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E’de Qin,
Qingyu Zhu,
Man Yu,
Baochang Fan,
Guohui Chang,
Bingyin Si,
Bao’an Yang,
Wenming Peng,
Tao Jiang,
Bohua Liu, [......],
Zongzhong Tong,
Feng Zhang,
Songgang Li,
Bin Liu,
Siqi Liu,
Wei Dong,
Jun Wang,
Gane K-S Wong,
Jun Yu,
Huanming Yang
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ABSTRACT: 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 be involved in the
immunoreactions between the virus and its host. Two amino acid changes have been detected in the M protein, which could be
related to viral envelope formation. Phylogenetic analysis suggests the possibility of non-human origin of the SARS-associated
viruses but provides no evidence 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 other possible SARS-related pathogen(s).
KeywordsSevere Acute Respiratory Syndrome (SARS)-coronavirus-genome-phylogeny
Chinese Science Bulletin 04/2012; 48(10):941-948. · 1.32 Impact Factor
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ABSTRACT: The published data on the curative effects of comparing the once weekly paclitaxel-based chemotherapies (W-paclitaxel) with the standard every 3 weeks paclitaxel-based chemotherapies (S-paclitaxel) in the first-line treatment of advanced non-small-cell lung cancer (NSCLC) were still controversial. To derive a more precise estimation of the two regimens, a meta-analysis was performed.
Medical databases and conference proceedings were searched for randomized controlled trials which compared W-paclitaxel with S-paclitaxel in patients with first-line treatment of advanced NSCLC. The following keywords were used: "paclitaxel", "weekly schedule" and "non-small cell lung cancer". Reference lists of original articles and review articles were also examined. The published languages and years were not limited. Endpoints were overall survival (OS), progression-free survival (PFS), overall response rate (ORR) and adverse events. Statistical tests for heterogeneity were one-sided; statistical tests for effect estimates were two-sided.
Five eligible trials involved 940 patients were identified. They were all published as full-text articles. The intention to treatment (ITT) analysis demonstrated that the ORR of W-paclitaxel regimens patients was 30.89% (143/463), whereas the ORR of S-paclitaxel regimens patients was 27.09% (123/454). The overall pooled relative ratio (RR) for ORR was 1.24 (95% confidence intervals (CI)=0.93-1.66; P=0.14) when W-paclitaxel regimens patients were compared with S-paclitaxel regimens patients. Although the patients with W-paclitaxel regimens had an similar OS and PFS in comparison with S-paclitaxel regimens (median OS was 9.8 versus 10.7 months; hazard ratio (HR)=1.00; 95%CI=0.86-1.17; P=0.99; median PFS was 5.2 versus 4.7 months; HR=0.90; 95%CI=0.79-1.03; P=0.13, respectively), the W-paclitaxel regimens led to significantly less frequent adverse events of hematological toxicities and nonhematological toxicities.
These results suggest that the W-paclitaxel is not superior than S-paclitaxel regimens. The paclitaxel-based chemotherapies given by every 3 weeks are still standard regimens. For patients, especially for the elder or the people with poor conditions who cannot tolerate the standard regimen, the weekly schedule can be considered.
Lung cancer (Amsterdam, Netherlands) 01/2012; 76(3):380-6. · 3.14 Impact Factor
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Jun Yu,
Jun Wang,
Wei Lin,
Songgang Li,
Heng Li,
Jun Zhou,
Peixiang Ni,
Wei Dong,
Songnian Hu,
Changqing Zeng, [......],
Bailin Hao,
Siqi Liu,
Wen Wang,
Longping Yuan,
Mengliang Cao,
Jason McDermott,
Ram Samudrala,
Jian Wang,
Gane Ka-Shu Wong,
Huanming Yang
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ABSTRACT: We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000-40,000. Only 2%-3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family.
PLoS Biology 03/2005; 3(2):e38. · 11.45 Impact Factor
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Gane Ka-Shu Wong,
Bin Liu,
Jun Wang,
Yong Zhang,
Xu Yang,
Zengjin Zhang,
Qingshun Meng,
Jun Zhou,
Dawei Li,
Jingjing Zhang, [......],
Caleb Webber,
Chris P Ponting,
Ian M Overton,
Paul E Boardman,
Haizhou Tang,
Simon J Hubbard,
Stuart A Wilson,
Jun Yu,
Jian Wang,
Huanming Yang
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ABSTRACT: We describe a genetic variation map for the chicken genome containing 2.8 million single-nucleotide polymorphisms (SNPs). This map is based on a comparison of the sequences of three domestic chicken breeds (a broiler, a layer and a Chinese silkie) with that of their wild ancestor, red jungle fowl. Subsequent experiments indicate that at least 90% of the variant sites are true SNPs, and at least 70% are common SNPs that segregate in many domestic breeds. Mean nucleotide diversity is about five SNPs per kilobase for almost every possible comparison between red jungle fowl and domestic lines, between two different domestic lines, and within domestic lines--in contrast to the notion that domestic animals are highly inbred relative to their wild ancestors. In fact, most of the SNPs originated before domestication, and there is little evidence of selective sweeps for adaptive alleles on length scales greater than 100 kilobases.
Nature 01/2005; 432(7018):717-22. · 36.28 Impact Factor
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Qingyou Xia,
Zeyang Zhou,
Cheng Lu,
Daojun Cheng,
Fangyin Dai,
Bin Li,
Ping Zhao,
Xingfu Zha,
Tingcai Cheng,
Chunli Chai, [......],
Jianguo Zhang,
Yong Zhang,
Hongkun Zheng,
Bingyu Mao,
Wen Wang,
Chen Ye,
Songgang Li,
Jian Wang,
Gane Ka-Shu Wong,
Huanming Yang
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ABSTRACT: We report a draft sequence for the genome of the domesticated silkworm (Bombyx mori), covering 90.9% of all known silkworm genes. Our estimated gene count is 18,510, which exceeds the 13,379 genes reported for Drosophila melanogaster. Comparative analyses to fruitfly, mosquito, spider, and butterfly reveal both similarities and differences in gene content.
Science 01/2005; 306(5703):1937-40. · 31.20 Impact Factor
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ABSTRACT: A large amount of data have been accumulated from the agro-ecosystem nutrient cycling research during recent years. It is necessary to develop a data management system for global decision-making and for preserving from loss. This paper outlined a conceptual model design based on Entity-Relation (E-R) model, presented the model constructing process from user query, and demonstrated a database system using a given model. The results showed that the database implemented from the designed model could provide the function of querying in terms of time, location and theme, and management of various types of data, such as field observation, theme map and research report, and fast extracting and analysis data with spatio-temporal characteristic.
Ying yong sheng tai xue bao = The journal of applied ecology / Zhongguo sheng tai xue xue hui, Zhongguo ke xue yuan Shenyang ying yong sheng tai yan jiu suo zhu ban 12/2003; 14(11):1873-8.
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Shengli Bi,
E'de Qin,
Zuyuan Xu,
Wei Li,
Jing Wang,
Yongwu Hu,
Yong Liu,
Shumin Duan,
Jianfei Hu,
Yujun Han, [......],
Ruifu Yang,
Bin Liu,
Siqi Liu,
Songgang Li,
Jun Wang,
Jian Wang,
Wuchun Cao,
Jun Yu,
Xiaoping Dong,
Huanming Yang
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ABSTRACT: Beijing has been one of the epicenters attacked most severely by the SARS-CoV (severe acute respiratory syndrome-associated coronavirus) since the first patient was diagnosed in one of the city's hospitals. We now report complete genome sequences of the BJ Group, including four isolates (Isolates BJ01, BJ02, BJ03, and BJ04) of the SARS-CoV. It is remarkable that all members of the BJ Group share a common haplotype, consisting of seven loci that differentiate the group from other isolates published to date. Among 42 substitutions uniquely identified from the BJ group, 32 are non-synonymous changes at the amino acid level. Rooted phylogenetic trees, proposed on the basis of haplotypes and other sequence variations of SARS-CoV isolates from Canada, USA, Singapore, and China, gave rise to different paradigms but positioned the BJ Group, together with the newly discovered GD01 (GD-Ins29) in the same clade, followed by the H-U Group (from Hong Kong to USA) and the H-T Group (from Hong Kong to Toronto), leaving the SP Group (Singapore) more distant. This result appears to suggest a possible transmission path from Guangdong to Beijing/Hong Kong, then to other countries and regions.
Genomics Proteomics & Bioinformatics 09/2003; 1(3):180-92.
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Yongwu Hu,
Jie Wen,
Lin Tang,
Haijun Zhang,
Xiaowei Zhang,
Yan Li,
Jing Wang,
Yujun Han,
Guoqing Li, Jianping Shi,
Xiangjun Tian,
Feng Jiang,
Xiaoqian Zhao,
Jun Wang,
Siqi Liu,
Changqing Zeng,
Jian Wang,
Huanming Yang
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ABSTRACT: We studied structural and immunological properties of the SARS-CoV M (membrane) protein, based on comparative analyses of sequence features, phylogenetic investigation, and experimental results. The M protein is predicted to contain a triple-spanning transmembrane (TM) region, a single N-glycosylation site near its N-terminus that is in the exterior of the virion, and a long C-terminal region in the interior. The M protein harbors a higher substitution rate (0.6% correlated to its size) among viral open reading frames (ORFs) from published data. The four substitutions detected in the M protein, which cause non-synonymous changes, can be classified into three types. One of them results in changes of pI (isoelectric point) and charge, affecting antigenicity. The second changes hydrophobicity of the TM region, and the third one relates to hydrophilicity of the interior structure. Phylogenetic tree building based on the variations of the M protein appears to support the non-human origin of SARS-CoV. To investigate its immunogenicity, we synthesized eight oligopeptides covering 69.2% of the entire ORF and screened them by using ELISA (enzyme-linked immunosorbent assay) with sera from SARS patients. The results confirmed our predictions on antigenic sites.
Genomics Proteomics & Bioinformatics 06/2003; 1(2):118-30.
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E'de Qin,
Xionglei He,
Wei Tian,
Yong Liu,
Wei Li,
Jie Wen,
Jingqiang Wang,
Baochang Fan,
Qingfa Wu,
Guohui Chang, [......],
Songgang Li,
Xuehai Tan,
Siqi Liu,
Wei Dong,
Jun Wang,
Gane Ka-Shu Wong,
Jun Yu,
Jian Wang,
Qingyu Zhu,
Huanming Yang
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ABSTRACT: We report a complete genomic sequence of rare isolates (minor genotype) of the SARS-CoV from SARS patients in Guangdong, China, where the first few cases emerged. The most striking discovery from the isolate is an extra 29-nucleotide sequence located at the nucleotide positions between 27,863 and 27,864 (referred to the complete sequence of BJ01) within an overlapped region composed of BGI-PUP5 (BGI-postulated uncharacterized protein 5) and BGI-PUP6 upstream of the N (nucleocapsid) protein. The discovery of this minor genotype, GD-Ins29, suggests a significant genetic event and differentiates it from the previously reported genotype, the dominant form among all sequenced SARS-CoV isolates. A 17-nt segment of this extra sequence is identical to a segment of the same size in two human mRNA sequences that may interfere with viral replication and transcription in the cytosol of the infected cells. It provides a new avenue for the exploration of the virus-host interaction in viral evolution, host pathogenesis, and vaccine development.
Genomics Proteomics & Bioinformatics 06/2003; 1(2):101-7.
