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PubMed1993

DNA fingerprinting for genetic monitoring of inbred laboratory rats and mice.

DNA fingerprinting using a nonisotopically labeled minisatellite probe provided a valuable technique for genetic monitoring/quality control of laboratory rodents. Each of 12 inbred rat strains had a unique fingerprint pattern, and colonies separated for over 20 years had identical or nearly identical patterns. Strain LOU/Iap, which is known to have been genetically contaminated in the past, was clearly different from strain LOU/CN, supporting previous findings of studies using biochemical markers. Inbred strains of mice were also found to differ from each other. The F1 hybrid between C57BL/6 and CBA/Ca could not be distinguished from C57BL/6 by using DNA fingerprints, although they could be distinguished by using biochemical markers. Some congenic strains differed from their inbred partner. A suspected genetic contamination of MRL/Mp-lpr mice could not be detected in a sample of the breeding colony by using biochemical markers; however, DNA fingerprints from the suspect animals clearly demonstrated genetic segregation. DNA fingerprinting will be of particular value in investigating suspected problems as only a small sample of fresh, frozen, or ethanol-preserved tissue is needed. Thus, the actual suspect animals can be studied, rather than samples from a breeding colony from which contaminated animals may already have been eliminated.

Animals↗
PubMed1994

Application of DNA fingerprinting in the Hokkaido brown bear (Ursus arctos yesoensis).

DNA fingerprinting employing a minisatellite Myo probe was used for individual identification and paternity determination in Hokkaido brown bears (Ursus arctos yesoensis). We used two restriction enzymes, HinfI and HaeIII to make DNA fingerprints. Band patterns obtained from randomly selected bears were compared with each other, and the probability x that fragment in an individual was also present in the other was 0.69 for HinfI and 0.83 for HaeIII. The value for HinfI (0.69) was similar to that obtained from other species, such as dog and domestic animals, and the mean probability of all fragments was calculated to be 2.5 x 10(-2). The results suggest that DNA fingerprinting applying the combination of HinfI and Myo is available for individual identification. On the other hand, the ability to determine paternity seemed to be insufficient owing to the lack of paternal fragments, although the band patterns reflected the correct relationships between child and father.

Animals↗
PubMed1989

DNA fingerprints of poultry.

Human minisatellite probes cross-hybridize to DNA of several species of poultry (chicken, duck, turkey and goose), and detect high levels of polymorphism. The resulting DNA fingerprints are individual specific, and allow the discrimination even between closely related birds. The pattern of poultry DNA fingerprints is different from that of humans and other animals, having a higher average proportion of large DNA fragments. Pedigree analysis revealed a low number of allelic pairs of variable DNA fragments, indicating that most of the alleles are unresolved in the DNA fingerprint or too small to be detected. The total number of detectable loci in broilers, using probe 33.6, was estimated as 62, of which 13 loci are on average scoreable and available for use. Poultry DNA fingerprints can be used for individual identification, linkage studies and as an aid in breeding programmes.

Alleles↗
PubMed1988

Differences in DNA-fingerprints between remission and relapse in childhood acute lymphoblastic leukemia.

DNA "fingerprint" (DNA-F) analysis, based on the polymorphism caused by numeric variations in the tandem repeats of minisatellite areas of the human genome, has a potential capacity to reveal even minor genomic changes. In this study we have applied DNA-F to the detection of residual disease in leukemia. In order to identify normal and leukemic cell populations, we used two molecular probes: Jeffrey's minisatellite probes and M13 wild type phage probe, which detect different sets of polymorphic fragments in the human genome. Comparison of varying minisatellite fragments between remission and relapse was performed by Southern blot hybridization in seven patients with acute lymphoblastic leukemia (ALL). The results suggest that Southern hybridization with DNA "fingerprint" probes can prove to be a sensitive method in the detection of minimal residual disease in ALL.

Adolescent↗
PubMed1993

[An evaluation of DNA fingerprinting with oligonucleotide probe for forensic purposes].

The synthetic oligonucleotide probe (CAC)5/(GTG)5 for DNA, fingerprinting was studied in this paper. The incomplete pattern of DNA fingerprints was obtained from bloodstains up to three years old, which were kept at room temperature. The identical results were achieved from various human organ tissues of the same individual. DNA fingerprints from vaginal swabs was the same as that obtained from the male donor's blood. The discernible DNA fingerprints were obtained with as little as 250ng of genomic DNA. Besides, using restriction enzyme Hae III instead of Hinf I to digest human DNA, the highly polymorphic hybridization pattern was also obtained. A practical case was tested by Hinf I and Hae III digestion, respectively. The results demonstrated that the (CAC)5/(GTG)5 was a suitable probe for DNA fingerprinting in forensic practice.

Base Sequence↗
PubMedDate not supplied

DNA fingerprinting analysis of vegetative compatibility groups in Aspergillus caelatus.

Forty-three isolates of Aspergillus caelatus, whose vegetative compatibility groups (VCGs) have been identified, were assessed by DNA fingerprinting using a repetitive sequence DNA probe (pAF28) cloned from A. flavus. Thirteen distinct DNA fingerprint groups or genotypes were identified among the 43 isolates. Twenty-four isolates belonging to VCG 1 produced identical DNA fingerprints and included isolates from the United States and Japan. Four other DNA fingerprint groups had multiple isolates sharing identical fingerprints corresponding to VCGs 2, 3, 12 and 13. Eight of the 13 fingerprint groups corresponding to VCGs 4-11 were represented by a single isolate with a unique fingerprint pattern. These results provide further confirmation that the pAF28 probe can distinguish VCGs of species within Aspergillus section Flavi based on DNA fingerprint patterns and that the probe can be used to estimate the number of VCGs in a sample population. Most of the A. caelatus isolates produced fewer restriction fragments and weakly hybridized with the repetitive DNA probe pAF28 compared to hybridization patterns obtained with A. flavus, suggesting less homology of the probe to A. caelatus genomic DNA.

Arachis↗
PubMed1994

Demonstration by DNA fingerprint analysis of genomic instability in mouse BALB 3T3 cells during cell transformation.

We employed DNA fingerprint analysis to monitor DNA rearrangements in BALB 3T3 cells transformed spontaneously or by treatment with 3-methylcholanthrene (MCA) and UV-C. The effect of 12-O-tetradecanoyl-phorbol-13-acetate (TPA) in combination with MCA was also examined. Twenty-three spontaneously transformed cells, 28 induced transformed cells (18 by 1 microgram/ml MCA, six by 5 micrograms/ml MCA, and four by UV-C), and 31 non-transformed subclones were isolated from parental BALB 3T3 A31-1-1 cells. The DNAs were digested with HinfI and subjected to DNA fingerprint analysis with three multi-locus minisatellite probes, Per-6, Core, and Ins. Per-6 was the most effective probe for detecting DNA rearrangements. Rearranged bands detected by the Per-6 probe were observed in 9/31 (29%) of non-transformed subclones, 14/23 (61%) of spontaneously transformed cells, 16/18 (89%) of cells transformed by 1 microgram/ml of MCA, 6/6 (100%) of cells transformed by 5 micrograms/ml MCA, and 4/4 (100%) of UV-C-transformed cells. Higher numbers of DNA rearrangements (> or = 3) occurred most frequently in the induced transformed cells. TPA enhanced the frequency of DNA rearrangements in cells transformed by MCA. These data indicate that (1) genomic DNA in BALB 3T3 cells is unstable and susceptible to rearrangement, (2) its instability is elevated during cell transformation, and (3) MCA and UV-C induce DNA rearrangements, and TPA enhances the effect of the former, probably via the recombination process. DNA fingerprint analysis is valuable for monitoring genomic instability during cell transformation.

3T3 Cells↗
PubMed1989

Individual identification from semen by the deoxyribonucleic acid (DNA) fingerprint technique.

For individual identification from semen, the deoxyribonucleic acid (DNA) fingerprint technique was used. In a blind trial, we succeeded in determining the semen donors among several volunteers comparing the DNA fingerprints of the blood and semen samples, respectively. Thereafter, we examined semen in a condom left beside a naked female dead body. The DNA fingerprint of the semen was recognized to be identical to that of the blood from a suspected man arrested later. This is the first report that the DNA fingerprint technique was practically used in a criminal investigation in Japan.

DNA↗
PubMed2000

DNA fingerprinting of a national sample of Mycobacterium tuberculosis isolates, Botswana, 1995-1996.

DNA fingerprinting may be useful to elucidate tuberculosis (TB) transmission in community settings, but its utility is limited if only few fingerprint patterns are observed or band numbers are low. We performed DNA fingerprinting on a national, population-based sample of Mycobacterium tuberculosis isolates from Botswana. During 1995-1996, a random sample of 213 isolates, representing 5% of all smear-positive TB cases, underwent DNA fingerprinting using restriction fragment length polymorphism (RFLP) IS6110 analysis. Eighty-two (38%) of the 213 isolates belonged to one of 18 clusters, with 2-9 isolates/cluster. The median number of bands was 10 (range 1-19); 183 (86%) had six or more bands. Sixty-three (49%) of 128 patients tested were infected with the human immunodeficiency virus (HIV). The degree of RFLP pattern heterogeneity and high band number support the feasibility of a prospective DNA fingerprinting study in Botswana.

Adult↗
PubMed1996

Prediction of heterosis from DNA fingerprints in chickens.

To assess the value of DNA fingerprints for the prediction of heterosis in chickens, retrospective analyses of data from three crossbreeding experiments and DNA fingerprints (DEP) of parental strains were conducted using two minisatellite and one middle-repetitive DNA probes. DEP bands were assessed on pooled DNA samples of 10-15 individuals per parental genetic group. The number of DEP bands evaluated in the experiments ranged from 81 to 139. The probes varied in their predictive value, but predictability of heterosis generally increased with multiple probes. Highly significant correlations (0.68-0.87) between band sharing ratios (SH) and heterosis were found in 25 crosses of White Leghorns in the first egg production cycle for age at sexual maturity, egg production, and mature body weight: traits with heterosis of 10% or more of the means. Regressions on SH explained 78.4% of the variation in heterosis in age at sexual maturity, 60.2% in egg production and 46.4% in mature body weight. For "broiler" traits with heterosis of < 1%, none of the correlations, based on 13 crosses, were significant. It was concluded that multilocus probe DFP of pooled DNA samples show promise as predictors of heterosis.

Animals↗
PubMed1996

Measurement of genetic parameters within and between turkey lines using DNA fingerprinting.

An experiment was conducted to estimate genetic parameters in six experimental and five commercial primary breeding turkey lines using DNA fingerprinting. Eighteen individual DNA samples per line were digested with an HaeIII restriction enzyme and hybridized with Jeffreys' 33.6 probe. The DNA fingerprints were analyzed with computer programs to measure band sharing (BS) and band frequencies. Within lines, BS ranged from 0.39 to 0.62 and reflected the history of the experimental lines. Among lines, BS ranged from 0.21 to 0.33 with an average of 0.26. The BS among the experimental lines reflected known relationships. All lines were subdivided based on indices of population subdivision. About 26 hypervariable loci were estimated from band frequencies. Average heterozygosity and genetic variability estimated from band frequencies were significantly different among lines and displayed a result very similar to the BS among lines. Genetic distance indices among lines were also significantly different and reflected known relationships between the experimental lines. The experimental selected lines displayed lower genetic diversity than did the other lines. The parameters measuring genetic diversity within lines had higher correlation coefficients among them than did the parameters between lines. The computer program used in this study made DNA fingerprinting easier to use in population analysis.

Animals↗
PubMed2001

Identifying the origin of single corneal cells by DNA fingerprinting: part I--implications for corneal limbal allografting.

PURPOSE: To demonstrate that the combination of impression cytology and single cell DNA fingerprinting represents a powerful tool that is suitable for detecting transplanted cells after corneal limbal allografting. METHODS: Fifty single cells were obtained by corneal impression cytology from 12 patients undergoing cataract surgery. Individual cells were isolated from samples by micromanipulation. Polymerase chain reaction and short tandem repeat profiling was used to obtain forensic standard "DNA fingerprints" from single cells. Blood samples taken at the time of impression cytology provided control "fingerprints." RESULTS: Informative DNA fingerprints were obtained from all corneal samples and 66% (33 of 50 cells) of isolated single cells. Of all fingerprints obtained, most (91%, 30 of 33 fingerprints) corneal fingerprints matched corresponding blood sample fingerprints. At least one corneal fingerprint matched the corresponding blood sample fingerprint in 83% (10 of 12 patients) of the patients in the study. CONCLUSIONS: This extremely specific single cell DNA fingerprinting system permits accurate identification of individual corneal epithelial cells, allowing very reliable determination of their origin, which will enable host and donor cells to be distinguished from each other after keratolimbal allografting procedures, even if the host and donor are the same sex or siblings. These DNA fingerprinting methods allow assessment of quality and quantity of donor cell survival, as well as survival time. The extreme sensitivity and accuracy of the technique means that should contamination occur, it would be identified, thus ensuring meaningful results.

Cell Transplantation↗
PubMed1995

[Analysis of human DNA fingerprints by using fluorescein labelled probe JH12.6].

A method of analysis of human DNA fingerprints has been established by using fluorescein (Fl-11-dUTP) labelled probe JH12.6. The clear and high distinctive patterns of human DNA fingerprints were obtained with this method. The DNA fingerprints of 78 unrelated individuals living in Yunnan province of China were detected, and their probability of chance association between random individuals was calculated as 7.4 x 10(-11), and their mean allelic frequency as 0.09. Comparing of DNA fingerprints with labelling probe JH12.6 by using between radioactive 32P and fluorescein showed that the method by using fluorescein labelled probe JH12.6 was simple, fast, safe and economical. It can totally replace the method by using radioactive 32P labelled probe JH12.6, and it can be broadly applied in forensic medicine and other fields.

DNA Fingerprinting↗
PubMed1992

Estimation of heterozygosity for single-probe multilocus DNA fingerprints.

In spite of the increasing application of DNA fingerprinting to natural populations and to the genetic identification of humans, explicit methods for estimation of basic population genetic parameters from DNA fingerprinting data have not been developed. Contributing to this omission is the inability to determine, for multilocus fingerprinting probes, relatively important genetic information, such as the number of loci, the number of alleles, and the distribution of these alleles into specific loci. One of the most useful genetic parameters that could be derived from such data would be the average heterozygosity, which has traditionally been employed to measure the level of genetic variation within populations and to compare genetic variation among different loci. We derive here explicit formulas for both the estimation of average heterozygosity at multiple hypervariable loci and a maximum value for this estimate. These estimates are based upon the DNA restriction-pattern matrices that are typical for fingerprinting studies of humans and natural populations. For several empirical data sets from our laboratory, estimates of average and maximal heterozygosity are shown to be relatively close to each other. Furthermore, variances of these statistics based on simulation studies are relatively small. These observations, as well as consideration of the effect of missing alleles and alternate numbers of loci, suggest that the average heterozygosity can be accurately estimated using phenotypic DNA fingerprint patterns, because this parameter is relatively insensitive to the lack of certain genetic information.

Animals↗
PubMed1991

The efficiency of multilocus DNA fingerprint probes for individualization and establishment of family relationships, determined from extensive casework.

The properties of human DNA fingerprints detected by multilocus minisatellite probes 33.6 and 33.15 have been investigated in 36 large sibships and in 1,702 Caucasian paternity cases involving the analysis of over 180,000 DNA fingerprint bands. The degree of overlap of minisatellite loci detected by these two probes is shown to be negligible (approximately 1%), and the resulting DNA fingerprints are therefore derived from independent sets of hypervariable loci. The level of allelism and linkage between different hypervariable DNA fragments scored with these probes is also low, implying substantial statistical independence of DNA fragments. Variation between the DNA fingerprints of different individuals indicates that the probability of chance identity is very low (much less than 10(-7) per probe). Empirical observations and theoretical considerations both indicate that genetic heterogeneity between subpopulations is unlikely to affect substantially the statistical evaluation of DNA fingerprints, at least among Caucasians. In paternity analysis, the proportion of nonmaternal DNA fragments in a child which cannot be attributed to the alleged father is shown to be an efficient statistic for distinguishing fathers from nonfathers, even in the presence of minisatellite mutation. Band-sharing estimates between a claimed parent and a child can also distinguish paternity from nonpaternity, though with less efficiency than comparison of a trio of mother, child, and alleged father.

Alleles↗
PubMed2000

Low probe concentration can cause problems in multilocus DNA fingerprinting (cautionary notes III).

The power of multilocus DNA fingerprinting depends on the reliability with which the uniqueness of an individual's profile can be demonstrated. This cautionary note stresses the importance of the probe concentration in this procedure. In case of a probe shortage, DNA fragments rich in tandem repeats have the potential to impede hybridization in other parts of the gel, and thus interfere with bands that are part of a DNA fingerprinting profile.

Animals↗
PubMed1995

Long-term colonization with single and multiple strains of Helicobacter pylori assessed by DNA fingerprinting.

The gastric pathogen Helicobacter pylori establishes long-term chronic infections that can lead to gastritis, peptic ulcers, and cancer. The species is so diverse that distinctly different strains are generally recovered from each patient. To better understand the dynamics of long-term carriage, we characterized H. pylori isolates from initial and follow-up biopsy specimens from a patient population at high risk of H. pylori infection and gastric cancer. Eighty-five isolates were obtained from 23 patients and were analyzed by genomic restriction enzyme analysis, arbitrarily primed PCR fingerprinting, (random amplified polymorphic DNA analysis), and/or restriction of specific PCR-amplified genes (restriction fragment length polymorphism analysis). A single strain was found in sequential biopsy specimens from 12 of 15 patients (80%) receiving sucralfate. In the remaining three patients treated with sucralfate, two strains were identified in two patients and three strains were identified in the third patient. In contrast, a single strain was found in sequential biopsy specimens from only three of eight patients (37%) receiving bismuth, metronidazole, and nitrofurantoin. Two strains were identified in five other patients receiving bismuth-antibiotic (63%). Immunoglobulin G antibodies to H. pylori were present in the sera of all patients. Thus, H. pylori colonization can persist for long periods (up to at least 4 years), despite high titers of immunoglobulin G antibodies in serum. Resistance to metronidazole was noted in some strains before and/or after treatment, but all strains remained susceptible to amoxicillin, tetracycline, and nitrofurantoin. We conclude that H. pylori genotypes, as measured by several sensitive DNA fingerprinting methods, can remain stable for years in vivo, despite the acquisition or loss of drug resistance, circulating antibody, or exposure to antibiotics or sucralfate.

Anti-Bacterial Agents↗