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PubMedDate not supplied

Population characteristics of DNA fingerprints in humpback whales (Megaptera novaeangliae).

Humpback whales exhibit a remarkable social organization that is characterized by seasonal long-distance migration (> 10,000 km/year) between summer feeding grounds in high latitudes and winter calving and breeding grounds in tropical or near-tropical waters. All populations are currently considered endangered as a result of intensive commercial exploitation during the last 200 years. Using three hypervariable minisatellite DNA probes (33.15, 3'HVR, and M13) originally developed for studies of human genetic variation, we examined genetic variation within and among three regional subpopulations of humpback whales from the North Pacific and one from the North Atlantic oceans. Analysis of DNA extracted from skin tissues collected by biopsy darting from free-ranging whales revealed considerable variation in each subpopulation. The extent of this variation argues against a recent history of inbreeding among humpback whales as a result of nineteenth- and twentieth-century hunting. A canonical variate analysis suggested a relationship between scaled genetic distance, based on similarities of DNA fingerprints, and geographic distance (i.e., longitude of regional subpopulation). Significant categorical differences were found between the two oceanic populations using a multivariate analysis of variance (MANOVA) with a modification of the Mantel nonparametric permutation test. The relationship between DNA fingerprint similarities and geographic distance suggests that nuclear gene flow between regional subpopulations within the North Pacific is restricted by relatively low rates of migratory interchange between breeding grounds or assortative mating on common wintering grounds.

Animals↗
PubMed1990

The similarity index and DNA fingerprinting.

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

Alleles↗
PubMed1998

Genetic diversity of commercial turkey primary breeding lines as estimated by DNA fingerprinting.

The genetic diversity of primary breeding sire and dam lines from the three largest turkey breeders was estimated by band sharing of DNA fingerprints and by genetic distance estimated from band sharing. For comparison, experimental lines selected for increased egg production (E line) or increased 16-wk body weight (F line) were also included in the analysis. Eighteen individual DNA samples per line were digested with HaeIII restriction enzyme and hybridized with Jeffreys' 33.6 probe. The DNA fingerprints were analyzed with computer programs designed to measure band sharing. Within commercial lines, band sharing ranged from 0.370 to 0.508 and was greater in commercial sire lines (average = 0.475) than in commercial dam lines (average = 0.393), indicating that accumulated inbreeding was greater in the sire lines. Band sharing in the F and E lines was 0.479 and 0.522, respectively. The average band sharing among lines was higher for primary breeding sire lines (average = 0.267) than for primary breeding dam lines (0.207), suggesting more genetic diversity in the dam lines. Genetic distance estimated from band sharing was greater among commercial dam lines than commercial sire lines. Based on band sharing between lines and genetic distance estimates, it appears that the experimental E and F lines contain genetic variation not found in the commercial lines. The results of the present study, along with data published in the literature, suggest that commercial primary breeding turkey lines are as diverse, if not more diverse, than similar commercial chicken lines.

Animals↗
PubMed2001

Random amplified polymorphic DNA fingerprints for identification of species in poultry pâté.

Because some fraudulent or unintentional mislabeling occurs that can be undetected, resulting in lower quality pâté, and because some population groups, for philosophical or religious reasons, do not wish to eat meat from certain species, a new procedure was developed and evaluated to detect pâté species composition by randomly amplified polymorphic DNA (RAPD). The RAPD method was used to generate fingerprint patterns for pork, chicken, duck, turkey, and goose meats. Ten DNA samples from pork, chicken, turkey, and duck meats were tested to confirm the effectiveness and specificity. Specific results for each species were obtained by the RAPD method. Sensitivity of the method was studied by DNA dilution in each species, detecting as little as 250 pg of DNA. Isolations of DNA from 30 pâtés (tinned and untinned) were carried out, and an optimal DNA was obtained for using as template DNA in polymerase chain reaction (PCR). The RAPD-PCR pattern was useful to identify species composition of pork, duck, duck-pork, goose, and poultry pâtés. This study demonstrates the usefulness of RAPD fingerprinting to distinguish between species in pâtés.

Animals↗
PubMed1994

Use of DNA fingerprinting and biotyping methods to study a Candida albicans outbreak in a neonatal intensive care unit.

During a 15-day period, 7 premature infants hospitalized in a neonatal intensive care unit presented with sepsis caused by Candida albicans. The local environment and hands of all 54 persons involved in the intensive care unit were examined for the presence of this organism. Five techniques were used in the analysis of the isolates recovered from blood cultures of the children, the hands of personnel and 10 control isolates. The methods used were serotype determination, genetic fingerprinting, morphotyping, resistotyping and killer yeast typing. Morphotyping and genetic fingerprinting proved to be the most discriminatory techniques, and only combined analysis of the results obtained with these various methods allowed the source of the outbreak to be identified. An isolate from the hands of a healthy staff member and isolates from infected children all belonged to the same strain.

Adult↗
PubMed2001

Molecular pathogenesis of Epstein-Barr virus associated posttransplant lymphomas: new insights through latent membrane protein 1 fingerprinting.

BACKGROUND: Fingerprint amino acid patterns within the carboxy terminus of the latent membrane protein (LMP1) oncoprotein of Epstein-Barr virus (EBV) allow individual strain identification at the molecular level. LMP1 is expressed in the tumor cells of EBV-associated posttransplant lymphomas (PTLs) and the LMP1 genome is also identified in lymphocytes of most donors of allogeneic bone marrow. Therefore, LMP1 genotyping in donor lymphocytes and PTL tumor cells, together with sex chromatin determination of tumor cells, allows to determine the origin of PTL tumor cells and the origin of individual EBV strains harboured by them. METHODS: We traced the origin of aggressive PTLs occurring in six patients after allogeneic T cell-depleted stem cell transplantation (allo-SCT). DNA was extracted from donor lymphocytes and PTLs of recipients and amplified with LMP1-specific primers in each case. A comparative sequence analysis of the fingerprint LMP1 region identified in donor lymphocytes and lymphoma was performed. RESULTS: One lymphoma of donor origin occurred after highly selected CD34+ PBSCT and contained the same LMP1 genotype as the donor lymphocytes. Three lymphomas of recipient origin had deletions within the carboxy terminus of LMP1, not identified in the donor strains. All lymphomas occurred in the setting of allo-SCT and had a rapid clinical course. CONCLUSIONS: These results show that highly selected CD34+ PBSCT does not protect against transfer of EBV positive founder cells of donor type PTL and that, after allo-SCT, recipient type PTLs are not uncommon. Outgrowth of recipient type lymphoma may be favoured by LMP1 deletion variant strains present in recipient lymphocytes.

Adult↗
PubMed1996

Phylogeny of the Sphaerotilus-Leptothrix group inferred from morphological comparisons, genomic fingerprinting, and 16S ribosomal DNA sequence analyses.

Phase-contrast light microscopy revealed that only one of eight cultivated strains belonging to the Sphaerotilus-Leptothrix group of sheathed bacteria actually produced a sheath in standard growth media. Two Sphaerotilus natans strains produced branched cells, but other morphological characteristics that were used to identify these bacteria were consistent with previously published descriptions. Genomic fingerprints, which were obtained by performing PCR amplification with primers corresponding to enterobacterial repetitive intergenic consensus sequences, were useful for distinguishing between the genera Sphaerotilus and Leptothrix, as well as among individual strains. The complete 16S ribosomal DNA (rDNA) sequences of two strains of "Leptothrix discophora" (strains SP-6 and SS-1) were determined. In addition, partial sequences (approximately 300 nucleotides) of one strain of Leptothrix cholodnii (strain LMG 7171), an unidentified Leptothrix strain (strain NC-1), and four strains of Sphaerotilus natans (strains ATCC 13338T [T = type strain], ATCC 15291, ATCC 29329, and ATCC 29330) were determined. We found that two of the S. natans strains (ATCC 15291 and ATCC 13338T), which differed in morphology and in their genomic fingerprints, had identical sequences in the 300-nucleotide region sequenced. Both parsimony and distance matrix methods were used to infer the evolutionary relationships of the eight strains in a comparison of the 16S rDNA sequences of these organisms with 16S rDNA sequences obtained from ribosomal sequence databases. All of the strains clustered in the Rubrivivax subdivision of the beta subclass of the Proteobacteria, which confirmed previously published conclusions concerning selected individual strains. Additional analyses revealed that all of the S. natans strains clustered in one closely related group, while the Leptothrix strains clustered in two separate lineages that were approximately equidistant from the S. natans cluster. This finding suggests that the tentative species "L. discophora" needs to be more clearly defined and compared with other species belonging to the genus Leptothrix.

Base Sequence↗
PubMed1998

PCR fingerprinting of whole genomes: the spacers between the 16S and 23S rRNA genes and of intergenic tRNA gene regions reveal a different intraspecific genomic variability of Bacillus cereus and Bacillus licheniformis [corrected].

Genomic diversity in 21 strains of Bacillus cereus and 10 strains of Bacillus licheniformis was investigated by random amplified polymorphic DNA (RAPD) analysis, which samples the whole genome, and by two PCR fingerprinting techniques sampling the hypervariable spacers between the conserved 16S and 23S rRNA genes of the rRNA gene operon (ITS-PCR) and regions between tRNA genes (tDNA-PCR). RAPD analysis showed a remarkable diversity among strains of B. cereus that was not observed with the rRNA and tRNA intergenic-spacer-targeted PCR, where all the strains showed practically identical fingerprints. A wide variability among the B. cereus strains was also observed in the plasmid profiles, suggesting that the genetic diversity within B. cereus species can arise from plasmid transfer. One contribution to the diversity detected by RAPD analysis was determined by the presence of large extrachromosomal elements that were amplified during RAPD analysis as shown by Southern hybridization experiments. In contrast to the strains of B. cereus, the 10 strains of B. licheniformis were grouped into two clusters which were the same with all the methods employed. The 16S rRNA genes were identical in all 10 strains when examined using single strand conformation polymorphism analysis after digestion with Alul and Rsal. From these data we hypothesize two different evolutionary schemes for the two species.

Bacillus cereus↗
PubMed1999

Identification of Burkholderia species and genomovars from cystic fibrosis patients by AFLP fingerprinting.

AFLP is a genomic fingerprinting technique based on the selective amplification of restriction fragments from a total double-digest of genomic DNA. The applicability of this method to differentiate between species and genomovars of the genus Burkholderia was tested, with particular emphasis on taxa occurring in cystic fibrosis patients. In this study, 78 well-characterized strains and field isolates were investigated by two methods of AFLP fingerprinting. In the manual procedure, a radioactively labelled primer was used, amplified fragments were separated by conventional PAGE and the patterns were revealed by autoradiography. In the automated procedure, a fluorescently labelled primer was used in combination with electrophoresis and on-line data collection by means of an automated DNA sequencer. Overall, there was good agreement between the two AFLP procedures and the data were mostly consistent with results obtained from SDS-PAGE of whole-cell proteins and DNA-DNA hybridization experiments. The automated AFLP procedure has considerable technical advantages compared with the manual AFLP procedure, but a thorough visual analysis of the DNA profiles was required to avoid misidentification of some Burkholderia cepacia genomovar III strains.

Bacterial Typing Techniques↗
PubMed1992

The insertion sequence IS200 fingerprints chromosomal genotypes and epidemiological relationships in Salmonella heidelberg.

In Salmonella heidelberg the copy number of the Salmonella-specific insertion element IS200 was found to vary from four to six. All strains tested contained at least one common insertion site which was serovar specific, and most strains contained three common sites. Concurrent analysis of plasmids indicated that all insertion sequence copies were chromosomally located, and also supported the equivalence of an IS200 fingerprint and clonality. Seven intra-serovar clonal lines were thereby identified. One of these was associated with human infections, including septicaemias. Another was associated with chicken as a host: all these strains also carried a unique plasmid of 23 MDa, which was typed as a member of the IncX group. The chromosomal fingerprint of a third clone showed it to be a descendant of the chicken line marked by a single IS200 transposition. One or two representatives of four other clonal lines were identified. These lines of S. heidelberg could be related by divergent evolution, and the most recent relatives conformed to a continuous branching process model of IS200 transposition. This insertion sequence provided a highly discriminatory molecular marker of the S. heidelberg chromosome, and two of the seven clonal lines so identified were associated with distinct clinical/epidemiological contexts.

Animals↗
PubMed1993

Genotypes and phylogenetic relationships of Salmonella typhimurium are defined by molecular fingerprinting of IS200 and 16S rrn loci.

Molecular fingerprints of chromosomal genotypes in Salmonella typhimurium were generated by analysis of variation at the 16S rrn gene loci and the sites of the insertion sequence IS200. Genetic and reference strains of S. typhimurium were compared with clinical phage type strains from cases of human salmonellosis. Three 16S rrn profiles, one of which was predominant, were found. The copy number of the Salmonella-specific insertion sequence IS200 varied from 6 to 12, and all insertions were chromosomal. Three of the insertion sites shared by all strains were serovar-specific for S. typhimurium. Thirteen distinct profiles of IS200 were detected, providing a high level of intraserovar strain discrimination. Profiles were generally more conserved among genetic and reference strains; representatives of clinical phage type strains, which are recent human isolates, showed much greater diversity of IS200 profiles. Irrespective of their origin, strains could be assigned to IS200 profile groups, phylogenetically related lines identified by combinations of conserved insertion sites. Hybridization profiles of this mobile element are markers of intermediate and short-term evolution in S. typhimurium. They provide a fingerprinting scheme for the purposes of genetics, and delineate a molecular typing scheme for the purposes of epidemiology.

Base Sequence↗
PubMed1997

Development and verification of fingerprinting probes for Candida glabrata.

Since Candida glabrata has emerged as one of the most common Candida pathogens, DNA probes have been developed which fulfil the requirements for effective fingerprinting. Using a screen for complex genomic fragments containing moderately repetitive sequences, seven DNA probes were cloned which generate complex Southern blot hybridization patterns with EcoRI-digested C. glabrata DNA. All of the probes are species-specific and the majority cross-hybridize to varying degrees. The capacity of two of the probes, Cg6 and Cg12, to measure genetic distance between independent isolates is verified by comparing clustering in dendrograms based on similarity coefficients computed between all pairs of 39 independent isolates fingerprinted with Cg6, Cg12 and randomly amplified polymorphic DNA. The capacity of the probes Cg6 and Cg12 to assess microevolution in clonal populations of infecting C. glabrata over time is also demonstrated. These probes can now be used in large computer-assisted epidemiological studies.

AIDS-Related Opportunistic Infections↗
PubMed1995

Random amplified polymorphic DNA fingerprinting for rapid identification of leptospiras of serogroup Sejroe.

Eight leptospiral and three non-leptospiral primers were examined in the development of a random amplified polymorphic DNA (RAPD) fingerprinting method for identification of leptospiral serovars within the serogroup Sejroe. The strains examined comprised 19 reference strains of serogroup Sejroe, five field strains and 17 Leptospira borgpetersenii serovar hardjo type hardjobovis strains. Unique DNA banding patterns were obtained for each of the 17 reference strains with L. hardjo type hardjobovis-derived primers, and all clinical isolates were identified as L. hardjo type hardjobovis. Although the profiles were specific for each serovar, most serovars within serogroup Sejroe clustered into previously recognised genetic groups. RAPD fingerprinting is a simple, rapid method suitable for the identification of some Leptospira serovars.

Animals↗
PubMed2006

PCR fingerprinting of Trichophyton mentagrophytes var. interdigitale using polymorphic subrepeat loci in the rDNA nontranscribed spacer.

The sequence of the nontranscribed spacer (NTS) region of the rDNA of Trichophyton mentagrophytes var. interdigitale strain 2111 was determined, and three individual subrepeat loci identified. The first repeat region contained eight tandem copies of a degenerate 33-43 bp sequence, whilst the second had two complete and two partial 300 bp repeats. The third locus contained six tandemly repetitive elements of between 67 and 89 bp, which showed sequence identity to the TrS2 repeats of Trichophyton rubrum. PCR amplification of the individual repetitive regions from 42 random isolates of T. mentagrophytes var. interdigitale identified fragment length polymorphisms at each locus. Sequence analysis of the PCR products revealed that the size variations resulted from differences in the copy number of each of the three sets of subrepeat elements, TmiS0, TmiS1 and TmiS2. In addition, some indels were present in the flanking regions of the TmiS1 repeats. Combining PCR fingerprints from each of the three polymorphic loci produced a total of 19 individual strain profiles. The method was rapid, reproducible and discriminatory, and the fragment patterns simple to interpret. PCR fingerprint analysis of variable tandem repeat loci in the T. mentagrophytes var. interdigitale NTS represents a valuable molecular typing method for future epidemiological investigations in this species.

Belgium↗
PubMed1995

Genomic fingerprinting by microsatellite-primed PCR: a critical evaluation.

Single PCR primers complementary to microsatellite repeats were used to amplify genomic DNA samples from various plant species, as well as from human, yeast, and Escherichia coli DNA. Most primers generated distinct amplification products, resulting in fingerprint-like banding patterns after agarose gel electrophoresis and ethidium bromide staining. These fingerprints allowed distinction among different plant taxa at an interspecific as well as intraspecific level. Unexpectedly, some of the primers produced bands with the E. coli template DNA as well. A detailed examination of the influence of PCR conditions, especially the annealing temperature, on the quality of banding patterns suggested that the majority of bands were generated by mismatch priming in a way similar to random amplified polymorphic DNAs (RAPDs).

Cloning, Molecular↗
PubMed1991

Quercetin induces recombinational mutations in cultured cells as detected by DNA fingerprinting.

Quercetin, a flavonoid, is found in many fruits and vegetables. This drug was previously shown to affect the metastatic potential of mouse tumor cells. Mutagenicity of quercetin was examined by means of DNA fingerprint analysis using the Pc-1 probe that efficiently detects mutations due to recombination. Treatment of BMT-11 and FM3A tumor cells with 55 microM quercetin resulted in gain and loss of bands in the fingerprints in both cell lines. The frequencies of the clones having undergone mutation were 3/11 and 6/26, respectively. This suggests that quercetin is mutagenic and induces recombination. This result seems to provide a molecular basis for the phenotypic variations of BMT-11 tumor cells induced by quercetin.

Animals↗
PubMed1991

Repeat sequences from complex ds DNA viruses can be used as minisatellite probes for DNA fingerprinting.

In a search for new fingerprinting probes for use with sheep, repeat sequences derived from five poxviruses, an iridovirus and a baculovirus were screened against DNA from sheep pedigrees. Probes constructed from portions of the parapox viruses, orf virus and papular stomatitis virus and the baculovirus from the alfalfa looper, Autographa californica, nuclear polyhedrosis virus all gave fingerprint patterns. Probes from three other poxviruses and an iridovirus did not give useful banding patterns.

Animals↗
PubMed1993

DNA fingerprint bands applied to linkage analysis with quantitative trait loci in chickens.

An efficient approach to detect association between quantitative traits and bands of DNA fingerprint patterns uses intra-family tail analysis, which compares fingerprints of DNA mixes from individuals at the two tails of a phenotypic distribution. In analysis of 67 paternal half-sibs of a meat-type chicken family, of 57 sire bands generated by two probes, one sire-specific band (S6.6) was associated with abdominal fat deposition. The band effect was estimated by a linear model analysis to be 0.88 standard deviations, or about 30% of the family mean. The association between band S6.6 and abdominal fat was further examined by testing progeny of paternal half-sibs of the chickens which were used in the tail analysis, establishing genetic linkage between the DNA marker and a genetic locus affecting abdominal fat deposition.

Adipose Tissue↗