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PubMed1996

Evidence of nosocomial transmission of tuberculosis among AIDS patients by DNA fingerprinting.

DNA restriction fragment length polymorphism (RFLP) analysis was performed on Mycobacterium tuberculosis isolates from patients in the human immunodeficiency virus (HIV) Unit of a community hospital. It was found that M. tuberculosis isolates from two patients with AIDS shared an identical RFLP pattern. Such a fingerprint was not found in M. tuberculosis isolates from any of 40 HIV-negative patients hospitalized in different Units over the same period, assumed as representative of the strains present in the community, thus ruling out that the isolates from the two AIDS patients might match because only a few strains were present in the community. Clinical records of the two AIDS patients showed an 8-day concomitant hospitalization period in the same ward during which one of the two patients showed active tuberculosis; the second patient developed active tuberculosis less than two months later. These findings strongly support the possibility of nosocomial transmission of tuberculosis.

Acquired Immunodeficiency Syndrome↗
PubMed1991

"Sexing" deoxyribonucleic acid (DNA) on DNA fingerprint gel: an internal control for DNA fingerprint evidence.

Deoxyribonucleic acid (DNA) isolated from male and female fresh blood samples was processed exactly as for routine DNA fingerprint analysis; that is, the DNA was digested with particular restriction endonucleases and fractionated by agarose gel electrophoresis. Ultraviolet (UV) visualization of ethidium-bromide (EtBr)-stained gels revealed a sex-specific banding pattern, which depended only on the restriction enzyme used. By means of this test, which is based on direct detection of particular sex-specific restriction fragments in human DNA digests, the authors succeeded in determining the sex of DNA obtained from biological specimens recovered as criminal evidence in rape cases. The data obtained demonstrate that direct sexing of DNA on DNA fingerprint gel appears to be useful as an intermediate control step in DNA fingerprinting analysis used for the purpose of assailant identification.

DNA↗
PubMed1994

Estimation of genetic distance and coefficient of gene diversity from single-probe multilocus DNA fingerprinting data.

DNA fingerprinting exhibits multilocus genotypes of individuals, detected by the use of a single multilocus probe. Consequently, population data on DNA fingerprinting do not provide a complete characterization of the genetic variation in terms of allele-frequency distributions, since neither the number of loci nor the locus affiliation of alleles is directly observable. Yet DNA fingerprinting has been proved to be a cost-effective method of detecting hypervariable polymorphisms in several organisms, where the traditional loci fail to detect enough variation for microevolutionary studies. In the present paper we demonstrate that the above-mentioned features of DNA fingerprinting data do not cause any serious problem when they are used in evolutionary studies. Bias-corrected estimators of Nei's standard and minimum genetic distances are derived, and, by an application of this theory to data on seven short tandem repeat loci in three major human populations, it is shown that these modified measures of genetic distances based on DNA fingerprint patterns are quite close to Nei's distances based on locus-specific allele frequencies. Empirical as well as theoretical support of the adequacy of such genetic distances from DNA fingerprinting data is also discussed, and it indicates that the technical limitations of DNA fingerprinting should not deter the use of the method for short-term evolutionary studies.

Alleles↗
PubMed1993

Identification of inbred rat strains by using DNA fingerprinting method.

DNA fingerprinting method was applied to identify inbred strains of laboratory rats. By Southern blot hybridization with core sequence of minisatellite DNA as a probe, typical hypervariable patterns of DNA fingerprint were obtained in inbred rat strains. The patterns were completely different among 15 rat strains examined, and the patterns of the DNA fingerprint of samples obtained from the same strain were completely identical. The patterns of the DNA fingerprint of two substrains derived from the same strain were identical, indicating relative stability of the patterns over a large number of generations. Therefore, we concluded that the DNA fingerprinting method was useful for the identification of inbred strains in genetic monitoring of laboratory rats.

Animals↗
PubMed2001

Genetic variation in parthenogenetic Caucasian rock lizards of the genus Lacerta (L. dahli, L. armeniaca, L. unisexualis) analyzed by DNA fingerprinting.

Multilocus DNA fingerprinting has been used to study the variability of some mini- and microsatellite sequences in parthenogenetic species of Caucasian rock lizards of the genus Lacerta (L. dahli, L. armeniaca and L. unisexualis). We demonstrate that these clonally reproducing lizards possess species-specific DNA fingerprints with a low degree of intra- and interpopulation variation. Mean indices of similarity obtained using M13 DNA, (GACA)4 and (TCC)50 as probes were 0.962 and 0.966 in L. dahli and L. armeniaca, respectively. The mean index of similarity obtained using M 13 and GATA probes in L. unisexualis was estimated to be 0.95. However, despite the high degree of band-sharing, variable DNA fragments were revealed in all populations with the microsatellite probes. An particularly high level of variability was observed for (TCC)n microsatellites in populations of L. unisexualis. In fact TCC-derived DNA fingerprints were close to being individual-specific, with a mean index of similarity of 0.824. Fingerprint analysis of parthenogenetic families of L. armeniaca showed that all maternal fragments were inherited together by the progeny, and no differences in fingerprint patterns were observed. On the other hand, while identical DNA fingerprints were obtained from L. unisexualis families with M13 and (GATA)4 probes, use of the (TCC)50 probe revealed remarkable intrafamily variation in this species. It is assumed that the genetic heterogeneity observed in parthenogenetic populations may be explained, at least in part, by the existence of genetically unstable microsatellite loci. Our data serve to illustrate processes of spontaneous mutagenesis and the initial stages of clonal differentiation in natural populations of the lizard species studied.

Animals↗
PubMedDate not supplied

Re-evaluation of hydatidiform mole by DNA fingerprint method: the discrepancy in the diagnoses by pathological finding and the DNA fingerprint method.

Ten cases of hydatidiform mole (HM) were analysed by the DNA fingerprint method. DNA samples were prepared from HM tissue of HM and maternal and paternal bloods, followed by digestion with HaeIII restriction endonuclease, applied to agarose gel, and then transferred to a nitrocellulose filter. The filter was hybridized using mini-satellite DNA as a probe. A case of partial HM diagnosed by histological findings was revealed to be complete HM using DNA fingerprinting. The case was suggested to be a twin pregnancy with a cHM and an abortion, because the DNA fingerprint of hydropic tissue showed a paternal pattern and that of the non-hydropic tissue did not show such a pattern. DNA fingerprinting was considered to be useful in distinguishing complete HM from partial HM.

Adult↗
PubMed1992

Probing identity: the changing face of DNA fingerprinting.

DNA-fingerprinting technology has made a very rapid transition from being a research laboratory discovery to an applied science widely understood by, and of interest to, the general public. However, DNA fingerprinting is often portrayed as being a single generic technology, rather than a complex evolving mixture of methodologies, where specific applications demand selection of appropriate probes and techniques.

Animals↗
PubMed1994

Characterization of the formae speciales of Fusarium oxysporum causing wilts of cucurbits by DNA fingerprinting with nuclear repetitive DNA sequences.

The genetic relatedness of five formae speciales of Fusarium oxysporum causing wilts of cucurbit plants was determined by DNA fingerprinting with the moderately repetitive DNA sequences FOLR1 to FOLR4. The four FOLR clones were chosen from a genomic library made from F. oxysporum f. sp. lagenariae 03-05118. Total DNAs from 50 strains representing five cucurbit-infecting formae speciales, cucumerinum, melonis, lagenariae, niveum, and momordicae, and 6 strains of formae speciales pathogenic to other plants were digested with EcoRV and hybridized with 32P-labeled FOLR probes. The strains were clearly distinguishable at the formae specialis level on the basis of FOLR DNA fingerprints. Fifty-two fingerprint types were detected among the 56 strains by using all FOLR probes. These probes were used to infer phylogenetic relationships among the DNA fingerprint types by the unweighted pair group method using averages and parsimony analysis. The fingerprint types detected in each of the formae speciales cucumerinum, lagenariae, niveum, and momordicae were grouped into a single cluster. However, two different genetic groups occurred in the formae specialis melonis. The two groups also differed in pathogenicity: one group caused wilts of muskmelon and oriental melon, while the second was pathogenic only to muskmelon. The fingerprint types of different formae speciales pathogenic to plants other than cucurbits were distinguishable from one another and from the fingerprints of the cucurbit-infecting strains. These results suggest that the cucurbit-infecting formae speciales are intraspecific variants distinguishable at the DNA level and in their host range.

Cloning, Molecular↗
PubMed1990

DNA alterations in prostatic adenocarcinoma and benign prostatic hyperplasia: detection by DNA fingerprint analyses.

DNA fingerprinting can be utilized to examine a large number of autosomal loci throughout the human genome. Alterations in banding patterns observed on DNA fingerprint analyses reflect DNA alterations ranging from single base changes to complex chromosomal rearrangements. In this report, we describe the application of this technique to prostatic adenocarcinoma (CAP) and benign prostatic hyperplasia (BPH). The majority of CAP cases (12 of 14) displayed alterations in at least 1 of the approximately 30 resolvable bands obtained by fingerprint analyses when compared with DNA obtained from peripheral white blood cells. Unexpectedly, 5 of the 12 cases of BPH examined revealed at least 1 identifiable band alteration in the prostatic tissue. These findings demonstrate the usefulness of fingerprint analyses in the examination of cancer-associated genetic alterations. They also suggest the presence of observable genetic alterations in BPH.

Adenocarcinoma↗
PubMedDate not supplied

Evaluation of genetic variation within and between different chicken lines by DNA fingerprinting.

A DNA fingerprinting technique was used to assess the extent of genetic variation within and between 12 lines of chickens of different origin. DNA fingerprints were obtained with the restriction endonucleases AluI and HinfI and with the oligonucleotide probes (CA)8, (CAC)5, (GGAT)4, and (GACA)4. Different methods that are based on band sharing and band frequency were tested to estimate genetic variation within and between populations. The genetic variability was significantly different within the populations. It was highest in a commercial broiler line and lowest in a White Leghorn inbred line. All three measures of genetic variation within populations provided results that were highly correlated (r = 0.89-0.97). A lower degree of correspondence was observed for the estimation of genetic variation between populations by three different methods. This is shown by differences of the phylogenetic trees and by coefficients of correlation between these measures ranging from r = 0.51-0.96.

Animals↗
PubMed1990

The similarity index and DNA fingerprinting.

DNA-fingerprint similarity is being used increasingly to make inferences about levels of genetic variation within and between natural populations. It is shown that the similarity index--the average fraction of shared restriction fragments--provides upwardly biased estimates of population homozygosity but nearly unbiased estimates of the average identity-in-state for random pairs of individuals. A method is suggested for partitioning the DNA-fingerprint dissimilarity into within- and between-population components. Some simple expressions are given for the sampling variances of these estimators.

Alleles↗
PubMed1990

Detection of somatic mutations in tumours of diverse types by DNA fingerprinting with M13 phage DNA.

Hybridization of M13 phage DNA to Southern blots of human DNA produces an individual-specific DNA fingerprint. In this study, tumour and lymphocyte DNA from a series of patients with melanoma, Merkel-cell carcinoma, Burkitt's lymphoma and Wilms' tumour was probed with M13 DNA to detect somatic mutations in the DNA of the tumours. Somatic changes were observed in tumour DNA of 16 out of the 28 cases examined. This frequency compared favourably with the frequency with which tumour-specific changes have been found when using the Jeffreys DNA fingerprinting probe 33.15, and demonstrates that M13 DNA provides a useful additional probe for the study of somatic changes in tumours. The finding that multiple DNA fragments were lost or gained in DNA fingerprints from individual tumours indicates a marked degree of complexity in the genetic changes involved in the evolution of certain human cancers.

Bacteriophages↗
PubMed1990

Detection of genomic alterations in carcinogen-induced mouse liver tumors by DNA fingerprint analysis.

DNA fingerprint analysis was used to study structural abnormalities in the genome of mouse liver tumor cells. Liver tumors were induced in three strains of mice, namely C57BL/6J, C3H/He and B6C3F1, by a single injection of 20 micrograms/g body wt. diethylnitrosamine on day 15 after birth. DNA from liver tumors was digested with Hinfl restriction enzyme and hybridized on Southern blots with wild-type bacteriophage M13 DNA as probe. The resulting fingerprints of tumor DNA were compared with those of DNA from normal liver tissue. Genomic aberrations were detected in two out of 68 tumors analyzed, one stemming from a C57BL/6J and the other from a C3H/He mouse.

Animals↗
PubMed1990

Characterization of the sequence of colonization and nosocomial candidemia using DNA fingerprinting and a DNA probe.

The objective of this hospital-based study was to determine the relationship between colonizing and infecting strains of Candida species and Torulopsis glabrata. Surveillance cultures from high-risk patients were paired with subsequent bloodstream isolates. Organisms were typed by using restriction endonuclease digestion of chromosomal DNA with BstNI and EcoRI, followed by Southern hybridization with a DNA probe (pBD4) derived from Saccharomyces cerevisiae. Sixteen patients for whom documented colonization preceded documented bloodstream infection were identified. The mean time between obtainment of surveillance isolates and obtainment of bloodstream isolates was 8 days, with a range of 1 to 423 days. For 15 (94%) of 16 patients, the DNA fingerprint pattern (using BstNI) of the surveillance isolate was identical to that of the bloodstream isolate. Isolates from 13 (81%) of 16 patients were unique to those patients. Typing by Southern hybridization with the pBD4 probe was less discriminating. We conclude that for a well-defined subset of hospitalized patients who were colonized by Candida species before developing nosocomial candidemia, the colonizing and infecting strains were identical, suggesting endogenous acquisition of infection. Restriction endonuclease digestion of chromosomal DNA was shown to be a discriminating and reproducible typing method for Candida species and T. glabrata.

Blotting, Southern↗
PubMed2000

Forensic identification by DNA fingerprinting and mitochondrial DNA typing.

Short tandem repeats (STRs), that represent an important source of highly polymorphic markers in human genome, and mitochondrial DNA (mtDNA) typing, that its sequences were conserved within the same maternal lineage, facilitated by use of the polymerase chain reaction (PCR) provide a powerful tool for forensic identification. We report the analysis of 9 STR loci and mtDNA typing of a muscle biopsied sample with 2 months postmortem by comparison with the genotype of the relative. The DNA profile showed common alleles with that of the relative but only 12 from 20 alleles (60%) were identifiable. Then, we performed mt DNA sequencing of the hypervariable region I (HV I) and obtained 100 per cent homology with that of the relative. In conclusion, personal identification can be performed precisely by the data of DNA profile and mtDNA typing compared to the genotype of the relative.

Base Sequence↗
PubMed1988

Cross-contamination of human esophageal squamous carcinoma cell lines detected by DNA fingerprint analysis.

DNA "fingerprint" analysis has recently become known as a valuable technique for positive identification of any given individual. The chances for mistaken identity have been estimated to be 10(-6) for close siblings or as little as 10(-23) for randomly selected individuals. This methodology thus represents a significant improvement over previously established identification tests using protein or enzyme analysis techniques and has already found application in forensic medicine. One of the chief problems in tissue culture studies is the question of the unequivocal identity of the cultured cells used and the very real possibility of their being contaminated by cells of a similar morphological appearance. We report here the application of the DNA "fingerprint" technique to the genotypic analysis of cultured human squamous carcinoma cells. The results show that a number of lines, designation HCu, have become cross-contaminated. Lines SNO, HCu 10, and HCu 13 are genetically distinct, however lines HCu 10, 18, 33, 37, and 39 are genetically identical and are in fact subcultures of the same cells. In addition, a myocardial line known as Girardi is shown to be identical to HeLa cells. The introduction of this technique to tissue culture laboratories could therefore prevent contaminated cultures from being disseminated or used in research studies.

Carcinoma, Squamous Cell↗