RT-PCR测定组织纤溶酶原激活剂突变体(La-tPA)在转基因鼠乳腺表达的研究

利用所构建的乳腺表达组织纤溶酶原激活剂突变体（Ｌａ－ｔＰＡ）载体．对５４０枚小鼠受精卵进行显微注射,经ＰＣＰ和Ｓｏｕｔｈｅｒｎｂｌｏｔ检测,获得６只整合有人Ｌａ－ｔＰＡ转基因小鼠．为了精确研究转基因在小鼠体内的表达,采用ＲＴ－ＰＣＰ方法测定转基因鼠在泌乳期１～２０ｄＬａ－ｔＰＡ基因的转录,结果表明,在转基因鼠乳腺的Ｌａ－ｔＰＡｍＲＮＡ水平在１０～１５ｄ最高,在２０ｄ时降为最低．外源基因在转基因小鼠乳腺的表达规律研究为未来利用转基因动物生产Ｌａ－ｔＰＡ提供依据     

Allele-specific PCR method based on rfbS sequence for distinguishing Salmonella gallinarum from Salmonella pullorum: serotype-specific rfbS sequence polymorphism

Cloning and sequence analysis of rfbS gene identified two polymorphic nucleotides, one at position 598 (Salmonella gallinarum-specific) and other at position 237 (Salmonella pullorum-specific). Based on S. gallinarum-specific nucleotide found at position 598, an allele-specific PCR method was developed for serotype-specific detection of S. gallinarum. This PCR method was able to discriminate pure cultures of S. gallinarum from S. pullorum and other Salmonella serotypes from serogroup D in less than 3 h. Serotype-specific detection of S. gallinarum was possible in less than 24 h when the PCR was applied on the presumptive Salmonella colonies obtained after overnight incubation of selective media plates streaked with the clinical material from diseased chickens. As little as 100 pg of genomic DNA could be detected with S. gallinarum-specific primers; no PCR product was detected in non-S. gallinarum serotypes of serogroup D and other closely related non-salmonella organisms. This rfbS allele-specific amplification assay is specific, reproducible and less time consuming than the standard bacteriological methods used to detect S. gallinarum and could be an effective molecular tool for rapid definitive diagnosis of fowl typhoid in the areas of endemicity where fowl typhoid infection exists.     

Automated PCR/sequence template purification

A commercially available filtration method is described for the purification of polymerase chain reaction (PCR) templates and sequence-labeled products. The methodology is described for the automation of this application and its use on a high-throughput liquid handling robot and capillary-based automated DNA sequencer. The application provides good-quality DNA, is relatively cheap, and can be used in either 96- or 384-well format.     

用反转录—聚合酶链反应检测B组轮状病毒

轮状病毒（Ｒｏｔａｖｉｒｕｓ）是属于呼肠病毒科（Ｒｅｏｖｉｒｉｄａｅ）的双链ＲＮＡ（ｄｓＲＮＡ）病毒。至今已将轮状病毒分为七个组（Ａ～Ｇ）。已经发现的Ｂ组轮状病毒分别来自人、大鼠、牛、猪、羊。近十年来,通过轮状病毒的研究,轮状病毒Ｂ组已被公认为引起人...     

Simple and rapid PCR method for identification of streptococcal species relevant to animal infections based on 23S rDNA sequence

A PCR identification system targeting 23S rDNA sequences for the identification of eight streptococcal species relevant to animal infections (Streptococcus agalactiae, S. bovis, S. canis, S. dysgalactiae, S. equi, S. porcinus, S. suis and S. uberis) was developed. This system consists of two PCR reactions, A and B, in which seven and eight primers, respectively, are used simultaneously, and was designed so that each amplification product indicates a species by its size. A total of 111 cultures, including the type strain of eight species, could be successfully identified and differentiated as individual species, except for the cross reactivity between S. bovis and S. equinus. The developed PCR system can complete the identification procedure for eight streptococcal species through two tube reactions per isolate, and, therefore, might provide a rapid, simple and accurate diagnostic tool for veterinary laboratories.     

A rapid method for purifying PCR products for direct sequence analysis

An HPLC approach for purification and sequencing of double-stranded DNA obtained directly from a PCR is described. This simple and reliable procedure has several advantages; the DNA fragment is rapidly eluted (less than 7 minutes), requires no organic cleanup, produces several hundred bases of sequence and is sensitive enough to obtain DNA sequence from a single 100-microliters PCR. This method is demonstrated by sequencing tumor necrosis factor alpha (TNF alpha) gene amplified from mouse tail DNA.     

Determination of self-locompatibility genotypes of Korean apple cultivars based on S-RNase PCR

To prevent self-fertilization, apple has a gametophytic self-incompatibility mechanism, part of a widespread intraspecific system, that is controlled by a multi-allelic locus. This attribute has been exploited in breeding programs for new cultivars. Likewise, many apple orchards depend on artificial pollination. Therefore, molecular analysis and early identification of the self-incompatibility (S) genotype could greatly improve breeding schemes and pollen donors selection. Here, we PCR-amplified the S-RNase PCR fragments from a total of 14 cultivars and parents, using new primers (ASPF3+ASPR3) common to 23 S-alleles in apple. The S-genotypes were determined for the following: ‘Hongro’ (S₁S₃), ‘Gamhong’ (S₁S₉), ‘Saenara’ (S₁S₃), ‘Chukwang’ (S₃S₉), ‘Hwahong’ (S₃S₉), ‘Seokwang’ (S₃S₃), ‘Hwarang’ (S₁S₉), ‘Sunhong’ (S₃S₉), ‘S.E.B.’ (S₁S₁₉), ‘S.G.D.’ (S₂S₃), and ‘Mollie’s Delicious’ (S₃S₇). We also confirmed the characteristics of the S-genotypes for eight Korean apple cultivars by PCR-Southern blot analysis, using seven S-RNases as probes.     

PCR法对鸡卵黄中Coxiella burnetii菌的测定

[目的]通过用定量PCR加巢式PCR方法,提高了对Coxiella burnetii (C.b)CoMl基因的检出率;通过对鸡卵中病原微生物Coxiella burnetii的基因检测,明确鸡卵的食品安全性;并对明确Coxiella burnetii的流行病学有重要意义.[方法]提取鸡卵DNA,用定量PCR加巢式PCR方法检测上述基因,并对PCR产物进行测序分析,通过间接免疫荧光法观察鸡血白细胞中的微生物.[结果]用定量PCR加巢式PCR方法可检出4个以上的Coxiella burnetii Coml基因,用此方法可测出鸡卵中Coxiella burnetii Coml基因达104-106个,阳性率为5％-22％;对阳性鸡卵Coml基因PCR产物的测序结果显示有变异菌株的存在;免疫荧光法可见鸡卵中含有该微生物.[结论]由此认为鸡卵中存在病原微生物Coxiella burnetii,可能是Q热传染源.     

逆转录-聚合酶链式反应技术检测"歇马杏"主要病毒

目的：调查“歇马杏”携带主要病毒的情况。方法：利用作者已建立的ACLSV、PNRSV和PDVRT—PCR检测体系对4宁省大连市地方特产“歇马杏”田间植株携带三种病毒的情况进行了调查。结果：被检植株ACLSV、PNRSV和PDV的单独感染率分别为83．33％、83．33％和190％,复合感染率达到76．67％,但带毒程度不同。     

Development of Porphyromonas gingivalis-specific quantitative real-time PCR primers based on the nucleotide sequence of rpoB

Species-specific quantitative real-time PCR (qPCR) primers were developed for the detection of Porphyromonas gingivalis. These primers, Pg-F/Pg-R, were designed based on the nucleotide sequences of RNA polymerase β-subunit gene (rpoB). Species-specific amplicons were obtained from the tested P. gingivalis strains but not in any of the other strains (46 strains of 46 species). The qPCR primers could detect as little as 4 fg of P. gingivalis chromosomal DNA. These findings suggest that these qPCR primers are suitable for applications in epidemiological studies.     

Analyzing ligation mixtures using a PCR based method

We have developed a simple and effective method (Lig-PCR) for monitoring ligation reactions using PCR and primers that are common to many cloning vectors. Ligation mixtures can directly be used as templates and the results can be analyzed by conventional gel electrophoresis. The PCR products are representative of the recombinant molecules created during ligation and the corresponding transformants. Orientation of inserts can also be determined using an internal primer. The usefulness of this method has been demonstrated using ligation mixtures of two cDNA’s derived from the salivary glands of Aedes aegypti mosquitoes. The method described here is sensitive and easy to perform compared to currently available methods.     

ADLAPH: A molecular haplotyping method based on allele-discriminating long-range PCR

We present a method, called Allele-Discriminating Long and Accurate PCR Haplotyping (ADLAPH), for directly determining haplotypes from an extended genomic region. This method uses allele-discriminating primers in long-range PCR to amplify only one of the two chromosome homologues for the region of interest. Haplotypes are then determined from these phase-separated PCR fragments by conventional single nucleotide polymorphism (SNP) genotyping methods. This simple robust procedure makes it practical for high-throughput haplotyping of unrelated individuals, and potentially allows direct observation of haplotype information for up to 40 kb or more. We demonstrate the feasibility of this molecular haplotyping procedure by generating apolipoprotein E (APOE) haplotypes from 100 unrelated subjects.     

Mouse genomics: making sense of the sequence

Interpretation of the human genome sequence relies on studies of model genetic organisms. Mouse genetics and genomics will help to identify all the genes, and to determine their function.     

Making sense of score statistics for sequence alignments

The search for similarity between two biological sequences lies at the core of many applications in bioinformatics. This paper aims to highlight a few of the principles that should be kept in mind when evaluating the statistical significance of alignments between sequences. The extreme value distribution is first introduced, which in most cases describes the distribution of alignment scores between a query and a database. The effects of the similarity matrix and gap penalty values on the score distribution are then examined, and it is shown that the alignment statistics can undergo an abrupt phase transition. A few types of random sequence databases used in the estimation of statistical significance are presented, and the statistics employed by the BLAST, FASTA and PRSS programs are compared. Finally the different strategies used to assess the statistical significance of the matches produced by profiles and hidden Markov models are presented.     

Analysis of sequence diversity among IS6110 sequence of Mycobacterium tuberculosis: possible implications for PCR based detection

The IS6110 belongs to the family of insertion sequences (IS) of the IS3 category. This insertion sequence was reported to be specific for Mycobacterium tuberculosis complex and hence is extensively exploited for laboratory detection of the agent of tuberculosis and for epidemiological investigations based on polymerase chain reaction. IS6110 is 1361-bp long and within this sequence different regions have been utilized as targets in the identification of M. tuberculosis by PCR. However, the results are not always consistent, specific and sensitive. In recent years, a few clinical investigations raised concerns over IS6110 specificity and sensitivity in the diagnosis of tuberculosis due to false-positive (homology with other target DNA besides M. tuberculosis) or false negative (due to absence of copies of IS6110) results with IS6110 specific primers. To unravel the variations in IS6110 sequences, an insilico analysis of IS6110 sequence of different strains of M. tuberculosis was carried out. Our results of comparative analysis of IS6110 insertion sequences of M. tuberculosis complex suggests that, IS6110 insertion sequences harbored variations in its sequence, which is evident from the phylogenetic analysis. Importantly, IS6110 sequence has divergence within the copies of same strain and formed different clusters. A list of IS6110 specific primers used in various clinical investigation of tuberculosis was obtained from the literature and their performance scrutinized. Our study emphasizes the need to develop PCR assays (multiplex format) targeting more than one region of the genome of M. tuberculosis.