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The Epitope Study on the SARS-CoV Nucleocapsid Protein

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genomics, Proteomics & Bioinformatics 2003年第3期1卷 198-206页

作者： 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,{3., China & beijing Proteomics institute,{3., China beijing genomics institute Chinese Academy of Sciences Beijing 101300 China.

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 3.1 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.

关键词： SARS coronavirus nucleocapsid protein antigenicity epitope

On the Organizational Dynamics of the Genetic Code

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genomics,Proteomics & Bioinformatics 2011年第Z1期 21-29页

作者： Zhang Zhang1 and Jun Yu1,2* 1Plant Stress genomics Research Center, Division of Chemical and Life Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23.55-6900, Saudi Arabia 2CAS Key Laboratory of Genome Sciences and Information, beijing institute of genomics, Chinese Academy of Sciences, beijing 100029, China.

The organization of the canonical genetic code needs to be thoroughly illuminated. Here we reorder the four nucleotides-adenine, thymine, guanine and cytosine-according to their emergence in evolution, and apply the organizational rules to devising an algebraic representation for the canonical genetic code. Under a framework of the devised code, we quantify codon and amino acid usages from a large collection of 917 prokaryotic genome sequences, and associate the usages with its intrinsic structure and classification schemes as well as amino acid physicochemical properties. Our results show that the algebraic representation of the code is structurally equivalent to a content-centric organization of the code and that codon and amino acid usages under different classification schemes were correlated closely with GC content, implying a set of rules governing composition dynamics across a wide variety of prokaryotic genome sequences. These results also indicate that codons and amino acids are not randomly allocated in the code, where the six-fold degenerate codons and their amino acids have important balancing roles for error minimization. Therefore, the content-centric code is of great usefulness in deciphering its hitherto unknown regularities as well as the dynamics of nucleotide, codon, and amino acid compositions.

关键词： genetic code codon GC content purine content organizational dynamics compositional dynamics

Applications using next generation sequencing technology

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Applications using next generation sequencing technology

Cloning and characterization of an up-regulated GA 20-oxidase gene in hybrid maize

第八次全国医学遗传学学术会议(中华医学会2009年医学遗传学年会)

作者： Wang Jun,Zhang Yong beijing genomics institute-Shenzhen

In the past,traditional disease research is only focus on single/a few *** is hypothesis-driven research *** two years,Functional genome research takes advantage of newly available genome sequences and high-throughput genome technologies to study genes and/or proteins to inform the perspective of entire biological *** next generation sequencing technology speed up the whole research *** research became to *** can use the next-generation of sequencing applied as follows;Whole genome resequencing,Exome-capture sequencing,Transcriptome,Digital gene expression profiling,MicroRNA, Epigenome,Pathogen,In order to define structural rearrangements and CNV,to define coding sequence mutation,to define alteration in expression levels,aberrant splicing and fusion transcripts,to defined the relation with the *** costs has enabled the sequencing of individual human *** data of the Chinese population will be rapidly accumulated and will result in the identification of new gene-disease associations and wide applications of genomics in clinics.

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Progress in Natural Science:Materials International 2009年第2期19卷 161-166页

作者： Jinkun Du,Yingyin Yao,Zhongfu Ni,Qixin Sun Department of Plant Genetics & Breeding and State Key Laboratory for Agrobiotechnology,Key Laboratory of Crop genomics and Genetic Improvement,Ministry of Agriculture/beijing Key Laboratory of Crop Genetic Improvement,China Agricultural University,beijing 100094,China Department of Plant Genetics & Breeding and State Key Laboratory for Agrobiotechnology Key Laboratory of Crop Genomics and Genetic Improvement Ministry of Agriculture/Beijing Key Laboratory of Crop Genetic Improvement China Agricultural University Beijing 100094 China

Previous studies revealed that GA content and metabolism are positively correlated with a faster shoot growth rate of hybrid,and recently,genes participating in both GA biosynthesis and GA response pathways were also found to be differentially expressed between wheat hybrid and its parental inbreds. In this study,an up-regulated GA 20-oxidase gene in a maize hybrid,designated ZmGA20,was cloned. ZmGA20 contains an open reading frame (ORF) encoding 3.1 amino acid residues. BLASTX searches in GenBank revealed that the ZmGA20 is homologous to the sequences of GA20ox proteins from different species,and analysis also indicated that ZmGA20 had typical features of GA 20-oxidase proteins,including a "LPWKET" sequence. Semi-quantitative RT-PCR analysis showed that ZmGA20 was expressed in different tissues and/or organs. The expression level of ZmGA20 in the hybrid was higher than that in two parents (in roots,leaves,stems and embryo,and ears). The abundance of ZmGA20 transcript was equal to that of the highly expressed parents,which provided molecular evidence for the observed GA content heterosis in maize hybrids.

关键词： GA 20-oxidase Gene expression Maize Heterosis

A novel model-free approach for reconstruction of time-delayed gene regulatory networks

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中国科学：生命科学英文版 2006年第2期49卷 190-200页

作者： JIANG Wei1,2, LI Xia1,2,3.4, GUO Zheng1,2,3. LI Chuanxing1, WANG Lihong1 & RAO Shaoqi1,5 1. Department of Bioinformatics, Harbin Medical University, Harbin 150086, China 2. Department of Computer Science, Harbin institute of Technology, Harbin 150080, China 3. School of Life Science and Technology, Tongji University, Shanghai 200092, China 4. Biomedical Engineering institute, Capital University of Medical Sciences, beijing 100054, China 5. Departments of Cardiovascular Medicine and Molecular Cardiology, Cleveland Clinic Foundation, Cleveland, Ohio 44195, USA Department of Bioinformatics Harbin Medical University Harbin China Department of Computer Science Harbin Institute of Technology Harbin China School of Life Science and Technology Tongji University Shanghai China Departments of Cardiovascular Medicine and Molecular Cardiology Cleveland Clinic Foundation Cleveland USA

Reconstruction of genetic networks is one of the key scientific challenges in functional genomics. This paper describes a novel approach for addressing the regulatory dependencies be-tween genes whose activities can be delayed by multiple units of time. The aim of the proposed ap-proach termed TdGRN (time-delayed gene regulatory networking) is to reversely engineer the dy-namic mechanisms of gene regulations, which is realized by identifying the time-delayed gene regu-lations through supervised decision-tree analysis of the newly designed time-delayed gene expres-sion matrix, derived from the original time-series microarray data. A permutation technique is used to determine the statistical classification threshold of a tree, from which a gene regulatory rule(s) is ex-tracted. The proposed TdGRN is a model-free approach that attempts to learn the underlying regula-tory rules without relying on any model assumptions. Compared with model-based approaches, it has several significant advantages: it requires neither any arbitrary threshold for discretization of gene transcriptional values nor the definition of the number of regulators (k). We have applied this novel method to the publicly available data for budding yeast cell cycling. The numerical results demonstrate that most of the identified time-delayed gene regulations have current biological knowledge supports.

关键词： gene regulatory networks, time delayed, decision tree.

Complete Resequencing of 40 Genomes Reveals Domestication Events and Genes in Silkworm（Bombyx）

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Complete Resequencing of 40 Genomes Reveals Domestication Ev...

Gene expression profiling in porcine mammary gland during lactation and identification of breed- and developmental-stage-specific genes

第十五次全国动物遗传育种学术讨论会

作者： Qingyou Xia,~(1,2)*.Yiran Guo,~(3.)Ze Zhang,~(1,2*) Dong Li,~(1,3.*Zhaoling Xuan,~(3.) Zhuo Li,~(3.) Zhi Jiang,~3.Zhonghuai Xiang,~1 Jun Wang~3.1.The Key Sericultural Laboratory of Agricultural Ministry,College of Biotechnology,Southwest University,Chongqing 400715, China 2.institute of Agronomy and Life Sciences,Chongqing University,Chongqing 400044,China 3.beijing genomics institute at Shenzhen,Shenzhen 518083.China.~*These authors contributed equally to this work.

＜正＞Introduction The genetic variations can be analyzed by comparing the sequences of individuals or at the population level. whole-genome resequencing is considered to be the most efficient approach for studying ge... 详细信息

关键词： silkworm resequencing SNP domestication gene

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Science China(Life Sciences) 2006年第1期49卷 26-36页

作者： SU Zhixi1, DONG Xinjiao2, ZHANG Bing1, ZENG Yanwu1, FU Yan1, YU Jun1,3.& HU Songnian1,3.1. James D. Watson institute of Genome Sciences, Zhejiang University, Hangzhou 3.0008, China 2. School of Life and Environmental Sciences, Wenzhou Normal College, Wenzhou 3.5027, China 3. beijing institute of {3., Chinese Academy of Sciences, beijing 1013.0, China James D. Watson institute of Genome Sciences Zhejiang University Hangzhou 310008 China School of Life and Environmental Sciences Wenzhou Normal College Wenzhou 325027 China James D. Watson institute of Genome Sciences Zhejiang University Hangzhou 310008 China beijing institute of genomics Chinese Academy of Sciences Beijing 101300 China

A total of 28941 ESTs were sequenced from five 5′-directed non-normalized cDNA libraries, which were assembled into 2212 contigs; 5642 singlets using CAP3. These sequences were annotated; clustered into 6857 unique genes, 2072 of which having no functional annotations were considered as novel genes. These genes were further classified into Gene Ontology categories. By comparing the expression profiles, we identified some breed-and developmental-stage-specific gene groups. These genes may be relative to reproductive performance or play important roles in milk synthesis, secretion; mammary involution. The unknown EST sequences; expression profiles at different developmental stages; breeds are very important resources for further research.

关键词： expressed sequence tags, expression profile, domestic pig, mammary gland.

Isolation and characterization of rice lesion mimic mutants from a T-DNA tagged population

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Progress in Natural Science:Materials International 2005年第1期 18-24页

作者： LI Shutian 1,2, PEI Zhongyou 1, LUO Lijuan 3. TIAN Yingchuan 1 and HE Chaozu 1* (1. National Key Laboratory of Plant genomics, institute of Microbiology, The Chinese Academy of Sciences, beijing 100080, China 2. Graduate School of the Chinese Academy of Sciences, beijing 10003., China 3. College of Agronomy, South China University of Tropical Agriculture, Danzhou 57173., China)

A rice (Oryza sativa L. ssp. japonica cv. Nipponbare) T-DNA tagged population consisting of about 7000 individual lines was generated and screened for rice lesion mimic mutants in the T 1 generation. Ten lines were found to develop spontaneous lesions in the absence of pathogen infection and displayed distinct lesion phenotypes. These mutants were tentatively designated as lm1—lm10 (for lesion mimic), respectively. Lesion formation of lm mutants was developmentally regulated, and all the mutants showed stunted growth and reduced fertility. Genetic analysis demonstrated that all the mutations were recessive, and five partially fertile mutants (lm4—lm8) were derived from different loci. Mimic lesions occurring on the leaves of lm mutants resulted from cell death as revealed by trypan blue staining. Six of them (lm3.lm8) exhibited enhanced resistance to five bacterial blight isolates, indicating their wide-spectrum resistance to this pathogen. These results imply that some lesion mimic mutations of rice might be involved in disease resistance signaling pathways, and that isolation of these mutated genes may be useful for elucidating molecular mechanisms of plant disease resistance. Among the mutants, only one mutant, lm6, was preliminarily shown to cosegregate with the inserted T-DNA in its T 1 generation, making it feasible to isolate the gene responsible for the phenotype of this mutant.

关键词： T-DNA tagging lesion mimic hypersensitive response Xanthomonas oryzae pv. Oryzae Oryza sativa.

Finding Signals for Plant Promoters

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genomics, Proteomics & Bioinformatics 2003年第1期1卷 68-73页

作者： Weimou Zhenginstitute of Theoretical Physics, Chinese Academy of Sciences, beijing 100080, China beijing {3.institute, Chinese Academy of Sciences, beijing 1013.0, China institute of Theoretical Physics Chinese Academy of Sciences Beijing 100080 China beijing genomics institute Chinese Academy of Sciences Beijing 101300 China

The strongest signal of plant promoter is searched with the model of single motif with two types. It turns out that the dominant type is the TATA-box. The other type may be called TATA-less signal, and may be used in gene finders for promoter recognition. While the TATA signals are very close for the monocot and the dicot, their TATA-less signals are significantly different. A general and flexible multi-motif model is also proposed for promoter analysis based on dynamic programming. By extending the Gibbs sampler to the dynamic programming and introducing temperature, an efficient algorithm is developed for searching signals in plant promoters.

关键词： for on is as et Pro Finding Signals for Plant Promoters been of into