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sequence analysis of Polypeptide by Mass Spectrometry

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Chemical Research in Chinese Universities 1993年第4期9卷 288-295页

作者： YANG Hou-jun , LI Xiao-ling, HU Xiao-yu and CHEN Yao-zu (State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou, 730000)

The method described in this work provides a sensitive and fast technique for investigating the primary structure of peptides with molecular weight up to 3340 amu. Usually, the metastable ion kinetic energy spectra (MIKES) and collisional activated decomposition (CAD) spectra provide complementary information for the FAB mass spectra, the MIKES and CAD spectra generally contain high-mass sequence ions.

关键词： Peptide sequence analysis Mass spectrometry.

Gene cloning and sequence analysis of the cold-adapted chaperones DnaK and DnaJ from deep-sea psychrotrophic bacterium Pseudoalteromonas sp. SM9913

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Acta Oceanologica Sinica 2007年第6期26卷 91-100页

作者： ZHAO Dianli CHEN Xiulan HE Hailun SHI Mei ZHANG Yuzhong State Key Laboratory of Microbial Technology Marine Biotechnology Research Center Shandong University Jinan 250100 China

Pseudoalteromonas sp. SM9913 is a phychrotmphic bacterium isolated from the deep-sea sediment. The genes encoding chaperones DnaJ and DnaK of P. sp. SM9913 were cloned by normal PCR and TAIL - PCR （GenBank accession Nos DQ640312, DQ504163 ）. The chaperones DnaJ and DnaK from the strain SM9913 contain such conserved domains as those of many other bacteria, and show some cold-adapted characteristics in their structures when compared with those from psychro-, meso-and themophilic bacteria. It is indicated that chaperones DnaJ and DnaK of P. sp. SM9913 may be adapted to low temperature in deep-sea and function well in assisting folding, assembling and translocation of proteins at low temperature. This research lays a foundation for the further study on the cold-adapted mechanism of chaperones DnaJ and DnaK of cold-adapted microorganisms.

关键词： cold-adapted chaperone DnaJ DnaK deep-sea Pseudoalteromonas sp. SM9913 gene cloning sequence analysis

sequence analysis and Quantitative Detection of Norwalk-like Viruses in Cultured Oysters of China

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Journal of Ocean University of China 2008年第2期7卷 223-227页

作者： WANG Jun TANG Qingjuan YUE Zhiqin LI Zhaojie ZHANG Jin XUE Changhu Institute of Food Science and Technology Ocean University of China Qingdao 266003 P. R. China Inspection and Quarantine Bureau of Shandong Qingdao 266003 P. R. China

We isolated 4 Norwalk-like viruses （NLVs） contaminated oysters from 33 Chinese oysters collected from local commercial sources of Shandong Province. After amplification of the RNA-dependent RNA polymerase （RdRp） region of NLVs genomes with RT-PCR, the open reading frame 1 （ORF 1） of the RdRp was sequenced and subjected to multiple-sequence alignment. The results showed that NLVs in the four isolates belong to genogroup Ⅱ. The sequence comparison showed that the similarity between four Chinese oyster isolates were higher than 99.0%, which indicated that NLVs prevalent in close areas have high homogeneity in genome sequences. In addition, the most conserved sequences between diverse NLVs were used to design primers and TaqMan probes, then the real-time quantitative PCR assay was performed. According to the standard curve of GII NLVs, the original amounts （copies） of NLVs in positive patient＇s fecal isolate, positive Japanese oyster isolate, and the Chinese oyster isolate were 8.9× 10^8, 1.25× 10^8 and 4.7× 10^1 respectively. The detecting limit of NLVs was 1 × 10^1 copies. This study will be helpful for routine diagnosis of NLVs pathogens in foods and thus for avoiding food poisoning in the future.

关键词： oysters Norwalk-like viruses (NLVs) reverse transcription polymerase chain reaction (RT-PCR) sequence analysis real time quantitative PCR

Cloning and sequence analysis of the Full-Length Genome of Japanese encephalitis virus Strain SXBJ07 Isolated from Swine

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Agricultural Sciences in China 2009年第11期8卷 1392-1402页

作者： WANG Wei-hua,ZHANG Yan-ming,XU Xin-gang,XING Fu-shan and TANG Qing-hai College of Veterinary Medicine,Northwest A&F University,Yangling 712000,P.R.China College of Veterinary Medicine Northwest A&F University Yangling 712000 P.R. China

A virus strain, showing cytopathic effect in BHK-21 cell, was isolated from swine brains in Shaanxi Province, China, in 2007. The isolate was confirmed as Japanese encephalitis virus （JEV） by immunofluorescence assay （IFA） and reverse transcription polymerase chain reaction （RT-PCR）, and named SXBJ07. The complete nueleotide and deduced amino acid sequences of the JEV strain SXBJ07 were determined. Its single open reading frame has a total of 3 432 amino acid residues. An extensive E gene based phylogenetic analysis was performed, the result showed that SXBJ07 strain belongs to genotype I. Comparison of the SXBJ07 genomic sequence with those of the 24 fully sequenced JEV strains in published databases showed nucleotide homology ranging from 99.0 to 83.7%; amino acid homology ranged from 99.8 to 94.8%. Compared SXBJ07 with SA14-14-2 strain, the current live vaccine strain in China, the homology of amino acid in envelope gene was 97.0%; and there were amino acid substitutions in 13 sites of the active domains of E protein （E1-E411）.

关键词： Japanese encephalitis virus (JEV) full-length genome sequence analysis

Vitis amuerensis CBF3 Gene Isolation,sequence analysis and Expression

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Agricultural Sciences in China 2010年第8期9卷 1127-1132页

作者： WANG Zhan-bin FENG Lian-rong WANG Jin-jie WANG Zhi-ying Northeast Forestry University/Key Labotatory of Forest Tree Genetic Improvement and Biotechnology Ministry of Agricuture Harbin 150040 P.R.China Institute of Poplar of Liaoning Province Gaizhou 115200 P.R. China

The full length cDNA sequence of CBF3 （CRT/DRE-binding factor） was cloned from Vitis amurensis by reverse transcription polymerase chain reaction （RT-PCR） using the primers designed based on CBF genes available in GenBank. sequence analysis showed that the gene had 854 bp long and its coding sequence contained 720 bp, encoding a protein with 239 amino acids and an AP2 structural domain. The molecular mass of CBF3 was predicted to be 25.9 kDa and its theoretical isoelectric point was 7.02 and aliphatic index was 59.29. The average hydropathicity of the protein was -0.551. The tertiary structures of CBF3 were also analyzed. The prokaryotic expression vector pGEX-4T-CBF3 containing CBF3 gene was constructed and CBF3 fusion protein （52 kDa） was produced in Escherichia coli after induction with 1 mmol L-1 IPTG. Further studies are needed to evaluate its potential application for improving plant resistance to cold and other stress condition such as drought and salinity.

关键词： Vitis amurensis CBF gene cloning sequence analysis expression in prokaryote

Molecular Cloning and cDNA sequence analysis of Two New Lepidopteran OR83b Orthologue Chemoreceptors

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Agricultural Sciences in China 2010年第8期9卷 1160-1166页

作者： XIU Wei-ming ZHANG Yi-fan YANG Dian-lin DONG Shuang-lin LIU Yu-sheng Agro-Environmental Protection Institute Ministry of Agriculture/Farmland Ecosystem Observation and Experiment Station of Genetically Modified Organisms in Wuqing Chinese Academy of Agricultural Sciences Tianjin 300191 P.R.China Key Laboratory of Monitoring and Management of Plant Diseases and Insects Ministry of Agriculture/Entomology Department Plant Protection College Nanjing Agricultural University Nanjing 210095 P.R. China Plant Protection College Shandong Agricultural University Tai ＇an 271018 P.R. China

The aim of this study was to isolate the full-length cDNA sequences of an unusually highly conserved olfactory receptor （orthologue to the Drosophila melanogaster DOR83b） from the antennae of Spodoptera exigua and S. litura by using reverse transcription-polymerase chain reaction （RT-PCR） and rapid amplification of cDNA ends （RACE） methods. Bioinformatics methods were used to further analyze the cDNA sequences and putative amino acid sequences. The two full-length cDNA sequences from olfactory receptor （OR） of male S. exigua and S. litura were named as SexiOR2 and SlitOR2, respectively. SexiOR2 and SlitOR2 consisted of nucleotide sequence of 1 906 and 2 483 bp, respectively, and both with deduced amino acid sequences of 473 residues. The sequence analysis indicated that the deduced amino acid sequences of the cDNA shared the high homologies with OR83b orthologue chemoreceptor sequences from previously reported moths, implying that the cDNA sequences were of OR83b orthologue chemoreceptor genes.

关键词： Spodoptera exigua Spodoptera litura olfactory receptor gene sequence analysis

Cloning and sequence analysis of the partial sequence of the rbcL from Bryopsis hypnoides

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Acta Oceanologica Sinica 2005年第5期24卷 150-161页

作者： TIAN Chao WANG Guangce YE Naihao ZHANG Baoyu FAN Xiaolei ZENG Chengkui Institute of Oceanology Chinese Academy of Sciences Qingdao 266071 China Graduate School of the Chinese Academy of Sciences Beijing 100039 China Yellow Sea Fisheries Research Institute Chinese Academy of Fishery Sciences Qingdao 266071 China

The partial sequence of the rbcL from Bryopsis hypnoides, including the sequences of the upstream, extron and partial intron, was amplified by PCR and their sequences were determined. With Spinacia oleracea as the outgroup, neighbor-joining method and maximum parsimony method were used respectively to build phylogenetic trees according to the rbcL exon sequence among 13 species that were the typical species of six phyla. Two kinds of trees showed clearly that there were two groups among those species, the green lineage and the non-green lineage. And the relationships of algae in the green lineage were similar in the two trees but those in the non-green lineage were not consistent. analysis of codon preference indicated that the codon preference of the rbcL exon of Bryopsis hypnoides distinctly differed from that of the relevant sequence of photosynthetic bacteria.

关键词： rbcL Bryopsis hypnoides sequence analysis phylogenetic analysis codon preference

Isolation and identification of a sulfate reducing bacteria and sequence analysis of its dissimilatory sulfite reductase gene

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Journal of Harbin Institute of Technology(New Series) 2009年第6期16卷 854-858页

作者：魏利马放魏继承李艳萍 SHAIK FIRDOZ 吕晓磊 School of Municipal and Environmental Engineering Harbin Institute of Technology Mudanjiang Teachers College Indian Institute of Technoogy

A sulfate reducing bacteria was isolated from mining sewage of Daqing Oilfield by Hungate anaerobic technology. Physiological-biochemical analysis showed that the strain could utilize polyacrylamide as sole carbon and nitrogen source. The sequence analysis of 16S rDNA illustrated that the similarity of F8 and Desulfovibrio desulfuricans (AF192153) was 99%, and the similarity sequence of dissimilatory sulfite reductase gene (DSR) cloned from the strain and Desulfovibrio desulfuricans (AF273034) was 98%. Their phylogenitic analysis was basically anastomosed, and thus temporarily named as Desulfovibrio desulfuricans F8. The DSR cloned from F8 strain was 2740 bp in length consisting of three ORF, DSRA, DSRB and DSRD as a single operon (DSRABD) regulated by the same operator. DSRA contained typical conservative box of sulfate—sulfite reducing enzyme (SiteⅠand SiteⅡ), which could bind siroheme and [Fe4S4]. DSRB retained a [Fe4S4] binding site, with an uncomplimentary structure for siroheme binding. There was no conservative box in DSRD. sequence analysis of DSR will provide a theoretical basis for quantitative detection, metabolic pathway modification through gene engineering, and sulfate reducing bacteria (SRB) suppression.

关键词： sulfate reducing bacteria DSR 16S rDNA sequence DSRABD zene sequence analysis

Facility Layout Based on sequence analysis:Design of Flowshops

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Journal of Shanghai Jiaotong university(Science) 2009年第6期14卷 686-689页

作者：周瑾吴智铭 School of Electronic and Electrical Engineering Shanghai Second Polytechnic University Department of Automation Shanghai Jiaotong University

A computer-aided method to design a hybrid layout--tree-shape planar flowlines is presented. In newtype fiowshop layout, the common machines shared by several flowlines could be located together in functional sections. The approach combines traditional cell formation techniques with sequence alignment algorithms. Firstly, a sequence analysis based cell formation procedure is adopted; then the operation sequences for parts are aligned to maximize machines adjacency in hyperedge representations; finally a tree-shape planar flowline will be obtained for each part family. With the help of a sample of operation sequences obtained from industry, this algorithm is illustrated.

关键词： workshop layout flowlines sequence analysis sequence alignment algorithm