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PubMed1992

Direct detection of circulating free radicals in the rat using electron spin resonance spectrometry.

We developed a new technique for directly observing in vivo free radical formation in the circulating blood of living rats using electron spin resonance (ESR) spectrometry without any labeling or trapping agents. It was found that a doublet peak spectrum was obtained following ferric citrate and ascorbic acid injection. The signals were confirmed in different ways to be due to ascorbic acid radicals. These results provide evidence to support the involvement of free radical intermediates in iron-ascorbic acid reactions, and further confirm the suggested mechanisms of both the adverse and protective effects of ascorbic acid in biological systems. Furthermore, this method of direct observation is a new application of ESR spectrometry to living animals.

Animals↗

PubMedDate not supplied

Direct detection of HBV preC mutants in heterogeneous viral populations by a modified DNA sequencing method.

A modified method for the direct sequencing of double-stranded DNA products of PCR amplification is described and has been applied to the analysis of hepatitis B virus (HBV) preC/C region in samples from persistently infected patients with chronic hepatitis. Data was obtained from both hepatitis B e antigen (HBeAg)-positive and -negative chronic carriers. A high prevalence of mixed viral populations (wild-type genomes and mutated sequences with a TAG stop codon in the distal preC region at position 1895-1897) was shown in the HBeAg-positive group; a homogeneous (either mutated or wild-type) viral population was detected in all but one of the long-term HBeAg-negative, untreated chronic carriers, thus suggesting that pre-core mutants can be rapidly generated and selected during the natural course of HBV infection.

Base Sequence↗

PubMed1987

[Diagnosis of ocular Chlamydia infections by direct detection].

Conjunctival smears of 75 patients with a presumptive diagnosis of oculogenital chlamydial infection were evaluated with the monoclonal antibody direct test (SyvaMerck and Orion Research). 69 isolates were correlated with McCoy cell cultures and serum IgG immunofluorescent tests. Sensitivity (100%) and specificity (56-76%) of the monoclonal antibody direct test was comparable to data from recently published studies on genital smears.

Antibodies, Monoclonal↗

PubMed1997

Cross-linking hybridization assay for direct detection of factor V Leiden mutation.

A nucleic acid photocross-linking technology was used in the development of a direct assay for factor V Leiden, a point mutation in the factor V gene (G1691A) that is the most common inherited risk factor for thrombosis. This cross-linking hybridization assay included two allele-specific capture probes and six signal-generating reporter probes; all were modified with a photoactivated cross-linking compound. By using two different capture probes complementary to a 16-base sequence at the factor V Leiden mutation site, but differing in the nucleotide opposite the mutation site (C vs T), wild-type and factor V Leiden alleles were differentiated in purified DNA specimens. The assay was also successfully applied to genomic DNA in leukocytes isolated from whole blood; the factor V status of 122 patients as determined by this method was in complete concordance with a standard PCR-based assay and clearly discriminated between healthy individuals and factor V Leiden heterozygotes.

Alleles↗

PubMed1991

Branched DNA amplification multimers for the sensitive, direct detection of human hepatitis viruses.

Branched oligonucleotides (bDNA) have been synthesized containing a unique primary segment and a set of identical secondary fragments covalently attached to the primary sequence through branch points. The primary sequence is designed to hybridize (directly or indirectly) to a target nucleic acid, such as hepatitis B virus (HBV) or hepatitis C virus (HCV) genomic DNA or RNA, respectively. The secondary fragments are used to direct the binding of multiple copies of a small oligonucleotide labelled with alkaline phosphatase. Assays for the presence of HBV and HCV based on the application of these branched amplification multimers have been devised. It is possible to detect as few as 1,000 hepatitis viral genomes directly.

Base Sequence↗

PubMed2006

Use of smear-positive samples to assess the PCR-based genotype MTBDR assay for rapid, direct detection of the Mycobacterium tuberculosis complex as well as its resistance to isoniazid and rifampin.

Isoniazid (INH) and rifampin (RIF) are two of the most important antituberculosis drugs, and resistance to both of these drugs can often result in treatment failure and fatal clinical outcome. Resistance to these two first-line drugs is most often attributed to mutations in the katG, inhA, and rpoB genes. Historically, the identification and testing of the susceptibility of Mycobacterium tuberculosis complex (MTBC) strains takes weeks to complete. Rapid detection of resistance using the PCR-based Genotype MTBDR assay (Hain Lifescience GmbH, Nehren, Germany) has the potential to significantly shorten the turnaround time from specimen receipt to reporting of results of susceptibility testing. Therefore, the aim of the present study was to determine (i) the sensitivity and accuracy of the Genotype MTBDR assay for the detection of MTBC strains and (ii) the ability of the assay to detect the presence of INH and RIF resistance-associated mutations in katG and rpoB from samples taken directly from smear-positive clinical specimens. The results were compared with those obtained with the reference BACTEC 460TB system combined with standard DNA sequencing analysis methods for katG, inhA, and rpoB. A total of 92 drug-resistant and 51 pansusceptible smear-positive specimens were included in the study. The Genotype MTBDR assay accurately and rapidly detected MTBC strains in 94.4% of the 143 specimens and showed a sensitivity of 94.4% for katG and 90.9% for rpoB when used directly on smear-positive specimens. The assay correctly identified INH resistance in 48 (84.2%) of the 57 specimens containing strains with resistance to high levels of INH (0.4 microg/ml) and RIF resistance in 25 (96.2%) of the 26 specimens containing RIF-resistant strains.

Antitubercular Agents↗

PubMed1989

Direct detection of beta-1,3-glucanase isozymes on polyacrylamide electrophoresis and isoelectrofocusing gels.

A procedure to assay isozymes of beta-1,3-glucanase directly on polyacrylamide gel electrophoresis (PAGE) and isoelectrofocusing (IEF) gels by using 2,3,5-triphenyltetrazolium chloride is described. The reagent reacts with reducing sugars released by beta-1,3-glucanases from the substrate laminarin. Acidic and neutral isozymes of beta-1,3-glucanase were detected and quantified on 17.5% native PAGE gels run with an anodic buffer system. A significant linear relationship (alpha = less than 0.01, R = 0.991) was observed between amounts of beta-1,3-glucanase loaded and intensity of bands stained with the reagent on native PAGE gels. A full isozyme pattern was obtained on 7.5% IEF gels with a pH range of 3.5-9.5. The IEF gels were heated in a microwave oven during the staining process to minimize diffusion.

Electrophoresis, Polyacrylamide Gel↗

PubMed1985

Direct detection of the human papovavirus BK in urine of bone marrow transplant recipients: comparison of DNA hybridization with ELISA.

Urine specimens from bone marrow transplant (BMT) recipients and from controls were directly tested for BK virus (BKV) DNA sequences by dot hybridization and for BKV antigen by a double-antibody indirect ELISA. A total of 158 specimens from 55 BMT patients (57 collected prior to or at the time of transplantation and 101 in the posttransplant period) and single urines from 125 control subjects were examined by both methods. A molecularly cloned, 32P-labelled BKV probe was hybridized with urine sediments that were spotted directly on nitrocellulose filters and denatured in situ. BKV DNA sequences were detected in 1 (1.8%) pretransplant and 22 (21.8%) posttransplant urines of BMT patients, and in none of control urines. In ELISA of urine supernatants, BKV antigen was detected in 1 (1.8%) pretransplant and 21 (20.8%) posttransplant urines of BMT patients and in 1 (0.8%) of the control urines. The results of the two tests correlated as follows: 16 urines were positive and 253 urines negative by both methods; seven specimens were positive by DNA hybridization only and seven were positive by ELISA alone. Virus excretion in urine was demonstrated in 20 (36.4%) patients by DNA hybridization, in 19 (34.5%) patients by ELISA, in 15 (27.3%) patients by both methods, and in 24 (44%) patients by at least one of the two tests.

Adolescent↗

PubMed2003

Direct detection of particles formed by laser ablation of matrices during matrix-assisted laser desorption/ionization.

We report the detection of nanoparticles formed by irradiating matrix-assisted laser desorption/ionization (MALDI) matrix samples. This is direct evidence for the ejection of large size aggregates in the MALDI process. Nanometer-size particles were generated via a tunable solid-state UV laser, irradiating a sample placed in a nitrogen atmosphere. Size distribution measurements were performed using a differential mobility analyzer and a condensation particle counter. Particles in the 10-1000 nm size range were detected. The dependence of the particle size distribution on the laser fluence, wavelength and matrix was investigated. The observed effects are discussed and related to the MALDI ablation dynamics and gas-phase processes.

Journal Article↗

PubMed1994

Direct detection of nucleic acid hybridization on the surface of a charge coupled device.

A method is described for the detection of DNA hybrids formed on a solid support, based upon the pairing of oligonucleotide chemistry and the technologies of electronic microdevice design. Surface matrices have been created in which oligonucleotide probes are covalently linked to a thin SiO2 film. 32P labeled target nucleic acid is then hybridized to this probe matrix under conditions of high stringency. The salient feature of the method is that to achieve the highest possible collection efficiency, the hybridization matrix is placed directly on the surface of a charge coupled device (CCD), which is used to detect 32P decay from hybridized target molecules (1, Eggers, M.D., Hogan, M.E., Reich, R.K., Lamture, J.B., Beattie, K.L., Hollis, M.A., Ehrilich, D.J., Kosicki, B.B., Shumaker, J.M., Varma, R.S., Burke, B.E., Murphy, A., and Rathman, D.D., (1993), Advances in DNA Sequencing Technology, Proc. SPIE, 1891, 13-26). Two implementations of the technology have been employed. The first involves direct attachment of the matrix to the surface of a CCD. The second involves attachment of the matrix to a disposible SiO2 coated chip, which is then placed face to face upon the CCD surface. As can be predicted from this favorable collection geometry and the known characteristics of a CCD, it is found that as measured by the time required to obtain equivalent signal to noise ratios, 32P detection speed by the direct CCD approach is at least 10 fold greater than can be obtained with a commercial gas phase array detector, and at least 100 fold greater than when X-ray film is used for 32P detection. Thus, it is shown that excellent quality hybridization signals can be obtained from a standard hybridization reaction, after only 1 second of CCD data acquisition.

Base Sequence↗

PubMed1987

Direct detection of free radicals in the reperfused rat heart using electron spin resonance spectroscopy.

The purpose of this study was to use a direct method, that of electron spin resonance (ESR) spectroscopy, to demonstrate that reperfusion after a period of ischemia results in a sudden increase in the production of free radicals in the myocardium. The isolated buffer-perfused rat heart was used with N-tert-butyl-alpha-phenylnitrone (PBN) as a spin-trapping agent. Samples of coronary effluent were taken and extracted into toluene for detection of radical adducts by ESR spectroscopy. After 15 minutes of total, global ischemia, aerobic reperfusion resulted in a sudden burst of radical formation that peaked at 4 minutes. When hearts were reperfused with anoxic buffer, no dramatic increase in radical production was observed. Subsequent reintroduction of oxygen, however, resulted in an immediate burst of radical production of a similar magnitude to that seen in the wholly aerobic reperfusion experiments. The ESR signals obtained (aN = 13.60 G, aH = 1.56 G) are consistent with the spin-trapping by PBN of either a carbon-centered species or an alkoxyl radical, both of which could be formed by secondary reactions of initially-formed oxygen radicals with membrane lipid components.

Animals↗

PubMed2005

A simple method for the direct detection of Salmonella and Escherichia coli O157:H7 from raw alfalfa sprouts and spent irrigation water using PCR.

The U.S. Food and Drug Administration recognizes that raw seed sprouts are an important cause of foodborne disease and is now recommending that either spent irrigation water or final product be screened for Salmonella and Escherichia coli O157:H7 as a means of assuring the safety of product intended for consumption. In an effort to streamline such testing efforts, a simple method to preconcentrate pathogens from sprouts and spent irrigation water was investigated to facilitate the direct (without prior cultural enrichment) detection of pathogens using the PCR technique. Alfalfa sprouts and spent irrigation water were seeded with Salmonella enterica serovar Typhimurium and E. coli O157:H7 at 10(-1) to 106 CFU/g or CFU/ml, respectively. Samples were blended (sprouts only) and then centrifuged at high speed to sediment the total bacterial population. The precipitate was processed for DNA isolation, PCR amplification, and amplicon confirmation by Southern hybridization. Mean pathogen recoveries after centrifugation ranged from 96 to 99% for both pathogens in both matrices. Using primers targeting the invA gene for Salmonella Typhimurium and the stx genes of E. coli O157:H7, it was possible to detect both pathogens in alfalfa sprouts at seeding concentrations as low as 10 CFU/g. PCR detection limits for both pathogens from spent irrigation water were 10(-1) CFU/ml, the equivalent of 100 CFU/liter of water. Because spent irrigation water is constitutionally simple, it is particularly well suited for bacterial concentration by simple centrifugation steps. In this study, progress was made toward development of a rapid, inexpensive, and sensitive method for the detection of sprout-associated pathogens that is relevant to current industrial practices and needs.

Colony Count, Microbial↗

PubMed1998

Direct detection of Mycobacterium tuberculosis complex and M. avium complex in tissue specimens from cattle through identification of specific rRNA sequences.

Mycobacterium Tuberculosis Direct test and Accuprobe M. avium Complex test, rely on recognition of specific rRNA sequences. The present investigation included sequentially a pre-evaluation study and a study on non-visible lesion tuberculin reactor cattle. As regards the first study, tests were performed on tissue samples from 14 reactors with tuberculous-like lesions and from as many lesion-free non-reactors, using culture findings as a reference. MTD and Accuprobe M. Avium Complex tests proved positive in 12 and 2 reactors respectively. Both tests proved negative in all non-reactors. Data consisted with culture findings. The aim of the second study was to verify the presence of mycobacteria in lymph node and tonsil homogenates from 32 non-visible lesion cattle. MTD and Accuprobe M. avium Complex test proved positive in 10 and 14 subjects respectively; no overlap was found. Our research demonstrates that low to minimal amounts of the main pathogenic mycobacteria can be reliably identified from cattle tissues by commercially available tests, which give simple, more rapid results than conventional techniques.

Animals↗

PubMed1995

Direct detection of Shiga-like toxin-producing Escherichia coli in ground beef using the polymerase chain reaction.

We recently reported the development and assessment of a technique for the detection of Shiga-like toxin-producing Escherichia coli (SLTEC) using the polymerase chain reaction (PCR) and a digoxigenin-11-dUTP-labelled DNA probe. This technique has now been adapted for the direct identification of SLTEC in ground beef. Ground beef homogenates were diluted 1000-fold to reduce the concentration of components which inhibit the thermostable polymerase. Assessment of four different ground beef samples using the PCR detection technique revealed that fat content was a major inhibitory component. As few as 30 SLTEC ml-1 of a ground beef homogenate were detected using the PCR technique, although it was necessary to enrich six of the samples for positive detection. These findings indicate that the PCR detection technique is suitable for the identification of SLTEC directly from contaminated ground beef without isolation of the bacterium or purification of its DNA.

Animals↗

PubMed1999

Poly(ethylene glycol) hydrogel-encapsulated fluorophore-enzyme conjugates for direct detection of organophosphorus neurotoxins.

A simple approach is described for preparing poly-(ethylene glycol) hydrogel materials with encapsulated seminapthofluorescein (SNAFL)-organophosphorus hydrolase enzyme conjugates. Direct determination of enzyme-catalyzed neurotoxin hydrolysis is provided by the self-referencing, pH-sensitive dye SNAFL-1, whose emission spectrum changes at lambda = 550 in response to pH. Using spectrofluorimetry and paraoxon as a model organophosphate, paraoxon concentrations as low as 8 x 10(-7) M could be readily detected. On the basis of the signal-to-noise ratio, a detection limit of 16 nM was determined. The materials demonstrated high stability against enzyme-denaturing, leaching, and photobleaching when stored under ambient conditions.

Aryldialkylphosphatase↗

PubMed1995

Direct detection of verotoxin-producing Escherichia coli in stool samples by PCR.

A method for the rapid detection of verotoxin-producing Escherichia coli in stool samples by PCR was evaluated. Verotoxin-1 and verotoxin-2 genes in DNA extracted directly from stool samples were amplified with oligonucleotide primers. Stools spiked with control organisms, E. coli C600 (H19B) (verotoxin-1) or E. coli C600 (933W) (verotoxin-2), demonstrated that verotoxin-1-containing organisms could be detected at 10(2) CFU per 0.1 g of stool and verotoxin-2-containing organisms could be detected at 10(7) CFU per 0.1 g of stool. Testing of stool samples from patients with diarrhea showed a high concordance between PCR positivity and the presence of verotoxin-producing E. coli, determined by isolation of serotype O157:H7 on sorbitol-MacConkey medium (34 of 35 stool samples) or by colony blots with gene probes (19 of 21 stool samples). Conversely, only 1 of 20 (5.0%) stool samples that were O157:H7 culture negative and colony blot negative and that contained free verotoxin only was positive by PCR. As well, only 4 of 145 (2.8%) stool samples that were negative for serotype O157:H7 or free verotoxin were PCR positive. PCR of DNA extracted directly from stool samples provides a rapid method for the detection of stool samples containing verotoxin-producing E. coli compared with colony blot testing.

Animals↗

PubMed2003

The direct detection and identification of staining dyes from security inks in the presence of other colorants, on currency and fabrics, by laser desorption mass spectrometry.

Laser desorption mass spectrometry (LDMS) is useful for the direct desorption and MS analysis of dyes off materials such as paper. Here it is shown that staining dyes, produced by currency degradation devices, such as those used by financial institutions or armored transport companies, can be detected by LDMS. These staining dye packs are commonly used in bank security programs to deter theft or unauthorized removal of currency from teller stations or from ATM cash cassettes. Working automatically, these technologies release a security dye to degrade the surface of the notes and possibly mark the assailant involved in the attack. These dyes can be characterized and identified directly from paper currency, and from fabrics, and uniquely identified in the presence of other dyes that are used in the printing and dying of such materials, by LDMS. In these experiments, no extraction step is required. A pulsed UV laser directly irradiates a paper or fabric sample--colorants are desorbed, ionized and detected using time-of-flight MS. Results shown here suggest that dyes such as Basic Red 1:1 and Basic Violet 11:1 are used in such devices.

Journal Article↗

PubMed1991

Direct detection of free radical generation in an in vivo model of acute lung injury.

Electron spin resonance (ESR) spectroscopy has been used to provide direct evidence that free radical production occurs in an in vivo model of acute lung injury. Two experimental groups of rabbits were given the spin trap alpha-phenyl N-tert.-butyl nitrone (PBN), together with endotoxin in the test group, and saline in the control group. Both groups were subsequently briefly ventilated with air containing cigarette smoke. Plasma samples from the endotoxin pretreated group showed a sudden burst of radical formation, detected as PBN spin adduct, which peaked in the first ten minutes after smoke exposure. No signals were detected in the control group. Permeability of the alveolar capillary barrier of the lung, measured by the clearance of 99mTc-DTPA, demonstrated significantly greater damage following smoke in the endotoxin primed animals than in the controls. Temporal studies suggest that this increase in permeability occurred after a burst of radical production. These studies provide supportive evidence for the hypothesis that endotoxin promotes the accumulation of a population of primed white cells within the lung, which when triggered by cigarette smoke, are able to generate a burst of free radicals which produce tissue damage and acute lung injury.

Animals↗