嗜水气单胞菌气溶素基因的克隆与序列分析

以嗜水气单胞菌BZ和NK分离株的DNA为模板,采用PCR技术,扩增气溶素基因(aerA)的DNA片段,将其克隆到pMDl8-T载体上.通过序列测定,分析结果表明:所克隆的1393 bp片段为aerA部分序列,编码产生464个氨基酸.BZ与NK之间aerA核苷酸同源性为97.6%.氨基酸同源性为98.3%,与其它分离物核苷酸同源性为71.6%～97.5%,氨基酸同源性为68.0%～98.9%.利用邻接法构建了aerA分子树状图,树状图分析表明:气单胞菌属各分离物聚为三支,其中嗜水气单胞菌各菌株之间关系密切,被聚类为同一支.     

和厚朴酚对嗜水气单胞菌气溶素表达的抑制作用

为了研究不同浓度和厚朴酚对嗜水气单胞菌(Aeromonas hydrophila)致病力的影响, 筛选抗嗜水气单胞菌感染的天然化合物, 通过溶血试验、免疫印记试验、荧光定量PCR试验和动物试验进行了研究。结果发现, 和厚朴酚能在亚抑菌浓度下降低嗜水气单胞菌培养物上清中的溶血活性; 蛋白免疫印迹试验发现和厚朴酚能降低嗜水气单胞菌气溶素的分泌; 荧光定量PCR试验进一步表明和厚朴酚与嗜水气单胞菌共培养后降低了气溶素编码基因aerA的转录而降低气溶素的分泌。此外, 通过动物试验发现和厚朴酚治疗能显著提高斑点叉尾鮰( Ictalurus punctatus )嗜水气单胞菌感染模型的存活率。以上研究表明, 和厚朴酚能通过降低气溶素编码基因aerA的转录而降低嗜水气单胞菌的致病力, 和厚朴酚是一种潜在的新型抗嗜水气单胞菌感染的先导化合物。     

人乙型肝炎病毒前表面抗原preS基因的克隆与序列分析

从杭州、兰州两地各一例乙型肝炎病毒(HBV)表面抗原阳性血清中提取病毒DNA,采取PCR技术扩增出前表面抗原(preS)基因片段,重组到质粒载体上,对该基因进行了全序列测定[GenBank索取号CpreS-HZAF325674;preS-LZAF325675].克隆的HBVpreS基因杭州分离物(preS-HZ)和兰州分离物(preS-LZ)全长522个核苷酸,编码174个氨基酸.preS-HZ与已发表的HBVadr亚型上海分离物[8]、北京分离物[9]、日本分离物[5]、HBVadw亚型[10]和ayw亚型[11]preS基因的核苷酸序列同源性分别为96.7%、96.2%、97.3%、88.7%和84.1%,氨基酸序列同源性分别为96.0%、94.9%、97.1%、85.1%和85.4%;preS-LZ与相应序列的核苷酸序列同源性分别为96.4%、96.2%、96.9%、88.7%、83.7%,氨基酸序列同源性分别为94.9%、94.9%、96.0%、85.1%、84.1%.分子进化分析(DNASTAR,1999)表明,克隆的两例HBVpreS基因属于adr亚型.preS-LZ与preS-HZ之间有两个核苷酸变异(对应两个氨基酸变异),相对于以上报道的序列二者含有四个特异的氨基酸突变位点.在免疫保护区内二者具有较好的保守性,可用于表达乙肝重组亚单位疫苗.     

病毒性脑炎病例中埃可病毒11型病毒的基因特征分析

分析埃可病毒11型(Echovirus 11,ECHO 11)福建龙岩分离株的分子生物学特征。收集龙岩市第一医院2011年1~12月临床诊断为病毒性脑炎或中枢神经系统感染的住院病例脑脊液标本进行病毒分离鉴定,从7株经血清中和鉴定的ECHO 11分离株中,选取4株测定VP1完整编码区序列,与GenBank上已发表的ECHO 11型病毒VP1区进行同源性比较及遗传进化分析。4株ECHO 11分离株VPl区序列长度为600个核苷酸,编码200个氨基酸;4株之间的核苷酸同源性为100%,氨基酸同源性为99%~100%;与1953年Gregory原型株之间的核苷酸同源性为75%~76%,氨基酸同源性为90%;与2007年荷兰株(GU393773)之间核苷酸的同源性为94%~95%,氨基酸同源性为98%~99%,同源性最高;与国内2010年山东株之间核苷酸的同源性为74%,氨基酸同源性为88%~89%。系统进化树分析显示,4株龙岩分离株同属D5型,其与D5型病毒株(GU393713)之间核苷酸的同源性为93%,氨基酸同源性为99%。国内分离株之间相对较低的相似性提示国内ECHO 11病毒可能存在不同的传播链。     

甘蔗花叶病毒3’末端基因的克隆及外壳蛋白序列分析比较

选取我国SCMV优势株系A株系的分离物SCMV-CA为材料,经过病毒和病毒RNA的提纯,反转录获得病毒cDNA,并克隆到载体pUC19的SmaI位点上,筛选得到多个重组质粒。选取其中一个克隆SCMV-CA54进行测序,得到一个全长为1296 bp的核苷酸序列。这段序列由一个长为1044 bp的开放阅读框架（ORF）和一个长279 bp的3’末端非编码区序列（3'-UTR）及poly(A)尾巴组成。这个ORF包括病毒完整的外壳蛋白（CP）及部分核内含体蛋白b（NIb）基因序列。将所得序列同已知SCMV亚组中各株系分离物的核苷酸和氨基酸进行同源性比较,结果表明该序列与其它株系分离物CP核苷酸序列的同源性介于63.7%～77.6%之间,氨基酸的同源性介于64%～89%之间。根据马铃薯Y病毒属的序列同源性划分标准,SCMV-CA与其它株系或分离物的同源性关系均介于种与株系划分标准之间。这是我国首次报道SCMVCP基因序列。     

翘嘴鳜病原嗜水气单胞菌分子特征及LAMP检测方法的建立

嗜水气单胞菌(Aeromonas hydrophila)是一种危害鳜鱼养殖生产的重要病原细菌, 为进一步明确该病原菌的分子特征及建立快速检测技术, 实验对引起翘嘴鳜(Siniperca chuatsi)暴发性死亡的病原嗜水气单胞菌进行了致病性、菌株毒力特征研究, 同时以嗜水气单胞菌气溶素基因aerA为分子靶标设计引物, 利用环介导等温扩增技术(Loop-mediated isothermal amplification, LAMP)建立了病原嗜水气单胞菌的快速检测方法。结果表明, 本次引起翘嘴鳜暴发性死亡的病原嗜水气单胞菌半致死浓度为1.6×106 CFU/mL, 携带aerA等14种毒力基因, 此14种毒力基因可用于其致病性分析及分子检测。以气溶素基因aerA设计引物进行的环介导恒温扩增, 结果显示可扩增出阶梯状条带, 加入SYBR Green I染色后呈现绿色的阳性反应, 而对照组均未出现任何扩增条带且反应体系呈现橙色, 表明LAMP检测方法对于嗜水气单胞菌检测具有很好的特异性; 灵敏度检测的最低检测限为4.6×101 CFU/mL; 10种经人工感染的淡水养殖鱼虾组织匀浆增菌液, 提取DNA后进行LAMP方法检测, 结果均可获得阳性扩增结果, 而对照未染菌组呈阴性, 表明该方法具有较好的应用性, 可应用于嗜水气单胞菌引起的水生动物疾病的检测。     

水稻条叶枯病毒(RStV)基因组组分4的克隆与序列分析

利用RTPCR技术合成并扩增了水稻条叶枯病毒(RStV)中国云南分离物基因组组分4的全长cDNA,将PCR产物克隆在载体pCRII上,并进行全序列测定,所得核苷酸序列及推测的氨基酸序列与日本分离物T进行比较。结果表明,在核苷酸水平,两分离物的vORF、vcORF及基因间非编码区序列的同源性分别为94.9%、94.1%、86.1%,5’端非编码区序列相同,而3’非编码区同源性为96.1%,仅有两个核苷酸不同;在氨基酸水平,vORF及vcORF编码蛋白的同源性分别为99.4%和98.3%。可见,编码区的大小及其氨基酸序列和两末端序列都是很保守的。因此,中国云南分离物Y与日本分离物T可能有很近的亲缘关系。     

马铃薯X病毒湖南分离物的鉴定与分组研究

从湖南石门采集表现重花叶症状的马铃薯叶片中分离纯化到一株线状病毒HN021.经双链RNA(ds-RNA)抽提、寄主反应测定、病毒粒子和内含体的形状观察, 初步确定该病毒为马铃薯X病毒 (Potato virus X).以ds-RNA作为模板,用相应引物对HN021分离物的ORF4-UTR-ORF5片段进行RT-PCR,得到1kb左右的双链cDNA片段.对该片段进行克隆和测序,并将测序所得的核苷酸序列与Genbank登录的11株不同分离物的相应片段的核苷酸序列进行同源性比较和分析.结果表明,HN021与分离自南美洲的三株分离物(COAT,KPA和HB)的同源性为78.4%~79.4%,与其它8株(分离自亚洲、欧洲、大洋州和北美洲)分离物的同源性为96.4%-97.8%.从氨基酸水平比较,HN021与COAT,KPA和HB三者CP和8kDa蛋白氨基酸序列同源性分别为86.5%~89.0%和74.3%~75.7%,相应地与其它8株分离物的同源性分别为97.1%-98.7% 和97.1%-100%.序列分析的结果证实了HN021分离物为马铃薯X病毒,同时表明PVX明显存在两个组(组Ⅰ和组Ⅱ),HN021和其它来自亚洲、欧洲、大洋州、北美洲分离物的组II,3个南美洲分离物属于组I.     

药用植物柴胡病毒病病原物的分子鉴定

利用非序列依赖性扩增(Sequence-independent amplification,SIA)方法对所采柴胡病样进行分子鉴定。序列测定及分析发现,伴有花叶症状的柴胡受到黄瓜花叶病毒(Cucumber mosaic virus,CMV)和蚕豆萎蔫病毒2号(Broad bean wilt virus 2,BBWV2)的复合侵染。为明确柴胡CMV分离物(CMV-SXCH)和柴胡BBWV2分离物(BBWV2-CH)的分类地位,进一步克隆CMV-SXCH的CP、MP和BBWV2-CH的LCP、SCP;序列比对发现,CMV-SXCH与CMV亚组ⅠB中株系XJ2相似性最高,其核苷酸和氨基酸序列同源性分别为99.1%、99.5%;BBWV2-CH与BBWV2中的K株系相似性最高,核苷酸和氨基酸序列同源性分别为95.4%、99.2%。系统进化树分析表明,CMV-SXCH与大多数CMV中国分离物聚类为一簇,同属于CMV亚组ⅠB;BBWV2-CH与BBWV2韩国K株系聚类为一簇,亲缘关系最近。     

湖北地区暴发病池塘中嗜水气单胞菌的遗传多样性和毒力特征研究

为了调查引起鱼类运动型气单胞菌败血症(俗称暴发病)的嗜水气单胞菌的遗传多样性和毒力特征, 阐明其流行规律, 研究于2006-2009年度从湖北省内3个不同地区的6个发病鱼塘中分离了30株嗜水气单胞菌, 其中20株为临床株(分离自血液、肝脏、肾脏或腹水), 6株为肠道株, 4株为池水株。基于所有菌株gyrB基因序列, 构建了系统发育树; 通过ERIC (Enterobacterial repetitive intergenic consensus, 肠道细菌基因间重复序列)指纹图谱进行菌株的遗传分型; 用PCR方法检测了7个毒力基因在菌株中的分布模式。这7个基因包括气溶素(aerA)、溶血素(hlyA)、热不稳定性细胞兴奋性肠毒素(alt)、热稳定性细胞兴奋性肠毒素(ast)、弹性蛋白酶(ahpB)、脂酶(lip)和鞭毛基因(fla)。此外, 以斑马鱼为感染对象, 通过腹腔注射测定了15株代表菌株的毒力。结果表明: 不同来源的20株临床株、1株肠道株和3株池水株具有相同的遗传特性, 体现为在系统树上聚为一枝, 序列相似性为100%, 具有相同的ERIC指纹图谱, 毒力基因分布模式为: aerA+hlyA+alt+ast+ahpB+lip+fla+, 且均为强毒株(LD50 9.74104cfu/尾)。与临床株相比, 其余5株肠道株和1株池水株或具有不同的ERIC指纹图谱或具有不同的毒力基因分布模式, 显示出了遗传多样性, 且毒力均弱于临床株(LD501.01106cfu/尾)。这说明在一定时间、一定区域内, 作为暴发病病原的嗜水气单胞菌为同一克隆系在流行, 不存在明显的变异或遗传多样性。此结果有助于阐明嗜水气单胞菌引起的暴发病的流行规律, 制定相应的防御措施。多种毒力基因在致病性菌株中的联合流行为发病机理的解析奠定了基础。此外, 鉴于毒力基因谱与致病性之间的相关性, 表明毒力基因可作为标记基因, 用于致病性菌株的检测。       

Sequence analysis of amplified DNA fragments containing the region encoding the putative lipase substrate-binding domain and genotyping of Aeromonas hydrophila

DNA fragments were amplified by PCR from all tested strains of Aeromonas hydrophila, A. caviae, and A. sobria with primers designed based on sequence alignment of all lipase, phospholipase C, and phospholipase A1 genes and the cytotonic enterotoxin gene, all of which have been reported to have the consensus region of the putative lipase substrate-binding domain. All strains showed lipase activity, and all amplified DNA fragments contained a nucleotide sequence corresponding to the substrate-binding domain. Thirty-five distinct nucleotide sequence patterns and 15 distinct deduced amino acid sequence patterns were found in the amplified DNA fragments from 59 A. hydrophila strains. The deduced amino acid sequences of the amplified DNA fragments from A. caviae and A. sobria strains had distinctive amino acids, suggesting a species-specific sequence in each organism. Furthermore, the amino acid sequence patterns appear to differ between clinical and environmental isolates among A. hydrophila strains. Some strains whose nucleotide sequences were identical to one another in the amplified region showed an identical DNA fingerprinting pattern by repetitive extragenic palindromic sequence-PCR genotyping. These results suggest that A. hydrophila, and also A. caviae and A. sobria strains, have a gene encoding a protein with lipase activity. Homologs of the gene appear to be widely distributed in Aeromonas strains, probably associating with the evolutionary genetic difference between clinical and environmental isolates of A. hydrophila. Additionally, the distinctive nucleotide sequences of the genes could be attributed to the genotype of each strain, suggesting that their analysis may be helpful in elucidating the genetic heterogeneity of Aeromonas.     

Identification of a new hemolysin from diarrheal isolate SSU of Aeromonas hydrophila

A clinical strain SSU of Aeromonas hydrophila produces a potent cytotoxic enterotoxin (Act) with cytotoxic, enterotoxic, and hemolytic activities. A new gene, which encoded a hemolysin of 439-amino acid residues with a molecular mass of 49 kDa, was identified. This hemolysin (HlyA) was detected based on the observation that the act gene minus mutant of A. hydrophila SSU still had residual hemolytic activity. The new hemolysin gene (hlyA) was cloned, sequenced, and overexpressed in Escherichia coli. The hlyA gene exhibited 96% identity with its homolog found in a recently annotated genome sequence of an environmental isolate, namely the type strain ATCC 7966 of A. hydrophila subspecies hydrophila. The hlyA gene did not exhibit any homology with other known hemolysins and aerolysin genes detected in Aeromonas isolates. However, this hemolysin exhibited significant homology with hemolysin of Vibrio vulnificus as well as with the cystathionine beta synthase domain protein of Shewanella oneidensis. The HlyA protein was activated only after treatment with trypsin and the resulting hemolytic activity was not neutralizable with antibodies to Act. The presence of the hlyA gene in clinical and water Aeromonas isolates was investigated and DNA fingerprint analysis was performed to demonstrate its possible role in Aeromonas virulence.     

牦牛与其他物种ZFX/ZFY基因片段间的进化关系

利用PCR扩增、克隆和序列分析法对牦牛ZFX/ZFY基因第11外显子部分片段进行了研究,并同来自于NCBI GenBank中人、猩猩、普通牛等9个物种的ZFX/ZFY基因核苷酸及其氨基酸序列进行了进化分析.结果表明,牦牛ZFX、ZFY基因间核苷酸序列同源性为94.1%,显示同一物种同源基因ZFX/ZFY间存在变异;比较的10个物种间ZFX基因核苷酸序列同源性为87.7%、ZFY基因为81.7%,相应ZFX、ZFY氨基酸同源性分别为96.6%、91.0%,ZFY基因的变异性大于ZFX基因,显示X染色体与Y染色体可能是独立进化.     

我国部分地区H9亚型禽流感病毒血凝素基因序列比较与遗传发生关系分析

为从分子水平掌握我国H9亚型AIV的遗传变异情况和流行规律,本研究汇集近年来从我国12个省、市、自治区的发病鸡群中分离到的23株H9亚型禽流感病毒,通过RT-PCR方法和核苷酸序列测定获得了23个毒株的HA基因cDNA核苷酸序列。核苷酸和推导的氨基酸序列同源性比较结果表明,这些毒株HA基因的核苷酸序列同源性为94．1％～100％,氨基酸序列同源性为95．4％～100%;将这23个毒株和来自亚洲及世界其它地区的另外31株的HA基因cDNA序列同源性进行比较发现,分离自香港的HK170499株与日本的2个毒株关系较近;氨基酸序列分析发现,CKGS199、CKTJ196、CKTJ296、CKSH300和CKBJ197五个毒株各发生了一个潜在的糖基化位点的丢失。54株H9亚型AIVHA基因55bp～1152bp的氨基酸序列分析发现,裂解位点尽管有10种基序,但本研究中的23株和近年来从我国大陆和香港地区的分离的毒株则均为RSSR↓GLF;构成受体结合位点的191位氨基酸有一个规律,即所有中国大陆毒株与部分香港毒株都为N,其它毒株均为H,141aa～143aa处的糖基化位点有与191aa类似的规律,即：凡是191aa为N的毒株,该处均为NVS（CKBJ194除外）,凡是191aa为H的毒株,则该处均为NVT;遗传发生关系分析,中国大陆毒株处于欧亚谱系的第一支。本研究结果表明近年来我国鸡群中H9N2亚型禽流感病毒的感染流行可能有一个共同的来源,这为制定防治该亚型禽流感流行的有效对策提供了重要的科学依据。     

Sequence analysis of NS3 protease gene in clinical strains of hepatitis C virus

The amino terminal region of the non structural gene 3 (NS3) of hepatitis C virus (HCV) is a chymotripsinlike serine-protease responsible for cleavage of the non structural proteins of Hepatitis C virus (HCV). In order to investigate the genetic variation of this region, we developed a nested PCR to obtain NS3 protease sequences from 54 patients chronically infected with HCV genotypes 1a, 1b and 3, respectively. Comparison of nucleotide and amino acids sequences of NS3 protease domain with consensus sequence obtained within the same genotype, showed 3.73% nucleotide divergence and 1.64% amino acid divergence in isolates of genotype 3a, whereas isolates 1a exhibited 4.45% nucleotide and 4% amino acid change, respectively. Finally, NS3 sequence from 1b isolates revealed 6.47% nucleotide and 3.5 % aa changes. Comparison of consensus amino acid sequences derived from isolates 1a, 1b and 3, with the HCV prototypes showed a low amino acid sequence diversity. However, the consensus sequence of HCV genotype 3 isolates showed an amino acid changed from the prototype, that was located within a region important for enzyme structure and activity. These results indicated that the NS3 protease gene is highly conserved within the same HCV genotype. The domains involved in enzyme function were highly conserved in 1a and 1b strains, whereas consensus sequence of isolates 3a showed that the majority of these strains were not perfectly conserved in one of such regions. These findings altogether suggested that the NS3 protease enzyme of HCV may constitute an important target for antiviral therapy, but the NS3 protease variability of isolates 3 within a region that is a potential target for antiviral therapy could pose a problem for structure based drug development.     

The cDNA sequence and chromosomal location of the murine GABAA alpha 1 receptor gene.

The murine GABAA/benzodiazepine (GABAA/BZ) receptor alpha 1 subunit cDNA has been isolated from a BALB/c mouse brain library and sequenced. The cDNA is 2665 nucleotides long with an open reading frame of 455 amino acids. It shows significant homology to the GABAA receptor alpha 1 subunit cDNA sequences of other species. Excluding deletions, the murine GABAA alpha 1 receptor exhibits 96% nucleotide and 100% amino acid sequence homology to the rat alpha 1 receptor cDNA and over 91% nucleotide and 98% amino acid sequence homology to the bovine and human alpha 1 receptor cDNAs in the protein coding region. This murine cDNA was used to locate the alpha 1 receptor subunit gene, Gabra-1, to murine Chromosome 11 between Il-3 and Rel. This assignment extends proximally the segment of mouse Chromosome 11 with known homology to human chromosome 5.     

Cloning, expression, and mapping of the Aeromonas hydrophila aerolysin gene determinant in Escherichia coli K-12.

DNA sequences corresponding to the aerolysin gene (aer) of Aeromonas hydrophila AH2 DNA were identified by screening a cosmid gene library for hemolytic and cytotoxic activities. A plasmid containing a 5.8-kilobase EcoRI fragment of A. hydrophila DNA was required for full expression of the hemolytic and cytotoxic phenotype in Escherichia coli K-12. Deletion analysis and transposon mutagenesis allowed us to localize the gene product to 1.4 kilobases of Aeromonas DNA and define flanking DNA regions affecting aerolysin production. The reduced hemolytic activity with plasmids lacking these flanking regions is associated with a temporal delay in the appearance of hemolytic activity and is not a result of a loss of transport functions. The aerolysin gene product was detected as a 54,000-dalton protein in E. coli maxicells harboring aer plasmids and by immunoblotting E. coli whole cells carrying aer plasmids. We suggest that the gene coding aerolysin be designated aerA and that regions downstream and upstream of aerA which modulate its expression and activity be designated aerB and aerC, respectively.