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PubMed1993

[Application of DNA fingerprinting to investigation of genetic relationships between laboratory rabbit strains].

It is well known that laboratory rabbits are not controlled genetically like laboratory mice and rats. In order to test the usefulness of DNA fingerprinting in investigation of genetic uniformity of the laboratory rabbits strains and their relationships, we applied DNA fingerprinting using bacteriophage M13 probe to five strains (2 inbreds (JWY-NIBS and DuY-NIBS) and 3 outbreds (JW-NIBS, Icl:JW and WHHL)). DNA fingerprints of 2 inbred strains showed the same banding patterns within each strain but the strain-specific patterns. Although there were no rabbits showing the same banding patterns in 3 outbred strains, average percent differences (APD) were 13.7 to 18.6. A dendrogram based on APD of DNA fingerprints was constructed by 2 large clusters, JW group and DuY. The dendrogram was essentially similar to that based on rabbit mandible measurements. These results suggest that DNA fingerprinting is available not only for the genetic monitoring of the laboratory rabbit strains but also for the investigation of their genetic relationships.

Animals↗
PubMed1996

Generation of sequence signatures from DNA amplification fingerprints with mini-hairpin and microsatellite primers.

DNA amplification fingerprinting (DAF) with mini-hairpins harboring arbitrary "core" sequences at their 3' termini were used to fingerprint a variety of templates, including PCR products and whole genomes, to establish genetic relationships between plant tax at the interspecific and intraspecific level, and to identify closely related fungal isolates and plant accessions. No correlation was observed between the sequence of the arbitrary core, the stability of the mini-hairpin structure and DAF efficiency. Mini-hairpin primers with short arbitrary cores and primers complementary to simple sequence repeats present in microsatellites were also used to generate arbitrary signatures from amplification profiles (ASAP). The ASAP strategy is a dual-step amplification procedure that uses at least one primer in each fingerprinting stage. ASAP was able to reproducibly amplify DAF products (representing about 10-15 kb of sequence) following careful optimization of amplification parameters such as primer and template concentration. Avoidance of primer sequences partially complementary to DAF product termini was necessary in order to produce distinct fingerprints. This allowed the combinatorial use of oligomers in nucleic acid screening, with numerous ASAP fingerprinting reactions based on a limited number of primer sequences. Mini-hairpin primers and ASAP analysis significantly increased detection of polymorphic DNA, separating closely related bermudagrass (Cynodon) cultivars and detecting putatively linked markers in bulked segregant analysis of the soybean (Glycine max) supernodulation (nitrate-tolerant symbiosis) locus.

DNA Fingerprinting↗
PubMed1999

Deoxyribonucleic acid fingerprinting of Staphylococcus aureus from heifer mammary secretions and from horn flies.

Staphylococcus aureus isolated from heifer mammary secretions, streak canals, and horn flies (Haematobia irritans) were evaluated by randomly amplified polymorphic DNA fingerprinting. The relationship between DNA fingerprint patterns of S. aureus isolated from horn flies and S. aureus isolated from heifer mammary glands was examined. Amplified DNA fragments were visualized by agarose gel electrophoresis and were analyzed by densitometry. Analysis of DNA fingerprint patterns of 56 S. aureus isolates that were obtained from heifer mammary secretions or streak canals resulted in three distinct subtypes of S. aureus. Of these, 31 isolates (55%) belonged to subtype 1, 22 isolates (39%) belonged to subtype 2, and 3 (5%) belonged to subtype 3. Eight of 10 S. aureus isolates from horn flies belonged to subtype 1, and 2 isolates belonged to subtype 2. Thus, all of the S. aureus isolates from horn flies had DNA fingerprint patterns identical to the majority (95%) of S. aureus isolates from heifer mammary secretions or streak canals. In addition, 10 S. aureus isolates from multiparous cows from the same herd were examined by randomly amplified polymorphic DNA. All S. aureus isolates from multiparous cows belonged to subtype 3. Results of this study suggest that horn flies may play an important role in the transmission of S. aureus to nulligravid and primigravid heifers. Furthermore, this study demonstrates the usefulness of randomly amplified polymorphic DNA fingerprinting to distinguish between different subtypes of S. aureus and to draw epidemiological inferences from the information it provides.

Animals↗
PubMed2002

Mycobacterium tuberculosis transmission between cluster members with similar fingerprint patterns.

Molecular epidemiologic studies provide evidence of transmission of Mycobacterium tuberculosis within clusters of patients whose isolates share identical IS6110-DNA fingerprint patterns. However, M. tuberculosis transmission among patients whose isolates have similar but not identical DNA fingerprint patterns (i.e., differing by a single band) has not been well documented. We used DNA fingerprinting, combined with conventional epidemiology, to show unsuspected patterns of tuberculosis transmission associated with three public bars in the same city. Among clustered TB cases, DNA fingerprinting analysis of isolates with similar and identical fingerprints helped us discover epidemiologic links missed during routine tuberculosis contact investigations.

Adult↗
PubMed1999

First searchable database for DNA profiles of human cell lines: sequential use of fingerprint techniques for authentication.

The authenticity and freedom from cross-contaminants of a cell line are important prerequisites for any research, development or production programs involving cell lines. Mini- and microsatellites in the human genome harboring variable-numbers of tandem repeat (VNTR) DNA markers allow individualization at the DNA level and are of practical value for genetic linkage mapping, forensic legal medicine, paternity testing, monitoring of bone marrow transplants, and individualization of established cell lines. We have validated fingerprint techniques of different single- and multiple-locus VNTRs enabling the establishment of a searchable database of DNA profiles. As a result, multiplexed polymerase chain reaction amplification fragment length polymorphism (AmpFLP) of four prominent and highly polymorphic minisatellite VNTR loci was proven as the best tool for screening the uniqueness of DNA profiles in a fingerprint database. In order to avoid false positivity, identical or similar DNA profiles based on AmpFLP VNTR were tested further using a multi-locus fingerprint system. Our data demonstrate that misidentification remains a chronic problem among human continuous cell lines (detailed information at URL http://www.dsmz.de). The combination of rapidly generated DNA profiles based on single-locus VNTR loci, their authentication by screening the fingerprint database, and confirmation of duplicate banding patterns using multilocus fingerprints constitute a highly reliable and robust method, which enables high fidelity and quality of maintenance independent from the quantity of individual cell lines.

Cell Line↗
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↗
PubMed2000

[Analysis of lymphocytic clone formation after stem cell transplantation and immunological reconstitution by gene fingerprinting].

OBJECTIVE: To analyze T lymphocytic clone formation in patients with malignant disease after bone marrow or peripheral blood stem cell transplantation and to understand the relationship between immunological reconstitution and clinic remission. METHODS: Due to the different TCRgamma gene rearrangements in different gamma/delta T cell clones, a gene fingerprinting was set up by PCR and denatured gel electrophoresis. The gene fingerprinting was used to analyze the gamma-delta T cell clone variations in 8 patients who received stem transplantation. In order to identify the source of the regenerated lymphocytes, the polymorphism of microsatellite was used at mean time. RESULTS: After PCR amplification and electrophoresis of each TCRgammaV region gene on a 60 cm sequence gel, a gene fingerprinting composed of about a hundred bands was set up. It showed the basic distribution of the dominant gamma/delta T cell clones in the body. Usually, a new band presenting after transplantation represented an expansive lymphocytic clone. Successful immunological reconstitution led to a good prognosis; and unsuccessful immunological reconstitution led to bad prognosis. After transplantation, some T cell clones expanded. Comparing the sequences of a expansive T cell clone in a multiple myeloma patient after auto-stem cell transplantation with 230 000 genes of immunoglobulin and T cell receptor in GeneBank, we found that two T cell line had homogenous sequences. Both T cell clones recognized homogeneous antigen. CONCLUSION: A new method to observe the distribution of gamma/delta T cells called gene fingerprinting was set up. Gene fingerprinting is useful in the analysis of immunological reconstitution after stem cells transplantation. The effect of transplantation is correlated to immunological reconstitution. Transplantation patients may appear some expansive T cell clones; probably they have anti - tumor effect.

Adult↗
PubMed1999

[Methodology of DNA fingerprinting and its application in identification of M. tuberculosis].

OBJECTIVE: To explore methodology of DNA fingerprinting technique and its application in identification of strains of M. tuberculosis. METHODS: This research was based on different copy numbers and location of chromosome DNA IS6110 in M. tuberculosis genome. After DNA of M. tuberculosis were cut by endonuclease PvuII, the products were transferred to nylon membrane, then detected and hybridized by enhanced chemiluminescent (ECL) labeling techniques. RESULTS: Fifty clinical isolates from different TB patients had unidentical DNA fingerprinting patterns. DNA fingerprinting patterns showed a great difference from sputum and pus specimens of the same patient. H(37) R(v) ofloxacin resistant and sensitive strains had an identical DNA fingerprinting pattern. CONCLUSIONS: Identification of M. tuberculosis strains is feasible by DNA fingerprinting technique.

DNA Fingerprinting↗
PubMed2001

[Authentication of traditional Chinese herbal medicines (TCHM) by fingerprints of characteristic general constituents].

OBJECTIVE: To describe the theory, scientific significance, distinguishing features and authentication feasibility of TCHMs by spectral fingerprints of characteristic general constituents. METHOD: Previous relevant investigations and literatures were summed up in the field, and the present situation on the authentication of TCHMs at home and abroad was analysed. RESULT: The characteristic general constituents of TCHMs can be obtained by an appropriate procedure. Their compositions and structures can be determined by spectral fingerprints, especially the 1HNMR fingerprint. The species of TCHMs can be identified accurately by these fingerprints. Besides, the quality of TCHMs can be evaluated by the contents of their GCEs. CONCLUSION: Fingerprint authentication of characteristic general constituents of TCHMs has profound significance for the species identification and quality evaluation of TCHMs.

DNA Fingerprinting↗
PubMed2002

Application of DNA fingerprinting in medicolegal practice.

Fingerprinting is thought to establish the identify of an individual in forensic cases. The technique is extensively used for forensic purposes. Deoxyribonucleic acid (DNA) is the vehicle of generational transference of heritable unit. While arching markers for genetic disease professor Alec Jeffreys discovered that certain regions of DNA showed variations in the number of tandem repeats known as variable number of tandem repeats (VNTRs). Thus DNA fingerprint was named by observing the number of repeated sequences which differ from individual to individual. The structure of DNA is quite flexible, within the nucleus of each cell resides an identical copy of the individual's genetic material, DNA. The coding regions of the genomic DNA are known as genes. The DNA fingerprinting in forensic science has generated considerable excitement in the criminal justice community. DNA fingerprinting can be applied to identify an individual in criminal and civil cases. Polymerase chain reaction has revolutionised molecular biology it has an ability to amplify (usually fewer than 3000 bp) a particular sequence of DNA into million of copies in a very short period. Consequently only a very tiny amount of an organism's DNA needs to be available originally. This property of polymerase chain reaction has enabled to analyse many forensic samples particularly which are degraded. Microsatellite DNA or commonly as short tandem repeats are scattered throughout the human genome and occur on an average of every 10,000 nucleotides. Microsatellite markers are considered to be the most powerful genetic markers. Collection, preservation and handling are the integral part of DNA fingerprinting analysis. There are various methods to isolate DNA from different biological materials but presently most of the laboratories prefer using FTA paper. The age of humans can be estimated by using DNA based on telomere shortening.

Clinical Medicine↗
PubMed1992

DNA fingerprinting in the Chinese with an oligonucleotide probe (GTG)5.

DNA fingerprinting is a very powerful tool that enables specific identification of individuals. In order to study fingerprinting patterns in the Chinese, the oligonucleotide probe designed by Epplen et al was used. Peripheral blood leukocyte DNA was digested with restriction enzyme Hinf I and probed by (GTG)5. Normal females and males were tested; all revealed very different DNA fingerprints. Most of the discernible bands in the gel were polymorphic; there was no specific association between any polymorphic band and the sex of the individual tested. In situ gel-hybridization was used with the oligonucleotide probe, and after electrophoresis, all procedures could be completed within one working day. Three patients who had received bone marrow transplants from their respective siblings had the same fingerprints as their donors. The inheritance of all bands from either the father or mother proved parents' authenticity. DNA fingerprinting with a oligonucleotide probe is obviously a useful technique. Clinical application may include engraftment monitoring, zygosity determination and paternity testing.

Base Sequence↗
PubMed1992

DNA fingerprinting survey of various human tumors and their metastases.

DNA fingerprinting with the minisatellite probes 33.6 and 33.15 was used to screen for genetic abnormalities in primary tumors of a variety of organs and, where appropriate, their metastases, obtained from 32 patients. The constitutional DNA of each host, obtained from blood leukocytes or normal tissue, was used to produce control, individual-specific fingerprints for comparison with those of their tumor. Fingerprints obtained with probe 33.6 showed differences between tumor and host fingerprints in 69% of patients and those produced with 33.15 in 55%. The most common change was loss or reduction in the intensity of one or more bands, but the appearance of new bands, not present in the fingerprint of the constitutional DNA, was also noted in several tumor DNA samples. The findings are interpreted as indicating loss or rearrangement of expressed sequences in the chromosomal regions adjacent to the hypervariable tandem repeat intron arrays which are detected by these probes. In three patients further differences were identified between primary tumors and their metastatic deposits. With this technique it is possible to perform simultaneous multilocus screening of the genome and the present results show that it has potential for identification of as yet unknown abnormalities in DNA constitution, which may be of pathogenetic significance.

Autoradiography↗
PubMed2003

Clustering binary fingerprint vectors with missing values for DNA array data analysis.

Oligonucleotide fingerprinting is a powerful DNA array based method to characterize cDNA and ribosomal RNA gene (rDNA) libraries and has many applications including gene expression profiling and DNA clone classification. We are especially interested in the latter application. A key step in the method is the cluster analysis of fingerprint data obtained from DNA array hybridization experiments. Most of the existing approaches to clustering use (normalized) real intensity values and thus do not treat positive and negative hybridization signals equally (positive signals are much more emphasized). In this paper, we consider a discrete approach. Fingerprint data are first normalized and binarized using control DNA clones. Because there may exist unresolved (or missing) values in this binarization process, we formulate the clustering of (binary) oligonucleotide fingerprints as a combinatorial optimization problem that attempts to identify clusters and resolve the missing values in the fingerprints simultaneously. We study the computational complexity of this clustering problem and a natural parameterized version, and present an efficient greedy algorithm based on MINIMUM CLIQUE PARTITION on graphs. The algorithm takes advantage of some unique properties of the graphs considered here, which allow us to efficiently find the maximum cliques as well as some special maximal cliques. Our experimental results on simulated and real data demonstrate that the algorithm runs faster and performs better than some popular hierarchical and graph-based clustering methods. The results on real data from DNA clone classification also suggest that this discrete approach is more accurate than clustering methods based on real intensity values, in terms of separating clones that have different characteristics with respect to the given oligonucleotide probes.

Algorithms↗
PubMed1991

Genome fingerprinting as a typing method used on polyagglutinable Pseudomonas aeruginosa isolates from cystic fibrosis patients.

Phenotypical changes occur in the surface of Pseudomonas aeruginosa during the chronic lung infection of cystic fibrosis patients. It is difficult with the classical typing methods, such as serotyping, phage typing and pyocin typing, to decide if a patient has been colonized with a new strain or whether it is the same strain which has reappeared, for instance after chemotherapy in the lungs. This investigation was carried out to evaluate genome fingerprinting as a typing method and to see how it correlated with classical methods and with DNA probe typing. Forty Pseudomonas aeruginosa isolates, 34 polyagglutinable and six monoagglutinable, from 14 cystic fibrosis patients were analysed using genome fingerprinting. The bacterial chromosomes were digested with the restriction endonucleases Dra 1 and Xbal, and separated by field inversion gel electrophoresis. The results were compared with those of a previous work (Ojeniyi et al. 1990) concerning typing with a DNA probe, serotyping using both polyclonal and monoclonal sera, phage typing, pyocin typing and reverse phage typing. The results of genome fingerprinting and DNA probe typing showed the best correlation, followed by pyocin typing. The correlation between the results of genome typing and the other typing methods was low. The discriminatory effect of genome fingerprinting was higher than that of DNA probe typing, and genome fingerprinting was found to be the best single method for epidemiological investigations of polyagglutinable isolates from cystic fibrosis patients.

Antibodies, Monoclonal↗
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↗
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↗
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↗
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↗