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Nucleotide sequence characterization and phylogenetic analysis of hantaviruses isolated in Shandong Province,China

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Chinese Medical Journal 2007年第9期120卷 825-830页

作者： LI Jian ZHAO Zhong-tang WANG Zhi-qiang LIU Yun-xi HU Mao-hong Department of Epidemiology and Health Statistics School of Public Health Shandong University Jinan 250012 China Institute for Infectious Disease Control and Prevention Shandong Centre for Disease Control and Prevention Jinan 250014 China Department of Nosocomial Infection Management and Disease Control Beijing Institute of Microbiology and Epidemiology Beijing 100071 China

Background China is the most severe endemic area of hemorrhagic fever with renal syndrome （HFRS） in the world with 30 000-50 000 cases reported annually, which accounts for more than 90% of total number of cases worldwide. The incidence rate of the syndrome in Shandong Province is one of the highest in China, which has ever reached 50 per 100 000 persons per year. However, the molecular characteristics of hantaviruses （HV） epidemic in Shandong Province remain unclear. Therefore it is useful to clarify nucleotide sequence and phylogenetic characteristics of HV isolated in Shandong Province in order to provide better advices to control and prevent HFRS. Methods RNAs were extracted from sera of clinically diagnosed patients and positive rodent lungs that were detected by indirect immunofluorescent assay （IFA）. Partial M segments of HV were amplified from the RNAs with reverse transcription nested polymerase chain reactions （nested PCR） using hantavirus genotype specific primers. The nested PCR products were sequenced and compared with those from previously epidemic isolates in Shandong and with other representative HV sequences from GenBank. Phylogenetic tree analyses were performed based on the sequences of the M genes. Results Thirty-four HV isolates in Shandong showed 67.1%-100% nucleotide identities. The nucleotide homologies among 6 Hantaan viruses （HTNV） isolates in Shandong were 78.1%-98.7%, while the homologies among 28 Seoul virus （SEOV） isolates in Shandong were 93.7%-100%. There were at least 3 subtypes HTNV （H2, H5, H9） and 2 subtypes SEOV （S2, S3） in Shandong Province. Conclusions In Shandong Province, the homologies of HTNV were lower and there were no predominant subtypes, while the homologies of SEOV were higher and S3 was the predominant subtype. The homologies of SEOV from rodents were higher than those from patients. The distribution of subtypes in Shandong was similar to that of the adjoining provinces. Phylogenetic analyses of the sequences showed geographic clustering of HV in Shandong.

关键词： hantavirus sequence analysis phylogenetic analysis

Subtype and sequence analysis of HIV-1 strains in Heilongjiang Province

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Chinese Medical Journal 2007年第22期120卷 2006-2010页

作者： WANG Fu-xiang ZHOU Hui LING Hong ZHOU Hai-zhou LIU Wei-hua SHAO Yi-ming ZHOU Jin Department of Infectious Diseases First Clinical College of Harbin Medical University Harbin 150001 China Department of Hematology First Clinical College of Harbin Medical University Harbin 150001 China Department of Microbiology Harbin Medical University Harbin 150081 China Agriculture General Hospital Harbin 150001 China National Center for AIDS/STD Control and Prevention Chinese Center for Disease Control and Prevention Beijing 100050 China

Background Human immunodeficiency virus （HIV-1） is divided into two types, HIV-1 （groups M, N and O） and HIV-2. Heilongjiang Province located in the northeast of China, and the feature of the subtype distribution and sequence characteristics of HIV-1 strains prevalent in Heilongjiang Province is still uncertain. The aim of this study was to investigate the subtype distribution and genetic characteristics of HIV-1 strains in one hospital in Heilongjiang Province. Methods HIV-1 env gene was amplified by nested-PCR from peripheral blood mononuclear cells （PBMCs） obtained from 19 HIV-1 seropositive individuals in Heilongjiang Province. The C2-V3 region was sequenced. Aligned the nucleotide sequence of 19 samples with CLUSTAL W （BioEdit） software, results were acquired and used for phylogenetic tree analysis after artificial adjustment. Reference sequence, downloaded from Los Alamos HIV sequence Database, was used to identify the subtype of obtained sequence. Genetic distance between sequences was assessed using the software MEGA 3.1 Kimura 2-parameter, and the Phylogenetic tree was reestablished with Neighbor-Joining method. Results Phylogenetic tree analysis showed that 19 Heilongjiang strains clustered closely to subtype B strain from Thailand and were far from other international subtype reference strains. Statistical test showed no significant discrepancy between the genetic distance of interclass and intra-class （P〉0.05）. The analysis of V3 loop amino sequence of 19 Heilongjiang B strains revealed that V3 tip motif of 10 samples （52.63%） was GPGQ, and of 4 samples （21.53%） was GPGR. Conclusions The subtype of 19 HIV-1 seropositive individuals in Heilongjiang Province is B′, and it is introduced from He＇nan Province. V3 tip motifs of the HIV-1 isolates are mainly GPGQ and GPGR.

关键词： human immunodeficiency virus type 1 sequence analysis

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

Complete Genome sequence analysis of Guangdong Isolates of Cymbidium Mosaic Virus

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Plant Diseases and Pests 2022年第3期13卷 15-20页

作者： Yonglu WEI Rui REN Jie GAO Weiping LIU Qi XIE Genfa ZHU Fengxi YANG Environmental Horticulture Research Institute Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and UtilizationGuangzhou 510640China Guangdong Wengshan Orchid Research Co. LtdWengyuan 512600China

[Objectives]The paper was to explore the genetic information and evolution of CymMV,and to provide an important scientific basis for monitoring and early warning of orchid virus disease and anti-virus genetic engineering of orchid in Guangdong Province.[Methods]RT-PCR and DASELISA were used to detect and identify CymMV from leaves with suspected virus disease of Cymbidium sinense collected from Guangzhou area.The genome sequence assembly,annotation,phylogeny and selection pressure analysis of CymMV isolates were performed with related molecular biology software.[Results]Two CymMV isolates(GZV013 and ZC29)were found in Guangdong Province for the first time in this study.The genome of both GZV013 and ZC29 were 6227 nt in length,encoding 5 functional proteins.The similarity analysis of the full sequence showed that the nucleotide sequence identity of GZV013 and Taiwan isolate M2 was 97.03% and that of ZC29 and Nanjing isolate NJ-1 was 97.11%.The complete genome sequence identity among CymMV isolates ranged from 86.85% to 98.31%,and the differentiation of diverse populations was closely related to host species and geographical isolation.Each region of CymMV genome was affected by negative selection and conformed to the neutral evolution model.The genes encoding RdRp,TGB1 and TGB2 had the highest mutation rates in the genome.[Conclusions]GZV013 was most closely related to Taiwan isolate M2,and ZC29 was most closely related to Nanjing isolate NJ-1,belonging to the same branch of a family.

关键词： Orchid Virus detection Cymbidium mosaic virus(CymMV) sequence analysis Selection pressure

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

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 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

Isolation and sequence analysis of HMW Glutenin Subunit 1Dy10.1 Ecoding Gene from Xinjiang Wheat (Triticum petropavlovskyi Udacz. et Migusch)

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Journal of Integrative Agriculture 2006年第2期5卷 81-89页

作者： JIANG Qian-tao1, 2*, WEI Yu-ming1, 2*, WANG Ji-rui1, 2, YAN Ze-hong1, 2 and ZHENG You-liang1, 2 1 Triticeae Research Institute, Sichuan Agricultural University, Ya’an 625014, P.R.China 2 Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education/Sichuan Agricultural University, Ya’an 625014, P.R.China Triticeae Research Institute Sichuan Agricultural University Ya'an 625014 P.R. China Key Laboratory of Crop Genetic Resources and Improvement Ministry of Education/Sichuan Agricultural University Ya'an 625014 P.R. China

A novel HMW glutenin subunit gene 1Dy10.1 was isolated and characterized from Xinjiang wheat (Triticum petropavlovskyi. Udacz. et Migusch) accession Daomai 2. The complete open reading frame (ORF) of 1Dy10.1 was 1 965 bp, encoding 655 amino acids. The numbers and distribution of cysteines in 1Dy10.1 were similar to those of 1Dy10 and other y-type subunits. In the N-terminal of 1Dy10.1, an amino acid was changed from L (leucine) to P (proline) at position 55. The repetitive domain of 1Dy10.1 differed from those of known HMW subunits by substitutions, insertions or/and deletions involving single or more amino acid residues. In the repetitive domain of subunit 1Dy10.1, the deletion of tripeptide GQQ in the consensus unit PGQGQQ resulted in the appearance of the motif PGQ that have not been observed in other known y-type HMW subunits. In comparison with the subunit 1Dy12, a deletion of dipeptide GQ, which occurred in subunit 1Dy10, was also observed in subunit 1Dy10.1. The cloned 1Dy10.1 gene had been successfully expressed in Escherichia coli, and the expressed protein had the identical mobility with the endogenous subunit 1Dy10.1 from seed.

关键词： Triticum petropavlovskyi sequence analysis HMW-GS gene bacterial expression