Sequencing and Phylogenetic Analysis of Potato virus Y Liaoning Isolate in China

Complete genome sequence of Potato virus Y Liaoning isolate (PVY-LN) causing tobacco vein necrosis symptoms were isolated from Liaoning Province in China. Genome sequences of PVY-LN was 9 714 nucleotides in length, excluding the 3′- terminal poly (A) tail. PVY-LN encodes a single long open reading frame (ORF) of polyprotein that is predicted to be cleaved into ten mature proteins by three viral proteases. No recombination can be predicted in PVY-LN sequences compared with that of the other PVY strains using Recombination Detection Programe v. 4.16 (RDP4). Complete genome sequence comparison and phylogenetic analysis indicated that PVY-LN is closely related to PVY necrosis strain (PVYN).     

Genome Analysis of the Bombyx mori Infectious Flacherie Virus Isolated in China

We reported here the complete genome of the Bombyx mori infectious flacherie virus （BmlFV）, BmlFV-CHN01, isolated in China and compared it with the Japanese strain IFV （BmIFV-JAN） sequence. BmIFV-JAN and BmIFV-CHN01 were 99% identical in nucleotide and amino acid sequences. The amino acid sequences of the three structural proteins （VP1, VP3 and VP4） and L protein were 100% identical between the two strains. Phylogenetic analyses based on conserved domains in RNA-dependent RNA polymerases （RdRps） by the neighbor-joining method showed that these two strains were from the same virus. The gain of the whole genome of the BmIFV isolated in China and its weak mutation character established a great foundation to the study of functional genome and the molecular epidemiology of BmIFV.     

Cloning and Sequence Analysis of gyrB Gene of Fluoroquinolones-resistant Salmonella Isolated from Chickens

Nine strains resistant to five fluoroquinolones (Ciprofloxacin, Ofloxacin, Enrofloxacin, Danofloxacin,Sarafloxacin) were isolated from clinical samples and extracted the chromosomal DNA of these strains. Designed primers to amplify the Quinolone-resistance-determining region (QRDR) of gyrB gene, then the PCR products were cloned and the sequence was analyzed. In comparison with the standarded strain NCTC5776, no mutation was found in the QRDR of gyrB gene of all resistant strains. The result indicated that the QRDR of gyrB has little relationship with fluoroquinolone resistance to salmonella.     

一株海洋细菌HZBN43的鉴定(英文)

[Objective] The aim of this study is to identify a bacterial strain isolated from ocean water from the Yellow Sea.[Method]Using 16S rRNA technique,a strain from Yellow Sea was preliminarily identified and analyzed.[Result]One 1 521 bp fragment of 16S rRNA was amplified from the strain HZBN43;homology analysis between the yielded sequence and the 16S rRNA sequences accessed in NCBI from other strains showed that HZBN43 belonged to Bacillus,and shared 99.79% homologue with the known species of Bacillus selenatarsenatis.[Conclusion]The sequence of strain HZBN43 was obtained.However,because of the incomplete sequence,the confidence level is just 46,so other corroborations are still required for grouping HZBN43 into an exact species.     

Sequence and phylogenetic analysis of chicken reoviruses in China

Avian reovirus(ARV) has been responsible for many cases of chicken tenosynovitis in China in recent years,causing high morbidity among layer and broiler chickens.To study the degree of genetic divergence and evolution among ARVs,the fulllength nucleotide sequences of the σC-encoding gene of eight ARV field isolates and the entire coding-region sequences of four isolates were determined and analyzed.The sequence analysis revealed that the eight aC-encoding genes shared99.0-99.9%nucleotide sequence identity with each other and over 99%with the chicken reovirus reference strain S1133.However,the nucleotide sequences of the eight aC-encoding genes varied extensively from that of isolate AVS-B(GenBank accession no.FR694197),with only 55.5%identity.A sequence analysis of the whole ARV-coding region showed some nucleotide substitutions in the open reading frames encoding AA,AB,AC,uA,uB,uNS,aC,aA,aB,and aNS in the field strains.A phylogenetic analysis showed that all eight isolates clustered in group I with S1133,but that four field isolates shared less homology with strain S1133 than the others,indicating that they had been evolved in the field.We also studied the pathogenicity of two strains.No characteristic lesions were observed in vaccinated chickens,and no virus was detected in sampled tissues.However,an enzyme-linked immunosorbent assay revealed significant differences between the antibody responses of the inoculated groups and the negative controls.These results revealed that Chinese isolates shared the highest sequence homologies with S1133,grouped together in one cluster.Although the vaccination against ARV is used in farms,the pathogens still persist in Chinese poultry flocks.     

Comparison of Acetylcholinesterase Characteristics Between Resistant and Susceptible Strains of Helicoverpa armigera （Hubner）

The sensitivity of a susceptible and two resistant strains of cotton bollworm, Helicoverpa armigera, to phoxim, malathion and methomyl was determined by a topical application of bioassay method. YG strain, collected from field of Yanggu, Shandong Province of China, possessed 7-, 13- and 20-fold of resistance to the above three antiacetylcholinesterases based on the comparison of LD50 values with a laboratory susceptible strain. There were not significant difference of the specific activity and the Vmax value among the three strains. But the affinity of AChE tO acetylthiocholine （ATCh）, in YG strain was the lowest among the three strains tested. A cDNA encoding partial AChE gene was cloned from the three strains by RT-PCR and there was one nucleotide acid difference between YG strain and other two strains which resulted in no amino acid mutation. This partial AChE gene was used as a probe to perform Southern blot. The results indicated that there was no gene amplification in resistant cotton bollworm. Altered AChE with a decreased sensitivity to inhibitors appeared to be one of important resistance mechanisms in cotton bollworm against OP and carbamate compounds.     

Isolation and Expression Analysis of Two Genes Encoding Cinnamate 4-Hydroxylase from Cotton （Gossypium hirsutum）

Two genes （GhC4H1 and GhC4H2） that encode putative cotton cinnamate 4-hydroxylases that catalyze the second step in the phenylpropanoid pathway were isolated from developing cotton fibers. GhC4H1 and GhC4H2 each contain open reading frames of 1 518 base pairs （bp） in length and both encode proteins consisting of 505 amino acid residues. They are 90.89% identical to each other at the amino acid sequence level and belong to class I of plant C4Hs. GhC4H1 and GhC4H2 genomic DNA are 2 247 and 2 161 bp long, respectively, and contain two introns located at conserved positions relative to the coding sequence. GhC4HI and GhC4H2 promoters were isolated and found to contain many cis-elements （boxes P, L and AC-1 element） previously identified in the promoters of other phenylpropanoid pathway genes. Histochemical staining showed GUS expression driven by the GhC4H1 and GhC4H2 promoters in ovules and fibers tissues. GhC4H1 and GhC4H2 were also widely expressed in other cotton tissues. GhC4H2 expression reached its highest level during the elongation stage of fiber development, whereas GhC4H1 expression increased during the secondary wall development period in cotton fibers. Our results contribute to a better understanding of the biochemical role of GhC4H1 and GhC4H2 in cotton fiber development.     

Identification and Characterization of Putative Virulent Genes in Streptococcus equi ssp. zooepidemicus

Suppression subtractive hybridization (SSH) was performed with virulent strain ATCC35246 and avirulent strain ST171 to identify novel genes associated with virulence in Streptococcus equi ssp. zooepidemicus (SEZ). There were fourteen genomic regions that only presented in virulent strain ATCC35246. These regions encoded 14 proteins, some of them were homologous to proteins associated with cellular surface structure, molecular synthesis, energy metabolism, regulation, transport systems, and other unknown functions. Primers for 6 particular regions were designed from the already published SEZ sequence. Then, we used PCR to evaluate the distribution and conservation of these 6 DNA fragments in various SEZ strains collected from different sources, regions, groups, and times. The results showed that these 6 DNA fragments were widely distributed in SEZ strains, yet they were not existence in the avirulent strain ST171. Moreover, these fragments could not be detected in other Streptococcus groups.     

Molecular Comparisons of Marek＇s disease virus strains of different pathotypes for their gⅠ, gE, pp38 and meq genes

Five to ten serotype I Marek‘ s disease virus (MDV1) strains of different pathotypes were compared for their DNA sequences of gⅠ, gE, pp38 and meq genes. The reference strains were vMDV GA and JM, vvMDV RB1B and Mdll(pl6), vv MDV strains 648A and 584A, vaccine strain CVI988/Rispens; Chinese strains were: v MDV strain N, vvMDV strain G2, vaccine strain 814. Only random aa changes were found in 12 positions within gE of 497 aa among 10 analyzed strains and in 10 positions within gⅠ of 355 aa among 5 strains. There was no relationship found between virus pathotypes and aa changes of both glycoproteins. The aa changes happened in 14 positions within meq of 339 aa among 5 compared strains. But a proline deletion at aa # 194 in a proline- rich domain of meq were shared by two vaccine strains CVI988/Rispens and 814, the latter was a non - pathogenic vaccine strain of serotype 1 isolated in 1983 in China. In another hand, vv MDV strains 648A demonstrated 5 unique aa changes and 4 of them also located in the proline - rich region. The pp38 was very conservative among sequenced 10 strains, there were only two positions at # 107 and # 109 with an altered in its 290 aa. All tested MDV1 strains had glufamine at # 107, instead, only vaccine CVI988 had arginine at the position and lost its epitope reactive with Mab H19, to which all ether tested MDV1 strains were positive. However, CVI988 and vMDV GA shared a Mab T65 - recognized epitope when there was glyeine at aa # 109. It was glutamie acid at aa # 109 in all other MDV1 strains which were not reactive with Mab T65. It seems like that there is some relationship between pathotypes and sequences of pp38 and meq, but more strains need to be compared.     

鸡卡氏杆菌的分子鉴定及其16S rRNA基因序列分析

2003年Christensen等将过去归为输卵管炎放线杆菌、禽溶血性巴氏杆菌及鸭巴氏杆菌的细菌归为巴氏杆菌科中的一个新属——卡氏杆菌属。卡氏杆菌主要引起产蛋母鸡发病,可以导致输卵管炎、卵巢炎、腹膜炎、败血症、心包炎、肝炎、肠炎和呼吸道疾病等。     

2株枯草芽孢杆菌的分离鉴定及特性研究

【目的】寻求适合制作水产类微生态制剂的益生菌。【方法】从养鱼塘底泥和健康鲫鱼Carassius auratus肠道中分离芽孢杆菌,结合细菌形态学、生理生化特征和16S rRNA序列分析对其进行鉴定,对菌株安全性、高温耐受性、酸性耐受性、拮抗性及产酶情况等特性进行研究。【结果】分离到2株芽孢杆菌,分别命名为B1和B2,细菌形态学、生理生化特征和16S rRNA序列分析的结果显示,B1和B2均为枯草芽孢杆菌Bacillus subtilis。特性研究结果证实B1、B2菌株都具有较好的安全性、高温耐受性和酸性耐受性,可对致病性大肠埃希菌Escherichia coli、金黄色葡萄球菌Staphylococcus aureus、嗜水气单胞菌Aeromonas hydrophila以及温和气单胞菌A.sobria有良好的体外抑菌能力,均具有产脂肪酶、淀粉酶、蛋白酶和纤维素酶的能力。【结论】分离到2株性能优良的枯草芽孢杆菌,可将其作为水产微生态制剂的候选菌株。     

多环芳烃厌氧降解菌的筛选与鉴定

[目的]筛选并鉴定多环芳烃厌氧降解茵。[方法]通过富集,在厌氧条件下从受焦油长期污染的土壤中筛选出多环芳烃的高效厌氧降解茵,并对其进行了生理生化试验和16SrDNA鉴定。[结果]从受焦油长期污染的土壤中分离出2株多环芳烃降解茵W2和Y3,经综合表征和16SrDNA序列分析,初步鉴定菌株W2为鞘氨醇单胞茵属（Sphingomonas sp．）,菌株Y3为芽孢杆菌属（Bacillussp．）。[结论]为多环芳烃的生物降解研究提供了理论依据。     

开菲尔粒中醋酸菌的分离鉴定

从开菲尔粒中分离出2株醋酸菌FJAT-13764和FJAT-13780.利用形态学观察、生理生化和16S rDNA方法对菌株进行分类鉴定.菌株FJAT-13764和FJAT-13780的菌体形态均为圆端直杆菌,单个或成对,无芽孢,其生理生化特征与醋杆菌属Acetobacter基本一致.经16S rDNA基因序列同源性比较和系统发育分析,鉴定菌株FJAT-13764为Acetobacter orientalis(东方醋酸菌),菌株FJAT-13780为Acetobacter syzygii.     

副猪嗜血杆菌的分离与鉴定及其16S rRNA 生物信息学分析

从湖南省内送检的疑似患多发性浆膜炎与关节炎的猪病料中分离到12株细菌,细菌学试验证明12株细菌均符合副猪嗜血杆菌(Haemophilus parasuis,HPS)形态、培养和生化特性.根据HPS 16S rRNA序列设计引物对12株细菌进行PCR扩增,均得到预期目的条带,将扩增片段测序并运用DNAStar软件与GenBank中不同血清型HPS基因序列进行比对,表明其与Genbank中已公布的不同血清型HPS菌株16S rRNA序列的同源性为90.4%~99.9%,其中与血清5型同源性最高,对所测序列与参考序列进行遗传进化树分析,结果表明其中11株属于血清5型HPS.     

不同根际细菌对南方根结线虫抑制效果的研究

采用稀释平板涂布方法从番茄根结土壤中初步筛选出对明胶有水解作用的菌株。通过各菌株发酵上清液对南方根结线虫二龄幼虫死亡率和虫卵孵化率抑制作用,以及拮抗菌悬浮处理番茄根系30 d后观察番茄根结数量变化,进一步筛选获得高效菌株。通过16S rDNA基因序列分析,对能显著抑制根结线虫生长的2株菌株进行了鉴定。结果表明:筛选出了10株对明胶有明显水解圈的细菌,其中菌株BTG和X5具有较强的明胶水解能力。菌株BTG和X5发酵的上清液处理二龄幼虫24 h后的死亡率比无菌上清液处理死亡率提高了72.13%和62.14%;而用菌株上清液处理14 d后的虫卵孵化率比无菌上清液处理的孵化率降低了38.62%和30.73%。菌株BTG和X5的菌悬液处理的番茄根结数比不加菌悬液对照处理根结数分别降低了80.49%和73.17%。经16S rDNA基因序列分析表明,菌株BTG和X5都属于芽孢杆菌。通过比较各株细菌对二龄幼虫(J2)死亡率,虫卵孵化率及番茄根结数量的影响,筛选出了2株可用于生物防治作物根结线虫的芽孢杆菌。     

盐泽地分离的耐盐性芽孢杆菌菌株的分子鉴定

采用生理生化检测、Rep-PCR指纹图谱分析、16S rDNA及gyrB基因序列分析技术,对在青海尕海盐泽地植物根际土壤中分离得到的几株菌落形态较为特殊的芽孢杆菌菌株进行鉴定。生理生化分析结果表明:分离的芽孢杆菌菌株革兰氏染色为阳性。Rep-PCR指纹图谱表明,不同分离菌株间的指纹图谱完全相同,为同种芽孢杆菌。16S rDNA及gyrB基因序列鉴定结果显示,菌株与地衣芽孢杆菌(Bacillus licheniformis)的亲缘关系最近。综合几种鉴定结果,最终将分离自盐泽地的芽孢杆菌菌株鉴定为B.licheniformis。     

采用16S rDNA片段鉴定鳗鲡病原菌的初步研究

初步探讨了采用16S rDNA片段鉴定鳗鲡病原菌的方法.根据已知细菌16S rDNA序列的高度保守区设计引物,利用PCR法扩增16株已鉴定的鳗鲡病原菌的16S rDNA片段,测序分析后,通过Gen-Bank数据库进行同源性检索,并构建相应的系统发育树.结果表明：16株鳗鲡病原菌均扩增到了400bp左右的基因片段,其中14株菌的16S rDNA片段序列与网上已发表的同属菌株的同源性为100%,其余2株为99%;8株病原菌被鉴定到种,分别属于嗜水气单胞菌和温和气单胞菌,其余8株被鉴定到属,分别属于气单胞菌属、假单胞菌属和肠杆菌属;鉴定结果与生化鉴定结果在属的分类单元上符合程度高达82%.     

氨基糖苷类药物高水平耐药16S rRNA甲基化酶基因在动物源大肠杆菌中的检测

为了解郑州地区氨基糖苷类药物高水平耐药16S rRNA甲基化酶基因(armA、rmtA、rmtB、rmtC、rmtD和npmA)在健康动物大肠杆菌中的流行情况,对2009年在郑州地区鸡、犬、猪的肛门拭子中分离保存的231株大肠杆菌进行了药敏试验,并分别设计特异性引物对其进行16S rRNA甲基化酶基因的聚合酶链式反应扩增。结果显示:在6种基因中,鸡、犬源大肠杆菌可检测到armA和rmtB,而猪源大肠杆菌仅检测出rmtB。鸡、犬源大肠杆菌armA的检测率分别为7.6%和3.3%;鸡、犬、猪源大肠杆菌rmtB的检出率分别为47.8%、20.0%和0.9%。其中,鸡、犬中分别有3.3%的大肠杆菌可同时检测到armA和rmtB。     

乳杆菌的分离及鉴定

从健康学龄儿童的新鲜粪便样品中分离得到6株乳杆菌,并对其进行属和种的鉴定。首先通过形态学观察及H2O2酶、糖发酵等生理生化试验对所分得菌株进行初步鉴定,然后利用16S rDNA序列同源性分析方法,对所分得菌株进行16S rDNA基因扩增与测序,测序结果与GenBank中该属内菌株的16S rDNA基因序列进行同源性分析,从而准确鉴定所分得菌株,并申请各菌株的GenBank登录号。经鉴定,其中1株为卷曲乳杆菌,2株为植物乳杆菌,1株为发酵乳杆菌,1株为黏液乳杆菌,1株为唾液乳杆菌。