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At least 847 records · Page 47Linked to original sources
PubMed2004

Direct electrochemiluminescence detection of oxidized DNA in ultrathin films containing [Os(bpy)2(PVP)10]2+.

Direct electrochemiluminescence (ECL) involving oxidized DNA was demonstrated in ultrathin films of cationic polymer [Os(bpy)2(PVP)10]2+ [PVP = poly(vinyl pyridine)] assembled layer-by-layer with DNA or oligonucleotides. Electrochemically oxidized Os(II) sites generated ECL from films containing oxo-guanines on DNA formed by chemical oxidation using Fenton reagent. Films combining DNA, [Ru(bpy)2(PVP)10]2+, and [Os(bpy)2(PVP)10]2+ had Os(II) sites that produced ECL specific for oxidized DNA, and Ru(II) sites gave ECL from reaction with oxo-adenines, chemically damaged DNA, and possibly from cleaved DNA strands.

Biosensing Techniques↗
PubMed1991

Detection and direct sequencing of hepatitis B virus genome by DNA amplification method.

Hepatitis B virus (HBV) DNA was detected with amplification by the polymerase chain reaction method. Cloned HBV DNA equivalent to one virus genome (3 x 10(-6) pg) was detectable by ethidium bromide staining after 50 cycles of polymerase chain reaction. By applying this method, presence of HBV DNA was studied in 23 hepatitis B surface antigen (HBsAg)-positive and 11 HBsAg-negative sera from patients with chronic liver disease. Hepatitis B virus DNA was positive in 8 of 8 hepatitis B e antigen (HBeAg)-positive, in 2 of 2 HBeAg- and anti-HBe-negative, and in 12 of 13 anti-HBe-positive sera. Hepatitis B virus DNA was undetectable in all HBsAg-negative sera even with amplification. To confirm specificity, the amplified product was directly sequenced. Sequences around 122nd and 160th codon of HBs gene, which determines subtypes d/y and w/r, respectively, were analyzed. The results were compatible with recent reports regarding the relation between HBV subtypes and HBV DNA sequence at those codons. Hepatitis B virus DNA could be detected at the level of one virion by gene amplification method, and its sequence could be determined by direct sequencing in a few days.

Base Sequence↗
PubMed1996

Polymerase chain reaction-mediated site-directed mutagenesis detection of Z and S alpha-1-antitrypsin alleles in family members.

Alpha-1-antitrypsin (A1AT) deficiency is an autosomal hereditary disorder with a reduction in serum A1AT levels. In a large family, we used a polymerase chain reaction (PCR)-mediated, site-directed mutagenesis assay to detect the two most common A1AT deficient variants, Z and S. By coamplification, using primers for both the Z and S mutations, we were able to detect heterozygous and homozygous genotypes for both mutations in a single reaction. We compared our results with phenotype studies obtained by standard immunofixation and isoelectric focusing techniques at two reference laboratories. Whereas PCR and isoelectric focusing agreed completely, there were five discrepancies in the results obtained by the immunofixation procedure. The reference laboratory that provided these discrepant results later informed us of a quality control problem that accounted for their error. The family study included 12 individuals representing three generations. Two individuals were MM homozygotes, three were MZ heterozygotes, four were MS heterozygotes, and three were SZ heterozygotes. A thirteenth family member was diagnosed as a ZZ homozygote at another institution. We have shown that this PCR coamplification technique provides accurate information about the M, S, and Z alleles that is at least as useful as current reference laboratory methodologies.

Alleles↗
PubMed1996

Application of molecular biology-based methods to the diagnosis of infectious diseases.

The basis for effective treatment and cure of a patient is the rapid diagnosis of the disease and its causative agent, which is founded on the analysis of the clinical symptoms coupled with laboratory tests. As we approach the 21st century, clinicians are becoming increasingly able to diagnose and treat diseases at the molecular level. The rapid development of new methods and techniques in the area of molecular biology has gained new insights into the genetic and structural features of a considerable number of human pathogens. These results obtained by intensive basic research are currently leading to improved diagnostic procedures. Basically, there are four different possibilities for laboratory diagnosis of infections: 1. direct detection of the pathogens (e.g., microscopy and/or culture), 2. detection of protein components of the pathogens with the help of specific antibodies (e.g., antigen capture ELISA) 3. IgA-, IgM- and IgG-specific detection of antibodies directed against a given pathogen and changes in their corresponding titer, and as the most sensitive method, 4. specific detection of nucleic acids (e.g., PCR) of the pathogens. Here, the human immunodeficiency virus (HIV) and Mycobacterium tuberculosis are serving as examples to review the recent developments as well as the future perspectives in molecular biology-based laboratory diagnosis.

Bacterial Infections↗
PubMed2006

High-speed interferometric detection of label-free immunoassays on the biological compact disc.

BACKGROUND: We describe a direct-detection immunoassay that uses high-speed optical interferometry on a biological compact disc (BioCD). METHODS: We fabricated phase-contrast BioCDs from 100-mm diameter 1.1-mm thick borosilicate glass disks coated with a 10-layer dielectric stack of Ta2O5/SiO2 that serves as a mirror with a center wavelength at 635 nm. The final layer is a lambda/4 layer of SiO2 onto which protein patterns are immobilized through several different chemical approaches. Protein on the disc is scanned by a focused laser spot as the disc spins. Interaction of the light with the protein provides both a phase-modulated signal and a local reference that are combined interferometrically to convert phase into intensity. A periodic pattern of protein on the spinning disc produces an intensity modulation as a function of time that is proportional to the surface-bound mass. The binding of antigen or antibodies is detected directly, without labels, by a change in the interferometric intensity. The technique is demonstrated with a reverse assay of immobilized rabbit and mouse IgG antigen incubated against anti-IgG antibody in a casein buffer. RESULTS: The signal increased with increased concentration of analyte. The current embodiment detected a concentration of 100 ng/L when averaged over approximately 3000 100-micron-diameter protein spots. CONCLUSIONS: High-speed interferometric detection of label-free protein assays on a rapidly spinning BioCD is a high-sensitivity approach that is amenable to scaling up to many analytes.

Animals↗
PubMed2001

The role of motility in the in vitro attachment of Pseudomonas putida PaW8 to wheat roots.

The attachment of motile and non-motile strains of Pseudomonas putida PaW8 to sterile wheat roots was assessed in both non-competitive and intra-specific competitive assays. The motile strain showed significantly greater attachment to wheat roots than non-motile strains in phosphate buffer. Overall, the motile strain attached better than the non-motile strain at 10(6), 10(7) and 10(8) cfu ml(-1) in competitive assays and at 10(6) and 10(7) cfu ml(-1) in non-competitive assays. When attachment was studied in Luria broth no significant difference between motile and non-motile strains was detected. P. putida PaW8 cells marked with the luxAB genes were used to compare direct detection of attached cells by luminometry with indirect detection by dilution plate counts following extraction from root material. Although direct detection permitted a rapid assessment (60 s) of attachment to surfaces, dilution plate counts provided a more sensitive method for quantification of bacteria. The detection limits were approximately 10 cfu root(-1) using dilution plate counts compared with 1000 cfu root(-1) using luminometry. All results highlighted the importance of motility for the attachment of P. putida to plant roots in simple model systems. To take this work further, studies to assess the role of motility using complex non-sterile systems are needed.

Journal Article↗
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↗
PubMed2003

Nitric oxide imaging in living neuronal tissues using fluorescent probes.

Nitric oxide (NO) is a major modulator of neural functions. Since NO is a gaseous molecule with very short half-life, the spatial distribution of NO and its relationship to neuronal activity are difficult to resolve. Non-invasive and direct visualization of NO in neuronal tissues had been hampered by the lack of a suitable method to identify NO directly. A fluorescent indicator, which directly detects NO under physiological conditions, would be advantageous. Several indicators for direct detection of NO have been developed, which react with NO by forming a fluorescent complex. However, some of these dyes have cytotoxic properties or have been found to be rather unspecific under certain conditions. Fortunately, some of the indicators, which change their fluorescent pattern in the presence of NO, appear to be promising for the visualization of NO. Since little is known about the spatial spread and the temporal aspects of NO release after a specific stimulus, the use of the specific and non-toxic fluorescent NO indicators could provide a potentially powerful tool to study these aspects of NO release in neuronal tissues in vitro and in vivo. Such measurements, especially in combination with electrophysiological recordings, would greatly further NO research. In addition, based on their fluorescent pattern, these NO-sensitive dyes can be distinguished from the calcium-sensitive dye Fura-2, which allows NO-imaging together with calcium-imaging. This article summarizes recent advances and current trends in the visualization of NO in living neuronal tissues.

Animals↗
PubMed2003

Direct PCR detection of Escherichia coli O157:H7.

AIMS: This paper reports a simple, rapid approach for the detection of Shiga toxin (Stx)-producing Escherichia coli (STEC). METHODS AND RESULTS: Direct PCR (DPCR) obviates the need for the recovery of cells from the sample or DNA extraction prior to PCR. Primers specific for Stx-encoding genes stx1 and stx2 were used in DPCR for the detection of E. coli O157:H7 added to environmental water samples and milk. CONCLUSIONS: PCR reactions containing one cell yielded a DPCR product. SIGNIFICANCE AND IMPACT OF THE STUDY: This should provide an improved method to assess contamination of environmental and other samples by STEC and other pathogens.

Animals↗
PubMed2004

Ultrasensitive detection of DNA sequences in solution by specific enzymatic labeling.

We present a newly developed technique for the direct detection of very low concentrations of specific nucleic acid sequences in homogeneous solution based on a polymerase extension reaction. This method consists of synthesizing a highly fluorescent nucleic acid reporter molecule using a sequence of the target as a template. Synthesis of the reporter molecule is accomplished by hybridizing a short complementary oligonucleotide primer to the target and extending the reporter using a polymerase and free nucleotides. One of these nucleotides is partially labeled with a fluorophore. The reaction sample is then flowed through the capillary cell of a single molecule detector. Detection of the reporter signifies the presence of the target being sought. Under carefully selected conditions, fluorescence from the reporter molecule is much stronger than that of the free nucleotide background over the detection time. We have derived practical equations that allow us to determine an optimal range of values for the relative reporter and free-nucleotide concentrations. This method allows for the rapid, direct detection of individual targets at femtomolar concentrations without the use of an amplification procedure, such as the polymerase chain reaction.

Affinity Labels↗
PubMed2006

Improved resolution in two-dimensional 1H NMR spectra of peptides by band-selective, homonuclear decoupling during both the evolution and acquisition periods: application to characterization of the binding of peptides by heparin.

Two-dimensional 1H NMR experiments that achieve band-selective, homonuclear decoupling in both the indirectly detected F1 and directly detected F2 dimensions were used to assign the highly overlapped 1H NMR spectrum of the peptide Ac-SRGKARVRAKVKDQTK-NH2, both free in solution and bound to heparin. Band-selective, homonuclear decoupling during the evolution period was achieved using a double pulsed field gradient spin-echo (DPFGSE) with semi-selective shaped pulses; band-selective, homonuclear decoupling during the acquisition period was achieved by time-shared semi-selective shaped pulse decoupling. Regular TOCSY, ROESY and NOESY spectra and TOCSY, ROESY and NOESY spectra measured with band-selective, homonuclear decoupling in the evolution (F1) dimension (BASHD-TOCSY, ROESY and NOESY spectra) and with band-selective, homonuclear decoupling in both the F1 and F2 dimensions (D-(or Double)-BASHD-TOCSY, ROESY and NOESY spectra) are reported and compared for the peptide and its heparin complex. Complete assignment of the 1H-NMR spectra of the free and heparin-complexed peptide was achieved with the high resolution of the D-BASHD-TOCSY, ROESY and NOESY spectra. Characterization of the heparin-complexed peptide is of interest because of the ability of the peptide to neutralize the anticoagulant activity of heparin.

Amino Acid Sequence↗
PubMed1997

Quantitative digital analysis of diffuse and concentrated nuclear distributions of nascent transcripts, SC35 and poly(A).

Digital imaging microscopy was used to analyze the spatial distribution and levels of newly synthesized RNA in relation to steady-state poly(A) RNA and to the splicing factor SC35. Transcription was monitored over time after microinjection of BrUTP and was detected using antibodies. Poly(A) RNA was detected with probes directly conjugated to fluorochromes, allowing direct detection of the hybrids. Objective methods were used to determine genuine signal. A defined threshold level to separate signal from noise was established for each nucleus. The nucleolus was used to determine poly(A) and SC35 background and the juxtanuclear cytoplasm was used for the BrUTP background. The remaining signal was segmented into high (concentrated) and low (diffuse) levels. Surprisingly, for all probes examined, most of the signal was not in concentrated areas, but rather was diffusely spread throughout the nucleoplasm. A minority (20-30%) of the SC35 signal was in concentrated areas ("speckles") and the rest was dispersed throughout the nucleoplasm. In addition, the concentrated areas had a mean intensity only twice the average. The amount and significance of the colocalization of the diffuse, or concentrated, areas of SC35 [or poly(A)] with BrUTP incorporation were analyzed. The image from one probe was translated with respect to the other in three dimensions to compare colocalization with random alignments. Both poly(A) and SC35 were found to have low colocalization with the total BrU signal. Sites of transcription were determined using an algorithm to find maxima of BrUTP signal within clusters. From 849 to as many as 3888 sites per nucleus were detected. A rim of hybridization to poly(A) coinciding with the nuclear envelope was eliminated by actinomycin treatment, suggesting that these transcripts were exiting from the nucleus. These results emphasize the importance of utilizing the full dynamic range of the image before drawing conclusions as to the distribution of nuclear components.

Algorithms↗
PubMed1988

Acetaminophen and analogs as cosubstrates and inhibitors of prostaglandin H synthase.

Previous studies have shown that acetaminophen (APAP) is converted by prostaglandin H synthase (PGHS) to both one-electron oxidized products and the two-electron oxidized product, N-acetyl-p-benzoquinone imine (NAPQI). The present study further characterizes this reaction and shows that relatively low concentrations (20-200 microM) of APAP stimulate PGHS activity in ram seminal vesicle microsomes, whereas high concentrations (greater than 10 mM) inhibit the conversion of arachidonic acid (AA) to 15-hydroperoxy-9,11-peroxidoprosta-5,13-dienoic acid (PGG2). Stimulatory and inhibitory activities apparently involve the reduction of oxidized complexes of PGHS, and stimulatory and inhibitory activities roughly correlate with the electrochemical half-wave oxidation potentials of a series of hydroxyacetanilides. Using APAP as a probe, it was found that at low concentrations, APAP is converted in a cooxidation reaction with arachidonic acid to a dimer, 4'4"'-dihydroxy-3', 3"'-biacetanilide (bi-APAP), and other polymeric products. Moreover, an electrophilic metabolite of acetaminophen, NAPQI, was detected directly and also detected indirectly by its reaction with glutathione (GSH) to form 3'-(S-glutathionyl)acetaminophen (GS-APAP). The formation of all products was inhibited by indomethacin and the reductants, ascorbic acid and butylated hydroxyanisole (BHA). However, in the presence of GSH, ascorbic acid only partially inhibited the formation of GS-APAP while almost completely inhibiting the formation of bi-APAP. The same products of APAP (bi-APAP and NAPQI) were formed by PGHS and hydrogen peroxide in reactions that were not inhibited by indomethacin. At high concentrations of APAP that inhibit PGHS, the formation of products in the presence of arachidonic acid but not H2O2 was inhibited. These findings are generally consistent with a mechanism of acetaminophen oxidation by PGHS that involves common intermediate enzyme forms for both cyclooxygenase- and hydroperoxidase-catalyzed reactions. At least one of the intermediate complexes is reduced by relatively low concentrations of APAP and stimulates PGHS, whereas another intermediate complex is reduced by APAP at higher concentrations to inhibit the enzyme.

Acetaminophen↗
PubMed2006

Design of a continuous wave blood flow bi-directional Doppler system.

This paper describes the design of a continuous wave blood flow bi-directional Doppler system based on an open, high-resolution architecture that is portable and low cost. The system incorporates the advantages of expensive systems with dedicated hardware. The system is composed of a flow detector probe, a signal conditioning stage, a direction detection module, a signal processing stage and a graphic user interface. The direction detection of the signal is achieved using a fast digital phasing filter. The Doppler signal is processed using a short-time Fourier transform-based algorithm. This is commonly used as a reference. Nevertheless, the system allows us to incorporate alternative high-resolution spectral estimation methods that might offer more precise information to the specialist.

Algorithms↗
PubMed2007

Second-order motion without awareness: passive adaptation to second-order motion produces a motion aftereffect.

Although second-order motion may be detected by early and automatic mechanisms, some models suggest that perceiving second-order motion requires higher-order processes, such as feature or attentive tracking. These types of attentionally mediated mechanisms could explain the motion aftereffect (MAE) perceived in dynamic displays after adapting to second-order motion. Here we tested whether there is a second-order MAE in the absence of attention or awareness. If awareness of motion, mediated by high-level or top-down mechanisms, is necessary for the second-order MAE, then there should be no measurable MAE if the ability to detect directionality is impaired during adaptation. To eliminate the subject's ability to detect directionality of the adapting stimulus, a second-order drifting Gabor was embedded in a dense array of additional crowding Gabors. We found that a significant MAE was perceived even after adaptation to second-order motion in crowded displays that prevented awareness. The results demonstrate that second-order motion can be passively coded in the absence of awareness and without top-down attentional control.

Adaptation, Physiological↗
PubMed1994

Use of nuclear magnetic resonance in probing ligand-macromolecule interactions.

Nuclear magnetic resonance techniques can be used to study ligand-macromolecule interactions under a wide variety of conditions. There are a number of different approaches, which are generally applicable under different conditions of exchange rate and binding constant. In the tight binding limit direct structural studies using NOE are possible using labeled ligand (13C, 15N) and/or labeled macromolecule. In the intermediate exchange regime, line broadening complicates the analysis of bound conformations of ligands. However, a good deal of information can be obtained about the binding kinetics and about the number and nature of binding modes when several are present. In such cases it is often best to use an NMR active nucleus which can be directly detected, with high sensitivity. Tritium has good characteristics in this respect, and has been effective in a number of cases. In the fast exchange limit it is often best to use the rapid dissociation of the ligand to transfer structural information from the bound form to the free, where it can be sensitively and selectively detected, often by direct observation of 1H values. There are a number of conditions on the binding kinetics which must be met, and systems with multiple binding sites generally cannot be analyzed. The large number of different NMR approaches which can be used, often only under special conditions of exchange, complicates planning of NMR studies of ligand-macromolecule interactions. However, once the characteristics of binding affinity and exchange rate have been determined, it is usually possible to apply NMR spectroscopy to obtain information about the binding. The instrumental demands for carrying out ligand-macromolecule interactions are generally not more than those required for studies of the macromolecules alone.

Amino Acid Isomerases↗
PubMed2000

Comparison of bacterial cultivation, PCR, in situ hybridization and immunohistochemistry as tools for diagnosis of Haemophilus somnus pneumonia in cattle.

The aim of the present study was to compare the potential of bacterial cultivation (BC), PCR, in situ hybridisation (ISH), and immunohistochemistry (IHC) in the diagnosis of Haemophilus somnus, when applied to pneumonic bovine tissue. Lungs from 65 field cases submitted for bacteriological examination were included in the study. The PCR-detection was performed on three different samples: plate-PCR (detection on plate washes after incubation of lung tissue on agar plates); swab-PCR (direct detection on a swab from the cut surface); and, whenever possible, a bronchus-PCR (direct detection on a swab from the main bronchus of the right cranial lung lobe). In order to examine the pathological significance of the findings, a histopathological examination of the cases was performed. H. somnus was detected by one or more techniques in 33 cases in total. By BC the bacterium was isolated from 10 cases, IHC and ISH were positive in 17 and 19 cases, and plate- and swab-PCR were positive in 21 and 29 cases, respectively. The bronchus-PCR was positive in 30 out of 61 cases examined. The PCR-technique was the most sensitive method, and as this technique is fast and relatively inexpensive, it should be considered as a supplementary tool in the diagnosis of H. somnus induced calf pneumonia.

Animals↗
PubMed1997

Performance of an automated Q-beta replicase amplification assay for Mycobacterium tuberculosis in a clinical trial.

We present data from a clinical trial study in which an automated version (Galileo) of a previously described Q-Beta replicase-amplified probe assay (J. S. Shah et al., J. Clin. Microbiol. 33:1435-1441, 1995) was used for the direct detection of Mycobacterium tuberculosis complex in sputum. The assay was designed to target specific regions of 23S rRNA found in M. tuberculosis, Mycobacterium bovis, Mycobacterium africanum, and Mycobacterium microti and had a sensitivity ranging from approximately <10 to 300 CFU. The assay was tested for cross-hybridization by using large numbers (e.g., 10(5)to 10(10) CFU/assay) of 133 other organisms commonly found in respiratory tract samples, including non-M. tuberculosis Mycobacterium spp., other bacteria, fungi, and viruses. All of these competitors tested negative by the assay. Automated assay results for 780 respiratory tract samples (sputum or bronchoalveolar lavage specimens) collected and tested at three trial sites in the United States) were compared with the results of culture and acid-fast microscopy. Aliquots of conventionally digested and decontaminated sputum pellets were heated at 100 degrees C and mechanically disrupted prior to hybridization and background reduction, amplification, and detection in a closed disposable test pack. Pertinent elements of individual patient histories relating to tuberculosis exposure, previous active disease, antituberculosis therapy status, etc., were considered in the resolution of discrepant results for 48 (assay false-positive) samples. Seventy-one of 90 (78.9%) culture-positive samples were positive when tested in the Galileo assay, while 7% of culture-negative samples were assay positive, corresponding to a sensitivity of 79% and a specificity of 93%. Following resolution of discrepant results by chart review, the sensitivity and specificity for the Q-Beta replicase amplification assay with the Galileo analyzer were 84 and 97%, respectively. A total of 69.2% of smear-negative (culture positive) samples were detected by the assay. Ten test packs at a time were automatically processed by the Galileo analyzer without operator intervention following loading of samples. The first result was reported in approximately 3 h, and the last result was available in 6.5 h. To our knowledge, this is the first report of a clinical study with a fully automated amplification probe hybridization assay for the detection of pathogens directly from a clinical specimen.

Bronchoalveolar Lavage Fluid↗