Heterologous modules for efficient and versatile PCR-based gene targeting in Schizosaccharomyces pombe

We describe a straightforward PCR-based approach to the deletion, tagging, and overexpression of genes in their normal chromosomal locations in the fission yeast Schizosaccharomyces pombe. Using this approach and the S. pombe ura4⁺ gene as a marker, nine genes were deleted with efficiencies of homologous integration ranging from 6 to 63%. We also constructed a series of plasmids containing the kanMX6 module, which allows selection of G418-resistant cells and thus provides a new heterologous marker for use in S. pombe. The modular nature of these constructs allows a small number of PCR primers to be used for a wide variety of gene manipulations, including deletion, overexpression (using the regulatable nmt1 promoter), C- or N-terminal protein tagging (with HA, Myc, GST, or GFP), and partial C- or N-terminal deletions with or without tagging. Nine genes were manipulated using these kanMX6 constructs as templates for PCR. The PCR primers included 60 to 80 bp of flanking sequences homologous to target sequences in the genome. Transformants were screened for homologous integration by PCR. In most cases, the efficiency of homologous integration was ≥50%, and the lowest efficiency encountered was 17%. The methodology and constructs described here should greatly facilitate analysis of gene function in S. pombe. © 1998 John Wiley & Sons, Ltd.     

New modules for PCR-based gene targeting in Candida albicans: rapid and efficient gene targeting using 100 bp of flanking homology region

The use of PCR-based techniques for directed gene alterations has become a standard tool in Saccharomyces cerevisiae. In our efforts to increase the speed of functional analysis of Candida albicans genes, we constructed a modular system of plasmid vectors and successfully applied PCR-amplified functional analysis (FA)-cassettes in the transformation of C. albicans. These cassettes facilitate: (a) gene disruptions; (b) tagging of 3'-ends of genes with green fluorescent protein (GFP); and (c) replacements of endogenous promoters to achieve regulated expression. The modules consists of a core of three selectable marker genes, CaURA3, CaHIS1 and CaARG4. Modules for C-terminal GFP-tagging were generated by adding GFP-sequences flanked at the 5'-end by a (Gly-Ala)3-linker and at the 3'-end by the S. cerevisiae URA3-terminator to these selection markers. Promoter exchange modules consist of the respective marker genes followed by the regulatable CaMAL2 or CaMET3 promoters at their 3'-ends. In order to ensure a reliably high rate of homologous gene targeting, the flanking homology regions required a size of 100 bp of gene-specific sequences, which were provided with the oligonucleotide primers. The use of shorter flanking homology regions produced unsatisfactory results with C. albicans strain BWP17. With these new modules only a minimal set of primers is required to achieve the functional analysis of C. albicans genes and, therefore, provides a basic tool to increase the number of functionally characterized C. albicans genes of this human pathogen in the near future.     

Cassettes for the PCR-mediated construction of regulatable alleles in Candida albicans

The recent availability of genome sequence information for the opportunistic pathogen Candida albicans has greatly facilitated the ability to perform genetic manipulations in this organism. Two important molecular tools for studying gene function are regulatable promoters for generating conditional mutants and fluorescent proteins for determining the subcellular localization of fusion gene products. We describe a set of plasmids containing promoter-GFP cassettes (P(MET3)-GFP, P(GAL1)-GFP, and P(PCK1)-GFP), linked to a selectable nutritional marker gene (URA3). PCR-mediated gene modification generates gene-specific promoter, or gene-specific promoter-GFP, fusions at the 5'-end of the gene of interest. One set of primers can be used to generate three strains expressing a native protein of interest, or an amino-terminal GFP-tagged version, from three different regulatable promoters. Thus, these promoter cassette plasmids facilitate construction of conditional mutant strains, overexpression alleles and/or inducible amino-terminal GFP fusion proteins.     

转基因玉米59122品系的特异性检测

使用反向聚合酶链式反应(PCR)技术克隆了转基因玉米59122的外源基因与玉米基因组之间的两段侧翼序列,并据其左侧侧翼序列设计了具品系特异性的引物,运用半巢式PCR技术建立了59122的品系特异性二重PCR检测方法,扩增片段100bp,横跨pat终止子与转基因玉米侧翼基因之间。以转基因玉米59122、MON863、MON810、GA21、NK603,转基因大豆Roundup Ready和转基因油菜GT73等为材料,证明本方法与其他转基因作物具有高特异性。本方法在检测59122时,确定出连接体系中线性DNA的最佳质量浓度为1ng/μL左右,检出限达到0.1%,灵敏度为38个单倍体基因组拷贝数。因此可准确、快速、高效地检测转基因玉米及其产品,或作为常规PCR定性检测后的验证方法。     

水产品中创伤弧菌ddPCR定量方法的建立

选取创伤弧菌单拷贝基因met为靶基因,设计引物探针,建立对创伤弧菌准确定量的微滴式数字聚合酶链式反应（droplet digital polymerase chain reaction,ddPCR）方法,并进行特异性、灵敏度和重复性实验,同时与实时PCR（real-time PCR）方法进行比较。结果显示,所建立的ddPCR方法可以快速、高效地检测出创伤弧菌,细菌纯培养物中其定量限可达323 拷贝数/mL,检测限可达61 拷贝数/mL,人工污染牡蛎样品中能最低能检测到1.13×102 拷贝数/g的目标菌。对人工污染样品中目标菌的检测,ddPCR的定量结果约为平板计数结果的1.4 倍,比real-time PCR方法的检测更加稳定准确。本研究建立的ddPCR检测方法能快速准确、特异、灵敏地定量检测创伤弧菌。     

Adaptor polymerase chain reaction for single molecule amplification

The adaptor polymerase chain reaction (PCR) permits the amplification of DNA fragments with arbitrary sequences. In this paper, we describe the successful amplification of plasmid-derived single molecule DNAs digested by a restriction enzyme. By using adaptors made of short and long oligonucleotides, nonspecific interactions during PCR were suppressed. The method will be applicable to the detection of single molecule DNA fragments even if their sequence is unknown.     

2种检测变形杆菌PCR方法的比较研究

选取atpD基因作为靶序列设计了2对引物,分别采用不同的PCR扩增条件,对3株变形杆菌属标准菌株,67株样品分离株及13株非变形杆菌属菌株进行扩增实验,结果2种PCR方法对3株标准菌株和66株样品分离株分别扩增出348 bp和596 bp的特异性片断,实验结果呈阴性的1株分离株经全自动微生物鉴定仪鉴定为阴沟肠杆菌。13株非变形杆菌属菌株均未有特异性条带产生。2种PCR方法检测变形杆菌,均具有快速、准确、灵敏、特异的优点。建立的引物2的PCR方法在检测时间、特异性、灵敏度方面比引物1的PCR方法更具优势。     

赤小豆加工食品中红豆成分定性和定量PCR检测

目的 为实现赤小豆加工食品的真伪和品质鉴别,建立赤小豆加工食品中被误用或混用的红豆成分实时荧光聚合酶链式反应（PCR）定性和微滴数字聚合酶链式反应（ddPCR）定量检测方法。方法 根据赤小豆和红豆基因组DNA中保守基因,分别设计适用于赤小豆和红豆成分实时荧光PCR定性检测的特异性引物探针,并设计适用于赤小豆加工食品中红豆成分双重ddPCR定量检测的通用引物探针,建立赤小豆加工食品中红豆成分质量百分比-DNA拷贝数浓度百分比线性关系式。结果 本方法对赤小豆和红豆基因组DNA检测低限分别为0.1和0.01 ng/μL,对赤小豆和红豆基因组DNA拷贝数浓度定量检测限均为6 copies/μL,可对赤小豆加工食品中质量百分比为5%～80%的红豆成分准确定量。结论 本方法可用于赤小豆加工食品中红豆成分的定性和质量百分比定量检测。     

基于实时聚合酶链式反应检测特种乳中牛乳的掺伪

分别基于SYBR Green实时聚合酶链式反应（real-time polymerase chain reaction;real-time PCR）和TaqMan real-time PCR技术检测特种乳及其热处理加工产品中掺假的牛乳成分;同时探讨不同热处理方式对掺假检测的影响;以满足不同商品化特种乳制品的检测要求。结果表明;所设计的牛特异性引物可以扩增牛乳中的DNA;与非目标动物无交叉反应性;具有较高的特异性。两种real-time PCR方法对于牛乳DNA的检测限分别为1 pg（SYBR Green）和10 pg（TaqMan）;且均可以最低检测出特种乳混合物中0.1%（m/m）牛乳成分掺伪。为评估掺假模拟的重现性;在3 d内共进行了9 次重复实验;验证了方法具有较高的重复性。同时;为检测本研究中所建立实验方法的可用性;对20 种商业加工特种乳制品进行了真实性分析;其中在7 种产品中检测出牛乳成分;显示出所建立的检测方法具有较高的分辨率和实际应用价值。     

鱼翅类食品中鲨鱼成分PCR鉴定方法研究

本文针对鱼翅中的鲨鱼成分进行检测鉴定开发了一种快速灵敏的PCR检测方法,可检测鱼翅类食品中是否存在鲨鱼成分。根据鲨鱼线粒体的细胞色素亚基I基因序列设计了鲨鱼特异性引物,扩增长度为228 bp;为了评价方法的特异性,将设计的引物分别针对22份鱼翅样品DNA和37种其它种类DNA进行PCR检测,结果显示,只在鲨鱼鱼翅中能检测出特异的228 bp条带,其它37种物种中均无条带检出。为了评价方法的灵敏度,将鱼翅DNA中掺入了不同比例土豆DNA的样品采用本方法进行了PCR分析,显示方法可检测灵敏度为0.1%(m/m)。随机抽取45份不同类型的鱼翅样品,检测出22份鲨鱼翅均含鲨鱼成分,而21份仿鱼翅均不含鲨鱼成分而含有植物成分。该样品前处理方法、DNA提取方法以及PCR检测方法可广泛应用于食品中鲨鱼成分检测鉴定。     

副溶血弧菌的多重PCR检测

副溶血弧菌是一种致病性弧菌,毒力因子主要有不耐热溶血毒素、耐热直接溶血毒素和相对耐热直接溶血毒素三种。本实验根据FDA标准推荐的引物对其进行了检验,发现副溶血弧菌环境分离株中没有耐热直接溶血毒素和相对耐热直接溶血毒素基因,仅有不耐热溶血毒素基因。     

Evaluating a commercial PCR assay against bacterial culture for diagnosing Streptococcus uberis and Staphylococcus aureus throughout lactation

The performance of a commercial, real-time PCR assay was compared with traditional bacterial culture for the identification of Streptococcus uberis and Staphylococcus aureus in bovine milk collected at different stages of lactation. Initial validation tests using fresh and frozen quarter milk samples identified factors that affected the success of the PCR. Therefore, the standard protocol was adjusted for samples collected at the first milking postpartum (colostrum) and from clinical mastitis cases. The adjustment involved PCR testing both undiluted and diluted (1 in 10 with sterile water) DNA extracts. The performance comparison between culture and the PCR assay used milk samples collected aseptically from individual quarters of mixed-age spring-calving dairy cows, during early, mid, and late lactation. Bacterial culture results were used to select a subset of samples for PCR testing (n = 315) that represented quarters with a current or prior Strep. uberis or Staph. aureus infection. Compared with culture, PCR had a sensitivity of 86.8% and specificity of 87.7% for detecting Strep. uberis (kappa = 0.74) and 96.4% and 99.7%, respectively, for detecting Staph. aureus (kappa = 0.96). The dilution of DNA extracts for colostrum and clinical samples increased the relative sensitivity from 79.2% to 86.8% for Strep. uberis detection and from 92.9% to 96.4% for Staph. aureus, presumably through diluting unidentified PCR inhibitors. The sensitivity for detecting Strep. uberis using PCR, relative to culture, was similar throughout lactation (85–89%), whereas relative specificity was lowest immediately postcalving (64%) but improved in mid and late lactation (98%). Specificity estimates for samples collected in early lactation can be optimized by reducing the cutoff cycle threshold (Ct) value from the recommended value of 37 to 34. Although using this value improved specificity (77%), it reduced test sensitivity (77%). The PCR assay lacked agreement with culture in early lactation, specifically for diagnosing Strep. uberis. Thus, PCR should not be used as the only tool for diagnosing mastitis in early lactation.