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PubMed2005

Development of a rapid assay for the diagnosis of Myxobolus cerebralis in fish and oligochaetes using loop-mediated isothermal amplification.

A loop-mediated isothermal amplification assay was developed for the rapid detection of Myxobolus cerebralis in both fish and oligochaete hosts. The assay was optimized to amplify parasitic DNA by incubation with Bst DNA polymerase and a set of six specially constructed primers at 65 degrees C for 60 min. The amplification products were detected visually using SYBR Green I dye which gave identical results to gel electrophoresis analysis. Parasite DNA was detected from infected oligochaetes, and from the anal fin, caudal fin, dorsal fin and operculum of clinically infected fish. This 'Myxo-LAMP' assay has a detection limit similar to that of a polymerase chain reaction assay (10(-6)), but is more rapid and only requires a water bath for amplification and is therefore practical for simple and rapid diagnosis of infected tissue.

Animals↗

PubMed1991

Design, development, and interpretation of HIV neutralization assays.

In developing therapeutic reagents for the control of HIV infection, it is necessary to screen candidate products in vitro for their ability to reduce or neutralize viral infection. Although the current literature describes numerous neutralization assays, no universally accepted standards have been adopted. In this article, we briefly review the available neutralization assays and describe in detail the methods we have selected in our laboratory for the screening and characterization of reagents with potential anti-HIV properties. After evaluating many different technical protocols and experimental procedures, we have found the syncytium inhibition and syncytial focus assays to be particularly useful and have found p24 gag antigen production to be an excellent objective measure of HIV infection under a variety of conditions. These assays proved reproducible and sensitive and are suitable for use in the majority of laboratories.

Animals↗

PubMedDate not supplied

Direct multiplex assay of enzymes in dried blood spots by tandem mass spectrometry for the newborn screening of lysosomal storage disorders.

Tandem mass spectrometry is currently used in newborn screening programmes to quantify the level of amino acids and acylcarnitines in dried blood spots for detection of metabolites associated with treatable diseases. We have developed assays for lysosomal enzymes in rehydrated dried blood spots in which a set of substrates is added and the set of corresponding enzymatic products are quantified using tandem mass spectrometry with the aid of mass-differentiated internal standards. We have developed a multiplex assay of the set of enzymes that, when deficient, cause the lysosomal storage disorders Fabry, Gaucher, Hurler, Krabbe, Niemann-Pick A/B and Pompe diseases. These diseases were selected because treatments are now available or expected to emerge shortly. The discovery that acarbose is a selective inhibitor of maltase glucoamylase allows the Pompe disease enzyme, acid alpha-glucosidase, to be selectively assayed in white blood cells and dried blood spots. When tested with dried blood spots from 40 unaffected individuals and 10-12 individuals with the lysosomal storage disorder, the tandem mass spectrometry assay led to the correct identification of the affected individuals with 100% sensitivity. Many of the reagents needed for the new assays are commercially available, and those that are not are being prepared under Good Manufacturing Procedures for approval by the FDA. Our newborn screening assay for Krabbe disease is currently being put in place at the Wadsworth Center in New York State for the analysis of approximately 1000 dried blood spots per day. Summary We have developed tandem mass spectrometry for the direct assay of lysosomal enzymes in rehydrated dried blood spots that can be implemented for newborn screening of lysosomal storage disorders. Several enzymes can be analysed by a single method (multiplex analysis) and in a high-throughput manner appropriate for newborn screening laboratories.

Blood Specimen Collection↗

PubMed2003

Development of a microplate assay for the detection of single plaque-forming units of bacteriophage PhiX174 in crude lysates.

Mice containing the PhiX174 am3 transgene can be used for measuring in vivo mutation; however, the single burst analysis method used for distinguishing in vivo mutations from mutations generated during sample processing is labor-intensive. A liquid microplate assay was developed that detects a single mutant plaque-forming unit (PFU) of PhiX174 bacterial virus in the presence of excess nonmutant virus. The assay is based on inhibiting reduction of the tetrazolium dye, MTS, by bacterial cells selective for mutant virus. The assay is performed with crude lysates of infected bacteria and is as accurate as scoring viral plaques on a bacterial lawn. This microplate assay may have application in increasing throughput of the single burst analysis of PhiX174 in transgenic mouse mutation assays.

Animals↗

PubMed2004

Development of an HTS assay for Na+, K+-ATPase using nonradioactive rubidium ion uptake.

A high-throughput screening (HTS) assay was developed for the Na(+),K(+)-ATPase channel in order to study rubidium uptake as a measure of the functional activity and modulation of this exchanger. The assay uses elemental rubidium as a tracer for K(+) ions. Three cell lines were used to study the exchanger, and the assay was performed in a 96-well microtiter plate format. Rb(+) uptake was carried by the CHO-K1 cells at 37 degrees C; the maximum ion influx was at 80 min of incubation of the cell line in the medium containing 5.4 mM RbCl. The cells were incubated in Rb(+) uptake buffer (5.4 mM) and with the pump blocker ouabain for 1, 2, and 3 h, respectively. A complete block of the Rb(+) uptake was observed with a 5 mM concentration of ouabain for all the three time intervals. The ouabain 50% inhibitory concentration (IC(50)) value for CHO-K1 cell line ATPase was observed to be 298 microM after 3 h of incubation. In addition, IC(50) values of 94 and 89 microM were observed at 30 min of incubation, indicating that the protocol shows reproducible results. A Z' factor higher than 0.7 was observed in the assays. These studies extend the profile of Na(+),K(+)-ATPases and demonstrate the feasibility of this HTS assay system to screen for compounds that pharmacologically modulate the function of Na(+),K(+)-ATPase.

Animals↗

PubMed2004

Fluorescence stopped-flow studies of single turnover kinetics of E.coli RecBCD helicase-catalyzed DNA unwinding.

We have developed and optimized a stopped-flow fluorescence assay for use in studying DNA unwinding catalyzed by Escherichia coli RecBCD helicase. This assay monitors changes in fluorescence resonance energy transfer (FRET) between a pair of fluorescent probes (Cy3 donor and Cy5 acceptor) placed on opposite sides of a nick in duplex DNA. As such, this is an "all-or-none" DNA unwinding assay. Single turnover DNA unwinding experiments were performed using a series of eight fluorescent DNA substrates containing duplex DNA regions ranging from 24 bp to 60 bp. The time-courses obtained by monitoring Cy3 fluorescence display a distinct lag phase that increases with increasing duplex DNA length, reflecting the transient formation of partially unwound DNA intermediates. These Cy3 FRET time-courses are identical with those obtained using a chemical quenched-flow kinetic assay developed previously. The signal from the Cy5 fluorescence probe shows additional effects that appear to specifically monitor the RecD helicase subunit. The continuous nature of this fluorescence assay enabled us to acquire more precise time-courses for many more duplex DNA lengths in a significantly reduced amount of time, compared to quenched-flow methods. Global analysis of the Cy3 and Cy5 FRET time-courses, using an n-step sequential DNA unwinding model, indicates that RecBCD unwinds duplex DNA with an average unwinding rate constant of kU = 200(+/-40) steps s(-1) (mkU = 680(+/-12)bp s(-1)) and an average kinetic step size, m = 3.4 (+/-0.6) bp step(-1) (5 mM ATP, 10 mM MgCl(2), 30 mM NaCl, pH 7.0, 5% (v/v) glycerol, 25.0 degrees C), in excellent agreement with the kinetic parameters determined using quenched-flow techniques. Under these same conditions, the RecBC enzyme unwinds DNA with a very similar rate. These methods will facilitate detailed studies of the mechanisms of DNA unwinding and translocation of the RecBCD and RecBC helicases.

Base Sequence↗

PubMed2006

Development of a genetic assay to distinguish between Leishmania viannia species on the basis of isoenzyme differences.

BACKGROUND: Tegumentary leishmaniasis in Latin America is caused mainly by Leishmania viannia braziliensis complex parasites. L. braziliensis and Leishmania viannia peruviana are the 2 predominant Leishmania species in Peru. L. braziliensis is more virulent, because it can cause mucocutaneous leishmaniasis, known as espundia, that results in severe facial destruction. Early identification of the species that causes the initial cutaneous infection would greatly help to prevent mucocutaneous leishmaniasis, because it would allow more aggressive treatment and follow-up. However, because of the close genetic similarity of L. braziliensis and L. peruviana, there currently exists no simple assay to distinguish between these species. METHODS: We cloned the mannose phosphate isomerase gene from both L. braziliensis and L. peruviana. It is the only known isoenzyme capable of differentiating between L. braziliensis and L. peruviana in multilocus enzyme electrophoresis. Interestingly, only a single nucleotide polymorphism was found between the mannose phosphate isomerase genes from L. braziliensis and L. peruviana, resulting in an amino acid change from threonine to arginine at amino acid 361. A polymerase chain reaction assay was developed to distinguish the single nucleotide polymorphism of the mannose phosphate isomerase gene to allow for the specific identification of L. braziliensis or L. peruviana. RESULTS: This assay was validated with 31 reference strains that were previously typed by multilocus enzyme electrophoresis, successfully applied to patient biopsy samples, and adapted to a real-time polymerase chain reaction assay. CONCLUSIONS: This innovative approach combines new genetic knowledge with traditional biochemical fundamentals of multilocus enzyme electrophoresis to better manage leishmaniasis in Latin America.

Amino Acid Sequence↗

PubMed1994

Improved LC assay for the determination of mitozantrone in plasma: analytical considerations.

Preliminary method development studies on mitozantrone (MTZ) revealed a number of characteristics which were found to be important in the analysis of patient samples for pharmacokinetic studies. MTZ rapidly bound to glass, particularly at low concentrations (< 10 ng ml-1), necessitating the use of silanized glassware or polypropylene tubes for the handling of all solutions containing MTZ. MTZ was also found to react with two commonly-used antioxidants; sodium metabisulphite and EDTA. However, solutions containing MTZ were found to be stabilized by the addition of ascorbic acid (0.5% w/v). In the absence of ascorbic acid, MTZ underwent rapid, biphasic degradation in plasma at 24 and 37 degrees C, with terminal half-lives of approximately 70 h. Ascorbic acid (0.5% 2/v) was found to stabilize plasma samples containing MTZ throughout work-up procedures and during frozen storage. The addition of ascorbic acid to the sample collection vial was also necessary to prevent MTZ degradation in the eluting solvent of the solid-phase extraction system. Another important consideration was the requirement for an equilibration period of > 5 min after the addition of ametantrone (AM) internal standard to plasma samples. This was essential, since the slope of the calibration plot obtained using non-equilibrated plasma was approximately 30% of that obtained for calibration plots using equilibrated plasma, and would result in erroneous determination of MTZ plasma concentrations. The fully developed assay was rapid, precise and sensitive (relative errors at 1 ng ml-1 = 2.3%). MTZ concentrations determined using the LC method described in this report correlated well with an independently developed ELISA technique (r = 0.995, n = 20).

Antineoplastic Agents↗

PubMed1999

New perspectives in the diagnosis of hepatitis C.

Since the identification and molecular characterization of the non-A, non-B hepatitis virus (HCV) in 1989, a variety of diagnostic tests based on the detection of hepatitis virus antibodies or HCV RNA in the serum have been developed and refined. The enzyme-linked immunosorbent assays (ELISAs) and the recombinant immunoblot assays (RIBAs) exhibit improved sensitivity and specificity for HCV antibodies compared with their predecessors, and the ELISA-3 is at the forefront of HCV screening. Furthermore, the advent of molecular assays that employ quantitative reverse-transcriptase polymerase chain reaction to detect HCV RNA has allowed clinicians to track the natural history of HCV and to monitor the progress of therapy. A role for further refinement of an HCV diagnosis using tests to determine genotype, subtype, and quasispecies is explored. In addition, the role of liver biopsy and non-invasive markers of histologic status are placed into the context of patient prognosis. This article reviews the state-of-the-art tests and assays developed for the diagnosis and management of HCV infection.

Enzyme-Linked Immunosorbent Assay↗

PubMed2006

Detection of the nifH gene of Methanobrevibacter smithii: a potential tool to identify sewage pollution in recreational waters.

AIMS: The goal of this study was to develop and test the efficacy of a PCR assay for the environmental detection of the nifH gene of Methanobrevibacter smithii, a methanogen found in human faeces and sewage. METHODS AND RESULTS: PCR primers for the nifH gene of M. smithii were designed, tested and used to detect the presence or absence of this organism in faecal and environmental samples. Specificity analysis showed that the Mnif primers amplified products only in M. smithii pure culture strains (100%), human faeces (29%), human sewage samples (93%) and sewage-contaminated water samples (100%). No amplification was observed when primers were tested against 43 bacterial stock cultures, 204 animal faecal samples, 548 environmental bacterial isolates and water samples from a bovine waste lagoon and adjacent polluted creek. Sequencing of PCR products from sewers demonstrated that a 222-bp product was the nifH gene of M. smithii. The minimal amount of total DNA required for the detection of M. smithii was 10 ng for human faeces, 10 ng for faecally contaminated water and 5 ng for sewage. Recreational water seeded with M. smithii established a lower detection limit of 13 cells ml(-1). CONCLUSIONS: The Mnif assay developed during this investigation showed successful detection of M. smithii in individual human faecal samples, sewage and sewage-contaminated water but not in uncontaminated marine water or bovine-contaminated waters. The Mnif assay appears to be a potentially useful method to detect sewage-polluted coastal waters. SIGNIFICANCE AND IMPACT OF THE STUDY: This study was the first to utilize methanogens as an indicator of sewage pollution. Mnif PCR detection of M. smithii was shown to be a rapid, inexpensive and reliable test for determining the presence or absence of sewage pollution in coastal recreational waters.

Animals↗

PubMed2006

Simultaneous estimation of six anti-diabetic drugs--glibenclamide, gliclazide, glipizide, pioglitazone, repaglinide and rosiglitazone: development of a novel HPLC method for use in the analysis of pharmaceutical formulations and its application to human plasma assay.

This paper describes a convenient method for the separation and simultaneous determination of six anti-diabetic drugs viz., glibenclamide (GLB), gliclazide (GLC), glipizide (GLZ), pioglitazone (PGL), repaglinide (RPG) and rosiglitazone (RGL) in pharmaceutical formulations. Also, the assay has been shown applied to support quantification of the six anti-diabetic drugs in human plasma. The analytes were either injected directly onto the column after suitable dilution (pharmaceutical formulation analysis) or a simple extraction procedure, using acetonitrile, from human plasma spiked with anti-diabetic drugs and internal standard (IS). Ternary gradient elution at a flow rate of 1 mL/min was employed on an Intertisl ODS 3V column (4.6 x 250 mm, 5 microm) at ambient temperature. The mobile phase consisted of 0.01 m formic acid (pH 3.0), acetonitrile, Milli Q water and methanol. Celecoxib was used as an IS. The six anti-diabetic drugs were monitored at a wavelength of 260 nm. The nominal retention times of RGL, PGL, GLZ, GLC, GLB, IS and RGL were 11.4, 13.3, 14.8, 17.6, 20.78, 22.1 and 25.4 min, respectively. The assay developed for formulation analysis was found to be accurate and precise. The calibration curves ranged from 0.1 to 100 microg/mL for all analytes with the exception of GLB, where the range was 0.3-100 microg/mL. The plasma assay was validated for parameters such as specificity, accuracy and extraction recovery. The proposed method is simple, selective and can be extended for routine analysis of anti-diabetics in pharmaceutical preparations and in biological matrices.

Carbamates↗

PubMed2003

Rapid and standardized detection of Chlamydia pneumoniae using LightCycler real-time fluorescence PCR.

In order to meet the need of many microbiological laboratories for a standardized system for detecting Chlamydia pneumoniae in respiratory specimens, a hybridization probe-based LightCycler (Roche Diagnostics, Germany) PCR assay was developed. The assay's analytical sensitivity and specificity were evaluated according to the recommendations of the Centers for Disease Control and Prevention (USA) and Laboratory Centre for Disease Control (Canada). Seventy-four bacterial species other than Chlamydia pneumoniae, including strains of Chlamydia trachomatis, Chlamydia psittaci, and Chlamydia pecorum, tested negative. Six of six representative Chlamydia pneumoniae strains tested positive. An analytical sensitivity of 1 inclusion forming unit per ml of bronchoalveolar lavage fluid, corresponding to 0.02 inclusion forming units per PCR reaction, was observed. The assay showed 100% specificity and sensitivity for Chlamydia pneumoniae when testing DNA preparations from 12 specimens of patients with known pulmonary Chlamydia pneumoniae infection and from 78 specimens of patients with respiratory tract disease of other origin. The newly developed LightCycler assay may contribute to the urgently needed standardization of laboratory diagnosis of Chlamydia pneumoniae.

Bacteriological Techniques↗

PubMed2000

Development of an improved assay for purine nucleoside kinase activity in cell extracts and detection of inosine kinase activity in Brevibacterium acetylicum ATCC 953, related species, and Corynebacterium flaccumfaciens ATCC 6887.

An improved assay was developed to detect direct purine nucleoside phosphorylating activity in cell-free extracts. Direct inosine phosphorylating activity was detected in 2 of 70 species tested. Both activities, which depended on magnesium ion and ATP, phosphorylated a hydroxyl group at the 5' position of inosine. The new assay was shown to be useful for screening of direct purine nucleoside phosphorylating activity and have the potential to detect inosine kinase in the presence of a background of nucleoside phosphorylase and purine phosphoribosyltransferase activities. Previously, the latter two activities made it difficult to correctly detect direct phosphorylation of inosine by inosine kinase.

Adenosine Triphosphate↗

PubMed1990

Development of an Adhesion Assay and Characterization of an Adhesion-Deficient Mutant of Pseudomonas fluorescens.

A sand column adhesion assay was developed which distinguishes the adhesion abilities of a number of pseudomonads isolated from fine sandy loam. Pseudomonas fluorescens Pf0-1 which adhered at >90% of the total cells added was subjected to transposon Tn5 insertion mutagenesis. From 2,500 Pf0-1::Tn5 mutants examined in the sand column assay, two adhesion-deficient Pf0-1 mutants showing <50% attachment were isolated. Marker exchange analysis of one of these mutants, Pf0-5, confirmed that the decreased adhesion was linked to the Tn5 insertion in the chromosome. The growth rate of Pf0-5 in enriched media and sterile soil was similar to that of the wild type; in minimal medium, however, Pf0-5 grew faster. In a soil column assay, less Pf0-5 than wild-type bacteria were recovered, suggesting a decreased ability to persist in soil. A 34-kilodalton major outer membrane protein present in the wild type was missing in Pf0-5. Transmission electron microscopy of the cell surface revealed that the wild-type possessed polar flagella which were absent in the mutant.

Journal Article↗

PubMed1992

[Clinical evaluation of SD-8828 (antibody coated bacteria assay kit) in urinary tract infection].

Clinical usefulness of a newly developed assay kit for ACB (SD-8828) which detects urinary bacteria coating IgG was evaluated and compared to the enzyme antibody plate method. A total of 48 patients including 20 patients with acute simple cystitis and 28 patients with acute or chronic pyelonephritis, who were shown to have pyuria of at least 5 cells/HPF, bacteriuria of at least 10(4) CFU/ml were enrolled in this study. By enzyme antibody method. ABC was positive in 92.9% of patients with upper urinary tract infection and negative in 100% of patients with lower UTI, this difference being statistically significant (p < 0.02). By SD-8828, 85% of positive coincidence rate and 100% of negative coincidence rate, compared to the enzyme antibody technique, was obtained. The overall coincidence rate was high (91.7%). This SD-8828, a new simple assay for ACB, which detects IgG alternating the plate method, may be used as a convenient method in clinical practice.

Acute Disease↗

PubMed2001

Development of an immunoassay for diagnosis of exposure to toxic organophosphorus compounds.

Currently, diagnosis of exposure to toxic low-molecular-weight compounds is effected by the use of chromatographic techniques. Such an approach is limited by the need for expensive equipment and sample clean-up before carrying out the analysis. To overcome those drawbacks, we have been involved in the development of an immunoassay for diagnosis of exposure to toxic organophosphorus compounds such as pinacolylmethyl phosphonofluoridate (soman), which is a chemical warfare agent. Prior estimates suggested that it is necessary to be able to detect soman at a concentration below 2.5 x 10(-7) M. Using four previously developed monoclonal antibodies, an enzyme-linked immunosorbant assay (ELISA) was used to optimize assay conditions and identify the antibody with the highest apparent affinity. The minimum required assay time was 2.0-2.5 h with no loss in sensitivity. To determine the specificity of the highest affinity antibody, a competitive inhibition enzyme immunoassay (CIEIA) was performed with six structural analogs of soman. The IC50 values for these analogues were 5 x 10(-7) M for 4-nitrophenylpinacolylmethylphosphonate, 8 x 10(-7) M for dipinacolylmethylphosphonate, 2 x 10(-6) M for diisopropylmethylphosphonate, 3 x 10(-5) M for 4-nitrophenylmethyl(phenylphosphinate) and 6.5 x 10(-5) M for 4-nitrophenylethyl(phenyl)phosphinate. 4-Nitrophenyl-di(n-butyl)phosphinate did not inhibit binding. Those inhibitors with branched alkyl side-chains, similar to the soman molecule, were effective inhibitors. Compounds, which contained predominately aromatic groups, were poor inhibitors. We are continuing to probe the binding specificity of the monoclonal antibody to determine its utility in further assay development. Our present results suggest that the antibody chosen may have the appropriate specificity and affinity for immunodiagnosis of exposure to soman.

Antibodies, Monoclonal↗

PubMed1994

Development of nested PCR assays for detection of bovine respiratory syncytial virus in clinical samples.

Two nested PCR assays were developed for the detection of bovine respiratory syncytial virus (BRSV). Primers were selected from the gene encoding the F fusion protein (PCR-F) and the gene encoding the G attachment protein (PCR-G). Biotinylated oligonucleotide probes, termed F and G, were selected for the hybridization of the respective PCR products. The sensitivities of the PCR-F and PCR-G assays were similar, both detecting 0.1 tissue culture infective dose of the virus. The PCR-F assay amplified all bovine strains and one human strain (RS32) tested. No cross-reactions were observed with nine heterologous respiratory viruses. PCR-F products of bovine and human RSV strains were discriminated by using endonuclease restriction enzyme ScaI, which specifically cleaved, products of BRSV. Oligonucleotide probe F was also specific for products of BRSV. The PCR-G assay detected all bovine strains and none of the human strains tested. A faint electrophoretic band was also observed with products of Sendai virus. However, probe G did not hybridize with this product, only with products of BRSV. Nasal swabs collected from cattle with no symptoms and cattle in the acute stage of respiratory disease were analyzed for BRSV by the immunofluorescence (IF) method and by the PCR-F and PCR-G assays. The virus was detected by the PCR assays in 31 of 35 (89%) samples tested. Only 23 samples (66%) were positive by the IF method, and these samples were also positive by both the PCR-F and PCR-G assays. The 31 samples detected as positive by PCR originated from cattle presenting clinical signs of acute respiratory disease; the four PCR-negative samples originated from clinically asymptomatic neighboring cattle. All sampled animals subsequently seroconverted and became reactive to BRSV. Thus, the detection of BRSV by PCR correlated with clinical observations and was considerably more sensitive (66 versus 89%) than IF. These results indicate that both nested PCR assays provide rapid and sensitive means for the detection of BRSV infection in cattle. Considering its higher specificity, the PCR-F assay can be recommended as the method of choice in the analysis of clinical specimens of BRSV.

Acute Disease↗

PubMed1998

AP endonuclease activity in humans: development of a simple assay and analysis of ten normal individuals.

The human AP endonuclease (APE) activity counteracts the mutagenic and cytotoxic effects of the frequent genomic lesions abasic (AP) sites. In order to investigate the interindividual variability of APE levels, a simple and quantitative assay was developed. Crude lymphocyte extracts were incubated with a depurinated or a control supercoiled plasmid substrate, and the accumulation of nicked circular plasmid forms was monitored by agarose gel electrophoresis. The detected incision activity was AP sites-dependent and EDTA-sensitive. The unit of enzymatic activity was defined as that amount able to incise 1 ng of plasmid DNA carrying 1 AP site/plasmid at 30 degrees C in 10 min. The assay was used to measure the APE activity in 10 healthy individuals ages 25-48 years. Values ranged from 0.38 to 0.94 units/ng protein, with a mean value of 0.62. The use of the assay for screening of people with DNA base excision repair (BER) defects is proposed.

Adult↗