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Journal of Environmental Sciences 2008年第12期20卷 1501-1507页

作者： ZHANG, Xuexia JIA, Yongfeng WANG, Xin XU, Liying Institute of Applied Ecology Chinese Academy of Sciences Shenyang 110016 China Graduate University Chinese Academy of Sciences Beijing 100039 China

Microbial reduction of As(V)(i.e.,arsenate)plays an important role in arsenic(As)mobilization in aqueous *** this study,we investigated As(V)reduction characteristics of the bacteria enriched from the arsenic-contaminated soil at an abandoned smelter *** was found that As(V)was completely reduced to As(III)(i.e.,arsenite)in 21 *** 3-d incubation,a yellow solid was precipitated and the concentration of As(III)decreased *** 150 h incubation,ca.65%of soluble arsenic was removed fro...

关键词： microbial reduction arsenic phylogenetic analysis

phylogenetic analysis of mtDNA from the Ancient Human of Yuan Dynasty in Inner Mongolia in China

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Chemical Research in Chinese Universities 2006年第2期22卷 177-180页

作者： FU Yu-qin XU Xue-lian ZHANG Xiao-lei ZHANG Quan-chao ZHOU Hui ZHU Hong Ancient DNA Laboratory Research Center for Chinese Frontier Archaeology Jilin UniversityChangchun 130012 P. R. China College of Life Science Jilin University 130021 P. R. China

A study of the genetic structure of an ancient human excavated from the Yikeshu site of Yuanshangdu ancient city in Inner Mongolia and the relationships between the ancient population and the extant populations was carried out. Sequences of the control region and coding region of mtDNA from the ancient human were analyzed by using direct sequencing and restriction-fragment length polymorphism （RFLP） methods, phylogenetic analysis and multidimensional scaling analysis were also performed on the mtDNA data of the ancient population and 12 extant populations. These results show that the ancient individuals of Yikeshu site can be assigned to D, G, B and Z haplogroups that are prevalent in Duars and Mongolians from Inner Mongolia. The ancient population is also closer to Duar and Mongolian populations in genetic distance than other compared populations. This study reveals that the ancient population from Yikeshu site in the Yuan Dynasty shares a common ancestor with Mongolic-speaking Daur and Mongolian tribes.

关键词： MtDNA Polymorphism phylogenetic analysis

phylogenetic analysis revealed the central roles of two African countries in the evolution and worldwide spread of Zika virus

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Virologica Sinica 2016年第2期31卷 118-130页

作者： Shu Shen Junming Shi Jun Wang Shuang Tang Hualin Wang Zhihong Hu Fei Deng State Key Laboratory of Virology Wuhan Institute of Virology Chinese Academy of Sciences

Recent outbreaks of Zika virus （ZIKV） infections in Oceania＇s islands and the Americas were characterized by high numbers of cases and the spread of the virus to new areas. To better understand the origin of ZIKV, its epidemic history was reviewed. Although the available records and information are limited, two major genetic lineages of ZIKV were identified in previous studies. However, in this study, three lineages were identified based on a phylogenetic analysis of all virus sequences from GenBank, including those of the envelope protein （E） and non-structural protein 5 （NS5） coding regions. The spatial and temporal distributions of the three identified ZIKV lineages and the recombination events and mechanisms underlying their divergence and evolution were further elaborated. The potential migration pathway of ZIKV was also characterized. Our findings revealed the central roles of two African countries, Senegal and Cote d＇lvoire, in ZIKV evolution and genotypic divergence. Furthermore, our results suggested that the outbreaks in Asia and the Pacific islands originated from Africa. The results provide insights into the geographic origins of ZlKV outbreaks and the spread of the virus, and also contribute to a better understanding of ZlKV evolution, which is important for the prevention and control of ZlKV infections.

关键词： Flaviviridae Zika virus (ZIKV) phylogenetic analysis lineages recombination migration

A survey on porcine circovirus type 2 infection and phylogenetic analysis of its ORF2 gene in Hangzhou,Zhejiang Province,China

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2008年第2期9卷 148-153页

作者： Zong-zhao YANG Jiang-bing SHUAI Xian-jun DAI Wei-huan FANG Institute of Preventive Veterinary Medicine Zhejiang University Hangzhou 310029 China Hangzhou Husbandry and Veterinary Station Hangzhou 310020 China College of Life Science China Jiliang University Hangzhou 310018 China

Porcine circovirus type 2 (PCV2) is closely related to the postweaning multisystemic wasting syndrome (PMWS). In this study, the pig serum and tissue samples collected from different regions of Hangzhou District in Zhejiang Province of China between 2003 and 2005 were analyzed by enzyme-linked immunosorbent assay (ELISA) for PCV2 antibody and by polymerase chain reaction (PCR) for ORF2 gene. The results show that out of 1250 randomly collected serum samples, 500 sera (40%) were seropositive for PCV2. PCR results demonstrate that Hangzhou PCV2 with more than 50% Chinese PCV2 strains and French PCV2 formed Cluster A. Only one PCV2 from Hangzhou belonged to Cluster B with some other Chinese PCV2 and Netherlands’s isolates. Cluster C consisted of PCV2 isolates from China, US, Canada, UK and Germany. The results indicate that the PCV2 infection was widespread in Hangzhou.

关键词： Porcine circovirus type 2 (PCV2) Seroprevalence ORF2 phylogenetic analysis

phylogenetic analysis and Expression Patterns of the MAPK Gene Family in Wheat (Triticum aestivum L.)

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Journal of Integrative Agriculture 2012年第8期11卷 1227-1235页

作者： LIAN Wei-wei TANG Yi-miao GAO Shi-qing ZHANG Zhao ZHAO Xin ZHAO Chang-ping Beijing Engineering and Technique Research Center of Hybrid Wheat Beijing Academy of Agricultural and Forestry Sciences Beijing 100097 P.R.China College of Life Science Capital Normal University Beijing 100048 P.R. China

Mitogen activated protein kinases （MAPK） cascades based on protein phosphorylation play an important role in plant growth and development. In this study, we have identified 15 putative members of the wheat MAPK gene （TaMPK） family through an in silico search of wheat expressed sequence tags （EST） databases based on the presence of amino acid sequence of Arabidopsis and rice MAPKs. phylogenetic analyses of MAPKs from wheat, rice and Arabidopsis genomes have classified them into seven subgroups （A, B, C, D, E, F, and G）. Using the available EST information as a source of expression data, the MAPK family genes from Triticum aestivum were detected in diverse tissues. Further expression analysis of the MAPKs in NCBI EST database revealed that their transcripts were most abundant in callus （20%）, followed by leaf （12%） and inflorescence （12%）. Most MAPK family genes showed some tissue specificity.

关键词： wheat MAPK EST phylogenetic analysis profile

phylogenetic analysis of the Non-structural (NS) Gene of Influenza A Viruses Isolated in Kazakhstan in 2002-2009

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Virologica Sinica 2011年第6期26卷 376-385页

作者： Andrey Bogoyavlenskiy Vladimir Berezin Alexey Prilipov Ilya Korotetskiy Irina Zaitseva Aydyn Kydyrmanov Kobey Karamedin Nailya Ishmukhametova Saule Asanova Marat Sayatov Kainar Zhumatov Institute of Microbiology & Virology 103 Bogenbay batyr StrAlmaty 050010Kazakhstan Ivanovsky Institute of Virology 16Gamaleya strMoscow 123098Russia

Although the important role of the non-structural (NS1 and NEP) gene of influenza A in virulence of the virus is well established, our knowledge about the extent of variation in the NS gene pool of influenza A viruses in their natural reservoirs in Kazakhstan is incomplete. 17 influenza A viruses of different subtypes were studied in this paper. Seven types of haemagglutinin and five different neuraminidase subtypes in eight combinations were found among the isolated viruses. A comparison of nucleotide sequences of isolated viruses revealed a substantial number of silent mutations, which results in high degree of homology in amino acid sequences. By phylogenetic analysis it was shown that two distinct gene pools, corresponding to both NS allele A with 5 Clades and B, were present at the same time in Kazakhstan. The degree of variation within the alleles was very low. In our study allele A viruses had a maximum of 5% amino acid divergence in Clade while allele B viruses had only 4% amino acid divergence.

关键词： Influenza Nonstructural gene phylogenetic analysis

Characterization and phylogenetic analysis of a phenanthrene-degrading strain isolated from oil-contaminated soil

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Journal of Environmental Sciences 2004年第4期16卷 589-593页

作者： XIAYing MINHang LUZhen-mei YEYang-fang CollegeofLifeScience ZhejiangUniversityHangzhou310029China

Bacterium strain EVA17 was isolated from an oil-contaminated soil, and identified as Sphingomonas sp. based on analysis of 16S rDNA sequence,cellular fatty acid composition and physiological-chemical tests. The salicylate hydroxylase and catechol 2,3-dioxygenase(C23O) were detected in cell-free lysates, suggesting a pathway for phenanthrene catabolism via salicylate and catechol. Alignment showed that both of the C23O and GST genes of the strain EVA17 had high similarity with homologues of strains from genus Sphingomonas. The phylogenetic analysis based on 16S rDNA and C23O gene sequence indicated that EVA17 should be classified into genus Sphingomonas, although the two phylogenetic trees were slightly different from each other. The results of co-amplification and sequence determination indicated that GST gene should be located upstream of the C23O gene.

关键词： phenanthrene 16S rDNA glutathione S-transferase catechol 2,3-dioxygenase phylogenetic analysis

Characterization of the Complete Mitochondrial Genome of the Hybrid Epinephelus moara♀ × Epinephelus lanceolatus♂,and phylogenetic analysis in Subfamily Epinephelinae

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Journal of Ocean University of China 2017年第3期16卷 555-563页

作者： GAO Fengtao WEI Min ZHU Ying GUO Hua CHEN Songlin YANG Guanpin College of Marine Life Science Ocean University of China Yellow Sea Fisheries Research Institute Chinese Academy of Fishery Sciences (CAFS)Key Laboratory for Sustainable Development of Marine FisheriesMinistry of Agriculture Wuxi Fisheries College Nanjing Agricultural University

This study presents the complete mitochondrial genome of the hybrid Epinephelus moara♀× Epinephelus lanceolatus♂. The genome is 16886 bp in length, and contains 13 protein-coding genes, 2 r RNA genes, 22 t RNA genes, a light-strand replication origin and a control region. Additionally, phylogenetic analysis based on the nucleotide sequences of 13 conserved protein-coding genes using the maximum likelihood method indicated that the mitochondrial genome is maternally inherited. This study presents genomic data for studying phylogenetic relationships and breeding of hybrid Epinephelinae.

关键词： Epinephelus moara♀× Epinephelus lanceolatus♂ mitochondrial genome phylogenetic analysis

Application of Human Adenovirus Genotyping by phylogenetic analysis in an Outbreak to Identify Nosocomial Infection

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Virologica Sinica 2021年第3期36卷 393-401页

作者： Chuanyu Yang Chunmei Zhu Yuan Qian Jie Deng Baoyuan Zhang Runan Zhu Fang Wang Yu Sun Dongmei Chen Qi Guo Yutong Zhou Lei Yu Ling Cao Linqing Zhao Laboratory of Virology Beijing Key Laboratory of Etiology of Viral Diseases in ChildrenCapital Institute of PediatricsBeijing 100020China Department of Respiratory Medicine Affiliated Children's HospitalCapital Institute of PediatricsBeijing 100020China Hospital Infection-Control Department Affiliated Children’s HospitalCapital Institute of PediatricsBeijing 100020China

Nosocomial infections are common in pediatric patients and can be fatal in infants and immunocompromised patients. In September 2018, a high positive rate of human adenovirus HAdV was occurred among hospitalized children in the Children's Hospital Affiliated to the Capital Institute of Paediatrics in Beijing. To investigate whether this outbreak of HAdV was related to nosocomial infections or the result of community infections, we collected respiratory specimens from patients with acute respiratory infections in a respiratory ward during June to December 2018, and screened for respiratory viruses. Among 1,840 cases included, 95(5.2%, 95/1840) were positive for HAdV and 81 were genotyped based on phylogenetic analysis, including seven as HAdV-1(8.6%), 30 HAdV-3(37.0%), two HAdV-6(2.5%), and 42 HAdV-7(51.9%). More HAdV-positive samples were collected in August(4.7%, 12/255), September(15.0%, 41/274) and October(6.9%, 17/247), with a peak in September 2018. By combining the results of HAdV phylogenetic analysis with clinical data of patients, there were 77 cases(4.2%, 77/1840;81.1%, 77/95) excluded from nosocomial infections, eight cases representing possible infections transmitted by visitors or attending parents, three cases without sequences that might have been due to infection transmitted by roommates positive for HAdV, one case of a roommate without an HAdV sequence, and six cases that shared highly homologous sequences with those of their roommates, for which nosocomial infections might be considered. In conclusion, genotyping of HAdVs based on phylogenetic analysis combined with clinical information provides a powerful method to distinguish nosocomial infections from community acquired infection, especially when tracing the origins of nosocomial infections.

关键词： Acute respiratory tract infection Human adenovirus(HAdV) phylogenetic analysis Nosocomial infection

Identification and phylogenetic analysis of an Orf Virus Isolated from an Outbreak in Boer Goat in Shanxi Province

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Agricultural Sciences in China 2011年第6期10卷 946-953页

作者： GU Shao-peng SHI Xin-tao SHI Zhong-yong WANG Zhong-bing ZHENG Ming-xue College of Animal Science and Veterinary Medicine Shanxi Agricultural University Taigu 030801 P.R.China Genetically Modified Testing Center Ministry of Agriculture/College of Life Science Shanxi Agricultural Universit Taigu 030801 P.R. China Center for Animal Disease Control and Prevention of Shanxi Province Taiyuan 030024 P.R.China

To identify and analyze the Orf virus in Shanxi Province, China, an Orf virus strain was successfully isolated from crust materials of boer goat with clinical sore mouth symptom from a goat farm of Shanxi Province by passaging in lamb testis （LT）. The Orf virus was identified by enzyme linked immunosorbent assay （ELISA） test, recurrent infection test, transmission electron microscopy, and PCR. The nucleotide and amino acid sequences of two genes of the Orf virus were analyzed. The results showed that under the electron microscopy the virus had a presence of typical parapoxvirus virions and there were many eosinophilic intracytoplasmic inclusions observed by hematoxylin-eosin （H＆E） stain. In ELISA test, optical density （OD） readings of the sample showed a positive result, and the rabbits infected with the virus showed a typically Orf virus-infected appearance. All these findings proved that the sample was an Orf virus. The phylogenetic studies of Orf B2L and Orf F1L genes showed that the virus clustered in different branches and were closer to the Orf virus Nantou （DQ904351） and the OV-SA00 isolates （AY386264）. Furthermore, the above results may provide some insight into the genotype of the etiological agent responsible for the Orf outbreak in Shanxi Province, and could also provide a comparative view of the B2L and F1L genes of parapoxvirus.

关键词： Orf virus boer goat identification phylogenetic analysis B2L F1L