗舞台的盐忍耐用 87 根基因渗入线(IL ) 被评估,它从在精英 indica 栽培变种 Teqing 和普通野米饭(Oryza rufipogon Griff ) 的就职之间的一个十字被导出。实质的变化为包括盐忍耐 20 的四个特点(圣) 被观察,相对的根干燥重量(RRW ) ,干燥重量(RSW ) 和相对总数弄干的相对射击重量(RTW ) 。圣断然显著地所有另外的三个特点地被相关。与这四个特点联系的 15 通常认为的量的特点 loci (QTL ) 的一个总数用单个点的分析被检测,它位于染色体 1, 2, 3, 6, 7, 9 和 10 与解释 phenotypic 变化的 8%26% 。O。在 13 QTL (86.7%) 的导出 rufipogon 的等位基因能在 Teqing 背景改进盐忍耐。影响 RRW, RSW 和 RTW 的四 QTL 簇在染色体上被发现 6, 7, 9 和 10 分别地。在这四 QTL 簇之中,包括三 QTL (qRRW10, qRSW10 和 qRTW10 ) 的主要的簇在染色体 10 的长手臂上在制造者 RM271 附近被发现,并且 O。分别地,当 phenotypic 变化由这解释为三个特点的三单个 QTL 从 19% ~ 26% 变化了时,在这三 loci 的导出 rufipogon 的等位基因与 22.7% , 17.3% 和 18.5% 的添加剂效果增加了 RRW, RSW 和 RTW。另外,几腌容忍的 IL 被选择并且能被用于识别并且利用有利的盐从普通野米饭的容忍的基因并且在盐使用容忍的米饭繁殖编程序。 | Lei Tian,Lubin Tan,Fengxia Liu,Hongwei Cai,Chuanqing Sun State Key Laboratory of Plant Physiology and Biochemistry,National Centre for Evaluation of Agricultural Wild Plant(Rice), Laboratory of Crop Heterosis and Utilization of Ministry of Education Beijing Key Laboratory of Crop Genetic Improvement and Genome of Ministry of Agriculture,Department of Plant Genetics and Breeding,China Agricultural University,Beijing 100193,China | 2011 | Journal of Genetics and Genomics2011，38，12： | 26 |
| 6 | Glutamine synthetase as an early marker for hepatocellular carcinoma based on proteomic analysis of resected smal hepatocel ular carcinomas显示文摘BACKGROUND:Hepatocellular carcinoma(HCC)is a highly malignant tumor with a poor prognosis.Because small HCCs possess most of the characteristics of early HCC,we investigated small HCCs to screen potential biomarkers for early diagnosis.METHODS:Proteins were extracted from 10 sets of paired tissue samples from HBV-infected small-HCC patients.The extracted proteins were well resolved by two-dimensional electrophoresis.These HCC-associated proteins were then identified by MALDI-TOF/TOF MS following image analysis.Western blotting and immunohistochemistry were used to assess glutamine synthetase(GS)and phenazine biosynthesislike domain-containing protein(PBLD)expression in liver tissue.Enzyme-linked immunosorbent assays in 152 serum samples(from 49 healthy donors,24 patients with liver cirrhosis,and 79 with HCC)were used to further assess the significance of GS clinically.RESULTS:Fifteen up-regulated and three down-regulated proteins were identified.Western blotting confirmed GS overexpression and decreased PBLD expression in liver tissue.Immunohistochemistry showed that GS was expressed in 70.0%(84/120)of HCCs and 35.8%(43/120)of nontumor tissues;PBLD was expressed in 74.2%(89/120) of nontumor tissues and 40.8%(49/120)of HCCs.The Chi-square test showed significant expression differences between HCCs and adjacent tissues.Consistent with this,serum GS levels in HCC patients were significantly higher than those in liver cirrhosis patients and healthy donors,while the latter two groups were also significantly different.In addition, a diagnostic cutoff value of 2.6 mg/ml was used for GS;it was elevated in 19(76.0%)of 25 HCC patients with AFP≤20 ng/ml and 47(88.7%)of 53 HCC patients with AFP≤200 ng/ml.CONCLUSION:GS and PBLD are abnormally expressed in most HCCs.GS may be a novel serum marker for early HCC, especially for those patients with low AFP levels(≤200 ng/ml). | Jiang Long,Zhen-Wei Lang,Hua-Guang Wang,Tai-Ling Wang,Bao-En Wang and Si-Qi Liu Liver Research Center,Beijing Friendship Hospital, Capital Medical University,Beijing 100050,China Department of Hepatology,Department of Pathology, Beijing Youan Hospital,Capital Medical University,Beijing 100069,China Department of Pharmaceutical Affairs,Beijing Chaoyang Hospital,Capital Medical University,Beijing 100020,China Department of Pathology,China-Japan Friendship Hospital,Beijing 100029,China Beijing Genomics Institute,Chinese Academy of Science,Beijing Airport Industrial Zone B-6,Shunyi,Beijing 101300,China | 2010 | Hepatobiliary & Pancreatic Diseases International2010，9，3： | 21 |
| 7 | Overexpression of a tobacco small G protein gene NtRop1 causes salt sensitivity and hydrogen peroxide production in transgenic plants显示文摘The small GTPases of Rop/Rho family is central regulators of important cellular processes in plants. Tobacco small G protein gene NtRop1 has been isolated; however, its roles in stress responses were unknown. In the present study, the genomic sequence of NtRop1 was cloned, which has seven exons and six introns, similar to the Rop gene structure from Arabidopsis. The NtRop1 gene was constitutively expressed in the different organs whereas the other six Rop genes from tobacco had differential expression patterns. The expression of the NtRop1 gene was moderately induced by methyl viologen, NaCl, and ACC treatments, but slightly inhibited by ABA treatment, with no significant induction by NAA treatment. The transgenic Arabidopsis plants overexpressing the NtRop1 showed increased salt sensitivity as can be seen from the reduced root growth and elevated relative electrolyte leakage. The hydrogen peroxide production was also promoted in the NtRop1-trangenic plants in comparison with wild type plants. These results imply that the NtRop1 may confer salt sensitivity through activation of H2O2 production during plant response to salt stress. | CAO YangRong1,2, LI ZhiGang1,2, CHEN Tao1,2, ZHANG ZhiGang1, ZHANG JinSong1 & CHEN ShouYi1 1 National Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China 2 Graduate School of Chinese Academy of Sciences, Beijing 100039, China | 2008 | Science China(Life Sciences)2008，51，5： | 18 |
| 8 | Intracellular compartmentation of CTP synthase in Drosophila显示文摘Compartmentation is essential for the localization of biological processes within a eukaryotic cell.ATP synthase localizes to organelles such as mitochondria and chloroplasts.By contrast,little is known about the subcellular distribution of CTP synthase,the critical enzyme in the production of CTP,a high-energy molecule similar to ATP.Here I describe the identification of a novel intracellular structure con-taining CTP synthase,termed the cytoophidium,in Drosophila cells.I find that cytoophidia are present in all major cell types in the ovary and exist in a wide range of tissues such as brain,gut,trachea,testis,accessory gland,salivary gland and lymph gland.In addition,I find CTP synthase-containing cytoophidia in other fruit fly species.The observation of compartmentation of CTP synthase now permits a broad range of questions to be addressed concerning not only the structure and function of cytoophidia but also the organization and regulation of CTP synthesis. | Ji-Long Liu Medical Research Council Functional Genomics Unit,Department of Physiology,Anatomy and Genetics,University of Oxford,Oxford,OX1 3QX,United Kingdom | 2010 | Journal of Genetics and Genomics2010，37，5： | 16 |
| 9 | Establishment of an artificial β-cell line expressing insulin under the control of doxycycline显示文摘AIM: Artificial β-cell lines may offer an abundant source of calls for the treatment of type Ⅰ diabetes, but insulin secretion in β-cells is tightly regulwted in physiological conditions The Tet-On system is a 'gene switch' system,which can induce gene expression by administration of tetracycline (Tet) derivatives such as doxcycline (D ox).Using this system, we established 293 cells to an artificial cell line secreting insulin in response to stimulation by Dox.METHODS: The mutated proinsulin cDNA was obtained fromplasmid pcDNA3.1/C-mlNS by the polymerase chain reaction(PCR), and was inserted downstream from the promoter onthe expression vector pTRE2, to construct a recombinedexpression vector pTRE2mlNS. The promoter on pTRE2consists of the tetracycline-response element and the CMVminimal promoter and is thus activated by the reversetetracycline-controlled transactivator (rtTA) when Dox isadministrated. pTRE2mlNS and plasmid pTK-Hyg encodinghygromycin were co-transfected in the tet293 cells, whichexpress rtTA stably. Following hygromycin screening, thesurvived cells expressing insulin were selected andenriched. Dox was used to control the expression of insulinin these cells. At the levels of mRNA and protein, theregulating effect of Dox in culture medium on the expressionof proinsulin gene was estimated respectively with Northernblot, RT-PCR, and radioimmunoassay.RESULTS: From the 28 hygromycin-resistant cell strains, weselected one cell strain (tet293/Ins6) secreting insulin notonly automatically, but in response to stimulation by Dox.The amount on insulin secretion was dependent on the Doxdose (0,10,100,200,400,800 and 1000 μg@ L-1 ), the level ofinsulin secreted by the cells treated with Dox ( 1000μg. L-1 )wes 241.0 pU@d1 @cell-1 , which was 25-fold that of 9.7 pU@d1@ cell-1 without Dox treatment. Northern blot analyses andRT-PCR further confinned that the transcription of insulingene had already been up-regulated after exposing tet293/Ins6 cells to Dox for 15 minutes, and was also induced in adose-depeodent manner. However, the concentration ofinsulin in the media did not increase significantly until 5hours following the addition of Dox.CONCLUSION: Human proinsulin gene was transfectedsuccessfully and expressed efficiently in 293 cells, and theexpression was modulated by tetracycline and itsderivatives, improving the accuracy, safety, and reliabilityof gene therapy, suggesting that conditional establishmentof artificial β-cells may be a useful approach to developcellular therapy for diabetes mellitus. | Xin-Yu Qin Kun-Tang Shen,Department of General Surgery,Zhongshan Hospital,Fudan University,Shanghai 200032,China Xin Zhang Zhi-Hong Cheng Xiang-Ru Xu Ze-Guang Han,Functional Genomics Division,Chinese National Human Genome Center At Shanghai,Shanghai 201203,China | 2002 | World Journal of Gastroenterology2002，8，2： | 15 |
| 10 | Perspectives of DNA microarray and next-generation DNA sequencing technologies显示文摘DNA microarray and next-generation DNA sequencing technologies are important tools for high-throughput genome research,in revealing both the structural and functional characteristics of genomes.In the past decade the DNA microarray technologies have been widely applied in the studies of functional genomics,systems biology and pharmacogenomics.The next-generation DNA sequencing method was first introduced by the 454 Company in 2003,immediately followed by the establishment of the Solexa and Solid techniques by other biotech companies.Though it has not been long since the first emergence of this technology,with the fast and impressive improvement,the application of this technology has extended to almost all fields of genomics research,as a rival challenging the existing DNA microarray technology.This paper briefly reviews the working principles of these two technologies as well as their application and perspectives in genome research. | TENG XiaoKun1 & XIAO HuaSheng1,2 1 National Engineering Center for Biochip at Shanghai,Shanghai 201203,China 2 Shanghai-MOST Key Laboratory of Health and Disease Genomics,Chinese National Human Genome Center,Shanghai 201203,China | 2009 | Science China(Life Sciences)2009，52，1： | 15 |
| 11 | The study of neighboring nucleotide composition and transition/transversion bias显示文摘Base substitution is one of the raw fuels that produce genetic variation and drive evolu-tion. Recent studies have shown that the genome components affect mutation patterns to some extent. In order to infer the correlation between the Transition/Transversion ratio (Ts/Tv) and the number of immediately adjacent A&T nucleotides, we investigated 3611007 Oryza sativa SNPs (including 45462 coding SNPs, and 242811 intronic SNPs) and 32019 Arabidopsis SNPs. The results show that Ts/Tv is negatively correlated with the number of immediately adjacent A&T in O. sativa and Arabidopsis. We further calculated AT2 (the number of SNPs whose immediately adjacent nucleotides are either A or T) and AT0 (the number of SNPs whose immediately adjacent nucleotides are either C or G) for all 6 types of SNPs. C/G SNP of O. sativa and Arabidopsis has the highest AT2/AT0, which denotes C/G SNP may be influenced by the adjacent A&T nucleotides mostly. For SNPs in O. sativa, the neighboring effect of A&T nucleotides is limited to 2 nucleotides on both sides; for SNPs in Arabidop-sis, the effect extends no more than 4 nucleotides on both sides. | ZHAO Hui1,3*, LI Qizhai1,2,3*, LI Jun1, ZENG Changqing1, HU Songnian1 & YU Jun1 1. Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100030, China 2. Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100080, China 3. Graduate University of Chinese Academy of Sciences, Beijing 100039, China | 2006 | Science China(Life Sciences)2006，49，4： | 12 |
| 12 | A seed-specific AP2-domain transcription factor from soybean plays a certain role in regulation of seed ger-mination显示文摘Plant seed development and germination are under strict temporal and spatial regulation, and tran-scription factors play important roles in this regulation. In the present study we identified an EST ex-pressed specifically in the developing soybean seeds. The full length of the gene was obtained through further RACE analysis and the gene was named GmSGR. Sequence analysis revealed that this gene belonged to the AP2/ERF transcription factor family. Its AP2 domain had the highest similarity with that of the A-3 member AtABI4 of DREB subgroup in the AP2/ERF family in Arabidopsis. GmSGR did not exhibit transcriptional activation activity in the yeast assay system. GmSGR was overexpressed in Arabidopsis and the germination rates of the transgenic seeds were significantly higher than that of the wild type seeds under higher concentrations of ABA and glucose respectively. However, the germina-tion rates of the transgenic seeds were lower than that of control under salt stress. The expression of AtEm6 and AtRD29B was higher in the seedlings of the transgenic plants than that in the wild-type seedlings. These results suggest that GmSGR may confer reduced ABA sensitivity and enhanced salt sensitivity to the transgenic seeds through regulating the expression of AtEm6 and AtRD29B genes. | WANG ChunMei, WANG HuiWen, ZHANG JinSong & CHEN ShouYi National Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Bei-jing 100101, China | 2008 | Science China(Life Sciences)2008，51，4： | 11 |
| 13 | Genome size and sequence composition of moso bamboo: A comparative study显示文摘Moso bamboo (Phyllostachys pubescens) is one of the world's most important bamboo species. It has the largest area of all planted bamboo―over two-thirds of the total bamboo forest area―and the highest economic value in China. Moso bamboo is a tetraploid (4x=48) and a special member of the grasses family. Although several genomes have been sequenced or are being sequenced in the grasses family, we know little about the genome of the bambusoids (bamboos). In this study, the moso bamboo genome size was estimated to be about 2034 Mb by flow cytometry (FCM), using maize (cv. B73) and rice (cv. Nipponbare) as internal references. The rice genome has been sequenced and the maize genome is being sequenced. We found that the size of the moso bamboo genome was similar to that of maize but significantly larger than that of rice. To determine whether the bamboo genome had a high proportion of repeat elements, similar to that of the maize genome, approximately 1000 genome survey sequences (GSS) were generated. Sequence analysis showed that the proportion of repeat elements was 23.3% for the bamboo genome, which is significantly lower than that of the maize ge-nome (65.7%). The bamboo repeat elements were mainly Gypsy/DIRS1 and Ty1/Copia LTR retrotrans-posons (14.7%), with a few DNA transposons. However, more genomic sequences are needed to con-firm the above results due to several factors, such as the limitation of our GSS data. This study is the first to investigate sequence composition of the bamboo genome. Our results are valuable for future genome research of moso and other bamboos. | GUI YiJie1, WANG Sheng1, QUAN LiYan1, ZHOU ChangPing2, LONG ShiBao2, ZHENG HuaJun3, JIN Liang1, ZHANG XianYin 1, MA NaiXun 4 & FAN LongJiang1 1 Institute of Crop Science/Institute of Bioinformatics, Zhejiang University, Hangzhou 310029, China 2 Zhejiang Anji Bamboo Exposition Garden, Anji 313300, China 3 Chinese National Human Genome Center at Shanghai, Shanghai 201203, China 4 The Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang 311400, China | 2007 | Science China(Life Sciences)2007，50，5： | 10 |
| 14 | Genetic regulation by non-coding RNAs显示文摘Large scale cDNA sequencing and genome tiling array studies have shown that around 50% of genomic DNA in humans is transcribed, of which 2% is translated into proteins and the remaining 98% is non-coding RNAs (ncRNAs). There is mounting evidence that these ncRNAs play critical roles in regulating DNA structure, RNA expression, protein translation and protein functions through multiple genetic mechanisms, and thus affect normal development of organisms at all levels. Today, we know very little about the regulatory mechanisms and functions of these ncRNAs, which is clearly essential knowledge for understanding the secret of life. To promote this emerging research subject of critical importance, in this paper we review (1) ncRNAs' past and present, (2) regulatory mechanisms and their functions, (3) experimental strategies for identifying novel ncRNAs, (4) experimental strategies for investigating their functions, and (5) methodologies and examples of the application of ncRNAs. | QI Liwang, LI Xinmin, ZHANG Shougong & AN Daochang Laboratory of Cell Biology, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China Functional Genomics Facility, Division of Biological Science, University of Chicago, Chicago 60637, USA China National Center for Biotechnology and Development, Ministry of Science and Technology, Beijing 100081, China | 2006 | Science China(Life Sciences)2006，49，3： | 10 |
| 15 | Current progress in epigenetic research for hepato-carcinomagenesis显示文摘Hepatocellular carcinoma is the main type of primary liver cancer,and also one of the most malignant tumors.At present,the pathogenesis mechanisms of liver cancer are not entirely clear.It has been shown that inactivation of tumor suppressor genes and activation of oncogenes play a significant role in carcinogenesis,caused by the genetic and epigenetic aberrance.In the past,people generally thought that genetic mutation is a key event of tumor pathogenesis,and somatic mutation of tumor suppressor genes is in particular closely associated with oncogenesis.With deeper understanding of tumors in recent years,increasing evidence has shown that epigenetic silencing of those genes,as a result of aberrant hypermethylation of CpG islands in promoters and histone modification,is essential to carcinogenesis and metastasis.The term epigenetics refers to heritable changes in gene expression caused by regulation mechanisms,other than changes in the underlying DNA sequence.Specific epigenetic processes include DNA methylation,genome imprinting,chromotin remodeling,histone modification and microRNA regulations.This paper reviews recent epigenetics research progress in the hepatocellular carcinoma study,and tries to depict the relationships between hepatocellular carcinomagenesis and DNA methylation as well as microRNA regulation. | HUANG Jian National Human Genome Research Center at Shanghai-Ministry of Science and Technology to build a healthy and disease Ge-nomics Laboratory,Shanghai 201203,China | 2009 | Science China(Life Sciences)2009，52，1： | 9 |
| 16 | The Epitope Study on the SARS-CoV Nucleocapsid Protein显示文摘The nucleocapsid protein (N protein) has been found to be an antigenic protein in a number of coronaviruses. Whether the N protein in severe acute respiratory syndrome-associated coronavirus (SARS-CoV) is antigenic remains to be elucidated. Using Western blot and Enzyme-linked Immunosorbent Assay (ELISA),the recombinant N proteins and the synthesized peptides derived from the N protein were screened in sera from SARS patients. All patient sera in this study displayed strong positive immunoreactivities against the recombinant N proteins,whereas normal sera gave negative immunoresponses to these proteins, indicating that the N protein of SARS-CoV is an antigenic protein. Furthermore, the epitope sites in the N protein were determined by competition experiments, in which the recombinant proteins or the synthesized peptides competed against the SARS-CoV proteins to bind to the antibodies raised in SARS sera. One epitope site located at the C-terminus was confirmed as the most antigenic region in this protein. A detailed screening of peptide with ELISA demonstrated that the amino sequence from Codons 371 to 407 was the epitope site at the C-terminus of the N protein. Understanding of the epitope sites could be very significant for developing an effective diagnostic approach to SARS. | Shuting Li, Liang Lin, Hao Wang, Jianning Yin, Yan Ren, Zhe Zhao, Jie Wen, Cuiqi Zhou, Xumin Zhang, Xiaolei Li, Jingqiang Wang, Zhengfeng Zhou, Jinxiu Liu, Jianmin Shao, Tingting Lei, Jianqiu Fang, Ningzhi Xu, and Siqi LiuBeijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China & Beijing Proteomics Institute, Beijing 101300, China | 2003 | Genomics, Proteomics & Bioinformatics2003，1，3： | 9 |
| 17 | Analysis of ESTs and gene expression patterns of the posterior silkgland in the fifth instar larvae of silkworm, Bombyx mori L.显示文摘The fibroin gene expression pattern and regulation of the posterior silkgland were studied by means of expressed sequence tags (ESTs) using the first and fifth day larvae of the fifth instar of silkworm, Bombyx mori L (strain: C 108). The results showed that there were 911 repetitive ESTs and 1950 single sequences (Singlets) among total 2861 consentient sequences, which were spliced. 1335 sequences were identified and the other 1526 were unknown. 5560 sequences (55.89%) in the posterior silkgland cell of the silkworm were new ESTs without homology with EST data published by Mita et al. The number of repetitive ESTs and single sequences from the first day larvae of the fifth instar was double more than that of the fifth day of the same instar in the silkworms. The unigenes which were more than 50 in repetitive EST size (contig size) came to only about 0.5% in total consentient sequences. There were significant differences between gene expression frequencies, and expressed genes were related to fibroin synthesis and its secretion and fibroin composition. Comparing the fifth day with the first day of the fifth instar, the genes-expressed quantity of fibroin heavy-chain gene was 18 fold higher, fibroin light-chain gene 9 fold and fibroin P52 gene 8 fold. 508 genes functioned for cellular component and 315 for enzyme after function tracing. These results implied that the gene expression of the first day was mainly for preparation for fibroin synthesis except for the growth of silkgland cells, and the gene expression of the fifth day of the fifth instar was mainly for synthesizing and excreting fibroin. Because the ratio of heavy chain, light chain and p25 of fibroin was not 6:6:1 as theoretically expected, or its special H-chain structure, the H-chain gene was not easy to detect through EST technique. Most of genes among total 2861 consentient sequences functioned for fibroin synthesis and secretion. This suggested the fibroin synthesis and secretion procedure of the posterior silkgland was more complex than the knowledge we have. | ZHONG Boxiong, YU Yingpo, XU Yusong, YU Hong, LU Xingmeng, MIAO Yungen, YANG Jun, XU Hao, HU Songnian & LOU Chengfu College of Animal Sciences, Zhejiang University, Hangzhou 310029, China Hangzhou Huada Gene Research and Development Center, Southern Base of Genomic Information, Chinese Academy of Sciences, Hangzhou 310007, China | 2005 | Science China(Life Sciences)2005，48，1： | 8 |
| 18 | Genomic research for important pathogenic bacteria in China显示文摘Rapid accumulation of bacterial genomic data offered an unprecedented opportunity to understand bacterial biology from a holistic view of point.We can thus closely look at the way in which a pathogen is evolved,and these data has been applied to molecular epidemiology and microbial forensics,and screening of novel diagnostic,vaccine and drug targets.The newly developed high-throughput low-cost sequencing technologies,such as 454,Solexa and SOLiD,will promote the acquisition and application of genomic data in new research areas that we dared not imagine previously,such as the metagenomics of human gastric-intestinal tract,for better and comprehensive understanding of human health and disease. | YANG RuiFu1,GUO XiaoKui2,YANG Jian3,JIANG YongQiang1,PANG Bo4,CHEN Chen5,YAO YuFeng2,QIN JinHong2 & LI QingTian2 1 Laboratory of Analytical Microbiology,State Key Laboratory of Pathogen and Biosecurity,Beijing Institute of Microbiology and Epidemiology,Beijing 100071,China 2 Department of Medical Microbiology and Parasitology,Institutes of Medical Sciences,Shanghai Jiao Tong University School of Medicine,Shanghai 200025,China 3 State Key Laboratory for Molecular Virology and Genetic engineering,Institute of Pathogen Biology,Chinese Academy of Medical Sciences,Beijing 100176,China 4 State Key Laboratory for Infectious Disease Prevention and Control,Institute for Communicable Disease Control and Prevention,Chinese Center for Disease Control and Prevention,Beijing 102206,China 5 Beijing Genomics Institute at Shenzhen,Shenzhen 518083,China | 2009 | Science China(Life Sciences)2009，52，1： | 8 |
| 19 | Phylogenomic Mining of the Mints Reveals Multiple Mechanisms Contributing to the Evolution of Chemical Diversity in Lamiaceae显示文摘化学复杂性的进化是植物多样化的一位主要司机,与用作关键革新的新奇混合物。充满种类的薄荷家庭(Lamiaceae ) 生产在自然充当引诱剂和防卫分子的混合物的一个庞大的变化并且被人广泛地用作风味添加剂,芬芳,和 anti-herbivory 代理人。阐明如此的差异由演变的机制,我们从 48 Lamiaceae 种类和四个外集团把叶 transcriptome 数据与柔韧的发展史和为先锋分享并且竞争的三个 terpenoid 班(monoterpenes, sesquiterpenes,和 iridoids ) 的化学分析相结合。我们的综合 chemical-genomic-phylogenetic 途径揭示了那:(1 ) 基因家庭扩大而非萜烯 synthases 的增加的酶乱交被相关与单音 -- 并且 sesquiterpene 差异;(2 ) 在 iridoid biosynthetic 小径以内的核心基因的微分表示与 iridoid 存在 / 缺席被联系;(3 ) 通常, iridoids 的生产和正规 monoterpenes 看起来相反地被相关;并且(4 ) iridoid 生合成显著地与香叶醇的表示被联系 synthase,转移新陈代谢的流动离开正规 monoterpenes,为普通先锋建议那场比赛能是在专业化新陈代谢的一个中央控制点。这些结果建议多重机制在这个经济地重要的家庭贡献了 chemodiversity 的进化。 | Mint Evolutionary Genomics Consortium | 2018 | Molecular Plant2018，11，8： | 8 |
| 20 | Recent progress in 8igenomic research of liver cancer显示文摘Along the course of occurrence and development of liver cancer,the corresponding somatic cells accumulate some important genetic variations.These variations may be divided into two categories.For the genetic changes closely related to etiology of liver cancer,the well-known cases include insertion and integration of the hepatitis B virus(HBV) DNA after infection,and mutations at site 249 of the tumor suppressor gene p53 induced by exposure to aflatoxin B1.The secondary genetic changes include amplification and deletion of certain chromosome regions,mutations in p53 at the sites other than 249,as well as the mutational activation of the Wnt/β-catenin signal pathway.The tumor cells with these genetic variations may gradually become the dominant clones under evolutionary selection.Besides,identification of genetic susceptible against risk of liver malignancy is also an important aspect of research in this field. | HAN ZeGuang Shanghai-MOST Key Laboratory for Disease and Health Genomics,Chinese National Human Genome Center at Shanghai,Shanghai 201203,China | 2009 | Science China(Life Sciences)2009，52，1： | 7 |
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