基因芯片技术在检测肠道致病菌方面的应用

基因芯片技术具有高通量、自动化、快速检测等特点,因此被广泛地应用于各种研究领域,如细菌分子流行病学、细菌基因鉴定、致病分子机理、基因突变及多态性分析、表达谱分析、DNA测序和药物筛选等。现介绍基因芯片检测肠道致病菌方面的国外研究进展,基因芯片应用于检测肠道致病菌的3个方面:结合多重PCR对致病菌的毒力因子或者特异性基因进行鉴定;直接检测细菌的DNA或者RNA;以致病细菌核糖体RNA作为检测的靶基因同时检测多种肠道致病菌。由于其检测的高效率,该技术要优于其他分子生物学检测方法。基因芯片技术在肠道致病菌检测中有着巨大的应用价值,具有广阔的应用前景。     

食源性致病菌多重PCR快速检测方法建立与应用

利用PCR技术,建立多组多重食源性致病菌PCR快速检测方法。设计受试菌特异性引物,反应体系中加入多对引物和多种DNA模板,采用正交试验优化PCR反应条件,进行特异性引物的PCR扩增。建立了多组多重食源性致病菌PCR快速检测方法,方法中所检测受试菌株和模拟样品均出现特异性扩增条带,结果与实际相符。所建立多组多重PCR快速检测体系符合设计要求,可以应用于食源性突发公共卫生事件的应急检测和日常样品检测工作。     

寡核苷酸探针悬浮芯片在病原体检测中的应用

悬浮芯片与固体芯片、荧光定量PCR并列成为核酸序列鉴定中的重要的分子生物学工具,并在病原菌检测方面显示出不同的应用领域.悬浮芯片能同时检测多种病原菌,具有处理多样本能力、使用灵活、低成本等特点,适合对未知样本检测及环境监控.能够在生物安全、公共卫生、工农业生产中发挥重要作用;而固体芯片能耦联成千上百个探针,但由于在多样本处理、成本方面欠缺,因此适合于对重要的未知病原体的鉴定;荧光定量PCR具较好特异性、灵敏度,以及多样本处理能力,但在高通量方面欠缺.适合有目的地检测已知病原体.目前已建立三种基于悬浮芯片的检测方法:多重PCR扩增、通用引物扩增16S/23S rDNA、直接对实际样本杂交检测.多重PCR具较好特异性,但其多重能力还难以满足悬浮芯片的高通量的需要;通用引物具较好灵敏度及扩增多靶分子能力,但也存在交叉反应等缺陷.同时,采用PCR扩增方法,悬浮芯片检测的是PCR产物,不能客观反应实际样本中存在病原菌数量及是否具生命力.直接杂交环境样本尽管避免了PCR的缺陷,但在灵敏度方面非常欠缺.目前,在环境样本处理上,仍然缺乏有效的、高通量、自动化的方法,不能满足PCR与悬浮芯片多样本检测的需要.     

多重PCR快速检测化妆品中三种致病菌的研究

利用多重PCR技术建立快速检测化妆品中三种致病菌的方法。根据已报道的大肠杆菌phoA基因、铜绿假单胞菌外膜蛋白基因oprL和金黄色葡萄球菌特异性序列SmaI选择特异性引物,对人工染菌化妆品进行多重PCR检测。结果显示,三种致病菌的基因组DNA均可与各自引物特异性结合,扩增产物大小分别为622 bp、504 bp和426 bp。该方法用于人工污染的化妆品中,大肠杆菌的检出限浓度为103 CFU/mL,铜绿假单胞菌和金黄色葡萄球菌的检出限浓度为105 CFU/mL。作者建立的多重PCR方法可同时快速、特异地对化妆品中三种致病菌进行检测,在化妆品行业具有较大的应用价值。     

饮用水中5种致病菌多重PCR技术检测研究

沙门氏菌(Salmonella sp．)、志贺氏菌(Shigella sp．)、绿脓杆菌(Pseudonmnas aeruginosa)、肠出血型大肠杆菌O157(Eterohaemorrhagic O157)和副溶血弧菌(Vibrio rahaemolyticus)是5种饮用水中不得检出食源性致病菌,根据它们的毒素基因、高度保守基因及特异性基因,设计合成5对寡核苷酸引物,应用PCR技术对10个属的30株细菌进行引物特异性检测。通过对多重PCR反应体系、条件进行优化,显提高了检测灵敏度。初步应用于水样分析中,极大的缩短了检测时间、降低了成本。实验结果表明：5对寡核苷酸引物都具较高的特异性和专一性,多重PCR检测灵敏度达到10^1～10^2cfu,检测需5～6h,在水样检测的初步应用中得到了均一、稳定、清晰的结果,可推广应用于环境监测、水源检测、食品卫生监督、商品检验检疫等领域。     

多种食源性致病菌检测的多重PCR 方法的研究

目的:利用多重PCR技术,建立可以同时检测多种食源性致病菌的多重PCR方法。方法:分别选择沙门氏菌invA基因,志贺氏菌的ipaH基因,单核细胞增生李斯特氏菌的hlyA基因,大肠杆菌O157:H7的eaeA基因,副溶血弧菌的toxR基因,设计多重PCR引物,建立多重PCR检测体系,并对该体系进行特异性和灵敏度实验。结果:通过对19株菌株进行实验,所有的目标菌株均为阳性,而其余菌株为阴性。对多重PCR体系的灵敏度进行考察,沙门菌的灵敏度为5000 CFU/mL;志贺氏菌的灵敏度为5500CFU/mL;单核细胞增生李斯特氏菌的灵敏度为5200 CFU/mL;O157:H7的灵敏度为5000CFU/mL;副溶血弧菌的灵敏度为6300CFU/mL。结论:建立的多重PCR体系能实现多种致病菌同时检测。     

3种粪便标本保存方法对肠道菌群检测结果影响的比较研究

比较3种粪便标本保存方法对肠道菌群检测结果的影响,为采集粪便标本后短期保存方法的选择提供参考。收集10名志愿者的新鲜粪便标本,对每份标本分别采用4℃、室温(25℃)、无水乙醇保存4 h,然后统一放入-80℃低温冰箱冻存。随后进行细菌DNA提取,并对16S rRNA V4区基因进行扩增,应用Illumina MiSeq平台进行高通量测序,比较3种保存方法下肠道菌群多样性和组成差异。结果表明,3种保存方法下,肠道菌群在Alpha多样性方面无统计学差异(P0.05)。肠道菌群属水平比较,毛螺旋菌属(Lachnospira)在无水乙醇组中相对丰度高于4℃组和室温组(P0.05),萨特菌属(Sutterella)在无水乙醇组中相对丰度高于4℃组(P0.05),而真杆菌属(Eubacterium)在无水乙醇组中相对丰度低于室温组(P0.05)。PCoA分析发现,当UniFrac距离加权后,4℃和无水乙醇保存同一受试者粪便标本,菌群结果较为接近,而室温保存会导致个别受试者菌群出现离散现象。无水乙醇短期保存粪便标本,肠道菌群多样性、组成以及结构保持稳定,能满足不同研究的需要。此外,无水乙醇具备价格低廉、便于携带等优点。因此,在新鲜粪便标本不能立即低温冻存时,无水乙醇保存可以作为首要选择。     

三种食源性致病菌的多重PCR快速检测及应用

针对常见的3种食源性致病菌肠出血性大肠杆菌O157H7的rfbE基因、金黄色葡萄球菌的nuc基因及沙门氏菌的hilA基因,使用Primer 5.0软件设计出相对应的特异性引物,预计PCR产物的分子大小为287、354及468 bp。通过单一、双重及三重PCR对样品进行检测,并对人工感染的鲜奶进行检测。结果表明,3种食源性致病菌的单一、双重和三重PCR均能成功扩增出与预计大小一致的片段,无非特异性扩增。人工感染食品的PCR检测也获得了目的菌的特异性片段,并且结果稳定。这说明此3对引物可分别用于3个菌靶基因的PCR检测。     

悬浮芯片技术应用进展

悬浮芯片技术(SAT)是一种新型、高通量的生物芯片技术,它是将流式细胞术、激光技术及应用流体学等技术结合在一起,利用悬浮在液相中的分类荧光编码微球作为检测载体,具有高通量、速度快、灵敏度高、特异性强及检测范围广等特点.近几年来,悬浮芯片技术在免疫学、基因组学、蛋白质组学及临床诊断检测等方面应用较广泛.就其原理、技术特点...     

通用引物PCR检测临床常见致病菌的实验研究

通用引物可一次性扩增18种临床常见致病菌和耐药菌株的DNA,扩增片段长度在220bp左右,18种特异性探针分别与18种标准菌株的PCR扩增产物杂交结果显示探针都具有高度特异性;5种37例经法国梅里埃API细菌鉴定系统确定的临床分离菌株进行杂交鉴定,鉴定结果与分离株一致,表明设计的探针具有高度特异性及准确性。80例临床标本分别用法国梅里埃API细菌鉴定系统及PCR杂交法进行检测,阳性率分别为(52.5%)和(67.5%),表明PCR结合寡核苷酸杂交法比传统的生物学培养法更为灵敏,值得推广。     

High-throughput molecular identification of fish eggs using multiplex suspension bead arrays

The location and abundance of fish eggs provide information concerning the timing and location of spawning activities and can provide fishery-independent estimates of spawning biomass. However, the full value of egg and larval surveys is severely restricted because many species' eggs and larvae are morphologically similar, making species-level identification difficult. Recent efforts have shown that nearly all species of fish may be identified by mitochondrial DNA (mtDNA) sequences (e.g. via 'DNA barcoding'). By taking advantage of a DNA barcode database, we have developed oligonucleotide probes for 23 marine fish species that produce pelagic eggs commonly found in California waters. Probes were coupled to fluorescent microspheres to create a suspension bead array. Biotin-labelled primers were used to amplify the mitochondrial cytochrome oxidase subunit I (COI) and 16S ribosomal rRNA genes from individual fish eggs. The amplicons were then hybridized to the bead array, and after the addition of a reporter fluorophore, samples were analysed by flow cytometry with Luminex 100 instrumentation. Probes specifically targeted eggs that are abundant and/or from morphologically indistinguishable species pairs. Results showed that the 33 different probes designed for this study accurately identified all samples when PCR was successful. Suspension bead arrays have a number of benefits over other methods of molecular identification; these arrays permit high multiplexing, simple addition of new probes, high throughput and lower cost than DNA sequencing. The increasing availability of DNA barcode data for numerous fish faunas worldwide suggests that bead arrays could be developed and widely used for fish egg, larval and tissue identifications.     

Rapid multiplex PCR based species identification of wild tigers using non-invasive samples

Conservation and management of rare and elusive species requires accurate data on presence or absence. In such cases, molecular genetics based species identification approaches can prove invaluable, especially in conjuncture with non-invasive DNA sampling. However, non-invasive sources yield DNA in low concentration that is degraded, which could result in false negatives for species identification. In this paper, we developed a set of primers for PCR-based species identification of tigers. Our results reveal high rates (upto 90%) of species identification for both fresh (less than 48 h) and old (between 7 days and 3 months) fecal samples from the field. Experiments reveal that multiplex PCR (amplifying more than one genomic region) results in an increase in conclusive species identification (and a consequent decrease in the number of false negatives) from 55% to 89% for old fecal samples. We demonstrate that this increased success is because we experimentally overcome the problems of low DNA template quantity (using the multiplex PCR kit, increases species identification from 55% to 72%) and low template DNA quality (two sets of primers increase the species identification success from 72% to 89%). We recommend that multiplex PCR based methods be used (in conjuncture with species specific primers) for other rare and elusive species since such methods will potentially significantly decrease error in species identification.     

Copy number variation detection using SNP genotyping arrays in three Chinese pig breeds

We performed genome‐wide CNV detection based on SNP genotyping data of 96 Chinese‐native Tibetan, Dahe and Wuzhishan pigs. These pigs are particularly interesting because of their excellent adaptation to hypoxia or small body size, which facilitates the use of them as models of different human diseases in addition to valuable agricultural animals. A total of 105 CNV regions (CNVRs) were identified, encompassing 16.71 Mb of the pig genome. Seven of 10 (70%) CNVRs selected randomly were validated by quantitative real‐time PCR. Comparison with previous studies revealed 25 (23.81%) novel CNVRs, indicating that CNV coverage of the pig genome is still incomplete and there exists large diversity between pig breeds. Functional analysis of genes located in these CNVRs confirmed the high representation of genes involved in sensory perception, neurological system processes and other basic metabolic processes. In addition, the majority of these CNVRs were detected to span reported pig QTL that affect various traits, which highlighted three biologically interesting genes with copy number changes (i.e., ANKRD34B, FAM110B and ABCG1). These genes may have economic importance in pig breeding and are worth being further investigated. We also obtained some CNVRs harboring genes that had human orthologs involved in human diseases such as cardiovascular disease and Alzheimer's disease. The findings of this study are a significant extension of the coverage of CNVRs in the pig genome and provide valuable resources for follow‐up‐associated studies of CNVs in pig complex traits as well as important implications of human diseases.     

Enzyme microgels in packed-bed bioreactors with downstream amperometric detection using microfabricated interdigitated microsensor electrode arrays.

In this article, we describe the use of pH- responsive hydrogels as matrices for the immobilization of two enzymes, glucose oxidase (GOx) and glutamate oxidase (GlutOx). Spherical hydrogel beads were prepared by inverse suspension polymerization and the enzymes were immobilized by either physical entrapment or covalent immobilization within or on the hydrogel surface. Packed-bed bioreactors were prepared containing the bioactive hydrogels and these incorporated into flow injection (FI) systems for the quantitation of glucose and monosodium glutamate (MSG) respectively. The FI amperometric detector comprised a microfabricated interdigitated array within a thin-layer flow cell. For the FI manifold incorporating immobilized GOx, glucose response curves were found to be linear over the concentration range 1.8-280 mg dL(-1) (0.1-15.5 mM) with a detection limit of 1.4 mg dL(-1) (0.08 mM). Up to 20 samples can be manually analyzed per hour, with the hydrogel-GOx bioreactor exhibiting good within-day (0.19%) precision. The optimized FI manifold for MSG quantitation yielded a linear response range of up to 135 mg dL(-1) (8 mM) with a detection limit of 3.38 mg dL(-1) (0.2 mM) and a throughput of 30 samples h(-1). Analysis of commercially produced soup samples gave a within-day precision of 3.6%. Bioreactors containing these two physically entrapped enzymes retained > 60% of their initial activities after a storage period of up to 1 year.     

Rapid detection of low‐level HeLa cell contamination in cell culture using nested PCR

HeLa cells are a commonly used cell line in many biological research areas. They are not picky for culture medium and proliferate rapidly. HeLa cells are a notorious source of cell cross‐contamination and have been found to be able to contaminate a wide range of cell lines in cell culture. In this study, we reported a simple and efficient method for detecting the presence of HeLa cell contamination in cell culture. HPV‐18 was used as a biomarker. The cell culture supernatant was used directly as the template for nested PCR without extracting nucleic acid. By PCR amplification of the cell culture supernatant with the designed primers, we were able to detect the presence of HeLa cells in the culture. The sensitivity of this method can reach 1%, which is 10‐fold higher than Short tandem repeat sequence (STR) profiling. This simple, rapid, and “noninvasive” quality checking method should find applications in routine cell culture practice.     

应用PCR技术快速检测熊蜂短膜虫

【目的】近年来,熊蜂作为温室作物的理想授粉者在国外已被广泛利用,并且获得很好的经济效益和生态效益,所以国外熊蜂经常被进口用于设施农业。熊蜂短膜虫Crithidia bombi是熊蜂的一种重要寄生虫病,一旦随进口熊蜂传入,将给国内熊蜂蜂群带来严重危害,因此迫切需要建立一种熊蜂短膜虫检测方法。【方法】基于熊蜂短膜虫基因内转录间隔区(internal transcribed space,ITS)基因序列设计了一对引物(Cri-F/R),建立了熊蜂短膜虫的PCR检测方法,并对退火温度、引物浓度和循环个数等反应条件进行了优化,同时验证了该PCR方法的灵敏性、特异性和稳定性。【结果】以熊蜂短膜虫ITS基因保守区设计特异性引物建立的熊蜂短膜虫PCR检测方法是可行的。优化的PCR反应条件为:退火温度59℃,引物浓度0.5μmol/L,扩增循环数35次。对感染熊蜂短膜虫的熊蜂总DNA的灵敏度达到13.24×10-5ng/μL,并具有良好的特异性和稳定性。将该方法应用于熊蜂短膜虫的检测,整个检测过程不超过4 h,具有良好的适用性。【结论】研究建立了熊蜂短膜虫检测方法,能用于疫情监测和进境熊蜂的检验检疫。     

Rapid and effective detection of anthrax spores in soil by PCR

AIMS: To detect Bacillus anthracis DNA from soil using rapid and simple procedures. METHODS AND RESULTS: Various amounts of B. anthracis Pasteur II spores were added artificially to 1 g of soil, which was then washed with ethanol and sterile water. Enrichment of the samples in trypticase soy broth was performed twice. A DNA template was prepared from the second enrichment culture using a FastPrep instrument. The template was then used for nested and real-time polymerase chain reaction (PCR) with B. anthracis-specific primers, to confirm the presence of B. anthracis chromosomal DNA and the pXO1/pXO2 plasmids. CONCLUSIONS: One cell of B. anthracis in 1 g of soil could be detected by nested and real-time PCR. The usefulness of the PCR method using field samples was also confirmed. SIGNIFICANCE AND IMPACT OF THE STUDY: The results indicate that this could be a useful method for detecting anthrax-spore contaminated soil with high sensitivity. Its application could have great impact on the progress of epidemiological surveillance.     

Rapid detection of Salmonella subspecies I by PCR combined with non-radioactive hybridisation using covalently immobilised oligonucleotide on a microplate

Abstract A polymerase chain reaction (PCR)-based test was developed for the detection of Salmonella . One pair of oligonucleotide primers was designed to amplify a 93-bp fragment of a gene required for the invasion of HeLa cells by Salmonella ser Typhi strain Ty2. The amplified product was analysed by non-radioactive sandwich hybridisation in microtiter plates using two oligonucleotides. The capture oligonucleotide was covalently linked onto aminated wells of microtiter plates. The detection oligonucleotide was labelled with biotine. The hybrid molecules were detected by avidine conjugated with alkaline phosphatase and chromogenic substrate. The described combination of microplate sandwich hybridisation and PCR seems to be a suitable method for rapid detection of Salmonella subspecies I. It only requires a thermal cycler and a conventional microtiter reader, and can be readily done on a large scale.     

Rapid detection and quantification of five periodontopathic bacteria by real-time PCR

The quantity of periodontopathic bacteria in plaque samples is an important determinant for understanding the etiologic role of bacteria. The real-time PCR method was used to detect and quantify periodontopathic bacteria, such as Actinobacillus actinomycetemcomitans, Bacteroides forsythus, Porphyromonas gingivalis, Treponema denticola, and Treponema socranskii, in saliva and subgingival plaque samples. There was good agreement between the results of conventional PCR and real-time PCR methods. Using the LightCycler system we were able to determine the amount of periodontopathic bacteria within an hour. The real-time PCR method was linear for samples containing from 10(3) to more than 10(8) cells (r2 = 0.999). The application of the real-time PCR method should be useful in the rapid detection and quantification of periodontopathic bacteria in clinical samples.