Quantitative Detection System Research Articles

Monitoring the Dissemination of the Broad-Host-Range Plasmid pB10 in Sediment Microcosms by Quantitative PCR

Studying the transfer of specific mobile genetic elements in complex environmental matrices remains difficult because suitable molecular tools are not yet available to back up classical culture-dependent approaches. In this report, we show that quantitative PCR could be used to monitor the dissemination of the broad-host-range plasmid pB10 in sediment microcosms. This approach lies in the differential measurement of the host and plasmid DNAs used to inoculate the microcosms, using a particular design of quantitative PCR primers/probes where we took advantage of the mosaic aspect of the bacterial genomes to achieve a highly specific quantitative PCR detection system.

Development of a quantitative detection system for cereulide, the emetic Bacillus cereus toxin

Development of a quantitative detection system for cereulide, the emetic Bacillus cereus toxin

Open Sandwich-Based Immuno-Transistor for Label-Free and Noncompetitive Detection of Low Molecular Weight Antigen

In this study, we proposed a new detection method, open sandwich-based immuno-field effect transistor (OS-FET) for label-free and noncompetitive detection of low molecular weight antigen. The principle of OS-FET is based on the detection of intrinsic molecular charges caused by the small antigen-dependent interchain interaction of separated V(L) and V(H) chains from a single antibody variable region using the field effect. Introducing V(H) chain and small antigen bisphenol A into the OS-FET with the immobilized V(L) chain on the gate, we could detect electrically and directly the binding of bisphenol A by V(H) and V(L) chains. Although the detection limit of OS-FET was 1 nM to detect bisphenol A for the standard deviation of control signal, the addition of isothiocyanobenzyl-EDTA with negative charges to the V(L) chain enhanced the detection limit to 1 pM. We could directly transduce the charge density changes based on the capture of target on the gate into the electrical signals using the OS-FET. The platform based on the FETs is suitable for a label-free, noncompetitive, and quantitative detection system for small antigen analysis in environmental, food, and clinical research.

A new single‐step quantitative pathogen detection system: Template‐tagging followed by multiplex asymmetric PCR using common primers and CE‐SSCP

Rapid diagnosis of bacterial infection is important for patient management and appropriate therapy during the early phase of bacteria-induced disease. Among the existing techniques for identifying microbial, CE-SSCP combined with 16S ribosomal RNA gene-specific PCR has the benefits of excellent sensitivity, resolution, and reproducibility. However, even though CE-SSCP can separate PCR products with high-resolution, multiplex detection and quantification are complicated by primer-dimer formation and non-specific amplification. Here, we describe a novel technique for multiplex detection and quantification of pathogens by template-tagging followed by multiplex asymmetric PCR and subsequent CE-SSCP. More specifically, we reverse transcribed 16S ribosomal RNAs from seven septicemia-inducing pathogens, tagged the templates with common end sequences, and amplified them using common primers. The resulting amplicons could be successfully separated by CE-SSCP and quantified by comparison to an internal standard. This method yielded results that illustrate the potential of this system for diagnosing infectious disease.

Real-time monitoring of odorant-induced cellular reactions using surface plasmon resonance

Surface plasmon resonance (SPR) is a powerful technique for measuring molecular interaction in real-time. SPR can be used to detect molecule to cell interactions as well as molecule to molecule interactions. In this study, the SPR-based biosensing technique was applied to real-time monitoring of odorant-induced cellular reactions. An olfactory receptor, OR I7, was fused with a rho-tag import sequence at the N-terminus of OR I7, and expressed on the surface of human embryonic kidney (HEK)-293 cells. These cells were then immobilized on a SPR sensor chip. The intensity of the SPR response was linearly dependent on the amount of injected odorant. Among all the aldehyde containing odorants tested, the SPR response was specifically high for octanal, which is the known cognate odorant for the OR I7. This SPR response is believed to have resulted from intracellular signaling triggered by the binding of odorant molecules to the olfactory receptors expressed on the cell surface. This SPR system combined with olfactory receptor-expressed cells provides a new olfactory biosensor system for selective and quantitative detection of volatile compounds.

A web-based quantitative signal detection system on adverse drug reaction in China

To establish a web-based quantitative signal detection system for adverse drug reactions (ADRs) based on spontaneous reporting to the Guangdong province drug-monitoring database in China. Using Microsoft Visual Basic and Active Server Pages programming languages and SQL Server 2000, a web-based system with three software modules was programmed to perform data preparation and association detection, and to generate reports. Information component (IC), the internationally recognized measure of disproportionality for quantitative signal detection, was integrated into the system, and its capacity for signal detection was tested with ADR reports collected from 1 January 2002 to 30 June 2007 in Guangdong. A total of 2,496 associations including known signals were mined from the test database. Signals (e.g., cefradine-induced hematuria) were found early by using the IC analysis. In addition, 291 drug-ADR associations were alerted for the first time in the second quarter of 2007. The system can be used for the detection of significant associations from the Guangdong drug-monitoring database and could be an extremely useful adjunct to the expert assessment of very large numbers of spontaneously reported ADRs for the first time in China.

Lentiviral vector-based assay system for quantitative detection of intracellular translocations of recombinant proteins

An enzymatic assay system is described that allows quantitative localization within different cellular structures of recombinant proteins. The system is based on alpha-complementation of beta-galactosidase. The large omega-fragment of beta-galactosidase is expressed in predefined cellular structures with the aid of attached protein localization signals. The obtained reporter cell lines are used for the introduction of a second construct that expresses a protein of study fused with a shorter alpha-fragment of beta-galactosidase. Physical proximity of the two recombinant proteins carrying beta-galactosidase fragments results in reconstitution of an active enzyme, and the activity can be measured in a plate reader. The recombinant constructs are based on lentiviral vectors, which allows rapid and efficient introduction of recombinant proteins into cells by infection with stocks of lentiviral particles. The efficiency of the system is demonstrated with transcriptional factor FOXO3A, which is shuttling between cytoplasm and nuclei in model colon carcinoma cell line RKO.

Quantitative assessment of minimal residual disease (MRD) in canine lymphoma by using real-time polymerase chain reaction

Lymphoma is the most common hematopoietic malignancy in dogs. Although a large proportion of dogs with lymphoma can achieve clinical remission by initial chemotherapy, most dogs die as a consequence of tumor relapse. We established a quantitative detection system for minimal residual disease (MRD) in canine lymphoma by using real-time polymerase chain reaction (PCR). A canine T-cell lymphoma-derived cell line, namely, UL-1, was used to examine the specificity and sensitivity of the MRD detecting system. Allele-specific oligonucleotide primers and probes were designed based on the sequence of T-cell receptor γ chain (TCRγ) gene fragment of UL-1 cells in conjunction with its downstream sequence, which were obtained from the dog genome database. The real-time PCR system for plasmid DNA containing the TCRγ gene derived from UL-1 cells and the genomic DNA of UL-1 cells revealed that the system was accurate for 10–100,000 copies per reaction and its sensitivity was 1 cell per 10,000 cells. In order to monitor the kinetics of tumor cell number in canine lymphoma, we quantified the level of MRD in the peripheral blood of 7 dogs with lymphoma under chemotherapy. Since the lymphoma cells from the 7 patients were shown to be B-cell origin from the finding of clonal rearrangement of immunoglobulin heavy chain (IgH) gene, allele-specific oligonucleotide primers and probes were prepared based on the sequence of rearranged IgH gene in each case. The number of peripheral blood tumor cells measured by the real-time PCR was comparable to that estimated by conventional hematological examination in 2 cases of stage V lymphoma. MRD in the peripheral blood was detectable in all 7 cases, even in the complete remission (CR) phase. In the 7 lymphoma dogs, changes in the MRD levels of peripheral blood generally paralleled with the changes in the volumes of lymph nodes. Molecular CR, in which the MRD level was below the detection limit, was not observed in any of these 7 patients under chemotherapy. The MRD level detected by the real-time PCR method described here would be useful for investigating the kinetics of tumor cell growth and its regression in canine lymphoma patients.

A two-step quantitative pathogen detection system based on capillary electrophoresis

Rapid identification of bacterial pathogens is important for patient management and initiation of appropriate antibiotic therapy in the early stages of infection. Among the several techniques, capillary electrophoresis single-strand conformation polymorphism (CE-SSCP) analysis combined with small subunit rRNA gene-specific polymerase chain reaction (PCR) has come into the spotlight owing to its sensitivity, resolution, and reproducibility. Despite the advantages of the method, the design of PCR primers and optimization of multiplex PCR conditions remain to be studied so that as many pathogens as possible can be analyzed in a single run. Here we describe a novel two-step technique involving multiplex PCR pathogen detection by CE-SSCP analysis followed by singleplex PCR pathogen quantification by CE-SSCP. Specific PCR primers were designed for optimal separation of their products by CE-SSCP based on molecular weight. PCR conditions were then optimized for multiplex analysis of the targets. Subsequently, detected pathogens were quantified by PCR with specific primers. Eight clinically important strains were simultaneously identified under the optimized conditions. Each individual pathogen was then quantified at a level of sensitivity of tens of cells per milliliter. In conclusion, the two-step pathogen detection method based on CE-SSCP described here allows for sensitive detection of pathogens by multiplex PCR (first step) and quantification by specific PCR (second step). The results illustrate the potential of the method in clinical applications.

Quantitative real-time PCR assay to detect transgene copy number in cotton (Gossypium hirsutum)

A TaqMan quantitative real-time PCR detection system was developed to examine transgene copy number in cotton. GhUBC1, a gene validated to be present as a single copy per haploid Gossypium hirsutum genome, was used as the endogenous reference to estimate copy number of GFP and selection marker NPTII in 28 T0 plants. This system was found to be more accurate than genomic Southern blot hybridization and could effectively tell homozygotes from heterozygotes in a T1 transgenic cotton population. Therefore it is suitable for efficient and cost effective early screening of transgenic seedlings and identifying transgene homozygotes in segregation populations.

Green and Orange CdTe Quantum Dots as Effective pH-Sensitive Fluorescent Probes for Dual Simultaneous and Independent Detection of Viruses

One of the most highlighted and fastest moving interfaces of nanotechnology is the application of quantum dots (QDs) in biology. The unparalleled advantages of the size-tunable fluorescent emission and the simultaneous excitation at a single wavelength make QDs the great possibility for use in optical encoding detection. In this paper, we report that green and orange CdTe QDs as convenient, cheap, reversible, and effective pH-sensitive fluorescent probes could monitor the proton (H+) flux driven by ATP synthesis for dual simultaneous and independent detection of viruses on the basis of antibody-antigen reactions. A new kind of biosensor (consisting of the mixture of green-QDs-labeled chromatophores and orange-QDs-labeled chromatophores) fluorescent measurement system was established for rapid, simultaneous, and independent detection of two different kinds of viruses (i.e., H9 avian influenza virus and MHV68 virus). It is crucial to find that the green and orange QDs labeled biosensors coexisting in the detection system can work independently and do not interfere with each another in the fluorescence assays. In addition, a primary steady electric double layer (EDL) model for the QDs biosensors was proposed to illustrate the mechanism of simultaneous and independent detection of the biosensors. We believe that the pH-sensitive CdTe QDs based detection system, described in this paper, is an important step toward optical encoding and has a great potential for simultaneous and independent qualitative and quantitative multiple detection systems.

Novel Real-Time Monitoring System for Human Cytomegalovirus- Infected Cells In Vitro That Uses a Green Fluorescent Protein-PML-Expressing Cell Line

Promyelocytic leukemia (PML) bodies are discrete nuclear foci that are intimately associated with many DNA viruses. In human cytomegalovirus (HCMV) infection, the IE1 (for "immediate-early 1") protein has a marked effect on PML bodies via de-SUMOylation of PML protein. Here, we report a novel real-time monitoring system for HCMV-infected cells using a newly established cell line (SE/15) that stably expresses green fluorescent protein (GFP)-PML protein. In SE/15 cells, HCMV infection causes specific and efficient dispersion of GFP-PML bodies in an IE1-dependent manner, allowing the infected cells to be monitored by fluorescence microscopy without immunostaining. Since a specific change in the detergent solubility of GFP-PML occurs upon infection, the infected cells can be quantified by GFP fluorescence measurement after extraction. With this assay, the inhibitory effects of heparin and neutralizing antibodies were determined in small-scale cultures, indicating its usefulness for screening inhibitory reagents for laboratory virus strains. Furthermore, we established a sensitive imaging assay by counting the number of nuclei containing dispersed GFP-PML, which is applicable for titration of slow-growing clinical isolates. In all strains tested, the virus titers estimated by the GFP-PML imaging assay were well correlated with the plaque-forming cell numbers determined in human embryonic lung cells. Coculture of SE/15 cells and HCMV-infected fibroblasts permitted a rapid and reliable method for estimating the 50% inhibitory concentration values of drugs for clinical isolates in susceptibility testing. Taken together, these results demonstrate the development of a rapid, sensitive, quantitative, and specific detection system for HCMV-infected cells involving a simple procedure that can be used for titration of low-titer clinical isolates.

Event-specific qualitative and quantitative PCR detection of MON863 maize based upon the 3′-transgene integration sequence

An event-specific detection method was developed based on the flanking sequence of an exogenous integrant in the transgenic maize MON863 which contains cry3Bb1 gene expressing a Bacillus thuringiensis Cry3Bb1 protein that is selectively toxic to a maize root worm pathogen. The 3′-integration junction between host plant DNA and integrated DNA of transgenic MON863 maize was isolated using thermal asymmetric interlaced (TAIL)-PCR. The event-specific primers and TaqMan probe were designed based upon the isolated 3′-integration junction sequence, and qualitative and quantitative PCR systems were established employing these designed primers and probe. In this system, the limit of detection of the qualitative PCR assay was estimated to be 40 initial haploid copies. The limit of quantitation of the quantitative PCR assay in authentic MON863 maize seeds was estimated to be approximately 80 haploid copies. GM MON863 contents were also quantified relative to endogenous maize starch synthase IIb ( zSSIIb) gene DNA, and the results were expressed as the percentage of genetically modified MON863 maize DNA relative to the total content of maize DNA. All the results indicated that the established MON863 event-specific qualitative and quantitative PCR detection system based on the 3′-integration junction was reliable, sensitive and accurate.

A Rapid and Quantitative Detection System for Streptococcus mutans in Saliva Using Monoclonal Antibodies

A new semiquantitative enumeration system was developed to detect Streptococcus mutans in saliva. Using species-specific monoclonal antibodies, the system quickly detected salivary S. mutans in 30 min and classified the results into three levels. In this study, saliva samples collected from 28 young adults aged between 22 and 24 years were subjected to the monoclonal antibody-based detecting system and selective medium-based detecting methods. The results generated from the PCR-confirmed culture method indicated the mean salivary S. mutans counts at level 1, 2 and 3 were 5.7 × 10⁴, 1.3 × 10⁵ and 3.4 × 10⁶ CFU/ml, respectively. The differences between level 3 and 1 and level 3 and 2 were statistically significant (one-way ANOVA; p < 0.01). The results generated from the system were consistent with the data generated from two culture-based commercial products.

Quantitative Detection System for Maize Sample Containing Combined-Trait Genetically Modified Maize

Various countries have established regulations that stipulate the labeling of agricultural commodities, feed, and food products that contain or are made from genetically modified (GM) material or that contain adventitious GM material in amounts that exceed certain threshold levels. While regulations in some countries refer to GM material on a weight per weight (w/w) percentage, the currently applied detection methods do not directly measure the w/w percentage of the GM material. Depending on the particular method and the sample matrix it is applied to, the conversion of analytical results to a w/w percentage is challenging or not possible. The first rapid PCR system for GM maize detection on a single kernel basis has been developed. The equipment for the grinding of individual kernels and a silica membrane-based 96-well DNA extraction kit were both significantly revised and optimized for this particular purpose, respectively. We developed a multiplex real-time PCR method for the rapid quantification of GM DNA sequences in the obtained DNA solutions. In addition, a multiplex qualitative PCR detection method allows for the simultaneous detection of different GM maize traits in each kernel and thereby for identification of individual kernels that contain a combination of two or more GM traits. Especially for grain samples that potentially contain combined-trait GM maize kernels, the proposed methods can deliver informative results in a rapid, precise, and reliable manner.

Recent Advances in GFP Folding Reporter and Split-GFP Solubility Reporter Technologies. Application to Improving the Folding and Solubility of Recalcitrant Proteins from Mycobacterium tuberculosis

We have improved our green fluorescent protein (GFP) folding reporter technology [Waldo et al., (1999) Nat. Biotechnol. 17, 691-695] to evolve recalcitrant proteins from Mycobacterium tuberculosis. The target protein is inserted into the scaffolding of the GFP, eliminating false-positive artifacts caused by expression of truncated protein variants from internal cryptic ribosome binding sites in the target RNA. In parallel, we have developed a new quantitative fluorescent protein tagging and detection system based on micro-domains of GFP. This split-GFP system, which works both in vivo and in vitro, is amenable to high-throughput assays of protein expression and solubility [Cabantous et al., (2005) Nat. Biotechnol. 23, 102-107]. Together, the GFP folding reporter and split-GFP technologies offer a comprehensive system for manipulating and improving protein folding and solubility.

Quantitative detection of Escherichia coli from urine of patients with bacteriuria by real-time PCR

Compared with the classical urine culture method, PCR is more rapid, and can detect smaller numbers of bacteria, however it is inferior for quantification. Because of the lack of quantification in routine PCR, the meaning of a positive PCR test result has not been validated for all infections. We report on the development of a novel quantitative detection system for the urinary tract infection (UTI) Escherichia coli using real-time PCR. We enrolled 200 patients with suspected bacteriuria. The gene encoding the universal stress protein (uspA) was found to be highly specific for E. coli. We quantified the copy numbers of E. coli in the urine of patients with UTI by using a real-time PCR assay (the TaqMan system) targeting uspA genes in genomic DNAs isolated from urine samples (n=200). To evaluate the feasibility of this method, the results were compared with those of a standard urine culture. The incidence of positive urine cultures was 75% (150 of 200), and various doses of E. coli were detected in 84 of 150 specimens. The real-time PCR method also detected 84 cases of urinary infections of E. coli in the same specimens. Furthermore, the result of the quantification of E. coli using real-time PCR strongly correlated (r2=0.925) with the result of urine culture. Our results suggest that using quantitative-PCR means a faster and simpler diagnosis of E. coli urinary infection can be made compared with the traditional urine culture method.

Real-time PCR designs to estimate nuclear and mitochondrial DNA copy number in forensic and ancient DNA studies

We explore different designs to estimate both nuclear and mitochondrial human DNA (mtDNA) content based on the detection of the 5′ nuclease activity of the Taq DNA polymerase using fluorogenic probes and a real-time quantitative PCR detection system. Human mtDNA quantification was accomplished by monitoring the real-time progress of the PCR-amplification of two different fragment sizes (113 and 287 bp) within the hypervariable region I (HV1) of the mtDNA control region, using two fluorogenic probes to specifically determine the mtDNA copy of each fragment size category. This mtDNA real-time PCR design has been used to assess the mtDNA preservation (copy number and degradation state) of DNA samples retrieved from 500 to 1500 years old human remains that showed low copy number and highly degraded mtDNA. The quantification of nuclear DNA was achieved by real-time PCR of a segment of the X–Y homologous amelogenin ( AMG) gene that allowed the simultaneous estimation of a Y-specific fragment (AMGY: 112 bp) and a X-specific fragment (AMGX: 106 bp) making possible not only haploid or diploid DNA quantitation but also sex determination. The AMG real-time PCR design has been used to quantify a set of 57 DNA samples from 4–5 years old forensic bone remains with improved sensitivity compared with the slot–blot hybridization method. The potential utility of this technology to improve the quality of some PCR-based forensic and ancient DNA studies (microsatellite typing and mtDNA sequencing) is discussed.

A specific real-time quantitative PCR detection system for event MON810 in maize YieldGard based on the 3'-transgene integration sequence.

The increasing presence of transgenic plant derivatives in a wide range of animal and human consumables has provoked in western Europe a strong demand for appropriate detection methods to evaluate the existence of transgenic elements. Among the different techniques currently used, the real-time quantitative PCR is a powerful technology well adapted to the mandatory labeling requirements in the European Union (EU). The use of transgene flanking genomic sequences has recently been suggested as a means to avoid ambiguous results both in qualitative and quantitative PCR-based technologies. In this study we report the identification of genomic sequences adjacent to the 3'-integration site of event MON810 in transgenic maize. This genetically modified crop contains transgene sequences leading to ectopic expression of a synthetic CryIA(b) endotoxin which confers resistance to lepidopteran insects especially against the European corn borer. The characterization of the genome-transgene junction sequences by means of TAIL-PCR has facilitated the design of a specific, sensitive and accurate quantification method based on TaqMan chemistry. Cloning of event MON810 3'-junction region has also allowed to compare the suitability of plasmid target sequences versus genomic DNA obtained from certified reference materials (CRMs), to prepare standard calibration curves for quantification.

下水中エストロゲン様物質検出のための酵母ｔｗｏ−ｈｙｂｒｉｄ法の最適化

The objective of this study was to optimize the yeast two-hybrid system for quantitative detection of the estrogenic activity of organics in sewage water. Most of the estrogenic activity of sewage water concentrates prepared by Amberlite XAD-2 resin column concentration method was due to that of 17β-estradiol (E2). As well as E2, sewage water concentrates showed higher estrogenic activity with the rise of assay pH than with the conventional pH (pH 4). When assay was performed at pH 7.6. the estrogenic activity of sewage water concentrates increased approximately 25 times as high as that in the case of the conventional pH. This increase was thought to be caused by the following reason: organic constituents of sewage water concentrates disturbed the detection of the activity of E2 at the conventional pH. but humic acid as an organic constituent did not interfere with the detection of the activity of E2 at pH 7.6. The estrogenic activity of sewage water concentrate assayed at pH 7.6 was almost the same as activity corresponding to E2 concentration that was measured by the ELISA method. This pH-optimized yeast two-hybrid system is useful for comprehensive evaluation of estrogenic substances in sewage water and environmental water.