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PubMed2004

Validation of quantitative trait loci for Ascochyta blight resistance in pea ( Pisum sativum L.), using populations from two crosses.

Resistance to Ascochyta blight of pea was genetically characterized by mapping quantitative trait loci (QTLs) using two crosses, 3147-A26 (A26, partially resistant) x cultivar Rovar (susceptible) and 3148-A88 (A88, partially resistant) x Rovar, with the aim of developing an increased understanding of the genetics of resistance and of identifying linked molecular markers that may be used to develop resistant germplasm. Molecular linkage maps for both crosses were aligned so that the results of QTL mapping could be compared. Ascochyta blight disease severity in response to natural epidemics was measured in field trials conducted in Western Australia and New Zealand. Eleven putative QTLs for Ascochyta blight resistance were identified from the A26 x Rovar population and 14 putative QTLs from the A88 x Rovar population. Six QTLs were associated with the same genomic regions in both populations. These QTLs reside on linkage groups II, III, IV, V, and VII (two QTLs). The severity of Ascochyta blight disease symptoms on pea increases during field epidemics as plants mature; therefore, QTLs for plant reproductive maturity were mapped. Six QTLs were detected for plant maturity in the A26 x Rovar population, while five plant maturity QTLs were mapped in the A88 x Rovar population. QTLs for plant maturity coincide with Ascochyta blight resistance QTLs in four genomic regions, on linkage groups II (two regions), III, and V. The plant maturity and Ascochyta blight resistance QTLs on III were linked in repulsion phase. Therefore, the coincidence of these QTLs may be explained by linkage of distinct loci for the two traits. The QTLs on linkage groups II and V were linked in coupling phase; therefore, linked QTLs for resistance and maturity may be present in these regions, or the Ascochyta blight resistance QTLs detected in these regions are the result of pleiotropic effects of plant-maturity genetic loci.

Ascomycota↗
PubMed1998

A RAPD-PCR method for large-scale typing of Bacillus cereus.

A robust RAPD-PCR procedure for large-scale typing of Bacillus cereus was developed. It is based on a simple DNA preparation, involving only freezing and boiling of cells in water with active carbon. By using a computerized system for data collection and processing, an efficient system for handling RAPD patterns for large-scale investigations was achieved. The procedure was highly discriminatory for Bacillus cereus strains and was found to give reproducible classification of RAPD fingerprints for five reference strains.

Animals↗
PubMedDate not supplied

Molecular epidemiology of serogroup a meningitis in Moscow, 1969 to 1997.

Molecular analysis of 103 serogroup A Neisseria meningitidis strains isolated in Moscow from 1969 to 1997 showed that four independent clonal groupings were responsible for successive waves of meningococcal disease. An epidemic from 1969 to the mid-1970s was caused by genocloud 2 of subgroup III, possibly imported from China. Subsequent endemic disease through the early 1990s was caused by subgroup X and then by subgroup VI, which has also caused endemic disease elsewhere in eastern Europe. A 1996 epidemic was part of the pandemic spread from Asia of genocloud 8 of subgroup III. Recent genocloud 8 epidemic disease in Moscow may represent an early warning for spread of these bacteria to other countries in Europe.

Bacterial Typing Techniques↗
PubMed2002

[DNA polymorphism in population genetics].

In the review, the literature evidence on DNA polymorphism obtained in the last 10-15 years using various molecular-genetic methods is summarized. All main types of DNA variation are considered but attention is focused on those extensively used in population genetics. The areas of using DNA markers are outlined and the limitations of their potential in analyzing genetic processes in populations are discussed. Particular emphasis is placed on the relationship between the earlier developed biochemical genetics based on protein polymorphism analysis and modern molecular population genetics based on DNA polymorphism. The possible role of selection in maintaining DNA variation is considered.

Animals↗
PubMed2001

Comparison of closely related orthopoxvirus isolates by random amplified polymorphic DNA and restriction fragment length polymorphism analysis.

The reliability and reproducibility of random amplified polymorphic DNA analysis (RAPD) was compared with restriction fragment length polymorphism (RFLP) by analysing three virus strains isolated from zoo animals in Berlin and three isolates which were cultivated from pets from Northern Germany. The RAPD technique was evaluated as a reliable tool with good reproducibility of the patterns for each virus strain investigated. Problems of interpretation due to inconsistent intensity of bands in different polymerase chain reaction runs may arise for less experienced personnel. The RAPD analysis can be performed within one working day and needs less DNA compared with RFLP so costs will be reduced. The obvious advantage of RFLP is that the pattern can be traced to the recognition site of the restriction enzyme whereas the RAPD primer sequence is not present in the orthopoxvirus genome at all. To the authors knowledge, the RAPD technique has never been applied in DNA viruses before and they conclude that this technique is a useful tool for the discrimination of closely related cowpoxviruses.

Animals↗
PubMed1999

Intra-specific diversity of Aureobasidium pullulans strains isolated from rocks and other habitats assessed by physiological methods and by random amplified polymorphic DNA (RAPD).

Intra-specific diversity of Aureobasidium pullulans strains isolated from environmental sources and from stones was studied by assessment of morphological, biochemical and physiological characters as well as random amplified polymorphic DNA (RAPD) using microsatellite or minisatellite DNA primers (GTG)5, (GACA)4, M13. The results showed that both classical and molecular techniques evidenced a phenotypic and genetic diversity of analysed A. pullulans strains. A different behaviour was observed in reference to the growth responses with D-glucosamine, citrate, galactitol and with different salt concentrations and range of growth temperature. Molecular analysis partially confirmed the data obtained with biochemical and physiological tests, additionally showing common fragments in all strains, to be used for a possible application as 'in situ' probes and for a rapid identification of A. pullulans strains.

Ascomycota↗
PubMed2005

Isolation of genes from plant Y chromosomes.

Few plant species are dioecious and only a small fraction of these species are known to have sex chromosomes. Considerable efforts to isolate sex-linked genes from dioecious Silene latifolia (Caryophillaceae) have resulted in the isolation of surprisingly few sex-linked genes, suggesting that the methods used previously were not efficient in plants. This chapter analyzes the methods that have been and can be used for isolation of genes from plant sex chromosomes. The most successful method used for the isolation of Y-linked genes included the screening of a male complementary DNA (cDNA) library with the probe obtained by degenerate oligonucleotide-primed polymerase chain reaction (PCR) of the microdissected Y chromosomes. However, chromosome microdissection requires sophisticated equipment and is difficult to apply to species with cytologically indistinguishable sex chromosomes. Genome and cDNA library subtraction methods were surprisingly unsuccessful, probably because of low divergence between the homologous X- and Y-linked genes in plants. Segregation testing and genomics-based methods are increasingly popular and are the most promising approaches for isolation of multiple genes from plant sex chromosomes.

Base Sequence↗
PubMed2005

The Bombyx mori karyotype and the assignment of linkage groups.

Lepidopteran species have a relatively high number of small holocentric chromosomes (Bombyx mori, 2n = 56). Chromosome identification has long been hampered in this group by the high number and by the absence of suitable markers like centromere position and chromosome bands. In this study, we carried out fluorescence in situ hybridization (FISH) on meiotic chromosome complements using genetically mapped B. mori bacterial artificial chromosomes (BACs) as probes. The combination of two to four either green or red fluorescence-labeled probes per chromosome allowed us to recognize unequivocally each of the 28 bivalents of the B. mori karyotype by its labeling pattern. Each chromosome was assigned one of the already established genetic linkage groups and the correct orientation in the chromosome was defined. This facilitates physical mapping of any other sequence and bears relevance for the ongoing B. mori genome projects. Two-color BAC-FISH karyotyping overcomes the problem of chromosome recognition in organisms where conventional banding techniques are not available.

Animals↗
PubMed1999

Molecular tools for identification of Penicillium starter cultures used in the food industry.

The main goal of this work was to develop rapid and accurate molecular tools to discriminate species of white industrial Penicillia. We applied three different polymerase chain reaction (PCR) based techniques. Sequences of the ITS region of the rRNA gene unit and of the 5' end of the beta tubulin gene yielded 1.2% and 5.8% nucleotide variability respectively, between Penicillium camembertii and Penicillium nalgiovense. Polymorphic restriction sites were found in both sequences. These may be used in diagnostic PCR-RFLP analysis to rapidly distinguish between the two Penicillium species. Random amplified polymorphic DNA (RAPD) markers were also useful to differentiate these two species, but no polymorphism was found at the subspecific level, which evidenced a high level of homogeneity of the isolates studied. By means of these three techniques, the real identity of industrial strains of Penicillium chrysogenum and P. nalgiovense could be demonstrated. The comparison of these isolates with type strains of the two species suggested that the former corresponds to P. nalgiovense. The genetic relatedness between P. naglovense and Penicillium dipodomyis was also confirmed.

Base Sequence↗
PubMed2000

Identification of Escherichia coli recovered from milk of sows with coliform mastitis by random amplified polymorphic DNA (RAPD) using standardized reagents.

A standardized-reagents commercial kit for random amplified polymorphic DNA (RAPD) analysis was used for typing 58 Escherichia coli strains that were recovered from the milk of sows, having coliform mastitis, within a single swineherd in Sweden. Previously, the 58 E. coli strains were characterized serologically and profiled biochemically. They were also evaluated for their serum resistance and their ability to adhere to fibronectin and bovine fetal fibroblasts. The RAPD analysis was fast, easily performed, and required only a nanogram of DNA. The indistinguishable banding patterns obtained with repeated analyses of 2 isolates from each strain demonstrated that RAPD analysis using standardized beads is a technique that provides reproducible results for typing E. coli strains that cause mastitis in sows. The results of the RAPD analyses demonstrated that E. coli sow mastitis strains are highly variable in serotype, biochemical profiles, virulence factors, and RAPD type, and that all 58 strains can be differentiated by means of the RAPD technique. The strains grouped into 24 RAPD types by combining the results of 2 primers, and into 38 groups by combining the results of serotype and RAPD type. No relationship between serotypes, virulence factors and RAPD types was found.

Animals↗
PubMed2001

Genetic diversity in the red yeast Cryptococcus hungaricus and its phylogenetic relationship to some related basidiomycetous yeasts.

Cryptococcus hungaricus is a basidiomycetous yeast with the abilities to synthesize carotenoid pigments and to grow under psychrophile conditions. Six C. hungaricus strains have been isolated so far from different habitats. In this study we wished to clarify the relationships amongst them. Morphological and physiological characters, mitochondrial DNA restriction profiles, and the presence of mycoviruses were examined. Internal transcribed spacers together with the 5.8S rDNA, the D1/D2 region of 26S rDNA, and partial sequences of the 18S rRNA gene were also analysed. On the basis of the phylogenetic analyses the type strain CBS 4214(T) together with four other C. hungaricus isolates were closely related to Bullera armeniaca and Bullera crocea, while strain CBS 6569 was much more similar to Cystofilobasidium than to the other C. hungaricus isolates.

Basidiomycota↗
PubMed2001

Random amplification of polymorphic DNA and phenotypic typing of Zimbabwean isolates of Pasteurella multocida.

Eighty-one isolates presumptively identified as Pasteurella multocida from a variety of diseases in animals in Zimbabwe were subjected to biochemical characterization, capsular typing and RAPD analysis. The majority of isolates (over 80%) were assigned into named taxa and were predominantly P. multocida subsp. multocida and P. multocida subsp. septica, whilst the remainder were unassigned. Serogroup A was predominant among the three capsular types (A, B and D) of P. multocida detected. Three main RAPD clusters and three subclusters were observed among the majority of isolates (93.8%), whilst the remainder was found to be weakly related. Nine different groups of strains with similar RAPD profiles (100% similarity) were also observed. The reference strain of capsular serogroup F clustered with the reference strain of P. multocida subsp. septica, whilst all other serogroups clustered with reference strains of subsp. multocida and gallicida. Notably, serogroups A and D were observed to be closely related to the reference strain of subsp. multocida. The relationship between biotype, capsular type, host origin and disease manifestation was not clear-cut. However, most pig isolates of subsp. multocida clustered together as did most cattle isolates of subsp. multocida. RAPD tended to separate subsp. multocida from septica.

Animals↗
PubMed1995

Random amplified polymorphic DNA and restriction enzyme analysis of PCR amplified rDNA in taxonomy: two identification techniques for food-borne yeasts.

The random amplified polymorphic DNA (RAPD) assay and the restriction enzyme analysis of PCR amplified rDNA are compared for the identification of the common spoilage yeasts Zygosaccharomyces bailii, Z. rouxii, Saccharomyces cerevisiae, Candida valida and C. lipolytica. Both techniques proved to be adequate tools for yeast identification. Since the RAPD does provide less stable patterns than restriction enzyme analysis of PCR amplified rDNA, and a large amount of data had to be compared without data reduction, Principal Component Analysis (PCA) was applied successfully for clustering the RAPD patterns. The success of PCA is highly influenced by the primer used in RAPD and the amount of reference samples. A large amount of reference samples improves the performance of clustering in PCA. The primer of choice was shown to be important with respect to the discriminatory power of the RAPD method. Some primers used enabled discrimination on the subspecies level. The results collected with both typing methods justify the conclusion that the present typing system can be applied for taxonomical purposes.

Base Sequence↗
PubMedDate not supplied

Identification of Serratia marcescens populations of nosocomial origin by RAPD-PCR.

BACKGROUND: Serratia marcescens has been increasingly identified as a cause of infection in the immunocompromised host and in high-mortality-rate nosocomial outbreaks. It is thus important to use identification methods that allow study of the dynamics and evolution of nosocomial S. marcescens strains. The aim of this study was to identify S. marcescens strains isolated from nosocomial outbreaks in two pediatric hospitals by random amplification polymorphic DNA polymerase chain reaction (RAPD-PCR). METHODS: RAPD-PCR was used to study five S. marcescens populations isolated from four different nosocomial outbreaks that occurred in two pediatric hospitals. This method was compared with the widely used biotyping system described by Grimont and Grimont. RESULTS: The combination of biotypification and RAPD-PCR allowed accurate identification of S. marcescens strains isolated in nosocomial outbreaks at pediatric hospitals; by RAPD-PCR, we were able to analyze clonal variations in S. marcescens populations. We established bacterial dissemination patterns in hospital environments according to hospital administration of medical services and compared changes in bacterial DNA amplification patterns in each hospital related with clonal variations by selective pressures. CONCLUSIONS: RAPD-PCR is a useful method to identify S. marcescens strains associated with nosocomial outbreaks.

Bacterial Typing Techniques↗
PubMed2005

The use of RAPD genomic fingerprinting to study relatedness in strains of Acidithiobacillus ferrooxidans.

Twelve strains of Acidithiobacillus ferrooxidans were recovered from acid mine drainage (AMD) sites from three different geographical locations: Copper Cliff, Ontario, Canada; Mineral City, OH, USA; and Cornwall, England. The spread-plate technique and various culture media were used to isolate and purify all strains. DNA was extracted from each purified culture and amplified using PCR and twenty, 10-mer primers. Amplification products were separated by gel electrophoresis and photographed under UV light. The RAPD (Randomly Amplified Polymorphic DNA) profiles were compared on the basis of the presence or absence of each DNA band and a data matrix was constructed. Strain diversity was calculated using the Jaccard's coefficient and UPGMA (Unweighted Pair-Group Arithmetic Average Clustering) cluster analysis. The variations in the banding patterns indicated genomic variability among the twelve A. ferrooxidans strains tested. The primers used in this study grouped the twelve strains into five major groups. Similarities between the strains ranged from 5.49% to 85.14%. These results show that the strains have a high degree of genomic diversity and that the RAPD procedure is a powerful technique to assess strain variability in this bacterium.

Acidithiobacillus↗
PubMed1997

Pulsed-field gel electrophoresis is more discriminating than multilocus enzyme electrophoresis and random amplified polymorphic DNA analysis for typing pyogenic streptococci.

The SmaI restriction endonuclease digestion patterns of chromosomal DNAs from 99 pyogenic streptococci belonging to Lancefield group A (41 Streptococcus pyogenes), group C (seven S.dysgalactiae, 11 "S. equisimilis", three S. equi, eight S. zooepidemicus) and group G (25 human group G Streptococcus, four S. canis) were analyzed by pulsed-field gel electrophoresis (PFGE), and the results were compared with those previously obtained by multilocus enzyme electrophoresis (MLEE) and random amplified polymorphic DNA analysis (RAPD). PFGE revealed 93 distinct types among the 99 strains, and no patterns were common to strains of different species. The discriminatory power of PFGE was greater than that of MLEE and RAPD for groups A and G streptococci. The polymorphism among group C streptococci was similar with the three techniques. PFGE is, therefore, the most efficacious method for epidemiological typing of pyogenic streptococci.

DNA, Bacterial↗
PubMed1999

Identification of oral mitis group streptococci by arbitrarily primed polymerase chain reaction.

"Mitis group" streptococci are commensal but may play some role in dental caries, septicemia or endocarditis. Rapid genotypic identification would aid studies of dental plaque ecology, or diagnostic use. AP-PCR with 58 unpaired arbitrary primers was used to characterize 7 Streptococcus gordonii, 11 Streptococcus sanguis, 2 Streptococcus crista, 5 Streptococcus parasanguis, 18 Streptococcus oralis, and 36 Streptococcus mitis (22 biovar 1 and 14 biovar 2). S. parasanguis 16S rRNA variable region primer RR2 produced species-specific bands with all S. gordonii and S. sanguis. Human V beta 1 T-cell receptor primer 434 yielded concordant genotypic identification of all phenotypically defined S. crista and S. parasanguis, 83% of S. oralis, and 74% of S. mitis biovar 1. Amplicon patterns for S. mitis biovar 2 were heterogeneous. Findings suggest that primers RR2 and 434 in succession will allow rapid identification of genotypic groups corresponding closely to mitis group species established by phenotype.

Bacterial Typing Techniques↗