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PubMedDate not supplied

Biocontrol strain Pseudomonas sp. W34: specific detection and quantification in the rhizosphere of Cucumis sativus with a DNA probe and genotypic characterization by DNA fingerprinting.

A DNA probe specific for biocontrol strains of Pseudomonas was produced by screening randomly amplified polymorphic DNA (RAPD) PCR fragments. Specificity of the probe was assessed by dot blot and colony hybridization. It was used to specifically determine the population of these strains on roots of Cucumis sativus cv. Delikatess. Two polymorphic RAPD fragments of 750 bp, and 550 bp showed identical specificity. The biocontrol strain Pseudomonas sp. W34 was shown to be competitive in the rhizosphere of cucumber and to maintain a stable population for at least 10 days when inoculated on the seed. The phylogenetic relationships between the biocontrol and reference strains were analyzed at the strain level by means of RAPD and repetitive sequence-based PCR genomic fingerprinting (rep-PCR), and at higher taxonomic levels by means of amplified 16S ribosomal DNA restriction analysis ARDRA. It was shown that the antagonistic strains are closely related, forming a separate cluster from other non-antagonistic and reference Pseudomonas strains, their taxonomic placement remaining uncertain.

Cucumis sativus↗
PubMed2003

[Differentiation of closely related and distant human populations by multilocus DNA fingerprinting].

Using multilocus DNA fingerprinting with phage M13 DNA as a probe, we have investigated a heterogeneous group of four human populations from Eastern Europe and Northeastern Asia. These populations belong to two language families: Indo-European (Eastern Slavonic branch: Russians, Belarussians) and Altaian (Turkic branch: Yakuts). The experimental results were treated by different statistical techniques: cluster analysis, multidimensional scaling, and multiple correspondence analysis. Coefficients of genetic differentiation were estimated using similarity indices and heterozygosities. The results of our study demonstrated similarity of Belarussian populations and significant differences between the group of Slavonic populations and Yakuts.

Asian People↗
PubMed1991

Principles and recent advances in human DNA fingerprinting.

Since 1985, DNA typing systems have played an increasingly important role in many aspects of human genetics, most notably in forensic and legal medicine. This article reviews the development of multilocus and single locus minisatellite DNA probes, and more recently the use of PCR to amplify hypervariable DNA loci, as well as discussing the biological properties of the unstable regions of DNA which form the basis of almost all DNA fingerprinting systems.

Base Sequence↗
PubMed1994

Genomic fingerprints of Staphylococcus aureus of bovine origin by polymerase chain reaction-based DNA fingerprinting.

Staphylococcus aureus (n = 75) isolated from mammary secretions of cows with subclinical and clinical mastitis from several geographic locations in the USA were examined using polymerase chain reaction-based DNA fingerprinting. DNA fingerprints were produced using a synthetic oligonucleotide primer (5'GTAACGCC3') to produce a distinct spectrum of amplified DNA fragments facilitating a high degree of resolution for differentiating S. aureus strains. PCR-based DNA fingerprinting grouped the 75 S. aureus isolates into 19 distinct profiles. The technique differentiated closely related strains within and between geographic locations. Findings suggest that certain types are found across geographic regions suggesting a common clonal type. Within herd data suggest heterogeneity among subclinical and clinical isolates of S. aureus strains. Compared to existing typing methods, PCR-based DNA fingerprinting is easy to perform and interpret. Use of PCR-based DNA fingerprinting may allow for a more detailed investigation of the epidemiology of S. aureus mastitis in dairy cows.

Animals↗
PubMed1995

Diversity of DNA fingerprints in Cryptococcus neoformans.

DNA fingerprint patterns of 156 Cryptococcus neoformans isolates (26 AIDS patients, 46 non-AIDS patients, and 40 environmental sources) from both varieties (126 C. neoformans var. neoformans and 30 C. neoformans var. gattii isolates) and from seven countries were analyzed by using the DNA probe UT-4p. Nine and twelve distinct DNA fingerprint patterns were observed for isolates of the C. neoformans var. neoformans and var. gattii, respectively. No pattern was unique to AIDS patients, non-AIDS patients, or the environment. Pattern II was observed more often in non-AIDS patients (8 of 23) than in AIDS patients (0 of 25). Pattern V was the most prevalent pattern (42 of 82) in clinical and environmental isolates. Isolates from three AIDS patients in Burundi and Zaire exhibited patterns identical to each other but different from those of isolates collected from their houses (i.e., dust of floors, walls, etc.) or a nearby pigeon coop. DNA fingerprint stability was determined for 53 isolates from nine non-AIDS patients at different time intervals during 5 to 128 weeks of antifungal therapy. For eight patients, the fingerprint pattern was stable while the ninth may have had a mixed infection. Pattern II was observed in 4 of 9 patients, which is similar to 4 of 14 in other non-AIDS patients as reported here. In spite of the extensive pattern heterogeneity among 15 C. neoformans var. gattii isolates in Australia, the patterns observed in seven California isolates were quite different from those in Australia. Among isolates of C. neoformans var. gattii, one fingerprint pattern (designated b) was observed in several countries of the Far East. The fingerprint patterns of two of three environmental isolates from Eucalyptus camaldulensis trees in Australia were identical to those of 2 of the 12 clinical isolates from the country.

AIDS-Related Opportunistic Infections↗
PubMed1991

[Analysis of genetic distances between populations using human DNA "fingerprints" detected by a phage M13 DNA probe].

The frequencies of different electrophoretic bands in DNA fingerprints detected by phage M13 DNA probe in two populations of the Kirov district were determined. The DNA polymorphisms observed in these two populations were compared with each other and with those of the Krasnodar populations, and pseudogenetic distances were calculated. The mean genetic distance between two Kirov populations was 0.072, this between every Kirov and Krasnodar population being 0.21 and 0.22.

Bacteriophages↗
PubMed1989

[DNA fingerprints and hypervariable regions: genetic marker with many application potentials in medicine and biology].

DNA polymorphisms are based on variations in the nucleotide sequences of the DNA within a given population and are transmitted from parents to offspring by Mendelian inheritance. Most of these mutations are phenotypically silent. Two different types of DNA polymorphisms are restriction fragment length polymorphisms and highly variable regions (HVRs), the latter with many different alleles at a given locus. Molecular probes for HVRs (or DNA minisatellites) can detect a great number of cross-hybridising fragments dispersed throughout the genome. The polymorphic patterns of these fragments are completely individual-specific, hence termed DNA "fingerprints". DNA "fingerprinting" has been shown to be a powerful tool for establishing family relationships, for example in paternity disputes, and for the positive identification of individuals in forensic medicine. The technique may be used to document marrow engraftment in patients who have undergone allogeneic bone marrow transplantation. DNA "fingerprinting" is a new method of assessing clonality in human tumours by identifying clonal somatic mutations in the tumour DNA. Cloning of individual DNA "fingerprint" fragments yields locus-specific HVR probes which, due to their high rate of heterozygosity, are ideal for linkage analysis and prenatal diagnosis in single gene disorders. This is exemplified by adult polycystic kidney disease, which has been found by a 3'alpha-globin-HVR probe to be closely linked to the alpha-globin-gene cluster on chromosome 16p. Locus-specific HVR probes have been used for the molecular diagnosis of clonal chromosomal deletions or loss of heterozygosity at particular loci in a large variety of tumours. These findings are the basis for the identification of anti-oncogenes or putative tumour-suppressor genes in the human genome.

Animals↗
PubMed1996

SINE sequences detect DNA fingerprints in salmonid fishes.

DNA probes homologous to two previously described salmonid short interspersed nuclear elements (SINEs) detected DNA fingerprint patterns in 14 species of salmonid fishes. The probes showed more homology to some species than to others and little homology to three nonsalmonid fishes. The DNA fingerprint patterns derived from the SINE probes are individual-specific and inherited in a Mendelian manner. Probes derived from different regions of the same SINE detect only partially overlapping banding patterns, reflecting a more complex SINE structure than has been previously reported. Like the human Alu sequence, the SINEs found in salmonids could provide useful genetic markers and primer sites for PCR-based techniques. These elements may be more desirable for some applications than traditional DNA fingerprinting probes that detect tandemly repeated arrays.

Animals↗
PubMed1994

Population dynamics of DNA fingerprint patterns within and between populations.

DNA fingerprint is a pattern of a variable number of bands (DNA fragments) with different sizes on a Southern gel for each individual, generated by one or many VNTR loci. Genetic divergence between individuals within and between populations can be studied in terms of number of shared bands between individuals. Using a population genetic model we show that the expectations of measures of genetic distance between populations based on band sharing data from DNA fingerprint patterns are functions of composite parameters M = 4Nv, and time of divergence (t) between populations, where N is the effective size of the populations, and v, the mutation rate. The expected genetic distance remains linear with time of divergence at least up to N generations as long as the average heterozygosity at the DNA fingerprint loci remains at or below 90%. Neither incomplete knowledge of the allele frequencies at each locus, nor the unknown number of loci underlying DNA fingerprint pattern, compromise these evolutionary dynamics of DNA fingerprint patterns. Applications of this theory to data on three human populations, and review of literature indicate that co-migration of alleles, and the presence of syntenic loci underlying the fingerprint pattern have little impact of the reliability of evolutionary conclusions from DNA fingerprint studies.

DNA Fingerprinting↗
PubMed1992

RAPD analysis of Campylobacter isolates: DNA fingerprinting without the need to purify DNA.

A method was developed to obtain reproducible DNA fingerprints from Campylobacter by PCR-based amplification, without the need to isolate total DNA. Randomly amplified polymorphic DNA (RAPD) profiles were generated with three randomly designed 10-mers, using each separately as an amplification primer. A range of C. jejuni serotypes could be typed by RAPD analysis. Depending on the primer, the analysis of RAPD profiles resulted in different levels of discrimination between the strains. Clear correlations were observed between results of RAPD analysis and serotyping. Two of the primers tested generated RAPD profiles which allowed discrimination of strains within given Penner and Lior serotypes.

Base Sequence↗
PubMed1992

Cell line characterisation by DNA fingerprinting; a review.

DNA fingerprinting using multi-locus probes has become established as the most powerful technology for the identification and characterisation of mammalian cell lines. However, care must be taken in the technical preparation and statistical evaluation of the DNA banding patterns.

Animals↗
PubMed2002

Randomly Amplified DNA Fingerprinting: A Culmination of DNA Marker Technologies Based on Arbitrarily-Primed PCR Amplification.

Arbitrarily-primed DNA markers can be very useful for genetic fingerprinting and for facilitating positional cloning of genes. This class of technologies is particularly important for less studied species, for which genome sequence information is generally not known. The technologies include Randomly Amplified Polymorphic DNA (RAPD), DNA Amplification Fingerprinting (DAF), and Amplified Fragment Length Polymorphism (AFLP). We have modified the DAF protocol to produce a robust PCR-based DNA marker technology called Randomly Amplified DNA Fingerprinting (RAF). While the protocol most closely resembles DAF, it is much more robust and sensitive because amplicons are labelled with either radioactive 33P or fluorescence in a 30-cycle PCR, and then separated and detected on large polyacrylamide sequencing gels. Highly reproducible RAF markers were readily amplified from either purified DNA or alkali-treated intact leaf tissue. RAF markers typically display dominant inheritance. However, a small but significant portion of the RAF markers exhibit codominant inheritance and represent microsatellite loci. RAF compares favorably with AFLP for efficiency and reliability on many plant genomes, including the very large and complex genomes of sugarcane and wheat. While the two technologies detect about the same number of markers per large polyacrylamide gel, advantages of RAF over AFLP include: (i) no requirement for enzymatic template preparation, (ii) one instead of two PCRs, and (iii) overall cost. RAF and AFLP were shown to differ in the selective basis of amplification of markers from genomes and could therefore be used in complementary fashion for some genetic studies.

Journal Article↗
PubMed1990

Application of DNA fingerprints for cell-line individualization.

DNA fingerprints of 46 human cell lines were derived using minisatellite probes for hypervariable genetic loci. The incidence of 121 HaeIII DNA fragments among 33 cell lines derived from unrelated individuals was used to estimate allelic and genotypic frequencies for each fragment and for composite individual DNA fingerprints. We present a quantitative estimate of the extent of genetic difference between individuals, an estimate based on the percentage of restriction fragments at which they differ. The average percent difference (APD) among pairwise combinations from the population of 33 unrelated cell lines was 76.9%, compared with the APD in band sharing among cell lines derived from the same individual (less than or equal to 1.2%). Included in this survey were nine additional cell lines previously implicated as HeLa cell derivatives, and these lines were clearly confirmed as such by DNA fingerprints (APD less than or equal to 0.6%). On the basis of fragment frequencies in the tested cell line population, a simple genetic model was developed to estimate the frequencies of each DNA fingerprint in the population. The median incidence was 2.9 X 10(-17), and the range was 2.4 X 10(-21) to 6.6 X 10(-15). This value approximates the probability that a second cell line selected at random from unrelated individuals will match a given DNA fingerprint. Related calculations address the chance that any two DNA fingerprints would be identical among a large group of cell lines. This estimate is still very slight; for example, the chance of two or more common DNA fingerprints among 1 million distinct individuals is less than .001. The procedure provides a straightforward, easily interpreted, and statistically robust method for identification and individualization of human cells.

Alleles↗
PubMed1998

Evaluation of oligonucleotide probes for simple tandem repeats (STR) to produce informative DNA fingerprints of the chicken.

1. DNA fingerprints of chickens from 2 commercial lines were used to identify oligonucleotide probes providing informative DNA fingerprints. 2. The oligonucleotides [CA]8, [CAC]5, [GGAT]4 and [GACA]4, producing a high number of bands of sufficient intensity and regular distribution, were chosen for further analysis out of 10 tested. 3. Analyses of banding patterns within families revealed Mendelian inheritance of the fragments detected. The DNA fingerprints obtained with the 4 chosen oligonucleotide probes showed about 40 scorable bands in total. 4. Comparison of banding patterns within and between the chicken lines for all 4 oligonucleotide probes revealed levels of bandsharing which did not differ significantly. The number of loci detected by these probes ranged from 25 to 30 each. 5. The probes [CA]8, [CAC]5, [GGAT]4 and [GACA]4 can be used to produce informative DNA fingerprints of chicken. These probes provide estimates of the genetic similarity/variability of individuals or of populations and provide a valid measure of the actual degree of genetic similarity/variability.

Animals↗
PubMed2004

Practical application of DNA fingerprinting to trace beef.

DNA fingerprinting allows the verification of conventional methods used to implement beef traceability. At any point along the supply chain, the identity of an animal or piece of meat can be checked by comparison of its DNA profile with an initial sample. Practical application of DNA fingerprinting to trace beef requires a choice of DNA markers as well as the optimization of sampling methods. This has been achieved as the result of collaboration between meat technicians and geneticists over a period of 4 years. The discrimination power of nine highly polymorphic microsatellite markers was evaluated. We propose that three markers (with a 0.001 probability that two individual profiles match by chance) are adequate for routine tests. Two key points along the production-commercialization chain where sampling must be systematic were defined: (i) the tagging of the calf (identity control) and (ii) after slaughter (slaughter control), before the animal loses its external appearance. The identity control was blood collected on a filter paper adapted to the ear tag; the slaughter control was the tagged ear itself. These constituted the control samples, which were archived with a code matching the individual tag number. Test samples were obtained on a random basis from live animals, carcasses, and pieces of meat at cutting halls and at the retail outlet and in cases when the verification of identity was needed. The DNA profiles of the test samples and the controls were then obtained and compared, to verify either an individual identity or the origin of a piece of meat from the stated animal.

Animal Identification Systems↗
PubMedDate not supplied

DNA fingerprinting: a versatile technology.

DNA fingerprinting originally developed as a genetic mapping strategy but has quickly found many other applications ranging from forensic casework to wildlife conservation. The versatility of various DNA fingerprinting methods is illustrated by a series of examples taken from the work of one laboratory in New Zealand.

Animals↗
PubMedDate not supplied

Parentage analysis for three Romanian families by DNA-fingerprinting.

In forensic medicine, DNA fingerprinting for human identification and paternity testing is becoming a necessary procedure. The genetic locus D1S80 (MCT118) with Hinf I polymorphism of its 5' flanking sequence, HUMTH01 and D21S11 have been successfully amplified from human genomic DNA isolated from blood (50 ng from each sample) by the polymerase chain reaction (PCR) using oligonucleotide primers complementary to the flanking sequences as primers for amplification. DNA bands were detected by ethidium bromide staining after electrophoresis on agarose gels or high-resolution SDS-PAGE. Analysis of these VNTR loci was thus achieved without the need for Southern blot or radioactive material. The small size of the DNA fragments produced in the PCR amplification permitted good resolution of individual alleles. The precise specification of the number of tandem repeats present in each allelic fragment was reproducible from one analysis to another. The aim of this study includes three paternity testing cases; they are the first three human DNA-fingerprints performed in Romania.

5' Untranslated Regions↗