问号钩端螺旋体基因组DNA芯片的研制

目的 研制并初步评估问号钩端螺旋体(简称钩体)赖型赖株的基因组DNA芯片。方法 利用Primegens引物设计软件筛选出问号钩体赖型赖株全基因组中的特异性基因进行引物设计。对成功设计出相应引物的3 290个基因用聚合酶链反应方法进行扩增,以纯化后的产物点样制备芯片。并用双色荧光杂交策略对芯片质量进行了初步平估。结果 共获得3 290个基因产物用于点样。参考株自身杂交实验结果表明:该芯片有较高的点一致性、信噪比和较低的假阳性率。结论 成功制备了包含问号钩体赖型赖株3 290个目的基因的基因组DNA芯片,并可用于基于该芯片的问号钩体比较基因组学的研究。     

钩端螺旋体liprmA基因的表达及其产物的纯化与功能分析

以钩端螺旋体基因组DNA为模板,通过酶联聚合反应（PCR）得到钩端螺旋体中prmA的同源基因liprmA的全基因编码序列,并克隆到原核表达载体pET22b中。通过优化大肠杆菌培养和诱导条件,含目的蛋白的融合蛋白可溶表达量达到40 mg/L,约占菌体总蛋白的40%。经Ni-NTA His Bind亲和柱纯化,得到纯度大于95%的目的蛋白。氨基酸序列同源性分析显示liPrmA与原核生物和真核生物的核糖体蛋白L11甲基化转移酶的功能域一级结构高度一致;活性分析显示,纯化的liPrmA有钩端螺旋体核糖体蛋白L11甲基化转移酶的活性。     

致病钩体表层膜蛋白新基因（Lslp）的克隆表达及免疫原性研究

克隆表达钩端螺旋体表层膜蛋白新基因Lslp并分析表达产物的免疫原性。根据前期研究得到的致病钩体新基因Lslp(GenBankAF32 5 80 7)的序列设计引物 ,在 6株致病钩体中扩增Lslp基因并测序。以BamHⅠ酶切Lslp和pGEX 1 λT ,构建重组质粒并用酶切和PCR鉴定 ,进一步在大肠杆菌中诱导表达 ,并进行免疫印迹分析 ;纯化表达产物免疫家兔 ,ELISA检测血清抗体滴度。结果显示Lslp在 6株致病钩体中均能扩增出相应片段 ,且序列同源性达到99 6 % ;构建高效原核表达重组质粒pGST LslP ,经IPTG诱导在大肠杆菌中可表达出 6 6kDGST融合蛋白 ,并能与全钩抗血清发生免疫印迹反应 ;将上述融合蛋白免疫新西兰大白兔产生 1 :5 1 2 0高滴度的IgG抗体。研究结果提示致病钩体膜蛋白新基因Lslp可在大肠杆菌进行高效表达 ,表达产物能被全钩抗血清识别 ,为研究钩体的致病机制和筛选保护性抗原提供了基础     

集胞藻ORFs侧翼序列的PCR扩增和定向基因插入失活策略

针对集胞藻PCC6803的1927个待定编码基因进行了两侧序列的PCR扩增。4个亚株基因组在sll0267-sll0269区域的PCR扩增产物与Kazusa DNA数据存在差异,以叶绿素合成基因chlH和chlL为例,显示三片段连接PCR产物可有效用于集胞藻6803基因组定向插入失活。     

降低mRNA差异显示技术假阳性率的一种方法

为了探讨降低mRNA差异显示技术假阳性率的方法 ,进一步提高此技术的可靠性 ,提取了手术切除肝癌及非癌肝组织成对标本的总RNA ,逆转录获得cDNA片段 ,以mRNA差异显示方法筛选差异表达基因 ,选取较明显的一条差异表达条带 ,行进一步PCR扩增 .分别对PCR产物及其经TA克隆后随机挑选的 6个单克隆质粒DNA进行序列分析 ,并通过GenBank BLAST数据库进行序列的同源性比较 ,以Northern杂交予以来源确认 .自 72 0余条扩增条带中共选出 2 8条差异条带 .序列分析及同源性比较表明 ,所选择条带的PCR产物为一可能的新基因片段 ;而随机选择的 6个TA克隆质粒DNA中 ,有 4个为同一已知基因片段 ,一个为另一已知基因片段 ,一个为一可能的新基因片段 .同源性比较表明 ,PCR产物直接测序所得序列与TA克隆质粒DNA的 6个片段不具同源性 .结果表明 ,mRNA差异显示条带可能由 1条以上分子量相似的片段构成 ,直接对PCR产物行序列分析并以其为探针进行Northern杂交 ,是导致出现假阳性片段的原因之一 .将PCR产物进行TA克隆 ,对单克隆质粒DNA进行序列分析并以其为探针进行Northern杂交 ,可能是解决此问题的一种较好方法 .     

大肠杆菌ubiC基因的克隆及序列分析

研究以克隆得到正确序列的大肠杆菌ubiC基因目的,实验通过PCR方法从大肠杆菌基因组中扩增得到了ubiC基因,扩增产物克隆到pUC118载体,转化大肠杆菌JM109,DNA序列分析结果表明克隆得到的大肠杆菌ubiC基因碱基序列正确。     

猪繁殖与呼吸综合征病毒S1株基因组序列测定和分析

应用RT-PCR方法分段扩增出PRRSV上海分离株S1毒株的4条基因大片段,扩增后的产物分别克隆于pCR-XL-TOPO载体鉴定后测序,同时应用RACE方法对S1毒株的3'和5'基因末端进行了成功的扩增并克隆于pMD-18T载体进行测序,按顺序将这些序列进行拼接得到PRRSV S1株全基因组cDNA序列.测序结果表明PRRSV S1株基因组全长15441 bp,包含9个开放式阅读框,5'UTR含有189nt,3'端UTR含有181nt,其中包含30nt Poly (A).基因组序列分析结果显示该病毒与ATCC VR-2332和BJ-4分离株的核苷酸同源性分别99.5%和99.6%.与另一国内分离株CH-1a的核苷酸同源性为90.8%.     

猪繁殖与呼吸综合征病毒S1株基因组序列测定和分析

应用RT-PCR方法分段扩增出PRRSV上海分离株S1毒株的4条基因大片段,扩增后的产物分别克隆于pCR-XL-TOPO载体鉴定后测序,同时应用RACE方法对S1毒株的3′和5′基因末端进行了成功的扩增并克隆于pMD-18T载体进行测序,按顺序将这些序列进行拼接得到PRRSVS1株全基因组cDNA序列。测序结果表明PRRSVS1株基因组全长15441bp,包含9个开放式阅读框,5′UTR含有189nt,3′端UTR含有181nt,其中包含30ntPoly(A)。基因组序列分析结果显示该病毒与ATCCVR-2332和BJ-4分离株的核苷酸同源性分别99.5%和99.6%。与另一国内分离株CH-1a的核苷酸同源性为90.8%。     

猪源肠出血性大肠杆菌CD18株fedA基因的克隆及表达

目的:获得重庆猪源肠出血性大肠杆菌(EHEC)强毒株CD18株fedA基因表达产物。方法:根据GenBank中的fedA基因序列设计引物,从重庆猪源EHEC强毒株CD18株基因组中经PCR扩增目的片段,克隆到pUC19质粒,亚克隆到表达载体pET28b( )的SalⅠ-HindⅢ位点后转化大肠杆菌BL21(DE3),经IPTG诱导表达,Ni柱法纯化,SDS-PAGE及Western印迹检验表达产物。结果:CD18株fedA与文献报道的fedA的序列同源性为99.3%,推导的氨基酸序列的同源性为98.7%,表达产物在50～100mmol/L咪唑洗脱时出峰,SDS-PAGE显示其相对分子质量20000,Western印迹证明该蛋白条带能与分子标记蛋白His6抗体发生特异反应。结论:克隆到猪源EHECCD18株fedA基因,并在大肠杆菌中得到表达。     

东方田鼠特异DNA片段的克隆及核苷酸序列分析

目的获得东方田鼠的特异DNA序列.方法Aβ基因使用PCR,基因克隆,斑点杂交,DNA序列分析,生物信息学技术.结果根据小鼠MHCⅡ外显子2及其两侧序列,合成引物并扩增东方田鼠基因组DNA,将PCR产物回收、测序后,分别设计内引物扩增东方田鼠基因组DNA,其中一对引物可得到特异性扩增带,将得到的DNA片段插入PGEM-Teasy载体,进行序列分析.用这对引物扩增人、昆明小鼠、BALB/c小鼠及C57BL/6J小鼠基因组DNA,均无扩增产物.以东方田鼠特异性扩增产物为探针进行斑点杂交,除东方田鼠基因组DNA外,其他几种动物基因组DNA均为阴性结果.进一步对该DNA片段进行了BLAST同源性搜索和外显子预测,在Genbank中没有发现高度同源序列,并且找到一个可能的外显子,该外显子由69个氨基酸组成.结论获得的DNA片段为东方田鼠的特异片段,这将为从分子水平深入研究东方田鼠的遗传背景、生物进化规律以及东方田鼠抗日本血吸虫的机理奠定基础.     

赖型钩端螺旋体外膜蛋白基因结构比较性研究

用ＰＣＲ方法扩增不同毒力赖型钩体ＯｍｐＬ１基因片段,进行序列测定,用相关软件比较分析核苷酸序列、蛋白质二级结构以及限制性内切酶谱,不同毒力赖型钩体能扩增出９６０ｂｐ的片段,非致病Ｐａｔｏｃ株未能扩出相应片段,中国赖型参考株ＯｍｐＬ１序列（ＧｅｎｅＢａｎｋ Ｎｏ．ＡＦ２５０３１８）与流感伤寒型相应序列比较有９８个核苷酸差异,同源性为８９．８％,二级结构预测和氨基酸疏水图显示变异主要发生在跨膜蛋白的膜     

Simultaneous detection and differentiation of pathogenic and nonpathogenic Leptospira spp. by multiplex real-time PCR (TaqMan) assay

Leptospirosis, caused by pathogenic Leptospira, is one of the most important zoonoses in the world. Several molecular techniques have been developed for detection and differentiation between pathogenic and saprophytic Leptospira spp. The aim of this study was to develop a rapid and simple assay for specific detection and differentiation of pathogenic Leptospira spp. by multiplex real-time PCR (TaqMan) assay using primers and probes targeting Leptospira genus specific 16S ribosomal RNA gene, the pathogen specific lig A/B genes and nonpathogen Leptospira biflexa specific 23S ribosomal RNA gene. Sixteen reference strains of Leptospira spp. including pathogenic and nonpathogenic and ten other negative control bacterial strains were used in the study. While the 16S primers amplified target from both pathogenic and non-pathogenic leptospires, the ligA/B and the 23S primers amplified target DNA from pathogenic and non-pathogenic leptospires, respectively. The multiplex real-time PCR (TaqMan) assay detection limit, that is, the sensitivity was found approximately 1 x 10(2) cells/ml for ligA/B gene and 23S ribosomal RNA gene, and 10 cells/ml 16S ribosomal RNA. The reaction efficiencies were 83-105% with decision coefficients of more than 0.99 in all multiplex assays. The multiplex real-time PCR (TaqMan) assay yielded negative results with the ten other control bacteria. In conclusion, the developed multiplex real-time PCR (TaqMan) assay is highly useful for early diagnosis and differentiation between pathogenic and non-pathogenic leptospires in a reaction tube as having high sensitivity and specificity.     

Molecular cloning and sequence analysis of the gene encoding OmpL1, a transmembrane outer membrane protein of pathogenic Leptospira spp.

Pathogenic Leptospira spp. are spirochetes that have a low transmembrane outer membrane protein content relative to that of enteric gram-negative bacteria. In a previous study we identified a 31-kDa surface protein that was present in strains of Leptospira alstoni in amounts which correlated with the outer membrane particle density observed by freeze fracture electron microscopy (D. A. Haake, E. M. Walker, D. R. Blanco, C. A. Bolin, J. N. Miller, and M. A. Lovett, Infect. Immun. 59:1131-1140, 1991). The N-terminal amino acid sequence was used to design a pair of oligonucleotides which were utilized to screen a lambda ZAP II library containing EcoRI fragments of L. alstoni DNA. A 2.5-kb DNA fragment which contained the entire structural ompL1 gene was identified. The structural gene deduced from the sequence of this DNA fragment would encode a 320-amino-acid polypeptide with a 24-amino-acid leader peptide and a leader peptidase I cleavage site. Processing of OmpL1 results in a mature protein with a predicted molecular mass of 31,113 Da. Secondary-structure prediction identified repeated stretches of amphipathic beta-sheets typical of outer membrane protein membrane-spanning sequences. A topological model of OmpL1 containing 10 transmembrane segments is suggested. A recombinant OmpL1 fusion protein was expressed in Escherichia coli in order to immunize rabbits with the purified protein. Upon Triton X-114 extraction of L. alstoni and phase separation, anti-OmpL1 antiserum recognized a single band on immunoblots of the hydrophobic detergent fraction which was not present in the hydrophilic aqueous fraction. Immunoelectron microscopy with anti-OmpL1 antiserum demonstrates binding to the surface of intact L. alstoni. DNA hybridization studies indicate that the ompL1 gene is present in a single copy in all pathogenic Leptospira species that have been tested and is absent in nonpathogenic Leptospira species. OmpL1 may be the first spirochetal transmembrane outer membrane protein for which the structural gene has been cloned and sequenced.     

Identification and Analysis of Genes Present in Leptospira interrogans serovar lai but Absent in L. biflexa serovar monvalerio

Leptospirosis is a globally important zoonotic diseasecaused by the pathogenic species of the spirochete genus,Leptospira including L. interrogans, L. kirschneri, L.noguchii, L. borgpetersenii, L. santarosai, L. weilii andetc. [1]. Pathogenic leptospires …     

Identification and analysis of genes present in Leptospira interrogans serovar lai but absent in L. biflexa serovar monvalerio

Genes present in virulent bacterial strains but absent in avirulent close relatives can be of great biologic and clinical interest. This project aimed to identify strain specific DNA sequences of Leptospira interrogens serovar lai, which is absent in the saprophytic L. biflexa serovar monvalerio, via suppression subtractive hybridization with the former as the tester while the latter as the driver. The mixture of PCR amplified DNA fragments from two subtractive hybridization experiments were cloned into pMD 18-T vector and the positive clones were identified by dot blotting against the chromosome DNA of the two strains individually. After DNA sequencing and analysis, the distribution of these genomic fragment sequences in a panel of pathogenic and nonpathogenic leptospires was investigated employing dot blot analysis. Among the 188 positive clones randomly chosen, 24 contained the tester strain specific genomic regions, of which, 5 were non-coding fragments while the others contained 23 distinct protein coding sequences. Besides 9 genes encoding functional proteins, 12 genes encode unknown proteins and the rest two genes encode proteins with recognizable domain structures, one for a putative leucine-rich repeats (LRR) family protein while the other as an outer-membrane protein. Our experiment results indicated that suppression subtractive hybridization is effective for screening specific DNA sequences between two leptospiral strains, and some of these sequences might be responsible for virulence determination. Further analysis of these DNA sequences will provide important information on the pathogenesis of Leptospira.     

Identification and partial characterization of a novel hemolysin from Leptospira interrogans serovar lai

It has been suggested that leptospiral hemolysins are important in the virulence and pathogenesis of leptospirosis. We have isolated an Escherichia coli clone carrying the 7.8kb DNA insert from a genomic library of Leptospira interrogans serovar lai by plaque hybridization using a sequence derived from the sphingomyelinase C gene (sphA) of L. borgpetersenii. The clone showed a clear beta-hemolytic zone on sheep blood agar and high hemolytic activities on both human and sheep erythrocytes in liquid assays. The clone carried at least two genes responsible for the hemolytic activities, encoded by two open reading frames of 1662 and 816 nucleotides, which are named sphH and hap-1 (hemolysis associated protein-1), respectively. The SphH showed 75% homology to the SphA at the amino acid level, and the Hap-1 showed no significant homology in major databases. Interestingly, however, E. coli cells harboring sphH did not show sphingomyelinase or phospholipase activities. Moreover, SphH-mediated hemolysis was osmotically protected by polyethylene glycol 5000, suggesting that the hemolysis is likely to be caused by pore formation on the membrane. The SphH was successfully expressed in E. coli as a histidine (His)-SphH fusion protein. Both sphH and hap-1 were highly conserved among the Leptospira species, except for the absence of sphH in non-pathogenic L. biflexa serovar patoc. We concluded that the SphH is a novel hemolysin of a pathogenic Leptospira species, which may be a putative pore-forming protein.     

Cloning of genes for a hemolytic factor of Leptospira interrogans serovar autumnalis strain Congo 21-543

A DNA fragment encoding a hemolytic factor was cloned from the parasitic spirochete Leptospira interrogans serovar autumnalis strain Congo 21-543. Initial clones were isolated by screening a genomic library in pBR322 in Escherichia coli for hemolytic activity. Hemolytic activity was coded by a 4.5 kilobase BamHI-HindIII fragment. Southern hybridization with DNAs from other strains of Leptospira using this gene as a probe showed that DNAs from non-parasitic strains failed to hybridize with the probe, whereas those from all parasitic strains tested had the sequence which hybridize to the probe.     

Isolation and characterization of the catalase gene from Rhizobium sp. SNU003, a root nodule symbiont of Canavalia lineata

A catalase gene from Rhizobium sp. SNU003, a root nodule symbiont of Canavalia lineata, was cloned and its nucleotide sequence was determined. The Rhizobium DNA of about 280 bp was amplified using two PCR primers synthesized from the conserved sequences of the type I catalase gene. The nucleotide sequence of the amplified fragment revealed three regions that were conserved in the catalase, showing it as being part of the catalase gene. A genomic Southern hybridization using this fragment as a probe showed that the 5.5 kb PstI, 1.8 kb EcoRI, and 0.7 kb StyI fragments hybridized strongly with the probe. The Rhizobium genomic library constructed into the EMBL3 vector was screened, and one catalase clone was selected. The nucleotide sequence of the 5.5 kb PstI fragment from the clone revealed an open reading frame of 1455 bp, encoding a polypeptide of 485 amino acids with a molecular mass of 54,958 Da and a pI of 6.54. The predicted amino acid sequence of the catalase is 66.3% identical to that of Bacteroides fragilis, but was only 53.3% identical to the Rhizobium meliloti catalase.     

Polymerase chain reaction assay specific for pathogenic Leptospira based on the gene hap1 encoding the hemolysis-associated protein-1

In this study, we used Southern hybridization of genomic DNA with the integral hap1 gene as a probe to show that this gene is only present in pathogenic Leptospira strains. We then selected PCR primers based on the hap1 gene, and tested them on several Leptospira strains and biological samples. Specific amplification was obtained for all pathogenic strains tested. Negative PCR results were observed with all saprophytic leptospire strains used as well as with other spirochetes and bacteria commonly found in biological samples. The results of direct PCR performed on biological samples, such as blood, urine or kidneys correlated with the results obtained with the classical Leptospira tests (culture and MAT). A PCR assay based on this gene would be a very useful tool for the rapid, sensitive and specific identification of pathogenic leptospires in samples for diagnosis or epidemiological survey.