烟草钾离子通道基因NKT5的克隆和序列分析

本研究运用已经获得的1条490bp的普通烟草钾离子(K~+)通道基因的中间片段来设计特异性引物,应用RACE方法获得其3'和5'末端cDNA序列。通过三段cDNA序列拼接结合全长克隆测序验证,获得一个未报道的普通烟草K~+通道基因,并将其命名为NKT5(NCBI登录号为HM010922)。NKT5的cDNA全长为2365bp,其中5'端非编码区190bp、3'端非编码区249bp、编码区1926bp,编码641AA。对该基因进行了序列分析及功能预测,为进一步阐明其在烟草吸钾及抗逆过程中的功能及分子机制奠定了基础。     

大豆膨胀素GmEXPA4基因的克隆及表达分析

根据植物膨胀素基因保守区设计简并引物,以大豆矮化突变体HK808幼芽的cDNA为模板,克隆到530bp的膨胀素基因保守区片段,并结合RACE技术克隆得到膨胀素基因全长序列,将其命名为GmEXPA4基因。生物信息学分析结果表明,该基因属于膨胀素中的α-expansin亚家族。GmEXPA4基因的实时荧光定量相对表达分析表明,该基因在东农42及其矮化突变体HK808中的各个时期都有表达,且与植物的生长量密切相关。     

标准分子构建及其在转基因玉米59122定量检测中的应用

根据转基因作物59122的外源基因与玉米基因组之间的左侧侧翼序列设计具品系特异性的荧光探针及引物,以实时荧光PCR技术建立59122的品系特定量检测方法,以重组PCR技术成功获得了标准分子(整合了内标基因序列与左侧翼序列)梯度范围为101～105,定量范围为0.01%～100%;建立了玉米内源基因与侧翼序列的标准曲线,变异系数CV值、标准偏差SD以及相关系数R2均可接受;检测5个已知转基因含量(0.1%、0.5%、1%、2%、5%)的混合样品中的转基因含量,结果分别为0.12%、0.56%、1.04%、1.61%、4.66%,实验误差小于25%,结果可信。     

Molecular beacon polymerase chain reaction detection of Escherichia coli O157:H7 in milk

A fluorescently labeled oligonucleotide probe (molecular beacon) was applied to detect Escherichia coli O157:H7 in artificially contaminated skim milk during polymerase chain reaction (PCR) amplification of extracted DNA. The probe was designed to hybridize with a region of the slt-II gene coding for the A subunit and to fluoresce when the hairpin-stem conformation was linearized upon hybridization to the target sequence. The molecular beacon was incorporated into PCR reactions containing DNA extracted from artificially contaminated skim milk. The degree of fluorescence was monitored in PCR reactions containing 10(3), 10(5), and 10(7) CFU of E. coli O157:H7 per ml and was found to correlate with the amount of template in each reaction. Fluorescence significantly increased above background levels by cycle 8, 14, or 14 in reactions containing DNA from the 10(7)-, 10(5)-, or 10(3)-CFU/ml template, respectively (P < 0.05). Molecular beacon PCR demonstrated positive results more rapidly than traditional agarose gel electrophoresis analysis of PCR products. Use of molecular beacons allows real-time monitoring of PCR reactions, and the closed-tube format allows simultaneous detection and confirmation of target amplicons without the need for agarose gel electrophoresis and/or Southern blotting. This is the first report of a stem-and-loop molecular beacon being applied for direct detection of a pathogen in food.     

TaqMan探针法实时荧光定量PCR快速检测沙门菌的探讨

为建立一种快速、灵敏、特异的实时荧光定量PCR法用于沙门菌的检验，根据GenBank上登录的编号为AE016841的沙门菌序列，应用生物学软件在fimY基因的保守区设计引物和TaqMan探针，同时应用BLAST程序进行网上序列比对，并进行筛选、优化。用鼠伤寒标准菌和60份食品样本进行本检测方法的特异性、敏感性和重复性试验，并与常规法和科玛嘉平板分离法做比较。本方法对沙门菌的检测具高度的特异性，检测的灵敏度这102CFU／ml，从增菌至完成检测仅需24h左右，是一种快速检测沙门菌的敏感、特异的新方法。     

巴氏杜氏藻ζ-胡萝卜素脱氢酶基因的克隆与分析

ζ-胡萝卜素脱氢酶(ZDS)基因是胡萝卜素生物合成途径中的一个关键酶之一。根据实验室已获得的巴氏杜氏藻ZDS基因的cDNA序列,设计引物,通过分段PCR的方法,获得ZDS基因的编码区序列。然后根据获得编码区序列,利用染色体步移的方法获得其两端侧翼序列:启动子和终止子,并利用生物信息学工具对获得序列进行分析。实验获得的完整ZDS基因全长11896 bp,其中编码区序列(从"ATG"到"TAA")长度为6435,编码区上游序列4091 bp(包括33 bp的5’UTR序列),编码区下游序列1370 bp(包括411 bp的3’UTR序列)。将编码序列与cDNA(开放阅读框)进行比对,发现整个编码区序列含有12个外显子和11个内含子,其中内含子长度达4686 bp,约为外显子长度的2.68倍,内含子均以GT开始,AG收尾,属于最常见的内含子类型。通过生物信息学分,发现ZDS启动子中具有多种转录因子结合位点,包括与光调控有关的GAGAbox,ASF1;与植物黄化反应有光的ACGTbox等。     

An improved method for specific-target preamplification PCR analysis of single blastocysts useful for embryo sexing and high-throughput gene expression analysis

Gene expression analysis in preimplantation embryos has been used for answering fundamental questions related to development, prediction of pregnancy outcome, and other topics. Limited amounts of mRNA in preimplantation embryos hinders progress in studying the preimplantation embryo. Here, a method was developed involving direct synthesis and specific-target preamplification (STA) of cDNA for gene expression analysis in single blastocysts. Effective cell lysis and genomic DNA removal steps were incorporated into the method. In addition, conditions for real-time PCR of cDNA generated from these processes were improved. By using this system, reliable embryo sexing results based on expression of sex-chromosome linked genes was demonstrated. Calibration curve analysis of PCR results using the Fluidigm Biomark microfluidic platform (Fluidigm, South San Francisco, CA) was performed to evaluate 96 STA cDNA from single blastocysts. In total, 93.75% of the genes were validated. Robust amplification was detected even when STA cDNA from a single blastocyst was diluted 1,024-fold. Further analysis showed that within-assay variation increased when cycle threshold values exceeded 18. Overall, STA quantitative real-time PCR analysis was shown to be useful for analysis of gene expression of multiple specific targets in single blastocysts.     

Marker-fusion PCR for one-step mutagenesis of essential genes in yeast.

We describe a one-step gene replacement method based on fusion PCR that can be used to mutagenize essential genes at their endogenous locus. Marker-fusion PCR can facilitate transfer of alleles between strains as well as PCR-based techniques, such as site-directed and error-prone PCR mutagenesis, all without cloning or strain constructions. With this method, PCR is used to fuse a mutagenized fragment to an overlapping fragment containing a selectable marker flanked by regions of homology to the target. By transforming yeast with these PCR products, specific mutations are introduced at the endogenous locus through homologous recombination. We tested the 'marker-fusion PCR' method using the budding yeast CDC28 gene and were able to efficiently introduce site-directed mutations and integrate genomic or plasmid-borne mutant alleles. As a further application for this method, we used a spiked oligonucleotide to randomize the coding sequence for a single domain of CDC28 and were able to construct highly mutagenized libraries for this region.     

Cloning and sequencing of the chromosomal DNA and cDNA encoding the mitochondrial citrate synthase of Aspergillus niger WU-2223L

The complementary DNA (cDNA) and chromosomal DNA encoding the citrate synthase (EC 4.1.3.7) gene (cit1) of Aspergillus niger WU-2223L, a citric acid-producing strain, were cloned. Synthetic oligonucleotide primers were designed according to the amino acid sequences of already known eukaryotic citrate synthases and the codon bias of A. niger genes. The 920-bp DNA fragment was amplified by polymerase chain reaction with these primers using chromosomal DNA of WU-2223L as a template, and was employed to screen a cDNA library of A. niger. One full-length cDNA clone was isolated and sequenced, within which an ORF of 1425 by encoding a protein of 475 as with a molecular weight of 52,153 Da was found. Its N-terminal region contains a typical mitochondrial-targeting motif. The predicted as sequence was 82, 68, and 65% homologous with the mitochondrial citrate synthases of Neurospora crassa, Saccharomyces cerevisiae, and pig, respectively, but it showed lower homology to bacterial citrate synthases. The full-length cDNA clone was used to screen a chromosomal library of A. niger WU-2223L, and a 7.5 kb-SalI fragment containing the corresponding chromosomal gene was isolated. Comparison of the chromosomal and cDNA sequences revealed that the cit1 gene is interrupted by six introns. In the chromosomal DNA, upstream of the coding region, a CT-rich region, but not the TATAAA or CAAT motifs, was found. Escherichia coli MOB150, a citrate synthase-deficient mutant showing a glutamate-requiring phenotype, was transformed with the plasmid pKAC-35S, which is the expression vector pKK223-3 containing the cDNA fragment encoding a putative mature protein of A. niger citrate synthase. The transformant harboring pKAC-35S showed citrate synthase activity and a glutamate-nonrequiring phenotype.     

通用多重不对称PCR结合寡核苷酸芯片检测7种食源性致病菌

应用通用多重不对称聚合酶链式反应(polymerase chain reaction,PCR)和寡核酸芯片技术建立一种同时检测7种常见食源性致病菌的方法。每种致病菌上游或下游引物5’端连接一段异源的共有序列。以荧光标记的该共有序列作为通用引物,与限制性特异引物经一步多重不对称PCR同时获得所有目标菌的单链标记靶序列,可被芯片上固定的特异性寡核苷酸探针捕获。通过芯片扫描、分析荧光信号完成检测。标准菌株检测结果证实,该方法可特异地检测单一和混合感染的目标菌,基因组DNA的检测灵敏度为0.1~1 pg。95份模拟污染和零售食品样本芯片检测结果与常规的分离与生化鉴定及荧光定量PCR结果一致。建立的寡核苷酸芯片方法可为快速、特异、灵敏及高通量地鉴定食源性致病菌提供一种有效的检测手段。     

实时荧光PCR定量检测食品中单增李斯特菌

目的建立快速、敏感、特异的食品中单增李斯特菌检测方法。方法针对单增李斯特菌溶素A基因（hlyA）设计一对引物和一条探针，并用该引物和探针运用实时荧光PCR技术对单增李斯特菌的DNA、细胞、质粒和样品进行实时荧光PCR定量检测。结果利用实时荧光PCR技术，建立了DNA校正曲线、细胞校正曲线和质粒校正曲线。DNA校正曲线在1～32CFU/ml、细胞校正曲线在32—320CFU／ml、质粒校正曲线在1—37Copies／ml，线形关系良好，且三种校正曲线检测样品得出的结果基本吻合。结论本试验建立起来的实时荧光PCR定量检测单增李斯特菌的方法灵敏度高、特异性好、准确，可应用于食品中单增李斯特菌的检测。     

Rapid DNA purification for Hal gene PCR diagnosis in porcine tissues and extension to other meat species

Two different halothane (Hal) gene polymerase chain reaction (PCR) tests were applied to genomic DNA extracted from porcine blood, semen, muscle and fat tissues by a rapid and simple Chelex-100 based method. One of the PCR procedure is designed from the ryanodine receptor coding sequence to produce a 81 base pair (bp) fragment, while the other is designed from pig intron sequences to produce a 659 bp fragment. Oligonucleotide primers derived from the coding sequence were also used for other meat species. Amplification products obtained from porcine, bovine, ovine, equine and deer genomic DNA were successfully digested with Hha I restriction enzyme to produce the same electrophoretic pattern as in the normal homozygous (NN) pig. No PCR products could be amplified from chicken and turkey DNA.     

Isolation of five laccase gene sequences from the white-rot fungus Trametes sanguinea by PCR, and cloning, characterization and expression of the laccase cDNA in yeasts

To obtain laccase-gene-specific sequences from the white-rot fungus Trametes sanguinea M85-2, a PCR screening method was used. Degenerate primers were designed based on highly conserved copper-binding regions I and IV of known laccases and used to amplify laccase sequences from T. sanguinea M85-2 genomic DNA. A single 1.6-kbp DNA band was amplified and cloned into a vector. Partial sequences of 21 clones were classified into five groups (lcc1-5) and the deduced amino acid sequences were all homologous to known laccase sequences. Based on the partial sequence of lcc1, the 5'-end of its cDNA was obtained by a PCR termed 5' rapid amplification of cDNA ends (5'-RACE), and RT-PCR was then carried out using the 5'-primer and the poly-dT primer to obtain the full-length lcc1 cDNA. The obtained cDNA encoded a protein consisting of 518 amino acid residues and its first 21 amino acid residues were predicted to be the signal peptide for secretion. The conserved characteristic structures of laccase, such as copper-binding ligands, N-glycosylation sites, and cysteine residues for disulfide bridges, were observed. The genomic DNA sequence of the lcc1 gene was also cloned by PCR method and the sequence revealed 10 introns. The lcc1 cDNA was inserted into yeast vectors for heterologous expression by Saccharomyces cerevisiae and Pichia pastoris. Phenol-oxidizing activity was detected from transformants of the yeasts, indicating that the obtained cDNA encodes a laccase. Previously, two laccase isozymes were biochemically characterized and purified from T. sanguinea M85-2. Using the sequential PCR method presented here, we have obtained partial sequences of at least five laccase genes and one cDNA clone encoding a protein with laccase activity but without any enzymatic information, suggesting that expressed enzymes under restricted conditions may not represent all the isozymes in target microorganisms. PCR cloning and heterologous expression of the cloned genes can be an alternative method of screening enzymes if these enzymes have conserved sequences.     

Cloning and sequencing of a complementary deoxyribonucleic acid coding for a bovine alpha s1-casein A from mammary tissue of a homozygous B variant cow

A cDNA clone for bovine alpha s1-casein variant A was isolated from a mammary gland cDNA library using a synthetic degenerate oligonucleotide probe. The largest Pst I insert containing an EcoR I site was sequenced. It contained 1090 base pairs, 47 in the 5' noncoding region, 603 in the coding region and 440 in the 3' noncoding region. The nucleotide sequence was compared with three published cDNA sequences for alpha s1-casein variant B. The most obvious difference was the absence of the 39 bases encoding the 13 amino acids that are present in the B variant but absent from the A variant. In addition, five other single base positions differed within individual codons among the four sequences at the third base for each codon, but this did not change the amino acids encoded. There were, however, a number of differences found in the 3' noncoding region. The isolated cDNA was subjected to site-directed mutagenesis to replace a Val-Ile dipeptide with Phe-Phe to increase the chymosin sensitivity of the protein. When the milk proteins from mammary gland tissue extracts were typed, the alpha s1-casein A gene product was not detected.     

Molecular cloning and expression of bovine kappa-casein in Escherichia coli

A cDNA library was constructed using poly(A) +RNA from bovine mammary gland. This cDNA library of 6000 clones was screened employing colony hybridization using 32P-labelled oligonucleotide probes and restriction endonuclease mapping. The cDNA from the selected plasmid, pKR76, was sequenced using the dideoxy-chain termination method. The cDNA insert of pKR76 carries the full-length sequence, which codes for mature kappa-casein protein. The amino acid sequence deduced from the cDNA sequence fits the published amino acid sequence with three exceptions; the reported pyroglutamic acid at position 1, tyrosine at position 35, and aspartic acid at position 81 are, respectively, a glutamine, a histidine, and an asparagine in the clone containing pKR76. The MspI-, NlaIV-cleaved fragment (630 base pair) from the kappa-casein cDNA insert has been subcloned into expression vectors pUC18 and pKK233-2, which contain a lac promoter and a trc promoter, respectively. Escherichia coli cells carrying the recombinant expression plasmids were shown to produce kappa-casein protein having the expected mobility on sodium dodecyl sulfate-polyacrylamide gel electrophoresis and being recognized by specific antibodies raised against natural bovine kappa-casein.     

常见肉类中鸭源性成分荧光PCR检测方法的建立

目的通过筛选引物、探针体系,优化PCR反应条件,建立常见肉品中鸭源性DNA的荧光PCR检测方法。方法针对线粒体基因设计50对引物探针,以鸭DNA为模板,利用PCR和荧光PCR方法筛选引物探针并确定反应条件,进行灵敏度、特异性和稳定性试验,最终确定荧光定量PCR方法的引物、探针及反应条件。结果当样本含量为0.1%时,本方法仍可特异、灵敏地检出鸭肉成分,检测Ct值可稳定在20以下。结论建立了常见肉品中鸭源性DNA的荧光PCR检测方法,可用于肉类制品中鸭源性成分的鉴定。     

Identification of Bacillus spp., Escherichia coli, Salmonella spp., Staphylococcus spp. and Vibrio spp. with 16S ribosomal DNA-based oligonucleotide array hybridization

Rapid identification of the genus and species of bacteria in foods and clinical specimens is important. In this report, DNA sequences of bacterial 16S rDNA were used to develop the oligonucleotide array for the identification of bacterial strains of Bacillus spp., Escherichia coli, Salmonella spp., Staphylococcus spp. and Vibrio spp. Most of these bacterial strains may cause food-borne outbreaks or sporadic cases. A rapid (<4 h) detection method that used universal PCR primers to amplify the variable regions of bacterial 16S rDNA, followed by reverse hybridization of the PCR products, which were biotin labeled, to the oligonucleotides arrayed on the chip was developed. Fifteen oligonucleotide probes were selected and spotted on the nylon strip to determine the array hybridization patterns. It was successful in discriminating Bacillus spp., E. coli, Salmonella spp., Staphylococcus spp. and Vibrio spp. with identification, in general, to the genus level, not species level. As 182 randomly selected strains were assayed, the detection rate was found higher than 98%. Except for 3 strains, the remaining 179 strains were correctly identified and no cross reactions were observed. These 179 strains generated five hybridization patterns. Adding more oligonucleotide probes to the array may allow the detection of more bacterial genera and species without significantly increasing the complexity or cost.     

食品中杏仁过敏原成分的检测

目的：建立检测食品中桃仁、杏仁过敏原成分的荧光PCR 方法,比较国外3 种ELISA 试剂盒效果。方法：针对杏仁Pru du1 基因设计引物及探针,建立荧光PCR 方法。利用杏仁过敏原参考物质对3 个品牌的ELISA试剂盒的回收率进行比较。结果：建立的荧光PCR 方法,具有很好的特异性;灵敏度为10mg/kg。结论：桃仁及杏仁过敏原成分荧光PCR 检测方法特异性好、灵敏度高,对食品中过敏原的检测有重要的实际意义。