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PubMed2006

Molecular beacons for DNA binding proteins: an emerging technology for detection of DNA binding proteins and their ligands.

Quantitation of the level or activity of specific proteins is one of the most commonly performed experiments in biomedical research. Protein detection has historically been difficult to adapt to high throughput platforms because of heavy reliance upon antibodies for protein detection. Molecular beacons for DNA binding proteins is a recently developed technology that attempts to overcome such limitations. Protein detection is accomplished using inexpensive, easy-to-synthesize oligonucleotides, accompanied by a fluorescence readout. Importantly, detection of the protein and reporting of the signal occur simultaneously, allowing for one-step protocols and increased potential for use in high throughput analysis. While the initial iteration of the technology allowed only for the detection of sequence-specific DNA binding proteins, more recent adaptations allow for the possibility of development of beacons for any protein, independent of native DNA binding activity. Here, we discuss the development of the technology, the mechanism of the reaction, and recent improvements and modifications made to improve the assay in terms of sensitivity, potential for multiplexing, and broad applicability.

Biotechnology↗

PubMed2004

A tagging-via-substrate technology for detection and proteomics of farnesylated proteins.

A recently developed proteomics strategy, designated tagging-via-substrate (TAS) approach, is described for the detection and proteomic analysis of farnesylated proteins. TAS technology involves metabolic incorporation of a synthetic azido-farnesyl analog and chemoselective derivatization of azido-farnesyl-modified proteins by an elegant version of Staudinger reaction, pioneered by the Bertozzi group, using a biotinylated phosphine capture reagent. The resulting protein conjugates can be specifically detected and/or affinity-purified by streptavidin-linked horseradish peroxidase or agarose beads, respectively. Thus, the technology enables global profiling of farnesylated proteins by enriching farnesylated proteins and reducing the complexity of farnesylation subproteome. Azido-farnesylated proteins maintain the properties of protein farnesylation, including promoting membrane association, Ras-dependent mitogen-activated protein kinase kinase activation, and inhibition of lovastatin-induced apoptosis. A proteomic analysis of farnesylated proteins by TAS technology revealed 18 farnesylated proteins, including those with potentially novel farnesylation motifs, suggesting that future use of this method is likely to yield novel insight into protein farnesylation. TAS technology can be extended to other posttranslational modifications, such as geranylgeranylation and myristoylation, thus providing powerful tools for detection, quantification, and proteomic analysis of posttranslationally modified proteins.

Animals↗

PubMed2006

Assay concordance between SPA and TR-FRET in high-throughput screening.

High-throughput screening (HTS) of large chemical libraries has become the main source of new lead compounds for drug development. Several specialized detection technologies have been developed to facilitate the cost- and time-efficient screening of millions of compounds. However, concerns have been raised, claiming that different HTS technologies may produce different hits, thus limiting trust in the reliability of HTS data. This study was aimed to investigate the reliability of the authors most frequently used assay techniques: scintillation proximity assay (SPA) and homogeneous time-resolved fluorescence resonance energy transfer (TR-FRET). To investigate the data concordance between these 2 detection technologies, the authors screened a large subset of the Schering compound library consisting of 300,000 compounds for inhibitors of a nonreceptor tyrosine kinase. They chose to set up this study in realistic HTS scale to ensure statistical significance of the results. The findings clearly demonstrate that the choice of detection technology has no significant impact on hit finding, provided that assays are biochemically equivalent. Data concordance is up to 90%. The little differences in hit findings are caused by threshold setting but not by systematic differences between the technologies. The most significant difference between the compared techniques is that in the SPA format, more false-positive primary hits were obtained.

Biological Assay↗

PubMed2001

[The ability of frequency doubling technology to detect abnormality of visual function in early glaucoma].

PURPOSE: To evaluate the ability of the Frequency Doubling Technology(FDT) threshold test in detecting abnormality of visual function in early glaucoma patients. SUBJECTS AND METHOD: The C-20 full threshold test of FDT was performed on 34 normal-tension glaucoma(NTG) patients and 39 primary open-angle glaucoma(POAG) patients with visual field defects limited to the upper or lower hemi-field as detected by Humphrey Field Analyzer(HFA) and on 79 normal control subjects. Optic disk findings and FDT results corresponding to the intact hemi-field were evaluated. FDT abnormalities in normal subjects were calculated as false positive rates in FDT. RESULT: The sensitivity and specificity of FDT, calculated based on optic disk findings, were 75.0% and 61.1% in POAG, and 61.1% and 66.7% in NTG, respectively, while the false positive rate in normal subjects was 11.4%. CONCLUSION: FDT can detect glaucomatous functional abnormality earlier than HFA.

Adult↗

PubMed2000

Comparison of two amplification technologies for detection and quantitation of human immunodeficiency virus type 1 RNA in the female genital tract. Division of AIDS Treatment Research Initiative 009 Study Team.

Human immunodeficiency virus type 1 (HIV-1) RNA levels in female genital tract and peripheral blood samples were compared using two commercial amplification technologies: the Roche AMPLICOR HIV-1 MONITOR test and either the Organon Teknika nucleic acid sequence-based amplification (NASBA-QT) assay or the NucliSens assay. Estimates of HIV-1 RNA copy number were derived from internal kit standards and analyzed unadjusted and adjusted to a common set of external standards. We found a discordance rate of approximately 18% between the two technologies for the detection of HIV-1 in either the genital tract or peripheral blood samples. Detection discordance was not consistent among specimens or among women. There were no significant differences in adjusted or unadjusted estimates of HIV-1 RNA copy number in the genital tract samples using the AMPLICOR HIV-1 MONITOR test and either the NASBA-QT assay or the NucliSens assay. In addition, the estimated HIV-1 RNA copy number in peripheral blood samples did not differ when tested with the NucliSens assay and the AMPLICOR HIV-1 MONITOR test using kit standards. However, there was a significant difference in estimated RNA copy number between the NASBA-QT assay and the AMPLICOR HIV-1 MONITOR test for internal kit standards, which, as we have previously shown, was eliminated after adjustment with the external standards. Our results suggest that the Roche and Organon Teknika assays are equivalent for quantifying HIV-1 RNA in female genital tract specimens, although variation in detection does exist.

Cross-Sectional Studies↗

PubMed2006

The use of DNA microarray technology for detection and genetic characterisation of chlamydiae.

Due to its highly parallel approach, DNA microarray technology opens up new possibilities that may be particularly beneficial for laboratory diagnosis of infectious diseases. We developed a microarray assay for detection and differentiation of all currently defined chlamydial species belonging to the genera Chlamydia and Chlamydophila using the ArrayTube system, which we found to be particularly user-friendly and economical. The test includes PCR amplification of a 23S rDNA target region with concurrent biotinylation and subsequent hybridisation in the ArrayTube, a micro-reaction tube carrying the microarray chip on the bottom. In addition to high specificity, the assay was shown to allow detection and genetic characterisation of single PCR-amplifiable target DNA copies.

Chlamydia↗

PubMed1993

Analysis of micronucleated cells by flow cytometry. 3. Advanced technology for detecting clastogenic activity.

Under optimum conditions, flow cytometry (FCM) can provide a powerful technology for analyzing rare micronucleated cells in the peripheral blood. Our efforts in this endeavor have been directed toward a careful and meticulous optimization of experimental conditions, in order to achieve high resolution and high accuracy before introducing biological variation. We have achieved high resolution (Tometsko et al., 1993a) wherein the micronucleus signal is moved 100-fold upfield and away from the DNA deficient red blood cell (RBC) peak. In addition, we have demonstrated the high accuracy of our flow cytometry method in scoring rare micronucleated cells (Tometsko et al., 1993b). In the course of our studies, we rigorously pursued conditions which minimized experimental noise, demanding that FCM-scoring accuracy should approach theoretical limits. Thus, we laid the foundation for detecting clastogen activity with great sensitivity. The experiments described herein extend the previous studies by using high-speed flow cytometry to detect a clastogen-induced increase in MN cells in the total erythrocyte population. Methyl methanesulfonate (MMS) served as a model clastogen in these studies. This manuscript describes our development of a suitable blood-sampling regimen, the advantages of obtaining initial blood samples before dosing, the sex-linked difference in background micronucleus levels in BALB/c mice, and the analysis of a clastogen-induced biological response in male and female mice. As described, our flow cytometry method is able to provide a quantitative analysis of the net change in micronucleated cells (delta MN) for each mouse.

Animals↗

PubMed2000

Apolipoprotein B-100: employing the electrochemiluminescence technology of the Elecsys systems for the detection of the point mutation Arg(3500)Gln.

Apolipoprotein B-100 (apo B-100) plays an essential role in lipoprotein metabolism where it is involved in the clearance of LDL particles from the bloodstream. The mutation Arg3500Gln in the apo B-100 gene impairs the binding of the LDL particles to the LDL receptor, resulting in elevated LDL-cholesterol levels in the blood which, in turn, fuel the development of premature atherosclerosis. Here we describe a rapid, automated test for the detection of the most frequent mutation in the apo B-100 gene. This PCR-based test employs electrochemiluminescence as detection technology and allows the reliable discrimination of all genotypes. The assay has been especially developed for the non-specialized routine clinical chemistry laboratory by employing an analyzer and chemistry often present in this type of labof1tory. Because of its low costs and easy handling the assay can be performed on a daily basis.

Amino Acid Substitution↗

PubMed2004

Information technology for detecting medication errors and adverse drug events.

It is estimated that over three-quarters of a million people are injured or die in hospitals each year from adverse drug events (ADEs). The majority of medical errors result from poorly designed healthcare systems rather than from negligence on the part of healthcare providers. In general, healthcare systems rely on voluntary reporting, which seriously underestimates the number of medication errors and ADEs by as much as 90%. This paper reviews the causes and impact of medication errors and ADEs. It also reports studies that have used information technology (IT) to detect and prevent medication errors and ADEs. Significant reduction of medication errors and ADEs requires systemic implementation of IT, improvements in the reporting of errors, and integration of the components of the healthcare systems' information systems. At the present time, most healthcare systems should be able to use IT to detect and prevent ADEs.

Adverse Drug Reaction Reporting Systems↗

PubMed2005

Two high throughput technologies to detect segmental aneuploidies identify new Williams-Beuren syndrome patients with atypical deletions.

OBJECTIVE: To develop and compare two new technologies for diagnosing a contiguous gene syndrome, the Williams-Beuren syndrome (WBS). METHODS: The first proposed method, named paralogous sequence quantification (PSQ), is based on the use of paralogous sequences located on different chromosomes and quantification of specific mismatches present at these loci using pyrosequencing technology. The second exploits quantitative real time polymerase chain reaction (QPCR) to assess the relative quantity of an analysed locus. RESULTS: A correct and unambiguous diagnosis was obtained for 100% of the analysed samples with either technique (n = 165 and n = 155, respectively). These methods allowed the identification of two patients with atypical deletions in a cohort of 182 WBS patients. Both patients presented with mild facial anomalies, mild mental retardation with impaired visuospatial cognition, supravalvar aortic stenosis, and normal growth indices. These observations are consistent with the involvement of GTF2IRD1 or GTF2I in some of the WBS facial features. CONCLUSIONS: Both PSQ and QPCR are robust, easy to interpret, and simple to set up. They represent a competitive alternative for the diagnosis of segmental aneuploidies in clinical laboratories. They have advantages over fluorescence in situ hybridisation or microsatellites/SNP genotyping for detecting short segmental aneuploidies as the former is costly and labour intensive while the latter depends on the informativeness of the polymorphisms.

Aneuploidy↗

PubMed2002

Standard achromatic perimetry, short wavelength automated perimetry, and frequency doubling technology for detection of glaucoma damage.

OBJECTIVE: Reevaluation of the relationship between short wavelength automated perimetry (SWAP), standard achromatic perimetry (SAP), and frequency doubling technology (FDT) in glaucoma and ocular hypertensive patients and in glaucoma suspects. DESIGN: Prospective comparative observational study. PARTICIPANTS: Four age-matched groups were evaluated (42 patients with early to moderate glaucoma, 34 ocular hypertensives, 22 glaucoma suspects, and 25 normal controls) using SAP, SWAP, and FDT. INTERVENTION: All participants underwent full clinical ophthalmologic evaluation followed by SWAP, SAP, and FDT perimetry within a period of not more than 3 months. Mean defect (MD), pattern standard deviation (PSD), visual field (VF) indices, and the percentage of depressed visual field points with P value <5% and <1% in the pattern deviation plot were evaluated. MAIN OUTCOME MEASURES: For each of the four study groups, the MD, PSD, and the percentage of abnormal points significantly depressed <5% and <1% were compared for the three VF testing modalities. RESULTS: In the glaucoma group, the mean percentage of the total number of abnormal points in SWAP was significantly less than abnormal points in SAP and FDT, both for 5% (P values were 0.0001 and 0.0001, respectively) and 1% (P values were 0.0001 and 0.0001, respectively). The same applied to the ocular hypertensives group. However, in the suspects group, no significant difference was detected. In normal controls, the abnormal points in SWAP were significantly lower than those in SAP for 5% (P value was 0.01) and 1% (P value was 0.05). FDT detected significantly larger defects (percentage of points <5%) than SAP in ocular hypertensives and suspects (P values were 0.01 and 0.004, respectively). CONCLUSIONS: SWAP in its existing condition is markedly less efficient than either SAP or FDT in detecting VF defects, especially in glaucoma patients and ocular hypertensives (defects detected with SWAP are less than both SAP and FDT). Defects detected with FDT are equivalent to SAP and sometimes larger, especially in ocular hypertensives and glaucoma suspects; this makes it a useful tool for picking up early glaucomatous defects in populations at risk.

Adult↗

PubMed2005

Further comparison of primary hit identification by different assay technologies and effects of assay measurement variability.

High-throughput screening (HTS) has grown rapidly in the past decade, with many advances in new assay formats, detection technologies, and laboratory automation. Recently, several studies have shown that the choice of assay technology used for the screening process is particularly important and can yield quite different primary screening outcomes. However, because the screening assays in these previous studies were performed in a single-point determination, it is not clear to what extent the difference observed in the screening results between different assay technologies is attributable to inherent assay variability and day-to-day measurement variation. To address this question, a nuclear receptor coactivator recruitment assay was carried out in 2 different assay formats, namely, AlphaScreen and time-resolved fluorescence resonance energy transfer, which probed the same biochemical binding events but with different detection technologies. For each assay format, 4 independent screening runs in a typical HTS setting were completed to evaluate the run-to-run screening variability. These multiple tests with 2 assay formats allow an unambiguous comparison between the discrepancies of different assay formats and the effects of the variability of assay and screening measurements on the screening outcomes. The results provide further support that the choice of assay format or technology is a critical factor in HTS assay development.

Animals↗

PubMed2003

Development and validation of a quantitative real-time PCR assay using fluorescence resonance energy transfer technology for detection of Aspergillus fumigatus in experimental invasive pulmonary aspergillosis.

Invasive pulmonary aspergillosis (IPA) is a frequently fatal infection in immunocompromised patients that is difficult to diagnose. Present methods for detection of Aspergillus spp. in bronchoalveolar lavage (BAL) fluid and in tissue vary in sensitivity and specificity. We therefore developed an A. fumigatus-specific quantitative real-time PCR-based assay utilizing fluorescent resonance energy transfer (FRET) technology. We compared the assay to quantitative culture of BAL fluid and lung tissue in a rabbit model of experimental IPA. Using an enzymatic and high-speed mechanical cell wall disruption protocol, DNA was extracted from samples of BAL fluid and lung tissues from noninfected and A. fumigatus-infected rabbits. A unique primer set amplified internal transcribed spacer regions (ITS) 1 and 2 of the rRNA operon. Amplicon was detected using FRET probes targeting a unique region of ITS1. Quantitation of A. fumigatus DNA was achieved by use of external standards. The presence of PCR inhibitors was determined by use of a unique control plasmid. The analytical sensitivity of the assay was </=10 copies of target DNA. No cross-reactivity occurred with other medically important filamentous fungi. The assay results correlated with pulmonary fungal burden as determined by quantitative culture (r = 0.72, Spearman rank correlation; P </= 0.0001). The mean number of genome equivalents detected in untreated animals was 3.86 log(10) (range, 0.86 to 6.39 log(10)) in tissue. There was a 3.53-log(10) mean reduction of A. fumigatus genome equivalents in animals treated with amphotericin B (AMB) (95% confidence interval, 3.38 to 3.69 log(10); P </= 0.0001), which correlated with the reduction of residual fungal burden in lung tissue measured in terms of log(10) CFU/gram. The enhanced quantitative sensitivity of the real-time PCR assay was evidenced by detection of A. fumigatus genome in infarcted culture-negative lobes, by a greater number of mean genome equivalents compared to the number of CFU per gram in tissue and BAL fluid, and by superior detection of therapeutic response to AMB in BAL fluid compared to culture. This real-time PCR assay using FRET technology is highly sensitive and specific in detecting A. fumigatus DNA from BAL fluid and lung tissue in experimental IPA.

Aspergillosis, Allergic Bronchopulmonary↗

PubMed1999

Proteinchip(R) surface enhanced laser desorption/ionization (SELDI) mass spectrometry: a novel protein biochip technology for detection of prostate cancer biomarkers in complex protein mixtures.

Improving early detection, diagnosis, treatment monitoring and prognosis of cancer will require rapid and high throughput detection, identification, and measurement of multiple biomarkers. In this study, we demonstrate the versatility of the innovative SELDI ProteinChip(R) MS technology for the rapid, reproducible and simultaneous identification of four well-characterized prostate cancer-associated (PCA) biomarkers, prostate specific antigen (free and complexed forms), prostate specific peptide, prostate acid phophatase and prostate specific membrane antigen in cell lysates, serum and seminal plasma. Proteins corresponding to the mass of these biomarkers could readily be captured and detected using either chemically defined or antibody coated ProteinChip(R) arrays. Several (yet to be identified) proteins were found upregulated in cell lysates of pure populations of PCA cells procured by laser capture microdissection (LCM) when compared with mass spectra of normal cell lysates. Coupling LCM with SELDI provides tremendous opportunities to discover and identify the signature proteins associated with each stage of tumor development. Collectively, these observations demonstrate the potential of SELDI for the discovery and simultaneous detection of and clinical assay development for PCA biomarkers in complex biological mixtures.

Journal Article↗

PubMed2005

Computer technology in detection and staging of prostate carcinoma: a review.

After two decades of increasing interest and research activity, computer-assisted diagnostic approaches are reaching the stage where more routine deployment in clinical practice is becoming a possibility [Kruppinski, E.A., 2004. Computer-aided detection in clinical environment: Benefits and challenges for radiologists. Radiology 231, 7-9]. This is particularly the case in the analysis of mammographic images [Helvie, M.A., Hadjiiski, L., Makariou, E., Chan, H.P., Petrick, N., Sahiner, B., Lo, S.C., Freedman, M., Adler, D., Bailey, J., Blane, C., Hoff, D., Hunt, K., Joynt, L., Klein, K., Paramagul, C., Patterson, S.K., Roubidoux, M.A., 2004. Sensitivity of noncommercial computer-aided detection system for mammographic breast cancer detection: pilot clinical trial. Radiology 231, 208-214] and in the detection of pulmonary nodules [Reeves, A.P., Kostis, W.J., 2000. Computer-aided diagnosis for lung cancer. Radiol. Clin. North Am. 38, 497-509]. However, similar approaches can be applied more widely with the promise of increasing clinical utility in other areas. We review how computer-aided approaches may be applied in the diagnosis and staging of prostatic cancer. The current status of computer technology is reviewed, covering artificial neural networks for detection and staging, computerised biopsy simulation and computer-assisted analysis of ultrasound and magnetic resonance images.

Adenocarcinoma↗

PubMed2003

Detection of single nucleotide polymorphisms.

Single nucleotide polymorphism (SNP) detection technologies are used to scan for new polymorphisms and to determine the allele(s) of a known polymorphism in target sequences. SNP detection technologies have evolved from labor intensive, time consuming, and expensive processes to some of the most highly automated, efficient, and relatively inexpensive methods. Driven by the Human Genome Project, these technologies are now maturing and robust strategies are found in both SNP discovery and genotyping areas. The nearly completed human genome sequence provides the reference against which all other sequencing data can be compared. Global SNP discovery is therefore only limited by the amount of funding available for the activity. Local, target, SNP discovery relies mostly on direct DNA sequencing or on denaturing high performance liquid chromatography (dHPLC). The number of SNP genotyping methods has exploded in recent years and many robust methods are currently available. The demand for SNP genotyping is great, however, and no one method is able to meet the needs of all studies using SNPs. Despite the considerable gains over the last decade, new approaches must be developed to lower the cost and increase the speed of SNP detection.

Alleles↗

PubMedDate not supplied

Application of a novel protein biochip technology for detection and identification of rheumatoid arthritis biomarkers in synovial fluid.

We compared protein profiles of the synovial fluid of patients with rheumatoid arthritis and osteoarthritis by using surface-enhanced laser desorption/ionization mass spectrometry technology. With this approach, we identified a protein expressed specifically in the synovial fluid of the patients with rheumatoid arthritis. During the investigation, we found several reproducible and discriminatory biomarker candidates for distinction between rheumatoid arthritis and osteoarthritis. Among these candidates, a 10 850 Da protein peak was the clearest example of a single signal found specifically in the rheumatoid arthritis samples. This candidate was purified using a size-exclusion spin column followed by gel electrophoresis and subsequently identified by peptide mapping and post-source decay (PSD) analysis. The results clearly indicate that the protein is myeloid-related protein 8, which was verified by the enzyme immunoassay. It is known that the myeloid-related protein 8 level in serum and synovial fluid is related to disease activity in juvenile rheumatoid arthritis. The results suggest that the ProteinChip platform is useful to detect and identify protein biomarkers expressed specifically in diseases or in some stage of diseases.

Arthritis, Rheumatoid↗

PubMed2006

Kinetic mechanism of deoxyadenosine kinase from Mycoplasma determined by surface plasmon resonance technology.

Surface plasmon resonance (SPR) detection technology was employed to investigate the kinetic mechanism of deoxyadenosine kinase from Mycoplasma mycoides ssp. mycoides SC. In our experimental approach, the enzyme was attached to the sensor surface, the reactants were injected in the mobile phase, and the product-enzyme complex formation was measured using the fact that the rate of product formation exceeds that of its dissociation. The pre-steady-state analysis of deoxyguanosine phosphorylation showed the presence of a burst phase, which is consistent with product dissociation being a rate-limiting step. High activity of the immobilized enzyme was demonstrated by analyzing the reaction mixture eluted from the chip and by determining the Michaelis-Menten constants for several phosphate acceptors (e.g., deoxyadenosine) and phosphate donors (e.g., ATP) using SPR detection. These values were in good agreement with those reported previously [Wang, L. et al. (2001) Mol. Microbiol. 42, 1065-1073]. The bisubstrate initial rate pattern obtained was characteristic of a sequential kinetic mechanism. Because in the method applied here it is the mass change on the surface that is monitored, a new mathematical approach to interpreting product inhibition experiments was proposed. According to that approach, product inhibition studies, supported by product binding experiments, indicated that the reaction mechanism was of Bi Bi sequential ordered type, involving the formation of a ternary complex, in which ATP and deoxyadenosine bound sequentially, followed by a transfer of the phosphate group, and an ordered release of products with ADP dissociating before dAMP.

Adenosine Diphosphate↗