SEARCH · PubMed Health

Results for “DNA probe”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 253 records · Page 14Linked to original sources

PubMed1990

DNA Probe for Lactobacillus delbrueckii.

From a genomic DNA library of Lactobacillus delbrueckii subsp. bulgaricus, a clone was isolated which complements a leucine auxotrophy of an Escherichia coli strain (GE891). Subsequent analysis of the clone indicated that it could serve as a specific DNA probe. Dot-blot hybridizations with over 40 different Lactobacillus strains showed that this clone specifically recognizes L. delbrueckii subsp. delbrueckii, bulgaricus, and lactis. The sensitivity of the method was tested by using an alpha-P-labeled DNA probe.

Journal Article↗

PubMed1989

Isolation of a potential DNA probe for Toxoplasma gondii.

A genomic DNA library for Toxoplasma gondii has been constructed in plasmid pUC8. Some recombinant plasmids (pJMBG1-pJMBG55) were analysed by restriction endonuclease mapping and by hybridization to DNA isolated from T. gondii and from human tissue culture cells. A number of recombinant plasmids, or DNA fragments derived from these, hybridizing only to Toxoplasma DNA have been identified. These are currently being characterized for the development of diagnostic DNA probes for Toxoplasma.

Animals↗

PubMed1985

Comparison of gram stain, DNA probe, and culture for the identification of species of Mobiluncus in female genital specimens.

The detection of species of Mobiluncus in female genital specimens by DNA probe (with whole-chromosomal bacterial DNA), culture, and gram stain were compared by using specimens obtained from hospital patients, college students, and women attending a sexually transmitted disease clinic. Culture purification and speciation required an average of 37 days to complete, whereas the DNA-probe assay required five days. Gram stain was also rapid but did not allow speciation. There was 100% correlation between species identification by DNA probe and by conventional biochemical tests. Gram stain alone detected 90% of the samples that were positive by any method, whereas culture detected 77%-83% and DNA probe detected 52%-83%.

Bacteria, Anaerobic↗

PubMed1996

Design and validation of DNA probe sets for a comprehensive interphase cytogenetic analysis of acute myeloid leukemia.

The objective of this study was to design DNA probe sets that enable the detection of chromosome aberrations in acute myeloid leukemia (AML) by interphase cytogenetics using fluorescence in situ hybridization (FISH) and to compare the results of interphase cytogenetics with those of conventional chromosome banding analysis. One hundred five consecutive patients with adult AML entered on a multicenter treatment trial were studied with a comprehensive set of DNA probes recognizing the most relevant AML-associated structural and numerical chromosome aberrations: translocations t(8;21), t(15;17), and t(11q23); inversion inv(16);chromosomal deletions (5q-, 7q-, 9q-, 12p-, 13q-, 17p-, and 20q-); and chromosomal aneuploidies. Interphase cytogenetics was particularly sensitive for detecting the AML-specific gene fusions: 3 additional cases of inv(16) and 1 additional case of t(8;21) were identified by FISH that were missed by banding analysis, whereas equal numbers of t(11q23) and t(15;17) were detected. Five additional cases of trisomy 8q, 3 more cases of trisomy 11q, and 2 more cases of trisomies 21q and 22q were shown by FISH. These aberrations were either masked in complex karyo-types or identified in cases in which conventional banding analysis failed. On the other hand, the DNA probes selected were not informative to detect 1 case of 5q-, 9q-, and 20q-. In 5 cases, clonal aberrations were detected on banding analysis for which no FISH probes were selected. In conclusion, interphase cytogenetics proved to be more sensitive for detecting AML-specific chimeric gene fusions and some partial trisomies. Interphase cytogenetics provides a powerful technique complementary and, with further development of diagnostic DNA probes, even an alternative to chromosome banding studies for the cytogenetic analysis of AML.

Acute Disease↗

PubMed2005

Identification of an anonymous RFLP DNA probe through multiple arbitrary amplicon profiling and its use for strain differentiation in a field isolate of cellulose-degrading Aspergillus niger.

The genome of Aspergillus niger (MPS-002) was subjected to RAPD fingerprinting using none different random oligonucleotide primers. A 0.7 Kb PCR amplicon, generated by primer-3 could be used as a RFLP probe to differentiate A. niger (ATCC 16880) from A. niger (MPS-002). The probe revealed DNA polymorphism internal to two different EcoRI recognition sequences spaced apart at a distance of 0.4 Kb within a 4.0 Kb EcoRI fragment of the genome of both the strains. Localized genome mapping analysis further revealed that the 0.7 Kb RFLP probe was positioned at a distance of 2.7 Kb and 0.6 Kb from the two ends of a 4.0 Kb EcoRI fragment, respectively within the genome of the two strains of A. niger.

Aspergillus niger↗

PubMed1991

[Evaluation of DNA-probe assay for the clinical diagnosis of Mycoplasma pneumoniae infections].

DNA probe-assay using the Gen-Probe kit was carried out to detect Mycoplasma pneumoniae infections. Fifteen children visited Ota General Hospital complaining of dry cough and high grade fever. Throat swabs of the patients were examined to detect M. pneumoniae ribosomal RNA by Gen-Prove kit. Five out of 15 patients were positive for DNA probe assay of M. pneumoniae. Clinical and laboratory data including serological examinations were compatible with M. pneumoniae infection in these cases. Following the improvement of clinical symptoms and signs by receiving erythromycin or minocycline, the positivity for DNA probe assay turned to negative. Among the ten patients, who were negative for DNA probe assay, 2 cases were suspected of M. pneumoniae infection on the basis of clinical and laboratory findings. One patient had already taken antibiotics. Therefore, in these two patients, there was a possibility that the bacterial numbers were too small to be detected by DNA-probe assay. The data described above support that DNA-probe assay is useful for the diagnosis of M. pneumoniae infections in the early stage. DNA-probe assay is also valuable to follow up the clinical course of the patients.

Child↗

PubMed1987

DNA probes detect genomic diversity in Theileria parva stocks.

Different stocks of Theileria parva were analysed for restriction fragment length polymorphisms by agarose gel electrophoresis, orthogonal-field-alternation gel electrophoresis (OFAGE) and Southern hybridization with DNA probes. Polymorphisms seen with DNA from purified piroplasms of different T. parva stocks, after digestion with restriction enzymes, were more clearly apparent with OFAGE than with standard agarose gel electrophoresis. Genomic differences between these theilerial parasites were investigated further using three DNA probes, which were selected from a genomic library of T. parva (Muguga) piroplasm DNA cloned in lambda gt11. All three clones hybridized to T. parva DNA in preparations from schizont-infected bovine lymphoblastoid cells and to DNA from intraerythrocytic piroplasms. These probes did not, however, hybridize under high stringency conditions to DNA prepared from uninfected bovine lymphoblasts, T. mutans piroplasms, or bovine lymphoblasts infected with T. annulata or T. taurotragi. The five Kenyan stocks of T. parva that were tested showed characteristic hybridization patterns with these DNA probes. Our results show that DNA probes can be used to distinguish selected stocks of T. parva by hybridization to DNA either from intraerythrocytic piroplasms taken from infected cattle, or from isolates of schizont-infected bovine lymphoblastoid cells that are maintained continuously in vitro.

Animals↗

PubMed1994

Similarities between Fusobacterium nucleatum and bacteroides fragilis studied by two DNA probes derived from Fusobacterium nucleatum.

A polymerase chain reaction (PCR)-amplified oligonucleotide DNA probe corresponding to a Fusobacterium nucleatum Fevl DNA region coding for a 40-kDa major outer-membrane protein (OMP) and a randomly cloned 2.1 kb DNA probe were found to recognize DNA from the Gram-negative bacteria Fusobacterium nucleatum and Bacteroides fragilis on Southern blots and slot blots. The results indicate sequence similarity within the DNA fragments studied. Immunoblots tested with polyclonal antibodies against whole cells of F. nucleatum revealed only weak antigen similarity between these species.

Aggregatibacter actinomycetemcomitans↗

PubMed1996

Novel DNA probes capable of discriminating indica and japonica rice cultivars.

We obtained two DNA clones, G93 (1.6kb) and G318 (1.7kb) from indica rice (Oryza sativa L.) cultivar Culture 340. Southern hybridization analysis indicated that both DNA probes hybridized with DNA of indica cultivars but not with japonica cultivars. Some javanica cultivars DNAs did not hybridize with these probes. Nucleotide sequence (400bp) of a part of G93 showed a 65.8% G + C content. These novel DNA probes can be used for the study of evolutional fingerprinting of rice cultivars.

Base Sequence↗

PubMed1997

PCR-DNA probe assays for identification and detection of Prevotella intermedia sensu stricto and Prevotella nigrescens.

The purpose of this study was to construct PCR-DNA probe assays specific for Prevotella intermedia sensu stricto and Prevotella nigrescens based on the ability of randomly amplified polymorphic DNA (RAPD) fingerprinting to generate species-specific markers. The strategy included four steps: (i) construction of first-generation DNA probes from a 850-bp RAPD marker for P. intermedia sensu stricto and a 1,300-bp RAPD marker for P. nigrescens, (ii) cloning and sequencing of each RAPD marker, (iii) designing of primer pairs flanking specific internal sequences of 754 bp for P. intermedia sensu stricto and of ca. 1,100 bp for P. nigrescens, and (iv) synthesis (by PCR amplification) and digoxigenin labeling of quantities of DNA probes 754 and ca. 1,100 bp in size. The PCR-DNA probe assays combine either PCR amplification of a 754-bp specific sequence in the genomic DNA of strains of P. intermedia sensu stricto and hybridization with the 754-bp digoxigenin-labeled probe or amplification of a ca. 1,100-bp sequence of P. nigrescens and hybridization with the ca. 1,100-bp probe. Specific hybridization was observed with the amplified DNAs from 25 strains of P. intermedia and 24 strains of P. nigrescens, and no reaction was observed with the PCR products from 20 foreign species. The PCR-DNA probe assays described here should allow a highly specific and sensitive detection of P. intermedia sensu stricto and P. nigrescens in mixed infections.

Bacterial Typing Techniques↗

PubMed1986

A computer programme for estimation of genetic risk in X linked disorders, combining pedigree and DNA probe data with other conditional information.

A computer programme is presented for calculating the recurrence risk in X linked disorders, combining pedigree and DNA probe data with other conditional information such as carrier detection tests. The methods of computation are shown in the given examples. The programme can be used with either a single DNA probe or two 'flanking' DNA probes for both familial and isolated case pedigrees. For isolated case families the mutation rate at the disease locus can be taken into account in conjunction with the DNA probe data.

DNA↗

PubMed1989

Identification and partial characterization of Mycobacterium avium and Mycobacterium intracellulare by using DNA probes.

We attempted to identify the Mycobacterium avium complex (MAC) isolated in Japan by using DNA probes specific for M. avium or Mycobacterium intracellulare (Gen-Probe Rapid Diagnostic System for MAC; Gen-Probe, Inc., San Diego, Calif.). The source and drug susceptibility distributions were examined. This assay system proved to be rapid, sensitive, specific, and reliable for identification of MAC and of the species as either M. avium or M. intracellulare. The DNA probe test showed that of the generally accepted MAC serovars, serovars 1 to 6, 8 to 11, and 21 belonged to M. avium and 7 and 12 to 20 belonged to M. intracellulare. Moreover, with the DNA probe test we found that the distribution patterns of M. avium and M. intracellulare isolates in Japan differed depending on the district in which MAC was isolated. The ratio of M. avium was much higher in eastern Japan. In Tokai and Shimane districts, the ratio of M. avium and M. intracellulare isolates significant in human disease was related to that of isolates from soil and house dust (natural sources). In M. avium, human disease-associated isolates were more resistant to rifampin, streptomycin, and kanamycin than were isolates from natural sources. However, this source dependence was not evident for M. intracellulare. In human disease-associated MAC, M. avium isolates were more resistant to most agents, except for quinolones, than were M. intracellulare isolates.

Animals↗

PubMed2003

Identification of Streptococcus sanguinis with a PCR-generated species-specific DNA probe.

The objective of the present study was to design a PCR-generated DNA probe and determine the specificity of the probe for the identification of clinical isolates of Streptococcus sanguinis. To do this, we examined over 200 arbitrarily primed PCR (AP-PCR) amplicon patterns obtained with DNA from clinical isolates of S. sanguinis. A 1.6-kb DNA amplicon that was common to all AP-PCR profiles was extracted from agarose gels and then cloned and sequenced. A search for a similar sequence in the GenBank database with the BLASTN program revealed that the 1.6-kb DNA fragment comprised an intergenic region between two housekeeping genes, uncC (proton-translocating ATPase) and murA (UDP-N-acetylglucosamine enolpyruvyl transferase). Three digoxigenin-labeled DNA probes were synthesized on the basis of the sequence of the 1.6-kb fragment: the sequence of probe SSA-1 contained the proton-translocating ATPase (uncC) and the entire intergenic region, the sequence of probe SSA-2 contained only the intergenic region, and the sequence of probe SSA-3 contained an internal region of the murA gene. Dot blot hybridization showed that the three probes displayed signals for hybridization to both S. sanguinis strain ATCC 10556 and the S. sanguinis clinical isolates. Probe SSA-1, however, hybridized to DNA from S. oralis and S. mitis. Probe SSA-3 hybridized to DNA from S. gordonii, S. mitis, S. oralis, S. parasanguinis, and S. vestibularis. The probe SSA-2-specific intergenic region appeared to be specific for S. sanguinis. The results from this study suggest that probe SSA-2 may serve as a species-specific DNA probe for the identification of clinical isolates of S. sanguinis.

Base Sequence↗

PubMed1997

Usefulness of HCV-RNA assays in efficacy evaluation of interferon treatment for chronic hepatitis C: Amplicor HCV assay and branched DNA probe assay.

We investigated the usefulness of Amplicor HCV assay and branched DNA probe assay in efficacy evaluation of interferon therapies for chronic hepatitis C. Subjects were 164 HCV-RNA positive chronic hepatitis C patients who received interferon-alpha (IFN-alpha, HLBI) 3-6 MU per day for 14-24 weeks. Their HCV-RNA levels were examined five times by using reverse transcription-polymerase chain reaction (RT-PCR) assay, Amplicor HCV assay, and branched DNA probe assay. Complete response rate in the low virus level patients was significantly higher than in the high virus level patients (P < 0.001). In complete responders, the rate of HCV-RNA disappearance 2 weeks after the initiation of IFN therapy was higher than in non-responders (P < 0.001). The HCV-RNA positive rates in RT-PCR assay and Amplicor HCV assay agreed by 98% or more. The HCV-RNA negative patients 6 months later were still negative 12 months later by Amplicor HCV assay. Before starting interferon therapy for chronic hepatitis C, it is advisable to make a prediction of treatment efficacy by using branched DNA probe assay. In addition, disappearance of HCV-RNA after 2 weeks of treatment could be a useful predictor of the therapeutic efficacy of IFN. Amplicor HCV assay is useful in detecting HCV-RNA and for efficacy evaluation during and after a given interferon therapy.

Adult↗

PubMed1989

[Biotinylated DNA probe for detection of streptotricin acetylation genes].

The biotin-labelled DNA probe for identification of functioning and silent genes for streptotricin acetylation has been constructed. The probe is homologous to sat1 gene of the movable genetic element Tn1825. The simplified modification of the hybridization technique using the biotin-labelled DNA probe is described.

Acetylation↗

PubMed1992

[Detection of methicillin-resistant Staphylococcus aureus using PCR and non-radioactive DNA probe].

Two commonly used diagnostic tests for Staphylococcus aureus (MRSA) are cultivation of bacteria from clinical samples on mannitol-salt agar plate or on MRSA-screen agar plate with oxacillin. However, the use of PCR and DNA probes is considered more rapid and sensitive, as staphylococcal cells have high resistance to beta-lactam due to the novel penicillin-binding protein, PBP2'. Therefore, three different pairs of DNA primers (P1F-P1R, P2F-P2R and P3F-P3R) complementary with unique regions of the MRSA PBP2' gene were synthesized for use in polymerase chain reactions with DNA of MRSA. Amplified target DNA of 466, 480 and 630 bp could be resolved on ethidium bromide-stained gels, and hybridized with DNA probes conjugated to alkaline phosphatase. When applied to pure cultures on the MRSA screen agar, the DNA probes detected MRSA in 180 of 196 (P1F-P1R), 72 of 83 (P2F-P2R) and 66 of 71 (P3F-P3R) culture-positive specimens (accuracy range, 86.7-93.0%), while 61.6-89.3% of MRSA were detectable in culture-positive specimens streaked on the mannitol-salt agar. When applied directly to clinical samples, this DNA probe assay detected MRSA in culture-positive specimens within an accuracy range of 50.0-79.3%. It was thus clear that comparison of cultivation and DNA hybridization results yields good correlation with respect to detection of MRSA. These results suggest that the DNA probe assay may be useful in complementing existing culture techniques.

DNA Probes↗

PubMed1997

In vivo and in vitro detection of canine distemper virus nucleoprotein gene with digoxigenin-labelled RNA, double-stranded DNA probes and oligonucleotides by in situ hybridization.

A single-stranded RNA, two double-stranded (ds) DNA probes and 10 oligonucleotides labelled with digoxigenin were comparatively evaluated for their usefulness to detect canine distemper virus (CDV) nucleoprotein RNA in in vitro infected Vero cells and in tissues of dogs with spontaneous CDV infection by in situ hybridization (ISH). In addition, results were compared to CDV nucleoprotein antigen distribution as demonstrated by immunohistochemistry. The RNA probe was derived from the virulent A75/17 strain, the DNA and oligonucleotide probes from the avirulent Onderstepoort strain of CDV. The two DNA probes were 287 and 126 base pairs long. For ISH, various factors including fixatives, proteolytic digestion, probe concentration, hybridization conditions and detection systems were compared. All probes were suitable for demonstration of CDV RNA in in vitro infected cells, regardless of the CDV strain employed. In vivo CDV nucleic acid was detected by RNA and the dsDNA probes. However, the probes varied substantially with respect to sensitivity and specificity. The CDV RNA probe was far superior in sensitivity when compared to the DNA probes. Furthermore, the shorter DNA probe displayed a higher sensitivity, indicating that length of the probe is an important parameter when selecting probes. Oligonucleotides displayed only rarely a positive signal and caused frequently hybridization signals in the nucleus, which where considered not specific for CDV. Summarized, the present study reveals that RNA probes are currently the most sensitive tool for detection of CDV RNA in tissues.

Animals↗

PubMed1996

DNA probes for the Anopheles punctulatus complex.

Genomic DNA probes were made for two recently identified members of the Anopheles punctulatus complex; Anopheles sp. near punctulatus from Papua New Guinea and Anopheles farauti No. 7 from the Solomon Islands. The probes are species-specific and with the use of 32P labeling sensitive enough so that a squash blot of only a small segment of the mosquito is required for identification. The 119-basepair (bp) probe for An. sp. near punctulatus and the 1,106-bp probe for An. farauti No. 7 have been sequenced in full and the probes have been tested on field collected specimens. These probes now make it possible to distinguish An. sp. near punctulatus and An. farauti No. 7 from the other eight members of the An. punctulatus complex. A pan-species probe was also made from the 18S ribosomal DNA that binds to DNA from all members of the complex. These three probes complete the set required for distinguishing all known members of the An. punctulatus complex by DNA hybridization.

Animals↗