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PubMed2001

Comparison of DNA probe test and cultivation methods for detection of Mycobacterium avium subsp paratuberculosis in caprine and ovine faeces.

OBJECTIVE: To compare a DNA probe test with two cultivation methods for the detection of Mycobacterium avium subsp paratuberculosis in goat and sheep faeces. DESIGN: Comparison of the results of the three methods with histological examination as the reference standard. PROCEDURE: Faecal specimens were obtained from goats and sheep originating from flocks known to be affected with paratuberculosis and tested for Mycobacterium avium subsp paratuberculosis with a DNA probe test and two cultivation methods (old conventional culture and new double incubation method in Herrold's and Lowenstein-Jensen medium). RESULTS: In goats, the sensitivity of the various tests were for the DNA probe test 17.2%, for the double incubation culture method 25.4% and for the old conventional culture method 22.8% using the histopathological results as reference. In sheep the sensitivity of the various tests were for the DNA probe test 13.2%, for the double incubation culture method 8.8% and for the old conventional culture method 5.9% using the histopathological results as reference. The specificity of the above tests was 100% in goats and sheep and the specificity of the double incubation culture method in goats was 91%. CONCLUSIONS: The DNA probe test is a rapid and specific test that could be used in a control program if the sensitivity of the test were improved and possibly in combination with another test.

Animals↗

PubMed2001

[Localization of DNA probes for human ribosomal genes on barley chromosomes].

To estimate the possibility of plant genome mapping using human genome probes, the probes fluorescent in situ hybridization (FISH) of human 18S-28S rDNA (clon 22F9 from the LA-13NCO1 library) was carried out on chromosomes of the spring barley Hordeum vulgare L. As a control, wheat rDNA probe (clon pTa71) was taken. Hybridization of the wheat DNA probe revealed two major labelling sites on mitotic barley chromosomes 5I (7H) and 6I (6H), as well as several minor sites. With the human DNA probe, signals were detected in the major sites of the ribosomal genes on chromosomes 5I (7H) and 6I (6H) only when the chromosome preparations were obtained using an optimized technique with obligatory pepsin treatment followed by hybridization. Thus, this study demonstrates that physical mapping of plant chromosomes with human DNA probes that are 60 to 75% homologous to the plant genes is possible. It suggests principal opportunity for the FISH mapping of plant genomes using probes from human genome libraries, obtained in the course of the total sequencing of the human genomes and corresponding to the coding regions of genes with known functions.

Chromosomes↗

PubMed1992

Development of a species-specific DNA probe for Mycoplasma capricolum.

A specific DNA probe for the detection and identification of Mycoplasma capricolum, one of the causative agents of contagious agalactia syndrome, was selected from a genomic library. It consists of a 900bp RsaI genomic fragment of M. capricolum (reference strain), cloned into the EcoRV site of the plasmid Bluescript. By using the appropriate stringency this radiolabelled probe reacts specifically with M. capricolum when tested by dot blot hybridization against various mycoplasmal DNAs. The current level of sensitivity of the 32P-labelled 900bp RsaI probe is 500 pg of homologous DNA, corresponding to 5 x 10(4) mycoplasmas. A non radioactive labelling method, using the digoxigenin-11-dUTP, was also tested. The specificity of the digoxigenin-labelled probe was equivalent to that obtained with the radioactive probe. However the sensitivity of detection decreased to 1 ng of homologous DNA detected, corresponding to 1 x 10(5) mycoplasmas. Tests performed with milk samples have demonstrated that the radioactive 900 bp RsaI probe indeed detected M. capricolum contained in milk. A positive signal was obtained when 10(5) M. capricolum were present in the spot.

Animals↗

PubMed1994

Comparison of DNA probe and ELISA microbial analysis methods and their association with adult periodontitis.

The purposes of this study were two-fold: to compare the DNA probe and enzyme linked immunosorbent assay (ELISA) microbial identification tests and correlate the levels of microorganisms with adult periodontitis. A single plaque sample were taken from each of 2 sites in 52 patients. Twelve of these patients were also sampled during and after treatment. The experimental site had clinical indicators of disease (bleeding on probing, probing and attachment loss of > or = 6 mm) and the contralateral site (control) was clinically healthy. A total of 176 plaque samples were collected, divided, processed, and sent for both types of quantitative microbial analyses. All of these samples were used to compare the DNA probe and ELISA methods while only the initial 104 pretreatment sites were used to correlate microorganisms/method with clinical indicators of adult periodontitis. DNA probes were used to assay for A. actinomycetemcomitans, P. gingivalis, P. intermedia, E. corrodens, F. nucleatum, T. denticola, and C. rectus. An ELISA utilizing monoclonal antibodies was used to assay for P. gingivalis, E. corrodens, T. denticola, and C. rectus. Comparison of the two methods revealed that the ELISA test identified P. gingivalis and C. rectus significantly more often than the DNA probe method and that T. denticola was detected more frequently with the DNA probe. The sensitivities and specificities varied widely among organisms and by test. P. gingivalis, as identified by ELISA, had the highest degree of sensitivity and specificity (0.90 and 0.82 respectively) to clinical indicators of adult periodontitis.

Adult↗

PubMed1990

Practical and economical method for using biotinylated DNA probes with bacterial colony blots to identify diarrhea-causing Escherichia coli.

A simple and economical method was developed for using biotinylated DNA probes to hybridize with bacterial colonies belonging to the various categories of diarrhea-causing Escherichia coli. Simplification and cost containment were achieved by using Whatman no. 541 filter papers instead of nitrocellulose, by minimizing the concentration of proteinase K (an expensive but necessary reagent used to pretreat the colony blots prior to hybridization with biotin-labeled DNA probes) and by reusing hybridization solution containing labeled probe DNA. After exposing the colony blots to lysing solution and steam, followed by lysozyme (1.5 mg/ml), sucrose (25%), and proteinase K (10 micrograms/ml) treatments, biotinylated probes were used to detect enterotoxigenic, enteropathogenic, enterohemorrhagic, diffuse adherence, and enteroinvasive categories of diarrhea-causing E. coli with a high level of sensitivity and specificity. Three independent observers who were experienced in reading DNA blots recorded remarkably similar results, while less satisfactory results were obtained when the blots were read by an inexperienced observer. This technique will be useful in laboratories in which radioactive isotopes are unavailable or impractical and in which budgets are restricted.

Biotin↗

PubMed1992

Evaluation of a non-radioactive DNA probe for detecting Porphyromonas gingivalis in subgingival specimens.

This study compared the ability of a nonradioactive digoxigenin-labeled DNA probe and anaerobic culture to identify subgingival Porphyromonas gingivalis. Total cellular DNA from P. gingivalis ATCC 33277T was labeled using the Genius kit from Boehringer Mannheim Biochemicals. Anaerobic culture was performed using VMGA III transport medium and enriched brucella blood agar. The DNA probe could detect as little as 1000 P. gingivalis cells added to supragingival plaque. Also, the probe could detect P. gingivalis when it was present in proportions too low to be visualized on overgrown bacterial plates. The probe showed no visible reaction with strains of various oral species or with thousands of non-P. gingivalis colonies from plaque samples. VMGA III could maintain the viability of P. gingivalis for up to 6 days, as evidenced by DNA probing of colony blot of subgingival cultures. A total cellular DNA probe for detecting P. gingivalis seems to offer a simple and reliable method of detecting the organism in subgingival specimens.

Colony Count, Microbial↗

PubMed1987

Detection of enterotoxigenic Escherichia coli by dot blot hybridization with biotinylated DNA probes.

A dot blot hybridization test was developed for the detection of enterotoxigenic E. coli without the use of radioisotopes. Three biotin-labeled DNA (Bio-DNA) probes corresponding to structural genes specifying heat-labile and heat-stable enterotoxins of porcine and human origin were prepared by random priming; label incorporation was significantly higher than that obtained from the use of nick translation. Bio-DNA probes were highly specific when reacted with protein- and RNA-free DNA preparations in a dot blot hybridization assay. The Bio-DNA probe, in which 40% of available thymidines were replaced by a biotin-labeled deoxyuridine, readily detected 160 pg of target DNA mixed with 6 micrograms of carrier DNA. The minimum amount of total DNA required for reliable identification of a single-copy enterotoxin gene of porcine origin within a 5,000-kilobase chromosome was found to be approximately 5 micrograms. Complete agreement among the results of Bio-DNA probe hybridization, [32P]DNA hybridization, and biological assay was demonstrated for 15 (100%) of the clinical isolates. This procedure provides a more suitable approach for the diagnosis of enterotoxigenic E. coli infections in clinical settings than the hybridization assay based on 32P-labeled DNA probes.

Bacterial Toxins↗

PubMed1991

[Reactivities of various mycobacteria species against DNA probes (Gen-Probe Rapid Diagnostic System) specific to Mycobacterium tuberculosis complex, Mycobacterium avium and Mycobacterium intracellulare].

Various mycobacterial species (22 species, 178 strains) were studied for their reactivity to DNA probe specific for Mycobacterium tuberculosis complex (MTC), M. avium or M. intracellulare, using Gen-Probe Rapid Diagnostic System (Gen-Probe Inc., San Diego, Calif., U.S.A.). All the MTC strains, including M. tuberculosis, M. africanum, M. bovis and M. microti reacted with MTC-DNA probe at the % hybridization value of 42.8-51.9% (values higher than 10% are regarded as positive), but their reactivity to MAC-DNA probes (0.8-2.5%) was under the cut off value (10%). The test strains (28 strains) of M. avium complex (MAC) segregated into two groups on the basis of reactivity to DNA probes specific for M. avium and M. intracellulare, that is, one group (16 strains) positively reacted with M. avium-probe but not with M. intracellulare-probe, and the other group (12 strains) showed the converse reactivity. The two groups did not show a reactivity with MTC-probe higher than the cut off value. Nontuberculous mycobacteria other than MAC, including M. kansasii, M. marinum, M. simiae, M. asiaticum, M. scrofulaceum, M. gordonae, M. szulgai, M. malmoense, M. xenopi, M. gastri, M. nonchromogenicum, M. terrae, M. triviale, M. fortuitum, and M. chelonae (subsp. abscessus and chelonae) reacted with neither MTC- nor MAC-probe and values for % hybridization (0.6-3.6%) were lower than the cut off value. These findings indicate extremely superior specificity of the DNA probes (Gen-Probe) for MTC, M. avium and M. intracellulare, thereby indicating the usefulness of Gen-Probe Rapid Diagnostic System for the MTC and MAC in clinical use.

Animals↗

PubMed1991

Application of single-locus hypervariable region DNA probes to deficiency cases in paternity testing.

Seven DNA probes which recognize single-locus hypervariable region (HVR) were applied to a paternity test in which the putative father and his wife were deceased. Three legitimate children, an illegitimate child and her mother were available for analysis. The cumulative paternity index of the illegitimate child derived from 15 conventional blood group markers was 18.71 and from 7 DNA probes 92,572.08, that is, 4,948 times higher than the former. Thus the DNA analyses gave nearly conclusive evidence that the putative father was the biological father of the child. The application of highly discriminating polymorphisms of DNA which recognize single HVR loci is considered to be extremely informative in cases of disputed parentage.

Child↗

PubMed1990

Development of a gene probe assay suitable for use in routine diagnosis: a pilot study using a DNA probe for parvovirus B19.

Although DNA probes have been widely applied in research for many years, lengthy and complex protocols, together with the use of radio-labelled probes, have hindered their introduction into routine diagnosis. In this study conventional methods were adapted to make gene probes more suitable for routine work and a biotin-labelled probe for human parvovirus B19 was utilised. The gene probe assay was shown to detect 0.25 pg of viral DNA per 5 microliters of serum in 20 h. A comparative study was carried out to assess the difference in antigen detection by gene probe with that of the more conventional methods of counter-current immunoelectrophoresis and immune electron microscopy. The application of probes in this manner may lead to their increased use in routine virological diagnosis.

Cloning, Molecular↗

PubMed1996

A PCR-DNA probe assay specific for Bacteroides forsythus.

Bacteroides forsythus is a fastidious anaerobic Gram-negative organism associated with active periodontal disease. The ability of random amplified polymorphic DNA (RAPD) fingerprinting to generate species-specific markers was exploited towards the construction of a polymerase chain reaction (PCR)-DNA probe assay specific for B. forsythus. The strategy included the four following steps: (1) construction of a first generation DNA probe based on a 507-bp RAPD species-specific marker; (2) cloning and sequencing the 507-bp RAPD marker; (3) design of the primer pair Bf 392-1/Bf 392-2 flanking a 392-bp specific internal sequence; and (4) synthesis of quantities of a 392-bp second generation DNA probe by PCR amplification. The PCR-DNA probe assay includes a PCR amplification of a 392-bp specific sequence in the genomic DNA of B. forsythus strains followed by hybridization with the 392-bp digoxigenin-labelled second generation probe. We observed strong, specific hybridization with the amplified DNAs from 11 stains of B. forsythus and no cross-hybridization with the PCR products from 22 foreign species. The PCR-DNA probe assay must be seen as a highly specific and sensitive method for the detection of B. forsythus in mixed infections.

Bacteroides↗

PubMed2000

3'-minor groove binder-DNA probes increase sequence specificity at PCR extension temperatures.

DNA probes with conjugated minor groove binder (MGB) groups form extremely stable duplexes with single-stranded DNA targets, allowing shorter probes to be used for hybridization based assays. In this paper, sequence specificity of 3'-MGB probes was explored. In comparison with unmodified DNA, MGB probes had higher melting temperature (T(m)) and increased specificity, especially when a mismatch was in the MGB region of the duplex. To exploit these properties, fluorogenic MGB probes were prepared and investigated in the 5'-nuclease PCR assay (real-time PCR assay, TaqMan assay). A 12mer MGB probe had the same T(m)(65 degrees C) as a no-MGB 27mer probe. The fluorogenic MGB probes were more specific for single base mismatches and fluorescence quenching was more efficient, giving increased sensitivity. A/T rich duplexes were stabilized more than G/C rich duplexes, thereby leveling probe T(m)and simplifying design. In summary, MGB probes were more sequence specific than standard DNA probes, especially for single base mismatches at elevated hybridization temperatures.

Base Pair Mismatch↗

PubMed1989

Genetic services in the context of DNA probes: what do they cost?

We describe results from the first year of a three year economic evaluation of genetic services in the context of DNA probes provided at three genetic centres in Great Britain. The analysis so far has concentrated on the costs of providing DNA diagnostic services. Estimates are given of the total costs of providing DNA probe services at each of the three centres, together with information for assessing the cost implications of future developments in these services. DNA probe services are likely to be funded as a Regional specialty. This paper concludes that relative to other developing medical technologies and as an investment by Regions, DNA probe services are inexpensive. An appraisal of the benefits to be derived from DNA probe services is still to be undertaken.

Cost-Benefit Analysis↗

PubMed1992

A procedure for repeated usage of 33P-labeled DNA probes in hybridization experiments.

We describe a technique for repeated use of 33P-labeled DNA probes in Southern hybridization experiments. A nick-translated 33P-labeled DNA probe in a volume of 0.5-1.0 ml of hybridization mixture (final concentration, 10-100 ng/ml) is used to wet a sheet of filter paper (approx 10 microliters/cm2), which covers a nylon membrane with DNA transferred by Southern blotting, and both are set between two washed X-ray films. The "sandwich" is placed in a plastic bag for hybridization for 16-24 h at 42 degrees C. This very simple procedure using 33P-labeled DNA probes has a number of advantages over the standard method using 32P-labeled probes: (a) a significantly lower biohazard (body/arms exposure); (b) a very small volume of hybridization mixture in contact with a DNA-containing membrane and the higher probe concentrations attainable, causing some increase in sensitivity, and, finally, (c) repeated use of the probe-containing filter (over approx 3 days for unique sequences and up to 2 weeks for reiterated sequences) due to a relatively long 33P half-life (25.3 days).

Autoradiography↗

PubMed1993

A transcriptionally amplified DNA probe assay with ligatable probes and immunochemical detection.

Transcriptionally amplified DNA probes are valuable tools in the development of sensitive nucleic acid-based diagnostic assays. Here we describe a model assay using a novel oligonucleotide hairpin probe that encodes a T7 RNA polymerase promoter. The hairpin probe and an adjacently hybridizing biotinylated capture probe were hybridized to target DNA and the duplex was captured onto streptavidin-coated magnetic particles. After ligation of the immobilized probes, which served to maintain specificity, the hairpin probe was transcribed by T7 RNA polymerase. The amplified RNA product was hybridized to the capture probe and bound to the streptavidin-coated magnetic particles. The immobilized heteroduplex was detected with an antibody-alkaline phosphatase conjugate specific for DNA:RNA hybrids, and the chemiluminescent substrate adamantyl-1,2-dioxetane phenyl phosphate. Ten attomoles of target DNA could be detected in a background of 5 micrograms of unrelated DNA. The chemiluminescent immunoassay was as sensitive as radioactive detection of specific product after gel electrophoresis.

Base Sequence↗

PubMed2000

Whole genomic DNA probe for detection of Porphyromonas endodontalis.

The purpose of the present study was to develop a DNA probe for Porphyromonas endodontalis. Pure cultures of P. endodontalis were grown in TYP medium, in an anaerobic chamber. DNA was extracted from the P. endodontalis and labeled using the Genius System by Boehringer Mannheim. The labeled P. endodontalis DNA was used in dot-blot hybridization reactions with homologous (P. endodontalis) and unrelated bacterial samples. To determine specificity, strains of 40 other oral bacterial species (e.g. Porphyromonas gingivalis, Porphyromonas asaccharolytica, and Prevotella intermedia) were spotted and reacted with the P. endodontalis DNA probe. None of the panel of 40 oral bacteria hybridized with the P. endodontalis probe, whereas the blot of the homologous organism showed a strong positive reaction. To determine the sensitivity of the probe, dilutions of a P. endodontalis suspension of known concentration were blotted onto a nylon membrane and reacted with the probe. The results of our investigation indicate that the DNA probe that we have prepared specifically detects only P. endodontalis and can detect at least 3 x 10(4) cells.

Colony Count, Microbial↗

PubMed1990

Development of sensitive methods for the detection of mycobacteria by DNA probes.

A sensitive method allowing the detection of mycobacteria by DNA probing has been developed. Besides the choice of a relevant probe encoding for part of the ribosomal RNA genes, the critical step allowing this high sensitivity was the method by which mycobacteria were lysed. Sonication of mycobacteria in the presence of chloroform followed by dot blot by this lysate gave the highest sensitivity in the detection of sequences homologous to the DNA probes.

Cloning, Molecular↗

PubMed1992

A degenerate alpha satellite probe, detecting a centromeric deletion on chromosome 21 in an apparently normal human male, shows limitations of the use of satellite DNA probes for interphase ploidy analysis.

A degenerate alpha satellite DNA probe specific for a repeated sequence on human chromosomes 13 and 21 was synthesized using the polymerase chain reaction (PCR). Fluorescence in situ hybridization (FISH) with this probe to normal metaphase spreads revealed strong probe binding to the centromeric regions of human chromosomes 13 and 21 with negligible cross-hybridization with other chromosomes. FISH to normal interphase cell nuclei showed four distinct domains of probe binding. However, hybridization with probe to interphase and metaphase preparations from one apparently normal human male resulted in only three major binding domains. Metaphase chromosome analysis revealed a centromeric deletion on one chromosome 21 that caused greatly reduced probe binding. The result suggest caution in the interpretation of interphase ploidy studies performed with chromosome-specific alphoid DNA probes.

Adult↗