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PubMedDate not supplied

DNA fingerprinting using arbitrary primer technology (APT): a tool or a torment.

A recent variation of the PCR has allowed DNA fingerprints to be obtained independently of prior sequence information and with unparalleled ease. Several approaches, conveniently grouped under the general term of arbitrary primer technology (APT), include the popular RAPD, DAF, and AP-PCR methods. A great deal of attention has been focussed on these methods and questions have arisen regarding reproducibility, DNA fingerprint resolution, and even the future of the technology itself. Here we discuss these issues and examine some of the unique properties of DNA amplification using a single short arbitrary primer.

DNA Fingerprinting↗
PubMed1996

Typing of rhizobia by PCR DNA fingerprinting and PCR-restriction fragment length polymorphism analysis of chromosomal and symbiotic gene regions: application to Rhizobium leguminosarum and its different biovars.

Characterization of 43 strains of Rhizobium leguminosarum biovars viciae, trifolii, and phaseoli was performed by two methodologies based on PCR amplification, i.e., PCR DNA fingerprinting of interrepeat sequences and restriction fragment length polymorphism (RFLP) analysis of PCR -amplified chromosomal and symbiotic gene regions. Groupings generated by PCR DNA fingerprinting with either extragenic palindromic repetitive primers or two different single random primers were correlated with similar levels of resolution. Although less discriminating, PCR-RFLP analysis of intergenic spacer between genes coding for 16S and 23S rRNA (16S and 23S rDNA) yielded intraspecific polymorphisms. The classification of strains was independent of the biovar status and was in agreement with those obtained by PCR DNA fingerprinting. Intrabiovar variation within symbiotic gene regions was detected by PCR-RFLP analysis of nifDK and nodD gene regions, but the strains were grouped according to the biovar. The rDNA intergenic spacer and nif primers were verified to be universal for rhizobial species by testing of various reference strains, whereas the nod primers designed in this study were biovar or species specific for R. leguminosarum and Rhizobium etli. Classifications of R. leguminosarum strains by the PCR-based methods were correlated with those previously obtained by conventional total DNA restriction profile comparisons and RFLP analysis using chromosomal and symbiotic gene probes. Ranges of discriminating powers were also equivalent between the two approaches. However, the PCR-based methods are much less time-consuming and are therefore more convenient.

Bacterial Typing Techniques↗
PubMed1992

M13 DNA fingerprinting, a new tool for classification and identification of Lactobacillus spp.

The optimal conditions for the application of M13 DNA fingerprinting to the genus Lactobacillus were determined. Comparative fingerprint analysis of representative strains of Lactobacillus delbrueckii subsp. delbrueckii, Lact. delbrueckii subsp. lactis, Lact. delbrueckii subsp. bulgaricus, Lact. helveticus and Lact. casei permitted the differentiation of species, subspecies and individual strains and the quantitative determination of their genetic relatedness. The results confirm the high specificity of M13 DNA fingerprinting and indicate that it might be used in the classification of Lactobacillus spp.

Blotting, Southern↗
PubMed1996

Relationship between band sharing levels of DNA fingerprints and inbreeding coefficients and estimation of true inbreeding in turkey lines.

A regression analysis between band sharing of DNA fingerprints and calculated inbreeding coefficients was conducted using six experimental turkey lines. The DNA fingerprints were produced from 18 individual DNA samples per line representing different families. The DNA was digested with a HaeIII restriction enzyme and hybridized with Jeffreys' 33.6 probe. The band sharing within lines ranged from 0.42 to 0.62. The inbreeding coefficients of the lines were calculated based on population sizes and variation in family sizes. The inbreeding coefficients varied from 2.5 to 45%. Regression analysis between the two variables yielded a highly significant (P < or = 0.0001) linear model with a correlation coefficient of 0.992. The linear model was used to estimate the actual inbreeding in these lines.

Animals↗
PubMed1990

DNA fingerprinting for forensic identification: potential effects on data interpretation of subpopulation heterogeneity and band number variability.

Some methods of statistical analysis of data on DNA fingerprinting suffer serious weaknesses. Unlinked Mendelizing loci that are at linkage equilibrium in subpopulations may be statistically associated, not statistically independent, in the population as a whole if there is heterogeneity in gene frequencies between subpopulations. In the populations where DNA fingerprinting is used for forensic applications, the assumption that DNA fragments occur statistically independently for different probes, different loci, or different fragment size classes lacks supporting data so far; there is some contrary evidence. Statistical association of alleles may cause estimates based on the assumption of statistical independence to understate the true matching probabilities by many orders of magnitude. The assumptions that DNA fragments occur independently and with constant frequency within a size class appear to be contradicted by the available data on the mean and variance of the number of fragments per person. The mistaken use of the geometric mean instead of the arithmetic mean to compute the probability that every DNA fragment of a randomly chosen person is present among the DNA fragments of a specimen may substantially understate the probability of a match between blots, even if other assumptions involved in the calculations are taken as correct. The conclusion is that some astronomically small probabilities of matching by chance, which have been claimed in forensic applications of DNA fingerprinting, presently lack substantial empirical and theoretical support.

Alleles↗
PubMed1995

Involvement of multiple Cryptococcus neoformans strains in a single episode of cryptococcosis and reinfection with novel strains in recurrent infection demonstrated by random amplification of polymorphic DNA and DNA fingerprinting.

We compared the abilities of random amplification of polymorphic DNA and DNA fingerprinting, with oligonucleotide probes, to type five pairs of Cryptococcus neoformans clinical isolates recovered from five separate human immunodeficiency virus-positive patients in London, England. The two techniques had comparable discriminatory abilities when applied to these isolates. A total of eight different isolate types were demonstrated in these patients. No isolate type was observed in more than one patient. Two of the isolate pairs recovered from single episodes of cryptococcosis within 1 day of each other were genotypically indistinguishable by both methods. The other three pairs of isolates were all distinguishable. One of these isolate pairs was obtained from a single episode of cryptococcosis, while the other two were obtained from recurrent infections. These results indicate that multiple strains of C. neoformans may be responsible for a single episode of cryptococcosis and that recurrent infection may occur as a result of reinfection with a novel strain.

Base Sequence↗
PubMed1988

Detection of DNA "fingerprints" of cultivated rice by hybridization with a human minisatellite DNA probe.

A human minisatellite DNA probe detects several restriction fragment length polymorphisms in cultivars of Asian and African rice. Certain fragments appear to be inherited in a Mendelian fashion and may represent unlinked loci. The hybridization patterns appear to be cultivar-specific and largely unchanged after the regeneration of plants from tissue culture. The results suggest that these regions of the rice genome may be used to generate cultivar-specific DNA fingerprints. The demonstration of similarity between a human minisatellite sequence and polymorphic regions in the rice genome suggests that such regions also occur in the genomes of many other plant species.

Cloning, Molecular↗
PubMedDate not supplied

Serotypes and DNA fingerprint profiles of Pasteurella multocida isolated from raptors.

Pasteurella multocida isolates from 21 raptors were examined by DNA fingerprint profile and serotyping methods. Isolates were obtained from noncaptive birds of prey found in 11 states from November 28, 1979, through February 10, 1993. Nine isolates were from bald eagles, and the remaining isolates were from hawks, falcons, and owls. Seven isolates were members of capsule group A, and 14 were nonencapsulated. One isolate was identified as somatic type 3, and another was type 3,4,7; both had unique HhaI DNA fingerprint profiles. Nineteen isolates expressed somatic type 1 antigen; HhaI profiles of all type 1 isolates were identical to each other and to the HhaI profile of the reference somatic type 1, strain X-73. The 19 type 1 isolates were differentiated by sequential digestion of DNA with HpaII; four HpaII fingerprint profiles were obtained. The HpaII profile of one isolate was identical to the HpaII profile of strain X-73. Incidence of P. multocida somatic type 1 in raptors suggests that this type may be prevalent in other wildlife or wildlife environments.

Animals↗
PubMed1996

DNA fingerprinting and serotyping of Campylobacter jejuni isolates from epidemic outbreaks.

The aim of the present investigation was to compare DNA fingerprinting and serotyping (heat-stabile and heat-labile antigens) of isolates from epidemic outbreaks as well as of solitary isolates. Campylobacter jejuni isolates from two epidemic outbreaks in Sweden, one milkborne (35 isolates) and one waterborne (17 isolates), and one waterborne outbreak in Norway (11 isolates), as well as 30 solitary isolates from Swedish patients with gastroenteritis, were analyzed. A total of 93 isolates were analyzed. In the waterborne outbreak in Norway, only one serotype with one DNA pattern was found. In the milkborne outbreak in Sweden, two serotypes (HS2:HL4 and HSNT:HL4) with two different DNA patterns were found. The isolates from the waterborne outbreak in Sweden were different serotypes. For two isolates of the same serotype, different DNA patterns were seen. This was also recorded for isolates from solitary cases. It was concluded that serotyping is a useful tool in most epidemiological situations but sometimes lacks sufficient discriminatory power. DNA fingerprinting can add valuable epidemiological information to that supplied by serotyping and can in some situations provide sufficient epidemiological information when used alone.

Animals↗
PubMed1989

Demonstration of spontaneous XX/XY chimerism by DNA fingerprinting.

The M13 bacteriophage probe, which makes possible the establishment of DNA fingerprints, was used to study a phenotypically normal woman with a 46XY karyotype and her twin brother. Identical fingerprints and positive hybridization with a series of Y-specific probes were obtained on blood samples from the siblings. DNA from a skin biopsy of the woman yielded a clearly different pattern and displayed no Y-specific hybridization, indicating that she is a spontaneous chimera. This study illustrates the use of DNA fingerprinting as a powerful and simple aid to the diagnosis of natural chimerism.

Adult↗
PubMedDate not supplied

Forensic application of DNA 'fingerprints'.

Many highly polymorphic minisatellite loci can be detected simultaneously in the human genome by hybridization to probes consisting of tandem repeats of the 'core' sequence. The resulting DNA fingerprints produced by Southern blot hybridization are comprised of multiple hypervariable DNA fragments, show somatic and germline stability and are completely specific to an individual. We now show that this technique can be used for forensic purposes; DNA of high relative molecular mass (Mr) can be isolated from 4-yr-old bloodstains and semen stains made on cotton cloth and digested to produce DNA fingerprints suitable for individual identification. Further, sperm nuclei can be separated from vaginal cellular debris, obtained from semen-contaminated vaginal swabs, enabling positive identification of the male donor/suspect. It is envisaged that DNA fingerprinting will revolutionize forensic biology particularly with regard to the identification of rape suspects.

Blood Proteins↗
PubMed2004

[Identification of the resource suspected sperm by DNA fingerprinting].

OBJECTIVE: To identify the resource suspected sperm of donor in human sperm bank and apply the parentage testing between the donor and his offspring. METHODS: We took the 6 semen specimen of the donor involved and correspondently suspected semen as well as the semen of one volunteer and peripheral blood of his offspring. All specimens were amplified by PCR, and DNA fingerprint was detected by PAGE electrophoresis. RESULTS: By DNA fingerprinting we discovered that the 5 suspected sperm samples came from corresponding donors and the other sample from another. The volunteer and his offspring were identified as consanguinity. CONCLUSION: We can identify the difference between sperm of donors and the suspected sperm of donors, and sperm of donors and the peripheral blood of their offspring exactly by DNA fingerprinting.

Adult↗
PubMed2000

Persistence of cellulitis-associated Escherichia coli DNA fingerprints in successive broiler chicken flocks.

Avian cellulitis in broiler chickens is primarily caused by Escherichia coli. Previous research found that the E. coli isolates of cellulitis origin were unique to each ranch, suggesting that these E. coli were endemic within the ranch environment. To test the hypothesis that the E. coli associated with cellulitis are endemic in the litter of the broiler house, we designed a study to determine whether E. coli DNA fingerprints associated with cellulitis persist over successive flocks that are grown in the same house. In addition, we assessed the impact of different cleaning and disinfection strategies on this persistence. Two broiler houses were followed on each of five farms over 3-4 flocks. A total of 353 E. coli isolates from cellulitis lesions were analyzed in this study, and 314 of these isolates (89%) were DNA fingerprinted by PFGE. In each ranch, there were several DNA fingerprint patterns that were present over successive flocks, regardless of the cleaning and disinfection strategy utilized. Isolates persisted as long as 191 days, implying that these E. coli are capable of persisting in the broiler house environment for long periods of time. In addition, these E. coli isolates were associated with cellulitis lesions in successive flocks. Thus, the isolates of E. coli that are associated with cellulitis in broiler chickens appear to be endemic in the litter environment of the broiler house.

Animal Husbandry↗
PubMed1990

Probe-specific DNA fingerprinting applied to the epidemiology of localized juvenile periodontitis.

Although Actinobacillus actinomycetemcomitans has been recognized as a primary etiological agent in localized juvenile periodontitis, questions remain concerning the source of infection, mode of transmission, and relative virulence of strains. DNA fingerprinting analysis, using a randomly cloned chromosomal DNA fragment as a probe, revealed that previously characterized strains of A. actinomycetemcomitans displayed significant restriction site heterogeneity which could be applied to the typing of clinical isolates of this bacterium such that individual strains or variants could be traced within subjects from localized juvenile periodontitis families. Hybridization data derived from an analysis of bacterial isolates obtained from families participating in an ongoing longitudinal study of the disease showed that a single individual could be infected with more than one strain or variant of A. actinomycetemcomitans and that various members of the same family could harbor different strains or variants of the bacterium. In several cases the clinical isolates were matched to characterized laboratory strains by comparing hybridization patterns generated by digestion of the DNA with several restriction enzymes in independent reactions. Thus, probe-specific DNA fingerprinting of A. actinomycetemcomitans will permit us to determine if particular strains or variants are frequently associated with sites of periodontal destruction. Attention could then be focused on determining the virulence properties of those strains or variants that have in vivo significance.

Actinobacillus↗
PubMed1995

DNA fingerprinting of Musa cultivars with oligodeoxyribonucleotide probes specific for simple repeat motifs.

Using synthetic oligodeoxyribonucleotide probes against restriction-digested genomic DNA, we have established DNA fingerprinting of Musa cultivars. Of all the enzymes used, Eco RI and Hin dIII were found to be most informative, giving rise to individual specific band patterns with oligonucleotide probes of 15- to 18-base residues. Of the several probes and enzyme combinations used, the 15mer GACA probe with Eco RI and Hin dIII digests revealed a maximal level of polymorphism, and the probability of obtaining an identical band pattern between any two random genotypes was calculated to be 1.50 x 10(-9) and 1.59 x 10(-9), respectively. Oligonucleotide probes longer than 22 residues were also used but did not hybridize. The present approach is useful for cultivar identification and for overall genome analysis to establish relatedness among the various accessions of the Musa germplasm originating from different geographic locations. The relevance of using synthetic oligonucleotide probes based on simple repeat motifs for achieving DNA fingerprinting pattern is discussed.

Base Sequence↗
PubMed2005

Five-year follow-up study of mother-to-child transmission of Helicobacter pylori infection detected by a random amplified polymorphic DNA fingerprinting method.

Recent studies have speculated on the possible role of the mother in transmitting Helicobacter pylori infection to their children. In an attempt to either prove or disprove this supposition, we investigated the rates of infection of children born to H. pylori-positive mothers from birth to 5 years of age using serology and the stool antigen test. When infection of the children did occur, the strains from the children were compared to those of their mothers using DNA analysis. Sixty-nine of the 350 pregnant mothers (19.7%) had a positive serology for H. pylori. Fifty-one children underwent serological examinations and stool antigen tests at 4 to 6 days after birth, followed by 1, 3, and 6 months. They were continuously given the stool antigen test at 4- to 6-month intervals until the age of 5 years. Gastric juice samples were collected from the infected children and their mothers for culture and DNA analyses using a random amplified polymorphic DNA fingerprinting method. None of the 51 children acquired H. pylori infection during the first year of life. Of the 44 children enrolled in a 5-year follow-up study, five (11%) acquired H. pylori infection. They acquired the infection at the age of 1 year 2 months, 1 year 3 months, 1 year 6 months, 1 year 8 months, and 4 years 4 months. Random amplified polymorphic DNA fingerprinting confirmed that the strains of the five children exhibited DNA fingerprinting patterns identical to those of their mothers. These findings suggest that mother-to-child transmission is the most probable cause of intrafamilial spread of H. pylori.

Antibodies, Bacterial↗
PubMed1992

Analysis of mating systems in the schistosome-vector hermaphrodite snail Bulinus globosus by DNA fingerprinting.

Bulinus globosus, one of the intermediate hosts for Schistosoma, is a hermaphrodite freshwater snail. Multilocus DNA fingerprinting was applied in order to investigate the mating system of this facultatively self-fertilizing species. By analysing DNA fingerprints of eight broods, we have shown that selfed and outcrossed individuals could be unambiguously distinguished by comparison with their parent fingerprints. First, selfed offspring patterns shared a higher number of bands with their mother than did outcrossed ones. Secondly, at least three paternal bands could be detected per outcrossed offspring pattern.

Animals↗