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At least 919 records · Page 51Linked to original sources
PubMed1992

Dideoxy fingerprinting (ddE): a rapid and efficient screen for the presence of mutations.

We describe dideoxy fingerprinting (ddF), a hybrid between dideoxy sequencing and SSCP that can detect the presence of single base and other sequence changes in PCR-amplified segments. As implemented herein, ddF involves a Sanger sequencing reaction with one dideoxynucleotide followed by nondenaturing gel electrophoresis. When ddF was used to examine segments of the human factor IX gene, 84 of 84 different mutations were detected with a very low rate of false positive signals. The approximate locations of the sequence changes could be determined from the ddF pattern and samples with different sequence changes had different fingerprints. In addition, large segments could be amplified and rapidly screened by ddF in multiple smaller subsegments. The patterns observed with ddF are instructive in that they suggest an inherent limitation in the detection of certain mutations by SSCP.

DNA Fingerprinting↗
PubMed1995

DNA fingerprint analysis in chemically mutagenized Chinese hamster lung cells.

Using a multi-locus minisatellite Per-6 DNA probe, we performed DNA fingerprint analysis. Chinese hamster lung (CHL) cells were treated with six model chemicals: N-methyl-N'-nitro-N-nitrosoguanidine, mitomycin C, methyl methanesulfonate, furylfuramide, 2-acetylamino-fluorene, and cyclophosphamide, with or without S9 mix. 771 hypoxanthine phosphoribosyltransferase deficient clones (749 from mutagen-treated cells and 22 from untreated cells) and 90 unselected clones from untreated cells were isolated and analyzed. The spontaneous mutation frequency at CHL cell minisatellite loci was 0.31-0.63%. All the chemicals increased mutation frequencies. Almost all mutations localized to the three specific minisatellite loci corresponding to 4.2, 3.8, and 2.4 kb bands, suggesting that these regions are more unstable and susceptible to mutation. DNA fingerprint analysis is a promising technique for detecting mutations at neutral DNA regions, especially recombinational mutations, and may be useful for surveying genetic instability related to heritable defects or aging.

2-Acetylaminofluorene↗
PubMed1993

Diversity of ribosomal DNA fingerprints of Leptospira serovars provides a database for subtyping and species assignation.

Ribosomal DNA fingerprints from 103 pathogenic Leptospira strains were examined using EcoRI restriction and fragment length polymorphisms of rRNA genes. Sixty-nine new leptospiral ribotypes were described, in addition to 49 previously observed. Except for 5 strains, a good correlation between DNA homology data and ribotyping was observed. The genospecies of 31 reference strains could be presumed, since they shared 13 ribotypes with strain(s) previously studied by DNA homology. Furthermore, the definition of common rRNA hybridization fragments in each recognized DNA hybridization group provides information about the status of Leptospira reference strains yet to be classified. With 118 ribotypes now defined among the validated serovar reference strains, rRNA fingerprints constitute a database for subtyping Leptospira species.

DNA Fingerprinting↗
PubMedDate not supplied

DNA fingerprinting of yeast strains by restriction enzyme analysis.

Restriction endonuclease analysis was used as a new method to obtain genomic DNA fingerprints in yeast. Fifteen yeast strains belonging to the genera Saccharomyces and Zygosaccharomyces were examined. Restriction fragments obtained with ApaI or KspI endonucleases were separated by SDS-PAGE and silver-stained. Analysis of the fingerprints showed that restriction enzyme digestion of genomic DNA can be successfully applied to yeast, enabling the differentiation between strains belonging to different or to the same species or genera.

DNA Fingerprinting↗
PubMed1993

DNA fingerprints of Mycobacterium tuberculosis do not change during the development of rifampicin resistance.

Drug-resistant tuberculosis has become a major public health problem. Resistance to rifampicin probably arises through mutations in the mycobacterial RNA polymerase. Patients may acquire rifampicin resistant tuberculosis by three mechanisms: (1) infection with a resistant organism, (2) selection of a sub-population of resistant organisms that remain contained whilst the more virulent wild type is present, (3) mutations within the population of bacilli causing the original infection. Sequential isolates of Mycobacterium tuberculosis were collected from 2 patients who developed rifampicin resistance whilst on treatment. One patient was immunosuppressed with HIV-infection; in the other patient the original isolate was also resistant to isoniazid. DNA fingerprinting techniques were used to type the isolates. No differences were found between the fingerprints of isolates from before and after the development of resistance. These data suggest that the third of the mechanisms listed above was responsible for the acquisition of rifampicin resistance in these 2 patients.

Adult↗
PubMed1993

Application of DNA fingerprinting with IS986 to sequential mycobacterial isolates obtained from pulmonary tuberculosis patients in Hong Kong before, during and after short-course chemotherapy.

A total of 266 Mycobacterium tuberculosis isolates were subjected to DNA RFLP analysis. They were obtained from monthly sputum cultures from patients treated with short-course chemotherapy and then followed up for 2 years. They originated from 42 patients who relapsed after short-course chemotherapy and from a further 42 patients who yielded a single isolated positive culture after chemotherapy. The isolates consisted of one obtained pretreatment and the last obtained during chemotherapy, together with either two isolates cultured at least 2 months apart during relapse or the single post-chemotherapy isolate. They were coded before DNA RFLP analysis and assigned to groups with identical or near identical band patterns on visual inspection. After decoding, it was evident that almost every patient was infected with a strain with a different band pattern (fingerprint). In 100 comparisons of either the pretreatment isolate against the last positive isolate obtained during chemotherapy, or of the first relapse isolate against the second relapse isolate, 15 had been recorded as different; 4 of these were retrospectively found to be due to reading error (error rate 1.5%), leaving 11 (11%) with marked differences. For 5 (12%) of the 42 patients who relapsed, the fingerprint of the relapse isolate was markedly different from that of the pretreatment isolate. In contrast, the isolated positive culture was markedly different from that initially present in 36 (90%) of 40 comparisons. The relative contributions by clinical mixed infection and laboratory cross-contamination to the remaining 10-12% discrepancy rates could not be assessed.(ABSTRACT TRUNCATED AT 250 WORDS)

Antitubercular Agents↗
PubMed1995

DNA fingerprinting of Musa cultivars with oligodeoxyribonucleotide probes specific for simple repeat motifs.

Using synthetic oligodeoxyribonucleotide probes against restriction-digested genomic DNA, we have established DNA fingerprinting of Musa cultivars. Of all the enzymes used, Eco RI and Hin dIII were found to be most informative, giving rise to individual specific band patterns with oligonucleotide probes of 15- to 18-base residues. Of the several probes and enzyme combinations used, the 15mer GACA probe with Eco RI and Hin dIII digests revealed a maximal level of polymorphism, and the probability of obtaining an identical band pattern between any two random genotypes was calculated to be 1.50 x 10(-9) and 1.59 x 10(-9), respectively. Oligonucleotide probes longer than 22 residues were also used but did not hybridize. The present approach is useful for cultivar identification and for overall genome analysis to establish relatedness among the various accessions of the Musa germplasm originating from different geographic locations. The relevance of using synthetic oligonucleotide probes based on simple repeat motifs for achieving DNA fingerprinting pattern is discussed.

Base Sequence↗
PubMed2005

PCR primers based on different portions of insertion elements can assist genetic relatedness studies, strain fingerprinting and species identification in rhizobia.

Using the sequence of an insertion element originally found in Rhizobium sullae, the nitrogen-fixing bacterial symbiont of the legume Hedysarum coronarium, we devised three primer pairs (inbound, outbound and internal primers) for the following applications: (a) tracing genetic relatedness within rhizobia using a method independent of ribosomal inheritance, based on the presence and conservation of IS elements; (b) achieve sensitive and reproducible bacterial fingerprinting; (c) enable a fast and unambiguous detection of rhizobia at the species level. In terms of taxonomy, while in line with part of the 16S rRNA gene- and glutamine synthetase I-based clustering, the tools appeared nonetheless more coherent with the actual geographical ranges of origin of rhizobial species, strengthening the European-Mediterranean connections and discerning them from the asian and american taxa. The fingerprinting performance of the outward-pointing primers, designed upon the inverted repeats, was shown to be at least as sensitive as BOX PCR, and to be functional on a universal basis with all 13 bacterial species tested. The primers designed on the internal part of the transposase gene instead proved highly species-specific for R. sullae, enabling selective distinction from its most related species, and testing positive on every R. sullae strain examined, fulfilling the need of PCR-mediated species identification. A general use of other IS elements for a combined approach to rhizobial taxonomy and ecology is proposed.

Base Sequence↗
PubMed2006

Effect of 1,2-indanedione on PCR-STR typing of fingerprints deposited on thermal and carbonless paper.

1,2-Indanedione treated fingerprints deposited on two substrates (thermal and carbonless paper) were swabbed and tested to determine the effect of the chemical on PCR-STR DNA typing. Samples from 10 post-treatment intervals were analyzed. Two extraction methods, Chelex and Qiamp, were used to determine the effect of extraction procedure on the quality of the DNA profiles. The LCN DNA samples were concentrated using Microcon 100 and amplified using the Profiler Plus amplification kit. 1,2-Indanedione did not adversely affect the DNA profiles obtained from the treated fingerprints. Partial DNA profiles were obtained at all post-development time frames. Both extraction methods produced comparable profiles although more "drop-ins" were observed with the Qiamp method. More "drop-outs" occurred in the DNA profiles from samples deposited on the thermal substrate compared with carbonless substrate.

Alleles↗
PubMed2006

Diagnosis of ectopic tissue versus contamination by genetic fingerprinting in a routine surgical pathology specimen.

A 62-year-old woman presented with recurring right upper quadrant pain and underwent a routine laparoscopic cholecystectomy. A large gallstone was found impacted in the fundus of the gall bladder. Interestingly, aside from noting mild inflammation of the gall bladder wall, microscopic examination of the specimen identified 2 fragments of benign thyroid tissue. Given the routine nature of the surgical procedure and lack of abnormality detected during the operation, the attending pathologist suspected extraneous tissue contamination ("floater") of the pathology specimen and submitted the block and slides to Molecular Pathology. The thyroid tissue-containing fragments and gallbladder wall were independently isolated and subjected to genetic fingerprinting using a standard forensic DNA identification panel. All fragments showed the identical fingerprint, strongly suggesting that they belonged to the same patient. The results indicated that the thyroid tissue was from an ectopic rest adjacent to the gall bladder, which has been reported only very rarely in the previous literature and illustrates the unusual use of molecular genetic testing to confirm the presence of ectopic tissue versus contamination.

Choristoma↗
PubMed2004

Spectrum of bacteriocin activity of Lactobacillus plantarum BS and fingerprinting by RAPD-PCR.

The spectrum of antimicrobial activity of Lactobacillus plantarum BS against representative bacterial species was established through deferred assay and 'spot-on-lawn' assay using actively growing cells and partially purified bacteriocin extract, respectively. Only lactobacilli, pediococci, enterococci, bacilli and Listeria were inhibited from the test microorganisms. Slight bacteriocinogenic activity through 'spot-on-lawn' assay was detected against Staphylococcus aureus and Escherichia coli O157:H7. Random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) analysis was used to compare the fingerprint of L. plantarum BS with other strains of L. plantarum. Using the 16S rRNA-based primer, P32, the bacteriocinogenic isolate exhibited identical RAPD-PCR fingerprints to L. plantarum ATCC 14917. Dendrograms derived from the Unweighted Pair Group Method with Arithmetic Mean (UPGMA) were constructed to show the similarity relationships among the investigated strains based on RAPD-PCR analysis. Bands differentiating L. plantarum BS from L. plantarum ATCC 14917 were also identified by varying the annealing temperature.

Bacteriocins↗
PubMed2004

Ninhydrin-dyed latent fingerprints as a DNA source in a murder case.

In this case report, we describe the possibility of using ninhydrin-dyed fingerprints as a DNA source for STR typing. Preliminary tests prove that ninhydrin-dyed material still can be useful for STR typing. The case material consisted of seven ninhydrin-labeled latent fingerprints found at a murder crime site, which could not be typed in a classical manner. We were able to swap DNA from the ninhydrin-treated areas and successfully use it for STR typing.

DNA↗
PubMed2004

ERIC-PCR fingerprinting-based community DNA hybridization to pinpoint genome-specific fragments as molecular markers to identify and track populations common to healthy human guts.

Bacterial populations common to healthy human guts may play important roles in human health. A new strategy for discovering genomic sequences as markers for these bacteria was developed using Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR fingerprinting. Structural features within microbial communities are compared with ERIC-PCR followed by DNA hybridization to identify genomic fragments shared by samples from healthy human individuals. ERIC-PCR profiles of fecal samples from 12 diseased or healthy human and piglet subjects demonstrated stable, unique banding patterns for each individual tested. Sequence homology of DNA fragments in bands of identical size was examined between samples by hybridization under high stringency conditions with DIG-labeled ERIC-PCR products derived from the fecal sample of one healthy child. Comparative analysis of the hybridization profiles with the original agarose fingerprints identified three predominant bands as signatures for populations associated with healthy human guts with sizes of 500, 800 and 1000 bp. Clone library profiling of the three bands produced 17 genome fragments, three of which showed high similarity only with regions of the Bacteroides thetaiotaomicron genome, while the remainder were orphan sequences. Association of these sequences with healthy guts was validated by sequence-selective PCR experiments, which showed that a single fragment was present in all 32 healthy humans and 13 healthy piglets tested. Two fragments were present in the healthy human group and in 18 children with non-infectious diarrhea but not in eight children with infectious diarrhea. Genome fragments identified with this novel strategy may be used as genome-specific markers for dynamic monitoring and sequence-guided isolation of functionally important bacterial populations in complex communities such as human gut microflora.

Adult↗
PubMed2006

Development of a 9600-clone procedure for oligonucleotide fingerprinting of rRNA genes: utilization to identify soil bacterial rRNA genes that correlate in abundance with the development of avocado root rot.

Oligonucleotide fingerprinting of rRNA genes (OFRG) is an array-based method that generates microbial community profiles through analysis of rRNA gene clone libraries. The original OFRG method allowed 1536 clones to be analyzed per experiment. This report describes a procedure for analyzing 9600 clones per experiment, including a new probe set for bacterial analysis, and improved data processing and statistical analysis tools. The software tools are available at the OFRG website (). Use of the 9600-clone procedure was demonstrated by examining the bacterial rRNA gene compositions of soils subjected to various temperature treatments. These treatments produced a series of soils with a range of abilities to suppress avocado root rot, enabling the identification of bacterial rRNA genes that correlate in abundance with root rot suppressiveness. OFRG analysis of these soils produced 8876 bacterial rRNA gene fingerprints grouped into 5123 clusters, or operational taxonomic units (OTUs). Eleven OTUs exhibited a positive correlation between the number of clones and the percentage of healthy roots. An in silico analysis was performed to examine the relationship between the number of rRNA genes analyzed and the number of correlates (rRNA gene-avocado root rot symptoms) identified. As the number of clones decreased, fewer correlates were identified. To further increase the throughput of the OFRG method, use of a glass slide-fluorescent probe microarray format was also explored.

DNA Fingerprinting↗
PubMed2005

Grouping of streptomycetes using 16S-ITS RFLP fingerprinting.

A total of 463 Streptomyces and Kitasatospora type strains were screened using 16S-ITS RFLP fingerprinting (combined restriction digest using enzymes BstUI and HaeIII). In total, 59 clusters could be delineated, each comprising multiple strains with nearly identical patterns. Good correlation was found in general with phylogeny, as revealed by 16S rDNA sequencing. Most strains assigned to a particular 16S-ITS RFLP cluster were classified into the corresponding 16S sequencing cluster whether a 16S similarity cut-off value of 97 or 98% was used. We conclude that the taxonomic resolution of 16S-ITS RFLP fingerprinting is higher than that of 16S rDNA sequencing; this may provide a tool for reducing the number of laborious DNA-DNA hybridizations necessary for discovering potentially new species within Streptomyces.

Cluster Analysis↗
PubMed2005

PCR-based DGGE fingerprinting and identification of methanogens detected in three different types of UASB granules.

Methane is produced by various methanogenic bacteria present in upflow anaerobic sludge blanket (UASB) bioreactors. Methane can be used to predict and improve UASB bioreactor efficiency. The methanogen population in the granules can be influenced by the composition of the substrate. The aim of this study was to fingerprint and identify the methanogens present in three different types of UASB granules that had been used to treat winery, brewery and peach-lye canning effluents. This was done using polymerase chain reaction (PCR)-based denaturing gradient gel electrophoresis (DGGE) and DNA sequence analysis. The DGGE fingerprints obtained from the methanogen reference cultures of Methanosaeta concilii, Methanosaeta thermophila, Methanosarcina barkeri, Methanosarcina mazeii and Methanobacterium formicicum were compared to the DGGE profiles of the Archaea in the different granules. The positions of the DGGE bands that did not correspond well to the bands of the known species were sequenced and compared to sequences available on GenBank using the Blastn search option. The aligned DNA sequences were used to construct a phylogenetic tree. Based on the data obtained, a DGGE marker was constructed which was used to provide a quick method to identify the Archaeal members of the microbial consortium in UASB granules.

Base Sequence↗
PubMed2006

Efficacy of clone fingerprinting methodologies.

With the development of new high-information content fingerprinting techniques for constructing BAC-based physical maps, physical map construction is accelerating and it is important to determine which methodologies work best. In a recent publication (Z. Xu et al., 2004, Genomics 84:941-951), Xu et al. evaluated five different techniques (one agarose-based and four using multiple enzymes) and concluded that a two-enzyme technique was superior. In addition, they found that no benefit was gained from fingerprinting more than 10x coverage. In this paper we report our own extensive simulation results, which lead to contrasting conclusions. Our data indicate that the five-enzyme method known as SNaPshot is the most effective and that the assembly can in fact be significantly improved with greater than 10x coverage.

Arabidopsis↗
PubMedDate not supplied

A DNA fingerprinting band associated with the susceptibility to CAE virus-induced arthritis in goats.

Caprine arthritis-encephalitis (CAE) virus-induced arthritis can be found in all Swiss goat breeds and it has been shown that there is a genetic pre-disposition for this disease. The 10 Toggenburg, 32 Chamois coloured and 40 Saanen goats, specially selected for this study, were naturally infected with CAE virus. Within each breed there was an equal distribution between clinically healthy animals and animals suffering from arthritis. In the case of the Saanen goats, a DNA fingerprint band generated with the multi-locus probe pV47 was identified associated with susceptibility to CAE virus-induced arthritis. In the Chamois coloured goats, no association was found. Another candidate DNA fingerprint band was present in clinically healthy animals of the Toggenburg breed but their number was insufficient for analysis.

Animals↗