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Direct EPR detection of the carbonate radical anion produced from peroxynitrite and carbon dioxide.

The biological effects of peroxynitrite have been recently considered to be largely dependent on its reaction with carbon dioxide, which is present in high concentrations in intra- and extracellular compartments. Peroxynitrite anion (ONOO-) reacts rapidly with carbon dioxide, forming an adduct, nitrosoperoxocarboxylate (ONOOCO2-), whose decomposition has been proposed to produce reactive intermediates such as the carbonate radical (CO-3). Here, by the use of rapid mixing continuous flow electron paramagnetic resonance (EPR), we directly detected the carbonate radical in flow mixtures of peroxynitrite with bicarbonate-carbon dioxide over the pH range of 6-9. The radical was unambiguously identified by its EPR parameters (g = 2.0113; line width = 5.5 G) and by experiments with bicarbonate labeled with 13C. In this case, the singlet EPR signal obtained with 12C bicarbonate splits into the expected doublet because of 13C (a(13C)= 11.7 G). The singlet spectrum of the unlabeled radical was invariant between pH 6 and 9, confirming that in this pH range the detected radical is the carbonate radical anion (CO-3). Importantly, in addition to contributing to the understanding of nitrosoperoxocarboxylate decomposition pathways, this is the first report unambiguously demonstrating the formation of the carbonate radical anion at physiological pHs by direct EPR spectroscopy.

Carbon Dioxide↗

Measurement of 15N relaxation in deuterated amide groups in proteins using direct nitrogen detection.

15N chemical shielding tensors contain useful structural information, and their knowledge is essential for accurate analysis of protein backbone dynamics. The anisotropic component (CSA) of 15N chemical shielding can be obtained from 15N relaxation measurements in solution. However, the predominant contribution to nitrogen relaxation from 15N-(1)H dipolar coupling in amide groups limits the sensitivity of these measurements to the actual CSA values. Here we present nitrogen-detected NMR experiments for measuring 15N relaxation in deuterated amide groups in proteins, where the dipolar contribution to 15N relaxation is significantly reduced by the deuteration. Under these conditions nitrogen spin relaxation becomes a sensitive probe for variations in 15N chemical shielding tensors. Using the nitrogen direct-detection experiments we measured the rates of longitudinal and transverse 15N relaxation for backbone amides in protein G in D(2)O at 11.7 T. The measured relaxation rates are validated by comparing the overall rotational diffusion tensor obtained from these data with that from the conventional 15N relaxation measurements in H(2)O. This analysis revealed a 17-24 degree angle between the NH-bond and the unique axis of the 15N chemical shielding tensor.

Amides↗

Characteristics of humic substances in the Kuji River waters as determined by high-performance size exclusion chromatography with fluorescence detection.

Direct measurement by high-performance size exclusion chromatography with fluorescence detection was applied to the characterization of humic substances in river waters from the Kuji River system, which runs through forest hills and an agricultural plain in Japan. The monitoring wavelength of excitation 320 nm and emission 430 nm corresponds to the fluorescence maxima for aquatic fulvic acid. Chromatograms of the river waters showed four peaks; each peak position was in good agreement among these samples. Peak height ratios for the samples from the upstream Kuji River and its tributaries were different from those of the midstream and downstream sections of the Kuji River, which may reflect differences in the characteristics of humic substances and other organic materials supplied from soil to river.

Chromatography, Gel↗

Direct genotypic detection of Mycobacterium tuberculosis rifampin resistance in clinical specimens by using single-tube heminested PCR.

Recent analysis of the gene encoding the beta subunit of Mycobacterium tuberculosis RNA polymerase (rpoB) has demonstrated a small region that harbors the mutations most frequently associated with rifampin resistance. Earlier reports have described a high degree of sequence conservation of rpoB among mycobacteria other than M. tuberculosis and other GC-rich bacteria that can lead to false-positive amplification when applied directly to clinical specimens. We developed reagents for PCR amplification that are based on signature nucleotides discovered by comparative sequence analysis of the rpoB genes of organisms phylogenetically related to M. tuberculosis. The specificities of the reagents were challenged with 20 isolates of multiple-drug-resistant M. tuberculosis and more than 20 species of mycobacteria other than M. tuberculosis and other GC-rich organisms. A single-tube heminested PCR protocol was devised to obtain sensitivity equal to those of an IS6110-based PCR assay and culture in spiked sputum experiments. The assay correctly identified 21 of 24 (87.5%) culture-positive specimens, 13 of which were acid-fast smear-negative, in a panel of 51 clinical specimens. Three specimens that were false-positive initially were negative upon repeat testing when the assay was modified to eliminate the potential for aerosol carryover of the first-round amplification product during the open-tube addition of the second set of reaction reagents. This assay is the most sensitive and specific test to date for the direct detection of M. tuberculosis rpoB in clinical specimens. This rapid PCR-based assay can be used for the simultaneous identification of M. tuberculosis and its rifampin susceptibility genotype.

Amino Acid Sequence↗

Production of Monoclonal Antibodies against the Major Capsid Protein of the Lactococcus Bacteriophage ul36 and Development of an Enzyme-Linked Immunosorbent Assay for Direct Phage Detection in Whey and Milk.

The only major structural protein (35 kDa) of the lactococcal small isometric-headed bacteriophage ul36, a member of the P335 species, was isolated from a preparative sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis. Monoclonal antibodies (MAbs) were raised against the denatured 35-kDa protein. Six MAbs were selected and characterized. Western blots (immunoblots) showed that all MAbs recognized the 35 kDa but also a 45 kDa that is in lower concentration in the phage structure. Binding inhibition assays identified five families of MAbs that recognized nonoverlapping epitopes of the 35- and 45-kDa proteins. Immunoelectron microscopy showed that these two proteins are localized within the phage head, therefore indicating that the 35 kDa is a major capsid protein of ul36 and that the 45 kDa is a minor capsid protein. With two MAbs, a sandwich enzyme-linked immunosorbent assay (ELISA) was developed for direct detection of lactococcal phages in whey and milk samples. Whey and milk components, however, interfered with the conduct of the assay. Partial denaturation of milk samples by heat treatment in the presence of SDS and beta-mercaptoethanol removed the masking effect and increased the sensitivity of the assay by 100-fold. With the method used here, 10 PFU/ml were detected by the ELISA within 2 h without any steps to enrich or isolate bacteriophages.

Journal Article↗

Sensitive detection of Mycoplasma pulmonis by using the polymerase chain reaction.

Detection of Mycoplasma pulmonis was examined by using the polymerase chain reaction (PCR) for amplifying a specific DNA sequence. In gel electrophoresis which was conducted to detect the amplified products, only 1 pg of M. pulmonis DNA could be detected following 30 cycles of amplification, while no amplified product was detected even from 1 microgram of M. arthritidis or M. neurolyticum DNA. Furthermore, 10 colony-forming units of M. pulmonis could be detected by direct amplification from the mycoplasma suspension. These results suggest the usefulness of the PCR as a highly sensitive, specific, and rapid method for direct detection of M. pulmonis.

Base Sequence↗

Separation and direct UV detection of lanthanides complexed with pyridine-2-carboxylic acid by capillary electrophoresis.

Separation and detection of lanthanides by capillary zone electrophoresis in the presence of pyridine-2-carboxylic acid (picolinic acid) as UV-absorbing complexing agent were investigated. The resolution of partially complexed positively charged complexes is improved by using two buffer ligands competing with picolinic acid for metal ions. When hydroxyisobutyric acid (HIBA) and formic acid are used together as competing ligands, this provides complete separation of all 14 lanthanides with good peak shapes. An on-column separation of 14 lanthanides was achieved in only 9 min using 0.8 mmol/l picolinic acid, 10 mmol/l HIBA and 25 mmol/l formic acid at pH 4.7. Determination of lanthanide complexes was performed by direct detection at 210 nm. Detection limits (signal-to-noise ratio=3) are ca. 0.53-0.96 microg/ml.

Electrophoresis, Capillary↗

Luminance contrast and motion detection.

Direction discrimination was used to measure the minimum and maximum displacement for the detection of motion (Dmin and Dmax) for abruptly displaced sinewave gratings. This was measured for a range of contrast levels from 2 to 32 times the detection threshold for a range of spatially narrow band stimuli. Performance for Dmin (but not Dmax) was found to deteriorate with an increase in contrast, with the most sensitive values for Dmin obtained at contrast levels of 4-8 times detection threshold. This dependence on luminance contrast is thought to be due to the physiology of the visual system, rather than the physics of the stimulus.

Contrast Sensitivity↗

Detection of Chlamydia trachomatis by direct fluorescent antibody staining. Results of the College of American Pathologists Proficiency Testing Program, 1986-1992.

Since 1986 the College of American Pathologists has provided a proficiency testing program for laboratories that use the direct fluorescent antibody test for direct detection of Chlamydia trachomatis in clinical specimens. The number of survey participants increased from about 200 in 1986 to about 800 in 1992, and in all years the majority used reagents produced by Syva Co (Palo Alto, Calif), although the percentage decreased from 82% in 1986 to 68% in 1992. Performance on positive specimens varied based on specimen fixation method, number of elementary bodies present, serotype, and specific product used, and declined when the specimen was fixed with acetone prior to shipping or contained fewer than 50 elementary bodies, particularly when the elementary bodies were of serotype L2. Performance with negative specimens was also variable, with 79% to 96% of all participants, and over 90% since 1991, responding correctly. In the last 1992 survey, an ungraded specimen (a five-well slide containing latex beads incorporated with fluorescein isothiocyanate) and a questionnaire were included to assess the potential influence of laboratory operations on performance. Responses to the questionnaire and the ungraded specimen suggested that the level of experience of testing personnel affected performance. A test for trend in error rate across the number of years that a laboratory had offered the Chlamydia direct fluorescent antibody test indicated that error rate declined as degree of experience with the test increased.

Chlamydia trachomatis↗

Microfluidic genetic analysis with an integrated a-Si:H detector.

We have developed an integrated hydrogenated amorphous silicon (a-Si:H) fluorescence detector for microfluidic genetic analysis. It consists of a half-ball lens, a ZnS/YF3 multilayer optical interference filter with a pinhole, and an annular a-Si:H PIN photodiode allowing the laser excitation to pass up through the central aperture in the photodiode and the filter. Microfluidic separations of multiplex PCR products generated from methicillin-resistant/sensitive Staphylococcus aureus (MRSA/MSSA) DNA on microfluidic capillary electrophoresis (CE) devices are successfully detected with the integrated detector. Similarly, multiplex PCR amplicons from the kanamycin resistant and K12 serotype-specific genes of E. coli cells are detected. The direct detection of multiplex PCR amplicons indicates that the fluorescence detector can be successfully coupled with current microfluidic PCR-CE platforms. This work establishes that the integrated a-Si:H detector provides relevant limits of detection for point-of-care genetic and pathogen analysis with microfluidic devices.

DNA, Bacterial↗

RAS enzyme-linked immunoblot assay discriminates p21 species: a technique to dissect gene family expression.

The members of the RAS gene family of protooncogenes are of implied biological significance in oncogenesis. The precise role of these genes is unclear. One difficulty has been the inability to discriminate the individual p21 protein products of various ras genes in cell lines, de novo human tumors, and related normal tissues. In this report, specific proteins of the human c-Ha-ras-1, c-Ki-ras-2, and c-N-ras genes have been detected and discriminated by the differential use of various antisera recognizing these p21s. This enzyme-linked immunoblot assay utilizes a double antibody system in which monoclonal antibodies are initially used to immunoprecipitate the p21ras proteins. Immunoprecipitates are then subjected to one-dimensional Western blot analysis utilizing other antibodies raised against p21s, coupled with nonradiolabeled enzyme-linked colorimetric detection. By direct detection, the specific products of the three human ras genes can be discriminated. In addition, we describe the generation and characterization of a new anti-p21c-N-ras-specific antibody. The simultaneous expression into protein of multiple ras genes is unequivocally demonstrated in both homogeneous cell lines and heterogeneous human tissues. This new technique is also applicable for discrimination of the protein products of other gene families.

Animals↗

Prostate-specific antigen immunosensing based on mixed self-assembled monolayers, camel antibodies and colloidal gold enhanced sandwich assays.

Prostate-specific antigen (PSA) is a valuable biomarker for prostate cancer screening. We developed a PSA immunoassay on a commercially available surface plasmon resonance biosensor. Our PSA receptor molecule consists of a single domain antigen-binding fragment, cAbPSA-N7, derived from dromedary heavy-chain antibodies and identified after phage display. It binds PSA with a high k(on) value of 1.9x10(6) M-1 s-1, and was covalently immobilised on a gold substrate via a mixed self-assembled monolayer (SAM) of alkanethiols by using carbodiimide-coupling chemistry in 10mM acetate buffer pH 5.5 to obtain an optimal pre-concentration. The best performing and optimised mixed SAM consisted of (10%) 16-mercapto-1-hexadecanoic acid (16-MHA) for covalent cAbPSA-N7 immobilisation and (90%) 11-mercapto-1-undecanol (11-MUOH) to minimise non-specific adsorption of the analyte. In this way, two advantages are incorporated in a single coupling layer. Up to 28 fmol/mm2 of cAbPSA-N7 could be immobilised and 30% of its binding sites participate actively in PSA interaction. In addition, the optimised layer showed also optimal performance to assess physiological samples. Although PSA concentrations as low as 10 ng/ml could be detected directly, this detection limit could be enhanced to PSA levels in the sub ng/ml range by introducing a sandwich assay involving a biotinylated secondary antibody and streptavidin modified gold nanoparticles. This approach realizes the PSA detection at clinical relevant concentrations.

Adsorption↗

Eye contact does not facilitate detection in children with autism.

Eye contact is crucial in achieving social communication. Deviant patterns of eye contact behavior are found in individuals with autism, who suffer from severe social and communicative deficits. This study used a visual oddball paradigm to investigate whether children with high functioning autism have difficulty in detecting mutual gaze under experimental conditions. The results revealed that children with autism were no better at detecting direct gaze than at detecting averted gaze, which is unlike normal children. This suggests that whereas typically developing children have the ability to detect direct gaze, children with autism do not. This might result in altered eye-contact behavior, which hampers subsequent development of social and communicative skills.

Adolescent↗

Genetics of life history in Drosophila melanogaster. II. Exploratory selection experiments.

two types of small-scale selection experiments were performed. (1) Artificial selection experiments were performed on age-specific female fecundity. Selection for early fecundity over three generations produced a statistically detectable direct response. There was no detectable indirect response in other life-history characters. Selection for late fecundity over three generations did not produce any detectable direct response. Indirect responses were detected: early egg-laying decreased and longevity increased. (2) Natural selection for late-age fitness components increased late fecundity, female longevity, and the duration of female reproduction, while early fecundity and mean egg-laying rate decreased.

Aging↗

Candidate gene promoter polymorphisms and antibody response kinetics in chickens: interferon-gamma, interleukin-2, and immunoglobulin light chain.

An F2 population was produced from mating G0 highly inbred (>99%) males of two MHC-congenic Fayoumi lines with G-B1 Leghorn hens. The F2 population was essentially a full-sibship with the F1 sire line reflecting MHC effect. Adult F2 hens (n = 158) were injected twice with SRBC and whole fixed Brucella abortus (BA). Agglutinating antibody titer at 7 d after primary immunization and mean titer of the final three samples (Days 18, 32, and 63 after the second immunization) were used as parameters for primary and equilibrium phases, respectively. Secondary phase parameters of minimum (Ymin), maximum titers (Ymax) and time needed to achieve minimum (Tmin) and maximum (Tmax) titers were estimated from seven postsecondary titers with a nonlinear regression model. Three candidate genes, interferon-gamma (IFN-gamma), interleukin-2 (IL-2), and immunoglobulin G light chain (IgL) were studied. Primers for the promoter regions were designed from EMBL chicken genomic sequences. Polymorphisms between parental lines were detected by direct sequencing. Polymerase chain reaction-restriction fragment length polymorphism methods were then developed to directly detect the polymorphism. There were significant main effects (P < 0.05, general linear model analysis) of IFN-gamma polymorphism on Ymax of BA antibody and interaction of IFN-gamma by IgL on primary antibody response to SRBC and BA, and on Tmin and Ymin of antibody response to SRBC in F2 offspring of M5.1 grandsires. There were significant main effects of IFN-gamma polymorphism on Tmax of BA and interaction of IFN-gamma by IL-2 on Ymin to SRBC in F2 offspring of M15.2 grandsires. The results suggest that IFN-gamma genes play an important role in chicken primary and secondary antibody response to SRBC and BA antigens, and there exists interaction among genes for antibody production.

Agglutination Tests↗

Hemagglutination-inhibition method and immunofluorescence staining with Venezuelan equine encephalomyelitis virus.

Hemagglutination and fluorescent antibody (FA) are compared for the direct detection of virus devoid of host cells. A determination was made of the minimal number of tissue plaque-forming units of Venezuelan equine encephalomyelitis virus that could be detected by the hemagglutination technique. Similar concentrations of the virus in bovine albumin borate saline, Brain Heart Infusion broth (Difco), and demineralized water were tested by the FA technique. Somewhat higher concentrations of the virus in bovine albumin borate saline were used in the hemagglutination-inhibition test. The quantitative hemagglutination procedure employed for these studies was carried out at 37 C for 75 min with variations in concentration of goose red cells. As a result of lowering the red cell concentration, smaller concentrations of virus were detected. The direct FA staining procedure applied to slide preparations containing known numbers of tissue culture plaque-forming units of virus was negative. Adsorbed viral antigen on agglutinated goose erythrocytes was visualized by direct and indirect FA techniques.

Culture Media↗

Evaluation of a method for rapid detection of penicillinase-producing Neisseria gonorrhoeae in urethral exudates.

A substrate, pyridine-2-azo-p-dimethylaniline cephalosporin (PADAC; Diagnostic Pasteur, Marnes-La-Coquette, France), for detection of penicillinase-producing Neisseria gonorrhoeae (PPNG) on isolated colonies grown on agar was compared with the nitrocefin reference test (Cefinase; Biomerieux, Marcy l'Etoile, France). The PADAC test was also used to detect PPNG directly on urethral exudates. All 38 PPNG-containing and 29 of 30 PPNG-negative urethral pus isolates gave results in agreement with those obtained on cultured isolates. We conclude that direct detection of PPNG in urethral exudates from males is simple, rapid, reliable, and sensitive.

Cephalosporins↗

[Determination of lead in grape wine by graphite furnace atomic absorption spectrometry with ammonium dihydric phosphate as modifier].

Ammonium dihydric phosphate (NH4H2PO4), palladium chloride, nickelous nitrate and magnesium nitrate were used as modifiers respectively, to directly detect lead in grape wine with graphite furnace atomic absorption spectrometry(GFAAS). The results showed that NH4H2PO4 might be the best modifier. It was found that the organic matter in grape wine interfere with the determination. To remove the interference and detect lead directly with GFAAS, not only did samples need to be diluted with 4 to 10 times sample volumes of de-ionized water, but also the standard addition method was used. The method had good precision and accuracy when concentration of lead was above 10 micrograms.L-1, the relative standard deviations of lead were between -5.4% and 6.2%.

Food Contamination↗