DNA fingerprinting analysis ofPetromyces alliaceus(AspergillussectionFlavi)

2005 ◽  
Vol 51 (12) ◽  
pp. 1039-1044 ◽  
Author(s):  
Cesaria E McAlpin ◽  
Donald T Wicklow
Keyword(s):  
Dna Fingerprinting ◽  
Aspergillus Flavus ◽  
Genomic Dna ◽  
Genotypic Diversity ◽  
Dna Probe ◽  
Dna Fingerprint ◽  
Dna Fingerprints ◽  
Close Relationship ◽  
Aspergillus Alliaceus ◽  
Aspergillus Section

The objective of this study was to evaluate the ability of the Aspergillus flavus pAF28 DNA probe to produce DNA fingerprints for distinguishing among genotypes of Petromyces alliaceus (Aspergillus section Flavi), a fungus considered responsible for the ochratoxin A contamination that is occasionally observed in California fig orchards. P. alliaceus (14 isolates), Petromyces albertensis (one isolate), and seven species of Aspergillus section Circumdati (14 isolates) were analyzed by DNA fingerprinting using a repetitive sequence DNA probe pAF28 derived from A. flavus. The presence of hybridization bands with the DNA probe and with the P. alliaceus or P. albertensis genomic DNA indicates a close relationship between A. flavus and P. alliaceus. Twelve distinct DNA fingerprint groups or genotypes were identified among the 15 isolates of Petromyces. Conspecificity of P. alliaceus and P. albertensis is suggested based on DNA fingerprints. Species belonging to Aspergillus section Circumdati hybridized only slightly at the 7.0-kb region with the repetitive DNA probe, unlike the highly polymorphic hybridization patterns obtained from P. alliaceus and A. flavus, suggesting very little homology of the probe to Aspergillus section Circum dati genomic DNA. The pAF28 DNA probe offers a tool for typing and monitoring specific P. alliaceus clonal populations and for estimating the genotypic diversity of P. alliaceus in orchards, vineyards, or crop fields.Key words: Aspergillus alliaceus, Circumdati, DNA probe, genotypic diversity, hybridization patterns, ochratoxin, Southern blot.

scholarly journals DNA Fingerprinting Analysis of Vegetative Compatibility Groups in Aspergillus flavus from a Peanut Field in Georgia

Plant Disease ◽  
2002 ◽  
Vol 86 (3) ◽  
pp. 254-258 ◽  
Author(s):  
C. E. McAlpin ◽  
D. T. Wicklow ◽  
B. W. Horn
Keyword(s):  
Aspergillus Flavus ◽  
Dna Probe ◽  
Vegetative Compatibility ◽  
Dna Fingerprint ◽  
Sample Population ◽  
Dna Fingerprints ◽  
Banding Patterns ◽  
Vegetative Compatibility Groups ◽  
Species Specific ◽  
Multiple Strains

The ability of species-specific DNA probe pAF28 to correctly match 75 strains of Aspergillus flavus isolated from a peanut field in Georgia with 1 of 44 distinct vegetative compatibility groupings (VCGs) was assessed. Multiple strains belonging to the same VCG typically produced identical DNA fingerprints, with the exception of VCG 17 and VCG 24, which contained strains that showed 83 and 87% similarity, respectively. A. flavus isolates sharing more than 80% of the fragments are recognized as belonging to the same DNA fingerprint group. Each VCG represented by a single isolate produced unique DNA fingerprints. The results provide further evidence that the pAF28 probe is able to distinguish A. flavus VCGs based on DNA fingerprints and can be used to predict the approximate number of VCGs in a sample population. The DNA probe also hybridized strongly and displayed multiple and distinct bands with other species in Aspergillus section Flavi: A. bombycis, A. caelatus, A. nomius, A. pseudotamarii, and A. tamarii. Although individual strains representing Aspergillus spp. in section Flavi produced DNA fingerprints with multiple bands, the banding patterns could not be used to classify these strains according to species.

scholarly journals Genotypic Diversity of Aspergillus parasiticus in an Illinois Corn Field

Plant Disease ◽  
1998 ◽  
Vol 82 (10) ◽  
pp. 1132-1136 ◽  
Author(s):  
C. E. McAlpin ◽  
D. T. Wicklow ◽  
C. E. Platis
Keyword(s):  
Aspergillus Flavus ◽  
Genomic Dna ◽  
Aspergillus Parasiticus ◽  
Genotypic Diversity ◽  
Dna Fingerprint ◽  
Sample Population ◽  
Field Soil ◽  
Dark Incubation ◽  
Corn Field ◽  
Group Sharing

Aspergillus parasiticus was isolated from direct platings of soil from a corn field near Kilbourne, Illinois. Soil contained 0.2 to 4.0 CFU of Aspergillus flavus and/or A. parasiticus per g of soil. Sixty isolates of A. parasiticus, each from a separately collected soil sample, were examined for ability to produce sclerotia and aflatoxins, and were subjected to DNA fingerprinting. PstI digests of total genomic DNA from each isolate were probed using the pAF28 repetitive sequence. Among 60 isolates analyzed, 33 (55%) distinct DNA fingerprint groups were identified (each group sharing less than 80% pAF28 band similarity), including 50 distinct genotypes (83%) with less than 100% pAF28 band similarity. A single A. parasiticus fingerprint group represented 13% of the sample population. The 83% genotypic diversity of the A. parasiticus population was equivalent to the 81% genotypic diversity recorded earlier for a population of 31 A. flavus isolates from the same field soil. Sclerotia were produced by 82% of the 50 A. parasiticus genotypes during dark incubation at 25°C. All isolates of A. parasiticus producedaflatoxin B1B2 and G1G2, whereas only 36% of the 31 A. flavus isolates from these soils produced aflatoxins.

scholarly journals Sample Size, Library Composition, and Genotypic Diversity among Natural Populations of Escherichia coli from Different Animals Influence Accuracy of Determining Sources of Fecal Pollution

2004 ◽  
Vol 70 (8) ◽  
pp. 4478-4485 ◽  
Author(s):  
LeeAnn K. Johnson ◽  
Mary B. Brown ◽  
Ethan A. Carruthers ◽  
John A. Ferguson ◽  
Priscilla E. Dombek ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Dna Fingerprinting ◽  
Correlation Coefficient ◽  
Average Rate ◽  
Dna Fingerprint ◽  
Correct Classification ◽  
Dna Fingerprints ◽  
Rarefaction Analysis ◽  
E Coli ◽  
Jackknife Analysis

ABSTRACT A horizontal, fluorophore-enhanced, repetitive extragenic palindromic-PCR (rep-PCR) DNA fingerprinting technique (HFERP) was developed and evaluated as a means to differentiate human from animal sources of Escherichia coli. Box A1R primers and PCR were used to generate 2,466 rep-PCR and 1,531 HFERP DNA fingerprints from E. coli strains isolated from fecal material from known human and 12 animal sources: dogs, cats, horses, deer, geese, ducks, chickens, turkeys, cows, pigs, goats, and sheep. HFERP DNA fingerprinting reduced within-gel grouping of DNA fingerprints and improved alignment of DNA fingerprints between gels, relative to that achieved using rep-PCR DNA fingerprinting. Jackknife analysis of the complete rep-PCR DNA fingerprint library, done using Pearson's product-moment correlation coefficient, indicated that animal and human isolates were assigned to the correct source groups with an 82.2% average rate of correct classification. However, when only unique isolates were examined, isolates from a single animal having a unique DNA fingerprint, Jackknife analysis showed that isolates were assigned to the correct source groups with a 60.5% average rate of correct classification. The percentages of correctly classified isolates were about 15 and 17% greater for rep-PCR and HFERP, respectively, when analyses were done using the curve-based Pearson's product-moment correlation coefficient, rather than the band-based Jaccard algorithm. Rarefaction analysis indicated that, despite the relatively large size of the known-source database, genetic diversity in E. coli was very great and is most likely accounting for our inability to correctly classify many environmental E. coli isolates. Our data indicate that removal of duplicate genotypes within DNA fingerprint libraries, increased database size, proper methods of statistical analysis, and correct alignment of band data within and between gels improve the accuracy of microbial source tracking methods.

scholarly journals Assessment of inbreeding by DNA fingerprinting: development of a calibration curve using defined strains of chickens.

Genetics ◽  
1990 ◽  
Vol 125 (1) ◽  
pp. 161-165 ◽  
Author(s):  
U Kuhnlein ◽  
D Zadworny ◽  
Y Dawe ◽  
R W Fairfull ◽  
J S Gavora
Keyword(s):  
Dna Fingerprinting ◽  
Restriction Enzyme ◽  
Calibration Curve ◽  
Genomic Dna ◽  
Mutation Frequency ◽  
Allelic Frequency ◽  
Dna Fingerprints ◽  
Band Frequency ◽  
Genetic Groups ◽  
Bacteriophage M13

Abstract By analyzing DNA fingerprints of chickens from seven well-defined genetic groups, a calibration curve was established relating the degree of inbreeding with the average band frequency, allelic frequency and band sharing. The probe used was bacteriophage M13 DNA and digestion of the genomic DNA was carried out with the MspI restriction enzyme. The analysis also provided an estimate of the average allelic frequency at a hypervariable locus and the average mutation frequency per locus and generation. The values of 0.24 and 1.7 X 10(-3), respectively, are similar to the estimates for humans using other probes and hybridization protocols. It is suggested that the calibration curve established can be used for determining inbreeding not only in chickens, but also in other species.

scholarly journals Application of DNA Fingerprints for Identification and Genetic Analyses of Mango (Mangifera indica) Genotypes

1995 ◽  
Vol 120 (2) ◽  
pp. 259-264 ◽  
Author(s):  
A. Adato ◽  
D. Sharon ◽  
U. Lavi ◽  
J. Hillel ◽  
S. Gazit
Keyword(s):  
Genetic Analysis ◽  
Genomic Dna ◽  
Genetic Relatedness ◽  
Mangifera Indica ◽  
Genetic Distances ◽  
Dna Fingerprint ◽  
Dna Fingerprints ◽  
Genetic Analyses ◽  
Young Leaves ◽  
Relatedness Analysis

DNA fingerprint information was used for identification of mango (Mangifera indica L.) cultivars for genetic relatedness analysis of20 mango cultivars and for genetic analysis of a family structure. Genomic DNA was extracted from young leaves, digested with Hind III or Dra I, and hybridized with 10 different DNA probes. Jeffreys' minisatellite probe 33.6 was the most useful, resulting in well-resolved bands representing highly polymorphic loci. Specific patterns were obtained for each cultivar. The probability of obtaining a similar pattern for two different cultivars was 9.4 × 10-6. Based on DNA fingerprint information, genetic distances between 20 mango cultivars were evaluated and an evolutionary tree was established. Analysis of DNA fingerprint band patterns of 12 progeny resulting from a cross between `Tommy Atkins' and `Keitt' mango revealed neither linked nor allelic bands. Application of the reported results for identification, genetic analyses, and mango breeding is discussed.

Genetic Heterogeneity of Porphyromonas (Bacteroides) gingivalis by Genomic DNA Fingerprinting

1990 ◽  
Vol 69 (8) ◽  
pp. 1488-1493 ◽  
Author(s):  
B.G. Loos ◽  
D. Mayrand ◽  
R.J. Genco ◽  
D.P. Dickinson
Keyword(s):  
Dna Fingerprinting ◽  
Genetic Heterogeneity ◽  
Genomic Dna ◽  
Epidemiological Studies ◽  
Dna Fingerprint ◽  
Cross Sectional ◽  
Large Numbers ◽  
Clonal Lines ◽  
Bacteroides Gingivalis ◽  
Global Population

This study describes the use of total genomic DNA fingerprinting with the use of restriction endonucleases to characterize clinical isolates of Porphyromonas gingivalis (Bacteroides gingivalis) obtained from patients with periodontitis or with root-canal infections. The majority of independent isolates had a unique DNA fingerprint, indicating extensive genetic heterogeneity within this species. Twenty-nine distinct DNA fingerprints were found among the 33 isolates investigated. This is in contrast to biotyping and serotyping, where only one type and three types, respectively, have been reported. The observed heterogeneity indicates that DNA fingerprinting is a sensitive measure of genetic dissimilarity between P. gingivalis isolates and is able to characterize individual isolates. These results have ecological implications, indicating that there is considerable natural diversity in the global population of P. gingivalis, and that there are likely to be relatively large numbers of genetically distinct clonal lines. Furthermore, DNA fingerprinting is a sensitive and powerful tool for longitudinal and cross-sectional epidemiological studies. This technique provides far greater discrimination between isolates than either biotyping or serotyping, and will be most helpful in, for example, the analysis of distribution of clonal lines within one periodontal patient, or the analysis of the transmission to and turnover of strain populations within a patient population, since the probability of two strains with the same DNA fingerprint being found by chance is small.

scholarly journals Application of DNA Fingerprints for Identification and Genetic Analysis of Avocado

1991 ◽  
Vol 116 (6) ◽  
pp. 1078-1081 ◽  
Author(s):  
U. Lavi ◽  
J. Hillel ◽  
A. Vainstein ◽  
E. Lahav ◽  
D. Sharon
Keyword(s):  
Genetic Analysis ◽  
Family Structure ◽  
Genomic Dna ◽  
Persea Americana ◽  
Dna Fingerprint ◽  
Dna Fingerprints ◽  
Evolutionary Studies ◽  
Pattern Characteristic ◽  
The Individual

Application of four DNA fingerprint probes to avocado (Persea americana Mill.) resulted in identification of various cultivars, characterization of the three avocado races, and a genetic analysis of family structure. Genomic DNA from 14 cultivars was probed with four DNA fingerprint probes. Three of the probes gave well-resolved bands. The individual-specific patterns obtained for each cultivar validate the use of this technique for definitive cultivar characterization, with the probability of obtaining a similar pattern for two different cultivars being 2 × 10-9. DNA mixes representing either Mexican, Guatemalan, or West-Indian avocado races were hybridized with the DNA fingerprint probes, and a band pattern characteristic for each race was obtained. Progeny of a cross between the cultivars Ettinger and Pinkerton were analyzed. Their DNA fingerprints revealed one pair of linked bands and another band allelic to one of them. The application of these observations to identification, evolutionary studies, and breeding is discussed.

Multilocus DNA fingerprints in seven species of salmonids

1995 ◽  
Vol 73 (3) ◽  
pp. 600-606 ◽  
Author(s):  
Daniel D. Heath ◽  
Robert H. Devlin ◽  
Thomas J. Hilbish ◽  
George K. Iwama
Keyword(s):  
Dna Fingerprinting ◽  
Chinook Salmon ◽  
Oncorhynchus Tshawytscha ◽  
Signal Strength ◽  
Variable Number ◽  
Dna Fingerprint ◽  
Dna Fingerprints ◽  
Molecular Biological Technique ◽  
Evolutionary Studies ◽  
Biological Technique

DNA fingerprinting is a molecular biological technique that is widely used for identifying parentage and relatedness in plants and animals. To identify new DNA fingerprinting probes for use with salmonids, Southern blots of genomic DNA from chinook salmon (Oncorhynchus tshawytscha) were hybridized at low stringencies with 12 different oligonucleotides designed from published core sequences of variable number of tendem repeats. Seven of the 12 oligonucleotides produced highly variable fingerprint-like patterns; however, only 3 of these had clear, distinct bands. The estimated heterozygosity for one population of chinook salmon using the three oligonucleotides as probes ranged from 0.64 to 0.77. Those three oligonucleotides were further hybridized with DNA from two unrelated individuals from six other species of salmonids. A single-locus DNA fingerprint probe originally developed for chinook salmon was also hybridized with DNA from the other six species at moderate stringency. There were differences in the complexity and signal strength of the resulting banding pattern between species for a given probe. Estimates of variability (heterozygosity and band sharing) for the three oligonucleotide probes and OtSL1 were high, indicating that the probes were potentially useful genetic markers. The availability of these additional DNA fingerprint probes should assist in ecological and evolutionary studies in salmonids, as well as in efforts to estimate genetic diversity of populations.

scholarly journals Evidence of genetic heterogeneity in a BALB/c mouse colony as determined by DNA fingerprinting

1998 ◽  
Vol 32 (1) ◽  
pp. 80-85 ◽  
Author(s):  
F. Benavides ◽  
D. Cazalla ◽  
C. Pereira ◽  
A. Fontanals ◽  
M. Salaverri ◽  
...  
Keyword(s):  
Dna Fingerprinting ◽  
Genetic Heterogeneity ◽  
Flow Cytometric Analysis ◽  
Skin Grafting ◽  
Electrophoretic Analysis ◽  
Coat Colour ◽  
Dna Fingerprint ◽  
Line System ◽  
Flow Cytometric ◽  
Immunological Research

A genetic monitoring of the BALB/c mouse foundation colony in our animal facility was carried out. The techniques of choice were skin grafting, coat colour test, flow cytometric analysis for H2 antigens (loci H2-D and H2-A), electrophoretic analysis of isoenzymes (loci Idh1, Pep3, Es3 and Mod1), PCR-amplified microsatellites (loci Igh-V, Ngfg, Plau, Crp, Igh, D16Mit5, D3Mit49 and D17Mit16) and DNA fingerprinting (multilocus probes 33.6, 33.15 and (CAC)5). No evidence of genetic contamination was found, ruling out the possibility of an outcross with AKR, the other albino strain maintained at the facility. Nevertheless, DNA fingerprint patterns revealed evidence of genetic heterogeneity in four out of nine lines of the nucleus colony, interpreted as minisatellite mutations favoured for a single line system with more than 40 generations of separation from the ancestral pair. These mice are mainly used in cancer and immunological research within the institute.

Sign in / Sign up

Export Citation Format

Share Document