Article Online

Articles Online (Volume 1, Issue 2)

Editoral

Science and Technology Is Not Simply Equal to Sci-Tech

Xingmin Li

The terms "science" (Hanyu Pinyin: Kēxué) and"technology" (Jìshù), in western languages, are usu-ally used separately with different meanings or to-gether as "science and technology". However, theyare often mentioned as "Kēxué Jìshù", or even abbre-viated as "sci-tech (Kējì)" in China (It is used in asimilar way in Japan).
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Page 87-89

Review Article

Plant MITEs: Useful Tools for Plant Genetics and Genomics

Ying Feng

MITEs (Miniature inverted-repeat transposable elements) are reminiscence of non-autonomous DNA (class Ⅱ) elements, which are distinguished from other transpos-able elements by their small size, short terminal inverted repeats (TIRs), high copynumbers, genic preference, and DNA sequence identity among family members. Al-though MITEs were first discovered in plants and still actively reshaping genomes,they have been isolated from a wide range of eukaryotic organisms. MITEs canbe divided into Tourist-like, Stowaway-like, and pogo-like groups, according tosimilarities of their TIRs and TSDs (target site duplications). In despite of sev-eral models to explain the origin and amplification of MITEs, their mechanisms oftransposition and accumulation in eukaryotic genomes remain poorly understoodowing to insufficient experimental data. The unique properties of MITEs have beenexploited as useful genetic tools for plant genome analysis. Utilization of MITEsas effective and informative genomic markers and potential application of MITEsin plants systematic, phylogenetic, and genetic studies are discussed.
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Page 90-100

Research Article

A Genome Sequence of Novel SARS-CoV Isolates: the Genotype,GD-Ins29, Leads to a Hypothesis of Viral Transmission in South China

E'de Qin,Xionglei He,Wei Tian,Yong Liu,Wei Li,Jie Wen,Jingqiang Wang,Baochang Fan,Qingfa Wu,Guohui Chang,Wuchun Cao,Zuyuan Xu,Ruifu Yang,Jing Wang,Man Yu,Yan Li,Jing Xu,Bingyin Si,Yongwu Hu,Wenming Peng,Lin Tang,Tao Jiang,Jianping Shi,Jia Ji,Yu Zhang,Jia Ye,Cui'e Wang,Yujun Han,Jun Zhou,Yajun Deng,Xiaoyu Li,Jianfei Hu,Caiping Wang,Chunxia Yan,Qingrun Zhang,Jingyue Bao,Guoqing Li,Weijun Chen,Lin Fang,Changfeng Li,Meng Lei,Dawei Li,Wei Tong,Xiangjun Tian,Jin Wang,Bo Zhang,Haiqing Zhang,Yilin Zhang,Hui Zhao,Xiaowei Zhang,Shuangli Li,Xiaojie Cheng,Xiuqing Zhang,Bin Liu,Changqing Zeng,Songgang Li,Xuehai Tan,Siqi Liu,Wei Dong,Jun Wang,Gane Ka-Shu Wong,Jun Yu,Jian Wang,Qingyu Zhu,Huan-Ming Yang

We report a complete genomic sequence of rare isolates (minor genotype) of theSARS-CoV from SARS patients in Guangdong, China, where the first few casesemerged. The most striking discovery from the isolate is an extra 29-nucleotidesequence located at the nucleotide positions between 27,863 and 27,864 (referredto the complete sequence of B J01) within an overlapped region composed of BGI-PUP5 (BGI-postulated uncharacterized protein 5) and BGI-PUP6 upstream ofthe N (nucleocapsid) protein. The discovery of this minor genotype, GD-Ins29,suggests a significant genetic event and differentiates it from the previously re-ported genotype, the dominant form among all sequenced SARS-CoV isolates. A17-nt segment of this extra sequence is identical to a segment of the same size intwo human mRNA sequences that may interfere with viral genome replication andtranscription in the cytosol of the infected cells. It provides a new avenue for theexploration of the virus-host interaction in viral evolution, host pathogenesis, andvaccine development.
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Page 101-107

Research Article

The Structural Characterization and Antigenicity of the S Protein of SARS-CoV

Jingxiang Li,Chunqing Luo,Yajun Deng,Yujun Han,Lin Tang,Jing Wang,Jia Ji,Jia Ye,Fanbo Jiang,Zhao Xu,Wei Tong,Wei Wei,Qingrun Zhang,Shengbin Li,Wei Li,Hongyan Li,Yudong Li,Wei Dong,Jian Wang,Shengli Bi,Huan-Ming Yang

The corona-like spikes or peplomers on the surface of the virion under electronicmicroscope are the most striking features of coronaviruses. The S (spike) proteinis the largest structural protein, with 1,255 amino acids, in the viral genome. Itsstructure can be divided into three regions: a long N-terminal region in the exte-rior, a characteristic transmembrane (TM) region, and a short C-terminus in theinterior of a virion. We detected fifteen substitutions of nucleotides by comparisonswith the seventeen published SARS-CoV genome sequences, eight (53.3%) of whichare non-synonymous mutations leading to amino acid alternations with predictedphysiochemical changes. The possible antigenic determinants of the S protein arepredicted, and the result is confirmed by ELISA (enzyme-linked immunosorbentassay) with synthesized peptides. Another profound finding is that three disulfidebonds are defined at the C-terminus with the N-terminus of the E (envelope) pro-tein, based on the typical sequence and positions, thus establishing the structuralconnection with these two important structural proteins, if confirmed. Phyloge-netic analysis reveals several conserved regions that might be potent drug targets.
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Page 108-117

Research Article

The M Protein of SARS-CoV: Basic Structural and Immunological Properties

Yongwu Hu,Jie Wen,Lin Tang,Haijun Zhang,Xiaowei Zhang,Yan Li,Jing Wang,Yujun Han,Guoqiang Li,Jianping Shi,Xiangjun Tian,Feng Jiang,Xiaoqian Zhao,Jun Wang,Siqi Liu,Changqing Zeng,Jian Wang,Huan-Ming Yang

We studied structural and immunological properties of the SARS-CoV M (mem-brane) protein, based on comparative analyses of sequence features, phylogeneticinvestigation, and experimental results. The M protein is predicted to contain atriple-spanning transmembrane (TM) region, a single N-glycosylation site near itsN-terminus that is in the exterior of the virion, and a long C-terminal region inthe interior. The M protein harbors a higher substitution rate (0.6% correlated toits size) among viral open reading frames (ORFs) from published data. The foursubstitutions detected in the M protein, which cause non-synonymous changes,can be classified into three types. One of them results in changes of pI (isoelectricpoint) and charge, affecting antigenicity. The second changes hydrophobicity of theTM region, and the third one relates to hydrophilicity of the interior structure.Phylogenetic tree building based on the variations of the M protein appears tosupport the non-human origin of SARS-CoV. To investigate its immunogenicity,we synthesized eight oligopeptides covering 69.2% of the entire ORF and screenedthem by using ELISA (enzyme-linked immunosorbent assay) with sera from SARSpatients. The results confirmed our predictions on antigenic sites.
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Page 118-130

Research Article

The E Protein Is a Multifunctional Membrane Protein of SARS-CoV

Qingfa Wu,Yilin Zhang,Hong Lu,Jing Wang,Ximiao He,Yong Liu,Chen Ye,Wei Lin,Jianfei Hu,Jia Ji,Jing Xu,Jia Ye,Yongwu Hu,Wenjun Chen,Songgang Li,Jun Wang,Jian Wang,Shengli Bi,Huan-Ming Yang

The E (envelope) protein is the smallest structural protein in all coronaviruses andis the only viral structural protein in which no variation has been detected. Weconducted genome sequencing and phylogenetic analyses of SARS-CoV. Based ongenome sequencing, we predicted the E protein is a transmembrane (TM) pro-tein characterized by a TM region with strong hydrophobicity and α-helix con-formation. We identified a segment (NH2-_L-Cys-A-Y-Cys-Cys-N_-COOH) in thecarboxyl-terminal region of the E protein that appears to form three disulfide bondswith another segment of corresponding cysteines in the carboxyl-terminus of the S(spike) protein. These bonds point to a possible structural association between theE and S proteins. Our phylogenetic analyses of the E protein sequences in all pub-lished coronaviruses place SARS-CoV in an independent group in Coronaviridaeand suggest a non-human animal origin.
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Page 131-144

Research Article

The Structure Analysis and Antigenicity Study of the N Protein of SARS-CoV

Jingqiang Wang,Jia Ji,Jia Ye,Xiaoqian Zhao,Jie Wen,Wei Li,Jianfei Hu,Dawei Li,Min Sun,Haipan Zeng,Yongwu Hu,Xiangjun Tian,Xuehai Tan,Ningzhi Xu,Changqing Zeng,Jian Wang,Shengli Bi,Huan-Ming Yang

The Coronaviridae family is characterized by a nucleocapsid that is composed of thegenome RNA molecule in combination with the nucleoprotein (N protein) withina virion. The most striking physiochemical feature of the N protein of SARS-CoVis that it is a typical basic protein with a high predicted pI and high hydrophilicity,which is consistent with its function of binding to the ribophosphate backbone ofthe RNA molecule. The predicted high extent of phosphorylation of the N proteinon multiple candidate phosphorylation sites demonstrates that it would be relatedto important functions, such as RNA-binding and localization to the nucleolus ofhost cells. Subsequent study shows that there is an SR-rich region in the N proteinand this region might be involved in the protein-protein interaction. The abundantantigenic sites predicted in the N protein, as well as experimental evidence withsynthesized polypeptides, indicate that the N protein is one of the major antigensof the SARS-CoV. Compared with other viral structural proteins, the low variationrate of the N protein with regards to its size suggests its importance to the survivalof the virus.
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Page 145-154

Research Article

The R Protein of SARS-CoV: Analyses of Structure and Function Based on Four Complete Genome Sequences of Isolates BJ01-BJ04

Zuyuan Xu,Haiqing Zhang,Xiangjun Tian,Jia Ji,Wei Li,Yan Li,Wei Tian,Yujun Han,Lili Wang,Zizhang Zhang,Jing Xu,Wei Wei,Jingui Zhu,Haiyan Sun,Xiaowei Zhang,Jun Zhou,Songgang Li,Jun Wang,Jian Wang,Shengli Bi,Huan-Ming Yang

The R (replicase) protein is the uniquely defined non-structural protein (NSP)responsible for RNA replication, mutation rate or fidelity, regulation of transcrip-tion in coronaviruses and many other ssRNA viruses. Based on our completegenome sequences of four isolates (BJ01-BJ04) of SARS-CoV from Beijing, China,we analyzed the structure and predicted functions of the R protein in comparisonwith 13 other isolates of SARS-CoV and 6 other coronaviruses. The entire ORF(open-reading frame) encodes for two major enzyme activities, RNA-dependentRNA polymerase (RdRp) and proteinase activities. The R polyprotein under-goes a complex proteolytic process to produce 15 function-related peptides. Ahydrophobic domain (HOD) and a hydrophilic domain (HID) are newly identifiedwithin NSP1. The substitution rate of the R protein is close to the average ofthe SARS-CoV genome. The functional domains in all NSPs of the R proteingive different phylogenetic results that suggest their different mutation rate underselective pressure. Eleven highly conserved regions in RdRp and twelve cleavagesites by 3CLP (chymotrypsin-like protein) have been identified as potential drugtargets. Findings suggest that it is possible to obtain information about the phy-logeny of SARS-CoV, as well as potential tools for drug design, genotyping anddiagnostics of SARS.
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Page 155-165

Letter

Polymorphism Profile of Nine Short Tandem Repeat Loci in the Han Chinese

Shuangding Li,Chunxia Yan,Yajun Deng,Ruiling Wang,Jian Wang,Huan-Ming Yang,Shengbin Li

Nine short tandem repeat (STR) markers (D3S1358, VWA, FGA, THO1, TPOX,CSFIPO, D5S818, D13S317, and D7S820) and a sex-identification marker (Amel-ogenin locus) were amplified with multiplex PCR and were genotyped with afour-color fluorescence method in samples from 174 unrelated Han individuals inNorth China. The allele frequencies, genotype frequencies, heterozygosity, prob-ability of discrimination powers, probability of paternity exclusion and Hardy-Weinberg equilibrium expectations were determined. The results demonstratedthat the genotypes at all these STR loci in Han population conform to Hardy-Weinberg equilibrium expectations. The combined discrimination power (DP) was1.05 × 10-10 within nine STR loci analyzed and the probability of paternity exclusion(EPP) was 0.9998. The results indicate that these nine STR loci and the Amelo-genin locus are useful markers for human identification, paternity and maternitytesting and sex determination in forensic sciences.
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Page 166-170

Brief Report

Gene Expression Profiling in Porcine Fetal Thymus

Yanjiong Chen,Shengbin Li,Lin Ye,Jianing Geng,Yajun Deng,Songnian Hu

obtain an initial overview of gene diversity and expression pattern in porcinethymus, 11,712 ESTs (Expressed Sequence Tags) from 100-day-old porcine thymus(FTY) were sequenced and 7,071 cleaned ESTs were used for gene expressionanalysis. Clustered by the PHRAP program, 959 contigs and 3,074 singlets wereobtained. Blast search showed that 806 contigs and 1,669 singlets (totally 5,442ESTs) had homologues in GenBank and 1,629 ESTs were novel. According to theGene Ontology classification, 36.99% ESTs were cataloged into the gene expressiongroup, indicating that although the functional gene (18.78% in defense group) ofthymus is expressed in a certain degree, the 100-day-old porcine thymus still existsin a developmental stage. Comparative analysis showed that the gene expressionpattern of the 100-day-old porcine thymus is similar to that of the human infantthymus.
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Page 171-172