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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↗
PubMed2002

[IS6110-restriction fragment length polymorphism based DNA fingerprinting in molecular epidemiology of tuberculosis].

OBJECTIVE: To identify the IS6110-restriction fragment length polymorphism (RFLP) DNA fingerprinting patterns of some clinical isolates of Mycobacterium tuberculosis (MTB) isolated from Ningxia, Beijing and Shanghai in recent years, and to observe their epidemiological characteristics. METHODS: Chromosomal DNA of MTB was digested with endonuclease PvuII, then electrophoresed on agarose gel plate and transferred capillarilly to a nylon filter and hybridized with 245 bp fragment of IS6110 which labeled using random primer fluorescein labeling kit. The RFLP patterns of Southern hybridization were inspected autofluorographically and the chromosomal DNAs of MTB were thereby typed. RESULTS: Most of 103 isolates of MTB shared 8 approximately 21 copies. Some of them were clustered. Strains isolated from Ningxia and Beijing had similar DNA fingerprinting patterns. One zero copy strain and one single copy strain were found among isolates from Shanghai. CONCLUSIONS: IS6110-RFLP based typing is feasible for MTB molecular epidemiological study in China. Most of isolates of MTB show analyzable patterns. Isolates of MTB from Ningxia and Beijing have close genomic relation.

China↗
PubMed2002

[DNA fingerprinting of individual species and intergeneric and interspecific hybrids of genera Bos and Bison, subfamily Bovinae].

Genome fingerprinting with a hypervariable minisatellite sequence of phage M13 DNA was used to study the genetic variation in individual species of the genera Bos and Bison (subfamily Bovinae) and in their interspecific and intergeneric hybrids. DNA fingerprints were obtained for domestic cow Bos taurus primigenius, vatussy Bos taurus macroceros, banteng Bos javanicus, gaur Bos gaurus, wisent Bison bonasus, bison Bison bison, and for the interspecific and intergeneric hybrids. Compared with the original species, most hybrids showed a greater variation in number and size of hybridization fragments. An association was revealed between the number of hybridization fragments and blood composition of interspecific hybrids resulting from unique crossing of domestic cow and banteng. Pairwise similarity coefficients were calculated to construct a dendrogram of genetic similarity, which reflected the relationships between the parental species and hybrids varying in blood composition. The applicability of the method for identifying interspecific and intergeneric hybrids and for studying the consequences of distant hybridization in the subfamily Bovinae is discussed.

Animals↗
PubMedDate not supplied

[Genetic typing of Mycobacterium tuberculosis strains by spoligotyping and genome fingerprinting techniques].

A total of 122 M. tuberculosis clinical drug-resistant strains isolated in Central Russia were studied by spoligotyping and genome fingerprinting techniques. According to spoligotyping results 77% of M. tuberculosis strains were distributed to 13 oligotypes, while 23% of these strains were found to form unique patterns. Most of them belonged to the families Beijing and Haarlem (43.4% and 13.9% respectively). The patterns of the strains of oligotype 12 (7F-7F-7E-0E-78-3E) were identical to those of the strains isolated in Brazil, France and the Netherlands. The strains of the spoligotype 22 (7F-1E-7F-7F-07-3E) had the patterns identical to those of the strains of group S13, also isolated in Brazil. According to genome fingerprinting 31.4% of the strains were found to belong to clusters with the similarity coefficient equal to 1. The strains belonging to genotypes W and A1 were found to prevail in the analyzed group.

Antitubercular Agents↗
PubMed2002

Epidemiological typing of Streptococcus pneumoniae from various sources in India & Korea using Box A PCR fingerprinting.

BACKGROUND & OBJECTIVES: Epidemiological typing of Streptococcus pneumoniae is necessary to study genetic relatedness among strains. The Box A PCR assay, a good epidemiological tool for high resolution typing of pneumococcal isolates, was used for comparison of strains of S. pneumoniae from Korea, an area of high penicillin resistance and India with low resistance to penicillin. METHODS: The pneumococcal strains from Indian and Korean sources included in the study belonged to serotypes 19F, 23F, 6A & 6B. The penicillin susceptibility of the strains was confirmed by determination of minimum inhibitory concentration values. The strains were then fingerprinted using the Box A PCR protocol and the results were further analysed by Molecular Analyst Software. RESULTS: The Box fingerprinting technique produced sharp, clear and reproducible banding patterns for strains of S. pneumoniae included in the study. There was no similarity between Indian and Korean strains at the genetic level. Among the Korean strains with similar serotypes, the level of similarity varied. Except for one pair (serotype 23F), that showed a level of homology of about 90 per cent, almost all the others showed less than 80 per cent homology. It was also seen that there was a high percentage of homology (> 90% in nasopharyngeal isolates from India belonging to serotype 19F) between isolates from similar source. Comparison of the Indian and Korean isolates of similar serotype showed low homology, except for one cluster of two strains with serotype 6B which showed 84 per cent homology (blood isolates from India and Korea). INTERPRETATION & CONCLUSION: Box A PCR is a highly discriminatory and useful method for typing S. pneumoniae. The results of the study have shown low levels of homology between strains from within India and also between two geographically distinct areas.

Bacterial Typing Techniques↗
PubMed2003

DNA fingerprinting of mosses.

Our study introduces the use of DNA fingerprinting of clonal plants in combination with phylogenetic and vegetation studies as a prospective forensic tool in criminal investigations. In this homicide case, the bryophyte species found on the suspects were identified as Brachythecium albicans, Calliergonella lindbergii, and Ceratodon purpureus. Colonies of all three species occurred at the crime site. DNA fingerprinting analyses were conducted for B. albicans and C. lindbergii, which were expected to reproduce mainly clonally, unlike C. purpureus, and included samples found on the suspects and samples collected from the crime site and other locations. It was concluded that B. albicans found on the suspects was likely to originate from the crime scene and that the sample of C. lindbergii may also have originated from the same site.

Adult↗
PubMed2003

Insertion of a reamplification round into the ISSR-PCR protocol gives new flax fingerprinting patterns.

We expanded the basic ISSR-PCR protocol by an additional PCR reamplification round in order to detect whether increased PCR productivity would give new bands in ISSR patterns. We found that the reamplification step had a prominent impact on the quality of the inter-simple-sequence repeat (ISSR) PCR patterns of flax, depending on the particular primer used for PCR amplification. We could clearly distinguish between two types of reamplification effect. Most ISSR primers (16 out of 21) gave no reamplification effect as usual, but five primers (23.8%) provided a new ISSR fingerprinting pattern after the 2nd reamplification round, leaving the previous 1st round pattern completely blank. Therefore, we recommend the expansion of a basic ISSR-PCR protocol for another reamplification round in order to mine out full the fingerprinting potential from ISSR-PCR method.

DNA Fingerprinting↗
PubMed2003

[Study on DNA fingerprinting of Mycobacterium tuberculosis strains isolated in Southern Chinese army by IS6110-restriction fragment length polymorphism].

OBJECTIVE: To study the correlation between DNA fingerprinting of Mycobacterium tuberculosis (MTB) stains isolated from the Chinese army in the south and from local residents, and to investigate the molecular epidemiological characteristics of tuberculosis (TB) in the army, for the sake of TB prevention in the army. METHODS: MTB DNA was digested with restriction endonuclease PvuII and electrophoresed in agarose gel, after Southern Blotting, the membrane was hybridized with a 245 bp fragment of IS6110 which labeled [alpha(32)P]-dCTP as probe. Finally, a restriction fragment length polymorphism (RFLP) patterns was shown, and analyzed logestic with epidemiological data from the patients. RESULTS: A total number of 185 TB strains were detected and the IS6110 copy numbers ranged from 1 - 22. No significant difference was found in the IS6110 copy numbers between patients from army and local patients. IS6110 copy numbers of TB strains in army patients were centered in 6 - 20, however, with 7 - 20 copies in local TB patients. The TB strains were dispersed into 8 groups and the majority of TB strains in both army and local patients was centered in groups I, II, III. The distribution of DNA fingerprint for drug resistance TB strains was significantly different from those for sensitive strains. No different distribution of among groups was found regarding BCG history. CONCLUSIONS: The genetics of TB stains were roughly the same between the army patients and local ones, but there was a strong correlation in the gene levels. Data suggested that a close connection should be considered on TB prevention and treatment for TB patients in the army and local residents.

China↗
PubMed1992

The decision theory of paternity disputes: optimization considerations applied to multilocus DNA fingerprinting.

The solution of paternity disputes using results from scientific analyses is studied from a decision-theoretical viewpoint. Two alternative approaches to decision making, the so-called 'Bayes' and 'Minimax' strategies, are described and discussed. If prior probabilities of paternity are exactly known, then Bayes decisions are (a) independent of the source of evidence and (b) optimal with respect to average losses caused by wrong decisions. However, it is concluded that Minimax decisions, which depend upon the employed test system but not upon prior probabilities, are more appropriate in paternity cases if equal prior good will towards disclaimed children and alleged fathers is demanded. It is further demonstrated that, when major evidence about paternity comes from multilocus DNA fingerprinting, prior probabilities must be known quite accurately for Bayes decisions to be superior with respect to average losses. Finally, we are able to show that 'quasi' Bayes decision making, that is, adopting a neutral prior probability of 0.5 but leaving thresholds for decision making unchanged, coincides with Minimax decision making if multilocus DNA fingerprinting is employed.

Bayes Theorem↗
PubMed1992

[Genomic DNA fingerprinting by pulsed-field gel electrophoresis for study of nosocomial infection caused by methicillin-resistant Staphylococcus aureus].

In this study, we have compared genomic DNA fingerprintings among isolates of methicillin-resistant Staphylococcus aureus (MRSA) by using pulsed-field gel electrophoresis (PFGE). Chromosomal fragments digested with Sma I were most suitable for the PFGE separation, giving 15-20 fragments of sizes ranging from about 30-1,500 kb. Thirty-one distinctive fragment patterns were identified in 111 isolates of MRSA. On the basis of the genomic typing by PFGE, we performed an epidemiological investigation of an outbreak of nosocomial MRSA infection among 18 inpatients in Nagoya University Hospital. Ten types of chromosomal digestion were identified in 21 isolates of MRSA. The clarity and polymorphism of the chromosomal digestion patterns enabled us to discriminate between isolates. Classification of the genomic DNA fingerprinting patterns by PFGE is therefore proposed as a useful method for investigating the source, transmission, and spread of nosocomial MRSA infections.

Cross Infection↗
PubMed2004

DNA amplification fingerprinting using 10 x polymerase chain reaction buffer with ammonium sulfate for human identification.

OBJECTIVE: The polymerase chain reaction (PCR) - based DNA amplification fingerprinting (DAF) or randomly amplified polymorphic DNA (RAPD) is based on a strategy using a single arbitrary oligonucleotide primer to generate anonymous amplification of genomic DNA. On this basic strategy, in this study, we aimed to test individual differences and usefulness of 2 basic primers (5'-CGCGCCGG-3' and 5'-TGCCGAGCTG-3') and examined whether there is a positive effect on results of 10 x PCR buffer with ammonium sulfate. METHODS: A new approach in DNA fingerprinting, 10 x PCR buffer with ammonium sulfate, is presented in the study. Primers with single 8 and 10 nucleotides in length and 2 different PCR buffers with or without ammonium sulfate were used to identify 135 volunteers with no blood relationship. This study was carried out at the Pharmacology Laboratory, University of Gaziantep, School of Medicine, Turkey between 1999 and 2000. RESULTS: An average of 10 major bands representing 500-1500 base pair (bp) in length was determined as amplified DNA products on standard agarose gels for these volunteers. The use of ammonium sulfate in 10 x PCR buffers has increased to 92% success ratio of individual difference obtained from the 8 nucleotides primer. CONCLUSION: With this study, more reliable results can be obtained by using ammonium sulfate in 10 x PCR buffers.

Ammonium Sulfate↗
PubMed2004

[Application of M-RAPD technique to obtain the genomic fingerprints of various pathogenic microbials].

OBJECTIVE: To obtain genomic fingerprints of different pathogenic microbials and make certain whether their patterns can be used in the identification of microbials by means of multiplex random amplified polymorphic DNA analysis (M-RAPD). METHODS: Arbitrary primers of 10 oligonucleotides were randomly grouped, and various microbials chromosomal DNA were amplified with three combinatorial primers at a special higher annealing temperature. The products were detected by 15 g/L agarose electrophoresis and the patterns were analyzed by the software of Gelworks 1d Intermediate. RESULTS: Specific and resistant DNA fingerprints for different pathogenic microbials with combinatorial primers were gained. The profiles were clear, well-distributed and the number was great. The products of the three primers included most products of every two primers and would appear with no relation to their length, but small products had more opportunity; three primers could provide information contents half as many again as that two primers could provide for the same pathogenic microbials. There were obvious differences among different drug-resistant strains and between the drug-resistant strains and the corresponding reference strains, but different strains of the same microorganism had more similarity than discrepancy. The analytic data of the software of Gelworks 1d Intermediate also support our results. CONCLUSION: M-RAPD is a simple and rapid technique for the identification of different kinds of pathogenic microbials, and it can provide rich genetic information.

DNA Fingerprinting↗
PubMedDate not supplied

[An already archived latent fingerprint as a DNA source for STR typing in a murder case].

Former studies have shown that even a single skin contact, resulting in a latent fingerprint, can transfer enough DNA for genetic analysis. However, up to now latent fingerprints have usually not been used for DNA typing. In the present case the smeared trace of a hand was found in the suspect's car and archived. As it could not be evaluated in a classical manner, the evidence had to be examined by molecular genetic methods. DNA was extracted and typed in five different STR loci. Based on the yielded results, the significance of the findings is discussed.

DNA↗
PubMed2004

Diversity surveys of soil bacterial community by cultivation--based methods and molecular fingerprinting techniques.

By combining the cultivation methods with molecular fingerprinting techniques, the diversity surveys of soil bacterial community in 13 areas of China were carried out. The cultivable heterotrophic diversity was investigated by colony morphology on solid LB medium. Genetic diversity was measured as bands on denaturing gradient gel electrophoresis(DGGE) by the extraction and purification of the total soil DNA, and amplification of bacterial 16S rDNA fragments by polymerase chain reaction (PCR). The Shannon-Wiener indices of diversity (H), richness (S) and evenness (E(H)) were employed to estimate the diversity of soil bacterial community. The results showed that there was an obvious diversification existed in soil from the different areas. However, the genetic diversity estimated by PCR-DGGE can provide more comprehensive information on bacterial community than the cultivation-based methods. Therefore, it is suggested to combine the traditional methods with genetic fingerprinting techniques to survey and estimate soil bacterial diversity.

DNA Fingerprinting↗
PubMed2004

Random amplified polymorphic DNA fingerprinting as a marker for Paramecium jenningsi strains.

The aim of the present study is to establish a common RAPD marker for P. jenningsi using a series of Ro primers and to investigate if strains originating from distant and isolated localities (Japan, China, India, Saudi Arabia) have isolated gene pools and represent distinct species. An analysis of dendrograms constructed on the basis of RAPD-PCR fingerprints with four primers (Ro 460-04, 460-06, 460-07, and 460-10) from the first part of this project (SKOTARCZAK et al. 2004), assigns the strains to two groups consisting of the continental strains (India, Saudi Arabia, China) and Japanese strains that have been considered as a separate sibling species within P. jenningsi. The genetic similarity of the Indian and Arabian strains was ascertained, whereas the Chinese strain formed an independent branch in this sibling species. The primers Ro (460-01,460-02, 460-03, 460-05, 460-08) also distinguish between two groups of strains, although they divide the Japanese strains into two subgroups that are not reproductively isolated. This probably indicates genetic variation within this sibling species. However, it comprises one common gene pool (successful inter-strain crosses) and is reproductively isolated from the other sibling species. The results presented in these papers confirm that the construction of ten band patterns having marker attributes is possible on the basis of DNA amplification from 9 strains of P. jenningsi with the RAPD-PCR fingerprinting method using five primers from the Ro series. The patterns can be assigned to three marker-groups: a general species group, a group differentiating between sibling species, and accessory strain markers.

Animals↗
PubMed1997

[Analysis of clonality with immunoglobulin heavy chain gene rearrangement fingerprinting map in childhood acute lymphoblastic leukemia].

OBJECTIVE: To investigate the types of the immunoglobulin heavy chain (IgH) gene rearrangement and the co-existing clones in childhood acute lymphoblastic leukemia (ALL). METHODS: Polymerase chain reaction (PCR) amplification and single-strand conformation polymorphism (SSCP) were used to construct the IgH-PCR-SSCP gene fingerprinting. RESULTS: Of the 34 gene fingerprinting maps obtained from newly diagnosed ALL, 9 (32.14%) were one allelic rearrangement and 15 (53.75%) were biallelic in mono-clonal rearrangements. Four cases (14.29%) with high white cell count and precursor-B immunophenotype were oligoclonal rearrangements. CONCLUSION: There were multiple IgH bi-allelic rearrangements and co-existing clones in childhood ALL.

Adolescent↗
PubMed1992

Oligonucleotide fingerprinting to individualize ungulates.

The optimal combination of restriction enzyme and oligonucleotide probe has been determined for the individualization of hoofed animal species (cattle, pig, goat, sheep, horse and camel). Four different restriction endonucleases were used as well as five synthetic oligonucleotide probes hybridizing to different simple tandem repeats for fingerprint analyses in unrelated cattle (Swiss and German Simmental of unknown relationship and three families): 4 x 10(15) cows and oxes would reveal different banding patterns after HinfI digestion using the probe (CAC)5/(GTG)5. The other species were investigated using HinfI (and HaeIII) and five different oligonucleotide probes specific for simple tandem repeats. Using (CAC)5/(GTG)5 the discrimination potential in sheep was about one order of magnitude lower than in cattle while in goats 6 x 10(10) specimen are easily differentiated with (CA)8/(GT)8. From an evolutionary standpoint it may be of interest that also in all other ungulate species tested, (CAC)5/(GTG)5 and (CA)8/(GT)8 exhibited the highest potential for individualization. Advantages of oligonucleotide fingerprinting are discussed.

Animals↗
PubMed2005

Genetic variability of the mouse hepatoma cells MH-22a revealed by RAPD-PCR-fingerprinting under different conditions of cultivation.

AIM: to study genetic variability in clonal lines of the mouse hepatoma MH-22a and the dependence of the capability of different clonal line cells for differentiation on the amount of genetic disturbances revealed by the RAPD-PCR method. METHODS: The hepatoma MH-22a and its ten clonal lines were transplanted into subcutaneous connective tissue (SCT) and the eye anterior chamber (EAC) by injection of the cells to syngenic C3HA mice. The growth of transplants was checked in 15-20 days after transplantation. The tumors were fixed in neutral paraformaldehyde (10%), passed through ethanol of increasing concentrations, embedded in paraffin and stained by hematoxiline and eosine and Van Gisone. The genetic heterogeneity in the hepatoma cell population MH-22a and its clonal lines in vitro and in vivo was revealed by random amplified polymorphic DNA (RAPD-PCR). For the estimation of genetic variability revealed in the fingerprints was used the genetic variability index (GVI), based on the Bootstrep and Mikulinskaya's statistic programme. RESULTS: The comparative analysis of the genetic structure of the clonal line populations in vitro and in vivo has revealed that the amount of clones with the high, intermediate, and low variability is approximately the same in both cases. It was also shown that GVI in various clonal lines in vitro correlated with their vital ability: the clones yielding clone lines had the lowest GVI. The same GVI value was found in the clonal lines proliferated in the EAC regardless of their capability for differentiation. Intraclonal analysis has shown that the highest values of changes revealed on fingerprints of the amplification of DNA products do not prevent from differentiation of tumor hepatoma cells in the EAC. CONCLUSION: These data allow concluding that the mouse hepatoma cells MH-22a can preserve ability for differentiation in spite of significant changes in their genome.

Animals↗