采用基因微阵列技术对常见呼吸道病毒进行检测的初步研究

建立一种高通量的基因微阵列检测技术,对常见呼吸道病毒感染进行监控.根据公开发表的8个病毒科38种常见呼吸道病毒的序列,计算其保守区域,设计病毒的特异性检测探针,制备呼吸道病毒检测基因微阵列.利用随机引物PCR方法标记样品中的病毒靶序列,标记产物与基因微阵列上的探针杂交,清洗、扫描后进行结果分析.采用流感病毒、麻疹病毒、腮腺炎病毒和风疹病毒作为报告病毒,并对80例上呼吸道感染患者的咽拭子标本进行验证测试.初步结果表明,该呼吸道病毒微阵列基因芯片检测是可行的,在利用基因微阵列技术对病毒监控方面进行了有益的尝试,得到了有经验的信息.     

蛋白微阵列研究进展

蛋白微阵列是随着基因微阵列技术发展起来的,用于基因微阵列的制备方法、信号的检测及分析系统,也可用于蛋白微阵列。各种蛋白微阵列基质的发展,提高了蛋白的固定效率。放射性同位数、化学发光、激光共聚焦荧光扫描等技术都已用于微阵列的检测。重组蛋白技术的发展,提高了蛋白微阵列检测的通量和灵敏度。蛋白微阵列具有通量高、使用样品少、重复性好、可定量的特点,使其在生物医药科学研究中得到了广泛应用。本综述了蛋白微阵列的制备及其在免疫检测、医学诊断及蛋白组研究中的应用。     

Identification of HCV-1b by Low-Density cDNA Microarray-Based Assay

A rapid and sensitive microarray assay for the detection of HCV-1b was developed in our laboratory and a cDNA fragment library for HCV-1b cDNA microarray probes was constructed. The full-length cDNAs of HCV-1b were digested with restriction endonuclease Sau3A I and the fragments were cloned with the pMD18-T vectors. Positive clones were isolated and identified by sequencing. The cDNA microarray was prepared by spotting the gene fragment on the surface of an amido-modified glass slide using the robotics system and samples were fluorescent labeled by the restriction display PCR (RD-PCR) technique, In the present study, modified protocols were used for probe selection and hybridization temperature. The detection of a microarray was validated by the hybridization and the sequence analysis. A total of 22 different specific gene fragments of HCV-1b ranging from 250 to 750 bp were isolated and sequenced, and these fragments were further used as probes in the microarray preparation. The diagnostic validity of the microarray method was evaluated after the washing and scanning process. The results of hybridization and sequence data analysis showed a significant specificity and sensitivity in the detection of HCV-1b RNA. The method of preparing microarray probes by construction of cDNA fragments library was effective, rapid, and simple; the optimized microarray was sensitive in the clinical detection of HCV-1b. The RD-PCR technique for the sample labeling was useful for significantly increasing the sensitivity of the assay. The cDNA microarray assay can be widely used in the clinical diagnosis of HCV-1b.     

Signal and sensitivity enhancement through optical interference coating for DNA and protein microarray applications.

Optical inteference (OI) coated slides with unique optical properties were utilized in microarray analyses, demonstrating their enhanced detection sensitivity over traditional microarray substrates. The OI coating is comprised of a proprietary multilayered, dielectric, thin-film interference coating located beneath the functional coating (aminosilane or epoxysilane). It is designed to enhance the fluorescence in the Cy3 and Cy5 channel by increasing the light absorption of the dyes by about 6-fold and by redirecting emitted fluorescence into the detector during scanning, resulting in a theoretical limit of about 12-fold signal amplification. Two-color DNA microarray experiments conducted on the OI slides showed over 8-fold signal amplification, conservation of gene expression ratios, and increased signal-to-noise ratio when compared to control slides, indicating enhanced detection sensitivity. Protein microarray assays also exhibited over 8-fold signal amplification at three different target concentrations, demonstrating the versatility of the OI slides for different microarray applications. Further, the DNA and protein assays performed on the OI slides exhibited excellent detection sensitivity even at the low target amounts essential for diagnostic applications. The OI slides are compatible with commonly used protocols, printers, scanners and other microarray equipment. Therefore, the OI slides offer an attractive alternative to traditional microarray substrates, where enhanced detection sensitivity is desired.     

Development of multiplex DNA electronic microarrays using a universal adaptor system for detection of single nucleotide polymorphisms

The NanoChip electronic microarray is designed for the rapid detection of genetic variation in research and clinical diagnosis. We have developed a multiplex electronic microarray assay, specific for single nucleotide polymorphism (SNP) genotyping and mutation detection, using universal adaptor sequences tailed to the 5' end of PCR primers specific to each target. PCR products, amplified by primers directed to the universal adaptor sequence, are immobilized on the microarray either directly or via capture oligonucleotides complementary to the universal adaptor sequence. This simple modification results in a significant increase in fidelity with improved specificity and accuracy. In addition, the multiplexing of genetic variant detection allows increased throughput and significantly reduced cost per assay. This general schema can also be applied to other microarray and macroarray formats.     

An improved algorithm for the detection of genomic variation using short oligonucleotide expression microarrays

High‐throughput microarray experiments often generate far more biological information than is required to test the experimental hypotheses. Many microarray analyses are considered finished after differential expression and additional analyses are typically not performed, leaving untapped biological information left undiscovered. This is especially true if the microarray experiment is from an ecological study of multiple populations. Comparisons across populations may also contain important genomic polymorphisms, and a subset of these polymorphisms may be identified with microarrays using techniques for the detection of single feature polymorphisms (SFP). SFPs are differences in microarray probe level intensities caused by genetic polymorphisms such as single‐nucleotide polymorphisms and small insertions/deletions and not expression differences. In this study, we provide a new algorithm for the detection of SFPs, evaluate the algorithm using existing data from two publicly available Affymetrix Barley (Hordeum vulgare) microarray data sets and compare them to two previously published SFP detection algorithms. Results show that our algorithm provides more consistent and sensitive calling of SFPs with a lower false discovery rate. Simultaneous analysis of SFPs and differential expression is a low‐cost method for the enhanced analysis of microarray data, enabling additional biological inferences to be made.     

Pegylated, steptavidin-conjugated quantum dots are effective detection elements for reverse-phase protein microarrays

Protein microarray technologies provide a means of investigating the proteomic content of clinical biopsy specimens in order to determine the relative activity of key nodes within cellular signaling pathways. A particular kind of protein microarray, the reverse-phase microarray, is being evaluated in clinical trials because of its potential to utilize limited amounts of cellular material obtained through biopsy. Using this approach, cellular lysates are arrayed in dilution curves on nitrocellulose substrates for subsequent probing with antibodies. To improve the sensitivity and utility of reverse-phase microarrays, we tested whether a new reporter technology as well as a new detection instrument could enhance microarray performance. We describe the use of an inorganic fluorescent nanoparticle conjugated to streptavidin, Qdot 655 Sav, in a reverse-phase protein microarray format for signal pathway profiling. Moreover, a pegylated form of this bioconjugate, Qdot 655 Sav, is found to have superior detection characteristics in assays performed on cellular protein extracts over the nonpegylated form of the bioconjugate. Hyperspectral imaging of the quantum dot microarray enabled unamplified detection of signaling proteins within defined cellular lysates, which indicates that this approach may be amenable to multiplexed, high-throughput reverse-phase protein microarrays in which numerous analytes are measured in parallel within a single spot.     

AFP蛋白芯片技术的检测流程优化

目的:通过优化现有的蛋白芯片检测过程,在保证检测准确性的同时缩短甲胎蛋白(Alpha Fetal protein,AFP)的检测时间,提高检测效率,为原发性肝癌的筛查提供经济、便捷、省时、有效的检测方法。方法:本研究在传统蛋白芯片检测流程(1-1.5小时)的基础上,通过优化检测流程将检测时间缩短至18分钟,并且通过和传统方法进行比较,评价该优化方法的检测效能。结果:与传统蛋白芯片检测方法相比,本优化方法的检测时间缩短至18分钟。重复检测同一样本,传统方法 AFP水平为16.50±1.172ng/m L,优化方法 AFP水平为18.33±1.029 ng/m L,结果无明显统计学差异(P=0.251)。结论:本研究成功地优化了AFP的蛋白芯片检测流程,在缩短检测时间的同时,保证了检测的准确率,是一种经济省时易操作的AFP检测方法。     

ampliPHOX Colorimetric Detection on a DNA Microarray for Influenza

DNA microarrays have emerged as a powerful tool for pathogen detection.^1-5 For instance, many examples of the ability to type and subtype influenza virus have been demonstrated.^6-11 The identification and subtyping of influenza on DNA microarrays has applications in both public health and the clinic for early detection, rapid intervention, and minimizing the impact of an influenza pandemic. Traditional fluorescence is currently the most commonly used microarray detection method. However, as microarray technology progresses towards clinical use,¹ replacing expensive instrumentation with low cost detection technology exhibiting similar performance characteristics to fluorescence will make microarray assays more attractive and cost-effective.The ampliPHOX colorimetric detection technology is intended for research applications, and has a limit of detection within one order of magnitude of traditional fluorescence¹¹, with a main advantage being an approximate ten-fold lower instrument cost compared to the confocal microarray scanners required for fluorescence microarray detection. Another advantage is the compact size of the instrument which allows for portability and flexibility, unlike traditional fluorescence instruments. Because the polymerization technology is not as inherently linear as fluorescence detection, however, it is best suited for lower density microarray applications in which a yes/no answer for the presence of a certain sequence is desired, such as for pathogen detection arrays. Currently the maximum spot density compatible with ampliPHOX detection is ˜1800 spots/array. Because of the spot density limitations, higher density microarrays are not suitable for ampliPHOX detection.Here, we present ampliPHOX colorimetric detection technology as a method of signal amplification on a low density microarray developed for the detection and characterization of influenza viruses (FluChip). Although this protocol uses the FluChip (a DNA microarray) as one specific application of ampliPHOX detection, any microarray incorporating biotinylated target can be labeled and detected in a similar manner. The microarray design and biotinylation of the target to be captured are the responsibility of the user. Once the biotinylated target has been captured on the array, ampliPHOX detection can be performed by first tagging the array with a streptavidin-label conjugate (ampliTAG). Upon light exposure using the ampliPHOX Reader instrument, polymerization of a monomer solution (ampliPHY) occurs only in regions containing ampliTAG-labeled targets. The polymer formed can be subsequently stained with a non-toxic solution to improve visual contrast, followed by imaging and analysis using a simple software package (ampliVIEW). The entire FluChip assay from un-extracted sample to result can be performed in about 6 hours, and the ampliPHOX detection steps described above can be completed in about 30 min. Download video file.^{(61M, mov)}     

Detection of bacterial pathogens in municipal wastewater using an oligonucleotide microarray and real-time quantitative PCR

As a first step toward building a comprehensive microarray, two low density DNA microarrays were constructed and evaluated for the accurate detection of wastewater pathogens. The first one involved the direct hybridization of wastewater microbial genomic DNA to the functional gene probes while the second involved PCR amplification of 23S ribosomal DNA. The genomic DNA microarray employed 10 functional genes as detection targets. Sensitivity of the microarray was determined to be approximately 1.0 microg of Esherichia coli genomic DNA, or 2 x 10(8) copies of the target gene, and only E. coli DNA was detected with the microarray assay using municipal raw sewage. Sensitivity of the microarray was enhanced approximately by 6 orders of magnitude when the target 23S rRNA gene sequences were PCR amplified with a novel universal primer set and allowed hybridization to 24 species-specific oligonucleotide probes. The minimum detection limit was estimated to be about 100 fg of E. coli genomic DNA or 1.4 x 10(2) copies of the 23S rRNA gene. The PCR amplified DNA microarray successfully detected multiple bacterial pathogens in wastewater. As a parallel study to verify efficiency of the DNA microarray, a real-time quantitative PCR assay was also developed based on the fluorescent TaqMan probes (Applied Biosystems).     

SNP与基因检测及表达中的RCA技术

滚环扩增(rollingcircleamplification,RCA)技术是一种新的分子生物学检测方法。该方法不仅可以在体外等温条件下对核酸进行高度特异性的检测,而且还可通过线性或指数扩增来进行信号级联放大,其灵敏度能达到1个拷贝的核酸分子,因此,可用于痕量分子的检测。目前,滚环扩增技术广泛应用于全基因组DNA检测、核酸测序、单核苷酸多态性、DNA芯片及蛋白质芯片分析等领域。     

Detection of representative enteropathogenic bacteria, Vibrio spp., pathogenic Escherichia coli, Salmonella spp., Shigella spp., and Yersinia enterocolitica, using a virulence factor gene-based oligonucleotide microarray

Rapid identification of enteropathogenic bacteria in stool samples is critical for clinical diagnosis and antimicrobial therapy. In this study, we describe the development of an approach that couples multiplex PCR with hybridization to a DNA microarray, to allow the simultaneous detection of the 10 pathogens. The microarray was synthesized with 20-mer oligonucleotide probes that were designed to be specific for virulence-factor genes of each strain. The detection limit for genomic DNA from a single strain was approximately 10 fg. In the presence of heterogeneous non-target DNA, the detection sensitivity of the array decreased to approximately 100 fg. We did not observe any non-specific hybridization. In addition, we successfully used this oligonucleotide-based DNA microarray to identify the causative agents in clinical stool samples from patients with food-borne enteritis.     

DNA芯片技术在食品病原体检测中的应用

病原体的存在,尤其是食品中的病原体,给人类健康带来了威胁。DNA芯片技术是一种非常有效的病原体检测工具,具有众多传统检测方法所不具备的优势,受到广泛关注。我们简要论述了DNA芯片在细菌病原体、寄生虫、病毒病原体、微生物耐药性等的检测中的应用,并进一步综述了DNA芯片技术在食品检测中存在的问题、解决方法及发展方向。     

Multipathogen oligonucleotide microarray for environmental and biodefense applications

Food-borne pathogens are a major health problem. The large and diverse number of microbial pathogens and their virulence factors has fueled interest in technologies capable of detecting multiple pathogens and multiple virulence factors simultaneously. Some of these pathogens and their toxins have potential use as bioweapons. DNA microarray technology allows the simultaneous analysis of thousands of sequences of DNA in a relatively short time, making it appropriate for biodefense and for public health uses. This paper describes methods for using DNA microarrays to detect and analyze microbial pathogens. The FDA-1 microarray was developed for the simultaneous detection of several food-borne pathogens and their virulence factors including Listeria spp., Campylobacter spp., Staphylococcus aureus enterotoxin genes and Clostridium perfringens toxin genes. Three elements were incorporated to increase confidence in the microarray detection system: redundancy of genes, redundancy of oligonucleotide probes (oligoprobes) for a specific gene, and quality control oligoprobes to monitor array spotting and target DNA hybridization. These elements enhance the reliability of detection and reduce the chance of erroneous results due to the genetic variability of microbes or technical problems with the microarray. The results presented demonstrate the potential of oligonucleotide microarrays for detection of environmental and biodefense relevant microbial pathogens.     

生物素-亲和素偶联探针蛋白芯片检测技术

自行制备一种新型生物素-亲和素偶联探针分子并用于反相蛋白芯片的检测。首先, 将生物素-羊抗鼠IgG与亲和素按照不同比例混合后与鼠IgG蛋白芯片反应, 观察荧光信号的放大情况; 然后以鼠IgG-羊抗鼠IgG体系为研究模式, 对反相蛋白芯片的制备条件进行了考察和优化, 包括荧光分子的非特异性吸附、点样缓冲液的选择以及蛋白的活性等。最后, 采用此偶联探针对反相蛋白芯片进行了检测。结果表明, BSA缓冲液制备的反相蛋白芯片可以防止非特异性吸附, 并有利于保持固定蛋白活性和提高检测限; 另外, 与传统的与生物素-亲和素检测技术相比, 采用生物素-亲和素偶联探针对反相芯片的检测限可以提高4倍左右。表明亲和素-生物素偶联探针成本低、易于合成、并可以与其它的信号放大技术联用进一步提高检测的灵敏度, 有望用于蛋白质芯片的检测。     

基因芯片技术检测3种食源性致病微生物方法的建立

建立一种运用多重PCR和基因芯片技术检测和鉴定志贺氏菌、沙门氏菌、大肠杆菌O157的方法, 为3种食源性致病菌的快速检测和鉴定提供了准确、快速、灵敏的方法。分别选取编码志贺氏菌侵袭性质粒抗原H基因(ipaH)、沙门氏菌肠毒素(stn)基因和致泻性大肠杆菌O157志贺样毒素(slt)基因设计引物和探针, 进行三重PCR扩增, 产物与含特异性探针的芯片杂交。对7种细菌共26株菌进行芯片检测, 仅3种菌得到阳性扩增结果, 证明此方法具有很高的特异性。3种致病菌基因组DNA和细菌纯培养物的检测灵敏度约为8 pg。对模拟食品样品进行直接检测, 结果与常规细菌学培养结果一致, 检测限为50 CFU/mL。结果表明：所建立的基因芯片检测方法特异性好, 灵敏度高, 为食源性致病菌的检测提供了理想手段, 有良好的应用前景。     

Development of a biosensor microarray towards food screening, using imaging surface plasmon resonance

In this study we examined the possibilities of implementing direct and competitive immunoassay formats for small and large molecule detection on a microarray, using IBIS imaging surface plasmon resonance (iSPR) system. First, IBIS iSPR optics performance was evaluated. Using a glycerol calibration curve on underivatized surface we observed high baseline variability, but uniform and robust sensitivity between hundred regions of interest. Further on, a direct immunoassay for bovine IgG detection and a competitive immunoassay for gentamicin and neomycin were developed. The direct immunoassay for bovine IgG detection in a microarray format showed poor sensitivity in comparison to the assay performed in Biacore 3000, due to low immobilization efficiency on spots. The competitive immunoassay for parallel gentamicin and neomycin detection in a microarray format displayed sensitivity in the ngmL(-1) range, comparable with the sensitivity achieved in Biacore 3000 and in the range of maximum residue limits in milk, established in the European Union. We expect that, utilization of the IBIS iSPR system for food analysis, by screening high and low molecular weight compounds, will allow rapid and simultaneous detection of various ingredients and contaminants, providing the end-user with a detailed food profile. However, assay transfer from conventional SPR biosensors to the imaging microarray platform also presents new challenges, such as sufficient immobilization on spots, that must be addressed in future studies.     

生物素-亲和素偶联探针蛋白芯片检测技术

自行制备一种新型生物素-亲和素偶联探针分子并用于反相蛋白芯片的检测。首先, 将生物素-羊抗鼠IgG与亲和素按照不同比例混合后与鼠IgG蛋白芯片反应, 观察荧光信号的放大情况; 然后以鼠IgG-羊抗鼠IgG体系为研究模式, 对反相蛋白芯片的制备条件进行了考察和优化, 包括荧光分子的非特异性吸附、点样缓冲液的选择以及蛋白的活性等。最后, 采用此偶联探针对反相蛋白芯片进行了检测。结果表明, BSA缓冲液制备的反相蛋白芯片可以防止非特异性吸附, 并有利于保持固定蛋白活性和提高检测限; 另外, 与传统的与生物素-亲和素检测技术相比, 采用生物素-亲和素偶联探针对反相芯片的检测限可以提高4倍左右。表明亲和素-生物素偶联探针成本低、易于合成、并可以与其它的信号放大技术联用进一步提高检测的灵敏度, 有望用于蛋白质芯片的检测。     

An oligonucleotide microarray for microRNA expression analysis based on labeling RNA with quantum dot and nanogold probe

MicroRNAs (miRNAs) play important regulatory roles in animals and plants by targeting mRNAs for cleavage or translational repression. They have diverse expression patterns and might regulate various developmental and physiological processes. Profiling miRNA expression is very helpful for studying biological functions of miRNAs. We report a novel miRNA profiling microarray, in which miRNAs were directly labeled at the 3′ terminus with biotin and hybridized with complementary oligo-DNA probes immobilized on glass slides, and subsequently detected by measuring fluorescence of quantum dots labeled with streptavidin bound to miRNAs through streptavidin–biotin interaction. The detection limit of this microarray for miRNA was ~0.4 fmol, and the detection dynamic range spanned about 2 orders of magnitude. We made a model microarray to profile 11 miRNAs from leaf and root of rice (Oryza sativa L. ssp. indica) seedlings. The analysis results of the miRNAs had a good reproducibility and were consistent with the northern blot result. To avoid using high-cost detection equipment, colorimetric detection, a method based on nanogold probe coupled with silver enhancement, was also successfully introduced into miRNA profiling microarray detection.     

A simple, rapid, and sensitive integrated protein microarray for simultaneous detection of multiple antigens and antibodies of five human hepatitis viruses (HBV, HCV, HDV, HEV, and HGV)

Protein microarrays for parallel detection of multiple viral antigens and antibodies have not yet been described in the field of human hepatitis virus infections. Here, we describe a simple, rapid and sensitive integrated protein microarray with three different reaction models. The integrated protein microarray could simultaneously determine in human sera two viral antigens (HBsAg, HBeAg) and seven viral antibodies (HBsAb, HBcAb, HBeAb, HCVAb, HDVAb, HEVAb, HGVAb) of human hepatitis viruses within 20 min. The results of the protein microarray were assessed directly by the naked eye but can also be analyzed by a quantitative detector. The detection limit of this protein microarray was 0.1 ng/ml for HBsAg. Overall, >85% concordance was observed between the integrated protein microarrays and an enzyme-linked immunosorbent assay for above hepatitis viral antigen and antibody detections in human sera. This integrated protein microarray can be easily optimized for clinical use and epidemiological screening for multiple hepatitis virus infections.