Efficiency of ligation-mediated PCR and TAIL-PCR methods for isolation of <Emphasis Type="Italic">RbcS</Emphasis> promoter sequences from green microalga <Emphasis Type="Italic">Ankistrodesmus convolutus</Emphasis>

Isolation of promoter sequences from known gene sequences is a tedious task in genome-related research. An efficient method of obtaining the promoter sequences is necessary in order to successfully use targeted promoters for genetic manipulations. Here, efficiency and usefulness of two PCR-based methods, namely: ligation-mediated PCR and thermal asymmetric interlaced (TAIL) PCR, for isolation of promoter sequences of the ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit (RbcS) gene from green microalga Ankistrodesmus convolutus (A. convolutus) were evaluated. The results showed that the amplification efficiency of TAIL-PCR was higher than that of the ligation-mediated PCR method, i.e. the amplified promoter fragments of 1.2 and 0.8 kb in length or promoter sequences of 813 and 606 bp (after eliminating the unreadable sequences). The use of TAIL-PCR described here presents a low cost and efficient strategy for the isolation of promoter sequences of known genes, especially in GC-rich regions, and species with little or no available genome information such as A. convolutus.     

应用于染色体步移的PCR扩增技术的研究进展

各种建立在PCR基础上染色体步移的方法能够根据已知的基因序列得到侧翼的基因序列。染色体步移技术主要应用于克隆启动子、步查获得新物种中基因的非保守区域、鉴定T-DNA或转座子的插入位点、染色体测序工作中的空隙填补,从而获得完整的基因组序列等方面。其方法主要有3种：反向PCR的方法,连接法介导的PCR的方法以及特异引物PCR的方法。文章就各种方法进行举例说明并加以分析比较。     

连接介导PCR及其在体内足迹研究中的应用

连接介导聚合酶链反应是以连接反应为基础的单侧PCR技术,首先在DNA片段的一端连接上一个公共连接子,而后在这个连接子与另一个DNA序列特异的引物间扩增.Vent聚合酶的使用,延伸产物捕获及连接子标记选择策略的采用,大大提高了连接介导聚合酶链反应的敏感性.这一技术的发明大大促进了体内足迹等研究的进行.     

Efficient 5' ETS walking from conserved 18S rDNA sequences of the dinoflagellates <Emphasis Type="Italic">Alexandrium</Emphasis> and <Emphasis Type="Italic">Akashiwo sanguinea</Emphasis> (Dinophyceae)

An external transcribed spacer (ETS) walking PCR technique was developed for the isolation of unknown sequences adjacent to the 18S rDNA. This strategy relied on four "walking primers", which were designed to bind unknown sequences upstream from the 18S rDNA, and a specially programmed series of thermocycles. This method was successful in the isolation of the 5' ETS regions from harmful dinoflagellates, including Alexandrium affine, A. catenella, A. minutum, A. tamarense, and Akashiwo sanguinea. Mono-directional sequencing reactions revealed the PCR products to be 392–962 nucleotides in length, and the 5' ETS in these products were longer than 362 bp. These are the first such sequences available for A. sanguinea and the Alexandrium. In comparisons of the ETS sequences, genetic distance was considerably high within the Alexandrium. Furthermore, the sequences were significantly variable among the different strains of identical species: genetic distance was recorded at 0.0420 for A. tamarense strains and as less than 0.7841 within strains of A. sanguinea. The 5'-start nucleotide of 18S rDNA was variable between the two genera: the five species of Alexandrium contained a T base, and A. sanguinea contained an A base. These results demonstrate the effectiveness of the ETS walking PCR method. This method will be valuable in directional ETS walking from known regions to unknown regions, particularly concerning the boundary sequences of rRNA genes.     

Rapid detection and differentiation of Erysipelothrix spp. by a novel multiplex real‐time PCR assay

Aim: The aim of this study was to develop a multiplex real‐time PCR assay for the identification and discrimination of Erysipelothrix rhusiopathiae, tonsillarum and Erysipelothrix sp. strain 2 for direct detection of Erysipelothrix spp. from animal specimens. Methods and Results: A primer set and three species‐specific probes with different end labelling were designed from the noncoding region downstream of the 5S rRNA coding region. The sensitivity, specificity and repeatability of the assay were validated by analysing 27 Erysipelothrix spp. reference serotype strains and ten septicemia‐associated non‐Erysipelothrix spp. bacterial isolates. Cross‐reactivity with Erysipelothrix sp. strain 1 was not observed with any of the primer probe combinations. The detection limit was determined to be <10 colony forming units and as low as one genome equivalent per PCR . Further evaluation of the Erysipelothrix spp. multiplex PCR was performed by comparing an enrichment isolation culture method and a conventional differential PCR on 15 samples from pigs experimentally inoculated with Erysipelothrix spp. and 22 samples from pigs with suspected natural infection. Conclusion: The multiplex real‐time PCR assay was found to be simple, rapid, reliable, specific and highly sensitive. Significance and Impact of the Study: The developed real‐time multiplex PCR assay does not require cumbersome and lengthy cultivation steps prior to DNA extraction, obtained comparable results to enrichment isolation, and will be useful in diagnostic laboratories for rapid detection of Erysipelothrix spp.     

Template-blocking PCR: An advanced PCR technique for genome walking

This article describes the development of an improved method for the isolation of genomic fragments adjacent to a known DNA sequence based on a cassette ligation-mediated polymerase chain reaction (PCR) technique. To reduce the nonspecific amplification of PCR-based genome walking, the 3′ ends of the restriction enzyme-digested genomic DNA fragments were blocked with dideoxynucleoside triphosphate (ddNTP) and ligated with properly designed cassettes. The modified genomic DNA fragments flanked with cassettes were used as a template for the amplification of a target gene with a gene-specific primer (GSP) and a cassette primer (CP). The ddNTP blocking of the genomic DNA ends significantly reduced the nonspecific amplification and resulted in a simple and rapid walking along the genome. The efficiency of the template-blocking PCR method was confirmed by a carefully designed control experiment. The method was successfully applied for the cloning of the PGK1 promoter from Pichia ciferrii and two novel cellulase genes from Penicillium sp.     

Molecular Typing of Cyst‐Forming Nematodes Globodera pallida and G. rostochiensis,Using Real‐Time PCR and Evaluation of Five Methods for Template Preparation

Globodera pallida and G. rostochiensis are two cyst‐forming nematodes known to infest potato crops, causing severe economic losses worldwide. In this study, a real‐time TaqMan PCR assay was developed and optimized for the simultaneous detection of G. pallida and G. rostochiensis. The assay's analytical and diagnostic sensitivity and specificity were evaluated using reference isolates. Four different DNA extraction methods and one rapid crude template‐preparation procedure were compared in terms of extraction purity, efficiency for PCR applications, utility and cost. Extraction methods A and B included two commercially available kits that utilize silica columns and magnetic beads, respectively. Method C was based on DNA isolation using Chelex resin, and method D was a standard chemistry in‐house protocol. Procedure E included the direct use of crude mixture composed of disrupted cysts in Tris–EDTA buffer. The multiplex TaqMan PCR assay successfully discriminated the two nematode species from all reference cyst samples and its recorded diagnostic sensitivity (Dse) and specificity (Dsp) was 100%. On the contrary, in conventional (Co) PCR tests, the overall Dsp and Dse were lower and estimated at 94 and 87% for G. pallida, and 97 and 88% for G. rostochiensis, respectively. Spectrophotometric results showed that DNA extraction methods A, B and C yielded the purest DNA and gave the lowest mean C_t values as well as the most consistent results in Co PCR. Alternative crude preparation method E resulted in statistically similar and C_t values consistent with those obtained with methods A to C when tested by TaqMan PCR. The developed assay, using crude template‐preparation E, allows the simple, accurate and cost‐effective testing of a large number of cyst samples and can be applied in surveys and certification schemes.     

Polymerase Chain Reaction for the Detection of Chlamydia psittaci in the Feces of Budgerigars

The polymerase chain reaction (PCR) targeting the ompA gene of Chlamydia psittaci was evaluated for its ability to detect chlamydiae in fecal specimens of budgerigars as compared with isolation procedures using cell culture and embryonated egg inoculations. Several procedures for PCR template DNA preparation were compared so as to determine their detection levels for chlamydiae propagated in cell culture in the presence of fecal materials. Tween-20 and proteinase K treatments followed by centrifugation of the template DNA were found to be an appropriate procedure for DNA preparation for primary PCR. Subsequent nested PCR was shown to detect 4.8 IFU/ml or 84 particles/ml of chlamydiae. Chlamydiae in 50 fecal specimens from apparently healthy budgerigars were examined by nested PCR and several other methods. Nested PCR detected chlamydiae at a higher rate (12/50, 24%) than the isolation procedure in embryonated eggs (6/50, 12%). Primary PCR combined with the isolation procedure in cell culture gave a detection rate (5/50, 10%) similar to that of isolation from embryonated eggs. Detection rates by primary PCR (1/50, 2%) and in cell culture (0%) were inferior to the other procedures.     

Discrimination between cultivars of Vitis vinifera based on molecular variability concerning 5″ untranslated regions of the StSy-CHS genes

 The degree of polymorphism present in 5′ untranslated regions of stilbene synthase (StSy)-like loci was assessed. A ligation-mediated polymerase chain reaction (LM-PCR) cloning strategy was adopted to isolate sequences located immediately upstream of StSy coding regions. Among several clones, 13 randomly chosen fragments were analyzed at the sequence level. Four of the analyzed fragments appeared of particular interest. Two carried sequences reminiscent of micro-satellites, while the remaining fragments contained direct repeats. Oligonucleotides constructed against the specific DNA sequence of these clones disclosed a complex banding pattern when used in polymerase chain reaction (PCR)-analysis of 22 ancient varieties of grapevine. A total of 40 polymorphic bands could be identified and used to calculate coefficients of genetic similarity (GS) between varieties. GS values were used in cluster analysis to differentiate the 22 varieties. The data obtained are in good agreement with available information concerning the relationships between the varieties considered. This suggests the use of the method we have developed in fingerprinting studies of Vitis vinifera germ plasma. Received: 11 April 1996 / Accepted: 14 March 1997     

Isolation and functional expression of the bop gene from Halobiforma lacisalsi

A novel bop gene was described from Halobiforma lacisalsi strain AJ5^T, an extremely halophilic archaeon isolated from Ayakekum Lake, China. Following six rounds of PCR amplification based on the conserved fragment of the bop gene, the complete sequence of the bop gene, including the 5′ and 3′ flanking regions of the conserved fragment, was obtained by the ligation-mediated PCR amplification (LPA) approach. The data presented provide us with further insight into the distribution of bop-like genes in the family Halobacteriaceae. This is the first example of a bop-like gene in halophiles found in the high-pH environment. Alignment and hydropathy analysis of the deduced amino acid sequence identified the conserved functional sites as well as some variations compared with other bacterio-opsins. Molecular phylogenetic analysis revealed the position of the bacterio-opsin of strain AJ5, which is closest to that of Haloterrigena sp. arg-4 with 85% identity. In the presence of all-trans retinal, recombinant Escherichia coli cells expressing the gene turned dark purple. The purple membrane from the recombinant E. coli showed maximal absorption at 540 nm.     

Development and evaluation of a multiplex PCR for simultaneous detection of five foodborne pathogens

Aims: To develop a rapid multiplex PCR method for simultaneous detection of five major foodborne pathogens (Staphylococcus aureus, Listeria monocytogenes, Escherichia coli O157:H7, Salmonella Enteritidis and Shigella flexneri, respectively). Methods and Results: Amplification by PCR was optimized to obtain high efficiency. Sensitivity and specificity assays were investigated by testing different strains. With a multipathogen enrichment, multiplex PCR assay was able to simultaneously detect all of the five organisms in artificially contaminated pork samples. The developed method was further applied to retail meat samples, of which 80% were found to be positive for one or more of these five organisms. All the samples were confirmed by traditional culture methods for each individual species. Conclusions: This study reported a rapid multiplex PCR assay using five primers sets for detection of multiple pathogens. Higher consistency was obtained between the results of multiplex PCR and traditional culture methods. Significance and Impact of the Study: This work has developed a reliable, useful and cost‐effective multiplex PCR method. The assay performed equally as well as the traditional cultural method and facilitated the sensitive detection both in artificially contaminated and naturally contaminated samples.     

Comparison of pulsed‐field gel electrophoresis and three rep‐PCR methods for evaluating the genetic relatedness of Stenotrophomonas maltophilia isolates

Aims: In this study, three facile repetitive‐sequence PCR (rep‐PCR) techniques have been compared with the pulsed‐field gel electrophoresis (PFGE) method for differentiating the genetic relatedness of clinical Stenotrophomonas maltophilia isolates. Methods and Results: The dendrograms of 20 S. maltophilia isolates were constructed based on the data obtained from PFGE and three PCR‐based methods, i.e. enterobacterial repetitive intergenic consensus‐PCR (ERIC‐PCR), BOX‐PCR and repetitive extragenic palindromic‐PCR (REP‐PCR). When compared with PFGE, ERIC‐PCR displayed a much lower discriminatory power, whereas BOX‐PCR and REP‐PCR had a comparable discriminatory power for close genetic‐related isolates. Conclusion: BOX‐PCR and REP‐PCR can be convenient and effective methods for evaluating the close genetic relatedness of clinical S. maltophilia isolates. Significance and Impact of the Study: A rapid method for determining S. maltophilia’s close genetic relatedness provides a convenient tool for understanding the epidemiology of S. maltophilia.     

Efficiency of ligation-mediated PCR and TAIL-PCR methods for isolation of RbcS promoter sequences from green microalgae Ankistrodesmus convolutus

Isolation of promoter sequences from known gene sequences is a tedious task in genome-related research. An efficient method of obtaining the promoter sequences is necessary in order to successfully use targeted promoters for genetic manipulations. Here, efficiency and usefulness of two PCR-based methods, namely: ligation-mediated PCR and thermal asymmetric interlaced (TAIL) PCR, for isolation of promoter sequences of the ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit (RbcS) gene from green microalgae Ankistrodesmus convolutus (A. convolutus) were evaluated. The results showed that the amplification efficiency of TAIL-PCR was higher than that of the ligation-mediated PCR method, i.e. the amplified promoter fragments of 1.2 and 0.8 kb in length or promoter sequences of 813 and 606 bp (after eliminating the unreadable sequences). The use of TAIL-PCR described here presents a low cost and efficient strategy for the isolation of promoter sequences of known genes, especially in GC-rich regions, and species with little or no available genome information such as A. convolutus.     

Touchdown-touchup nested PCR for low-copy gene detection of benzimidazole-susceptible Wuchereria bancrofti with a Wolbachia endosymbiont imported by migrant carriers

A novel, sensitive and specific touchdown–touchup nested PCR (TNPCR) technique based on two useful molecular markers, a Wuchereria bancrofti β-tubulin gene involved in benzimidazole susceptibility and a Wolbachia ftsZ gene involved in cell division, was developed to simultaneously detect the parasite W. bancrofti (W1) with its Wolbachia endosymbiont (W2) from both microfilaremic and post-treatment samples of at-risk migrant carriers infected with geographical W. bancrofti isolates. The detection and characterization of authentically low-copy gene-derived amplicons revealed no false positive identifications in amicrofilaremia with or without antigenemia. The W1-TNPCR was 100-fold more sensitive than the W2-TNPCR regardless of the microfilarial DNA isolation method and compared well with the thick blood film and membrane filtration techniques. These locus-specific TNPCRs could also detect Wolbachia-carrying W. bancrofti genotype in addition to a link to benzimidazole sensitivity among those with unknown infection origins that exhibited microfilaremia responsiveness against treatment with diethylcarbamazine plus albendazole. These TNPCR methods can augment the results of microscopic detection of the parasite because these methods enhance DNA isolation and PCR amplification capabilities.     

PCR‐based Rapid Assay for Discriminative Detection of Latent Infections of Rice Bacterial Blight

A triplex PCR method has been developed for the race‐specific detection of Xanthomonas oryzae pv. oryzae (Xoo), the bacterial blight (BB) pathogen of rice. For this, three primer sets were designed: for specific internal regions of two genes (hpaA and XorII very‐short‐patch‐repair endonuclease) and for a genomic locus derived from an amplified fragment length polymorphism (AFLP) fragment specific for the K3 and K5 races. The sizes of the PCR products when using XOOF/XOOR, XRMF/XRMR and XAF3F/XAF3R primer pairs were 327, 427 bp and 1 kb, respectively, when the assay was applied to detect the pathogen in solution and lesion exudates, and as a template. Amplicons were obtained without the need for any prior processing (e.g. DNA preparation from infected leaf or bacterial cell isolation from the lesion). Furthermore, the pathogen could be quickly detected in the asymptomatic rice leaf 3 days after inoculation and at a distance of 6 cm from the lesion site. This PCR‐based simple and rapid assay will be a useful method for the detection and identification of Xoo as well as for disease forecasting in paddy fields.     

Comparison of culture and PCR for the detection of Brucella melitensis in blood and lymphoid tissues of serologically positive and negative slaughtered sheep

Aims: To compare the culture and PCR methods for detection of Brucella melitensis in blood and lymphoid tissue samples obtained from slaughtered sheep (n = 162) testing positive/negative in serological tests (Rose Bengal test and serum agglutination test). Methods and Results: Of 162 sheep examined, 45 were positive and 117 negative in serological tests. A PCR assay based on a pair of Br. melitensis‐specific primers was used to detect DNA in blood and lymphoid tissue. Brucella melitensis was isolated from 1·2% (2/162) and 17·2% (28/162) of the blood and lymphoid tissue samples respectively. Positive PCR products with a molecular size of 731 bp were obtained from 27·7% (45/162) of blood and 29·0% (47/162) of lymphoid tissue samples. Conclusions: The species‐specific PCR assay detected a higher number of Br. melitensis DNA both from serologically positive (P < 0·01 in blood PCR, P < 0·001 in tissue PCR) and serologically negative (P < 0·001 in both blood PCR and tissue PCR) sheep compared with classical bacteriological culture methods. Significance and Impact of the Study: The results emphasize the importance of using more than one type of diagnostic technique for the detection of animals positive for brucellosis, especially with epidemiological purposes.     

Characterization of extended-spectrum beta-lactamase-producing Enterobacterales from organic and conventional chicken meats

This study was conducted to isolate and identify extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales in conventional and organic chicken meats, which were sold in Turkey. A total of 200 raw chicken meat sample (100 conventional and 100 organic) were used as material. Classic culture technique based on chromogenic method was used for the isolation of bacteria, and the identification was performed with VITEK MS. Phenotypic ESBL production was detected by combined disc diffusion method. Gene regions responsible for ESBL production were determined by PCR. MIC values of isolates were detected by VITEK 2. Phenotypic ESBL-producing Enterobacterales were detected in 46% of conventional chicken meats and in 22% of organic chicken meats. Of the 115 isolates obtained, 97 (84%) were Escherichia coli, 12 (10%) were Klebsiella pneumoniae, four (3·48%) were Serratia fonticola, one (0·87%) was Rahnella aquatilis, and one (0·87%) was Serratia liquefaciens. PCR analysis revealed that 109 of 115 isolates (94·78%) contained at least one of the bla_CTX-M, bla_TEM, and bla_SHV genes. Of the 115 ESBL-producing isolates, 103 (89·57%) were found resistant to at least one antibiotic except for the β-lactam group. The contamination level of ESBL-producing Enterobacterales was higher in conventional chicken meats (P < 0·001).     

一种改良的启动子序列克隆的染色体步查法

利用染色体步行法,从已知DNA序列克隆侧翼未知序列是非常有效的方法之一,但由于所选用的特定限制性内切酶对目标基因组不能酶解成合适大小的片段,因而受PCR扩增能力的局限,往往扩增不出有效产物. 针对这一点,这里我们介绍一种简单有效的改良方法,它包括以下步骤：首先用不同的限制性内切酶(包括平末端和粘性末端) 酶解目标基因组DNA,接着,选择能将基因组酶切成弥散、分布均匀的限制性内切酶,如DraⅠ和HindⅢ,合成相对应的接头;然后,选择弥散的、分布均匀的限制性内切酶的酶解产物,构建成含相应接头的基因组DNA文库,用作PCR的模板;最后,用接头引物和特异引物,通过巢式PCR扩增目的片段,获得了理想的扩增效果.采用改进后的染色体步查法,有效地从较复杂的棉花核DNA中克隆出6个棉花启动子序列.     

Straight Walk: A modified method of ligation-mediated genome walking for plant species with large genomes

Polymerase chain reaction (PCR)-based genome walking techniques are commonly used to clone unknown genomic regions flanking known sequences. However, these methods are typically problematic when applied to highly complex DNA templates isolated from plants with large genomes. Here we describe a reliable and efficient genome walking method that is particularly effective for plants with large genomes. Our ligation-mediated PCR method, Straight Walk, has improved sensitivity and specificity due to optimization of sequences of adaptors and adaptor primers. Successful genome walking in lily, which has one of the largest genomes in plants, indicates that Straight Walk is applicable for most plant species.