Adaptation of aerobic, ethene-assimilating Mycobacterium strains to vinyl chloride as a growth substrate

Contamination of drinking water source zones by vinyl chloride (VC), a known human carcinogen and common groundwater contaminant, poses a public health risk. Bioremediation applications involving aerobic, VC-assimilating bacteria could be useful in alleviating environmental VC cancer risk, but their evolution and activity in the environment are poorly understood. In this study, adaptation of ethene-assimilating Mycobacterium strains JS622, JS623, JS624, and JS625 to VC as a growth substrate was investigated to test the hypothesis that VC-assimilating bacteria arise from naturally occurring ethene-assimilating bacteria. VC consumption in the absence of microbial growth was initially observed in cultures grown in both ethene and 1/10-strength trypticase soy agar + 1% (w/v) glucose. After extended incubations (55-476 days), all strains commenced growth-coupled VC consumption patterns. VC-adapted cultures grown on 20 mM acetate subsequently retained their ability to assimilate VC. Three independent purity check methods (streak plates, 16S rRNA gene sequencing, and repetitive extragenic palindromic polymerase chain reaction) verified culture purity prior to and following VC adaptation. Overall, our results suggest that ethene-assimilating mycobacteria have a widespread ability to adapt to VC as a growth substrate.     

肉制品中牛源性成分Taqman荧光定量PCR检测法的建立

本实验根据牛线粒体差异序列设计特异性PCR引物和Taqman探针,并基于16S rDNA内参基因设计通用引物及Taqman探针,绘制并通过标准曲线确定样品中总DNA浓度以及牛源性成分DNA浓度,采用相对定量法测定肉制品中牛源性成分的质量分数。并通过特异性、灵敏度实验,及混合肉样回收率及市售肉制品检测,对本方法进行验证。结果表明,方法特异性强,可对牛肉DNA进行特异性扩增。最低检出限为10 pg/μL,具有较高的灵敏度。并根据回收实验可知,平均回收率为98.62%。可以为肉制品中牛肉含量的测定提供技术参考。     

Development of a quantitative real-time PCR assay for the detection of Aspergillus carbonarius in grapes

Aspergillus carbonarius is the main species responsible for the production of ochratoxin A (OTA) in wine grapes. To monitor and quantify A. carbonarious in grapes, a quantitative real-time PCR assay was developed as a possible tool for predicting the potential ochratoxigenic risk. DNA extraction from grape berries was performed by using conventional extraction and clean up through EZNA Hi-bond spin columns. A TaqMan probe was used to quantify A. carbonarius genomic DNA in grape berries samples. An exogenous internal positive control was used to overcome DNA recovery losses due to matrix inhibition. The quantification of fungal genomic DNA in naturally contaminated grape was performed using the TaqMan signal versus spectrophotometrically measured DNA quantities (Log10) calibration curve with a linearity range from 50 to 5 x 10(-4) ng of DNA. A positive correlation (R2=0.92) was found between A. carbonarious DNA content and OTA concentration in naturally contaminated grape samples. This is the first application of TaqMan real-time PCR for identifying and quantifying A. carbonarius genomic DNA occurring in grapes. The rapid DNA extraction method for grapes, together with the commercial availability of reagents and instrumentation, allows to perform a remarkable number of reproducible assays (96-well format) in less than 4 h.     

一种快速鉴别普通高温放线菌的特异PCR方法

普通高温放线菌(Thermoactinomyces vulgaris)具有产生多种耐热酶的能力,在淀粉深加工、皮革制造、高温堆肥生产以及分子生物学等领域中均有重要应用,应用常规技术鉴别费时费力,无法满足普通高温放线菌筛选及其应用研究的要求,有必要建立一套快速、准确的鉴别方法。该研究根据普通高温放线菌的gyr B基因分别设计了普通高温放线菌的特异性引物,建立了快速筛选普通高温放线菌的特异PCR方法。实验结果表明所设计的特异性引物对普通高温放线菌具有较高的特异性,可以快速鉴别普通高温放线菌,与传统的菌种鉴定方法相比,具有高效、灵敏、便捷及成本低廉等显著优点。     

Use of the agar drop method for the quantitative calculation of mesophilic aerobic and facultatively anaerobic microorganisms and coliform bacteria in food products

The tests in agar dishes and agar drops were used simultaneously to determine the amount of mesophilic aerobic and facultative-anaerobic microorganisms and coliform bacteria in certain food products. The results of the analysis of more than 40 samples of different food products in both the tests have proved to be identical. The method can be recommended for practical use at laboratories of sanitary-epidemiological stations during prophylactic sanitary control, and at laboratories of food manufacturing enterprises.     

A collagenase-targeted multiplex PCR assay for identification of Vibrio alginolyticus, Vibrio cholerae, and Vibrio parahaemolyticus

A multiplex PCR assay using three collagenase-targeted primer pairs for the species-specific detection of Vibrio alginolyticus, Vibrio cholerae, and Vibrio parahaemolyticus was developed. The results highlight the species specificity of the three primer sets designed. Because of the increasing importance of Vibrio spp. in human foodborne diseases, molecular approaches for routine microbial screening and monitoring of clinical, environmental, and food samples also have become more important. The results of this study indicate that the gene coding for collagenase should be used as an alternative molecular target to discriminate among the three Vibrio species.     

多重PCR鉴定动物源空肠弯曲菌和结肠弯曲菌方法的建立

建立鉴定空肠弯曲菌和结肠弯曲菌的多重PCR(mPCR)方法。方法 分别以16S rRNA、马尿酸酶和16S-23S rRNA基因为靶序列设计特异性引物,建立多重PCR方法检测37株菌株样品,同时采用ⁱⁿgene CAM nested PCR检测试剂盒检测验证,进行结果比较分析。结果 该多重PCR方法可扩增出空肠弯曲菌和结肠弯曲菌的特异性条带,其他对照菌株均未扩增出条带,具有较好的特异性;检测敏感性可达0.81pg/μl空肠弯曲菌DNA,0.93pg/μl结肠弯曲菌DNA。多重PCR方法和试剂盒检测结果的符合率为100%,二者与国标GB/T 4789.9—2008方法的符合率达97%以上。结论 本试验建立的多重PCR方法操作快速方便、节约试验成本,具有较好的特异性、敏感性和重复性,可用于弯曲菌的鉴定。     

微生物酶制剂中转基因微生物的实时荧光PCR检测方法

针对微生物酶制剂中残留转基因微生物的检测问题,根据醇氧化酶-1（AOX1）启动子基因的序列信息设计一对引物及一条MGB探针,建立了转基因微生物的实时荧光PCR筛选检测方法。实验结果表明,该方法灵敏度达到1pg,可以准确判定生产线上不同分离阶段的微生物酶制剂中的转基因微生物残留情况。该方法准确度和灵敏度高,操作方便,可作为微生物酶制剂中转基因微生物分离状况的监测方法,也可为其他转基因微生物检测研究提供借鉴和参考。      

微生物酶制剂中转基因微生物的实时荧光PCR检测方法

针对微生物酶制剂中残留转基因微生物的检测问题,根据醇氧化酶-1(AOX1)启动子基因的序列信息设计一对引物及一条MGB探针,建立了转基因微生物的实时荧光PCR筛选检测方法.实验结果表明,该方法灵敏度达到1pg,可以准确判定生产线上不同分离阶段的微生物酶制剂中的转基因微生物残留情况.该方法准确度和灵敏度高,操作方便,可作为微生物酶制剂中转基因微生物分离状况的监测方法,也可为其他转基因微生物检测研究提供借鉴和参考.     

实时荧光定量PCR监测镇江香醋醋酸发酵过程中微生物变化

对镇江香醋醋酸发酵阶段醋醅中功能微生物的变化进行定量分析。建立了实时荧光定量PCR方法,对醋酸发酵阶段醋醅中总细菌、总真菌、醋酸菌、乳酸菌和酵母的动态变化进行了定量分析。研究结果表明,发酵起始阶段(1～7天)醋醅中总细菌、醋酸菌和乳酸菌的生物量快速上升,分别于第6、7、4天达到最大值,为4.85×1011,1.14×1010和3.37×1011copies/g干醅。随后各类细菌的生物量逐渐下降,并维持在一定水平。醋醅中总真菌和酵母的生物量在发酵前期变化不大,7天后至发酵结束总真菌的生物量逐渐下降为7.59×104copies/g干醅,而酵母生物量则在发酵8～12天内下降为0。     

基于内参系统的阪崎肠杆菌实时荧光定量PCR检测方法的建立

根据阪崎肠杆菌ompA靶基因设计特异性引物和探针,并加入内参(IAC),建立能够实时监控反应过程的荧光定量PCR检测方法。结果表明,该方法对阪崎肠杆菌基因组DNA的最低检测限为1pg;对细菌的最低检测限为1×10~4 CFU;对含有靶基因质粒的最低检测限为10~3拷贝;Ct值与模板拷贝数均呈良好的线性关系(R~2=0.999)。人工污染试验结果表明,在初始菌量为10CFU/25g奶粉样品时,采用水洗加试剂盒法和水煮法提取DNA,阪崎肠杆菌均在增菌10h时检出。研究结果为进一步优化和完善阪崎肠杆菌分子生物学方法的标准化提供了参考。     

基于内参的副溶血性弧菌实时荧光定量PCR快速检测方法的建立

目的建立基于内参的副溶血性弧菌实时荧光定量PCR方法,快速检测样品中的副溶血性弧菌。方法根据Gen Bank已公布的副溶血性弧菌基因组序列,筛选特异性靶基因,设计特异性引物探针,优化反应体系,并在体系中加入内参(IAC),通过标记不同荧光基团的Taq Man探针来监测IAC,进而实时监控整个PCR反应。按照5~50 cfu/25 g的细菌量人工污染样品,以评价所建立反应的体系。结果以副溶血性弧菌基因组DNA为模板,最低检测限为1 pg/μl;以10倍梯度稀释的菌液经水煮法提取的DNA为模板,最低检测限为4×102cfu/ml;以含有gyr B的质粒为模板,最低检测极限可以达到100 copies/μl;建立gyr B和gyr B-IAC标准曲线,Ct值与模板拷贝数均呈良好线性关系(r2=0.999);人工污染初始菌量为7 cfu/25 g时,样品中副溶血性弧菌增菌6 h即可检出。结论本研究所建立的gyr B-IAC实时荧光定量PCR方法,既能有效检测食品中副溶血性弧菌,又能实时监测PCR反应过程,有效防止"假阴性"的发生,结果可靠,有利于实现海产品中副溶血性弧菌实时荧光定量PCR检测方法的标准化。     

Development of a new real-time quantitative PCR assay for the detection of Staphylococcus aureus genotype B in cow milk,targeting the new gene adlb

The specific and reliable diagnosis of mastitis pathogens is essential for successful sanitation programs. The aim of the present study was to develop and evaluate a new real-time quantitative PCR (qPCR) assay for the very sensitive and specific detection of Staphylococcus aureus genotype B in cow milk samples. This mastitis pathogen is contagious and particularly prevalent in Switzerland and other central European countries. The new test is based on a rapid preparation of bacteria, followed by DNA isolation and qPCR for a unique target gene coding for the adhesion-like bovine protein (adlb). The inclusivity of the new target gene was 97% and the exclusivity 98%, meaning that other genotypes and bacterial species could be excluded with high reliability. The limit of detection of the new assay was 235 staphylococcal cell equivalents/mL of culture. The new test shows high intra- and interassay repeatability. Results are available within 2 d after sampling, allowing farmers and veterinarians to apply sanitation measures immediately. Based on the results of a preliminary field study, the diagnostic sensitivity and specificity of the new qPCR assay are 99 and 100%, respectively. The new analytical procedure is straightforward and can be applied for routine diagnostics.     

实时定量PCR法对羊肉中鸡源性成分的量化检测

为实现羊肉中鸡源性成分的量化检测,本文利用实时荧光PCR技术,通过在单拷贝基因上设计引物,DNA标准曲线绘制以及确定羊肉,鸡肉质量与DNA数学换算参数等方法,对四种不同掺混比例的鸡肉、猪肉混合样本掺混的质量百分比进行分析。结果显示,检测百分比与理论混合百分比间的绝对误差控制在5%以内,量化研究结果准确,该法为食品安全检测工作提供了技术支撑。      

Real-time PCR for quantitative detection of bovine tissues in food and feed

A real-time PCR approach with the SYBR Green detection system has been developed for the quantitative detection of bovine tissues in food and feedstuffs. The method combines the use of bovine-specific primers, which amplify an 84-bp fragment of the mitochondrial 12S rRNA gene, and universal primers, which amplify a 140-bp fragment of the nuclear 18S rRNA gene from eukaryotic DNA. The 18S rRNA primers are used as endogenous controls for the total content of PCR-amplifiable DNA in the sample. The specificity of the primers was tested against 18 animal species, including mammals, birds, and fish, as well as 6 plant species. Analysis of experimental bovine tissues-oats mixtures demonstrated the suitability of the assay for the detection of bovine DNA in mixtures containing as low as 0.1% of bovine tissues. The performance of the method is not affected by severe heat treatment (up to 133 degrees C for 20 min at 300 kPa). The reported PCR assay could be very useful for detecting bovine-derived ingredients in raw and heat-treated food and feedstuffs.     

Vanillin inhibits pathogenic and spoilage microorganisms in vitro and aerobic microbial growth in fresh-cut apples

The antimicrobial effect of vanillin against four pathogenic or indicator organisms; Escherichia coli, Pseudomonas aeruginosa, Enterobacter aerogenes, and Salmonella enterica subsp. enterica serovar Newport and four spoilage organisms; Candida albicans, Lactobacillus casei, Penicillum expansum, and Saccharomyces cerevisiae that could be associated with contaminated fresh-cut produce, was examined. The minimal inhibitory concentration (MIC) of vanillin was dependent upon the microorganism and this ranged between 6 and 18 mM. When incorporated with a commercial anti-browning dipping solution (calcium ascorbate, NatureSeal™), 12 mM vanillin inhibited the total aerobic microbial growth by 37% and 66% in fresh-cut ‘Empire’ and ‘Crispin’ apples, respectively, during storage at 4 °C for 19 days. Vanillin (12 mM) did not influence the control of enzymatic browning and softening by NatureSeal. These results provide a new insight for vanillin as a potential antimicrobial agent for refrigerated fresh-cut fruits and vegetables.     

A PCR assay for detection of acetic acid-tolerant lactic acid bacteria in acidic food products

A PCR assay for the detection of acetic acid-tolerant lactic acid bacteria in the genera of Lactobacillus and Pediococcus was developed in this study. Primers targeting the bacterial 16S rRNA gene were newly designed and used in this PCR assay. To determine the specificity of the assay, 56 different bacterial strains (of 33 genera), 2 fungi, 3 animals, and 4 plants were tested. Results were positive for most tested bacterial members of 16S rRNA gene-based phylogenetic groups (classified in the Lactobacillus casei and Pediococcus group), including Lactobacillus fructivorans, Lactobacillus brevis, Lactobacillus buchneri, Lactobacillus plantarum, and Lactobacillus paracasei. For all other bacterial strains and eukaryote tested, results were negative. Bacterial DNA for PCR was prepared with a simple procedure with the use of Chelex 100 resin from culture after growth in deMan Rogosa Sharpe broth (pH 6.0). To test this PCR assay for the monitoring of the acetic acid-tolerant lactic acid bacteria, L. fructivorans was inoculated into several acidic food as an indicator. Before the PCR, the inoculation of 10 to 50 CFU of bacteria per g of food was followed by a 28-h enrichment culture step, and the PCR assay allowed the detection of bacterial cells. Including the enrichment culture step, the entire PCR detection process can be completed within 30 h.     

Roundup Ready® soybean event-specific real-time quantitative PCR assay and estimation of the practical detection and quantification limits in GMO analyses

An event-specific real-time PCR method for detection and quantification of genetically modified Roundup Ready soybean with TaqMan chemistry on the LightCycler, targeting the nopaline synthase terminator (3') junction between recombinant and host plant DNA is described. We distinguish between three types of detection and quantification limits: the absolute limits (referring to the initial number of template copies in the PCR), the relative limits (referring to the relative percentage of initial template copies of the recombinant sequence to copies of the haploid soybean genome that is detected), and the practical limits (referring to what is applicable in the PCR with the DNA that is being analysed). The absolute detection limit was determined to be a single initial template copy, while the absolute quantification limit was determined to be approximately 30 initial template copies. We discuss the relative and practical limits, and provide guidelines to estimating the practical limits.