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At least 217 records · Page 12Linked to original sources
PubMed1992

Difficult diagnosis of the fragile X syndrome made possible by direct detection of DNA mutations.

Genetic recombination near the fragile X locus (Xq27.3) has frequently been a problem in linkage studies of families in which the fragile X is segregating. This case report illustrates the resolution of a difficult situation in a fragile X family for whom cytogenetic studies were inconclusive and where recombination had twice confounded attempts at prenatal DNA diagnosis by RFLP analysis. Using a newly developed DNA probe, StB12.3, for direct detection of DNA instability in the fragile X locus, the presence of the fragile X was ascertained definitively in a prenatal DNA sample.

Blotting, Southern↗
PubMed2004

Direct detection of renal function markers using microchip CE with pulsed electrochemical detection.

Creatinine, creatine, and uric acid are three important compounds that are measured in a variety of clinical assays, most notably for renal function. Traditional clinical assays for these compounds have focused on the use of enzymes or chemical reactions. Electrophoretic microchips have the potential to integrate separation power of capillary electrophoresis with devices that are small, portable, and have the speed of conventional sensors. The development of a microchip CE system for the direct detection of creatinine, creatine, and uric acid is presented. The device uses pulsed amperometric detection (PAD) to detect the nitrogen-containing compounds as well as the easily oxidizable uric acid. Baseline separation of creatinine, creatine and uric acid was achieved using 30 mM borate buffer (pH = 9.4) in less than 200 s. Linear calibration curves were obtained with limits of detection of 80 microM, 250 microM and 270 microM for creatinine, creatine and uric acid respectively. An optimization of the separation conditions and a comparison of PAD with other amperometric detection modes is also shown. Finally, analysis of a real urine sample is presented with validation of creatinine concentrations using a clinical assay kit based on the Jaffé reaction.

Biomarkers↗
PubMed2002

Direct detection of insertion/deletion polymorphisms in an autosomal region by analyzing high-density markers in individual spermatozoa.

Direct polymerase chain reaction (PCR) detection of insertion/deletion (indel) polymorphisms requires sample homozygosity. For the indel polymorphisms that have the deletion allele with a relatively low frequency in the autosomal regions, direct PCR detection becomes difficult or impossible. The present study is, to our knowledge, the first designed to directly detect indel polymorphisms in a human autosomal region (i.e., the immunoglobulin V(H) region), through use of single haploid sperm cells as subjects. Unique marker sequences (n=32), spaced at approximately 5-kb intervals, were selected near the 3' end of the V(H) region. A two-round multiplex PCR protocol was used to amplify these sequences from single sperm samples from nine unrelated healthy donors. The parental haplotypes of the donors were determined by examining the presence or absence of these markers. Seven clustered markers in 6 of the 18 haplotypes were missing and likely represented a 35-40-kb indel polymorphism. The genotypes of the donors, with respect to this polymorphism, perfectly matched the expectation under Hardy-Weinberg equilibrium. Three V(H) gene segments, of which two are functional, are affected by this polymorphism. According to these results, >10% of individuals in the human population may not have these gene segments in their genome, and approximately 44% may have only one copy of these gene segments. The biological impact of this polymorphism would be very interesting to study. The approach used in the present study could be applied to understand the physical structure and diversity of all other autosomal regions.

Genes, Immunoglobulin↗
PubMed2004

Direct detection of cell surface interactive forces of sessile, fimbriated and non-fimbriated Actinomyces spp. using atomic force microscopy.

Actinomyces species are predominant early colonizers of the oral cavity and prime mediators of inter-bacterial adhesion and coaggregation. Previous workers have evaluated the adhesion of Actinomyces spp. by quantitative assessment of sessile, as opposed to planktonic cells attached to substrates, but did not quantify the cell surface interactive forces. Therefore we used atomic force microscopy to directly detect the interactive force between an approaching silicon tip and sessile Actinomyces spp. adhering to a substrate, at nanonewton (nN) range force levels. A total of eight strains each belonging to fimbriated and non-fimbriated Actinomyces species were employed, namely A. bovis, A. gerencseriae, A. israelii, A. meyeri, A. naeslundii genospecies 1 and 2, A. odontolyticus and A. viscosus. The sterile mica discs, used as the adhesion substrate, were immersed in mono-species bacterial suspensions for five days to obtain a thin bacterial biofilm. Interactive forces were measured using a silicon nitride cantilever attached to a Nanoscope IIIA atomic force microscope. The interactive forces between the approaching silicon nitride tip and bacterial biofilm surfaces were randomly quantified at three different locations on each cell; namely, the cell surface proper, the periphery of the cell and the substrate and, the interface between two cells. When the interactive forces at these locations of the same species were compared, significantly higher force levels at the cell-cell interface than the other two locations were noted with A. gerencseriae (P < 0.001), A. viscosus (P < 0.01) and A. israelii (P < 0.05). When the interactive forces of different Actinomyces spp. at an identical location were compared, fimbriated A. naeslundii genospecies 2 showed the greatest interactive force at the cell surface proper (-32.6 +/- 8.7 nN, P < 0.01). A. naeslundii genospecies 1, 2 and A. viscosus demonstrated greater interactive force at the cell-mica periphery than the other five species (P < 0.05); A. viscosus (-34.6 +/- 10.5 nN) displayed greater interactive force at the cell-cell interface than the others (P < 0.01), except for A. gerencseriae (P > 0.05). These data indicate that fimbriated Actinomyces spp., including A. naeslundii genospecies 1, 2 and A. viscosus exert higher cell surface interactive forces than those devoid of fimbriae and, such variable force levels may modulate their adhesion and coaggregation during biofilm formation.

Actinomyces↗
PubMed1996

Direct detection of equine herpesvirus DNA in tissues of aborted equine fetuses.

Restriction endonuclease analysis of equine herpesviruses 1 (EHV-1) and 4 has been investigated using cultured cells infected with these viruses. The DNA cleavage patterns of these viruses were observed in the intracellular DNA after digestion with Eco RI and electrophoresis. This procedure was applied to the diagnosis of equine herpesvirus infection in aborted equine fetuses. The characteristic Eco RI restriction pattern of EHV-1 DNA was directly detectable in the emulsion of lungs collected from aborted equine fetuses.

Abortion, Veterinary↗
PubMed2006

Direct detection of glycogenin reaction products during glycogen initiation.

Glycogenin initiates glycogen synthesis in an autocatalytic reaction in which individual glucose residues are covalently linked to Tyrosine 194 in order to form a short priming chain of glucose residues that is a substrate for glycogen synthase which, combined with the branching enzyme, catalyzes the bulk synthesis of glycogen. We sought to develop a new enzymatic assay to better characterize both the chemical and enzymatic characteristics of this unusual reaction. By directly detecting the reaction products using electrospray mass spectrometry this procedure permits both the visualization of the intact individual reaction species produced as a function of time and quantitation of the levels of each of species. The quantitation of the reaction agrees well with previous measurements of both catalytic rate and the change in rate as a function of average glucosylation. The results from this assay provide new insight into the mechanism by which glycogenin catalyzes the initiation reaction.

Catalysis↗
PubMed2005

Multiplex PCR for direct detection of Shiga toxigenic Escherichia coli strains producing the novel subtilase cytotoxin.

We have recently described a novel AB5 subtilase cytotoxin produced by certain Shiga toxigenic Escherichia coli (STEC) strains. This potentially lethal toxin may contribute to severe gastrointestinal and systemic disease in humans. In this study we have developed a trivalent PCR assay for the detection of the novel toxin A subunit gene subA, as well as stx1 and stx2. The three primer pairs used in the assay do not interfere with each other and generate amplification products of 556, 180, and 255 bp, respectively. The assay can be used for determining the toxin genotype of STEC isolates, as well as for direct detection of toxin genes in primary fecal culture extracts.

Cytotoxins↗
PubMed1995

Direct detection of expanded (CAG/CTG) repeats in the myotonin-protein kinase genes of myotonic dystrophy patients using a high-stringency hybridization method.

Recent discoveries of genes containing (CAG/CTG) repeats as the causative genes for neuromuscular diseases suggest that trinucleotide repeat expansions are associated with a number of other neurodegenerative diseases, particularly in those showing genetic anticipation. In order to efficiently identify expanded trinucleotide repeats, we have developed a novel method using a single-stranded probe containing (CAG)55, which allows direct detection of expanded (CAG/CTG) repeats in the myotonin-protein kinase (Mt-PK) genes of patients with myotonic dystrophy without the need for any prior information of chromosomal localizations of the disease genes. This method is expected to be useful for identifying novel genes for diseases associated with expanded (CAG/CTG) repeats.

Base Sequence↗
PubMed1997

Evaluation of Amplicor- and IS6110-PCR for direct detection of Mycobacterium tuberculosis complex in Singapore.

One hundred and seventy-eight samples from 168 individuals were tested for Mycobacterum tuberculosis complex (Mtc) using Amplicor PCR, IS6110-PCR (in-house), acid fast (AF)-staining and culture. Thirty-one samples were positive by culture, but 37 samples were later resolved to be truly positive for Mtc. Of these, Amplicor detected 32 (86.5%), IS6110-PCR detected 31 (83.6%), and AF-staining 21 (56.8%). None of the 141 Mtc-negative samples was positive by these tests, thus giving 100% specificity. Although the IS6110-PCR was more sensitive than Amplicor in detecting spiked Mtc DNA, it was not more sensitive than the latter in detecting Mtc in clinical samples. Reasons likely to account for the PCR false negativity were (i) sample inoculum size, (ii) nonuniform samples due to clumping effect of Mtc and (iii) the absence of target gene sequences for IS6110-PCR. Culture negativity, on the other hand, was likely to be associated with nonviable Mtc. Amplicor PCR is promising for direct detection of Mtc. The IS6110-PCR, however, may not be as suitable because of possible existence of IS6110-deleted Mtc strain in Singapore.

DNA, Bacterial↗
PubMed2005

A theoretical look at the direct detection of giant planets outside the Solar System.

Astronomy is at times a science of unexpected discovery. When it is, and if we are lucky, new intellectual territories emerge to challenge our views of the cosmos. The recent indirect detections using high-precision Doppler spectroscopy of more than 100 giant planets orbiting more than 100 nearby stars is an example of such rare serendipity. What has been learned has shaken out preconceptions, for none of the planetary systems discovered so far is like our own. The key to unlocking a planet's chemical, structural, and evolutionary secrets, however, is the direct detection of the planet's light. Because there have been as yet no confirmed detections, a theoretical analysis of such a planet's atmosphere is necessary for guiding our search.

Journal Article↗
PubMed2001

Direct detection of galactic halo dark matter.

The Milky Way galaxy contains a large, spherical component which is believed to harbor a substantial amount of unseen matter. Recent observations indirectly suggest that as much as half of this "dark matter" may be in the form of old, very cool white dwarfs, the remnants of an ancient population of stars as old as the galaxy itself. We conducted a survey to find faint, cool white dwarfs with large space velocities, indicative of their membership in the galaxy's spherical halo component. The survey reveals a substantial, directly observed population of old white dwarfs, too faint to be seen in previous surveys. This newly discovered population accounts for at least 2 percent of the halo dark matter. It provides a natural explanation for the indirect observations, and represents a direct detection of galactic halo dark matter.

Journal Article↗
PubMed2002

Direct detection of Cryptosporidium parvum oocysts by immunomagnetic separation-polymerase chain reaction in raw milk.

Cryptosporidium parvum is an emerging protozoan parasite responsible for several serious outbreaks of cryptosporidiosis, an enteric infection characterized by severe intestinal distress. This parasite can be transmitted through contaminated water and raw food in the oocyst form, which is resistant to many environmental stresses and food processes. C. parvum is also commonly found on dairy farms and could be transmitted to humans through contaminated raw milk and dairy products. Thus, an immunomagnetic separation-polymerase chain reaction assay for direct detection of C. parvum oocysts in milk was developed. The procedure was able to detect < 10 C. parvum oocysts. Thus, it could be used for monitoring milk samples.

Animals↗
PubMed1992

Direct detection of Molluscum contagiosum virus in clinical specimens by in situ hybridization using biotinylated probe.

Molluscum contagiosum virus (MCV) is an unclassified poxvirus which has recently become recognized as causing a major sexually transmitted disease. At present no assay is available for specific detection of MCV because the virus cannot be serially propagated in cell culture. Since MCV produces an abortive, limited growth with some cytopathic effect in certain cell lines, we were able to develop an in situ hybridization assay for detection of MCV genome in clinical specimens. Human fetal diploid lung cell monolayers were infected with clinical specimens, and after proper incubation and fixation in paraformaldehyde, hybridization was performed under full stringency conditions with a molecularly cloned biotinylated probe. Only MCV infected cells showed homology to the MCV probe with a purple-brown cytoplasmic staining. Additionally, we have described an in situ hybridization assay for direct detection of MCV genome in formalin-fixed, paraffin-embedded biopsies. Characteristic intracytoplasmic Molluscum bodies (Henderson-Paterson bodies) were detected in stratum spinosum cells of the epidermis. Striking staining similarities have been observed between in situ hybridization and haematoxylin-eosin cytostaining. These procedures are the first successful identification of MCV genome in clinical samples by molecular hybridization, with sensitivity and specificity equal to or greater than electron microscopy.

Blotting, Southern↗
PubMed1993

Prenatal diagnosis of congenital adrenal hyperplasia by direct detection of mutations in the steroid 21-hydroxylase gene.

OBJECTIVE: Our aim was to develop a rapid and accurate method for the prenatal diagnosis of congenital adrenal hyperplasia using the polymerase chain reaction to detect mutations in the steroid 21-hydroxylase gene. These procedures will help to minimize exposure to dexamethasone treatment of either affected males or unaffected females. DESIGN AND PATIENTS: Chorionic villus biopsy samples were obtained between 10 and 11 weeks gestation from three females carrying fetuses at risk of steroid 21-hydroxylase deficiency. Blood samples were taken from parents and the index case in each family. MEASUREMENTS: Three common mutations in the 21-hydroxylase B gene were detected following DNA amplification. RESULTS: Prenatal diagnosis of congenital adrenal hyperplasia was successful in all three cases. One affected female was treated with dexamethasone to term. In the other two cases, one affected male and one carrier also male, dexamethasone was withdrawn at an early stage. CONCLUSIONS: First trimester prenatal diagnosis of steroid 21-hydroxylase deficiency was achieved in three pregnancies with a strategy based on direct detection of gene mutations.

Adrenal Hyperplasia, Congenital↗
PubMed2005

Direct detection of a magnetic field in the innermost regions of an accretion disk.

Models predict that magnetic fields play a crucial role in the physics of astrophysical accretion disks and their associated winds and jets. For example, the rotation of the disk twists around the rotation axis the initially vertical magnetic field, which responds by slowing down the plasma in the disk and by causing it to fall towards the central star. The magnetic energy flux produced in this process points away from the disk, pushing the surface plasma outwards, leading to a wind from the disk and sometimes a collimated jet. But these predictions have hitherto not been supported by observations. Here we report the direct detection of the magnetic field in the core of the protostellar accretion disk FU Orionis. The surface field reaches strengths of about 1 kG close to the centre of the disk, and it includes a significant azimuthal component, in good agreement with recent models. But we find that the field is very filamentary and slows down the disk plasma much more than models predict, which may explain why FU Ori fails to collimate its wind into a jet.

Journal Article↗
PubMed1991

Zidovudine resistance predicted by direct detection of mutations in DNA from HIV-infected lymphocytes.

Zidovudine-resistant strains of HIV have recently been isolated from individuals during prolonged treatment. Analysis of the HIV reverse transcriptase (RT) gene from clinical isolates revealed that resistance was due to multiple nucleotide changes conferring specific amino acid substitutions in this enzyme. In order to correlate the degree of resistance with these amino acid changes, we constructed a series of infectious HIV variants with specific combinations of mutations in the RT gene and assessed their sensitivity to zidovudine. The reproducible nature of the mutations seen in clinical isolates has enabled the polymerase chain reaction to be used to identify lesions associated with resistance. This procedure was validated by analysis of sensitive and resistant clinical isolates with RT genes of known DNA sequence. Using a 'double' amplification procedure, zidovudine sensitivity was assessed by direct detection of specific mutations in DNA from peripheral-blood lymphocyte samples. This should make it possible to test large numbers of individuals receiving zidovudine therapy, with the aim of establishing the clinical significance of the resistant isolates.

AIDS-Related Complex↗
PubMed2003

Comparison of the BDProbeTec ET system with the Cobas Amplicor PCR for direct detection of Mycobacterium tuberculosis in respiratory samples.

In the study presented here, the performance of the BDProbeTec ET system (Becton Dickinson, USA) was compared with the Roche Cobas Amplicor-PCR (Roche, Switzerland) to detect Mycobacterium tuberculosis complex (MTB) in clinical respiratory samples. The Bactec MGIT 960 liquid culture system (Becton Dickinson) was used as a reference method. A total of 411 samples were tested. Of the 93 culture-positive samples, both the BDProbeTec ET system and the Cobas Amplicor-PCR detected 87 (sensitivity, 93.5%). When only smear-negative samples were considered, the BDProbeTec ET exhibited a sensitivity of 50% and the Cobas Amplicor-PCR 60%. Specificity was 99.7% for the BDProbeTec ET system and 100% for the Cobas Amplicor-PCR. Percent agreement between the two nucleic amplification methods was 98.7%. Inhibition occurred in three (0.7%) samples in the BDProbeTec ET system. The high sensitivity and specificity of the BDProbeTec ET system suggest it is a useful method for the rapid and direct detection of MTB in smear-positive respiratory samples.

Bacteriological Techniques↗
PubMed1994

Direct detection of Vibrio cholerae in stool samples.

A direct method to detect Vibrio cholerae in stool samples was developed by using a PCR procedure that did not require a DNA purification step. Dilution (1/100) of stool samples prevented inhibition of the reaction by contaminants, and two consecutive PCRs, the second one with a nested primer, achieved the desired sensitivity. Comparison of the results obtained from stool swab samples processed by the two-step PCR and by an enzyme-linked immunosorbent assay using GM1 as the capture molecule showed that the former is more sensitive and gave positive results even when V. cholerae was not culturable or dead.

Argentina↗